Starting phenix.real_space_refine on Sun Dec 29 08:19:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cy7_27069/12_2024/8cy7_27069_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cy7_27069/12_2024/8cy7_27069.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8cy7_27069/12_2024/8cy7_27069.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cy7_27069/12_2024/8cy7_27069.map" model { file = "/net/cci-nas-00/data/ceres_data/8cy7_27069/12_2024/8cy7_27069_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cy7_27069/12_2024/8cy7_27069_trim.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.000 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 123 5.16 5 C 18023 2.51 5 N 4654 2.21 5 O 5583 1.98 5 H 26549 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 54932 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 16148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1050, 16148 Classifications: {'peptide': 1050} Link IDs: {'PTRANS': 52, 'TRANS': 997} Chain breaks: 5 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 16161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1050, 16161 Classifications: {'peptide': 1050} Link IDs: {'PTRANS': 52, 'TRANS': 997} Chain breaks: 5 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 16160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1050, 16160 Classifications: {'peptide': 1050} Link IDs: {'PTRANS': 52, 'TRANS': 997} Chain breaks: 5 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 1809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 1809 Classifications: {'peptide': 121} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "E" Number of atoms: 1809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 1809 Classifications: {'peptide': 121} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "F" Number of atoms: 1809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 1809 Classifications: {'peptide': 121} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 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: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 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: "L" 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: "M" 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: "N" 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: "O" 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: "P" 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: "Q" 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: "R" 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: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 238 Unusual residues: {'NAG': 17} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 17 Chain: "B" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Chain: "C" Number of atoms: 252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 252 Unusual residues: {'NAG': 18} Classifications: {'undetermined': 18} Link IDs: {None: 17} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 18 Time building chain proxies: 21.04, per 1000 atoms: 0.38 Number of scatterers: 54932 At special positions: 0 Unit cell: (160.5, 154.08, 196.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 123 16.00 O 5583 8.00 N 4654 7.00 C 18023 6.00 H 26549 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 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 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 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 480 " - pdb=" SG CYS B 488 " 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 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 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 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 95 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 95 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 95 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1303 " - " ASN A 331 " " NAG A1304 " - " ASN A 603 " " NAG A1306 " - " ASN A 657 " " NAG A1307 " - " ASN A 709 " " NAG A1308 " - " ASN A1074 " " NAG A1309 " - " ASN A 717 " " NAG A1311 " - " ASN A 801 " " NAG A1313 " - " ASN A 149 " " NAG A1314 " - " ASN A 234 " " NAG A1316 " - " ASN A 343 " " NAG B1301 " - " ASN B 61 " " NAG B1304 " - " ASN B 603 " " NAG B1306 " - " ASN B 657 " " NAG B1308 " - " ASN B1074 " " NAG B1310 " - " ASN B 343 " " NAG B1312 " - " ASN B 282 " " NAG B1313 " - " ASN B 234 " " NAG B1314 " - " ASN B 165 " " NAG C1302 " - " ASN C 61 " " NAG C1304 " - " ASN C 282 " " NAG C1305 " - " ASN C 331 " " NAG C1306 " - " ASN C 603 " " NAG C1307 " - " ASN C 616 " " NAG C1308 " - " ASN C 657 " " NAG C1309 " - " ASN C1074 " " NAG C1312 " - " ASN C 149 " " NAG C1313 " - " ASN C 165 " " NAG C1314 " - " ASN C 234 " " NAG G 1 " - " ASN A1134 " " NAG H 1 " - " ASN A 165 " " NAG I 1 " - " ASN A 282 " " NAG J 1 " - " ASN A1098 " " NAG K 1 " - " ASN B 801 " " NAG N 1 " - " ASN B1098 " " NAG P 1 " - " ASN C 801 " " NAG Q 1 " - " ASN C 343 " " NAG R 1 " - " ASN C1098 " Time building additional restraints: 10.83 Conformation dependent library (CDL) restraints added in 3.5 seconds 6942 Ramachandran restraints generated. 3471 Oldfield, 0 Emsley, 3471 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6564 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 54 sheets defined 23.1% alpha, 23.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.87 Creating SS restraints... 