Starting phenix.real_space_refine on Sun Jul 5 08:36:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7l56_23165/07_2026/7l56_23165.cif Found real_map, /net/cci-nas-00/data/ceres_data/7l56_23165/07_2026/7l56_23165.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7l56_23165/07_2026/7l56_23165.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7l56_23165/07_2026/7l56_23165.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7l56_23165/07_2026/7l56_23165.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7l56_23165/07_2026/7l56_23165.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7l56_23165/07_2026/7l56_23165.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7l56_23165/07_2026/7l56_23165.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.002 sd= 0.024 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 132 5.16 5 C 16951 2.51 5 N 4432 2.21 5 O 5068 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 150 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 26583 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 7128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 983, 7128 Classifications: {'peptide': 983} Incomplete info: {'truncation_to_alanine': 174} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 933} Chain breaks: 10 Unresolved non-hydrogen bonds: 552 Unresolved non-hydrogen angles: 682 Unresolved non-hydrogen dihedrals: 427 Unresolved non-hydrogen chiralities: 59 Planarities with less than four sites: {'ASN:plan1': 13, 'ASP:plan': 18, 'GLN:plan1': 11, 'HIS:plan': 1, 'GLU:plan': 14, 'ARG:plan': 10, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 255 Chain: "B" Number of atoms: 6870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 992, 6870 Classifications: {'peptide': 992} Incomplete info: {'truncation_to_alanine': 289} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 942} Chain breaks: 9 Unresolved non-hydrogen bonds: 888 Unresolved non-hydrogen angles: 1115 Unresolved non-hydrogen dihedrals: 676 Unresolved non-hydrogen chiralities: 93 Planarities with less than four sites: {'ASN:plan1': 26, 'ASP:plan': 39, 'GLN:plan1': 15, 'HIS:plan': 2, 'GLU:plan': 27, 'ARG:plan': 12, 'PHE:plan': 4, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 464 Chain: "C" Number of atoms: 6947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 994, 6947 Classifications: {'peptide': 994} Incomplete info: {'truncation_to_alanine': 263} Link IDs: {'PCIS': 1, 'PTRANS': 49, 'TRANS': 943} Chain breaks: 10 Unresolved non-hydrogen bonds: 818 Unresolved non-hydrogen angles: 1019 Unresolved non-hydrogen dihedrals: 630 Unresolved non-hydrogen chiralities: 82 Planarities with less than four sites: {'ASP:plan': 31, 'GLN:plan1': 13, 'HIS:plan': 2, 'GLU:plan': 31, 'ASN:plan1': 19, 'PHE:plan': 3, 'ARG:plan': 12, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 421 Chain: "F" Number of atoms: 872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 872 Classifications: {'peptide': 129} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 3, 'TRANS': 125} Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 159 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 7, 'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 54 Chain: "G" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 688 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'PTRANS': 5, 'TRANS': 104} Unresolved non-hydrogen bonds: 118 Unresolved non-hydrogen angles: 146 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 3, 'ASN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 41 Chain: "H" Number of atoms: 882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 882 Classifications: {'peptide': 129} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 3, 'TRANS': 125} Unresolved non-hydrogen bonds: 116 Unresolved non-hydrogen angles: 146 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 51 Chain: "J" Number of atoms: 901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 901 Classifications: {'peptide': 129} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 3, 'TRANS': 125} Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 123 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 2, 'GLU:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 39 Chain: "K" Number of atoms: 694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 694 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 5, 'TRANS': 104} Unresolved non-hydrogen bonds: 112 Unresolved non-hydrogen angles: 140 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 3, 'ASN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 41 Chain: "L" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 708 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 5, 'TRANS': 104} Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 124 Unresolved non-hydrogen dihedrals: 72 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 3, 'ASN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 32 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 97 Unusual residues: {'BMA': 1, 'GAL': 1, 'MAN': 3, 'NAG': 3} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "M" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 97 Unusual residues: {'BMA': 1, 'GAL': 1, 'MAN': 3, 'NAG': 3} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 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 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 chiralities: 2 Chain: "P" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 97 Unusual residues: {'BMA': 1, 'GAL': 1, 'MAN': 3, 'NAG': 3} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 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 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 chiralities: 2 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 5.79, per 1000 atoms: 0.22 Number of scatterers: 26583 At special positions: 0 Unit cell: (140.714, 136.482, 187.266, 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 132 16.00 O 5068 8.00 N 4432 7.00 C 16951 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, 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=2.04 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 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=2.04 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=2.01 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.08 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.02 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.02 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.04 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 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=2.03 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=2.04 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.04 Simple disulfide: pdb=" SG CYS F 100 " - pdb=" SG CYS F 100E" distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 100 " - pdb=" SG CYS H 100E" distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.04 Simple disulfide: pdb=" SG CYS J 100 " - pdb=" SG CYS J 100E" distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.02 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 ALPHA1-3 " BMA I 3 " - " MAN I 4 " " MAN I 7 " - " MAN I 8 " " BMA M 3 " - " MAN M 4 " " BMA P 3 " - " MAN P 7 " ALPHA1-6 " BMA I 3 " - " MAN I 7 " " BMA M 3 " - " MAN M 7 " " MAN M 7 " - " MAN M 8 " " BMA P 3 " - " MAN P 4 " " MAN P 7 " - " MAN P 8 " BETA1-2 " MAN I 4 " - " NAG I 5 " " MAN M 4 " - " NAG M 5 " " MAN P 4 " - " NAG P 5 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG I 5 " - " GAL I 6 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG M 5 " - " GAL M 6 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG P 5 " - " GAL P 6 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " NAG-ASN " NAG A1301 " - " ASN A1134 " " NAG A1302 " - " ASN A1074 " " NAG A1303 " - " ASN A 801 " " NAG A1304 " - " ASN A 709 " " NAG A1305 " - " ASN A 657 " " NAG A1306 " - " ASN A 616 " " NAG A1307 " - " ASN A 603 " " NAG A1308 " - " ASN A 61 " " NAG A1309 " - " ASN A 282 " " NAG A1310 " - " ASN A 331 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 282 " " NAG B1303 " - " ASN B 331 " " NAG B1304 " - " ASN B 603 " " NAG B1305 " - " ASN B 657 " " NAG B1306 " - " ASN B 709 " " NAG B1307 " - " ASN B 801 " " NAG B1308 " - " ASN B1074 " " NAG B1309 " - " ASN B1134 " " NAG B1310 " - " ASN B 165 " " NAG C1301 " - " ASN C 165 " " NAG C1302 " - " ASN C 282 " " NAG C1303 " - " ASN C 331 " " NAG C1304 " - " ASN C 603 " " NAG C1305 " - " ASN C 616 " " NAG C1306 " - " ASN C 657 " " NAG C1307 " - " ASN C 709 " " NAG C1308 " - " ASN C 801 " " NAG C1309 " - " ASN C1074 " " NAG C1310 " - " ASN C1134 " " NAG C1311 " - " ASN C 61 " " NAG D 1 " - " ASN A1098 " " NAG E 1 " - " ASN A 717 " " NAG I 1 " - " ASN A 343 " " NAG M 1 " - " ASN B 343 " " NAG N 1 " - " ASN B 717 " " NAG O 1 " - " ASN B1098 " " NAG P 1 " - " ASN C 343 " " NAG Q 1 " - " ASN C 717 " " NAG R 1 " - " ASN C1098 " Time building additional restraints: 3.36 Conformation dependent library (CDL) restraints added in 1.2 seconds 7220 Ramachandran restraints generated. 3610 Oldfield, 0 Emsley, 3610 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6818 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 68 sheets defined 22.0% alpha, 26.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.27 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 342 removed outlier: 3.909A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 removed outlier: 4.116A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.899A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.207A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.739A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.764A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 913 through 918 Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.685A pdb=" N THR A 941 " --> pdb=" O SER A 937 " (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 removed outlier: 4.653A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) 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: 3.646A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.485A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 341 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.221A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 542 through 546 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 4.634A pdb=" N ASN B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 805 removed outlier: 4.370A pdb=" N GLN B 804 " --> pdb=" O ASN B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.552A pdb=" N ASN B 824 " --> pdb=" O ASP B 820 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.703A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 918 Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.667A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.126A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.761A pdb=" N LEU B 981 " --> pdb=" O LEU B 977 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N SER B 982 " --> pdb=" O ASN B 978 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.688A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 342 removed outlier: 3.936A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 386 through 389 Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.260A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 616 through 620 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.614A pdb=" N ASN C 751 " --> pdb=" O THR C 747 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 4.111A pdb=" N ASN C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 805 removed outlier: 4.072A pdb=" N GLN C 804 " --> pdb=" O ASN C 801 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.789A pdb=" N ASN C 824 " --> pdb=" O ASP C 820 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.671A pdb=" N GLY C 885 " --> pdb=" O THR C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.673A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 939 Processing helix chain 'C' and resid 941 through 944 Processing helix chain 'C' and resid 945 through 967 removed outlier: 4.220A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N SER C 967 " --> pdb=" O VAL C 963 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.786A pdb=" N ARG C 983 " --> pdb=" O ASP C 979 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.195A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ASP C 994 " --> pdb=" O GLU C 990 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 32 removed outlier: 3.902A pdb=" N TYR F 32 " --> pdb=" O PHE F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 73 through 75 No H-bonds generated for 'chain 'F' and resid 73 through 75' Processing helix chain 'F' and resid 83 through 87 Processing helix chain 'H' and resid 28 through 30 No H-bonds generated for 'chain 'H' and resid 28 through 30' Processing helix chain 'H' and resid 73 through 75 No H-bonds generated for 'chain 'H' and resid 73 through 75' Processing helix chain 'H' and resid 83 through 87 removed outlier: 4.123A pdb=" N THR H 87 " --> pdb=" O SER H 84 " (cutoff:3.500A) Processing helix chain 'J' and resid 28 through 30 No H-bonds generated for 'chain 'J' and resid 28 through 30' Processing helix chain 'J' and resid 61 through 64 Processing helix chain 'J' and resid 73 through 75 No H-bonds generated for 'chain 'J' and resid 73 through 75' Processing helix chain 'K' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 7.780A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 51 removed outlier: 3.731A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA4, first strand: chain 'A' and resid 116 through 117 removed outlier: 3.733A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.450A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.623A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.633A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL A 524 " --> pdb=" O PHE A 392 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 538 through 541 removed outlier: 5.986A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 656 removed outlier: 6.099A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.401A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 8.471A pdb=" N VAL A 656 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 703 through 704 removed outlier: 6.642A pdb=" N ASN A 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.980A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.477A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1123 Processing sheet with id=AB7, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB8, first strand: chain 'B' and resid 29 through 30 removed outlier: 3.670A pdb=" N THR B 29 " --> pdb=" O VAL B 62 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL B 62 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 42 through 43 removed outlier: 6.078A pdb=" N PHE B 43 " --> pdb=" O ARG C 567 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.756A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 54 through 55 Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC4, first strand: chain 'B' and resid 134 through 135 Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 319 removed outlier: 7.026A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.649A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.649A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.726A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL B 524 " --> pdb=" O PHE B 392 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD1, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD2, first strand: chain 'B' and resid 538 through 541 removed outlier: 6.080A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N THR B 573 " --> pdb=" O ASP B 568 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N ASP B 568 " --> pdb=" O THR B 573 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 654 through 660 removed outlier: 3.684A pdb=" N GLU B 654 " --> pdb=" O ILE B 692 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N THR B 696 " --> pdb=" O VAL B 656 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ASN B 658 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 711 through 718 removed outlier: 6.931A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 721 through 728 removed outlier: 5.604A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.418A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 1120 through 1123 removed outlier: 3.681A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD9, first strand: chain 'C' and resid 28 through 30 removed outlier: 7.767A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.260A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.285A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 47 through 51 removed outlier: 3.750A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AE3, first strand: chain 'C' and resid 126 through 127 Processing sheet with id=AE4, first strand: chain 'C' and resid 134 through 135 Processing sheet with id=AE5, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.403A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.809A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.693A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL C 524 " --> pdb=" O PHE C 392 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE9, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AF1, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.139A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.511A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.891A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.891A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.504A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 1120 through 1123 Processing sheet with id=AF6, first strand: chain 'C' and resid 1094 through 1096 Processing sheet with id=AF7, first strand: chain 'F' and resid 3 through 6 removed outlier: 3.782A pdb=" N THR F 77 " --> pdb=" O ASP F 72 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'F' and resid 57 through 59 removed outlier: 5.176A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N VAL F 102 " --> pdb=" O ARG F 94 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'F' and resid 57 through 59 removed outlier: 5.176A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'G' and resid 21 through 22 Processing sheet with id=AG2, first strand: chain 'G' and resid 45 through 48 removed outlier: 6.283A pdb=" N TRP G 35 " --> pdb=" O MET G 47 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.673A pdb=" N THR H 77 " --> pdb=" O ASP H 72 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'H' and resid 57 through 59 removed outlier: 3.899A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LEU H 96 " --> pdb=" O TYR H 33 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N HIS H 35 " --> pdb=" O ARG H 94 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N ARG H 94 " --> pdb=" O HIS H 35 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N VAL H 37 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N CYS H 92 " --> pdb=" O VAL H 37 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N VAL H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'H' and resid 100G through 100I removed outlier: 6.222A pdb=" N GLY H 97 " --> pdb=" O ASP H 100H" (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'J' and resid 3 through 6 removed outlier: 3.998A pdb=" N THR J 77 " --> pdb=" O ASP J 72 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'J' and resid 57 through 59 removed outlier: 3.509A pdb=" N GLY J 49 " --> pdb=" O TRP J 36 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N LEU J 96 " --> pdb=" O TYR J 33 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N HIS J 35 " --> pdb=" O ARG J 94 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N ARG J 94 " --> pdb=" O HIS J 35 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL J 37 " --> pdb=" O CYS J 92 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N CYS J 92 " --> pdb=" O VAL J 37 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N VAL J 102 " --> pdb=" O ARG J 94 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'J' and resid 57 through 59 removed outlier: 3.509A pdb=" N GLY J 49 " --> pdb=" O TRP J 36 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N LEU J 96 " --> pdb=" O TYR J 33 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N HIS J 35 " --> pdb=" O ARG J 94 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N ARG J 94 " --> pdb=" O HIS J 35 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL J 37 " --> pdb=" O CYS J 92 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N CYS J 92 " --> pdb=" O VAL J 37 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'K' and resid 21 through 22 Processing sheet with id=AH1, first strand: chain 'K' and resid 45 through 48 removed outlier: 6.613A pdb=" N TRP K 35 " --> pdb=" O MET K 47 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASP K 85 " --> pdb=" O GLN K 38 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'K' and resid 45 through 48 removed outlier: 6.613A pdb=" N TRP K 35 " --> pdb=" O MET K 47 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASP K 85 " --> pdb=" O GLN K 38 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'L' and resid 20 through 22 Processing sheet with id=AH4, first strand: chain 'L' and resid 45 through 48 removed outlier: 6.458A pdb=" N TRP L 35 " --> pdb=" O MET L 47 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'L' and resid 45 through 48 removed outlier: 6.458A pdb=" N TRP L 35 " --> pdb=" O MET L 47 " (cutoff:3.500A) 1123 hydrogen bonds defined for protein. 2952 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: 7.18 Time building geometry restraints manager: 3.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.36: 8803 1.36 - 1.50: 8694 1.50 - 1.65: 9547 1.65 - 1.79: 84 1.79 - 1.94: 83 Bond restraints: 27211 Sorted by residual: bond pdb=" C1 NAG C1303 " pdb=" O5 NAG C1303 " ideal model delta sigma weight residual 1.406 1.502 -0.096 2.00e-02 2.50e+03 2.31e+01 bond pdb=" C1 NAG I 5 " pdb=" O5 NAG I 5 " ideal model delta sigma weight residual 1.406 1.496 -0.090 2.00e-02 2.50e+03 2.03e+01 bond pdb=" CB CYS B 379 " pdb=" SG CYS B 379 " ideal model delta sigma weight residual 1.808 1.936 -0.128 3.30e-02 9.18e+02 1.51e+01 bond pdb=" C1 NAG B1308 " pdb=" O5 NAG B1308 " ideal model delta sigma weight residual 1.406 1.479 -0.073 2.00e-02 2.50e+03 1.32e+01 bond pdb=" CB CYS B 432 " pdb=" SG CYS B 432 " ideal model delta sigma weight residual 1.808 1.692 0.116 3.30e-02 9.18e+02 1.23e+01 ... (remaining 27206 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.68: 37217 5.68 - 11.36: 99 11.36 - 17.03: 0 17.03 - 22.71: 0 22.71 - 28.39: 1 Bond angle restraints: 37317 Sorted by residual: angle pdb=" CA CYS B 432 " pdb=" CB CYS B 432 " pdb=" SG CYS B 432 " ideal model delta sigma weight residual 114.40 142.79 -28.39 2.30e+00 1.89e-01 1.52e+02 angle pdb=" C ASN F 52 " pdb=" CA ASN F 52 " pdb=" CB ASN F 52 " ideal model delta sigma weight residual 110.33 105.11 5.22 1.02e+00 9.61e-01 2.62e+01 angle pdb=" N ASP J 100H" pdb=" CA ASP J 100H" pdb=" C ASP J 100H" ideal model delta sigma weight residual 111.02 116.72 -5.70 1.22e+00 6.72e-01 2.18e+01 angle pdb=" N PHE C 565 " pdb=" CA PHE C 565 " pdb=" CB PHE C 565 " ideal model delta sigma weight residual 111.55 103.44 8.11 1.74e+00 3.30e-01 2.17e+01 angle pdb=" NE ARG A 328 " pdb=" CZ ARG A 328 " pdb=" NH2 ARG A 328 " ideal model delta sigma weight residual 119.20 115.13 4.07 9.00e-01 1.23e+00 2.05e+01 ... (remaining 37312 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.56: 14108 17.56 - 35.11: 922 35.11 - 52.67: 113 52.67 - 70.23: 32 70.23 - 87.79: 23 Dihedral angle restraints: 15198 sinusoidal: 4550 harmonic: 10648 Sorted by residual: dihedral pdb=" CB CYS B 480 " pdb=" SG CYS B 480 " pdb=" SG CYS B 488 " pdb=" CB CYS B 488 " ideal model delta sinusoidal sigma weight residual 93.00 154.04 -61.04 1 1.00e+01 1.00e-02 4.95e+01 dihedral pdb=" CB CYS B 379 " pdb=" SG CYS B 379 " pdb=" SG CYS B 432 " pdb=" CB CYS B 432 " ideal model delta sinusoidal sigma weight residual 93.00 37.36 55.64 1 1.00e+01 1.00e-02 4.18e+01 dihedral pdb=" CA ASP J 100H" pdb=" C ASP J 100H" pdb=" N TYR J 100I" pdb=" CA TYR J 100I" ideal model delta harmonic sigma weight residual -180.00 -149.09 -30.91 0 5.00e+00 4.00e-02 3.82e+01 ... (remaining 15195 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.331: 4471 0.331 - 0.663: 7 0.663 - 0.994: 1 0.994 - 1.326: 0 1.326 - 1.657: 2 Chirality restraints: 4481 Sorted by residual: chirality pdb=" C1 NAG M 1 " pdb=" ND2 ASN B 343 " pdb=" C2 NAG M 1 " pdb=" O5 NAG M 1 " both_signs ideal model delta sigma weight residual False -2.40 -0.74 -1.66 2.00e-01 2.50e+01 6.87e+01 chirality pdb=" C1 NAG P 1 " pdb=" ND2 ASN C 343 " pdb=" C2 NAG P 1 " pdb=" O5 NAG P 1 " both_signs ideal model delta sigma weight residual False -2.40 -0.96 -1.44 2.00e-01 2.50e+01 5.21e+01 chirality pdb=" C1 NAG B1303 " pdb=" ND2 ASN B 331 " pdb=" C2 NAG B1303 " pdb=" O5 NAG B1303 " both_signs ideal model delta sigma weight residual False -2.40 -1.60 -0.80 2.00e-01 2.50e+01 1.62e+01 ... (remaining 4478 not shown) Planarity restraints: 4850 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 328 " 0.124 9.50e-02 1.11e+02 8.16e-02 4.67e+01 pdb=" NE ARG A 328 " -0.046 2.00e-02 2.50e+03 pdb=" CZ ARG A 328 " 0.114 2.00e-02 2.50e+03 pdb=" NH1 ARG A 328 " -0.041 2.00e-02 2.50e+03 pdb=" NH2 ARG A 328 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 343 " 0.051 2.00e-02 2.50e+03 4.75e-02 2.82e+01 pdb=" CG ASN C 343 " -0.055 2.00e-02 2.50e+03 pdb=" OD1 ASN C 343 " 0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN C 343 " -0.054 2.00e-02 2.50e+03 pdb=" C1 NAG P 1 " 0.051 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 343 " -0.051 2.00e-02 2.50e+03 4.72e-02 2.79e+01 pdb=" CG ASN B 343 " 0.056 2.00e-02 2.50e+03 pdb=" OD1 ASN B 343 " -0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN B 343 " 0.053 2.00e-02 2.50e+03 pdb=" C1 NAG M 1 " -0.051 2.00e-02 2.50e+03 ... (remaining 4847 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 252 2.63 - 3.20: 25635 3.20 - 3.77: 38474 3.77 - 4.33: 51918 4.33 - 4.90: 88079 Nonbonded interactions: 204358 Sorted by model distance: nonbonded pdb=" OH TYR J 100F" pdb=" O4 BMA I 3 " model vdw 2.063 3.040 nonbonded pdb=" OE1 GLN B 784 " pdb=" OG SER B1030 " model vdw 2.114 3.040 nonbonded pdb=" O3 MAN P 4 " pdb=" O6 NAG P 5 " model vdw 2.180 3.040 nonbonded pdb=" O GLN A 675 " pdb=" N GLN A 690 " model vdw 2.227 3.120 nonbonded pdb=" O3 NAG D 1 " pdb=" O7 NAG D 1 " model vdw 2.227 3.040 ... (remaining 204353 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 28 through 68 or resid 81 through 100 or (resid 101 throug \ h 102 and (name N or name CA or name C or name O or name CB )) or resid 103 thro \ ugh 110 or (resid 115 through 130 and (name N or name CA or name C or name O or \ name CB )) or resid 131 or (resid 132 through 138 and (name N or name CA or name \ C or name O or name CB )) or resid 139 through 172 or resid 187 through 206 or \ (resid 207 and (name N or name CA or name C or name O or name CB )) or resid 208 \ through 215 or (resid 216 and (name N or name CA or name C or name O or name CB \ )) or resid 217 through 273 or (resid 274 and (name N or name CA or name C or n \ ame O or name CB )) or resid 275 through 283 or (resid 284 and (name N or name C \ A or name C or name O or name CB )) or resid 285 through 288 or (resid 289 throu \ gh 290 and (name N or name CA or name C or name O or name CB )) or resid 291 thr \ ough 292 or (resid 293 through 294 and (name N or name CA or name C or name O or \ name CB )) or resid 295 through 323 or (resid 324 through 325 and (name N or na \ me CA or name C or name O or name CB )) or resid 326 through 331 or (resid 332 a \ nd (name N or name CA or name C or name O or name CB )) or resid 333 through 334 \ or (resid 335 and (name N or name CA or name C or name O or name CB )) or resid \ 336 through 339 or (resid 340 and (name N or name CA or name C or name O or nam \ e CB )) or resid 341 through 344 or (resid 345 through 346 and (name N or name C \ A or name C or name O or name CB )) or resid 347 through 353 or (resid 354 and ( \ name N or name CA or name C or name O or name CB )) or resid 355 or (resid 356 t \ hrough 357 and (name N or name CA or name C or name O or name CB )) or resid 358 \ or (resid 359 and (name N or name CA or name C or name O or name CB )) or resid \ 360 through 363 or (resid 364 and (name N or name CA or name C or name O or nam \ e CB )) or resid 365 through 367 or (resid 368 and (name N or name CA or name C \ or name O or name CB )) or resid 369 through 372 or (resid 373 and (name N or na \ me CA or name C or name O or name CB )) or resid 374 or (resid 375 through 376 a \ nd (name N or name CA or name C or name O or name CB )) or resid 377 or (resid 3 \ 78 and (name N or name CA or name C or name O or name CB )) or resid 379 through \ 382 or (resid 383 and (name N or name CA or name C or name O or name CB )) or r \ esid 384 or (resid 385 through 386 and (name N or name CA or name C or name O or \ name CB )) or resid 387 or (resid 388 through 390 and (name N or name CA or nam \ e C or name O or name CB )) or resid 391 through 392 or (resid 393 and (name N o \ r name CA or name C or name O or name CB )) or resid 394 through 404 or (resid 4 \ 05 through 406 and (name N or name CA or name C or name O or name CB )) or resid \ 407 through 413 or (resid 414 through 415 and (name N or name CA or name C or n \ ame O or name CB )) or resid 416 through 419 or (resid 420 and (name N or name C \ A or name C or name O or name CB )) or resid 421 through 432 or (resid 433 and ( \ name N or name CA or name C or name O or name CB )) or resid 434 through 436 or \ (resid 437 and (name N or name CA or name C or name O or name CB )) or resid 438 \ through 440 or (resid 441 through 442 and (name N or name CA or name C or name \ O or name CB )) or resid 443 through 447 or (resid 448 and (name N or name CA or \ name C or name O or name CB )) or resid 449 through 451 or (resid 452 and (name \ N or name CA or name C or name O or name CB )) or resid 453 through 454 or (res \ id 455 and (name N or name CA or name C or name O or name CB )) or resid 456 or \ (resid 457 through 460 and (name N or name CA or name C or name O or name CB )) \ or resid 461 through 467 or (resid 468 through 469 and (name N or name CA or nam \ e C or name O or name CB )) or resid 470 or (resid 471 and (name N or name CA or \ name C or name O or name CB )) or resid 472 through 476 or (resid 477 through 4 \ 78 and (name N or name CA or name C or name O or name CB )) or resid 479 through \ 480 or (resid 481 and (name N or name CA or name C or name O or name CB )) or r \ esid 482 through 492 or (resid 493 and (name N or name CA or name C or name O or \ name CB )) or resid 494 through 500 or (resid 501 and (name N or name CA or nam \ e C or name O or name CB )) or resid 502 through 505 or (resid 506 and (name N o \ r name CA or name C or name O or name CB )) or resid 507 through 509 or (resid 5 \ 10 through 512 and (name N or name CA or name C or name O or name CB )) or resid \ 513 or (resid 514 and (name N or name CA or name C or name O or name CB )) or r \ esid 515 through 516 or (resid 517 through 520 and (name N or name CA or name C \ or name O or name CB )) or resid 521 through 523 or (resid 524 and (name N or na \ me CA or name C or name O or name CB )) or resid 525 through 528 or (resid 529 a \ nd (name N or name CA or name C or name O or name CB )) or resid 530 through 531 \ or (resid 532 through 537 and (name N or name CA or name C or name O or name CB \ )) or resid 538 through 539 or (resid 540 and (name N or name CA or name C or n \ ame O or name CB )) or resid 541 or (resid 542 and (name N or name CA or name C \ or name O or name CB )) or resid 543 or (resid 544 and (name N or name CA or nam \ e C or name O or name CB )) or resid 545 or (resid 546 and (name N or name CA or \ name C or name O or name CB )) or resid 547 through 550 or (resid 551 and (name \ N or name CA or name C or name O or name CB )) or resid 552 or (resid 553 throu \ gh 554 and (name N or name CA or name C or name O or name CB )) or resid 555 or \ (resid 556 through 558 and (name N or name CA or name C or name O or name CB )) \ or resid 559 or (resid 560 and (name N or name CA or name C or name O or name CB \ )) or resid 561 through 563 or (resid 564 and (name N or name CA or name C or n \ ame O or name CB )) or resid 565 through 570 or (resid 571 through 572 and (name \ N or name CA or name C or name O or name CB )) or resid 573 through 575 or (res \ id 576 and (name N or name CA or name C or name O or name CB )) or resid 577 or \ (resid 578 and (name N or name CA or name C or name O or name CB )) or resid 579 \ through 580 or (resid 581 through 586 and (name N or name CA or name C or name \ O or name CB )) or resid 587 or (resid 588 and (name N or name CA or name C or n \ ame O or name CB )) or resid 589 through 590 or (resid 591 through 592 and (name \ N or name CA or name C or name O or name CB )) or resid 593 through 613 or (res \ id 614 and (name N or name CA or name C or name O or name CB )) or resid 615 or \ (resid 616 and (name N or name CA or name C or name O or name CB )) or resid 617 \ through 618 or (resid 619 through 620 and (name N or name CA or name C or name \ O or name CB )) or resid 641 through 650 or (resid 651 and (name N or name CA or \ name C or name O or name CB )) or (resid 652 through 654 and (name N or name CA \ or name C or name O or name CB )) or resid 655 through 663 or (resid 664 and (n \ ame N or name CA or name C or name O or name CB )) or resid 665 through 676 or ( \ resid 690 and (name N or name CA or name C or name O or name CB )) or resid 691 \ through 697 or (resid 698 and (name N or name CA or name C or name O or name CB \ )) or resid 699 through 703 or (resid 704 and (name N or name CA or name C or na \ me O or name CB )) or resid 705 through 709 or (resid 710 and (name N or name CA \ or name C or name O or name CB )) or resid 711 through 718 or (resid 719 and (n \ ame N or name CA or name C or name O or name CB )) or resid 720 through 722 or ( \ resid 723 and (name N or name CA or name C or name O or name CB )) or resid 724 \ or (resid 725 and (name N or name CA or name C or name O or name CB )) or resid \ 726 through 729 or (resid 730 and (name N or name CA or name C or name O or name \ CB )) or resid 731 through 736 or (resid 737 and (name N or name CA or name C o \ r name O or name CB )) or resid 738 or (resid 739 through 740 and (name N or nam \ e CA or name C or name O or name CB )) or resid 741 through 744 or (resid 745 an \ d (name N or name CA or name C or name O or name CB )) or resid 746 or (resid 74 \ 7 through 748 and (name N or name CA or name C or name O or name CB )) or resid \ 749 through 750 or (resid 751 and (name N or name CA or name C or name O or name \ CB )) or resid 752 through 754 or (resid 755 and (name N or name CA or name C o \ r name O or name CB )) or resid 756 through 757 or (resid 758 and (name N or nam \ e CA or name C or name O or name CB )) or resid 759 through 760 or (resid 761 an \ d (name N or name CA or name C or name O or name CB )) or resid 762 through 764 \ or (resid 765 through 766 and (name N or name CA or name C or name O or name CB \ )) or resid 767 through 772 or (resid 773 and (name N or name CA or name C or na \ me O or name CB )) or resid 774 through 775 or (resid 776 and (name N or name CA \ or name C or name O or name CB )) or resid 777 through 778 or (resid 779 throug \ h 780 and (name N or name CA or name C or name O or name CB )) or resid 781 thro \ ugh 794 or (resid 795 through 796 and (name N or name CA or name C or name O or \ name CB )) or resid 797 through 809 or (resid 810 through 811 and (name N or nam \ e CA or name C or name O or name CB )) or resid 812 or (resid 813 through 814 an \ d (name N or name CA or name C or name O or name CB )) or resid 815 or (resid 81 \ 6 and (name N or name CA or name C or name O or name CB )) or resid 817 through \ 819 or (resid 820 and (name N or name CA or name C or name O or name CB )) or re \ sid 821 through 826 or (resid 827 through 828 and (name N or name CA or name C o \ r name O or name CB )) or (resid 855 and (name N or name CA or name C or name O \ or name CB )) or resid 856 through 857 or (resid 858 and (name N or name CA or n \ ame C or name O or name CB )) or resid 859 or (resid 860 and (name N or name CA \ or name C or name O or name CB )) or resid 861 through 866 or (resid 867 through \ 868 and (name N or name CA or name C or name O or name CB )) or resid 869 throu \ gh 874 or (resid 875 through 876 and (name N or name CA or name C or name O or n \ ame CB )) or resid 877 through 933 or (resid 934 and (name N or name CA or name \ C or name O or name CB )) or resid 935 through 936 or (resid 937 through 944 and \ (name N or name CA or name C or name O or name CB )) or resid 945 through 949 o \ r (resid 950 and (name N or name CA or name C or name O or name CB )) or resid 9 \ 51 through 973 or (resid 974 through 979 and (name N or name CA or name C or nam \ e O or name CB )) or resid 980 through 984 or (resid 985 and (name N or name CA \ or name C or name O or name CB )) or resid 986 through 987 or (resid 988 through \ 991 and (name N or name CA or name C or name O or name CB )) or resid 992 or (r \ esid 993 through 994 