Starting phenix.real_space_refine on Wed Jun 25 03:36:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k46_36878/06_2025/8k46_36878.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k46_36878/06_2025/8k46_36878.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8k46_36878/06_2025/8k46_36878.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k46_36878/06_2025/8k46_36878.map" model { file = "/net/cci-nas-00/data/ceres_data/8k46_36878/06_2025/8k46_36878.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k46_36878/06_2025/8k46_36878.cif" } resolution = 3.37 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.041 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 127 5.16 5 C 18409 2.51 5 N 4739 2.21 5 O 5633 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 2.50s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 28908 Number of models: 1 Model: "" Number of chains: 21 Chain: "E" Number of atoms: 987 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 124, 981 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Conformer: "B" Number of residues, atoms: 124, 981 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} bond proxies already assigned to first conformer: 1003 Chain: "G" Number of atoms: 977 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 124, 971 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 120} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 124, 971 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 120} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 993 Chain: "I" Number of atoms: 987 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 124, 981 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Conformer: "B" Number of residues, atoms: 124, 981 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} bond proxies already assigned to first conformer: 1003 Chain: "A" Number of atoms: 8410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1083, 8410 Classifications: {'peptide': 1083} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 57, 'TRANS': 1025} Chain breaks: 4 Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 67 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 3, 'GLU:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 52 Chain: "B" Number of atoms: 8413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1081, 8413 Classifications: {'peptide': 1081} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 57, 'TRANS': 1023} Chain breaks: 4 Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 6, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 39 Chain: "C" Number of atoms: 8448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1084, 8448 Classifications: {'peptide': 1084} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 58, 'TRANS': 1025} Chain breaks: 4 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 4, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 29 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: "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: "S" 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: "T" 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: "U" 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: "X" 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: "Y" 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: "Z" 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N ASER E 26 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER E 26 " occ=0.50 residue: pdb=" N ASER G 26 " occ=0.48 ... (10 atoms not shown) pdb=" OG BSER G 26 " occ=0.52 residue: pdb=" N ASER I 26 " occ=0.48 ... (10 atoms not shown) pdb=" OG BSER I 26 " occ=0.52 Time building chain proxies: 21.14, per 1000 atoms: 0.73 Number of scatterers: 28908 At special positions: 0 Unit cell: (139.536, 154.224, 199.104, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 127 16.00 O 5633 8.00 N 4739 7.00 C 18409 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=37, symmetry=0 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 97 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 97 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 97 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.05 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.05 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " 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=2.02 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.05 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " 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=2.02 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=2.06 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.02 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=2.04 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.06 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 K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " NAG-ASN " NAG A1301 " - " ASN A 234 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 603 " " NAG A1305 " - " ASN A 616 " " NAG A1308 " - " ASN A1074 " " NAG B1301 " - " ASN B 164 " " NAG B1302 " - " ASN B 234 " " NAG B1303 " - " ASN B 61 " " NAG B1304 " - " ASN B 282 " " NAG B1305 " - " ASN B 603 " " NAG B1306 " - " ASN B 616 " " NAG B1307 " - " ASN B 657 " " NAG B1308 " - " ASN B 709 " " NAG B1309 " - " ASN B1074 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 282 " " NAG C1303 " - " ASN C 603 " " NAG C1307 " - " ASN C 343 " " NAG K 1 " - " ASN C 717 " " NAG L 1 " - " ASN C 801 " " NAG M 1 " - " ASN C1098 " " NAG N 1 " - " ASN C1134 " " NAG R 1 " - " ASN B 717 " " NAG S 1 " - " ASN B 801 " " NAG T 1 " - " ASN B1098 " " NAG U 1 " - " ASN B1134 " " NAG X 1 " - " ASN A 717 " " NAG Y 1 " - " ASN A 801 " " NAG Z 1 " - " ASN A1098 " " NAG a 1 " - " ASN A1134 " Time building additional restraints: 7.84 Conformation dependent library (CDL) restraints added in 4.0 seconds 7186 Ramachandran restraints generated. 