Starting phenix.real_space_refine on Fri Mar 6 00:49:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7l56_23165/03_2026/7l56_23165.cif Found real_map, /net/cci-nas-00/data/ceres_data/7l56_23165/03_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_23165/03_2026/7l56_23165.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7l56_23165/03_2026/7l56_23165.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7l56_23165/03_2026/7l56_23165.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7l56_23165/03_2026/7l56_23165.map" } 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-5986/lib/python3.9/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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 24 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 dihedrals: 24 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 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 dihedrals: 24 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 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 dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 6.34, per 1000 atoms: 0.24 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: 3.07 Conformation dependent library (CDL) restraints added in 1.3 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: 1.34 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: 7.68 Time building geometry restraints manager: 3.90 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 - 23.28: 15798 23.28 - 46.56: 601 46.56 - 69.83: 109 69.83 - 93.11: 45 93.11 - 116.39: 22 Dihedral angle restraints: 16575 sinusoidal: 5927 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 16572 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: 4.710 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: 0.400 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 28.710 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.060 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:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 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 : 14.414 116.387 9613 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 covalent geometry : bond 0.00987 (27211) covalent geometry : angle 1.12663 (37317) SS BOND : bond 0.00951 ( 48) SS BOND : angle 2.45602 ( 96) hydrogen bonds : bond 0.13136 ( 1072) hydrogen bonds : angle 8.54666 ( 2952) link_ALPHA1-3 : bond 0.02052 ( 4) link_ALPHA1-3 : angle 3.38163 ( 12) link_ALPHA1-6 : bond 0.01208 ( 5) link_ALPHA1-6 : angle 2.93123 ( 15) link_BETA1-2 : bond 0.03447 ( 3) link_BETA1-2 : angle 5.80903 ( 9) link_BETA1-4 : bond 0.01257 ( 15) link_BETA1-4 : angle 5.58233 ( 45) link_NAG-ASN : bond 0.00798 ( 40) link_NAG-ASN : angle 5.53941 ( 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 : 0.961 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: 0.1587 time to fit residues: 67.2630 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 : 0.936 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3326 r_free = 0.3326 target = 0.087735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.077853 restraints weight = 81468.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.079605 restraints weight = 43509.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.080759 restraints weight = 27840.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.081550 restraints weight = 20063.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.082085 restraints weight = 15464.715| |-----------------------------------------------------------------------------| r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3200 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3200 r_free = 0.3200 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 = 0.3200 r_free = 0.3200 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3200 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 27326 Z= 0.140 Angle : 0.754 14.514 37614 Z= 0.372 Chirality : 0.050 0.616 4481 Planarity : 0.004 0.073 4810 Dihedral : 10.570 100.160 5288 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.36 % Allowed : 7.05 % Favored : 92.59 % 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: -0.88 (0.13), residues: 3610 helix: 1.04 (0.21), residues: 637 sheet: -0.40 (0.18), residues: 785 loop : -1.18 (0.13), residues: 2188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 71 TYR 0.029 0.002 TYR J 33 PHE 0.028 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 covalent geometry : bond 0.00290 (27211) covalent geometry : angle 0.70593 (37317) SS BOND : bond 0.00683 ( 48) SS BOND : angle 1.11642 ( 96) hydrogen bonds : bond 0.04321 ( 1072) hydrogen bonds : angle 6.14966 ( 2952) link_ALPHA1-3 : bond 0.00903 ( 4) link_ALPHA1-3 : angle 1.70086 ( 12) link_ALPHA1-6 : bond 0.00301 ( 5) link_ALPHA1-6 : angle 1.89544 ( 15) link_BETA1-2 : bond 0.01498 ( 3) link_BETA1-2 : angle 4.67774 ( 9) link_BETA1-4 : bond 0.01153 ( 15) link_BETA1-4 : angle 3.58408 ( 45) link_NAG-ASN : bond 0.00463 ( 40) link_NAG-ASN : angle 3.89368 ( 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 242 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 234 time to evaluate : 1.027 Fit side-chains REVERT: A 900 MET cc_start: 0.8136 (mtp) cc_final: 0.7687 (ttm) REVERT: B 353 TRP cc_start: 0.8201 (p-90) cc_final: 0.7275 (p-90) REVERT: B 484 GLU cc_start: 0.7703 (mt-10) cc_final: 0.7454 (mt-10) REVERT: B 