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 370 removed outlier: 4.235A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) 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 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 619 through 623 Processing helix chain 'A' and resid 632 through 637 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 757 removed outlier: 3.830A pdb=" N GLY A 757 " --> pdb=" O LEU A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.527A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 891 removed outlier: 4.055A pdb=" N GLY A 891 " --> pdb=" O PHE A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.484A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 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 Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.088A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 3.582A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N SER A1147 " --> pdb=" O PRO A1143 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.660A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 372 removed outlier: 4.241A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASN B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N SER B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 390 removed outlier: 4.079A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 407 No H-bonds generated for 'chain 'B' and resid 405 through 407' Processing helix chain 'B' and resid 418 through 423 removed outlier: 3.617A pdb=" N ASN B 422 " --> pdb=" O ILE B 418 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N TYR B 423 " --> pdb=" O ALA B 419 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 418 through 423' Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 616 through 620 Processing helix chain 'B' and resid 632 through 638 removed outlier: 3.719A pdb=" N TYR B 636 " --> pdb=" O THR B 632 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR B 638 " --> pdb=" O ARG B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 removed outlier: 3.624A pdb=" N ILE B 742 " --> pdb=" O CYS B 738 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N CYS B 743 " --> pdb=" O THR B 739 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 757 removed outlier: 3.706A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N TYR B 756 " --> pdb=" O LEU B 752 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLY B 757 " --> pdb=" O LEU B 753 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.765A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 891 removed outlier: 4.057A pdb=" N GLY B 891 " --> pdb=" O PHE B 888 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.562A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 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 Processing helix chain 'B' and resid 985 through 1032 removed outlier: 3.557A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 3.882A pdb=" N SER B1147 " --> pdb=" O PRO B1143 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 385 through 390 removed outlier: 3.553A pdb=" N ASP C 389 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 407 No H-bonds generated for 'chain 'C' and resid 405 through 407' Processing helix chain 'C' and resid 418 through 423 removed outlier: 4.254A pdb=" N TYR C 423 " --> pdb=" O ALA C 419 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 757 removed outlier: 3.664A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N TYR C 756 " --> pdb=" O LEU C 752 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLY C 757 " --> pdb=" O LEU C 753 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 825 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 891 removed outlier: 4.020A pdb=" N GLY C 891 " --> pdb=" O PHE C 888 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.503A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.097A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 4.647A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 90 Processing helix chain 'E' and resid 86 through 90 Processing helix chain 'F' and resid 86 through 90 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 4.028A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 52 removed outlier: 4.245A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 225 through 229 removed outlier: 5.475A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU A 96 " --> pdb=" O ASN A 188 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 125 through 129 Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 316 removed outlier: 6.941A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 326 through 328 Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.894A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 553 through 554 removed outlier: 3.703A pdb=" N THR A 553 " --> pdb=" O ASP A 586 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.791A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.409A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 702 through 703 Processing sheet with id=AB4, first strand: chain 'A' and resid 712 through 713 Processing sheet with id=AB5, first strand: chain 'A' and resid 717 through 728 removed outlier: 6.300A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB7, first strand: chain 'A' and resid 788 through 789 removed outlier: 5.866A pdb=" N ILE A 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1123 Processing sheet with id=AB9, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC1, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.956A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 48 through 52 removed outlier: 4.027A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.651A pdb=" N LEU B 84 " --> pdb=" O PHE B 238 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 316 removed outlier: 6.938A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 326 through 328 Processing sheet with id=AC6, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.127A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 448 through 453 removed outlier: 6.980A pdb=" N TYR B 449 " --> pdb=" O PHE B 497 " (cutoff:3.500A) removed outlier: 8.645A pdb=" N PHE B 497 " --> pdb=" O TYR B 449 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N TYR B 451 " --> pdb=" O TYR B 495 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 553 through 554 removed outlier: 3.695A pdb=" N THR B 553 " --> pdb=" O ASP B 586 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.587A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.280A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 712 through 713 Processing sheet with id=AD2, first strand: chain 'B' and resid 717 through 728 removed outlier: 6.423A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 717 through 728 removed outlier: 6.423A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 735 through 736 Processing sheet with id=AD5, first strand: chain 'B' and resid 788 through 789 removed