and (name N or name CA or name C or name O or name CB )) or \ resid 995 through 1018 or (resid 1019 through 1020 and (name N or name CA or na \ me C or name O or name CB )) or resid 1021 through 1030 or (resid 1031 and (name \ N or name CA or name C or name O or name CB )) or resid 1032 through 1039 or (r \ esid 1040 through 1041 and (name N or name CA or name C or name O or name CB )) \ or resid 1042 through 1050 or (resid 1051 and (name N or name CA or name C or na \ me O or name CB )) or resid 1052 through 1054 or (resid 1055 through 1056 and (n \ ame N or name CA or name C or name O or name CB )) or resid 1057 through 1059 or \ (resid 1060 through 1061 and (name N or name CA or name C or name O or name CB \ )) or resid 1062 through 1065 or (resid 1066 and (name N or name CA or name C or \ name O or name CB )) or resid 1067 or (resid 1068 and (name N or name CA or nam \ e C or name O or name CB )) or resid 1069 through 1083 or (resid 1084 and (name \ N or name CA or name C or name O or name CB )) or resid 1085 or (resid 1086 thro \ ugh 1087 and (name N or name CA or name C or name O or name CB )) or resid 1088 \ through 1091 or (resid 1092 and (name N or name CA or name C or name O or name C \ B )) or resid 1093 through 1096 or (resid 1097 and (name N or name CA or name C \ or name O or name CB )) or resid 1098 through 1099 or (resid 1100 and (name N or \ name CA or name C or name O or name CB )) or resid 1101 through 1110 or (resid \ 1111 and (name N or name CA or name C or name O or name CB )) or resid 1112 thro \ ugh 1115 or (resid 1116 through 1118 and (name N or name CA or name C or name O \ or name CB )) or resid 1119 through 1121 or (resid 1122 through 1123 and (name N \ or name CA or name C or name O or name CB )) or resid 1124 or (resid 1125 and ( \ name N or name CA or name C or name O or name CB )) or resid 1126 or (resid 1127 \ through 1128 and (name N or name CA or name C or name O or name CB )) or resid \ 1129 or (resid 1130 and (name N or name CA or name C or name O or name CB )) or \ resid 1131 through 1132 or (resid 1133 and (name N or name CA or name C or name \ O or name CB )) or resid 1134 or (resid 1135 through 1136 and (name N or name CA \ or name C or name O or name CB )) or resid 1137 through 1138 or (resid 1139 and \ (name N or name CA or name C or name O or name CB )) or resid 1140 through 1143 \ or (resid 1144 and (name N or name CA or name C or name O or name CB )) or resi \ d 1301 through 1310)) selection = (chain 'B' and (resid 28 or (resid 29 through 30 and (name N or name CA or name \ C or name O or name CB )) or resid 31 through 49 or (resid 50 through 54 and (na \ me N or name CA or name C or name O or name CB )) or resid 55 through 61 or (res \ id 62 through 63 and (name N or name CA or name C or name O or name CB )) or res \ id 64 through 68 or resid 81 through 110 or (resid 115 through 130 and (name N o \ r name CA or name C or name O or name CB )) or resid 131 through 134 or (resid 1 \ 35 through 138 and (name N or name CA or name C or name O or name CB )) or resid \ 139 through 141 or resid 166 through 189 or (resid 190 through 191 and (name N \ or name CA or name C or name O or name CB )) or resid 192 through 194 or (resid \ 195 through 198 and (name N or name CA or name C or name O or name CB )) or resi \ d 199 or (resid 200 and (name N or name CA or name C or name O or name CB )) or \ resid 201 through 217 or (resid 218 and (name N or name CA or name C or name O o \ r name CB )) or resid 219 through 231 or resid 236 through 272 or (resid 273 thr \ ough 274 and (name N or name CA or name C or name O or name CB )) or resid 275 t \ hrough 283 or (resid 284 and (name N or name CA or name C or name O or name CB ) \ ) or resid 285 through 293 or (resid 294 and (name N or name CA or name C or nam \ e O or name CB )) or resid 295 through 297 or (resid 298 through 299 and (name N \ or name CA or name C or name O or name CB )) or resid 300 through 301 or (resid \ 302 and (name N or name CA or name C or name O or name CB )) or resid 303 throu \ gh 306 or (resid 307 and (name N or name CA or name C or name O or name CB )) or \ resid 308 through 314 or (resid 315 and (name N or name CA or name C or name O \ or name CB )) or resid 316 through 320 or (resid 321 and (name N or name CA or n \ ame C or name O or name CB )) or resid 322 through 324 or (resid 325 and (name N \ or name CA or name C or name O or name CB )) or resid 326 through 356 or (resid \ 357 and (name N or name CA or name C or name O or name CB )) or resid 358 throu \ gh 367 or (resid 368 and (name N or name CA or name C or name O or name CB )) or \ resid 369 through 389 or (resid 390 and (name N or name CA or name C or name O \ or name CB )) or resid 391 through 454 or (resid 455 and (name N or name CA or n \ ame C or name O or name CB )) or resid 456 through 459 or (resid 460 and (name N \ or name CA or name C or name O or name CB )) or resid 461 through 468 or (resid \ 469 and (name N or name CA or name C or name O or name CB )) or resid 470 throu \ gh 477 or (resid 478 and (name N or name CA or name C or name O or name CB )) or \ resid 479 through 480 or (resid 481 and (name N or name CA or name C or name O \ or name CB )) or resid 482 through 505 or (resid 506 and (name N or name CA or n \ ame C or name O or name CB )) or resid 507 through 518 or (resid 519 through 520 \ and (name N or name CA or name C or name O or name CB )) or resid 521 through 5 \ 28 or (resid 529 and (name N or name CA or name C or name O or name CB )) or res \ id 530 through 535 or (resid 536 through 537 and (name N or name CA or name C or \ name O or name CB )) or resid 538 through 539 or (resid 540 and (name N or name \ CA or name C or name O or name CB )) or resid 541 through 545 or (resid 546 and \ (name N or name CA or name C or name O or name CB )) or resid 547 through 559 o \ r (resid 560 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 61 through 618 or (resid 619 through 620 and (name N or name CA or name C or nam \ e O or name CB )) or resid 641 through 738 or (resid 739 through 740 and (name N \ or name CA or name C or name O or name CB )) or resid 741 through 746 or (resid \ 747 through 748 and (name N or name CA or name C or name O or name CB )) or res \ id 749 through 750 or (resid 751 and (name N or name CA or name C or name O or n \ ame CB )) or resid 752 through 757 or (resid 758 and (name N or name CA or name \ C or name O or name CB )) or resid 759 through 760 or (resid 761 and (name N or \ name CA or name C or name O or name CB )) or resid 762 through 772 or (resid 773 \ and (name N or name CA or name C or name O or name CB )) or resid 774 through 7 \ 75 or (resid 776 and (name N or name CA or name C or name O or name CB )) or res \ id 777 through 778 or (resid 779 through 780 and (name N or name CA or name C or \ name O or name CB )) or resid 781 through 794 or (resid 795 through 796 and (na \ me N or name CA or name C or name O or name CB )) or resid 797 through 809 or (r \ esid 810 through 811 and (name N or name CA or name C or name O or name CB )) or \ resid 812 through 815 or (resid 816 and (name N or name CA or name C or name O \ or name CB )) or resid 817 through 819 or (resid 820 and (name N or name CA or n \ ame C or name O or name CB )) or resid 821 through 859 or (resid 860 and (name N \ or name CA or name C or name O or name CB )) or resid 861 through 867 or (resid \ 868 and (name N or name CA or name C or name O or name CB )) or resid 869 throu \ gh 874 or (resid 875 through 876 and (name N or name CA or name C or name O or n \ ame CB )) or resid 877 through 933 or (resid 934 and (name N or name CA or name \ C or name O or name CB )) or resid 935 through 936 or (resid 937 through 944 and \ (name N or name CA or name C or name O or name CB )) or resid 945 through 976 o \ r (resid 977 through 979 and (name N or name CA or name C or name O or name CB ) \ ) or resid 980 through 990 or (resid 991 and (name N or name CA or name C or nam \ e O or name CB )) or resid 992 or (resid 993 through 994 and (name N or name CA \ or name C or name O or name CB )) or resid 995 through 1018 or (resid 1019 throu \ gh 1020 and (name N or name CA or name C or name O or name CB )) or resid 1021 t \ hrough 1030 or (resid 1031 and (name N or name CA or name C or name O or name CB \ )) or resid 1032 through 1059 or (resid 1060 through 1061 and (name N or name C \ A or name C or name O or name CB )) or resid 1062 through 1065 or (resid 1066 an \ d (name N or name CA or name C or name O or name CB )) or resid 1067 or (resid 1 \ 068 and (name N or name CA or name C or name O or name CB )) or resid 1069 throu \ gh 1072 or (resid 1073 and (name N or name CA or name C or name O or name CB )) \ or resid 1074 through 1096 or (resid 1097 and (name N or name CA or name C or na \ me O or name CB )) or resid 1098 through 1099 or (resid 1100 and (name N or name \ CA or name C or name O or name CB )) or resid 1101 through 1115 or (resid 1116 \ through 1118 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 119 through 1121 or (resid 1122 through 1123 and (name N or name CA or name C or \ name O or name CB )) or resid 1124 or (resid 1125 and (name N or name CA or nam \ e C or name O or name CB )) or resid 1126 through 1129 or (resid 1130 and (name \ N or name CA or name C or name O or name CB )) or resid 1131 through 1132 or (re \ sid 1133 and (name N or name CA or name C or name O or name CB )) or resid 1134 \ or (resid 1135 through 1136 and (name N or name CA or name C or name O or name C \ B )) or resid 1137 through 1310)) selection = (chain 'C' and (resid 28 through 29 or (resid 30 and (name N or name CA or name \ C or name O or name CB )) or resid 31 through 32 or (resid 33 and (name N or nam \ e CA or name C or name O or name CB )) or resid 34 through 35 or (resid 36 and ( \ name N or name CA or name C or name O or name CB )) or resid 37 through 41 or (r \ esid 42 and (name N or name CA or name C or name O or name CB )) or resid 43 thr \ ough 44 or (resid 45 through 48 and (name N or name CA or name C or name O or na \ me CB )) or resid 49 or (resid 50 through 54 and (name N or name CA or name C or \ name O or name CB )) or resid 55 through 61 or (resid 62 through 63 and (name N \ or name CA or name C or name O or name CB )) or resid 64 through 65 or (resid 6 \ 6 through 68 and (name N or name CA or name C or name O or name CB )) or resid 8 \ 1 through 82 or (resid 83 through 84 and (name N or name CA or name C or name O \ or name CB )) or resid 85 through 86 or (resid 87 through 88 and (name N or name \ CA or name C or name O or name CB )) or resid 89 through 99 or (resid 100 throu \ gh 102 and (name N or name CA or name C or name O or name CB )) or resid 103 thr \ ough 110 or (resid 115 through 130 and (name N or name CA or name C or name O or \ name CB )) or resid 131 through 140 or (resid 141 and (name N or name CA or nam \ e C or name O or name CB )) or resid 166 through 172 or (resid 187 through 188 a \ nd (name N or name CA or name C or name O or name CB )) or resid 189 or (resid 1 \ 90 through 191 and (name N or name CA or name C or name O or name CB )) or resid \ 192 through 194 or (resid 195 through 198 and (name N or name CA or name C or n \ ame O or name CB )) or resid 199 or (resid 200 and (name N or name CA or name C \ or name O or name CB )) or resid 201 through 206 or (resid 207 and (name N or na \ me CA or name C or name O or name CB )) or resid 208 through 210 or (resid 215 t \ hrough 216 and (name N or name CA or name C or name O or name CB )) or resid 217 \ through 220 or (resid 221 through 224 and (name N or name CA or name C or name \ O or name CB )) or resid 225 or (resid 226 through 229 and (name N or name CA or \ name C or name O or name CB )) or resid 230 or (resid 231 and (name N or name C \ A or name C or name O or name CB )) or resid 236 through 239 or (resid 240 throu \ gh 264 and (name N or name CA or name C or name O or name CB )) or resid 265 thr \ ough 272 or (resid 273 through 274 and (name N or name CA or name C or name O or \ name CB )) or resid 275 or (resid 276 through 278 and (name N or name CA or nam \ e C or name O or name CB )) or resid 279 through 288 or (resid 289 through 290 a \ nd (name N or name CA or name C or name O or name CB )) or resid 291 through 293 \ or (resid 294 and (name N or name CA or name C or name O or name CB )) or resid \ 295 through 297 or (resid 298 through 299 and (name N or name CA or name C or n \ ame O or name CB )) or