980 ILE cc_start: 0.9346 (tp) cc_final: 0.9129 (tt) REVERT: B 1050 MET cc_start: 0.8091 (ptp) cc_final: 0.7682 (ptp) REVERT: F 80 MET cc_start: 0.8488 (tmm) cc_final: 0.8121 (tmm) REVERT: F 91 TYR cc_start: 0.8799 (m-80) cc_final: 0.8564 (m-80) REVERT: F 100 ASN cc_start: 0.8423 (t0) cc_final: 0.8122 (t0) REVERT: H 80 MET cc_start: 0.8279 (tmm) cc_final: 0.7994 (tmm) REVERT: J 32 TYR cc_start: 0.8462 (m-80) cc_final: 0.8029 (m-10) REVERT: J 80 MET cc_start: 0.8427 (tmm) cc_final: 0.8197 (tmm) REVERT: J 91 TYR cc_start: 0.8683 (m-80) cc_final: 0.8263 (m-80) REVERT: L 36 TYR cc_start: 0.8585 (m-80) cc_final: 0.8142 (m-10) outliers start: 8 outliers final: 3 residues processed: 237 average time/residue: 0.1599 time to fit residues: 63.3487 Evaluate side-chains 185 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 182 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain C residue 738 CYS 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: 3.9990 chunk 138 optimal weight: 3.9990 chunk 289 optimal weight: 0.8980 chunk 199 optimal weight: 3.9990 chunk 110 optimal weight: 6.9990 chunk 104 optimal weight: 0.8980 chunk 310 optimal weight: 4.9990 chunk 274 optimal weight: 2.9990 chunk 130 optimal weight: 6.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 501 ASN A 532 ASN A1088 HIS A1135 ASN 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 = 0.3258 r_free = 0.3258 target = 0.080080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.070569 restraints weight = 79975.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.072116 restraints weight = 44055.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.073208 restraints weight = 29080.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.073855 restraints weight = 21264.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.074348 restraints weight = 17235.797| |-----------------------------------------------------------------------------| r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3138 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3138 r_free = 0.3138 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 = 0.3138 r_free = 0.3138 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3138 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.1714 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= 0.241 Angle : 0.752 15.833 37614 Z= 0.373 Chirality : 0.051 0.766 4481 Planarity : 0.005 0.065 4810 Dihedral : 9.964 101.317 5288 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 1.23 % Allowed : 9.96 % Favored : 88.81 % 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: -0.95 (0.14), residues: 3610 helix: 1.15 (0.21), residues: 653 sheet: -0.55 (0.18), residues: 820 loop : -1.25 (0.13), residues: 2137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 54 TYR 0.026 0.002 TYR H 33 PHE 0.020 0.002 PHE A 497 TRP 0.019 0.002 TRP B 104 HIS 0.006 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00540 (27211) covalent geometry : angle 0.70775 (37317) SS BOND : bond 0.00392 ( 48) SS BOND : angle 1.43878 ( 96) hydrogen bonds : bond 0.04254 ( 1072) hydrogen bonds : angle 5.82791 ( 2952) link_ALPHA1-3 : bond 0.00575 ( 4) link_ALPHA1-3 : angle 2.06151 ( 12) link_ALPHA1-6 : bond 0.00541 ( 5) link_ALPHA1-6 : angle 2.15062 ( 15) link_BETA1-2 : bond 0.01349 ( 3) link_BETA1-2 : angle 3.83106 ( 9) link_BETA1-4 : bond 0.01026 ( 15) link_BETA1-4 : angle 3.49917 ( 45) link_NAG-ASN : bond 0.00446 ( 40) link_NAG-ASN : angle 3.63967 ( 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 232 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 205 time to evaluate : 0.962 Fit side-chains REVERT: B 351 TYR cc_start: 0.8015 (OUTLIER) cc_final: 0.7734 (t80) REVERT: B 980 ILE cc_start: 0.9341 (tp) cc_final: 0.9027 (tt) REVERT: F 33 TYR cc_start: 0.8158 (m-10) cc_final: 0.7890 (m-10) REVERT: F 80 MET cc_start: 0.8365 (tmm) cc_final: 0.8107 (tmm) REVERT: F 100 ASN cc_start: 0.8490 (t0) cc_final: 0.7998 (t0) REVERT: J 52 ASN cc_start: 0.8330 (t0) cc_final: 0.7934 (t0) REVERT: J 80 MET cc_start: 0.8489 (tmm) cc_final: 0.8249 (tmm) REVERT: J 91 TYR cc_start: 0.8786 (m-80) cc_final: 0.8368 (m-80) REVERT: J 94 ARG cc_start: 0.8383 (ttp80) cc_final: 0.7267 (ttp80) REVERT: J 100 TYR cc_start: 0.7637 (m-10) cc_final: 0.7342 (m-10) REVERT: L 36 TYR cc_start: 0.8679 (m-80) cc_final: 0.8227 (m-10) outliers start: 27 outliers final: 15 residues processed: 218 average time/residue: 0.1499 time to fit residues: 55.1838 Evaluate side-chains 198 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 182 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 F residue 57 THR 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: 7.9990 chunk 13 optimal weight: 1.9990 chunk 222 optimal weight: 4.9990 chunk 271 optimal weight: 1.9990 chunk 328 optimal weight: 1.9990 chunk 144 optimal weight: 8.9990 chunk 339 optimal weight: 0.7980 chunk 363 optimal weight: 6.9990 chunk 219 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 955 ASN B 784 GLN B 955 ASN C 613 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.077078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.067128 restraints weight = 81779.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.068838 restraints weight = 44137.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.069974 restraints weight = 28435.