3593 Oldfield, 0 Emsley, 3593 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6754 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 62 sheets defined 21.5% alpha, 18.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.21 Creating SS restraints... Processing helix chain 'E' and resid 88 through 92 removed outlier: 4.084A pdb=" N THR E 92 " --> pdb=" O ALA E 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.650A pdb=" N THR A 299 " --> pdb=" O PRO A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.602A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 370 removed outlier: 3.903A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ASN A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 388 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 502 through 506 Processing helix chain 'A' and resid 633 through 637 Processing helix chain 'A' and resid 737 through 742 Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.526A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.633A pdb=" N GLN A 774 " --> pdb=" O ILE A 770 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 806 Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 4.167A pdb=" N GLY A 891 " --> pdb=" O PHE A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 919 removed outlier: 4.010A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 4.023A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.534A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.806A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLY A 999 " --> pdb=" O ARG A 995 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1150 Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 364 through 369 Processing helix chain 'B' and resid 383 through 390 removed outlier: 3.788A pdb=" N ASN B 388 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ASP B 389 " --> 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 502 through 505 Processing helix chain 'B' and resid 633 through 637 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.523A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 759 removed outlier: 6.936A pdb=" N SER B 758 " --> pdb=" O GLN B 755 " (cutoff:3.500A) Processing helix chain 'B' and resid 760 through 783 Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 852 through 856 removed outlier: 3.501A pdb=" N ASN B 856 " --> pdb=" O GLN B 853 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 4.060A pdb=" N GLY B 891 " --> pdb=" O PHE B 888 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 918 removed outlier: 4.205A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.687A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.628A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.678A pdb=" N GLU B 990 " --> pdb=" O PRO B 986 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY B 999 " --> pdb=" O ARG B 995 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER B1003 " --> pdb=" O GLY B 999 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1150 Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 383 through 387 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 416 through 421 removed outlier: 3.967A pdb=" N TYR C 421 " --> pdb=" O ASN C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 543 through 546 Processing helix chain 'C' and resid 633 through 637 Processing helix chain 'C' and resid 737 through 742 Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.632A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 760 through 783 removed outlier: 3.538A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 850 through 854 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.907A 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 918 removed outlier: 4.241A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.628A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 966 removed outlier: 3.558A pdb=" N ALA C 958 " --> pdb=" O HIS C 954 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.777A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 988 through 1033 removed outlier: 3.765A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE C1013 " --> pdb=" O THR C1009 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1150 removed outlier: 4.143A pdb=" N PHE C1148 " --> pdb=" O GLU C1144 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 6 through 8 removed outlier: 3.628A pdb=" N GLN E 6 " --> pdb=" O ALA E 24 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA E 24 " --> pdb=" O GLN E 6 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N SER E 22 " --> pdb=" O SER E 8 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 11 through 13 removed outlier: 4.298A pdb=" N THR E 121 " --> pdb=" O GLY E 11 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 46 through 52 removed outlier: 5.634A pdb=" N PHE E 48 " --> pdb=" O ARG E 39 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ARG E 39 " --> pdb=" O PHE E 48 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER E 50 " --> pdb=" O TRP E 37 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N PHE E 38 " --> pdb=" O TYR E 96 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N TYR E 96 " --> pdb=" O PHE E 38 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 10 through 13 Processing sheet with id=AA5, first strand: chain 'G' and resid 59 through 60 removed outlier: 6.486A pdb=" N TRP G 37 " --> pdb=" O VAL G 49 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N ALA G 51 " --> pdb=" O MET G 35 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N MET G 35 " --> pdb=" O ALA G 51 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR G 94 " --> pdb=" O GLN G 40 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR G 99 " --> pdb=" O TYR G 113 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 70 through 72 Processing sheet with id=AA7, first strand: chain 'I' and resid 4 through 8 Processing sheet with id=AA8, first strand: chain 'I' and resid 12 through 13 Processing sheet with id=AA9, first strand: chain 'I' and resid 34 through 