Starting phenix.real_space_refine on Sat Jul 4 15:13:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7t9a_25754/07_2026/7t9a_25754.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t9a_25754/07_2026/7t9a_25754.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7t9a_25754/07_2026/7t9a_25754.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t9a_25754/07_2026/7t9a_25754.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7t9a_25754/07_2026/7t9a_25754.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t9a_25754/07_2026/7t9a_25754.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7t9a_25754/07_2026/7t9a_25754.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7t9a_25754/07_2026/7t9a_25754.cif" } resolution = 3.54 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= 0.001 sd= 0.033 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 131 5.16 5 C 13459 2.51 5 N 3572 2.21 5 O 4355 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21517 Number of models: 1 Model: "" Number of chains: 41 Chain: "A" Number of atoms: 3418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3418 Classifications: {'peptide': 434} Link IDs: {'PTRANS': 23, 'TRANS': 410} Chain breaks: 3 Chain: "B" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 958 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain breaks: 1 Chain: "J" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 943 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "K" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 811 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "C" Number of atoms: 3410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3410 Classifications: {'peptide': 433} Link IDs: {'PTRANS': 23, 'TRANS': 409} Chain breaks: 3 Chain: "D" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 958 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain breaks: 1 Chain: "M" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 943 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "N" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 811 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "E" Number of atoms: 3418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3418 Classifications: {'peptide': 434} Link IDs: {'PTRANS': 23, 'TRANS': 410} Chain breaks: 4 Chain: "F" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 958 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain breaks: 1 Chain: "O" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 943 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "P" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 811 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "H" Number of atoms: 1052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1052 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 3, 'TRANS': 128} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'TYS:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "L" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 799 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Chain: "T" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen chiralities: 12 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen chiralities: 12 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen chiralities: 12 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 4.96, per 1000 atoms: 0.23 Number of scatterers: 21517 At special positions: 0 Unit cell: (120.51, 129.78, 188.49, 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 131 16.00 O 4355 8.00 N 3572 7.00 C 13459 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=38, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.05 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.04 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.05 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.02 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.04 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.02 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.02 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.04 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.02 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.05 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.05 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.02 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.04 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.02 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.02 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS D 605 " distance=2.02 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.04 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.02 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.06 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.05 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.04 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.04 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.02 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 92 " distance=2.04 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 88 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.02 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.08 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 Q 3 " - " MAN Q 4 " " BMA S 3 " - " MAN S 7 " " MAN S 4 " - " MAN S 5 " " BMA Y 3 " - " MAN Y 4 " " BMA e 3 " - " MAN e 4 " ALPHA1-6 " BMA S 3 " - " MAN S 4 " " MAN S 4 " - " MAN S 6 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " BETA1-6 " NAG T 1 " - " FUC T 2 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG U 1 " - " FUC U 2 " " NAG a 1 " - " FUC a 2 " " NAG b 1 " - " FUC b 2 " " NAG h 1 " - " FUC h 2 " " NAG i 1 " - " FUC i 2 " NAG-ASN " NAG A 601 " - " ASN A 88 " " NAG A 602 " - " ASN A 234 " " NAG A 603 " - " ASN A 137 " " NAG A 604 " - " ASN A 355 " " NAG A 605 " - " ASN A 276 " " NAG A 606 " - " ASN A 392 " " NAG A 607 " - " ASN A 339 " " NAG A 608 " - " ASN A 295 " " NAG A 609 " - " ASN A 448 " " NAG A 610 " - " ASN A 301 " " NAG A 611 " - " ASN A 197 " " NAG A 612 " - " ASN A 133 " " NAG B 701 " - " ASN B 637 " " NAG B 702 " - " ASN B 625 " " NAG C 601 " - " ASN C 88 " " NAG C 602 " - " ASN C 234 " " NAG C 603 " - " ASN C 137 " " NAG C 604 " - " ASN C 355 " " NAG C 605 " - " ASN C 276 " " NAG C 606 " - " ASN C 392 " " NAG C 607 " - " ASN C 339 " " NAG C 608 " - " ASN C 295 " " NAG C 609 " - " ASN C 448 " " NAG C 610 " - " ASN C 301 " " NAG C 611 " - " ASN C 197 " " NAG C 612 " - " ASN C 133 " " NAG D 701 " - " ASN D 625 " " NAG D 702 " - " ASN D 637 " " NAG E 601 " - " ASN E 88 " " NAG E 602 " - " ASN E 234 " " NAG E 603 " - " ASN E 137 " " NAG E 604 " - " ASN E 355 " " NAG E 605 " - " ASN E 276 " " NAG E 606 " - " ASN E 392 " " NAG E 607 " - " ASN E 339 " " NAG E 608 " - " ASN E 295 " " NAG E 609 " - " ASN E 448 " " NAG E 610 " - " ASN E 301 " " NAG E 611 " - " ASN E 197 " " NAG E 612 " - " ASN E 133 " " NAG F 701 " - " ASN F 637 " " NAG F 702 " - " ASN F 625 " " NAG G 1 " - " ASN A 386 " " NAG I 1 " - " ASN A 332 " " NAG Q 1 " - " ASN A 262 " " NAG R 1 " - " ASN A 156 " " NAG S 1 " - " ASN A 160 " " NAG T 1 " - " ASN B 618 " " NAG U 1 " - " ASN B 611 " " NAG V 1 " - " ASN C 160 " " NAG W 1 " - " ASN C 386 " " NAG X 1 " - " ASN C 332 " " NAG Y 1 " - " ASN C 262 " " NAG Z 1 " - " ASN C 156 " " NAG a 1 " - " ASN D 618 " " NAG b 1 " - " ASN D 611 " " NAG c 1 " - " ASN E 386 " " NAG d 1 " - " ASN E 332 " " NAG e 1 " - " ASN E 262 " " NAG f 1 " - " ASN E 156 " " NAG g 1 " - " ASN E 160 " " NAG h 1 " - " ASN F 618 " " NAG i 1 " - " ASN F 611 " Time building additional restraints: 2.02 Conformation dependent library (CDL) restraints added in 878.9 milliseconds 5072 Ramachandran restraints generated. 2536 Oldfield, 0 Emsley, 2536 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4760 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 36 sheets defined 19.1% alpha, 22.