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.070722 restraints weight = 20472.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.071238 restraints weight = 16072.046| |-----------------------------------------------------------------------------| r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3155 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3155 r_free = 0.3155 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3155 r_free = 0.3155 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3155 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 27326 Z= 0.184 Angle : 0.690 14.563 37614 Z= 0.340 Chirality : 0.049 0.657 4481 Planarity : 0.004 0.076 4810 Dihedral : 9.401 92.928 5288 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 1.86 % Allowed : 11.28 % Favored : 86.86 % 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: -0.84 (0.14), residues: 3610 helix: 1.44 (0.21), residues: 652 sheet: -0.52 (0.18), residues: 819 loop : -1.24 (0.13), residues: 2139 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 83 TYR 0.024 0.002 TYR H 33 PHE 0.016 0.002 PHE A 565 TRP 0.019 0.002 TRP C 104 HIS 0.005 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00409 (27211) covalent geometry : angle 0.64921 (37317) SS BOND : bond 0.00385 ( 48) SS BOND : angle 1.29255 ( 96) hydrogen bonds : bond 0.03877 ( 1072) hydrogen bonds : angle 5.58681 ( 2952) link_ALPHA1-3 : bond 0.00887 ( 4) link_ALPHA1-3 : angle 1.74515 ( 12) link_ALPHA1-6 : bond 0.00272 ( 5) link_ALPHA1-6 : angle 1.79901 ( 15) link_BETA1-2 : bond 0.01164 ( 3) link_BETA1-2 : angle 3.63744 ( 9) link_BETA1-4 : bond 0.00964 ( 15) link_BETA1-4 : angle 3.35317 ( 45) link_NAG-ASN : bond 0.00363 ( 40) link_NAG-ASN : angle 3.33156 ( 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 245 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 204 time to evaluate : 0.982 Fit side-chains REVERT: B 351 TYR cc_start: 0.8032 (OUTLIER) cc_final: 0.7764 (t80) REVERT: B 507 PRO cc_start: 0.8726 (Cg_exo) cc_final: 0.8480 (Cg_endo) REVERT: B 980 ILE cc_start: 0.9355 (tp) cc_final: 0.9080 (tt) REVERT: C 565 PHE cc_start: 0.7103 (OUTLIER) cc_final: 0.6127 (t80) REVERT: F 54 SER cc_start: 0.8732 (OUTLIER) cc_final: 0.8413 (m) REVERT: F 80 MET cc_start: 0.8426 (tmm) cc_final: 0.8127 (tmm) REVERT: F 100 ASN cc_start: 0.8340 (t0) cc_final: 0.8096 (t0) REVERT: J 10 GLU cc_start: 0.7068 (tm-30) cc_final: 0.6711 (tm-30) REVERT: J 52 ASN cc_start: 0.8380 (t0) cc_final: 0.8000 (t0) REVERT: J 80 MET cc_start: 0.8530 (tmm) cc_final: 0.8189 (tmm) REVERT: J 91 TYR cc_start: 0.8771 (m-80) cc_final: 0.8414 (m-80) REVERT: J 100 TYR cc_start: 0.7487 (m-10) cc_final: 0.7077 (m-10) REVERT: L 36 TYR cc_start: 0.8618 (m-80) cc_final: 0.8192 (m-10) outliers start: 41 outliers final: 23 residues processed: 232 average time/residue: 0.1504 time to fit residues: 58.5037 Evaluate side-chains 206 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 180 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 915 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 731 MET Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 968 SER 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 F residue 53 ASN Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain H residue 59 TYR Chi-restraints excluded: chain H residue 71 ARG 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: 6.9990 chunk 305 optimal weight: 10.0000 chunk 277 optimal weight: 0.9990 chunk 21 optimal weight: 8.9990 chunk 111 optimal weight: 0.9990 chunk 53 optimal weight: 9.9990 chunk 340 optimal weight: 5.9990 chunk 361 optimal weight: 10.0000 chunk 30 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 644 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.083082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.072999 restraints weight = 83067.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.074672 restraints weight = 45412.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.075759 restraints weight = 29576.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.076527 restraints weight = 21770.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.077067 restraints weight = 17130.353| |-----------------------------------------------------------------------------| r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3092 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3092 r_free = 0.3092 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 = 0.3092 r_free = 0.3092 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3092 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.067 27326 Z= 0.339 Angle : 0.816 13.676 37614 Z= 0.406 Chirality : 0.053 0.767 4481 Planarity : 0.005 0.071 4810 Dihedral : 9.738 92.930 5288 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 3.41 % Allowed : 11.51 % Favored : 85.08 % 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: -1.22 (0.14), residues: 3610 helix: 1.20 (0.21), residues: 645 sheet: -0.85 (0.18), residues: 843 loop : -1.47 (0.13), residues: 2122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 94 TYR 0.029 0.002 TYR C 265 PHE 0.023 0.003 PHE C 92 TRP 0.021 0.003 TRP C 104 HIS 0.006 0.002 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00759 (27211) covalent geometry : angle 0.77185 (37317) SS BOND : bond 0.00434 ( 48) SS BOND : angle 1.46937 ( 96) hydrogen bonds : bond 