35 Processing sheet with id=AB1, first strand: chain 'I' and resid 46 through 48 removed outlier: 3.979A pdb=" N GLN I 40 " --> pdb=" O THR I 94 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N THR I 94 " --> pdb=" O GLN I 40 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 71 through 73 Processing sheet with id=AB3, first strand: chain 'A' and resid 30 through 31 removed outlier: 3.721A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AB5, first strand: chain 'A' and resid 48 through 50 removed outlier: 3.607A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AB7, first strand: chain 'A' and resid 192 through 193 Processing sheet with id=AB8, first strand: chain 'A' and resid 103 through 105 Processing sheet with id=AB9, first strand: chain 'A' and resid 120 through 121 Processing sheet with id=AC1, first strand: chain 'A' and resid 130 through 131 removed outlier: 3.909A pdb=" N VAL A 130 " --> pdb=" O THR A 167 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 196 through 197 Processing sheet with id=AC3, first strand: chain 'A' and resid 310 through 318 removed outlier: 3.772A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TYR A 612 " --> pdb=" O CYS A 649 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N CYS A 649 " --> pdb=" O TYR A 612 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY A 648 " --> pdb=" O THR A 645 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 324 through 325 removed outlier: 7.412A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.528A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.231A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLY A 431 " --> pdb=" O TYR A 380 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'A' and resid 664 through 667 removed outlier: 6.724A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AC9, first strand: chain 'A' and resid 711 through 728 removed outlier: 7.110A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 1047 through 1051 removed outlier: 6.951A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 735 through 736 Processing sheet with id=AD3, first strand: chain 'A' and resid 787 through 790 removed outlier: 5.277A pdb=" N ILE A 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.541A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 30 through 31 removed outlier: 3.988A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 53 through 55 Processing sheet with id=AD7, first strand: chain 'B' and resid 224 through 230 removed outlier: 5.500A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE B 197 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N TYR B 204 " --> pdb=" O VAL B 193 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 104 through 105 removed outlier: 3.528A pdb=" N VAL B 120 " --> pdb=" O VAL B 127 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 187 through 190 removed outlier: 4.534A pdb=" N ILE B 210 " --> pdb=" O LYS B 187 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N LEU B 189 " --> pdb=" O THR B 208 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N THR B 208 " --> pdb=" O LEU B 189 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 276 through 279 removed outlier: 3.597A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 311 through 318 removed outlier: 7.148A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 326 through 327 Processing sheet with id=AE4, first strand: chain 'B' and resid 356 through 358 removed outlier: 3.614A pdb=" N ILE B 402 " --> pdb=" O TYR B 508 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 356 through 358 Processing sheet with id=AE6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AE7, first strand: chain 'B' and resid 664 through 665 removed outlier: 3.754A pdb=" N SER B 691 " --> pdb=" O GLN B 675 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 711 through 719 removed outlier: 6.577A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 725 through 728 removed outlier: 3.730A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'B' and resid 787 through 790 removed outlier: 5.250A pdb=" N ILE B 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'B' and resid 1081 through 1082 removed outlier: 4.621A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 48 through 51 Processing sheet with id=AF4, first strand: chain 'C' and resid 54 through 55 Processing sheet with id=AF5, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.544A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU C 117 " --> pdb=" O PHE C 106 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 225 through 229 removed outlier: 5.748A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 311 through 318 removed outlier: 7.150A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 325 through 326 removed outlier: 3.737A pdb=" N GLY C 550 " --> pdb=" O VAL C 539 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 375 through 380 Processing sheet with id=AG1, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AG2, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AG3, first strand: chain 'C' and resid 664 through 665 Processing sheet with id=AG4, first strand: chain 'C' and resid 711 through 722 removed outlier: 6.955A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'C' and resid 725 through 728 Processing sheet with id=AG6, first strand: chain 'C' and resid 733 through 735 removed outlier: 4.029A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.468A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'C' and resid 1094 through 1097 855 hydrogen bonds defined for protein. 2265 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: 12.94 Time building geometry restraints manager: 9.