resid 300 through 301 or (resid 302 and (name N or name C \ A or name C or name O or name CB )) or resid 303 through 304 or (resid 305 and ( \ name N or name CA or name C or name O or name CB )) or resid 306 through 313 or \ (resid 314 through 315 and (name N or name CA or name C or name O or name CB )) \ or resid 316 through 319 or (resid 320 through 321 and (name N or name CA or nam \ e C or name O or name CB )) or resid 322 through 324 or (resid 325 and (name N o \ r name CA or name C or name O or name CB )) or resid 326 through 358 or (resid 3 \ 59 and (name N or name CA or name C or name O or name CB )) or resid 360 through \ 363 or (resid 364 and (name N or name CA or name C or name O or name CB )) or r \ esid 365 through 382 or (resid 383 and (name N or name CA or name C or name O or \ name CB )) or resid 384 through 385 or (resid 386 and (name N or name CA or nam \ e C or name O or name CB )) or resid 387 or (resid 388 through 390 and (name N o \ r name CA or name C or name O or name CB )) or resid 391 through 413 or (resid 4 \ 14 through 415 and (name N or name CA or name C or name O or name CB )) or resid \ 416 through 419 or (resid 420 and (name N or name CA or name C or name O or nam \ e CB )) or resid 421 through 432 or (resid 433 and (name N or name CA or name C \ or name O or name CB )) or resid 434 through 436 or (resid 437 and (name N or na \ me CA or name C or name O or name CB )) or resid 438 or (resid 439 through 442 a \ nd (name N or name CA or name C or name O or name CB )) or resid 443 through 447 \ or (resid 448 and (name N or name CA or name C or name O or name CB )) or resid \ 449 through 456 or (resid 457 through 460 and (name N or name CA or name C or n \ ame O or name CB )) or resid 461 through 467 or (resid 468 through 469 and (name \ N or name CA or name C or name O or name CB )) or resid 470 through 492 or (res \ id 493 and (name N or name CA or name C or name O or name CB )) or resid 494 thr \ ough 500 or (resid 501 and (name N or name CA or name C or name O or name CB )) \ or resid 502 through 509 or (resid 510 through 512 and (name N or name CA or nam \ e C or name O or name CB )) or resid 513 or (resid 514 and (name N or name CA or \ name C or name O or name CB )) or resid 515 through 541 or (resid 542 and (name \ N or name CA or name C or name O or name CB )) or resid 543 or (resid 544 and ( \ name N or name CA or name C or name O or name CB )) or resid 545 through 552 or \ (resid 553 through 554 and (name N or name CA or name C or name O or name CB )) \ or resid 555 through 563 or (resid 564 and (name N or name CA or name C or name \ O or name CB )) or resid 565 through 575 or (resid 576 and (name N or name CA or \ name C or name O or name CB )) or resid 577 or (resid 578 and (name N or name C \ A or name C or name O or name CB )) or resid 579 or (resid 580 through 586 and ( \ name N or name CA or name C or name O or name CB )) or resid 587 through 590 or \ (resid 591 through 592 and (name N or name CA or name C or name O or name CB )) \ or resid 593 through 615 or (resid 616 and (name N or name CA or name C or name \ O or name CB )) or resid 617 or (resid 618 through 620 and (name N or name CA or \ name C or name O or name CB )) or resid 641 through 650 or (resid 651 and (name \ N or name CA or name C or name O or name CB )) or resid 652 through 663 or (res \ id 664 and (name N or name CA or name C or name O or name CB )) or resid 665 thr \ ough 709 or (resid 710 and (name N or name CA or name C or name O or name CB )) \ or resid 711 through 718 or (resid 719 and (name N or name CA or name C or name \ O or name CB )) or resid 720 through 722 or (resid 723 and (name N or name CA or \ name C or name O or name CB )) or resid 724 through 729 or (resid 730 and (name \ N or name CA or name C or name O or name CB )) or resid 731 through 795 or (res \ id 796 and (name N or name CA or name C or name O or name CB )) or resid 797 thr \ ough 812 or (resid 813 through 814 and (name N or name CA or name C or name O or \ name CB )) or resid 815 through 818 or (resid 819 through 820 and (name N or na \ me CA or name C or name O or name CB )) or resid 821 through 828 or resid 855 th \ rough 977 or (resid 978 through 979 and (name N or name CA or name C or name O o \ r name CB )) or resid 980 through 1310)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'N' selection = chain 'O' selection = chain 'Q' selection = chain 'R' } ncs_group { reference = (chain 'F' and (resid 1 through 50 or (resid 51 and (name N or name CA or name C \ or name O or name CB )) or resid 52 through 65 or (resid 66 through 68 and (nam \ e N or name CA or name C or name O or name CB )) or resid 69 through 88 or (resi \ d 89 and (name N or name CA or name C or name O or name CB )) or resid 90 throug \ h 113)) selection = (chain 'H' and ((resid 1 through 3 and (name N or name CA or name C or name O or \ name CB )) or resid 4 or (resid 5 through 7 and (name N or name CA or name C or \ name O or name CB )) or resid 8 through 44 or (resid 45 through 46 and (name N \ or name CA or name C or name O or name CB )) or resid 47 or (resid 48 and (name \ N or name CA or name C or name O or name CB )) or resid 49 through 60 or (resid \ 61 through 62 and (name N or name CA or name C or name O or name CB )) or resid \ 63 through 72 or (resid 73 and (name N or name CA or name C or name O or name CB \ )) or resid 74 through 113)) selection = (chain 'J' and (resid 1 through 9 or (resid 10 through 13 and (name N or name CA \ or name C or name O or name CB )) or resid 14 through 20 or (resid 21 and (name \ N or name CA or name C or name O or name CB )) or resid 22 through 24 or (resid \ 25 and (name N or name CA or name C or name O or name CB )) or resid 26 through \ 38 or (resid 39 through 40 and (name N or name CA or name C or name O or name C \ B )) or resid 41 through 42 or (resid 43 and (name N or name CA or name C or nam \ e O or name CB )) or resid 44 through 47 or (resid 48 and (name N or name CA or \ name C or name O or name CB )) or resid 49 through 50 or (resid 51 and (name N o \ r name CA or name C or name O or name CB )) or resid 52 through 60 or (resid 61 \ through 62 and (name N or name CA or name C or name O or name CB )) or resid 63 \ or (resid 64 and (name N or name CA or name C or name O or name CB )) or (resid \ 65 through 68 and (name N or name CA or name C or name O or name CB )) or resid \ 69 or (resid 70 and (name N or name CA or name C or name O or name CB )) or resi \ d 71 through 72 or (resid 73 and (name N or name CA or name C or name O or name \ CB )) or resid 74 through 113)) } ncs_group { reference = (chain 'G' and (resid 1 through 25 or (resid 26 through 27B and (name N or name \ CA or name C or name O or name CB )) or resid 27C through 74 or (resid 75 throug \ h 76 and (name N or name CA or name C or name O or name CB )) or resid 77 throug \ h 106A)) selection = (chain 'K' and (resid 1 through 13 or (resid 14 and (name N or name CA or name C \ or name O or name CB )) or resid 15 through 17 or (resid 18 through 22 and (nam \ e N or name CA or name C or name O or name CB )) or resid 23 through 25 or (resi \ d 26 through 27B and (name N or name CA or name C or name O or name CB )) or res \ id 27C through 58 or (resid 59 through 61 and (name N or name CA or name C or na \ me O or name CB )) or resid 62 or (resid 63 and (name N or name CA or name C or \ name O or name CB )) or resid 64 through 71 or (resid 72 through 76 and (name N \ or name CA or name C or name O or name CB )) or resid 77 through 106A)) selection = (chain 'L' and (resid 1 through 16 or (resid 17 through 22 and (name N or name C \ A or name C or name O or name CB )) or resid 23 through 26 or (resid 27 through \ 27B and (name N or name CA or name C or name O or name CB )) or resid 27C throug \ h 58 or (resid 59 through 61 and (name N or name CA or name C or name O or name \ CB )) or resid 62 through 64 or (resid 65 through 67 and (name N or name CA or n \ ame C or name O or name CB )) or resid 68 through 71 or (resid 72 through 76 and \ (name N or name CA or name C or name O or name CB )) or resid 77 through 106A)) \ } ncs_group { reference = chain 'I' selection = chain 'M' selection = chain 'P' } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 26.490 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.070 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: 0.000 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 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 : 0.010 0.128 27326 Z= 0.441 Angle : 1.194 28.390 37614 Z= 0.636 Chirality : 0.073 1.657 4481 Planarity : 0.008 0.118 4810 Dihedral : 12.551 87.786 8236 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 1.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 0.05 % Allowed : 1.18 % Favored : 98.77 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.85 (0.13), residues: 3610 helix: -0.87 (0.18), residues: 641 sheet: -0.57 (0.18), residues: 796 loop : -1.64 (0.12), residues: 2173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.116 0.010 ARG A 328 TYR 0.057 0.008 TYR F 100I PHE 0.052 0.004 PHE H 63 TRP 0.028 0.005 TRP H 50 HIS 0.017 0.003 HIS J 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00987 / 0.44 (27211) covalent geometry : angle 1.12663 / 0.62 (37317) SS BOND : bond 0.00951 / 0.45 ( 48) SS BOND : angle 2.45602 / 1.67 ( 96) hydrogen bonds : bond 0.13136 / 8.86 ( 1072) hydrogen bonds : angle 8.54666 / 5.94 ( 2952) link_ALPHA1-3 : bond 0.02052 / 0.92 ( 4) link_ALPHA1-3 : angle 3.38163 / 2.04 ( 12) link_ALPHA1-6 : bond 0.01208 / 0.67 ( 5) link_ALPHA1-6 : angle 2.93123 / 1.81 ( 15) link_BETA1-2 : bond 0.03447 / 1.56 ( 3) link_BETA1-2 : angle 5.80903 / 3.49 ( 9) link_BETA1-4 : bond 0.01257 / 0.86 ( 15) link_BETA1-4 : angle 5.58233 / 3.85 ( 45) link_NAG-ASN : bond 0.00798 / 0.44 ( 40) link_NAG-ASN : angle 5.53941 / 3.68 ( 120) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7220 Ramachandran restraints generated. 3610 Oldfield, 0 Emsley, 3610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7220 Ramachandran restraints generated. 3610 Oldfield, 0 Emsley, 3610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 253 time to evaluate : 0.654 Fit side-chains revert: symmetry clash REVERT: B 484 GLU cc_start: 0.7719 (mt-10) cc_final: 0.7376 (mt-10) REVERT: B 780 GLU cc_start: 0.8230 (tp30) cc_final: 0.7614 (tp30) REVERT: B 980 ILE cc_start: 0.9323 (tp) cc_final: 0.8958 (tp) REVERT: B 984 LEU cc_start: 0.8613 (mt) cc_final: 0.8373 (mp) REVERT: C 882 ILE cc_start: 0.9205 (mm) cc_final: 0.9000 (mt) REVERT: F 50 TRP cc_start: 0.7688 (p-90) cc_final: 0.7414 (p-90) REVERT: F 100 ASN cc_start: 0.8513 (t0) cc_final: 0.8047 (t0) REVERT: H 80 MET cc_start: 0.8338 (tmm) cc_final: 0.8012 (tmm) REVERT: J 32 TYR cc_start: 0.8894 (m-80) cc_final: 0.8548 (m-10) REVERT: J 77 THR cc_start: 0.9331 (p) cc_final: 0.9088 (p) REVERT: J 79 TYR cc_start: 0.8623 (m-10) cc_final: 0.8408 (m-10) REVERT: J 91 TYR cc_start: 0.8884 (m-80) cc_final: 0.8410 (m-80) REVERT: J 100 TYR cc_start: 0.7743 (m-10) cc_final: 0.7288 (m-10) REVERT: K 96 TRP cc_start: 0.8849 (m-90) cc_final: 0.8480 (m-90) REVERT: L 36 TYR cc_start: 0.8746 (m-10) cc_final: 0.8267 (m-10) outliers start: 1 outliers final: 0 residues processed: 254 average time/residue: 0.1520 time to fit residues: 63.7805 Evaluate side-chains 200 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 200 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.0970 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 0.6980 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.0770 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 0.8980 chunk 298 optimal weight: 1.9990 overall best weight: 0.5136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 606 ASN A 901 GLN A1101 HIS B 613 GLN C 710 ASN C 926 GLN F 35 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.088391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.078499 restraints weight = 81316.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.080253 restraints weight = 43462.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.081414 restraints weight = 27815.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.082204 restraints weight = 20015.