0.04446 ( 1072) hydrogen bonds : angle 5.82706 ( 2952) link_ALPHA1-3 : bond 0.00511 ( 4) link_ALPHA1-3 : angle 2.12453 ( 12) link_ALPHA1-6 : bond 0.00442 ( 5) link_ALPHA1-6 : angle 2.29800 ( 15) link_BETA1-2 : bond 0.01294 ( 3) link_BETA1-2 : angle 3.60047 ( 9) link_BETA1-4 : bond 0.00999 ( 15) link_BETA1-4 : angle 3.72311 ( 45) link_NAG-ASN : bond 0.00528 ( 40) link_NAG-ASN : angle 3.80462 ( 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 263 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 188 time to evaluate : 1.037 Fit side-chains REVERT: B 980 ILE cc_start: 0.9413 (tp) cc_final: 0.9175 (tt) REVERT: C 351 TYR cc_start: 0.8398 (OUTLIER) cc_final: 0.8175 (t80) REVERT: C 565 PHE cc_start: 0.7221 (OUTLIER) cc_final: 0.6075 (t80) REVERT: F 35 HIS cc_start: 0.8779 (OUTLIER) cc_final: 0.8575 (m90) REVERT: F 50 TRP cc_start: 0.8255 (p-90) cc_final: 0.8054 (p-90) REVERT: F 54 SER cc_start: 0.8689 (OUTLIER) cc_final: 0.8456 (m) REVERT: F 80 MET cc_start: 0.8405 (tmm) cc_final: 0.8079 (tmm) REVERT: H 33 TYR cc_start: 0.8822 (m-10) cc_final: 0.8606 (m-10) REVERT: J 32 TYR cc_start: 0.8430 (m-80) cc_final: 0.8202 (m-10) REVERT: J 52 ASN cc_start: 0.8366 (t0) cc_final: 0.7746 (t0) REVERT: J 80 MET cc_start: 0.8504 (tmm) cc_final: 0.8150 (tmm) REVERT: J 100 TYR cc_start: 0.8364 (OUTLIER) cc_final: 0.7674 (p90) REVERT: J 100 TYR cc_start: 0.7757 (m-10) cc_final: 0.7371 (m-10) REVERT: L 36 TYR cc_start: 0.8605 (m-80) cc_final: 0.8264 (m-10) outliers start: 75 outliers final: 46 residues processed: 243 average time/residue: 0.1520 time to fit residues: 62.8201 Evaluate side-chains 224 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 173 time to evaluate : 1.007 ------------------------------------------------------------------------------- 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 610 VAL Chi-restraints excluded: chain A residue 904 TYR Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 126 VAL 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 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 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 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 915 VAL Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain F residue 35 HIS 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 CYS Chi-restraints excluded: chain F residue 100 ASP Chi-restraints excluded: chain G residue 75 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 59 TYR Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain J residue 100 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 2 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 313 optimal weight: 0.3980 chunk 61 optimal weight: 0.7980 chunk 243 optimal weight: 6.9990 chunk 15 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 308 optimal weight: 6.9990 chunk 340 optimal weight: 10.0000 chunk 170 optimal weight: 0.9990 chunk 180 optimal weight: 0.5980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1088 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.077224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.067273 restraints weight = 81384.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.068990 restraints weight = 43910.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.070111 restraints weight = 28260.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.070860 restraints weight = 20412.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.071354 restraints weight = 15991.296| |-----------------------------------------------------------------------------| r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3158 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3158 r_free = 0.3158 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3158 r_free = 0.3158 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3158 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 27326 Z= 0.140 Angle : 0.663 12.039 37614 Z= 0.326 Chirality : 0.048 0.568 4481 Planarity : 0.004 0.059 4810 Dihedral : 9.098 89.496 5288 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.86 % Allowed : 12.46 % Favored : 84.67 % 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: -0.88 (0.14), residues: 3610 helix: 1.59 (0.21), residues: 644 sheet: -0.66 (0.18), residues: 849 loop : -1.28 (0.13), residues: 2117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 83 TYR 0.021 0.001 TYR H 32 PHE 0.019 0.001 PHE A 565 TRP 0.022 0.002 TRP C 104 HIS 0.006 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00306 (27211) covalent geometry : angle 0.62373 (37317) SS BOND : bond 0.00352 ( 48) SS BOND : angle 1.16303 ( 96) hydrogen bonds : bond 0.03714 ( 1072) hydrogen bonds : angle 5.44521 ( 2952) link_ALPHA1-3 : bond 0.00999 ( 4) link_ALPHA1-3 : angle 1.67061 ( 12) link_ALPHA1-6 : bond 0.00360 ( 5) link_ALPHA1-6 : angle 1.69089 ( 15) link_BETA1-2 : bond 0.01284 ( 3) link_BETA1-2 : angle 3.60199 ( 9) link_BETA1-4 : bond 0.00945 ( 15) link_BETA1-4 : angle 3.18111 ( 45) link_NAG-ASN : bond 0.00343 ( 40) link_NAG-ASN : angle 3.20442 ( 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 271 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 208 time to evaluate : 0.995 Fit side-chains revert: symmetry clash REVERT: B 507 PRO cc_start: 0.8632 (Cg_exo) cc_final: 0.8384 (Cg_endo) REVERT: B 565 PHE cc_start: 0.7245 (OUTLIER) cc_final: 