outlier: 5.628A pdb=" N ILE B 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'B' and resid 1120 through 1123 removed outlier: 3.564A pdb=" N CYS B1082 " --> pdb=" O VAL B1133 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD8, first strand: chain 'C' and resid 27 through 30 removed outlier: 3.881A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA C 93 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 48 through 55 removed outlier: 4.357A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.842A pdb=" N TRP C 104 " --> pdb=" O ILE C 119 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 311 through 317 removed outlier: 4.164A pdb=" N GLY C 311 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.881A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE5, first strand: chain 'C' and resid 538 through 543 removed outlier: 3.686A pdb=" N THR C 553 " --> pdb=" O ASP C 586 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ILE C 584 " --> pdb=" O SER C 555 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 664 through 667 removed outlier: 6.441A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 712 through 713 Processing sheet with id=AE8, first strand: chain 'C' and resid 717 through 728 removed outlier: 6.463A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU C1063 " --> pdb=" O PHE C1052 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N PHE C1052 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1120 through 1123 Processing sheet with id=AF1, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AF2, first strand: chain 'D' and resid 4 through 8 Processing sheet with id=AF3, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.079A pdb=" N ARG D 37 " --> pdb=" O PHE D 46 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N PHE D 46 " --> pdb=" O ARG D 37 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'D' and resid 10 through 13 removed outlier: 7.296A pdb=" N GLY D 99 " --> pdb=" O VAL D 108 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N VAL D 108 " --> pdb=" O GLY D 99 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 4 through 8 Processing sheet with id=AF6, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.184A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N SER E 120 " --> pdb=" O GLY E 10 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N VAL E 12 " --> pdb=" O SER E 120 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ARG E 37 " --> pdb=" O PHE E 46 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N PHE E 46 " --> pdb=" O ARG E 37 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.184A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N SER E 120 " --> pdb=" O GLY E 10 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N VAL E 12 " --> pdb=" O SER E 120 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N GLY E 99 " --> pdb=" O VAL E 108 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N VAL E 108 " --> pdb=" O GLY E 99 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'F' and resid 5 through 8 Processing sheet with id=AF9, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.101A pdb=" N GLY F 10 " --> pdb=" O THR F 118 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N SER F 120 " --> pdb=" O GLY F 10 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N VAL F 12 " --> pdb=" O SER F 120 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ARG F 37 " --> pdb=" O PHE F 46 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N PHE F 46 " --> pdb=" O ARG F 37 " (cutoff:3.500A) 1079 hydrogen bonds defined for protein. 2946 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: 21.51 Time building geometry restraints manager: 13.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 26537 1.03 - 1.23: 92 1.23 - 1.42: 12252 1.42 - 1.62: 16531 1.62 - 1.81: 156 Bond restraints: 55568 Sorted by residual: bond pdb=" C1 NAG C1304 " pdb=" O5 NAG C1304 " ideal model delta sigma weight residual 1.406 1.459 -0.053 2.00e-02 2.50e+03 7.01e+00 bond pdb=" C1 NAG I 1 " pdb=" O5 NAG I 1 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.71e+00 bond pdb=" C1 NAG P 1 " pdb=" O5 NAG P 1 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.53e+00 bond pdb=" C1 NAG B1306 " pdb=" O5 NAG B1306 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.52e+00 bond pdb=" C1 NAG L 2 " pdb=" O5 NAG L 2 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.17e+00 ... (remaining 55563 not shown) Histogram of bond angle deviations from ideal: 0.00 - 9.22: 99118 9.22 - 18.43: 71 18.43 - 27.65: 147 27.65 - 36.87: 226 36.87 - 46.09: 26 Bond angle restraints: 99588 Sorted by residual: angle pdb="HD21 ASN B 657 " pdb=" ND2 ASN B 657 " pdb="HD22 ASN B 657 " ideal model delta sigma weight residual 120.00 73.91 46.09 3.00e+00 1.11e-01 2.36e+02 angle pdb="HD21 ASN B 801 " pdb=" ND2 ASN B 801 " pdb="HD22 ASN B 801 " ideal model delta sigma weight residual 120.00 74.14 45.86 3.00e+00 1.11e-01 2.34e+02 angle pdb="HD21 ASN A1134 " pdb=" ND2 ASN A1134 " pdb="HD22 ASN A1134 " ideal model delta sigma weight residual 120.00 74.15 45.85 3.00e+00 1.11e-01 2.34e+02 angle pdb="HD21 ASN C 801 " pdb=" ND2 ASN C 801 " pdb="HD22 ASN C 801 " ideal model delta sigma weight residual 120.00 74.20 45.80 3.00e+00 1.11e-01 2.33e+02 angle pdb="HD21 ASN A 801 " pdb=" ND2 ASN A 801 " pdb="HD22 ASN A 801 " ideal model delta sigma weight residual 120.00 74.25 45.75 3.00e+00 1.11e-01 2.33e+02 ... (remaining 99583 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.51: 26365 25.51 - 51.02: 1109 51.02 - 76.52: 204 76.52 - 102.03: 21 102.03 - 127.54: 1 Dihedral angle restraints: 27700 sinusoidal: 15439 harmonic: 12261 Sorted by residual: dihedral pdb=" CB CYS B 131 " pdb=" SG CYS B 131 " pdb=" SG CYS B 166 " pdb=" CB CYS B 166 " ideal model delta sinusoidal sigma weight residual 93.00 134.64 -41.64 1 1.00e+01 1.00e-02 2.43e+01 dihedral pdb=" CA VAL C 620 " pdb=" C VAL C 620 " pdb=" N PRO C 621 " pdb=" CA PRO C 621 " ideal model delta harmonic sigma weight residual -180.00 -155.70 -24.30 0 5.00e+00 4.00e-02 2.36e+01 dihedral pdb=" C ILE B 624 " pdb=" N ILE B 624 " pdb=" CA ILE B 624 " pdb=" CB ILE B 624 " ideal model delta