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.082734 restraints weight = 15447.477| |-----------------------------------------------------------------------------| r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3203 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3203 r_free = 0.3203 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3202 r_free = 0.3202 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (6 function evaluations) r_final: 0.3202 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 27326 Z= 0.138 Angle : 0.743 14.329 37614 Z= 0.370 Chirality : 0.049 0.521 4481 Planarity : 0.004 0.071 4810 Dihedral : 6.065 35.426 3911 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.45 % Allowed : 7.00 % Favored : 92.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.14), residues: 3610 helix: 0.97 (0.20), residues: 647 sheet: -0.33 (0.18), residues: 787 loop : -1.20 (0.13), residues: 2176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG J 94 TYR 0.026 0.002 TYR G 49 PHE 0.026 0.002 PHE A 497 TRP 0.025 0.002 TRP B 104 HIS 0.005 0.001 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.14 (27211) covalent geometry : angle 0.70104 / 0.36 (37317) SS BOND : bond 0.00401 / 0.19 ( 48) SS BOND : angle 1.06250 / 0.70 ( 96) hydrogen bonds : bond 0.04275 / 2.88 ( 1072) hydrogen bonds : angle 6.13119 / 4.28 ( 2952) link_ALPHA1-3 : bond 0.00659 / 0.34 ( 4) link_ALPHA1-3 : angle 1.91037 / 1.13 ( 12) link_ALPHA1-6 : bond 0.00502 / 0.29 ( 5) link_ALPHA1-6 : angle 1.55819 / 0.91 ( 15) link_BETA1-2 : bond 0.01303 / 0.61 ( 3) link_BETA1-2 : angle 3.65416 / 2.20 ( 9) link_BETA1-4 : bond 0.01122 / 0.85 ( 15) link_BETA1-4 : angle 3.03831 / 2.20 ( 45) link_NAG-ASN : bond 0.00466 / 0.28 ( 40) link_NAG-ASN : angle 3.76090 / 2.54 ( 120) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7220 Ramachandran restraints generated. 3610 Oldfield, 0 Emsley, 3610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7220 Ramachandran restraints generated. 3610 Oldfield, 0 Emsley, 3610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 234 time to evaluate : 0.764 Fit side-chains REVERT: A 900 MET cc_start: 0.8131 (mtp) cc_final: 0.7700 (ttm) REVERT: B 353 TRP cc_start: 0.8203 (p-90) cc_final: 0.7282 (p-90) REVERT: B 484 GLU cc_start: 0.7692 (mt-10) cc_final: 0.7440 (mt-10) REVERT: B 980 ILE cc_start: 0.9346 (tp) cc_final: 0.9090 (tt) REVERT: B 1050 MET cc_start: 0.8096 (ptp) cc_final: 0.7706 (ptp) REVERT: F 80 MET cc_start: 0.8491 (tmm) cc_final: 0.8122 (tmm) REVERT: F 100 ASN cc_start: 0.8413 (t0) cc_final: 0.8107 (t0) REVERT: H 80 MET cc_start: 0.8275 (tmm) cc_final: 0.7993 (tmm) REVERT: J 32 TYR cc_start: 0.8461 (m-80) cc_final: 0.7998 (m-10) REVERT: J 80 MET cc_start: 0.8429 (tmm) cc_final: 0.8201 (tmm) REVERT: J 91 TYR cc_start: 0.8678 (m-80) cc_final: 0.8454 (m-10) REVERT: J 100 TYR cc_start: 0.7528 (m-10) cc_final: 0.7155 (m-10) REVERT: L 36 TYR cc_start: 0.8574 (m-80) cc_final: 0.8139 (m-10) outliers start: 10 outliers final: 4 residues processed: 239 average time/residue: 0.1529 time to fit residues: 60.9176 Evaluate side-chains 193 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 189 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain J residue 73 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 276 optimal weight: 1.9990 chunk 351 optimal weight: 8.9990 chunk 305 optimal weight: 4.9990 chunk 138 optimal weight: 4.9990 chunk 289 optimal weight: 1.9990 chunk 199 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 chunk 104 optimal weight: 0.9990 chunk 310 optimal weight: 5.9990 chunk 274 optimal weight: 0.8980 chunk 130 optimal weight: 6.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 501 ASN A1088 HIS A1135 ASN C 613 GLN C 901 GLN K 6 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.080134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.070587 restraints weight = 80041.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.072230 restraints weight = 44212.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.073243 restraints weight = 28857.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.073978 restraints weight = 21315.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.074422 restraints weight = 16918.606| |-----------------------------------------------------------------------------| r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3142 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3142 r_free = 0.3142 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3142 r_free = 0.3142 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.3142 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 27326 Z= 0.226 Angle : 0.735 15.381 37614 Z= 0.366 Chirality : 0.050 0.608 4481 Planarity : 0.005 0.064 4810 Dihedral : 5.688 33.980 3911 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 1.09 % Allowed : 9.91 % Favored : 88.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.14), residues: 3610 helix: 1.18 (0.21), residues: 653 sheet: -0.55 (0.18), residues: 820 loop : -1.22 (0.13), residues: 2137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 54 TYR 0.024 0.002 TYR H 33 PHE 0.020 0.002 PHE A 497 TRP 0.018 0.002 TRP C 104 HIS 0.005 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00505 / 0.23 (27211) covalent geometry : angle 0.69863 / 0.36 (37317) SS BOND : bond 0.00410 / 0.24 ( 48) SS BOND : angle 1.38645 / 0.80 ( 96) hydrogen bonds : bond 0.04197 / 2.85 ( 1072) hydrogen bonds : angle 5.78406 / 4.05 ( 2952) link_ALPHA1-3 : bond 0.00430 / 0.22 ( 4) link_ALPHA1-3 : angle 1.80890 / 1.07 ( 12) link_ALPHA1-6 : bond 0.00318 / 0.15 ( 5) link_ALPHA1-6 : angle 1.79520 / 1.05 ( 15) link_BETA1-2 : bond 0.01375 / 0.63 ( 3) link_BETA1-2 : angle 3.29794 / 1.99 ( 9) link_BETA1-4 : bond 0.00976 / 0.74 ( 15) link_BETA1-4 : angle 2.79638 / 2.01 ( 45) link_NAG-ASN : bond 0.00448 / 0.27 ( 40) link_NAG-ASN : angle 3.42621 / 2.26 ( 120) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7220 Ramachandran restraints generated. 3610 Oldfield, 0 Emsley, 3610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7220 Ramachandran restraints generated. 3610 Oldfield, 0 Emsley, 3610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 209 time to evaluate : 1.074 Fit side-chains revert: symmetry clash REVERT: B 351 TYR cc_start: 0.7991 (OUTLIER) cc_final: 0.7709 (t80) REVERT: B 980 ILE cc_start: 0.9310 (tp) cc_final: 0.8979 (tt) REVERT: F 33 TYR cc_start: 0.8175 (m-10) cc_final: 0.7959 (m-10) REVERT: F 80 MET cc_start: 0.8359 (tmm) cc_final: 0.8108 (tmm) REVERT: F 100 ASN cc_start: 0.8505 (t0) cc_final: 0.8015 (t0) REVERT: J 52 ASN cc_start: 0.8348 (t0) cc_final: 0.7986 (t0) REVERT: J 80 MET cc_start: 0.8473 (tmm) cc_final: 0.8246 (tmm) REVERT: J 91 TYR cc_start: 0.8741 (m-80) cc_final: 0.8308 (m-80) REVERT: J 94 ARG cc_start: 0.8392 (ttp80) cc_final: 0.7278 (ttp80) REVERT: J 100 TYR cc_start: 0.7737 (m-10) cc_final: 0.7296 (m-10) REVERT: L 36 TYR cc_start: 0.8677 (m-80) cc_final: 0.8226 (m-10) outliers start: 24 outliers final: 15 residues processed: 221 average time/residue: 0.1503 time to fit residues: 56.0474 Evaluate side-chains 199 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 183 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain F residue 53 ASN Chi-restraints excluded: chain H residue 59 TYR Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 98 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 215 optimal weight: 0.0970 chunk 13 optimal weight: 6.9990 chunk 222 optimal weight: 4.9990 chunk 271 optimal weight: 1.9990 chunk 328 optimal weight: 6.9990 chunk 144 optimal weight: 8.9990 chunk 339 optimal weight: 1.9990 chunk 363 optimal weight: 5.9990 chunk 219 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 955 ASN B 784 GLN B 955 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.086387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.076389 restraints weight = 82411.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.078114 restraints weight = 44539.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.079217 restraints weight = 28656.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.079983 restraints weight = 20885.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.080524 restraints weight = 16376.996| |-----------------------------------------------------------------------------| r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3132 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3132 r_free = 0.3132 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3132 r_free = 0.3132 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3132 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 27326 Z= 0.224 Angle : 0.710 12.988 37614 Z= 0.353 Chirality : 0.049 0.534 4481 Planarity : 0.005 0.075 4810 Dihedral : 5.479 34.200 3911 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.36 % Allowed : 11.05 % Favored : 86.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.14), residues: 3610 helix: 1.35 (0.21), residues: 651 sheet: -0.56 (0.18), residues: 823 loop : -1.29 (0.13), residues: 2136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 83 TYR 0.024 0.002 TYR H 33 PHE 0.019 0.002 PHE J 63 TRP 0.019 0.002 TRP C 104 HIS 0.005 0.001 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00501 / 0.22 (27211) covalent geometry : angle 0.67694 / 0.35 (37317) SS BOND : bond 0.00378 / 0.19 ( 48) SS BOND : angle 1.30159 / 0.77 ( 96) hydrogen bonds : bond 0.03993 / 2.72 ( 1072) hydrogen bonds : angle 5.63704 / 3.94 ( 2952) link_ALPHA1-3 : bond 0.00432 / 0.22 ( 4) link_ALPHA1-3 : angle 1.73857 / 1.04 ( 12) link_ALPHA1-6 : bond 0.00324 / 0.16 ( 5) link_ALPHA1-6 : angle 1.74235 / 1.03 ( 15) link_BETA1-2 : bond 0.01450 / 0.65 ( 3) link_BETA1-2 : angle 3.18415 / 1.92 ( 9) link_BETA1-4 : bond 0.00812 / 0.61 ( 15) link_BETA1-4 : angle 2.57238 / 1.85 ( 45) link_NAG-ASN : bond 0.00389 / 0.23 ( 40) link_NAG-ASN : angle 3.20869 / 2.11 ( 120) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7220 Ramachandran restraints generated. 3610 Oldfield, 0 Emsley, 3610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7220 Ramachandran restraints generated. 3610 Oldfield, 0 Emsley, 3610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 194 time to evaluate : 0.926 Fit side-chains revert: symmetry clash REVERT: B 351 TYR cc_start: 0.8068 (OUTLIER) cc_final: 0.7831 (t80) REVERT: B 980 ILE cc_start: 0.9331 (tp) cc_final: 0.9031 (tt) REVERT: C 565 PHE cc_start: 0.7147 (OUTLIER) cc_final: 0.6119 (t80) REVERT: F 54 SER cc_start: 0.8751 (OUTLIER) cc_final: 0.8436 (m) REVERT: F 80 MET cc_start: 0.8450 (tmm) cc_final: 0.8123 (tmm) REVERT: F 100 ASN cc_start: 0.8400 (t0) cc_final: 0.8179 (t0) REVERT: J 52 ASN cc_start: 0.8362 (t0) cc_final: 0.7928 (t0) REVERT: J 80 MET cc_start: 0.8495 (tmm) cc_final: 0.8167 (tmm) REVERT: J 91 TYR cc_start: 0.8794 (m-80) cc_final: 0.8460 (m-80) REVERT: J 100 TYR cc_start: 0.7852 (m-10) cc_final: 0.7366 (m-10) REVERT: L 36 TYR cc_start: 0.8594 (m-80) cc_final: 0.8220 (m-10) outliers start: 52 outliers final: 33 residues processed: 228 average time/residue: 0.1470 time to fit residues: 56.6058 Evaluate side-chains 213 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 177 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 690 GLN Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain F residue 53 ASN Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 100 ASP Chi-restraints excluded: chain H residue 59 TYR Chi-restraints excluded: chain H residue 71 ARG Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain J residue 59 TYR Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 98 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 113 optimal weight: 20.0000 chunk 305 optimal weight: 7.9990 chunk 277 optimal weight: 0.9980 chunk 21 optimal weight: 7.9990 chunk 111 optimal weight: 0.9990 chunk 53 optimal weight: 9.9990 chunk 340 optimal weight: 10.0000 chunk 361 optimal weight: 9.9990 chunk 30 optimal weight: 5.9990 chunk 48 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.086102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.076071 restraints weight = 82752.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.077796 restraints weight = 44794.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.078895 restraints weight = 28824.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.079683 restraints weight = 20996.