0.5530 (p90) REVERT: B 980 ILE cc_start: 0.9380 (tp) cc_final: 0.9132 (tt) REVERT: C 351 TYR cc_start: 0.8161 (OUTLIER) cc_final: 0.7841 (t80) REVERT: C 565 PHE cc_start: 0.7203 (OUTLIER) cc_final: 0.6182 (t80) REVERT: F 32 TYR cc_start: 0.8106 (m-80) cc_final: 0.7737 (m-10) REVERT: F 50 TRP cc_start: 0.8154 (p-90) cc_final: 0.7695 (p-90) REVERT: F 54 SER cc_start: 0.8603 (OUTLIER) cc_final: 0.8344 (m) REVERT: F 80 MET cc_start: 0.8406 (tmm) cc_final: 0.8135 (tmm) REVERT: F 100 ASN cc_start: 0.8170 (t0) cc_final: 0.7948 (t0) REVERT: J 10 GLU cc_start: 0.7203 (tm-30) cc_final: 0.6848 (tm-30) REVERT: J 36 TRP cc_start: 0.9054 (m100) cc_final: 0.8658 (m100) REVERT: J 80 MET cc_start: 0.8485 (tmm) cc_final: 0.8207 (tmm) REVERT: J 100 TYR cc_start: 0.7323 (m-10) cc_final: 0.6895 (m-10) REVERT: L 36 TYR cc_start: 0.8550 (m-80) cc_final: 0.8257 (m-10) outliers start: 63 outliers final: 38 residues processed: 256 average time/residue: 0.1538 time to fit residues: 66.9002 Evaluate side-chains 233 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 191 time to evaluate : 0.956 ------------------------------------------------------------------------------- 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 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 662 CYS Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 904 TYR Chi-restraints excluded: chain A residue 931 ILE 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 326 ILE Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 565 PHE 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 915 VAL 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 489 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 F residue 53 ASN Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain F residue 100 CYS 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 J residue 51 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 Chi-restraints excluded: chain K residue 49 TYR 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: 0.0010 chunk 255 optimal weight: 1.9990 chunk 259 optimal weight: 4.9990 chunk 126 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 184 optimal weight: 3.9990 chunk 102 optimal weight: 0.1980 chunk 274 optimal weight: 2.9990 chunk 324 optimal weight: 3.9990 chunk 194 optimal weight: 0.9990 overall best weight: 1.2392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 644 GLN A1135 ASN C 969 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.076706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.066773 restraints weight = 81587.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.068494 restraints weight = 44022.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.069612 restraints weight = 28273.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.070359 restraints weight = 20439.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.070864 restraints weight = 16011.912| |-----------------------------------------------------------------------------| r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 27326 Z= 0.160 Angle : 0.661 12.054 37614 Z= 0.323 Chirality : 0.048 0.580 4481 Planarity : 0.004 0.056 4810 Dihedral : 8.800 86.921 5288 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 2.91 % Allowed : 12.64 % Favored : 84.45 % 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: -0.83 (0.14), residues: 3610 helix: 1.69 (0.21), residues: 644 sheet: -0.64 (0.18), residues: 849 loop : -1.26 (0.13), residues: 2117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 83 TYR 0.023 0.002 TYR H 33 PHE 0.019 0.001 PHE A 565 TRP 0.019 0.002 TRP B 104 HIS 0.011 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00357 (27211) covalent geometry : angle 0.62072 (37317) SS BOND : bond 0.00378 ( 48) SS BOND : angle 1.17800 ( 96) hydrogen bonds : bond 0.03642 ( 1072) hydrogen bonds : angle 5.37516 ( 2952) link_ALPHA1-3 : bond 0.00824 ( 4) link_ALPHA1-3 : angle 1.60471 ( 12) link_ALPHA1-6 : bond 0.00292 ( 5) link_ALPHA1-6 : angle 1.76831 ( 15) link_BETA1-2 : bond 0.01239 ( 3) link_BETA1-2 : angle 3.45881 ( 9) link_BETA1-4 : bond 0.00923 ( 15) link_BETA1-4 : angle 3.21952 ( 45) link_NAG-ASN : bond 0.00319 ( 40) link_NAG-ASN : angle 3.25831 ( 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 263 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 199 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 507 PRO cc_start: 0.8703 (Cg_exo) cc_final: 0.8457 (Cg_endo) REVERT: B 565 PHE cc_start: 0.7265 (OUTLIER) cc_final: 0.5513 (p90) REVERT: B 980 ILE cc_start: 0.9378 (tp) cc_final: 0.9081 (tt) REVERT: B 984 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8353 (mp) REVERT: C 351 TYR cc_start: 0.8160 (OUTLIER) cc_final: 0.7824 (t80) REVERT: C 565 PHE cc_start: 0.7216 (OUTLIER) cc_final: 0.6177 (t80) REVERT: F 32 TYR cc_start: 0.8057 (m-80) cc_final: 0.7763 (m-10) REVERT: F 54 SER cc_start: 0.8501 (OUTLIER) cc_final: 0.8248 (m) REVERT: F 80 MET cc_start: 0.8399 (tmm) cc_final: 0.8144 (tmm) REVERT: F 100 ASN cc_start: 0.8130 (t0) cc_final: 0.7888 (t0) REVERT: J 80 MET cc_start: 0.8444 (tmm) cc_final: 0.8175 (tmm) REVERT: J 100 TYR cc_start: 0.7179 (m-10) cc_final: 0.6822 (m-10) REVERT: L 36 TYR cc_start: 0.8506 (m-80) cc_final: 0.8168 (m-10) outliers start: 64 outliers final: 44 residues processed: 250 average time/residue: 0.1577 time to fit residues: 