harmonic sigma weight residual -122.00 -133.29 11.29 0 2.50e+00 1.60e-01 2.04e+01 ... (remaining 27697 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.349: 4575 0.349 - 0.698: 39 0.698 - 1.047: 0 1.047 - 1.396: 6 1.396 - 1.745: 43 Chirality restraints: 4663 Sorted by residual: chirality pdb=" CG LEU B 878 " pdb=" CB LEU B 878 " pdb=" CD1 LEU B 878 " pdb=" CD2 LEU B 878 " both_signs ideal model delta sigma weight residual False -2.59 -0.85 -1.74 2.00e-01 2.50e+01 7.61e+01 chirality pdb=" CG LEU B1004 " pdb=" CB LEU B1004 " pdb=" CD1 LEU B1004 " pdb=" CD2 LEU B1004 " both_signs ideal model delta sigma weight residual False -2.59 -0.86 -1.73 2.00e-01 2.50e+01 7.51e+01 chirality pdb=" CG LEU C1004 " pdb=" CB LEU C1004 " pdb=" CD1 LEU C1004 " pdb=" CD2 LEU C1004 " both_signs ideal model delta sigma weight residual False -2.59 -0.86 -1.73 2.00e-01 2.50e+01 7.50e+01 ... (remaining 4660 not shown) Planarity restraints: 8345 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL C 620 " -0.050 5.00e-02 4.00e+02 7.66e-02 9.38e+00 pdb=" N PRO C 621 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO C 621 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO C 621 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 861 " 0.025 5.00e-02 4.00e+02 3.73e-02 2.22e+00 pdb=" N PRO C 862 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO C 862 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 862 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 861 " 0.023 5.00e-02 4.00e+02 3.47e-02 1.93e+00 pdb=" N PRO B 862 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO B 862 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 862 " 0.019 5.00e-02 4.00e+02 ... (remaining 8342 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.16: 2106 2.16 - 2.77: 101164 2.77 - 3.38: 142505 3.38 - 3.99: 183049 3.99 - 4.60: 282005 Nonbonded interactions: 710829 Sorted by model distance: nonbonded pdb=" H ASN C1125 " pdb=" HA ASN C1125 " model vdw 1.551 1.816 nonbonded pdb=" H LYS B 187 " pdb=" HA LYS B 187 " model vdw 1.564 1.816 nonbonded pdb=" H HIS C 66 " pdb=" HA HIS C 66 " model vdw 1.567 1.816 nonbonded pdb=" H ILE B 584 " pdb=" HA ILE B 584 " model vdw 1.568 1.816 nonbonded pdb=" H HIS B1088 " pdb=" HA HIS B1088 " model vdw 1.568 1.816 ... (remaining 710824 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 25 through 615 or (resid 616 and (name N or name CA or nam \ e C or name O or name CB or name CG or name OD1 or name ND2 or name H or name HA \ or name HB2 or name HB3 or name HD21)) or resid 617 through 801 or (resid 802 a \ nd (name N or name CA or name C or name O or name CB or name CG or name CD1 or n \ ame CD2 or name CE1 or name CE2 or name CZ or name HA or name HB2 or name HB3 or \ name HD1 or name HD2 or name HE1 or name HE2 or name HZ )) or resid 803 through \ 1147 or resid 1301 through 1315)) selection = (chain 'B' and (resid 25 through 320 or (resid 321 and (name N or name CA or nam \ e C or name O or name CB or name H or name HA )) or resid 322 through 615 or (re \ sid 616 and (name N or name CA or name C or name O or name CB or name CG or name \ OD1 or name ND2 or name H or name HA or name HB2 or name HB3 or name HD21)) or \ resid 617 through 656 or (resid 657 and (name N or name CA or name C or name O o \ r name CB or name CG or name OD1 or name ND2 or name H or name HA or name HB2 or \ name HB3 or name HD21)) or resid 658 through 800 or (resid 801 and (name N or n \ ame CA or name C or name O or name CB or name CG or name OD1 or name ND2 or name \ HA or name HB2 or name HB3 or name HD21 or name HD22)) or resid 802 or (resid 8 \ 03 and (name N or name CA or name C or name O or name CB or name OG or name HA o \ r name HB2 or name HB3 or name HG )) or resid 804 through 1133 or (resid 1134 th \ rough 1135 and (name N or name CA or name C or name O or name CB or name CG or n \ ame OD1 or name ND2 or name HA or name HB2 or name HB3 or name HD21 or name HD22 \ )) or resid 1136 through 1147 or resid 1301 through 1315)) selection = (chain 'C' and (resid 25 through 320 or (resid 321 and (name N or name CA or nam \ e C or name O or name CB or name H or name HA )) or resid 322 through 800 or (re \ sid 801 and (name N or name CA or name C or name O or name CB or name CG or name \ OD1 or name ND2 or name HA or name HB2 or name HB3 or name HD21 or name HD22)) \ or resid 802 or (resid 803 and (name N or name CA or name C or name O or name CB \ or name OG or name HA or name HB2 or name HB3 or name HG )) or resid 804 throug \ h 1133 or (resid 1134 through 1135 and (name N or name CA or name C or name O or \ name CB or name CG or name OD1 or name ND2 or name HA or name HB2 or name HB3 o \ r name HD21 or name HD22)) or resid 1136 through 1147 or resid 1301 through 1315 \ )) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } 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: 5.220 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: 0.910 Extract box with map and model: 1.890 Check model and map are aligned: 0.390 Set scattering table: 0.480 Process input model: 92.460 Find NCS groups from input model: 2.250 Set up NCS constraints: 0.290 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:10.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 114.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 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 : 0.003 0.053 29019 Z= 0.223 Angle : 0.757 15.504 39504 Z= 0.368 Chirality : 0.172 1.745 4663 Planarity : 0.003 0.077 5011 Dihedral : 13.015 127.538 11496 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.75 % Favored : 96.11 % Rotamer: Outliers : 0.26 % Allowed : 0.13 % Favored : 99.60 % Cbeta Deviations : 0.30 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.15), residues: 3471 helix: 3.33 (0.21), residues: 647 sheet: 0.91 (0.19), residues: 712 loop : -0.33 (0.14), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP C 886 HIS 0.001 0.000 HIS A 207 PHE 0.010 0.001 PHE B 592 TYR 0.010 0.000 TYR A1067 ARG 0.001 0.000 ARG A 328 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6942 Ramachandran restraints generated. 3471 Oldfield, 0 Emsley, 3471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6942 Ramachandran restraints generated. 