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'A' and resid 98 through 117 removed outlier: 4.115A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU A 116 " --> pdb=" O TRP A 112 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS A 117 " --> pdb=" O ASP A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 151 Processing helix chain 'A' and resid 335 through 350 Processing helix chain 'A' and resid 368 through 373 removed outlier: 3.535A pdb=" N THR A 373 " --> pdb=" O LEU A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 484 removed outlier: 3.593A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 526 removed outlier: 4.401A pdb=" N GLY B 525 " --> pdb=" O GLY B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 527 through 532 Processing helix chain 'B' and resid 534 through 540 Processing helix chain 'B' and resid 572 through 596 Processing helix chain 'B' and resid 618 through 623 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 662 removed outlier: 3.504A pdb=" N ILE B 642 " --> pdb=" O TYR B 638 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLY B 644 " --> pdb=" O GLN B 640 " (cutoff:3.500A) Processing helix chain 'J' and resid 28 through 32 Processing helix chain 'J' and resid 61 through 64 Processing helix chain 'J' and resid 83 through 87 Processing helix chain 'K' and resid 79 through 83 Processing helix chain 'C' and resid 99 through 115 Processing helix chain 'C' and resid 139 through 151 Processing helix chain 'C' and resid 335 through 350 Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 475 through 484 removed outlier: 3.952A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 521 through 526 removed outlier: 4.382A pdb=" N GLY D 525 " --> pdb=" O GLY D 522 " (cutoff:3.500A) Processing helix chain 'D' and resid 527 through 532 Processing helix chain 'D' and resid 534 through 540 Processing helix chain 'D' and resid 572 through 596 removed outlier: 3.514A pdb=" N LEU D 576 " --> pdb=" O GLY D 572 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 625 Processing helix chain 'D' and resid 627 through 635 Processing helix chain 'D' and resid 639 through 662 Processing helix chain 'M' and resid 28 through 32 Processing helix chain 'M' and resid 61 through 64 Processing helix chain 'M' and resid 83 through 87 Processing helix chain 'N' and resid 79 through 83 Processing helix chain 'E' and resid 99 through 115 Processing helix chain 'E' and resid 139 through 151 Processing helix chain 'E' and resid 195 through 197 No H-bonds generated for 'chain 'E' and resid 195 through 197' Processing helix chain 'E' and resid 335 through 350 Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 475 through 484 removed outlier: 3.962A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 527 through 532 Processing helix chain 'F' and resid 534 through 540 Processing helix chain 'F' and resid 572 through 596 Processing helix chain 'F' and resid 618 through 623 Processing helix chain 'F' and resid 627 through 633 Processing helix chain 'F' and resid 635 through 637 No H-bonds generated for 'chain 'F' and resid 635 through 637' Processing helix chain 'F' and resid 638 through 662 removed outlier: 3.638A pdb=" N ALA F 662 " --> pdb=" O GLN F 658 " (cutoff:3.500A) Processing helix chain 'O' and resid 28 through 32 Processing helix chain 'O' and resid 61 through 64 Processing helix chain 'O' and resid 83 through 87 Processing helix chain 'P' and resid 79 through 83 removed outlier: 3.508A pdb=" N GLU P 83 " --> pdb=" O ALA P 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 52A through 54 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 removed outlier: 4.129A pdb=" N THR H 87 " --> pdb=" O THR H 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 29 through 31 No H-bonds generated for 'chain 'L' and resid 29 through 31' Processing helix chain 'L' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.394A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.712A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA4, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AA5, first strand: chain 'A' and resid 201 through 203 removed outlier: 6.466A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 259 through 261 current: chain 'A' and resid 284 through 312 removed outlier: 6.889A pdb=" N ASN A 301 " --> pdb=" O ILE A 323 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ILE A 323 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 315 through 323A current: chain 'A' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 381 through 385 current: chain 'A' and resid 466 through 470 Processing sheet with id=AA7, first strand: chain 'J' and resid 3 through 6 Processing sheet with id=AA8, first strand: chain 'J' and resid 11 through 12 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 11 through 12 current: chain 'J' and resid 45 through 51 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 57 through 59 current: chain 'J' and resid 100H through 103 Processing sheet with id=AA9, first strand: chain 'K' and resid 12 through 13 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 12 through 13 current: chain 'K' and resid 45 through 48 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 45 through 48 current: chain 'K' and resid 96 through 98 No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'K' and resid 19 through 24 Processing sheet with id=AB2, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.445A pdb=" N VAL D 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N VAL C 38 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N THR D 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N TYR C 40 " --> pdb=" O CYS D 604 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N CYS D 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.589A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 75 through 76 Processing sheet with id=AB5, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AB6, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AB7, first strand: chain 'C' and resid 201 through 203 removed outlier: 6.539A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 259 through 261 current: chain 'C' and resid 284 through 312 removed outlier: 6.839A pdb=" N ASN C 301 " --> pdb=" O ILE C 323 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ILE C 323 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 315 through 323A current: chain 'C' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 381 through 385 current: chain 'C' and resid 466 through 470 Processing sheet with id=AB9, first strand: chain 'M' and resid 3 through 6 Processing sheet with id=AC1, first strand: chain 'M' and resid 11 through 12 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 11 through 12 current: chain 'M' and resid 46 through 51 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 57 through 59 current: chain 'M' and resid 100H through 103 Processing sheet with id=AC2, first strand: chain 'N' and resid 12 through 13 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 12 through 13 current: chain 'N' and resid 45 through 48 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 45 through 48 current: chain 'N' and resid 96 through 98 No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'N' and resid 19 through 24 Processing sheet with id=AC4, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.401A pdb=" N VAL F 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N VAL E 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N THR F 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N TYR E 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 8.235A pdb=" N CYS F 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.522A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N THR E 244 " --> pdb=" O ILE E 84 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AC7, first strand: chain 'E' and resid 91 through 94 removed outlier: 3.522A pdb=" N GLU E 91 " --> pdb=" O CYS E 239 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 169 through 177 Processing sheet with id=AC9, first strand: chain 'E' and resid 201 through 203 removed outlier: 6.425A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 259 through 261 current: chain 'E' and resid 284 through 312 removed outlier: 3.750A pdb=" N ASN E 301 " --> pdb=" O ILE E 323A" (cutoff:3.500A) removed outlier: 5.994A pdb=" N LYS E 305 " --> pdb=" O THR E 320 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N THR E 320 " --> pdb=" O LYS E 305 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N ILE E 307 " --> pdb=" O TYR E 318 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N TYR E 318 " --> pdb=" O ILE E 307 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ILE E 309 " --> pdb=" O ALA E 316 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N ALA E 316 " --> pdb=" O ILE E 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 315 through 323A current: chain 'E' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 381 through 385 current: chain 'E' and resid 466 through 470 Processing sheet with id=AD2, first strand: chain 'O' and resid 3 through 6 Processing sheet with id=AD3, first strand: chain 'O' and resid 11 through 12 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 11 through 12 current: chain 'O' and resid 46 through 51 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 57 through 59 current: chain 'O' and resid 100H through 103 Processing sheet with id=AD4, first strand: chain 'P' and resid 12 through 13 WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 12 through 13 current: chain 'P' and resid 45 through 48 WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 45 through 48 current: chain 'P' and resid 96 through 98 No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'P' and resid 19 through 24 Processing sheet with id=AD6, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AD7, first strand: chain 'H' and resid 34 through 39 removed outlier: 6.754A pdb=" N MET H 34 " --> pdb=" O ARG H 50 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N ARG H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 57 through 59 current: chain 'H' and resid 100J through 103 Processing sheet with id=AD8, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AD9, first strand: chain 'L' and resid 11 through 12 removed outlier: 5.631A pdb=" N LEU L 11 " --> pdb=" O ASP L 105 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) 566 hydrogen bonds defined for protein. 