66.7234 Evaluate side-chains 237 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 188 time to evaluate : 1.010 ------------------------------------------------------------------------------- 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 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 644 GLN Chi-restraints excluded: chain A residue 662 CYS 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 931 ILE Chi-restraints excluded: chain A residue 1008 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 368 LEU Chi-restraints excluded: chain B residue 565 PHE 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 915 VAL 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 326 ILE Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 489 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 997 ILE Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain F residue 100 CYS 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 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 Chi-restraints excluded: chain K residue 49 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 246 optimal weight: 0.7980 chunk 279 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 252 optimal weight: 2.9990 chunk 133 optimal weight: 3.9990 chunk 332 optimal weight: 0.0030 chunk 47 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 153 optimal weight: 0.6980 chunk 328 optimal weight: 2.9990 chunk 318 optimal weight: 7.9990 overall best weight: 1.0792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 58 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.086710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.076652 restraints weight = 81570.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.078388 restraints weight = 43929.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.079507 restraints weight = 28231.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.080288 restraints weight = 20541.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.080831 restraints weight = 16067.850| |-----------------------------------------------------------------------------| r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 27326 Z= 0.144 Angle : 0.644 11.735 37614 Z= 0.314 Chirality : 0.047 0.555 4481 Planarity : 0.004 0.057 4810 Dihedral : 8.539 83.265 5288 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.59 % Allowed : 13.19 % Favored : 84.22 % 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: -0.76 (0.14), residues: 3610 helix: 1.86 (0.22), residues: 635 sheet: -0.67 (0.18), residues: 848 loop : -1.20 (0.13), residues: 2127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 83 TYR 0.036 0.001 TYR H 100J PHE 0.019 0.001 PHE A 565 TRP 0.024 0.002 TRP J 50 HIS 0.007 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00318 (27211) covalent geometry : angle 0.60628 (37317) SS BOND : bond 0.00382 ( 48) SS BOND : angle 1.13633 ( 96) hydrogen bonds : bond 0.03514 ( 1072) hydrogen bonds : angle 5.27479 ( 2952) link_ALPHA1-3 : bond 0.00992 ( 4) link_ALPHA1-3 : angle 1.49951 ( 12) link_ALPHA1-6 : bond 0.00344 ( 5) link_ALPHA1-6 : angle 1.73429 ( 15) link_BETA1-2 : bond 0.01210 ( 3) link_BETA1-2 : angle 3.47928 ( 9) link_BETA1-4 : bond 0.00934 ( 15) link_BETA1-4 : angle 3.15188 ( 45) link_NAG-ASN : bond 0.00352 ( 40) link_NAG-ASN : angle 3.07631 ( 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 260 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 203 time to evaluate : 0.739 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 565 PHE cc_start: 0.7323 (OUTLIER) cc_final: 0.5534 (p90) REVERT: B 980 ILE cc_start: 0.9370 (tp) cc_final: 0.9081 (tt) REVERT: B 984 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8356 (mp) REVERT: C 351 TYR cc_start: 0.8113 (OUTLIER) cc_final: 0.7778 (t80) REVERT: C 565 PHE cc_start: 0.7247 (OUTLIER) cc_final: 0.6206 (t80) REVERT: F 80 MET cc_start: 0.8382 (tmm) cc_final: 0.8100 (tmm) REVERT: F 100 ASN cc_start: 0.8405 (t0) cc_final: 0.8133 (t0) REVERT: J 80 MET cc_start: 0.8465 (tmm) cc_final: 0.8223 (tmm) REVERT: J 100 TYR cc_start: 0.7068 (m-10) cc_final: 0.6796 (m-10) REVERT: L 36 TYR cc_start: 0.8492 (m-80) cc_final: 0.8142 (m-10) outliers start: 57 outliers final: 43 residues processed: 250 average time/residue: 0.1508 time to fit residues: 63.7693 Evaluate side-chains 236 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 189 time to evaluate : 0.944 ------------------------------------------------------------------------------- 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 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 662 CYS Chi-restraints excluded: chain A residue 690 GLN 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 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 565 PHE Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 915 VAL 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 36 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 489 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 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 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 Chi-restraints excluded: chain K residue 49 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 234 optimal weight: 4.9990 chunk 125 optimal weight: 3.9990 chunk 257 optimal weight: 0.6980 chunk 169 optimal weight: 0.8980 chunk 219 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 252 optimal weight: 0.9990 chunk 95 optimal weight: 0.0970 chunk 126 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.087645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.077596 restraints weight = 81155.