3471 Oldfield, 0 Emsley, 3471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 147 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue LYS 147 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue LYS 147 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Evaluate side-chains 157 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 149 time to evaluate : 3.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 773 GLU cc_start: 0.8249 (tp30) cc_final: 0.7930 (tp30) REVERT: C 314 GLN cc_start: 0.8144 (tm-30) cc_final: 0.7911 (tm-30) REVERT: C 773 GLU cc_start: 0.8248 (tp30) cc_final: 0.7970 (tp30) REVERT: D 33 MET cc_start: -0.0686 (mmm) cc_final: -0.1464 (mmm) REVERT: F 21 SER cc_start: 0.7512 (m) cc_final: 0.7272 (p) REVERT: F 79 ASP cc_start: 0.6589 (t0) cc_final: 0.6059 (m-30) REVERT: F 105 PRO cc_start: 0.6547 (Cg_exo) cc_final: 0.6210 (Cg_endo) outliers start: 8 outliers final: 8 residues processed: 157 average time/residue: 1.7681 time to fit residues: 344.5878 Evaluate side-chains 100 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 92 time to evaluate : 3.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 603 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 296 optimal weight: 2.9990 chunk 266 optimal weight: 7.9990 chunk 147 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 179 optimal weight: 1.9990 chunk 142 optimal weight: 40.0000 chunk 275 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 167 optimal weight: 0.5980 chunk 204 optimal weight: 1.9990 chunk 318 optimal weight: 50.0000 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 774 GLN A1135 ASN E 81 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.1121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 29019 Z= 0.306 Angle : 0.763 15.573 39504 Z= 0.380 Chirality : 0.172 1.756 4663 Planarity : 0.004 0.089 5011 Dihedral : 8.785 120.002 5338 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.52 % Favored : 95.36 % Rotamer: Outliers : 0.56 % Allowed : 3.96 % Favored : 95.48 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.15), residues: 3471 helix: 3.16 (0.21), residues: 660 sheet: 0.81 (0.19), residues: 741 loop : -0.45 (0.14), residues: 2070 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 152 HIS 0.004 0.001 HIS B1048 PHE 0.013 0.001 PHE F 46 TYR 0.016 0.001 TYR B1067 ARG 0.014 0.000 ARG E 37 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6942 Ramachandran restraints generated. 3471 Oldfield, 0 Emsley, 3471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6942 Ramachandran restraints generated. 3471 Oldfield, 0 Emsley, 3471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 147 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue LYS 147 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue LYS 147 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Evaluate side-chains 112 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 95 time to evaluate : 3.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 773 GLU cc_start: 0.8375 (tp30) cc_final: 0.8125 (tp30) REVERT: C 773 GLU cc_start: 0.8491 (tp30) cc_final: 0.8106 (tp30) REVERT: D 33 MET cc_start: -0.0650 (mmm) cc_final: -0.1414 (mmm) REVERT: F 21 SER cc_start: 0.7528 (m) cc_final: 0.7314 (p) REVERT: F 79 ASP cc_start: 0.6452 (t0) cc_final: 0.6209 (m-30) REVERT: F 82 MET cc_start: -0.1872 (pmm) cc_final: -0.2096 (mpt) outliers start: 17 outliers final: 14 residues processed: 109 average time/residue: 1.6383 time to fit residues: 228.1277 Evaluate side-chains 99 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 85 time to evaluate : 3.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 1138 TYR Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 950 ASP Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 858 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 177 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 265 optimal weight: 2.9990 chunk 217 optimal weight: 5.9990 chunk 87 optimal weight: 4.9990 chunk 319 optimal weight: 8.9990 chunk 344 optimal weight: 20.0000 chunk 284 optimal weight: 1.9990 chunk 316 optimal weight: 30.0000 chunk 108 optimal weight: 3.9990 chunk 256 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN A1135 ASN B 717 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 29019 Z= 0.360 Angle : 0.782 15.539 39504 Z= 0.390 Chirality : 0.172 1.768 4663 Planarity : 0.004 0.074 5011 Dihedral : 8.347 117.326 5336 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.10 % Favored : 94.79 % Rotamer: Outliers : 0.76 % Allowed : 5.25 % Favored : 93.99 % Cbeta Deviations : 0.30 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.61 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.15), residues: 3471 helix: 2.85 (0.21), residues: 658 sheet: 0.46 (0.19), residues: 752 loop : -0.68 (0.14), residues: 2061 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP F 100 HIS 0.004 0.001 HIS A 207 PHE 0.034 0.002 PHE D 67 TYR 0.019 0.001 TYR B1067 ARG 0.008 0.000 ARG E 37 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6942 Ramachandran restraints generated. 3471 Oldfield, 0 Emsley, 3471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6942 Ramachandran restraints generated. 3471 Oldfield, 0 Emsley, 3471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 147 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue LYS 147 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue LYS 147 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Evaluate side-chains 115 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 92 time to evaluate : 3.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1138 TYR cc_start: 0.4195 (OUTLIER) cc_final: 0.3279 (p90) REVERT: D 33 MET cc_start: -0.0813 (mmm) cc_final: -0.1466 (mmm) outliers start: 23 outliers final: 11 residues processed: 107 average time/residue: 1.6533 time to fit residues: 224.5920 Evaluate side-chains 89 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 3.