1494 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: 4.06 Time building geometry restraints manager: 2.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.42: 9029 1.42 - 1.66: 12747 1.66 - 1.90: 175 1.90 - 2.14: 0 2.14 - 2.38: 1 Bond restraints: 21952 Sorted by residual: bond pdb=" C SER L 94 " pdb=" N PHE L 96 " ideal model delta sigma weight residual 1.333 2.382 -1.049 1.28e-02 6.10e+03 6.72e+03 bond pdb=" CB ASP K 27B" pdb=" CG ASP K 27B" ideal model delta sigma weight residual 1.516 1.351 0.165 2.50e-02 1.60e+03 4.34e+01 bond pdb=" NE ARG E 503 " pdb=" CZ ARG E 503 " ideal model delta sigma weight residual 1.326 1.398 -0.072 1.10e-02 8.26e+03 4.33e+01 bond pdb=" CB LEU L 33 " pdb=" CG LEU L 33 " ideal model delta sigma weight residual 1.530 1.656 -0.126 2.00e-02 2.50e+03 3.94e+01 bond pdb=" CB LEU K 107 " pdb=" CG LEU K 107 " ideal model delta sigma weight residual 1.530 1.652 -0.122 2.00e-02 2.50e+03 3.71e+01 ... (remaining 21947 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.01: 28759 4.01 - 8.02: 1014 8.02 - 12.02: 28 12.02 - 16.03: 3 16.03 - 20.04: 2 Bond angle restraints: 29806 Sorted by residual: angle pdb=" C SER L 94 " pdb=" N PHE L 96 " pdb=" CA PHE L 96 " ideal model delta sigma weight residual 122.05 102.01 20.04 1.48e+00 4.57e-01 1.83e+02 angle pdb=" O SER L 94 " pdb=" C SER L 94 " pdb=" N PHE L 96 " ideal model delta sigma weight residual 123.34 110.98 12.36 1.37e+00 5.33e-01 8.14e+01 angle pdb=" CA SER L 94 " pdb=" C SER L 94 " pdb=" N PHE L 96 " ideal model delta sigma weight residual 116.50 127.89 -11.39 1.44e+00 4.82e-01 6.26e+01 angle pdb=" C CYS C 239 " pdb=" N PRO C 240 " pdb=" CA PRO C 240 " ideal model delta sigma weight residual 119.56 126.77 -7.21 1.01e+00 9.80e-01 5.10e+01 angle pdb=" C GLU E 492 " pdb=" N PRO E 493 " pdb=" CA PRO E 493 " ideal model delta sigma weight residual 119.87 127.12 -7.25 1.04e+00 9.25e-01 4.86e+01 ... (remaining 29801 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 11657 17.78 - 35.57: 425 35.57 - 53.35: 144 53.35 - 71.13: 66 71.13 - 88.92: 15 Dihedral angle restraints: 12307 sinusoidal: 4875 harmonic: 7432 Sorted by residual: dihedral pdb=" CA THR E 77 " pdb=" C THR E 77 " pdb=" N ASP E 78 " pdb=" CA ASP E 78 " ideal model delta harmonic sigma weight residual -180.00 -151.57 -28.43 0 5.00e+00 4.00e-02 3.23e+01 dihedral pdb=" CA ASP C 78 " pdb=" C ASP C 78 " pdb=" N PRO C 79 " pdb=" CA PRO C 79 " ideal model delta harmonic sigma weight residual -180.00 -154.43 -25.57 0 5.00e+00 4.00e-02 2.61e+01 dihedral pdb=" CA ASN E 94 " pdb=" C ASN E 94 " pdb=" N MET E 95 " pdb=" CA MET E 95 " ideal model delta harmonic sigma weight residual 180.00 155.94 24.06 0 5.00e+00 4.00e-02 2.32e+01 ... (remaining 12304 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.264: 3347 0.264 - 0.528: 248 0.528 - 0.792: 3 0.792 - 1.056: 2 1.056 - 1.320: 1 Chirality restraints: 3601 Sorted by residual: chirality pdb=" C1 FUC b 2 " pdb=" O6 NAG b 1 " pdb=" C2 FUC b 2 " pdb=" O5 FUC b 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.08 -1.32 2.00e-02 2.50e+03 4.36e+03 chirality pdb=" C1 MAN S 6 " pdb=" O6 MAN S 4 " pdb=" C2 MAN S 6 " pdb=" O5 MAN S 6 " both_signs ideal model delta sigma weight residual False 2.40 1.73 0.67 2.00e-02 2.50e+03 1.13e+03 chirality pdb=" C1 MAN S 5 " pdb=" O3 MAN S 4 " pdb=" C2 MAN S 5 " pdb=" O5 MAN S 5 " both_signs ideal model delta sigma weight residual False 2.40 1.91 0.49 2.00e-02 2.50e+03 5.91e+02 ... (remaining 3598 not shown) Planarity restraints: 3736 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG g 1 " 0.327 2.00e-02 2.50e+03 2.78e-01 9.67e+02 pdb=" C7 NAG g 1 " -0.081 2.00e-02 2.50e+03 pdb=" C8 NAG g 1 " 0.174 2.00e-02 2.50e+03 pdb=" N2 NAG g 1 " -0.488 2.00e-02 2.50e+03 pdb=" O7 NAG g 1 " 0.069 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG R 2 " -0.326 2.00e-02 2.50e+03 2.77e-01 9.61e+02 pdb=" C7 NAG R 2 " 0.081 2.00e-02 2.50e+03 pdb=" C8 NAG R 2 " -0.175 2.00e-02 2.50e+03 pdb=" N2 NAG R 2 " 0.486 2.00e-02 2.50e+03 pdb=" O7 NAG R 2 " -0.066 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 701 " 0.312 2.00e-02 2.50e+03 2.72e-01 9.27e+02 pdb=" C7 NAG D 701 " -0.069 2.00e-02 2.50e+03 pdb=" C8 NAG D 701 " 0.125 2.00e-02 2.50e+03 pdb=" N2 NAG D 701 " -0.489 2.00e-02 2.50e+03 pdb=" O7 NAG D 701 " 0.120 2.00e-02 2.50e+03 ... (remaining 3733 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 6170 2.83 - 3.35: 18758 3.35 - 3.87: 36185 3.87 - 4.38: 43141 4.38 - 4.90: 69274 Nonbonded interactions: 173528 Sorted by model distance: nonbonded pdb=" O5 NAG T 1 " pdb=" O6 NAG T 1 " model vdw 2.315 2.432 nonbonded pdb=" N ASP M 84 " pdb=" OD1 ASP M 84 " model vdw 2.372 3.120 nonbonded pdb=" N ASP J 84 " pdb=" OD1 ASP J 84 " model vdw 2.373 3.120 nonbonded pdb=" N ASP O 84 " pdb=" OD1 ASP O 84 " model vdw 2.375 3.120 nonbonded pdb=" O5 NAG R 2 " pdb=" O6 NAG R 2 " model vdw 2.383 2.432 ... (remaining 173523 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 33 through 57 or resid 68 through 612)) selection = chain 'C' selection = (chain 'E' and (resid 33 through 57 or resid 68 through 612)) } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = (chain 'G' and resid 1) selection = (chain 'I' and resid 1) selection = (chain 'T' and resid 1) selection = (chain 'U' and resid 1) selection = (chain 'V' and resid 1) selection = (chain 'W' and resid 1) selection = (chain 'X' and resid 1) selection = (chain 'Z' and resid 1) selection = (chain 'a' and resid 1) selection = (chain 'b' and resid 1) selection = (chain 'c' and resid 1) selection = (chain 'd' and resid 1) selection = (chain 'f' and resid 1) selection = (chain 'g' and resid 1) selection = (chain 'h' and resid 1) selection = (chain 'i' and resid 1) } ncs_group { reference = chain 'J' selection = chain 'M' selection = chain 'O' } ncs_group { reference = chain 'K' selection = chain 'N' selection = chain 'P' } ncs_group { reference = chain 'Q' selection = chain 'Y' selection = chain 'e' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 4.040 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: 0.030 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 19.880 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 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 : 0.022 1.049 22086 Z= 1.249 Angle : 1.766 20.039 30170 Z= 1.142 Chirality : 0.133 1.320 3601 Planarity : 0.016 0.278 3673 Dihedral : 12.007 88.917 7433 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 1.30 Ramachandran Plot: Outliers : 0.71 % Allowed : 3.59 % Favored : 95.70 % Rotamer: Outliers : 2.68 % Allowed : 1.74 % Favored : 95.58 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.95 % 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: 0.35 (0.16), residues: 2536 helix: -0.21 (0.25), residues: 375 sheet: 0.91 (0.18), residues: 800 loop : 0.04 (0.17), residues: 1361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG O 71 TYR 0.052 0.006 TYR N 96 PHE 0.036 0.006 PHE L 98 TRP 0.063 0.007 TRP A 96 HIS 0.009 0.002 HIS F 585 Details of bonding type rmsd/Z covalent geometry : bond 0.02174 / 1.24 (21952) covalent geometry : angle 1.73753 / 1.14 (29806) SS BOND : bond 0.01379 / 0.70 ( 38) SS BOND : angle 2.72983 / 1.92 ( 76) hydrogen bonds : bond 0.16917 / 11.20 ( 566) hydrogen bonds : angle 6.91855 / 5.03 ( 1494) link_ALPHA1-3 : bond 0.06218 / 3.60 ( 5) link_ALPHA1-3 : angle 3.64231 / 2.07 ( 15) link_ALPHA1-6 : bond 0.00632 / 0.30 ( 2) link_ALPHA1-6 : angle 3.57903 / 2.34 ( 6) link_BETA1-4 : bond 0.05908 / 3.48 ( 20) link_BETA1-4 : angle 4.31213 / 3.11 ( 60) link_BETA1-6 : bond 0.01861 / 1.19 ( 6) link_BETA1-6 : angle 5.79527 / 3.06 ( 18) link_NAG-ASN : bond 0.06557 / 3.99 ( 63) link_NAG-ASN : angle 2.81694 / 1.86 ( 189) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5072 Ramachandran restraints generated. 2536 Oldfield, 0 Emsley, 2536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5072 Ramachandran restraints generated. 