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.080205 restraints weight = 16354.584| |-----------------------------------------------------------------------------| r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3135 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3135 r_free = 0.3135 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3135 r_free = 0.3135 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3135 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 27326 Z= 0.222 Angle : 0.700 12.892 37614 Z= 0.346 Chirality : 0.048 0.504 4481 Planarity : 0.005 0.064 4810 Dihedral : 5.353 34.497 3911 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 3.05 % Allowed : 11.73 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.14), residues: 3610 helix: 1.44 (0.21), residues: 650 sheet: -0.64 (0.18), residues: 826 loop : -1.29 (0.13), residues: 2134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 94 TYR 0.023 0.002 TYR C 265 PHE 0.017 0.002 PHE A 392 TRP 0.020 0.002 TRP C 104 HIS 0.005 0.001 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00495 / 0.22 (27211) covalent geometry : angle 0.66783 / 0.34 (37317) SS BOND : bond 0.00400 / 0.20 ( 48) SS BOND : angle 1.29554 / 0.79 ( 96) hydrogen bonds : bond 0.03942 / 2.70 ( 1072) hydrogen bonds : angle 5.54739 / 3.87 ( 2952) link_ALPHA1-3 : bond 0.00404 / 0.20 ( 4) link_ALPHA1-3 : angle 1.73184 / 1.04 ( 12) link_ALPHA1-6 : bond 0.00323 / 0.16 ( 5) link_ALPHA1-6 : angle 1.75920 / 1.05 ( 15) link_BETA1-2 : bond 0.01379 / 0.61 ( 3) link_BETA1-2 : angle 3.16064 / 1.90 ( 9) link_BETA1-4 : bond 0.00786 / 0.59 ( 15) link_BETA1-4 : angle 2.39707 / 1.70 ( 45) link_NAG-ASN : bond 0.00379 / 0.23 ( 40) link_NAG-ASN : angle 3.12173 / 2.05 ( 120) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7220 Ramachandran restraints generated. 3610 Oldfield, 0 Emsley, 3610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7220 Ramachandran restraints generated. 3610 Oldfield, 0 Emsley, 3610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 193 time to evaluate : 1.144 Fit side-chains revert: symmetry clash REVERT: B 507 PRO cc_start: 0.8751 (Cg_exo) cc_final: 0.8495 (Cg_endo) REVERT: B 980 ILE cc_start: 0.9344 (tp) cc_final: 0.9050 (tt) REVERT: C 351 TYR cc_start: 0.8231 (OUTLIER) cc_final: 0.7969 (t80) REVERT: C 565 PHE cc_start: 0.7145 (OUTLIER) cc_final: 0.6073 (t80) REVERT: F 54 SER cc_start: 0.8564 (OUTLIER) cc_final: 0.8320 (m) REVERT: F 80 MET cc_start: 0.8420 (tmm) cc_final: 0.8112 (tmm) REVERT: F 100 ASN cc_start: 0.8370 (t0) cc_final: 0.7896 (t0) REVERT: J 10 GLU cc_start: 0.7113 (tm-30) cc_final: 0.6754 (tm-30) REVERT: J 32 TYR cc_start: 0.8488 (m-80) cc_final: 0.8037 (m-80) REVERT: J 36 TRP cc_start: 0.9037 (m100) cc_final: 0.8654 (m100) REVERT: J 52 ASN cc_start: 0.8325 (t0) cc_final: 0.7803 (t0) REVERT: J 80 MET cc_start: 0.8471 (tmm) cc_final: 0.8212 (tmm) REVERT: J 100 TYR cc_start: 0.7899 (m-10) cc_final: 0.7433 (m-10) REVERT: L 36 TYR cc_start: 0.8563 (m-80) cc_final: 0.8226 (m-10) outliers start: 67 outliers final: 40 residues processed: 242 average time/residue: 0.1472 time to fit residues: 60.5205 Evaluate side-chains 220 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 177 time to evaluate : 1.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 690 GLN Chi-restraints excluded: chain A residue 904 TYR Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 484 GLU Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain F residue 53 ASN Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 100 ASP Chi-restraints excluded: chain H residue 59 TYR Chi-restraints excluded: chain H residue 71 ARG Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain J residue 59 TYR Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 98 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 2 optimal weight: 0.5980 chunk 34 optimal weight: 5.9990 chunk 313 optimal weight: 0.4980 chunk 61 optimal weight: 2.9990 chunk 243 optimal weight: 1.9990 chunk 15 optimal weight: 9.9990 chunk 37 optimal weight: 4.9990 chunk 308 optimal weight: 8.9990 chunk 340 optimal weight: 6.9990 chunk 170 optimal weight: 1.9990 chunk 180 optimal weight: 0.6980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.086393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.076387 restraints weight = 81478.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.078117 restraints weight = 44060.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.079211 restraints weight = 28338.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.080001 restraints weight = 20704.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.080533 restraints weight = 16085.322| |-----------------------------------------------------------------------------| r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 27326 Z= 0.149 Angle : 0.644 11.834 37614 Z= 0.318 Chirality : 0.047 0.404 4481 Planarity : 0.004 0.054 4810 Dihedral : 5.029 33.248 3911 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 2.82 % Allowed : 12.32 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.14), residues: 3610 helix: 1.66 (0.21), residues: 645 sheet: -0.69 (0.18), residues: 860 loop : -1.20 (0.13), residues: 2105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 83 TYR 0.020 0.001 TYR H 33 PHE 0.017 0.001 PHE A 565 TRP 0.020 0.002 TRP C 104 HIS 0.006 0.001 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.15 (27211) covalent geometry : angle 0.61298 / 0.31 (37317) SS BOND : bond 0.00330 / 0.16 ( 48) SS BOND : angle 1.17061 / 0.71 ( 96) hydrogen bonds : bond 0.03624 / 2.48 ( 1072) hydrogen bonds : angle 5.36292 / 3.73 ( 2952) link_ALPHA1-3 : bond 0.00533 / 0.26 ( 4) link_ALPHA1-3 : angle 1.69373 / 1.02 ( 12) link_ALPHA1-6 : bond 0.00473 / 0.25 ( 5) link_ALPHA1-6 : angle 1.54539 / 0.92 ( 15) link_BETA1-2 : bond 0.01350 / 0.60 ( 3) link_BETA1-2 : angle 3.11180 / 1.87 ( 9) link_BETA1-4 : bond 0.00734 / 0.54 ( 15) link_BETA1-4 : angle 2.10201 / 1.47 ( 45) link_NAG-ASN : bond 0.00332 / 0.19 ( 40) link_NAG-ASN : angle 3.01604 / 2.06 ( 120) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7220 Ramachandran restraints generated. 3610 Oldfield, 0 Emsley, 3610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7220 Ramachandran restraints generated. 3610 Oldfield, 0 Emsley, 3610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 207 time to evaluate : 0.650 Fit side-chains REVERT: B 507 PRO cc_start: 0.8712 (Cg_exo) cc_final: 0.8469 (Cg_endo) REVERT: B 980 ILE cc_start: 0.9334 (tp) cc_final: 0.9043 (tt) REVERT: C 351 TYR cc_start: 0.8154 (OUTLIER) cc_final: 0.7874 (t80) REVERT: C 565 PHE cc_start: 0.7164 (OUTLIER) cc_final: 0.6134 (t80) REVERT: F 32 TYR cc_start: 0.7989 (m-80) cc_final: 0.7580 (m-10) REVERT: F 80 MET cc_start: 0.8429 (tmm) cc_final: 0.8123 (tmm) REVERT: F 100 ASN cc_start: 0.8297 (t0) cc_final: 0.7686 (t0) REVERT: J 52 ASN cc_start: 0.8283 (t0) cc_final: 0.7659 (t0) REVERT: J 80 MET cc_start: 0.8380 (tmm) cc_final: 0.8136 (tmm) REVERT: J 100 TYR cc_start: 0.7803 (m-10) cc_final: 0.7429 (m-10) REVERT: L 36 TYR cc_start: 0.8517 (m-80) cc_final: 0.8165 (m-10) outliers start: 62 outliers final: 38 residues processed: 252 average time/residue: 0.1500 time to fit residues: 63.6807 Evaluate side-chains 230 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 190 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 690 GLN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 904 TYR Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain H residue 59 TYR Chi-restraints excluded: chain H residue 71 ARG Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 75 ILE Chi-restraints excluded: chain J residue 98 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 37 optimal weight: 3.9990 chunk 159 optimal weight: 0.0770 chunk 255 optimal weight: 0.0030 chunk 259 optimal weight: 0.6980 chunk 126 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 184 optimal weight: 3.9990 chunk 102 optimal weight: 6.9990 chunk 274 optimal weight: 2.9990 chunk 324 optimal weight: 5.9990 chunk 194 optimal weight: 0.9980 overall best weight: 0.9550 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1135 ASN C1088 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.087585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.077585 restraints weight = 80693.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.079314 restraints weight = 43337.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.080441 restraints weight = 27861.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.081225 restraints weight = 20194.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.081781 restraints weight = 15705.638| |-----------------------------------------------------------------------------| r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 27326 Z= 0.136 Angle : 0.623 11.581 37614 Z= 0.307 Chirality : 0.046 0.357 4481 Planarity : 0.004 0.053 4810 Dihedral : 4.803 30.837 3911 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.68 % Allowed : 13.14 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.14), residues: 3610 helix: 1.78 (0.21), residues: 641 sheet: -0.66 (0.18), residues: 849 loop : -1.10 (0.13), residues: 2120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 83 TYR 0.025 0.001 TYR H 100J PHE 0.016 0.001 PHE A 565 TRP 0.018 0.002 TRP C 104 HIS 0.005 0.001 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 (27211) covalent geometry : angle 0.59503 / 0.30 (37317) SS BOND : bond 0.00349 / 0.17 ( 48) SS BOND : angle 1.13164 / 0.68 ( 96) hydrogen bonds : bond 0.03486 / 2.39 ( 1072) hydrogen bonds : angle 5.23257 / 3.63 ( 2952) link_ALPHA1-3 : bond 0.00542 / 0.26 ( 4) link_ALPHA1-3 : angle 1.65238 / 1.00 ( 12) link_ALPHA1-6 : bond 0.00462 / 0.24 ( 5) link_ALPHA1-6 : angle 1.54543 / 0.92 ( 15) link_BETA1-2 : bond 0.01243 / 0.55 ( 3) link_BETA1-2 : angle 2.96694 / 1.78 ( 9) link_BETA1-4 : bond 0.00713 / 0.52 ( 15) link_BETA1-4 : angle 1.93334 / 1.34 ( 45) link_NAG-ASN : bond 0.00343 / 0.21 ( 40) link_NAG-ASN : angle 2.79966 / 1.89 ( 120) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7220 Ramachandran restraints generated. 3610 Oldfield, 0 Emsley, 3610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7220 Ramachandran restraints generated. 3610 Oldfield, 0 Emsley, 3610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 207 time to evaluate : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 980 ILE cc_start: 0.9313 (tp) cc_final: 0.8968 (tt) REVERT: B 984 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8318 (mp) REVERT: C 351 TYR cc_start: 0.8117 (OUTLIER) cc_final: 0.7825 (t80) REVERT: C 565 PHE cc_start: 0.7166 (OUTLIER) cc_final: 0.6113 (t80) REVERT: F 80 MET cc_start: 0.8415 (tmm) cc_final: 0.8130 (tmm) REVERT: F 100 ASN cc_start: 0.8156 (t0) cc_final: 0.7944 (t0) REVERT: J 80 MET cc_start: 0.8450 (tmm) cc_final: 0.8236 (tmm) REVERT: J 100 TYR cc_start: 0.7653 (m-10) cc_final: 0.7309 (m-10) REVERT: L 36 TYR cc_start: 0.8487 (m-80) cc_final: 0.8128 (m-10) outliers start: 59 outliers final: 37 residues processed: 253 average time/residue: 0.1484 time to fit residues: 63.0956 Evaluate side-chains 238 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 198 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 904 TYR Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain H residue 59 TYR Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 98 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 246 optimal weight: 0.8980 chunk 279 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 252 optimal weight: 5.9990 chunk 133 optimal weight: 2.9990 chunk 332 optimal weight: 0.0870 chunk 47 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 153 optimal weight: 2.9990 chunk 328 optimal weight: 0.2980 chunk 318 optimal weight: 8.9990 overall best weight: 0.8360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.088703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.078751 restraints weight = 81449.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.080522 restraints weight = 43464.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.081695 restraints weight = 27672.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.082418 restraints weight = 19715.