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 1138 TYR Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain D residue 67 PHE Chi-restraints excluded: chain E residue 46 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 315 optimal weight: 30.0000 chunk 240 optimal weight: 0.6980 chunk 165 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 chunk 152 optimal weight: 2.9990 chunk 214 optimal weight: 0.7980 chunk 320 optimal weight: 5.9990 chunk 339 optimal weight: 30.0000 chunk 167 optimal weight: 2.9990 chunk 303 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1142 GLN ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 29019 Z= 0.188 Angle : 0.739 15.396 39504 Z= 0.364 Chirality : 0.171 1.757 4663 Planarity : 0.003 0.130 5011 Dihedral : 7.829 115.156 5332 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.26 % Favored : 95.62 % Rotamer: Outliers : 0.76 % Allowed : 6.01 % Favored : 93.23 % Cbeta Deviations : 0.30 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.61 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.15), residues: 3471 helix: 2.90 (0.21), residues: 658 sheet: 0.57 (0.19), residues: 744 loop : -0.58 (0.14), residues: 2069 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 100 HIS 0.005 0.001 HIS C 69 PHE 0.086 0.001 PHE E 46 TYR 0.016 0.001 TYR C 380 ARG 0.002 0.000 ARG A 983 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6942 Ramachandran restraints generated. 3471 Oldfield, 0 Emsley, 3471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6942 Ramachandran restraints generated. 3471 Oldfield, 0 Emsley, 3471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 147 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue LYS 147 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue LYS 147 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Evaluate side-chains 103 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 80 time to evaluate : 3.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1002 GLN cc_start: 0.9112 (tt0) cc_final: 0.8507 (tm-30) REVERT: D 33 MET cc_start: -0.0850 (mmm) cc_final: -0.1532 (mmm) outliers start: 23 outliers final: 16 residues processed: 97 average time/residue: 1.6776 time to fit residues: 208.7171 Evaluate side-chains 92 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 76 time to evaluate : 3.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain E residue 46 PHE Chi-restraints excluded: chain F residue 80 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 282 optimal weight: 1.9990 chunk 192 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 252 optimal weight: 0.0170 chunk 139 optimal weight: 30.0000 chunk 289 optimal weight: 1.9990 chunk 234 optimal weight: 0.0270 chunk 0 optimal weight: 3.9990 chunk 173 optimal weight: 3.9990 chunk 304 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 overall best weight: 0.9680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 29019 Z= 0.204 Angle : 0.737 15.499 39504 Z= 0.363 Chirality : 0.171 1.750 4663 Planarity : 0.003 0.045 5011 Dihedral : 7.542 113.684 5332 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.24 % Favored : 95.65 % Rotamer: Outliers : 0.73 % Allowed : 6.37 % Favored : 92.90 % Cbeta Deviations : 0.30 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.61 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.15), residues: 3471 helix: 2.98 (0.21), residues: 654 sheet: 0.58 (0.19), residues: 752 loop : -0.58 (0.14), residues: 2065 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 35 HIS 0.005 0.001 HIS C 69 PHE 0.083 0.001 PHE E 46 TYR 0.013 0.001 TYR B1067 ARG 0.002 0.000 ARG A 983 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6942 Ramachandran restraints generated. 3471 Oldfield, 0 Emsley, 3471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6942 Ramachandran restraints generated. 3471 Oldfield, 0 Emsley, 3471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 147 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue LYS 147 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue LYS 147 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Evaluate side-chains 103 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 81 time to evaluate : 3.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1002 GLN cc_start: 0.9128 (tt0) cc_final: 0.8527 (tm-30) REVERT: C 988 GLU cc_start: 0.8754 (mp0) cc_final: 0.8547 (mp0) REVERT: D 33 MET cc_start: -0.0841 (mmm) cc_final: -0.1568 (mmm) outliers start: 22 outliers final: 14 residues processed: 98 average time/residue: 1.7938 time to fit residues: 226.4609 Evaluate side-chains 92 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 78 time to evaluate : 3.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain F residue 21 SER Chi-restraints excluded: chain F residue 80 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 114 optimal weight: 7.9990 chunk 305 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 199 optimal weight: 0.6980 chunk 83 optimal weight: 1.9990 chunk 339 optimal weight: 30.0000 chunk 281 optimal weight: 0.2980 chunk 157 optimal weight: 0.8980 chunk 28 optimal weight: 20.0000 chunk 112 optimal weight: 5.9990 chunk 178 optimal weight: 0.0070 overall best weight: 0.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 804 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 29019 Z= 0.180 Angle : 0.729 15.389 39504 Z= 0.359 Chirality : 0.171 1.750 4663 Planarity : 0.003 0.044 5011 Dihedral : 7.253 111.991 5332 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.26 % Favored : 95.65 % Rotamer: Outliers : 0.73 % Allowed : 6.80 % Favored : 92.47 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.61 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.15), residues: 3471 helix: 2.98 (0.21), residues: 656 sheet: 0.64 (0.19), residues: 736 loop : -0.56 (0.14), residues: 2079 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 35 HIS 0.005 0.000 HIS C 69 PHE 0.017 0.001 PHE D 46 TYR 0.013 0.001 TYR B1067 ARG 0.002 0.000 ARG B 634 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6942 Ramachandran restraints generated. 3471 Oldfield, 0 Emsley, 3471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6942 Ramachandran restraints generated. 