2536 Oldfield, 0 Emsley, 2536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 318 time to evaluate : 0.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 ILE cc_start: 0.8925 (OUTLIER) cc_final: 0.8704 (mp) REVERT: A 215 ILE cc_start: 0.9239 (mt) cc_final: 0.9033 (pt) REVERT: J 28 THR cc_start: 0.8600 (m) cc_final: 0.8347 (p) REVERT: K 94 ARG cc_start: 0.6261 (OUTLIER) cc_final: 0.5632 (tpt170) REVERT: M 3 GLN cc_start: 0.8305 (mt0) cc_final: 0.7989 (mt0) REVERT: N 26 THR cc_start: 0.8860 (t) cc_final: 0.8256 (t) REVERT: N 94 ARG cc_start: 0.5883 (mpt180) cc_final: 0.3607 (mmt180) REVERT: E 69 TRP cc_start: 0.7257 (OUTLIER) cc_final: 0.6103 (m100) REVERT: E 95 MET cc_start: 0.9054 (ptm) cc_final: 0.8767 (ptm) REVERT: E 137 ASN cc_start: 0.8056 (OUTLIER) cc_final: 0.7782 (m-40) REVERT: F 635 ILE cc_start: 0.8977 (OUTLIER) cc_final: 0.8704 (pp) REVERT: O 6 GLU cc_start: 0.7865 (mp0) cc_final: 0.7509 (mp0) REVERT: P 94 ARG cc_start: 0.5913 (OUTLIER) cc_final: 0.4032 (tpp-160) REVERT: H 29 PHE cc_start: 0.5122 (m-10) cc_final: 0.4653 (m-10) REVERT: H 43 LYS cc_start: 0.8849 (mmtt) cc_final: 0.8543 (pttt) REVERT: H 78 LEU cc_start: 0.7352 (tp) cc_final: 0.6915 (tp) REVERT: H 82 MET cc_start: 0.7848 (mtm) cc_final: 0.7631 (mpp) REVERT: L 5 THR cc_start: 0.8802 (p) cc_final: 0.8504 (m) REVERT: L 33 LEU cc_start: 0.7479 (tp) cc_final: 0.6659 (tt) REVERT: L 37 GLN cc_start: 0.6040 (tt0) cc_final: 0.5660 (tt0) REVERT: L 46 LEU cc_start: 0.7230 (tp) cc_final: 0.6773 (tp) REVERT: L 47 LEU cc_start: 0.7905 (mt) cc_final: 0.7673 (mt) REVERT: L 70 ASP cc_start: 0.8341 (t0) cc_final: 0.8053 (t0) REVERT: L 71 PHE cc_start: 0.3022 (m-80) cc_final: 0.2562 (m-10) REVERT: L 96 PHE cc_start: 0.7241 (OUTLIER) cc_final: 0.6753 (m-80) outliers start: 60 outliers final: 12 residues processed: 366 average time/residue: 0.1742 time to fit residues: 93.7527 Evaluate side-chains 172 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 153 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain K residue 94 ARG Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 169 ARG Chi-restraints excluded: chain C residue 184 MET Chi-restraints excluded: chain C residue 188 SER Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 137 ASN Chi-restraints excluded: chain E residue 188 SER Chi-restraints excluded: chain E residue 423 ILE Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain P residue 94 ARG Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 96 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 216 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 1.9990 chunk 227 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 0.8980 chunk 247 optimal weight: 4.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.8980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 80 ASN A 82 GLN A 425 ASN J 3 GLN J 13 GLN J 52 ASN ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 ASN D 577 GLN D 616 ASN D 650 GLN D 653 GLN N 17 GLN L 90 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.083827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.065528 restraints weight = 65623.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.067713 restraints weight = 36252.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.069089 restraints weight = 24916.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.069935 restraints weight = 19562.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.070379 restraints weight = 16821.218| |-----------------------------------------------------------------------------| r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 22086 Z= 0.154 Angle : 0.707 13.508 30170 Z= 0.350 Chirality : 0.047 0.274 3601 Planarity : 0.004 0.038 3673 Dihedral : 6.363 68.965 2831 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.23 % Favored : 96.41 % Rotamer: Outliers : 1.74 % Allowed : 6.47 % Favored : 91.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.95 % 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: 0.51 (0.17), residues: 2538 helix: 1.85 (0.28), residues: 355 sheet: 0.84 (0.18), residues: 784 loop : -0.32 (0.17), residues: 1399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 66 TYR 0.014 0.001 TYR M 100F PHE 0.025 0.002 PHE H 27 TRP 0.030 0.002 TRP L 35 HIS 0.004 0.001 HIS A 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (21952) covalent geometry : angle 0.67170 / 0.34 (29806) SS BOND : bond 0.00252 / 0.15 ( 38) SS BOND : angle 1.04022 / 0.71 ( 76) hydrogen bonds : bond 0.05314 / 3.57 ( 566) hydrogen bonds : angle 5.08977 / 3.65 ( 1494) link_ALPHA1-3 : bond 0.01148 / 0.60 ( 5) link_ALPHA1-3 : angle 1.43627 / 0.78 ( 15) link_ALPHA1-6 : bond 0.01638 / 0.79 ( 2) link_ALPHA1-6 : angle 1.43474 / 1.20 ( 6) link_BETA1-4 : bond 0.00691 / 0.46 ( 20) link_BETA1-4 : angle 2.57096 / 1.90 ( 60) link_BETA1-6 : bond 0.01444 / 0.74 ( 6) link_BETA1-6 : angle 2.09559 / 1.39 ( 18) link_NAG-ASN : bond 0.00383 / 0.22 ( 63) link_NAG-ASN : angle 2.33789 / 1.57 ( 189) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 193 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.9008 (mtp) cc_final: 0.8737 (mtp) REVERT: J 28 THR cc_start: 0.8589 (m) cc_final: 0.8368 (p) REVERT: J 87 THR cc_start: 0.8464 (m) cc_final: 0.8257 (p) REVERT: K 27 ASP cc_start: 0.8571 (OUTLIER) cc_final: 0.8296 (t70) REVERT: K 94 ARG cc_start: 0.5544 (mpt180) cc_final: 0.4546 (mmt180) REVERT: C 475 MET cc_start: 0.7690 (tpp) cc_final: 0.7307 (mmm) REVERT: D 621 GLU cc_start: 0.7303 (mt-10) cc_final: 0.7076 (mp0) REVERT: D 632 ASP cc_start: 0.8407 (t70) cc_final: 0.8185 (t0) REVERT: M 11 LEU cc_start: 0.7451 (tp) cc_final: 0.7030 (mp) REVERT: N 94 ARG cc_start: 0.5380 (mpt180) cc_final: 0.3212 (mmt180) REVERT: E 69 TRP cc_start: 0.8159 (OUTLIER) cc_final: 0.7227 (m100) REVERT: P 94 ARG cc_start: 0.5099 (mpt180) cc_final: 0.3681 (tpp-160) REVERT: H 34 MET cc_start: 0.6608 (mtm) cc_final: 0.5373 (mtm) REVERT: H 38 ARG cc_start: 0.8274 (ptt180) cc_final: 0.7995 (ptm160) REVERT: H 67 PHE cc_start: 0.6131 (m-10) cc_final: 0.5774 (m-10) REVERT: H 75 LYS cc_start: 0.8807 (pttp) cc_final: 0.8598 (mmmt) REVERT: H 78 LEU cc_start: 0.7196 (tp) cc_final: 0.6386 (tp) REVERT: H 82 LEU cc_start: 0.7417 (pp) cc_final: 0.6219 (mp) REVERT: L 33 LEU cc_start: 0.8212 (tp) cc_final: 0.8011 (tt) REVERT: L 75 ILE cc_start: 0.8208 (mp) cc_final: 0.7464 (tp) REVERT: L 79 GLU cc_start: 0.8287 (mm-30) cc_final: 0.7961 (mm-30) outliers start: 39 outliers final: 17 residues processed: 224 average time/residue: 0.1713 time to fit residues: 57.8049 Evaluate side-chains 164 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 145 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain J residue 101 ASP Chi-restraints excluded: chain J residue 111 VAL Chi-restraints excluded: chain K residue 27 ASP Chi-restraints excluded: chain C residue 188 SER Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain N residue 106 VAL Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 188 SER Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 96 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 162 optimal weight: 0.6980 chunk 204 optimal weight: 5.9990 chunk 134 optimal weight: 9.9990 chunk 224 optimal weight: 1.9990 chunk 235 optimal weight: 30.0000 chunk 209 optimal weight: 9.9990 chunk 113 optimal weight: 5.9990 chunk 87 optimal weight: 0.9980 chunk 179 optimal weight: 6.9990 chunk 39 optimal weight: 5.9990 chunk 56 optimal weight: 8.9990 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 103 GLN A 195 ASN J 3 GLN ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 31 ASN ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 616 ASN ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.079509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.060690 restraints weight = 66421.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.062686 restraints weight = 36810.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.063996 restraints weight = 25872.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.064786 restraints weight = 20799.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.065227 restraints weight = 18164.610| |-----------------------------------------------------------------------------| r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 22086 Z= 0.253 Angle : 0.707 10.750 30170 Z= 0.352 Chirality : 0.048 0.305 3601 Planarity : 0.005 0.048 3673 Dihedral : 5.466 51.518 2802 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.26 % Favored : 95.47 % Rotamer: Outliers : 1.74 % Allowed : 7.68 % Favored : 90.