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.079346 restraints weight = 43544.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.080494 restraints weight = 27980.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.081272 restraints weight = 20231.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.081822 restraints weight = 15743.878| |-----------------------------------------------------------------------------| r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 27326 Z= 0.122 Angle : 0.642 16.200 37614 Z= 0.312 Chirality : 0.047 0.515 4481 Planarity : 0.004 0.059 4810 Dihedral : 8.229 78.117 5288 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 2.55 % Allowed : 13.55 % Favored : 83.90 % 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: -0.66 (0.14), residues: 3610 helix: 1.90 (0.21), residues: 640 sheet: -0.65 (0.18), residues: 864 loop : -1.11 (0.14), residues: 2106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 94 TYR 0.035 0.001 TYR F 32 PHE 0.030 0.001 PHE A 374 TRP 0.028 0.002 TRP J 50 HIS 0.006 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00267 (27211) covalent geometry : angle 0.60120 (37317) SS BOND : bond 0.00446 ( 48) SS BOND : angle 1.35276 ( 96) hydrogen bonds : bond 0.03395 ( 1072) hydrogen bonds : angle 5.15964 ( 2952) link_ALPHA1-3 : bond 0.01013 ( 4) link_ALPHA1-3 : angle 1.35768 ( 12) link_ALPHA1-6 : bond 0.00412 ( 5) link_ALPHA1-6 : angle 1.72568 ( 15) link_BETA1-2 : bond 0.01263 ( 3) link_BETA1-2 : angle 3.47666 ( 9) link_BETA1-4 : bond 0.00932 ( 15) link_BETA1-4 : angle 3.06965 ( 45) link_NAG-ASN : bond 0.00346 ( 40) link_NAG-ASN : angle 3.22347 ( 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 266 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 210 time to evaluate : 0.964 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 507 PRO cc_start: 0.8603 (Cg_exo) cc_final: 0.8252 (Cg_endo) REVERT: B 565 PHE cc_start: 0.7284 (OUTLIER) cc_final: 0.5533 (p90) REVERT: B 980 ILE cc_start: 0.9349 (tp) cc_final: 0.9051 (tt) REVERT: B 984 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8337 (mp) REVERT: C 565 PHE cc_start: 0.7219 (OUTLIER) cc_final: 0.6192 (t80) REVERT: F 50 TRP cc_start: 0.8141 (p-90) cc_final: 0.7525 (p-90) REVERT: F 80 MET cc_start: 0.8419 (tmm) cc_final: 0.8180 (tmm) REVERT: F 100 ASN cc_start: 0.8257 (t0) cc_final: 0.7984 (t0) REVERT: J 10 GLU cc_start: 0.6957 (tm-30) cc_final: 0.6634 (tm-30) REVERT: J 80 MET cc_start: 0.8414 (tmm) cc_final: 0.8157 (tmm) REVERT: J 100 TYR cc_start: 0.8166 (p90) cc_final: 0.7926 (p90) REVERT: J 100 TYR cc_start: 0.7118 (m-10) cc_final: 0.6751 (m-10) REVERT: L 36 TYR cc_start: 0.8443 (m-80) cc_final: 0.8063 (m-10) outliers start: 56 outliers final: 42 residues processed: 252 average time/residue: 0.1555 time to fit residues: 65.6890 Evaluate side-chains 243 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 198 time to evaluate : 0.967 ------------------------------------------------------------------------------- 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 690 GLN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 904 TYR 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 301 CYS Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 565 PHE 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 915 VAL 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 36 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 489 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 F residue 75 ILE Chi-restraints excluded: chain F residue 100 CYS Chi-restraints excluded: chain F residue 100 ASP 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 73 THR Chi-restraints excluded: chain J residue 75 ILE Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain K residue 49 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 336 optimal weight: 0.0970 chunk 230 optimal weight: 4.9990 chunk 360 optimal weight: 8.9990 chunk 90 optimal weight: 0.8980 chunk 151 optimal weight: 3.9990 chunk 328 optimal weight: 5.9990 chunk 205 optimal weight: 9.9990 chunk 269 optimal weight: 3.9990 chunk 43 optimal weight: 0.0870 chunk 298 optimal weight: 8.9990 chunk 66 optimal weight: 0.5980 overall best weight: 1.1358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.087135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.077096 restraints weight = 81017.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.078826 restraints weight = 43310.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.079978 restraints weight = 27813.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.080764 restraints weight = 20052.