3471 Oldfield, 0 Emsley, 3471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 147 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue LYS 147 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue LYS 147 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Evaluate side-chains 100 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 78 time to evaluate : 3.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1002 GLN cc_start: 0.9123 (tt0) cc_final: 0.8518 (tm-30) REVERT: C 988 GLU cc_start: 0.8738 (mp0) cc_final: 0.8528 (mp0) REVERT: D 33 MET cc_start: -0.0567 (mmm) cc_final: -0.1356 (mmm) outliers start: 22 outliers final: 15 residues processed: 96 average time/residue: 1.7015 time to fit residues: 209.8789 Evaluate side-chains 92 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 77 time to evaluate : 3.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain F residue 21 SER Chi-restraints excluded: chain F residue 80 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 327 optimal weight: 30.0000 chunk 38 optimal weight: 6.9990 chunk 193 optimal weight: 3.9990 chunk 248 optimal weight: 6.9990 chunk 192 optimal weight: 2.9990 chunk 285 optimal weight: 5.9990 chunk 189 optimal weight: 2.9990 chunk 338 optimal weight: 9.9990 chunk 211 optimal weight: 2.9990 chunk 206 optimal weight: 1.9990 chunk 156 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 218 GLN ** B 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 29019 Z= 0.406 Angle : 0.792 15.785 39504 Z= 0.396 Chirality : 0.174 1.782 4663 Planarity : 0.003 0.048 5011 Dihedral : 7.484 112.313 5332 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.11 % Favored : 93.78 % Rotamer: Outliers : 0.59 % Allowed : 7.33 % Favored : 92.08 % Cbeta Deviations : 0.30 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.61 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.15), residues: 3471 helix: 2.73 (0.20), residues: 663 sheet: 0.30 (0.19), residues: 763 loop : -0.76 (0.14), residues: 2045 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 886 HIS 0.005 0.001 HIS B1048 PHE 0.020 0.002 PHE C 92 TYR 0.021 0.001 TYR B1067 ARG 0.004 0.000 ARG B1014 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6942 Ramachandran restraints generated. 3471 Oldfield, 0 Emsley, 3471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6942 Ramachandran restraints generated. 3471 Oldfield, 0 Emsley, 3471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 147 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue LYS 147 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue LYS 147 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Evaluate side-chains 98 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 80 time to evaluate : 3.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1138 TYR cc_start: 0.4491 (OUTLIER) cc_final: 0.4061 (p90) REVERT: C 988 GLU cc_start: 0.8829 (mp0) cc_final: 0.8622 (mp0) REVERT: D 33 MET cc_start: -0.0637 (mmm) cc_final: -0.1422 (mmm) outliers start: 18 outliers final: 15 residues processed: 94 average time/residue: 1.6710 time to fit residues: 202.0434 Evaluate side-chains 88 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 72 time to evaluate : 3.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 1138 TYR Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 1029 MET Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 46 PHE Chi-restraints excluded: chain F residue 21 SER Chi-restraints excluded: chain F residue 80 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 209 optimal weight: 0.0670 chunk 135 optimal weight: 0.8980 chunk 202 optimal weight: 0.5980 chunk 101 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 65 optimal weight: 0.5980 chunk 215 optimal weight: 3.9990 chunk 230 optimal weight: 1.9990 chunk 167 optimal weight: 0.0870 chunk 31 optimal weight: 8.9990 chunk 265 optimal weight: 1.9990 overall best weight: 0.4496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 218 GLN ** B 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 29019 Z= 0.169 Angle : 0.738 16.370 39504 Z= 0.364 Chirality : 0.172 1.854 4663 Planarity : 0.003 0.045 5011 Dihedral : 7.120 110.813 5332 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.41 % Favored : 95.51 % Rotamer: Outliers : 0.56 % Allowed : 7.56 % Favored : 91.88 % Cbeta Deviations : 0.30 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.61 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.15), residues: 3471 helix: 2.86 (0.21), residues: 663 sheet: 0.43 (0.19), residues: 747 loop : -0.63 (0.14), residues: 2061 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 104 HIS 0.005 0.001 HIS C 69 PHE 0.012 0.001 PHE A 855 TYR 0.014 0.001 TYR D 93 ARG 0.003 0.000 ARG A 983 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6942 Ramachandran restraints generated. 3471 Oldfield, 0 Emsley, 3471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6942 Ramachandran restraints generated. 3471 Oldfield, 0 Emsley, 3471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 147 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue LYS 147 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue LYS 147 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Evaluate side-chains 93 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 76 time to evaluate : 3.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1002 GLN cc_start: 0.9134 (tt0) cc_final: 0.8489 (tm-30) REVERT: C 988 GLU cc_start: 0.8833 (mp0) cc_final: 0.8627 (mp0) REVERT: D 33 MET cc_start: -0.0669 (mmm) cc_final: -0.1461 (mmm) outliers start: 17 outliers final: 16 residues processed: 91 average time/residue: 1.6005 time to fit residues: 187.0310 Evaluate side-chains 87 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 71 time to evaluate : 3.