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.082972 restraints weight = 15459.448| |-----------------------------------------------------------------------------| r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 27326 Z= 0.127 Angle : 0.615 11.594 37614 Z= 0.303 Chirality : 0.046 0.329 4481 Planarity : 0.004 0.058 4810 Dihedral : 4.689 29.844 3911 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.46 % Allowed : 13.96 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.14), residues: 3610 helix: 1.84 (0.21), residues: 644 sheet: -0.65 (0.18), residues: 861 loop : -1.07 (0.14), residues: 2105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 83 TYR 0.034 0.001 TYR F 32 PHE 0.016 0.001 PHE A 565 TRP 0.017 0.002 TRP C 104 HIS 0.011 0.001 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 (27211) covalent geometry : angle 0.58903 / 0.30 (37317) SS BOND : bond 0.00336 / 0.17 ( 48) SS BOND : angle 1.11617 / 0.67 ( 96) hydrogen bonds : bond 0.03425 / 2.34 ( 1072) hydrogen bonds : angle 5.17729 / 3.59 ( 2952) link_ALPHA1-3 : bond 0.00559 / 0.27 ( 4) link_ALPHA1-3 : angle 1.62687 / 0.98 ( 12) link_ALPHA1-6 : bond 0.00485 / 0.25 ( 5) link_ALPHA1-6 : angle 1.50779 / 0.90 ( 15) link_BETA1-2 : bond 0.01284 / 0.58 ( 3) link_BETA1-2 : angle 2.89561 / 1.74 ( 9) link_BETA1-4 : bond 0.00674 / 0.49 ( 15) link_BETA1-4 : angle 1.84767 / 1.26 ( 45) link_NAG-ASN : bond 0.00328 / 0.19 ( 40) link_NAG-ASN : angle 2.67758 / 1.80 ( 120) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7220 Ramachandran restraints generated. 3610 Oldfield, 0 Emsley, 3610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7220 Ramachandran restraints generated. 3610 Oldfield, 0 Emsley, 3610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 209 time to evaluate : 0.827 Fit side-chains REVERT: B 980 ILE cc_start: 0.9306 (tp) cc_final: 0.8958 (tt) REVERT: B 984 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8329 (mp) REVERT: C 351 TYR cc_start: 0.8086 (OUTLIER) cc_final: 0.7776 (t80) REVERT: C 565 PHE cc_start: 0.7179 (OUTLIER) cc_final: 0.6175 (t80) REVERT: F 50 TRP cc_start: 0.8017 (p-90) cc_final: 0.7448 (p-90) REVERT: F 80 MET cc_start: 0.8392 (tmm) cc_final: 0.8144 (tmm) REVERT: F 100 ASN cc_start: 0.8051 (t0) cc_final: 0.7833 (t0) REVERT: J 10 GLU cc_start: 0.6958 (tm-30) cc_final: 0.6633 (tm-30) REVERT: J 80 MET cc_start: 0.8445 (tmm) cc_final: 0.8207 (tmm) REVERT: J 100 TYR cc_start: 0.7514 (m-10) cc_final: 0.7250 (m-10) REVERT: L 36 TYR cc_start: 0.8507 (m-80) cc_final: 0.8118 (m-10) outliers start: 54 outliers final: 38 residues processed: 252 average time/residue: 0.1547 time to fit residues: 66.1873 Evaluate side-chains 235 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 194 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 100 CYS Chi-restraints excluded: chain H residue 59 TYR Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 75 ILE Chi-restraints excluded: chain J residue 98 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 234 optimal weight: 3.9990 chunk 125 optimal weight: 3.9990 chunk 257 optimal weight: 0.6980 chunk 169 optimal weight: 0.3980 chunk 219 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 252 optimal weight: 0.9980 chunk 95 optimal weight: 0.9990 chunk 126 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.089567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.079653 restraints weight = 81165.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.081412 restraints weight = 43098.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.082550 restraints weight = 27529.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.083342 restraints weight = 19735.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.083880 restraints weight = 15263.460| |-----------------------------------------------------------------------------| r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.2868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 27326 Z= 0.121 Angle : 0.613 11.881 37614 Z= 0.301 Chirality : 0.046 0.534 4481 Planarity : 0.004 0.064 4810 Dihedral : 4.565 29.660 3911 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.41 % Allowed : 14.51 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.14), residues: 3610 helix: 1.90 (0.21), residues: 644 sheet: -0.62 (0.18), residues: 868 loop : -1.03 (0.14), residues: 2098 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 94 TYR 0.021 0.001 TYR H 32 PHE 0.015 0.001 PHE A 565 TRP 0.037 0.002 TRP J 50 HIS 0.007 0.001 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (27211) covalent geometry : angle 0.58505 / 0.29 (37317) SS BOND : bond 0.00351 / 0.17 ( 48) SS BOND : angle 1.12018 / 0.68 ( 96) hydrogen bonds : bond 0.03363 / 2.30 ( 1072) hydrogen bonds : angle 5.09140 / 3.54 ( 2952) link_ALPHA1-3 : bond 0.00565 / 0.27 ( 4) link_ALPHA1-3 : angle 1.62262 / 0.98 ( 12) link_ALPHA1-6 : bond 0.00494 / 0.25 ( 5) link_ALPHA1-6 : angle 1.48986 / 0.89 ( 15) link_BETA1-2 : bond 0.01243 / 0.56 ( 3) link_BETA1-2 : angle 2.85678 / 1.71 ( 9) link_BETA1-4 : bond 0.00646 / 0.46 ( 15) link_BETA1-4 : angle 1.76604 / 1.19 ( 45) link_NAG-ASN : bond 0.00332 / 0.19 ( 40) link_NAG-ASN : angle 2.80569 / 1.97 ( 120) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7220 Ramachandran restraints generated. 3610 Oldfield, 0 Emsley, 3610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7220 Ramachandran restraints generated. 3610 Oldfield, 0 Emsley, 3610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 206 time to evaluate : 1.002 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 980 ILE cc_start: 0.9293 (tp) cc_final: 0.8940 (tt) REVERT: B 984 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8323 (mp) REVERT: C 351 TYR cc_start: 0.8050 (OUTLIER) cc_final: 0.7729 (t80) REVERT: C 565 PHE cc_start: 0.7210 (OUTLIER) cc_final: 0.6177 (t80) REVERT: F 74 SER cc_start: 0.8857 (OUTLIER) cc_final: 0.8628 (p) REVERT: F 80 MET cc_start: 0.8319 (tmm) cc_final: 0.7904 (tmm) REVERT: F 100 ASN cc_start: 0.8305 (t0) cc_final: 0.8071 (t0) REVERT: J 80 MET cc_start: 0.8417 (tmm) cc_final: 0.8181 (tmm) REVERT: J 100 TYR cc_start: 0.7419 (m-10) cc_final: 0.7218 (m-10) REVERT: L 36 TYR cc_start: 0.8491 (m-80) cc_final: 0.8052 (m-10) outliers start: 53 outliers final: 40 residues processed: 247 average time/residue: 0.1606 time to fit residues: 66.5511 Evaluate side-chains 242 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 198 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 904 TYR Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain F residue 74 SER Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain H residue 59 TYR Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain J residue 57 THR Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 75 ILE Chi-restraints excluded: chain J residue 98 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 336 optimal weight: 0.0870 chunk 230 optimal weight: 4.9990 chunk 360 optimal weight: 3.9990 chunk 90 optimal weight: 0.0980 chunk 151 optimal weight: 3.9990 chunk 328 optimal weight: 0.0040 chunk 205 optimal weight: 1.9990 chunk 269 optimal weight: 2.9990 chunk 43 optimal weight: 0.3980 chunk 298 optimal weight: 7.9990 chunk 66 optimal weight: 0.6980 overall best weight: 0.2570 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.089995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.080074 restraints weight = 80593.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.081827 restraints weight = 42739.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.082949 restraints weight = 27260.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.083722 restraints weight = 19759.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.084257 restraints weight = 15284.362| |-----------------------------------------------------------------------------| r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.3055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.068 27326 Z= 0.106 Angle : 0.616 16.969 37614 Z= 0.304 Chirality : 0.045 0.354 4481 Planarity : 0.004 0.069 4810 Dihedral : 4.477 30.151 3911 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.82 % Allowed : 15.23 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.14), residues: 3610 helix: 2.09 (0.22), residues: 631 sheet: -0.53 (0.17), residues: 871 loop : -0.93 (0.14), residues: 2108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 94 TYR 0.031 0.001 TYR F 33 PHE 0.020 0.001 PHE A 374 TRP 0.036 0.002 TRP J 50 HIS 0.006 0.001 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.10 (27211) covalent geometry : angle 0.58625 / 0.30 (37317) SS BOND : bond 0.00472 / 0.20 ( 48) SS BOND : angle 1.84134 / 1.11 ( 96) hydrogen bonds : bond 0.03225 / 2.21 ( 1072) hydrogen bonds : angle 4.97690 / 3.46 ( 2952) link_ALPHA1-3 : bond 0.00674 / 0.32 ( 4) link_ALPHA1-3 : angle 1.62098 / 0.98 ( 12) link_ALPHA1-6 : bond 0.00609 / 0.32 ( 5) link_ALPHA1-6 : angle 1.36972 / 0.82 ( 15) link_BETA1-2 : bond 0.01242 / 0.56 ( 3) link_BETA1-2 : angle 2.91346 / 1.75 ( 9) link_BETA1-4 : bond 0.00643 / 0.44 ( 15) link_BETA1-4 : angle 1.68107 / 1.11 ( 45) link_NAG-ASN : bond 0.00399 / 0.24 ( 40) link_NAG-ASN : angle 2.64652 / 1.83 ( 120) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7220 Ramachandran restraints generated. 3610 Oldfield, 0 Emsley, 3610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7220 Ramachandran restraints generated. 3610 Oldfield, 0 Emsley, 3610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 212 time to evaluate : 1.051 Fit side-chains revert: symmetry clash REVERT: A 902 MET cc_start: 0.8305 (tpp) cc_final: 0.8091 (tpp) REVERT: B 980 ILE cc_start: 0.9254 (tp) cc_final: 0.8937 (tt) REVERT: C 565 PHE cc_start: 0.7186 (OUTLIER) cc_final: 0.6185 (t80) REVERT: F 74 SER cc_start: 0.8908 (OUTLIER) cc_final: 0.8658 (p) REVERT: F 80 MET cc_start: 0.8382 (tmm) cc_final: 0.8016 (tmm) REVERT: F 100 ASN cc_start: 0.8279 (t0) cc_final: 0.8057 (t0) REVERT: G 32 TYR cc_start: 0.8853 (m-80) cc_final: 0.8441 (m-10) REVERT: J 80 MET cc_start: 0.8386 (tmm) cc_final: 0.8135 (tmm) REVERT: J 100 TYR cc_start: 0.7440 (m-10) cc_final: 0.7175 (m-10) REVERT: L 36 TYR cc_start: 0.8436 (m-80) cc_final: 0.7982 (m-10) outliers start: 40 outliers final: 29 residues processed: 243 average time/residue: 0.1602 time to fit residues: 65.2157 Evaluate side-chains 226 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 195 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain F residue 74 SER Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 100 CYS Chi-restraints excluded: chain H residue 59 TYR Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 75 ILE Chi-restraints excluded: chain J residue 98 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 344 optimal weight: 1.9990 chunk 265 optimal weight: 0.0570 chunk 285 optimal weight: 0.3980 chunk 125 optimal weight: 4.9990 chunk 279 optimal weight: 3.9990 chunk 322 optimal weight: 3.9990 chunk 8 optimal weight: 0.0570 chunk 122 optimal weight: 0.1980 chunk 216 optimal weight: 8.9990 chunk 280 optimal weight: 0.9990 chunk 297 optimal weight: 7.9990 overall best weight: 0.3418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 644 GLN C 969 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.080154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.070400 restraints weight = 80424.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.072159 restraints weight = 42445.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.073315 restraints weight = 26768.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.074063 restraints weight = 18980.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.074579 restraints weight = 14698.700| |-----------------------------------------------------------------------------| r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.3203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.068 27326 Z= 0.107 Angle : 0.609 15.906 37614 Z= 0.300 Chirality : 0.045 0.293 4481 Planarity : 0.004 0.061 4810 Dihedral : 4.351 27.055 3911 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.77 % Allowed : 15.69 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.14), residues: 3610 helix: 2.11 (0.22), residues: 634 sheet: -0.52 (0.17), residues: 904 loop : -0.90 (0.14), residues: 2072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 83 TYR 0.041 0.001 TYR G 36 PHE 0.020 0.001 PHE B 759 TRP 0.034 0.002 TRP J 50 HIS 0.005 0.001 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.11 (27211) covalent geometry : angle 0.58343 / 0.29 (37317) SS BOND : bond 0.00438 / 0.19 ( 48) SS BOND : angle 1.68348 / 1.03 ( 96) hydrogen bonds : bond 0.03217 / 2.21 ( 1072) hydrogen bonds : angle 4.92576 / 3.43 ( 2952) link_ALPHA1-3 : bond 0.00638 / 0.30 ( 4) link_ALPHA1-3 : angle 1.64075 / 0.99 ( 12) link_ALPHA1-6 : bond 0.00550 / 0.28 ( 5) link_ALPHA1-6 : angle 1.41105 / 0.84 ( 15) link_BETA1-2 : bond 0.01257 / 0.57 ( 3) link_BETA1-2 : angle 2.84479 / 1.70 ( 9) link_BETA1-4 : bond 0.00609 / 0.42 ( 15) link_BETA1-4 : angle 1.64709 / 1.08 ( 45) link_NAG-ASN : bond 0.00364 / 0.22 ( 40) link_NAG-ASN : angle 2.46702 / 1.70 ( 120) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3784.55 seconds wall clock time: 81 minutes 33.72 seconds (4893.72 seconds total)