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.26 (0.16), residues: 2538 helix: 1.88 (0.27), residues: 355 sheet: 0.70 (0.18), residues: 807 loop : -0.61 (0.16), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 350 TYR 0.013 0.002 TYR P 96 PHE 0.022 0.002 PHE L 96 TRP 0.022 0.002 TRP L 35 HIS 0.007 0.001 HIS C 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00590 / 0.25 (21952) covalent geometry : angle 0.68346 / 0.35 (29806) SS BOND : bond 0.00368 / 0.24 ( 38) SS BOND : angle 1.18090 / 0.88 ( 76) hydrogen bonds : bond 0.05026 / 3.36 ( 566) hydrogen bonds : angle 4.87319 / 3.58 ( 1494) link_ALPHA1-3 : bond 0.00919 / 0.47 ( 5) link_ALPHA1-3 : angle 1.49319 / 0.93 ( 15) link_ALPHA1-6 : bond 0.01300 / 0.63 ( 2) link_ALPHA1-6 : angle 1.82353 / 1.63 ( 6) link_BETA1-4 : bond 0.00406 / 0.25 ( 20) link_BETA1-4 : angle 1.85234 / 1.28 ( 60) link_BETA1-6 : bond 0.00714 / 0.38 ( 6) link_BETA1-6 : angle 2.21170 / 1.34 ( 18) link_NAG-ASN : bond 0.00500 / 0.32 ( 63) link_NAG-ASN : angle 1.91912 / 1.32 ( 189) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 161 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.9031 (mtp) cc_final: 0.8743 (mtp) REVERT: J 75 LYS cc_start: 0.9063 (mmmt) cc_final: 0.8839 (mmmm) REVERT: J 87 THR cc_start: 0.8565 (m) cc_final: 0.8343 (p) REVERT: K 94 ARG cc_start: 0.5696 (mpt180) cc_final: 0.5202 (tpt170) REVERT: D 632 ASP cc_start: 0.8587 (t70) cc_final: 0.8256 (t0) REVERT: M 11 LEU cc_start: 0.7723 (tp) cc_final: 0.7165 (mp) REVERT: N 94 ARG cc_start: 0.5656 (mpt180) cc_final: 0.3466 (mmt180) REVERT: E 69 TRP cc_start: 0.8373 (OUTLIER) cc_final: 0.7198 (m100) REVERT: E 95 MET cc_start: 0.8906 (ptm) cc_final: 0.8606 (ptm) REVERT: E 129 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8767 (mt) REVERT: P 85 ASP cc_start: 0.8538 (m-30) cc_final: 0.8098 (m-30) REVERT: P 94 ARG cc_start: 0.5331 (mpt180) cc_final: 0.3658 (tpp-160) REVERT: P 107 LEU cc_start: 0.7133 (mp) cc_final: 0.6652 (mt) REVERT: H 19 ARG cc_start: 0.7101 (ttm170) cc_final: 0.6857 (ttm170) REVERT: H 34 MET cc_start: 0.5867 (mtm) cc_final: 0.5469 (mtm) REVERT: H 38 ARG cc_start: 0.8581 (ptt180) cc_final: 0.7933 (ptm160) REVERT: H 67 PHE cc_start: 0.6258 (m-10) cc_final: 0.5556 (m-10) REVERT: H 78 LEU cc_start: 0.7463 (tp) cc_final: 0.6894 (tp) REVERT: H 82 LEU cc_start: 0.7448 (pp) cc_final: 0.6299 (mp) REVERT: L 5 THR cc_start: 0.8816 (m) cc_final: 0.8390 (m) REVERT: L 90 GLN cc_start: 0.9238 (pt0) cc_final: 0.8856 (pp30) outliers start: 39 outliers final: 22 residues processed: 191 average time/residue: 0.1533 time to fit residues: 45.3222 Evaluate side-chains 161 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 137 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain J residue 101 ASP Chi-restraints excluded: chain J residue 111 VAL Chi-restraints excluded: chain K residue 52 THR Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 188 SER Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 68 THR Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 188 SER Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 430 ILE Chi-restraints excluded: chain F residue 526 SER Chi-restraints excluded: chain L residue 20 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 20 optimal weight: 3.9990 chunk 128 optimal weight: 1.9990 chunk 10 optimal weight: 8.9990 chunk 21 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 193 optimal weight: 6.9990 chunk 200 optimal weight: 4.9990 chunk 230 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 198 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 170 GLN A 195 ASN ** B 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 3 GLN ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 616 ASN ** P 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.079664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.060915 restraints weight = 66368.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.062920 restraints weight = 36604.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.064213 restraints weight = 25735.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 71)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.065021 restraints weight = 20641.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.065485 restraints weight = 17931.739| |-----------------------------------------------------------------------------| r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.3209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 22086 Z= 0.179 Angle : 0.612 10.423 30170 Z= 0.302 Chirality : 0.045 0.293 3601 Planarity : 0.004 0.059 3673 Dihedral : 5.023 48.448 2798 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.10 % Favored : 95.67 % Rotamer: Outliers : 1.56 % Allowed : 7.63 % Favored : 90.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.17 (0.17), residues: 2538 helix: 2.09 (0.28), residues: 355 sheet: 0.67 (0.18), residues: 786 loop : -0.76 (0.16), residues: 1397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 24 TYR 0.010 0.001 TYR M 100G PHE 0.015 0.002 PHE E 176 TRP 0.032 0.001 TRP L 35 HIS 0.005 0.001 HIS A 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.18 (21952) covalent geometry : angle 0.59003 / 0.30 (29806) SS BOND : bond 0.00262 / 0.17 ( 38) SS BOND : angle 1.07879 / 0.87 ( 76) hydrogen bonds : bond 0.04328 / 2.91 ( 566) hydrogen bonds : angle 4.56262 / 3.34 ( 1494) link_ALPHA1-3 : bond 0.00841 / 0.43 ( 5) link_ALPHA1-3 : angle 1.40821 / 0.87 ( 15) link_ALPHA1-6 : bond 0.01230 / 0.60 ( 2) link_ALPHA1-6 : angle 1.76745 / 1.47 ( 6) link_BETA1-4 : bond 0.00334 / 0.21 ( 20) link_BETA1-4 : angle 1.59061 / 1.10 ( 60) link_BETA1-6 : bond 0.00604 / 0.32 ( 6) link_BETA1-6 : angle 2.12631 / 1.24 ( 18) link_NAG-ASN : bond 0.00235 / 0.15 ( 63) link_NAG-ASN : angle 1.69770 / 1.19 ( 189) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 150 time to evaluate : 0.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 475 MET cc_start: 0.8860 (tpp) cc_final: 0.8546 (tpp) REVERT: J 75 LYS cc_start: 0.9033 (mmmt) cc_final: 0.8825 (mmmm) REVERT: J 87 THR cc_start: 0.8506 (m) cc_final: 0.8306 (p) REVERT: K 94 ARG cc_start: 0.5675 (mpt180) cc_final: 0.5140 (tpt170) REVERT: D 632 ASP cc_start: 0.8582 (t70) cc_final: 0.8316 (t0) REVERT: M 11 LEU cc_start: 0.7667 (tp) cc_final: 0.7130 (mp) REVERT: N 94 ARG cc_start: 0.5624 (mpt180) cc_final: 0.3511 (mmt180) REVERT: E 69 TRP cc_start: 0.8337 (OUTLIER) cc_final: 0.6906 (m100) REVERT: E 95 MET cc_start: 0.8838 (ptm) cc_final: 0.8523 (ptm) REVERT: E 129 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8703 (mt) REVERT: P 94 ARG cc_start: 0.5274 (mpt180) cc_final: 0.3613 (tpp-160) REVERT: P 107 LEU cc_start: 0.7106 (mp) cc_final: 0.6635 (mt) REVERT: H 19 ARG cc_start: 0.7144 (ttm170) cc_final: 0.6812 (ttm170) REVERT: H 38 ARG cc_start: 0.8530 (ptt180) cc_final: 0.7980 (ptm160) REVERT: H 64 LYS cc_start: 0.8450 (mmtt) cc_final: 0.8029 (mmmt) REVERT: H 67 PHE cc_start: 0.6094 (m-10) cc_final: 0.5518 (m-10) REVERT: H 82 LEU cc_start: 0.7346 (pp) cc_final: 0.6208 (mp) REVERT: L 90 GLN cc_start: 0.9236 (pt0) cc_final: 0.8743 (pp30) outliers start: 35 outliers final: 19 residues processed: 179 average time/residue: 0.1479 time to fit residues: 41.4883 Evaluate side-chains 155 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 134 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain J residue 111 VAL Chi-restraints excluded: chain K residue 27 ASP Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain D residue 543 LEU Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 188 SER Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 430 ILE Chi-restraints excluded: chain F residue 526 SER Chi-restraints excluded: chain O residue 97 MET Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 75 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 181 optimal weight: 9.9990 chunk 76 optimal weight: 4.9990 chunk 146 optimal weight: 8.9990 chunk 201 optimal weight: 4.9990 chunk 241 optimal weight: 4.9990 chunk 20 optimal weight: 0.0770 chunk 167 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 1 optimal weight: 7.9990 chunk 47 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 overall best weight: 2.2144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 195 ASN ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 ASN O 39 GLN P 38 GLN ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.075854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.056422 restraints weight = 68323.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.058324 restraints weight = 38032.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.059534 restraints weight = 26917.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.060245 restraints weight = 21748.