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 1029 MET Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 46 PHE Chi-restraints excluded: chain F residue 80 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 307 optimal weight: 0.0070 chunk 324 optimal weight: 50.0000 chunk 295 optimal weight: 1.9990 chunk 315 optimal weight: 20.0000 chunk 189 optimal weight: 3.9990 chunk 137 optimal weight: 7.9990 chunk 247 optimal weight: 10.0000 chunk 96 optimal weight: 1.9990 chunk 284 optimal weight: 2.9990 chunk 298 optimal weight: 0.6980 chunk 314 optimal weight: 0.0370 overall best weight: 0.9480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 29019 Z= 0.204 Angle : 0.744 15.405 39504 Z= 0.368 Chirality : 0.172 1.753 4663 Planarity : 0.003 0.045 5011 Dihedral : 7.030 109.508 5332 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.47 % Favored : 95.45 % Rotamer: Outliers : 0.59 % Allowed : 7.49 % Favored : 91.91 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.61 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.15), residues: 3471 helix: 2.94 (0.21), residues: 658 sheet: 0.51 (0.19), residues: 737 loop : -0.64 (0.14), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 886 HIS 0.005 0.001 HIS C 69 PHE 0.069 0.001 PHE D 46 TYR 0.013 0.001 TYR B1067 ARG 0.002 0.000 ARG B 634 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6942 Ramachandran restraints generated. 3471 Oldfield, 0 Emsley, 3471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6942 Ramachandran restraints generated. 3471 Oldfield, 0 Emsley, 3471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 147 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue LYS 147 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue LYS 147 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Evaluate side-chains 91 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 73 time to evaluate : 3.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 855 PHE cc_start: 0.6765 (m-80) cc_final: 0.6525 (m-10) REVERT: B 1002 GLN cc_start: 0.9150 (tt0) cc_final: 0.8516 (tm-30) REVERT: C 988 GLU cc_start: 0.8824 (mp0) cc_final: 0.8610 (mp0) REVERT: D 33 MET cc_start: -0.0546 (mmm) cc_final: -0.1313 (mmm) outliers start: 18 outliers final: 16 residues processed: 89 average time/residue: 1.6467 time to fit residues: 189.9224 Evaluate side-chains 87 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 71 time to evaluate : 3.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 1029 MET Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain F residue 21 SER Chi-restraints excluded: chain F residue 80 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 207 optimal weight: 1.9990 chunk 333 optimal weight: 10.0000 chunk 203 optimal weight: 1.9990 chunk 158 optimal weight: 2.9990 chunk 231 optimal weight: 2.9990 chunk 349 optimal weight: 7.9990 chunk 321 optimal weight: 10.0000 chunk 278 optimal weight: 3.9990 chunk 28 optimal weight: 20.0000 chunk 215 optimal weight: 2.9990 chunk 170 optimal weight: 0.7980 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.3070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 29019 Z= 0.329 Angle : 0.786 15.828 39504 Z= 0.391 Chirality : 0.173 1.801 4663 Planarity : 0.003 0.047 5011 Dihedral : 7.194 109.108 5332 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.91 % Favored : 94.01 % Rotamer: Outliers : 0.66 % Allowed : 7.49 % Favored : 91.85 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.61 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.15), residues: 3471 helix: 2.75 (0.20), residues: 664 sheet: 0.23 (0.19), residues: 771 loop : -0.77 (0.14), residues: 2036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 886 HIS 0.005 0.001 HIS A1048 PHE 0.021 0.001 PHE A 898 TYR 0.021 0.001 TYR A1138 ARG 0.004 0.000 ARG D 44 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6942 Ramachandran restraints generated. 3471 Oldfield, 0 Emsley, 3471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6942 Ramachandran restraints generated. 3471 Oldfield, 0 Emsley, 3471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 147 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue LYS 147 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue LYS 147 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Evaluate side-chains 92 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 72 time to evaluate : 3.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 780 GLU cc_start: 0.8733 (tp30) cc_final: 0.8455 (tp30) REVERT: A 855 PHE cc_start: 0.6724 (m-80) cc_final: 0.6518 (m-80) REVERT: C 988 GLU cc_start: 0.8856 (mp0) cc_final: 0.8649 (mp0) REVERT: D 33 MET cc_start: -0.0608 (mmm) cc_final: -0.1383 (mmm) outliers start: 20 outliers final: 18 residues processed: 91 average time/residue: 1.8132 time to fit residues: 215.3509 Evaluate side-chains 88 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 70 time to evaluate : 3.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 1029 MET Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain F residue 21 SER Chi-restraints excluded: chain F residue 80 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 221 optimal weight: 7.9990 chunk 296 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 256 optimal weight: 0.9980 chunk 41 optimal weight: 10.0000 chunk 77 optimal weight: 1.9990 chunk 278 optimal weight: 2.9990 chunk 116 optimal weight: 0.7980 chunk 286 optimal weight: 0.7980 chunk 35 optimal weight: 20.0000 chunk 51 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 218 GLN B 331 ASN ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.116747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.074122 restraints weight = 235396.058| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 3.67 r_work: 0.3203 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.3118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 29019 Z= 0.225 Angle : 0.750 15.504 39504 Z= 0.371 Chirality : 0.172 1.761 4663 Planarity : 0.003 0.079 5011 Dihedral : 6.993 108.144 5332 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.70 % Favored : 95.22 % Rotamer: Outliers : 0.66 % Allowed : 7.53 % Favored : 91.81 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.61 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.15), residues: 3471 helix: 2.85 (0.21), residues: 663 sheet: 0.31 (0.19), residues: 744 loop : -0.71 (0.14), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 886 HIS 0.005 0.001 HIS C 69 PHE 0.013 0.001 PHE A 898 TYR 0.013 0.001 TYR B1067 ARG 0.011 0.000 ARG B 815 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7396.94 seconds wall clock time: 129 minutes 48.90 seconds (7788.90 seconds total)