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 4705 1.31 - 1.44: 8456 1.44 - 1.57: 16280 1.57 - 1.69: 0 1.69 - 1.82: 166 Bond restraints: 29607 Sorted by residual: bond pdb=" CA SER B1097 " pdb=" CB SER B1097 " ideal model delta sigma weight residual 1.532 1.464 0.068 1.58e-02 4.01e+03 1.86e+01 bond pdb=" N PHE C 329 " pdb=" CA PHE C 329 " ideal model delta sigma weight residual 1.455 1.483 -0.028 7.00e-03 2.04e+04 1.58e+01 bond pdb=" C PRO A 897 " pdb=" O PRO A 897 " ideal model delta sigma weight residual 1.233 1.188 0.045 1.16e-02 7.43e+03 1.48e+01 bond pdb=" CA SER C1097 " pdb=" CB SER C1097 " ideal model delta sigma weight residual 1.532 1.470 0.062 1.62e-02 3.81e+03 1.46e+01 bond pdb=" CA SER A 803 " pdb=" CB SER A 803 " ideal model delta sigma weight residual 1.531 1.470 0.060 1.59e-02 3.96e+03 1.44e+01 ... (remaining 29602 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.20: 38444 2.20 - 4.39: 1692 4.39 - 6.59: 162 6.59 - 8.78: 32 8.78 - 10.98: 3 Bond angle restraints: 40333 Sorted by residual: angle pdb=" N VAL C 367 " pdb=" CA VAL C 367 " pdb=" C VAL C 367 " ideal model delta sigma weight residual 111.81 105.20 6.61 8.60e-01 1.35e+00 5.91e+01 angle pdb=" N LYS B 77 " pdb=" CA LYS B 77 " pdb=" C LYS B 77 " ideal model delta sigma weight residual 114.62 107.01 7.61 1.14e+00 7.69e-01 4.46e+01 angle pdb=" CA PHE C1121 " pdb=" CB PHE C1121 " pdb=" CG PHE C1121 " ideal model delta sigma weight residual 113.80 120.12 -6.32 1.00e+00 1.00e+00 4.00e+01 angle pdb=" C PRO A 521 " pdb=" CA PRO A 521 " pdb=" CB PRO A 521 " ideal model delta sigma weight residual 111.46 103.91 7.55 1.21e+00 6.83e-01 3.89e+01 angle pdb=" N VAL C 622 " pdb=" CA VAL C 622 " pdb=" C VAL C 622 " ideal model delta sigma weight residual 110.42 104.85 5.57 9.40e-01 1.13e+00 3.51e+01 ... (remaining 40328 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.08: 16416 26.08 - 52.15: 1445 52.15 - 78.23: 195 78.23 - 104.31: 54 104.31 - 130.39: 19 Dihedral angle restraints: 18129 sinusoidal: 7596 harmonic: 10533 Sorted by residual: dihedral pdb=" CB CYS C 743 " pdb=" SG CYS C 743 " pdb=" SG CYS C 749 " pdb=" CB CYS C 749 " ideal model delta sinusoidal sigma weight residual -86.00 -174.45 88.45 1 1.00e+01 1.00e-02 9.34e+01 dihedral pdb=" CB CYS C 336 " pdb=" SG CYS C 336 " pdb=" SG CYS C 361 " pdb=" CB CYS C 361 " ideal model delta sinusoidal sigma weight residual 93.00 8.23 84.77 1 1.00e+01 1.00e-02 8.73e+01 dihedral pdb=" CB CYS C 617 " pdb=" SG CYS C 617 " pdb=" SG CYS C 649 " pdb=" CB CYS C 649 " ideal model delta sinusoidal sigma weight residual 93.00 28.44 64.56 1 1.00e+01 1.00e-02 5.48e+01 ... (remaining 18126 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.213: 4594 0.213 - 0.426: 45 0.426 - 0.640: 2 0.640 - 0.853: 2 0.853 - 1.066: 2 Chirality restraints: 4645 Sorted by residual: chirality pdb=" C1 NAG Z 2 " pdb=" O4 NAG Z 1 " pdb=" C2 NAG Z 2 " pdb=" O5 NAG Z 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-02 2.50e+03 1.16e+02 chirality pdb=" C1 NAG M 2 " pdb=" O4 NAG M 1 " pdb=" C2 NAG M 2 " pdb=" O5 NAG M 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-02 2.50e+03 7.22e+01 chirality pdb=" C1 NAG A1305 " pdb=" ND2 ASN A 616 " pdb=" C2 NAG A1305 " pdb=" O5 NAG A1305 " both_signs ideal model delta sigma weight residual False -2.40 -1.33 -1.07 2.00e-01 2.50e+01 2.84e+01 ... (remaining 4642 not shown) Planarity restraints: 5197 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG Y 2 " 0.343 2.00e-02 2.50e+03 2.93e-01 1.07e+03 pdb=" C7 NAG Y 2 " -0.088 2.00e-02 2.50e+03 pdb=" C8 NAG Y 2 " 0.168 2.00e-02 2.50e+03 pdb=" N2 NAG Y 2 " -0.516 2.00e-02 2.50e+03 pdb=" O7 NAG Y 2 " 0.093 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1308 " 0.339 2.00e-02 2.50e+03 2.90e-01 1.05e+03 pdb=" C7 NAG B1308 " -0.084 2.00e-02 2.50e+03 pdb=" C8 NAG B1308 " 0.160 2.00e-02 2.50e+03 pdb=" N2 NAG B1308 " -0.514 2.00e-02 2.50e+03 pdb=" O7 NAG B1308 " 0.099 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG T 2 " -0.330 2.00e-02 2.50e+03 2.85e-01 1.01e+03 pdb=" C7 NAG T 2 " 0.075 2.00e-02 2.50e+03 pdb=" C8 NAG T 2 " -0.043 2.00e-02 2.50e+03 pdb=" N2 NAG T 2 " 0.499 2.00e-02 2.50e+03 pdb=" O7 NAG T 2 " -0.202 2.00e-02 2.50e+03 ... (remaining 5194 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 3253 2.74 - 3.28: 29954 3.28 - 3.82: 50873 3.82 - 4.36: 60017 4.36 - 4.90: 99728 Nonbonded interactions: 243825 Sorted by model distance: nonbonded pdb=" O ASN C 439 " pdb=" OG SER C 443 " model vdw 2.197 3.040 nonbonded pdb=" O CYS A 617 " pdb=" N GLU A 619 " model vdw 2.203 3.120 nonbonded pdb=" N ASN B 405 " pdb=" O GLY B 504 " model vdw 2.217 3.120 nonbonded pdb=" OG1 THR B 33 " pdb=" O GLY B 219 " model vdw 2.228 3.040 nonbonded pdb=" OH TYR A 369 " pdb=" O PRO A 384 " model vdw 2.231 3.040 ... (remaining 243820 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 29 and (name N or name CA or name C or name O or name CB \ )) or resid 30 through 66 or resid 73 through 236 or (resid 237 and (name N or n \ ame CA or name C or name O or name CB )) or resid 238 through 257 or (resid 258 \ and (name N or name CA or name C or name O or name CB )) or resid 259 through 32 \ 7 or (resid 328 and (name N or name CA or name C or name O or name CB )) or resi \ d 329 through 331 or (resid 332 and (name N or name CA or name C or name O or na \ me CB )) or resid 333 through 345 or (resid 346 and (name N or name CA or name C \ or name O or name CB )) or resid 347 through 356 or (resid 357 and (name N or n \ ame CA or name C or name O or name CB )) or resid 358 through 524 or resid 531 t \ hrough 1099 or (resid 1100 and (name N or name CA or name C or name O or name CB \ )) or resid 1101 through 1150 or resid 1301 through 1307)) selection = (chain 'B' and ((resid 29 and (name N or name CA or name C or name O or name CB \ )) or resid 30 through 66 or resid 73 through 77 or (resid 78 and (name N or nam \ e CA or name C or name O or name CB )) or resid 79 through 167 or (resid 168 and \ (name N or name CA or name C or name O or name CB )) or resid 169 through 330 o \ r (resid 331 through 332 and (name N or name CA or name C or name O or name CB ) \ ) or resid 333 through 337 or (resid 338 and (name N or name CA or name C or nam \ e O or name CB )) or resid 339 or (resid 340 and (name N or name CA or name C or \ name O or name CB )) or resid 341 through 356 or (resid 357 and (name N or name \ CA or name C or name O or name CB )) or resid 358 through 524 or resid 531 thro \ ugh 536 or (resid 537 and (name N or name CA or name C or name O or name CB )) o \ r resid 538 through 579 or (resid 580 and (name N or name CA or name C or name O \ or name CB )) or resid 581 through 853 or (resid 854 through 855 and (name N or \ name CA or name C or name O or name CB )) or resid 856 through 1117 or (resid 1 \ 118 and (name N or name CA or name C or name O or name CB )) or resid 1119 throu \ gh 1150 or resid 1301 through 1307)) selection = (chain 'C' and (resid 29 through 66 or resid 73 through 77 or (resid 78 and (nam \ e N or name CA or name C or name O or name CB )) or resid 79 through 167 or (res \ id 168 and (name N or name CA or name C or name O or name CB )) or resid 169 thr \ ough 236 or (resid 237 and (name N or name CA or name C or name O or name CB )) \ or resid 238 through 327 or (resid 328 and (name N or name CA or name C or name \ O or name CB )) or resid 329 through 330 or (resid 331 through 332 and (name N o \ r name CA or name C or name O or name CB )) or resid 333 through 337 or (resid 3 \ 38 and (name N or name CA or name C or name O or name CB )) or resid 339 or (res \ id 340 and (name N or name CA or name C or name O or name CB )) or resid 341 thr \ ough 345 or (resid 346 and (name N or name CA or name C or name O or name CB )) \ or resid 347 through 524 or resid 531 through 536 or (resid 537 and (name N or n \ ame CA or name C or name O or name CB )) or resid 538 through 579 or (resid 580 \ and (name N or name CA or name C or name O or name CB )) or resid 581 through 85 \ 3 or (resid 854 through 855 and (name N or name CA or name C or name O or name C \ B )) or resid 856 through 1099 or (resid 1100 and (name N or name CA or name C o \ r name O or name CB )) or resid 1101 through 1117 or (resid 1118 and (name N or \ name CA or name C or name O or name CB )) or resid 1119 through 1150 or resid 13 \ 01 through 1307)) } ncs_group { reference = (chain 'E' and (resid 1 through 25 or resid 27 through 72 or (resid 73 and (name \ N or name CA or name C or name O or name CB )) or resid 74 through 76 or (resid \ 77 and (name N or name CA or name C or name O or name CB )) or resid 78 through \ 126)) selection = (chain 'G' and (resid 1 through 25 or resid 27 through 124)) selection = (chain 'I' and (resid 1 through 25 or resid 27 through 72 or (resid 73 and (name \ N or name CA or name C or name O or name CB )) or resid 74 through 76 or (resid \ 77 and (name N or name CA or name C or name O or name CB )) or resid 78 through \ 124)) } ncs_group { reference = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' } 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=0.48 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: 12.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.350 Check model and map are aligned: 0.230 Set scattering table: 0.290 Process input model: 73.810 Find NCS groups from input model: 2.210 Set up NCS constraints: 0.180 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 93.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 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 : 0.007 0.068 29686 Z= 0.408 Angle : 0.955 20.858 40533 Z= 0.592 Chirality : 0.068 1.066 4645 Planarity : 0.016 0.293 5167 Dihedral : 19.292 130.386 11264 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 18.65 Ramachandran Plot: Outliers : 1.73 % Allowed : 11.19 % Favored : 87.08 % Rotamer: Outliers : 6.08 % Allowed : 26.48 % Favored : 67.44 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.62 (0.14), residues: 3593 helix: 0.36 (0.21), residues: 693 sheet: -2.07 (0.19), residues: 683 loop : -2.45 (0.13), residues: 2217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 64 HIS 0.005 0.001 HIS C 954 PHE 0.031 0.002 PHE C1121 TYR 0.039 0.002 TYR A 265 ARG 0.004 0.001 ARG B 44 Details of bonding type rmsd link_NAG-ASN : bond 0.01053 ( 30) link_NAG-ASN : angle 4.37170 ( 90) link_BETA1-4 : bond 0.00688 ( 12) link_BETA1-4 : angle 1.54258 ( 36) hydrogen bonds : bond 0.25178 ( 851) hydrogen bonds : angle 10.37671 ( 2265) SS BOND : bond 0.00979 ( 37) SS BOND : angle 2.04216 ( 74) covalent geometry : bond 0.00659 (29607) covalent geometry : angle 0.92916 (40333) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7186 Ramachandran restraints generated. 3593 Oldfield, 0 Emsley, 3593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7186 Ramachandran restraints generated. 3593 Oldfield, 0 Emsley, 3593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 3138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 186 poor density : 318 time to evaluate : 3.331 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: E 30 GLU cc_start: 0.7972 (tp30) cc_final: 0.7584 (mm-30) REVERT: E 74 ASP cc_start: 0.8290 (t0) cc_final: 0.8072 (p0) REVERT: E 84 MET cc_start: 0.1010 (ptp) cc_final: 0.0751 (mtt) REVERT: G 102 MET cc_start: 0.7512 (pmm) cc_final: 0.6758 (tmm) REVERT: I 68 ARG cc_start: 0.7210 (ptt90) cc_final: 0.6418 (ptm-80) REVERT: I 69 PHE cc_start: 0.7448 (m-80) cc_final: 0.6021 (m-80) REVERT: I 100 TRP cc_start: 0.8703 (m-90) cc_final: 0.8287 (m-90) REVERT: I 111 VAL cc_start: 0.8355 (OUTLIER) cc_final: 0.7966 (t) REVERT: A 65 PHE cc_start: 0.8093 (OUTLIER) cc_final: 0.7736 (t80) REVERT: A 130 VAL cc_start: 0.8394 (OUTLIER) cc_final: 0.7981 (t) REVERT: A 192 PHE cc_start: 0.8439 (m-80) cc_final: 0.7988 (m-10) REVERT: A 237 ARG cc_start: 0.8575 (mmm-85) cc_final: 0.8209 (mmm-85) REVERT: A 242 LEU cc_start: 0.7647 (mp) cc_final: 0.7369 (tp) REVERT: A 357 ARG cc_start: 0.7554 (tmm-80) cc_final: 0.7270 (tmm-80) REVERT: A 371 PHE cc_start: 0.5908 (t80) cc_final: 0.5429 (t80) REVERT: A 377 PHE cc_start: 0.8311 (m-10) cc_final: 0.7780 (m-10) REVERT: A 394 ASN cc_start: 0.7934 (OUTLIER) cc_final: 0.7657 (p0) REVERT: A 421 TYR cc_start: 0.8065 (m-10) cc_final: 0.6978 (m-10) REVERT: A 457 ARG cc_start: 0.6016 (ttm170) cc_final: 0.4575 (tpt90) REVERT: A 558 LYS cc_start: 0.9502 (OUTLIER) cc_final: 0.9271 (mmmt) REVERT: A 621 PRO cc_start: 0.6834 (Cg_exo) cc_final: 0.6628 (Cg_endo) REVERT: B 65 PHE cc_start: 0.7842 (m-80) cc_final: 0.7506 (m-80) REVERT: B 200 TYR cc_start: 0.8953 (m-80) cc_final: 0.8750 (m-10) REVERT: B 207 HIS cc_start: 0.8017 (m-70) cc_final: 0.7774 (m90) REVERT: B 329 PHE cc_start: 0.7894 (OUTLIER) cc_final: 0.7533 (t80) REVERT: B 347 PHE cc_start: 0.6698 (OUTLIER) cc_final: 0.5698 (t80) REVERT: B 382 VAL cc_start: 0.6097 (OUTLIER) cc_final: 0.5893 (t) REVERT: B 390 LEU cc_start: 0.9188 (OUTLIER) cc_final: 0.8963 (mm) REVERT: B 420 ASP cc_start: 0.8583 (m-30) cc_final: 0.8222 (m-30) REVERT: B 508 TYR cc_start: 0.7682 (m-80) cc_final: 0.7232 (m-10) REVERT: B 580 GLN cc_start: 0.7901 (OUTLIER) cc_final: 0.7418 (mt0) REVERT: B 710 ASN cc_start: 0.8980 (OUTLIER) cc_final: 0.8724 (p0) REVERT: B 1002 GLN cc_start: 0.8668 (tm-30) cc_final: 0.8191 (tm-30) REVERT: B 1005 GLN cc_start: 0.8964 (tp40) cc_final: 0.8737 (mm-40) REVERT: B 1101 HIS cc_start: 0.8607 (OUTLIER) cc_final: 0.8039 (m90) REVERT: C 118 LEU cc_start: 0.8649 (tp) cc_final: 0.8331 (tp) REVERT: C 153 MET cc_start: 0.6182 (mmm) cc_final: 0.5341 (ptp) REVERT: C 157 PHE cc_start: 0.8556 (p90) cc_final: 0.8313 (p90) REVERT: C 265 TYR cc_start: 0.7490 (p90) cc_final: 0.7180 (p90) REVERT: C 449 TYR cc_start: 0.8346 (m-80) cc_final: 0.8063 (m-80) REVERT: C 505 HIS cc_start: 0.8499 (t-90) cc_final: 0.8216 (t-90) REVERT: C 515 PHE cc_start: 0.8225 (m-80) cc_final: 0.7960 (m-80) REVERT: C 565 PHE cc_start: 0.7160 (m-80) cc_final: 0.6307 (m-10) REVERT: C 583 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.8134 (tp30) REVERT: C 584 ILE cc_start: 0.9015 (OUTLIER) cc_final: 0.8329 (tt) REVERT: C 994 ASP cc_start: 0.8774 (m-30) cc_final: 0.8530 (t0) outliers start: 186 outliers final: 59 residues processed: 489 average time/residue: 0.4189 time to fit residues: 327.0865 Evaluate side-chains 285 residues out of total 3138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 212 time to evaluate : 2.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 52 ILE Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain I residue 113 TYR Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 78 ARG Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 248 TYR Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 580 GLN Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 624 ILE Chi-restraints excluded: chain B residue 710 ASN Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 74 ASN Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 280 ASN Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 583 GLU Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 303 optimal weight: 8.9990 chunk 272 optimal weight: 2.9990 chunk 151 optimal weight: 0.9980 chunk 93 optimal weight: 0.7980 chunk 184 optimal weight: 7.9990 chunk 145 optimal weight: 0.4980 chunk 282 optimal weight: 5.9990 chunk 109 optimal weight: 0.6980 chunk 171 optimal weight: 4.9990 chunk 210 optimal weight: 0.6980 chunk 326 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 78 ASN I 59 HIS A 61 ASN ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 ASN A 542 ASN A 856 ASN A 926 GLN A 965 GLN A 992 GLN B 74 ASN B 239 GLN B 331 ASN B 394 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN B 644 GLN B 677 GLN ** C 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 519 HIS C 542 ASN ** C 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 751 ASN C1002 GLN C1101 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.129038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.085946 restraints weight = 151690.122| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 5.09 r_work: 0.3035 rms_B_bonded: 4.87 restraints_weight: 0.5000 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3037 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3037 r_free = 0.3037 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3037 r_free = 0.3037 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3037 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 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 : 0.004 0.058 29686 Z= 0.162 Angle : 0.768 22.711 40533 Z= 0.377 Chirality : 0.048 0.333 4645 Planarity : 0.005 0.079 5167 Dihedral : 11.803 104.963 5048 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.42 % Allowed : 9.10 % Favored : 90.49 % Rotamer: Outliers : 5.21 % Allowed : 27.25 % Favored : 67.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.35 (0.14), residues: 3593 helix: 0.71 (0.20), residues: 710 sheet: -2.01 (0.18), residues: 731 loop : -2.29 (0.13), residues: 2152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 104 HIS 0.006 0.001 HIS A 207 PHE 0.022 0.002 PHE I 38 TYR 0.021 0.002 TYR B 453 ARG 0.011 0.001 ARG C 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00798 ( 30) link_NAG-ASN : angle 4.13707 ( 90) link_BETA1-4 : bond 0.00418 ( 12) link_BETA1-4 : angle 1.35770 ( 36) hydrogen bonds : bond 0.04910 ( 851) hydrogen bonds : angle 7.13463 ( 2265) SS BOND : bond 0.00741 ( 37) SS BOND : angle 1.66952 ( 74) covalent geometry : bond 0.00354 (29607) covalent geometry : angle 0.74041 (40333) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7186 Ramachandran restraints generated. 3593 Oldfield, 0 Emsley, 3593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7186 Ramachandran restraints generated. 