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.060772 restraints weight = 19144.144| |-----------------------------------------------------------------------------| r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.3444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 22086 Z= 0.183 Angle : 0.603 10.254 30170 Z= 0.296 Chirality : 0.045 0.289 3601 Planarity : 0.004 0.064 3673 Dihedral : 4.659 37.216 2793 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.49 % Favored : 95.31 % Rotamer: Outliers : 1.38 % Allowed : 8.43 % Favored : 90.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.07 (0.17), residues: 2538 helix: 2.01 (0.28), residues: 365 sheet: 0.62 (0.18), residues: 779 loop : -0.84 (0.16), residues: 1394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 617 TYR 0.010 0.001 TYR H 100L PHE 0.014 0.002 PHE E 53 TRP 0.051 0.001 TRP L 35 HIS 0.005 0.001 HIS C 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.18 (21952) covalent geometry : angle 0.58345 / 0.29 (29806) SS BOND : bond 0.00273 / 0.17 ( 38) SS BOND : angle 0.98973 / 0.79 ( 76) hydrogen bonds : bond 0.04221 / 2.84 ( 566) hydrogen bonds : angle 4.49158 / 3.29 ( 1494) link_ALPHA1-3 : bond 0.00838 / 0.43 ( 5) link_ALPHA1-3 : angle 1.42949 / 0.90 ( 15) link_ALPHA1-6 : bond 0.01256 / 0.61 ( 2) link_ALPHA1-6 : angle 1.81819 / 1.51 ( 6) link_BETA1-4 : bond 0.00324 / 0.21 ( 20) link_BETA1-4 : angle 1.52562 / 1.04 ( 60) link_BETA1-6 : bond 0.00535 / 0.29 ( 6) link_BETA1-6 : angle 2.12997 / 1.22 ( 18) link_NAG-ASN : bond 0.00295 / 0.18 ( 63) link_NAG-ASN : angle 1.60269 / 1.12 ( 189) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 151 time to evaluate : 0.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 475 MET cc_start: 0.8906 (tpp) cc_final: 0.8628 (tpp) REVERT: J 3 GLN cc_start: 0.8042 (tp-100) cc_final: 0.7837 (tp40) REVERT: J 87 THR cc_start: 0.8540 (m) cc_final: 0.8261 (p) REVERT: K 94 ARG cc_start: 0.5609 (mpt180) cc_final: 0.5255 (tpt170) REVERT: D 632 ASP cc_start: 0.8643 (t70) cc_final: 0.8325 (t0) REVERT: M 11 LEU cc_start: 0.7817 (tp) cc_final: 0.7267 (mp) REVERT: N 94 ARG cc_start: 0.5723 (mpt180) cc_final: 0.3435 (mmt180) REVERT: E 69 TRP cc_start: 0.8437 (OUTLIER) cc_final: 0.7100 (m100) REVERT: E 95 MET cc_start: 0.8841 (ptm) cc_final: 0.8538 (ptm) REVERT: E 129 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8603 (mt) REVERT: O 3 GLN cc_start: 0.7743 (OUTLIER) cc_final: 0.7390 (mm110) REVERT: P 45 LYS cc_start: 0.8347 (ttmm) cc_final: 0.8133 (tttp) REVERT: P 94 ARG cc_start: 0.5262 (mpt180) cc_final: 0.3569 (tpp-160) REVERT: P 107 LEU cc_start: 0.7059 (mp) cc_final: 0.6632 (mt) REVERT: H 38 ARG cc_start: 0.8537 (ptt180) cc_final: 0.7824 (ptm160) REVERT: H 43 LYS cc_start: 0.6208 (pptt) cc_final: 0.5637 (pptt) REVERT: H 67 PHE cc_start: 0.6136 (m-10) cc_final: 0.5579 (m-10) REVERT: H 78 LEU cc_start: 0.7593 (tp) cc_final: 0.7385 (tp) REVERT: H 82 LEU cc_start: 0.7303 (pp) cc_final: 0.6205 (mp) REVERT: L 77 ARG cc_start: 0.8439 (mtp-110) cc_final: 0.8094 (ptm160) REVERT: L 90 GLN cc_start: 0.9160 (pt0) cc_final: 0.8716 (pp30) outliers start: 31 outliers final: 17 residues processed: 176 average time/residue: 0.1497 time to fit residues: 40.7974 Evaluate side-chains 162 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 142 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain K residue 27 ASP Chi-restraints excluded: chain K residue 52 THR Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain D residue 543 LEU Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 188 SER Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 430 ILE Chi-restraints excluded: chain F residue 526 SER Chi-restraints excluded: chain O residue 3 GLN Chi-restraints excluded: chain O residue 97 MET Chi-restraints excluded: chain L residue 75 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 144 optimal weight: 0.0870 chunk 74 optimal weight: 10.0000 chunk 93 optimal weight: 2.9990 chunk 252 optimal weight: 10.0000 chunk 48 optimal weight: 1.9990 chunk 121 optimal weight: 0.0370 chunk 187 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 chunk 152 optimal weight: 7.9990 chunk 68 optimal weight: 6.9990 chunk 8 optimal weight: 1.9990 overall best weight: 1.4242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 195 ASN B 653 GLN ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.077154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.058124 restraints weight = 67496.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.060042 restraints weight = 38069.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.061249 restraints weight = 26976.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.061913 restraints weight = 21824.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 65)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.062458 restraints weight = 19260.842| |-----------------------------------------------------------------------------| r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.3625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 22086 Z= 0.131 Angle : 0.555 10.062 30170 Z= 0.272 Chirality : 0.044 0.283 3601 Planarity : 0.003 0.061 3673 Dihedral : 4.386 36.213 2793 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.02 % Favored : 95.78 % Rotamer: Outliers : 1.12 % Allowed : 8.97 % Favored : 89.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.95 % 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: 0.14 (0.17), residues: 2538 helix: 2.18 (0.28), residues: 365 sheet: 0.58 (0.18), residues: 794 loop : -0.78 (0.16), residues: 1379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG P 103 TYR 0.011 0.001 TYR J 100G PHE 0.013 0.001 PHE C 53 TRP 0.049 0.001 TRP L 35 HIS 0.004 0.001 HIS A 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 (21952) covalent geometry : angle 0.53594 / 0.27 (29806) SS BOND : bond 0.00227 / 0.14 ( 38) SS BOND : angle 0.87200 / 0.70 ( 76) hydrogen bonds : bond 0.03806 / 2.57 ( 566) hydrogen bonds : angle 4.31398 / 3.17 ( 1494) link_ALPHA1-3 : bond 0.00814 / 0.42 ( 5) link_ALPHA1-3 : angle 1.42628 / 0.90 ( 15) link_ALPHA1-6 : bond 0.01186 / 0.58 ( 2) link_ALPHA1-6 : angle 1.77224 / 1.45 ( 6) link_BETA1-4 : bond 0.00319 / 0.20 ( 20) link_BETA1-4 : angle 1.39690 / 0.94 ( 60) link_BETA1-6 : bond 0.00409 / 0.23 ( 6) link_BETA1-6 : angle 2.11271 / 1.20 ( 18) link_NAG-ASN : bond 0.00200 / 0.12 ( 63) link_NAG-ASN : angle 1.49180 / 1.05 ( 189) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 156 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 475 MET cc_start: 0.8847 (tpp) cc_final: 0.8612 (tpp) REVERT: J 87 THR cc_start: 0.8483 (m) cc_final: 0.8161 (p) REVERT: K 94 ARG cc_start: 0.5587 (mpt180) cc_final: 0.5278 (tpt170) REVERT: D 632 ASP cc_start: 0.8619 (t70) cc_final: 0.8297 (t0) REVERT: M 11 LEU cc_start: 0.7776 (tp) cc_final: 0.7208 (mp) REVERT: N 94 ARG cc_start: 0.5715 (mpt180) cc_final: 0.3445 (mmt180) REVERT: E 95 MET cc_start: 0.8800 (ptm) cc_final: 0.8492 (ptm) REVERT: O 3 GLN cc_start: 0.7669 (OUTLIER) cc_final: 0.7321 (mm110) REVERT: O 6 GLU cc_start: 0.7968 (mp0) cc_final: 0.7715 (mp0) REVERT: P 47 MET cc_start: 0.6629 (mmt) cc_final: 0.6383 (mmt) REVERT: P 94 ARG cc_start: 0.5231 (mpt180) cc_final: 0.3552 (tpp-160) REVERT: P 107 LEU cc_start: 0.6912 (mp) cc_final: 0.6448 (mt) REVERT: H 38 ARG cc_start: 0.8521 (ptt180) cc_final: 0.7829 (ptm160) REVERT: H 43 LYS cc_start: 0.6333 (pptt) cc_final: 0.5824 (pptt) REVERT: H 67 PHE cc_start: 0.6170 (m-10) cc_final: 0.5705 (m-10) REVERT: H 78 LEU cc_start: 0.7682 (tp) cc_final: 0.7450 (tp) REVERT: H 82 LEU cc_start: 0.7254 (pp) cc_final: 0.6146 (mp) REVERT: L 90 GLN cc_start: 0.9028 (pt0) cc_final: 0.8692 (pp30) outliers start: 25 outliers final: 16 residues processed: 177 average time/residue: 0.1438 time to fit residues: 39.4001 Evaluate side-chains 154 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 137 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain J residue 111 VAL Chi-restraints excluded: chain K residue 52 THR Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain F residue 526 SER Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain O residue 3 GLN Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 75 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 75 optimal weight: 1.9990 chunk 37 optimal weight: 7.9990 chunk 17 optimal weight: 5.9990 chunk 183 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 89 optimal weight: 7.9990 chunk 1 optimal weight: 0.1980 chunk 62 optimal weight: 6.9990 chunk 35 optimal weight: 0.9980 chunk 137 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** J 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** 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 = 0.3528 r_free = 0.3528 target = 0.076966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.057977 restraints weight = 67056.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.059849 restraints weight = 37979.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.061048 restraints weight = 27077.