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.081295 restraints weight = 15597.517| |-----------------------------------------------------------------------------| r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 27326 Z= 0.152 Angle : 0.664 14.860 37614 Z= 0.323 Chirality : 0.048 0.553 4481 Planarity : 0.004 0.068 4810 Dihedral : 8.120 75.761 5288 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 2.32 % Allowed : 14.28 % Favored : 83.40 % 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: -0.67 (0.14), residues: 3610 helix: 1.91 (0.21), residues: 641 sheet: -0.69 (0.17), residues: 867 loop : -1.10 (0.14), residues: 2102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 94 TYR 0.029 0.001 TYR H 100J PHE 0.025 0.001 PHE A 374 TRP 0.040 0.002 TRP J 50 HIS 0.006 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00340 (27211) covalent geometry : angle 0.62345 (37317) SS BOND : bond 0.00448 ( 48) SS BOND : angle 1.78523 ( 96) hydrogen bonds : bond 0.03482 ( 1072) hydrogen bonds : angle 5.15651 ( 2952) link_ALPHA1-3 : bond 0.00916 ( 4) link_ALPHA1-3 : angle 1.42595 ( 12) link_ALPHA1-6 : bond 0.00361 ( 5) link_ALPHA1-6 : angle 1.87662 ( 15) link_BETA1-2 : bond 0.01210 ( 3) link_BETA1-2 : angle 3.36306 ( 9) link_BETA1-4 : bond 0.00910 ( 15) link_BETA1-4 : angle 3.04615 ( 45) link_NAG-ASN : bond 0.00350 ( 40) link_NAG-ASN : angle 3.16149 ( 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 250 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 199 time to evaluate : 0.864 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 980 ILE cc_start: 0.9356 (tp) cc_final: 0.9072 (tt) REVERT: B 984 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8347 (mp) REVERT: C 351 TYR cc_start: 0.8097 (OUTLIER) cc_final: 0.7786 (t80) REVERT: C 565 PHE cc_start: 0.7259 (OUTLIER) cc_final: 0.6237 (t80) REVERT: F 50 TRP cc_start: 0.7875 (p-90) cc_final: 0.7530 (p-90) REVERT: F 80 MET cc_start: 0.8374 (tmm) cc_final: 0.7912 (tmm) REVERT: F 100 ASN cc_start: 0.8362 (t0) cc_final: 0.8117 (t0) REVERT: J 10 GLU cc_start: 0.6915 (tm-30) cc_final: 0.6594 (tm-30) REVERT: J 80 MET cc_start: 0.8398 (tmm) cc_final: 0.8128 (tmm) REVERT: J 100 TYR cc_start: 0.7074 (m-10) cc_final: 0.6800 (m-10) REVERT: L 36 TYR cc_start: 0.8453 (m-80) cc_final: 0.8053 (m-10) outliers start: 51 outliers final: 42 residues processed: 241 average time/residue: 0.1560 time to fit residues: 63.0760 Evaluate side-chains 239 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 194 time to evaluate : 0.977 ------------------------------------------------------------------------------- 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 690 GLN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 904 TYR 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 301 CYS Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 484 GLU Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 915 VAL 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 36 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 489 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 F residue 75 ILE Chi-restraints excluded: chain F residue 100 ASP 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 73 THR Chi-restraints excluded: chain J residue 75 ILE Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain K residue 49 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 344 optimal weight: 6.9990 chunk 265 optimal weight: 0.0040 chunk 285 optimal weight: 2.9990 chunk 125 optimal weight: 3.9990 chunk 279 optimal weight: 2.9990 chunk 322 optimal weight: 0.9980 chunk 8 optimal weight: 20.0000 chunk 122 optimal weight: 0.0050 chunk 216 optimal weight: 9.9990 chunk 280 optimal weight: 0.5980 chunk 297 optimal weight: 8.9990 overall best weight: 0.9208 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 644 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.082526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.071846 restraints weight = 75842.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.073428 restraints weight = 43014.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.074482 restraints weight = 28996.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.075161 restraints weight = 21790.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.075655 restraints weight = 17867.337| |-----------------------------------------------------------------------------| r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.2998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 27326 Z= 0.137 Angle : 0.651 13.229 37614 Z= 0.318 Chirality : 0.047 0.527 4481 Planarity : 0.004 0.066 4810 Dihedral : 7.980 74.894 5288 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 2.55 % Allowed : 14.37 % 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: -0.66 (0.14), residues: 3610 helix: 1.89 (0.21), residues: 640 sheet: -0.68 (0.17), residues: 890 loop : -1.08 (0.14), residues: 2080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 71 TYR 0.032 0.001 TYR H 100J PHE 0.023 0.001 PHE A 374 TRP 0.034 0.002 TRP J 50 HIS 0.006 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00306 (27211) covalent geometry : angle 0.61048 (37317) SS BOND : bond 0.00480 ( 48) SS BOND : angle 1.84793 ( 96) hydrogen bonds : bond 0.03391 ( 1072) hydrogen bonds : angle 5.12280 ( 2952) link_ALPHA1-3 : bond 0.01013 ( 4) link_ALPHA1-3 : angle 1.30762 ( 12) link_ALPHA1-6 : bond 0.00424 ( 5) link_ALPHA1-6 : angle 1.94680 ( 15) link_BETA1-2 : bond 0.01260 ( 3) link_BETA1-2 : angle 3.40033 ( 9) link_BETA1-4 : bond 0.00892 ( 15) link_BETA1-4 : angle 2.99487 ( 45) link_NAG-ASN : bond 0.00336 ( 40) link_NAG-ASN : angle 3.04375 ( 120) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3831.64 seconds wall clock time: 67 minutes 6.20 seconds (4026.20 seconds total)