3593 Oldfield, 0 Emsley, 3593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 3138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 242 time to evaluate : 3.287 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: E 30 GLU cc_start: 0.7730 (tp30) cc_final: 0.7492 (mm-30) REVERT: E 74 ASP cc_start: 0.8241 (t0) cc_final: 0.8009 (p0) REVERT: G 52 ILE cc_start: 0.4596 (OUTLIER) cc_final: 0.4251 (mm) REVERT: I 35 MET cc_start: 0.7462 (mmm) cc_final: 0.7185 (tpt) REVERT: I 49 VAL cc_start: 0.7207 (OUTLIER) cc_final: 0.6988 (m) REVERT: I 84 MET cc_start: 0.5715 (ptp) cc_final: 0.4666 (mtp) REVERT: I 105 LEU cc_start: 0.6357 (tt) cc_final: 0.5649 (mm) REVERT: A 64 TRP cc_start: 0.6532 (t60) cc_final: 0.6211 (t60) REVERT: A 65 PHE cc_start: 0.8344 (OUTLIER) cc_final: 0.7877 (t80) REVERT: A 130 VAL cc_start: 0.8453 (OUTLIER) cc_final: 0.8222 (t) REVERT: A 228 ASP cc_start: 0.8585 (t0) cc_final: 0.8249 (t0) REVERT: A 237 ARG cc_start: 0.8473 (mmm-85) cc_final: 0.8201 (mmm-85) REVERT: A 258 TRP cc_start: 0.6813 (m-90) cc_final: 0.6057 (m-90) REVERT: A 294 ASP cc_start: 0.8308 (OUTLIER) cc_final: 0.8102 (t70) REVERT: A 357 ARG cc_start: 0.7430 (tmm-80) cc_final: 0.7097 (tmm-80) REVERT: A 374 PHE cc_start: 0.8363 (p90) cc_final: 0.8008 (p90) REVERT: A 377 PHE cc_start: 0.8560 (m-10) cc_final: 0.7754 (m-10) REVERT: A 421 TYR cc_start: 0.8081 (m-10) cc_final: 0.7173 (m-10) REVERT: A 457 ARG cc_start: 0.6028 (ttm170) cc_final: 0.4525 (tpt-90) REVERT: A 559 PHE cc_start: 0.8369 (OUTLIER) cc_final: 0.7572 (m-80) REVERT: A 721 SER cc_start: 0.9415 (OUTLIER) cc_final: 0.9208 (p) REVERT: A 967 SER cc_start: 0.9434 (OUTLIER) cc_final: 0.9188 (m) REVERT: A 979 ASP cc_start: 0.8855 (t70) cc_final: 0.8440 (t70) REVERT: A 1050 MET cc_start: 0.8871 (ptt) cc_final: 0.8590 (ptt) REVERT: B 157 PHE cc_start: 0.8316 (p90) cc_final: 0.7913 (p90) REVERT: B 207 HIS cc_start: 0.8080 (m-70) cc_final: 0.7859 (m90) REVERT: B 215 ASP cc_start: 0.7643 (OUTLIER) cc_final: 0.7421 (p0) REVERT: B 329 PHE cc_start: 0.8506 (OUTLIER) cc_final: 0.8013 (t80) REVERT: B 347 PHE cc_start: 0.6235 (OUTLIER) cc_final: 0.5563 (t80) REVERT: B 390 LEU cc_start: 0.9197 (OUTLIER) cc_final: 0.8951 (mm) REVERT: B 508 TYR cc_start: 0.7658 (m-10) cc_final: 0.7181 (m-10) REVERT: B 619 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7549 (mt-10) REVERT: B 973 ILE cc_start: 0.9593 (OUTLIER) cc_final: 0.9306 (mm) REVERT: B 979 ASP cc_start: 0.9012 (m-30) cc_final: 0.8793 (t70) REVERT: B 1002 GLN cc_start: 0.9066 (tm-30) cc_final: 0.8583 (tm-30) REVERT: C 65 PHE cc_start: 0.8328 (m-80) cc_final: 0.7805 (t80) REVERT: C 153 MET cc_start: 0.5567 (mmm) cc_final: 0.4744 (ptp) REVERT: C 157 PHE cc_start: 0.8132 (p90) cc_final: 0.7810 (p90) REVERT: C 259 THR cc_start: 0.7740 (OUTLIER) cc_final: 0.7278 (m) REVERT: C 265 TYR cc_start: 0.7829 (p90) cc_final: 0.7415 (p90) REVERT: C 449 TYR cc_start: 0.8623 (m-80) cc_final: 0.8282 (m-80) REVERT: C 477 ASN cc_start: 0.7494 (OUTLIER) cc_final: 0.6904 (t0) REVERT: C 495 TYR cc_start: 0.7248 (OUTLIER) cc_final: 0.6867 (m-80) REVERT: C 505 HIS cc_start: 0.8601 (t-90) cc_final: 0.8264 (t-90) REVERT: C 583 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7842 (tp30) REVERT: C 584 ILE cc_start: 0.8956 (OUTLIER) cc_final: 0.8678 (mm) REVERT: C 994 ASP cc_start: 0.8855 (m-30) cc_final: 0.8610 (t0) outliers start: 159 outliers final: 49 residues processed: 384 average time/residue: 0.5216 time to fit residues: 328.3609 Evaluate side-chains 279 residues out of total 3138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 211 time to evaluate : 3.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 52 ILE Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 186 PHE Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 967 SER Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 624 ILE Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 74 ASN Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 280 ASN Chi-restraints excluded: chain C residue 306 PHE Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 342 PHE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 477 ASN Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 583 GLU Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 973 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 193 optimal weight: 5.9990 chunk 147 optimal weight: 7.9990 chunk 302 optimal weight: 4.9990 chunk 66 optimal weight: 0.0970 chunk 333 optimal weight: 2.9990 chunk 19 optimal weight: 50.0000 chunk 230 optimal weight: 0.9980 chunk 356 optimal weight: 3.9990 chunk 33 optimal weight: 7.9990 chunk 69 optimal weight: 0.9980 chunk 82 optimal weight: 6.9990 overall best weight: 1.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 59 HIS ** I 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 422 ASN ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 564 GLN B1119 ASN C 81 ASN ** C 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 245 HIS C 394 ASN C 474 GLN C 709 ASN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.121750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.074954 restraints weight = 140162.546| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 5.20 r_work: 0.2986 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2987 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2987 r_free = 0.2987 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2987 r_free = 0.2987 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2987 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 29686 Z= 0.209 Angle : 0.721 18.127 40533 Z= 0.353 Chirality : 0.047 0.592 4645 Planarity : 0.005 0.076 5167 Dihedral : 10.070 106.497 4976 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.31 % Allowed : 9.71 % Favored : 89.98 % Rotamer: Outliers : 5.44 % Allowed : 27.32 % Favored : 67.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.14), residues: 3593 helix: 0.98 (0.20), residues: 689 sheet: -2.04 (0.18), residues: 719 loop : -2.19 (0.13), residues: 2185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP B 104 HIS 0.004 0.001 HIS B1083 PHE 0.028 0.002 PHE A 79 TYR 0.026 0.002 TYR B 495 ARG 0.016 0.001 ARG B 498 Details of bonding type rmsd link_NAG-ASN : bond 0.00719 ( 30) link_NAG-ASN : angle 3.44550 ( 90) link_BETA1-4 : bond 0.00246 ( 12) link_BETA1-4 : angle 1.52728 ( 36) hydrogen bonds : bond 0.04582 ( 851) hydrogen bonds : angle 6.56362 ( 2265) SS BOND : bond 0.00461 ( 37) SS BOND : angle 1.72352 ( 74) covalent geometry : bond 0.00475 (29607) covalent geometry : angle 0.69917 (40333) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7186 Ramachandran restraints generated. 