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.061805 restraints weight = 21941.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 63)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.062271 restraints weight = 19224.793| |-----------------------------------------------------------------------------| r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.3776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 22086 Z= 0.145 Angle : 0.566 10.070 30170 Z= 0.277 Chirality : 0.044 0.281 3601 Planarity : 0.004 0.059 3673 Dihedral : 4.285 29.241 2790 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.49 % Favored : 95.31 % Rotamer: Outliers : 1.25 % Allowed : 9.24 % Favored : 89.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.95 % 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: 0.10 (0.17), residues: 2538 helix: 2.22 (0.28), residues: 365 sheet: 0.54 (0.18), residues: 794 loop : -0.82 (0.16), residues: 1379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 103 TYR 0.012 0.001 TYR J 100G PHE 0.013 0.001 PHE C 53 TRP 0.059 0.001 TRP L 35 HIS 0.004 0.001 HIS C 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 (21952) covalent geometry : angle 0.54798 / 0.27 (29806) SS BOND : bond 0.00238 / 0.14 ( 38) SS BOND : angle 0.86471 / 0.69 ( 76) hydrogen bonds : bond 0.03815 / 2.57 ( 566) hydrogen bonds : angle 4.31547 / 3.17 ( 1494) link_ALPHA1-3 : bond 0.00784 / 0.40 ( 5) link_ALPHA1-3 : angle 1.42045 / 0.90 ( 15) link_ALPHA1-6 : bond 0.01154 / 0.57 ( 2) link_ALPHA1-6 : angle 1.77304 / 1.46 ( 6) link_BETA1-4 : bond 0.00311 / 0.20 ( 20) link_BETA1-4 : angle 1.41289 / 0.95 ( 60) link_BETA1-6 : bond 0.00291 / 0.17 ( 6) link_BETA1-6 : angle 2.01084 / 1.15 ( 18) link_NAG-ASN : bond 0.00199 / 0.12 ( 63) link_NAG-ASN : angle 1.46318 / 1.03 ( 189) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 151 time to evaluate : 0.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 370 GLU cc_start: 0.7911 (mp0) cc_final: 0.7673 (mp0) REVERT: A 475 MET cc_start: 0.8888 (tpp) cc_final: 0.8659 (tpp) REVERT: J 87 THR cc_start: 0.8436 (m) cc_final: 0.8108 (p) REVERT: K 94 ARG cc_start: 0.5657 (mpt180) cc_final: 0.5303 (tpt170) REVERT: D 632 ASP cc_start: 0.8607 (t70) cc_final: 0.8286 (t0) REVERT: N 94 ARG cc_start: 0.5740 (mpt180) cc_final: 0.3427 (mmt180) REVERT: E 69 TRP cc_start: 0.8384 (OUTLIER) cc_final: 0.6562 (m100) REVERT: E 95 MET cc_start: 0.8816 (ptm) cc_final: 0.8508 (ptm) REVERT: F 635 ILE cc_start: 0.8888 (OUTLIER) cc_final: 0.8501 (pp) REVERT: P 94 ARG cc_start: 0.5262 (mpt180) cc_final: 0.3556 (tpp-160) REVERT: P 107 LEU cc_start: 0.6954 (mp) cc_final: 0.6457 (mt) REVERT: H 34 MET cc_start: 0.5046 (mtm) cc_final: 0.4821 (mtm) REVERT: H 38 ARG cc_start: 0.8533 (ptt180) cc_final: 0.7840 (ptm160) REVERT: H 43 LYS cc_start: 0.6331 (pptt) cc_final: 0.5791 (pptt) REVERT: H 67 PHE cc_start: 0.6028 (m-10) cc_final: 0.5566 (m-10) REVERT: H 78 LEU cc_start: 0.7462 (tp) cc_final: 0.7116 (tp) REVERT: H 82 LEU cc_start: 0.7223 (pp) cc_final: 0.6091 (mp) REVERT: L 90 GLN cc_start: 0.8995 (pt0) cc_final: 0.8685 (pp30) outliers start: 28 outliers final: 19 residues processed: 174 average time/residue: 0.1512 time to fit residues: 40.8585 Evaluate side-chains 159 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 138 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain K residue 52 THR Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 95 THR Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 97 MET Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 72 HIS Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain F residue 526 SER Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain O residue 60 VAL Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 75 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 34 optimal weight: 7.9990 chunk 161 optimal weight: 0.5980 chunk 47 optimal weight: 2.9990 chunk 156 optimal weight: 0.6980 chunk 72 optimal weight: 6.9990 chunk 251 optimal weight: 10.0000 chunk 100 optimal weight: 5.9990 chunk 226 optimal weight: 0.0010 chunk 123 optimal weight: 0.6980 chunk 137 optimal weight: 2.9990 chunk 73 optimal weight: 7.9990 overall best weight: 0.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 39 HIS ** N 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 399 ASN ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 89 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.077707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.058762 restraints weight = 67250.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.060679 restraints weight = 38121.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.061892 restraints weight = 26975.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 62)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.062652 restraints weight = 21817.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.063068 restraints weight = 19079.797| |-----------------------------------------------------------------------------| r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.3901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 22086 Z= 0.110 Angle : 0.546 9.961 30170 Z= 0.268 Chirality : 0.043 0.275 3601 Planarity : 0.003 0.056 3673 Dihedral : 4.156 28.441 2790 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.10 % Favored : 95.74 % Rotamer: Outliers : 1.12 % Allowed : 9.50 % Favored : 89.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.95 % 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: 0.17 (0.17), residues: 2538 helix: 2.22 (0.28), residues: 371 sheet: 0.59 (0.18), residues: 794 loop : -0.78 (0.17), residues: 1373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 617 TYR 0.010 0.001 TYR J 100G PHE 0.013 0.001 PHE C 53 TRP 0.069 0.001 TRP L 35 HIS 0.004 0.001 HIS A 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 (21952) covalent geometry : angle 0.52931 / 0.26 (29806) SS BOND : bond 0.00198 / 0.12 ( 38) SS BOND : angle 0.95593 / 0.73 ( 76) hydrogen bonds : bond 0.03518 / 2.38 ( 566) hydrogen bonds : angle 4.23533 / 3.12 ( 1494) link_ALPHA1-3 : bond 0.00765 / 0.39 ( 5) link_ALPHA1-3 : angle 1.42338 / 0.90 ( 15) link_ALPHA1-6 : bond 0.01162 / 0.57 ( 2) link_ALPHA1-6 : angle 1.74128 / 1.42 ( 6) link_BETA1-4 : bond 0.00327 / 0.21 ( 20) link_BETA1-4 : angle 1.33837 / 0.90 ( 60) link_BETA1-6 : bond 0.00291 / 0.18 ( 6) link_BETA1-6 : angle 1.88230 / 1.08 ( 18) link_NAG-ASN : bond 0.00192 / 0.12 ( 63) link_NAG-ASN : angle 1.38468 / 0.97 ( 189) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 149 time to evaluate : 0.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 87 THR cc_start: 0.8369 (m) cc_final: 0.8027 (p) REVERT: K 94 ARG cc_start: 0.5633 (mpt180) cc_final: 0.5210 (tpt170) REVERT: D 632 ASP cc_start: 0.8596 (t70) cc_final: 0.8350 (t0) REVERT: N 94 ARG cc_start: 0.5721 (mpt180) cc_final: 0.3531 (mmt180) REVERT: E 95 MET cc_start: 0.8747 (ptm) cc_final: 0.8429 (ptm) REVERT: F 635 ILE cc_start: 0.8879 (OUTLIER) cc_final: 0.8496 (pp) REVERT: P 94 ARG cc_start: 0.5233 (mpt180) cc_final: 0.3568 (tpp-160) REVERT: P 107 LEU cc_start: 0.6891 (mp) cc_final: 0.6604 (mt) REVERT: H 38 ARG cc_start: 0.8550 (ptt180) cc_final: 0.7866 (ptm160) REVERT: H 43 LYS cc_start: 0.6434 (pptt) cc_final: 0.5866 (pptt) REVERT: H 67 PHE cc_start: 0.5975 (m-10) cc_final: 0.5423 (m-10) REVERT: H 78 LEU cc_start: 0.7609 (tp) cc_final: 0.7377 (tp) REVERT: H 82 LEU cc_start: 0.7276 (pp) cc_final: 0.6162 (mp) REVERT: L 82 ASP cc_start: 0.6449 (p0) cc_final: 0.6219 (p0) REVERT: L 90 GLN cc_start: 0.8996 (pt0) cc_final: 0.8698 (pp30) outliers start: 25 outliers final: 18 residues processed: 171 average time/residue: 0.1565 time to fit residues: 41.7051 Evaluate side-chains 159 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 140 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain K residue 52 THR Chi-restraints excluded: chain K residue 95 THR Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain D residue 638 TYR Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 97 MET Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain E residue 72 HIS Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain F residue 526 SER Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain O residue 60 VAL Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 75 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 169 optimal weight: 7.9990 chunk 15 optimal weight: 4.9990 chunk 166 optimal weight: 6.9990 chunk 24 optimal weight: 4.9990 chunk 146 optimal weight: 5.9990 chunk 39 optimal weight: 0.9990 chunk 180 optimal weight: 0.9980 chunk 210 optimal weight: 10.0000 chunk 77 optimal weight: 0.6980 chunk 2 optimal weight: 9.9990 chunk 147 optimal weight: 2.