3593 Oldfield, 0 Emsley, 3593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7186 Ramachandran restraints generated. 3593 Oldfield, 0 Emsley, 3593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 3138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 222 time to evaluate : 3.771 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: E 30 GLU cc_start: 0.7646 (tp30) cc_final: 0.7380 (mm-30) REVERT: E 74 ASP cc_start: 0.8208 (t0) cc_final: 0.8001 (p0) REVERT: I 35 MET cc_start: 0.7340 (mmm) cc_final: 0.7130 (tpt) REVERT: I 69 PHE cc_start: 0.6894 (m-80) cc_final: 0.6243 (m-80) REVERT: A 104 TRP cc_start: 0.6471 (m-90) cc_final: 0.6184 (m-90) REVERT: A 130 VAL cc_start: 0.8581 (OUTLIER) cc_final: 0.8322 (t) REVERT: A 237 ARG cc_start: 0.8553 (mmm-85) cc_final: 0.8235 (mmm-85) REVERT: A 357 ARG cc_start: 0.7499 (tmm-80) cc_final: 0.7140 (tmm-80) REVERT: A 374 PHE cc_start: 0.8473 (p90) cc_final: 0.7996 (p90) REVERT: A 377 PHE cc_start: 0.8645 (m-10) cc_final: 0.7849 (m-10) REVERT: A 391 CYS cc_start: 0.8455 (p) cc_final: 0.8239 (m) REVERT: A 421 TYR cc_start: 0.8065 (m-10) cc_final: 0.7186 (m-10) REVERT: A 457 ARG cc_start: 0.6105 (ttm170) cc_final: 0.4737 (tpt-90) REVERT: A 559 PHE cc_start: 0.8444 (OUTLIER) cc_final: 0.7515 (m-80) REVERT: A 661 GLU cc_start: 0.8473 (tp30) cc_final: 0.8260 (tp30) REVERT: B 65 PHE cc_start: 0.8141 (m-80) cc_final: 0.7792 (m-80) REVERT: B 157 PHE cc_start: 0.8411 (p90) cc_final: 0.8057 (p90) REVERT: B 212 LEU cc_start: 0.6117 (OUTLIER) cc_final: 0.5787 (pp) REVERT: B 347 PHE cc_start: 0.5987 (OUTLIER) cc_final: 0.5591 (t80) REVERT: B 492 LEU cc_start: 0.6649 (OUTLIER) cc_final: 0.5446 (mt) REVERT: B 619 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.7666 (mt-10) REVERT: B 740 MET cc_start: 0.9298 (mmm) cc_final: 0.9032 (tpp) REVERT: B 973 ILE cc_start: 0.9575 (OUTLIER) cc_final: 0.9302 (mm) REVERT: B 1002 GLN cc_start: 0.9051 (tm-30) cc_final: 0.8603 (tm-30) REVERT: C 65 PHE cc_start: 0.8347 (m-80) cc_final: 0.7934 (t80) REVERT: C 153 MET cc_start: 0.5704 (mmm) cc_final: 0.4840 (ptp) REVERT: C 157 PHE cc_start: 0.8202 (p90) cc_final: 0.7940 (p90) REVERT: C 226 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8835 (mm) REVERT: C 259 THR cc_start: 0.7912 (OUTLIER) cc_final: 0.7674 (m) REVERT: C 265 TYR cc_start: 0.7949 (p90) cc_final: 0.7574 (p90) REVERT: C 280 ASN cc_start: 0.7953 (OUTLIER) cc_final: 0.7741 (p0) REVERT: C 449 TYR cc_start: 0.8650 (m-80) cc_final: 0.8281 (m-80) REVERT: C 477 ASN cc_start: 0.7571 (OUTLIER) cc_final: 0.7007 (t0) REVERT: C 505 HIS cc_start: 0.8626 (t-90) cc_final: 0.8281 (t-90) REVERT: C 584 ILE cc_start: 0.8950 (OUTLIER) cc_final: 0.8653 (mm) REVERT: C 994 ASP cc_start: 0.8904 (m-30) cc_final: 0.8682 (t0) outliers start: 165 outliers final: 75 residues processed: 367 average time/residue: 0.4297 time to fit residues: 261.1206 Evaluate side-chains 288 residues out of total 3138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 201 time to evaluate : 3.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain I residue 38 PHE Chi-restraints excluded: chain I residue 78 ASN Chi-restraints excluded: chain I residue 95 TYR Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 134 GLN Chi-restraints excluded: chain A residue 186 PHE Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 78 ARG Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 624 ILE Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain C residue 74 ASN Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 280 ASN Chi-restraints excluded: chain C residue 306 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 342 PHE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 477 ASN Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 63.1725 > 50: distance: 74 - 170: 35.371 distance: 77 - 167: 26.702 distance: 90 - 157: 18.552 distance: 124 - 128: 28.092 distance: 128 - 129: 16.909 distance: 129 - 130: 10.097 distance: 130 - 131: 24.712 distance: 130 - 132: 9.881 distance: 132 - 133: 7.915 distance: 133 - 134: 19.682 distance: 133 - 136: 17.979 distance: 134 - 135: 42.569 distance: 134 - 139: 4.154 distance: 136 - 137: 28.200 distance: 136 - 138: 15.426 distance: 139 - 140: 21.229 distance: 140 - 141: 12.950 distance: 140 - 143: 19.755 distance: 141 - 142: 15.662 distance: 141 - 147: 11.084 distance: 143 - 144: 10.912 distance: 143 - 145: 20.099 distance: 144 - 146: 10.277 distance: 147 - 148: 16.884 distance: 148 - 149: 23.066 distance: 148 - 151: 5.851 distance: 149 - 150: 23.903 distance: 149 - 154: 32.508 distance: 151 - 152: 18.617 distance: 151 - 153: 19.232 distance: 154 - 155: 21.295 distance: 155 - 156: 11.900 distance: 155 - 158: 7.203 distance: 156 - 157: 24.953 distance: 156 - 162: 21.127 distance: 158 - 159: 7.088 distance: 159 - 160: 5.387 distance: 159 - 161: 7.830 distance: 162 - 163: 16.597 distance: 163 - 164: 46.442 distance: 163 - 166: 28.492 distance: 164 - 165: 39.554 distance: 164 - 167: 15.948 distance: 167 - 168: 42.887 distance: 168 - 169: 57.641 distance: 168 - 171: 50.881 distance: 169 - 170: 52.518 distance: 169 - 174: 63.172 distance: 171 - 172: 19.633 distance: 171 - 173: 15.186 distance: 174 - 175: 45.286 distance: 175 - 176: 29.261 distance: 175 - 178: 29.261 distance: 176 - 177: 17.913 distance: 176 - 182: 12.701 distance: 178 - 179: 19.585 distance: 179 - 180: 13.204 distance: 179 - 181: 14.169 distance: 182 - 183: 24.619 distance: 183 - 184: 42.933 distance: 183 - 186: 41.688 distance: 184 - 185: 44.750 distance: 184 - 188: 17.322 distance: 186 - 187: 33.634 distance: 187 - 221: 4.575 distance: 188 - 189: 41.358 distance: 189 - 190: 15.887 distance: 189 - 192: 45.533 distance: 190 - 191: 22.604 distance: 190 - 193: 26.916