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 570 HIS J 3 GLN J 39 GLN ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 38 GLN ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.077551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.058910 restraints weight = 66571.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.060829 restraints weight = 37576.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.062073 restraints weight = 26629.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.062851 restraints weight = 21404.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.063335 restraints weight = 18678.364| |-----------------------------------------------------------------------------| r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.4016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 22086 Z= 0.175 Angle : 0.597 10.127 30170 Z= 0.291 Chirality : 0.044 0.279 3601 Planarity : 0.004 0.055 3673 Dihedral : 4.298 29.145 2790 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.12 % Favored : 94.76 % Rotamer: Outliers : 1.16 % Allowed : 9.59 % Favored : 89.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.95 % 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: 0.07 (0.17), residues: 2538 helix: 2.22 (0.28), residues: 365 sheet: 0.50 (0.19), residues: 796 loop : -0.84 (0.17), residues: 1377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 617 TYR 0.026 0.001 TYR N 91 PHE 0.013 0.001 PHE E 53 TRP 0.049 0.001 TRP L 35 HIS 0.005 0.001 HIS C 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.18 (21952) covalent geometry : angle 0.57988 / 0.29 (29806) SS BOND : bond 0.00262 / 0.16 ( 38) SS BOND : angle 1.08367 / 0.85 ( 76) hydrogen bonds : bond 0.04034 / 2.69 ( 566) hydrogen bonds : angle 4.39257 / 3.23 ( 1494) link_ALPHA1-3 : bond 0.00751 / 0.38 ( 5) link_ALPHA1-3 : angle 1.44309 / 0.93 ( 15) link_ALPHA1-6 : bond 0.01136 / 0.56 ( 2) link_ALPHA1-6 : angle 1.69054 / 1.41 ( 6) link_BETA1-4 : bond 0.00309 / 0.19 ( 20) link_BETA1-4 : angle 1.45691 / 0.97 ( 60) link_BETA1-6 : bond 0.00313 / 0.18 ( 6) link_BETA1-6 : angle 1.88731 / 1.09 ( 18) link_NAG-ASN : bond 0.00235 / 0.15 ( 63) link_NAG-ASN : angle 1.45757 / 1.02 ( 189) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 138 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 87 THR cc_start: 0.8325 (m) cc_final: 0.7945 (p) REVERT: K 94 ARG cc_start: 0.5727 (mpt180) cc_final: 0.5322 (tpt170) REVERT: C 475 MET cc_start: 0.8117 (mmt) cc_final: 0.7720 (mmm) REVERT: D 632 ASP cc_start: 0.8589 (t70) cc_final: 0.8268 (t0) REVERT: N 94 ARG cc_start: 0.5995 (mpt180) cc_final: 0.3627 (mmt180) REVERT: E 95 MET cc_start: 0.8868 (ptm) cc_final: 0.8565 (ptm) REVERT: F 635 ILE cc_start: 0.8917 (OUTLIER) cc_final: 0.8512 (pp) REVERT: P 94 ARG cc_start: 0.5461 (mpt180) cc_final: 0.3531 (tpp-160) REVERT: P 107 LEU cc_start: 0.6453 (mp) cc_final: 0.6067 (mt) REVERT: H 38 ARG cc_start: 0.8444 (ptt180) cc_final: 0.7746 (ptm160) REVERT: H 43 LYS cc_start: 0.6397 (pptt) cc_final: 0.5774 (pptt) REVERT: H 67 PHE cc_start: 0.5766 (m-10) cc_final: 0.5312 (m-10) REVERT: H 78 LEU cc_start: 0.7491 (tp) cc_final: 0.7271 (tp) REVERT: H 82 LEU cc_start: 0.7096 (pp) cc_final: 0.5980 (mp) REVERT: L 90 GLN cc_start: 0.8937 (pt0) cc_final: 0.8439 (pm20) outliers start: 26 outliers final: 19 residues processed: 161 average time/residue: 0.1541 time to fit residues: 38.6924 Evaluate side-chains 154 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 134 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain K residue 27 ASP Chi-restraints excluded: chain K residue 52 THR Chi-restraints excluded: chain K residue 95 THR Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain D residue 638 TYR Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain N residue 81 ASP Chi-restraints excluded: chain E residue 72 HIS Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain F residue 526 SER Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain O residue 60 VAL Chi-restraints excluded: chain L residue 75 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 171 optimal weight: 0.8980 chunk 214 optimal weight: 0.7980 chunk 193 optimal weight: 7.9990 chunk 118 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 100 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 3 optimal weight: 9.9990 chunk 216 optimal weight: 0.8980 chunk 95 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 GLN ** N 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.078407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.059839 restraints weight = 66604.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.061818 restraints weight = 37446.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.062952 restraints weight = 26332.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.063740 restraints weight = 21409.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.064202 restraints weight = 18696.153| |-----------------------------------------------------------------------------| r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.4100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 22086 Z= 0.125 Angle : 0.559 9.984 30170 Z= 0.273 Chirality : 0.043 0.276 3601 Planarity : 0.003 0.054 3673 Dihedral : 4.156 28.491 2790 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.45 % Favored : 95.43 % Rotamer: Outliers : 0.89 % Allowed : 10.13 % Favored : 88.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.95 % 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: 0.13 (0.17), residues: 2538 helix: 2.31 (0.28), residues: 365 sheet: 0.56 (0.18), residues: 823 loop : -0.86 (0.17), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 617 TYR 0.018 0.001 TYR N 91 PHE 0.013 0.001 PHE C 53 TRP 0.047 0.001 TRP L 35 HIS 0.003 0.001 HIS A 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.12 (21952) covalent geometry : angle 0.54364 / 0.27 (29806) SS BOND : bond 0.00212 / 0.13 ( 38) SS BOND : angle 0.90624 / 0.70 ( 76) hydrogen bonds : bond 0.03588 / 2.41 ( 566) hydrogen bonds : angle 4.26223 / 3.15 ( 1494) link_ALPHA1-3 : bond 0.00738 / 0.38 ( 5) link_ALPHA1-3 : angle 1.44345 / 0.93 ( 15) link_ALPHA1-6 : bond 0.01074 / 0.53 ( 2) link_ALPHA1-6 : angle 1.70236 / 1.39 ( 6) link_BETA1-4 : bond 0.00290 / 0.18 ( 20) link_BETA1-4 : angle 1.32666 / 0.89 ( 60) link_BETA1-6 : bond 0.00290 / 0.17 ( 6) link_BETA1-6 : angle 1.74375 / 1.01 ( 18) link_NAG-ASN : bond 0.00185 / 0.12 ( 63) link_NAG-ASN : angle 1.36596 / 0.96 ( 189) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 140 time to evaluate : 0.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 87 THR cc_start: 0.8325 (m) cc_final: 0.7981 (p) REVERT: K 94 ARG cc_start: 0.5671 (mpt180) cc_final: 0.5293 (tpt170) REVERT: D 632 ASP cc_start: 0.8566 (t70) cc_final: 0.8312 (t0) REVERT: N 94 ARG cc_start: 0.5945 (mpt180) cc_final: 0.3664 (mmt180) REVERT: E 95 MET cc_start: 0.8779 (ptm) cc_final: 0.8470 (ptm) REVERT: F 635 ILE cc_start: 0.8898 (OUTLIER) cc_final: 0.8505 (pp) REVERT: P 94 ARG cc_start: 0.5269 (mpt180) cc_final: 0.3611 (tpp-160) REVERT: P 107 LEU cc_start: 0.6562 (mp) cc_final: 0.6193 (mt) REVERT: H 38 ARG cc_start: 0.8514 (ptt180) cc_final: 0.7824 (ptm160) REVERT: H 43 LYS cc_start: 0.6590 (pptt) cc_final: 0.6028 (pptt) REVERT: H 67 PHE cc_start: 0.5905 (m-10) cc_final: 0.5298 (m-10) REVERT: H 82 LEU cc_start: 0.7269 (pp) cc_final: 0.6203 (mp) REVERT: L 90 GLN cc_start: 0.9044 (pt0) cc_final: 0.8505 (pm20) outliers start: 20 outliers final: 18 residues processed: 160 average time/residue: 0.1421 time to fit residues: 35.5545 Evaluate side-chains 154 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 135 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain K residue 27 ASP Chi-restraints excluded: chain K residue 52 THR Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 95 THR Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain D residue 638 TYR Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain E residue 72 HIS Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain F residue 526 SER Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain O residue 60 VAL Chi-restraints excluded: chain L residue 75 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 47 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 216 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 chunk 126 optimal weight: 1.9990 chunk 121 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 80 optimal weight: 0.3980 chunk 199 optimal weight: 7.9990 chunk 33 optimal weight: 0.0170 chunk 144 optimal weight: 7.9990 overall best weight: 1.4824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 39 GLN N 38 GLN ** N 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.078310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.059693 restraints weight = 66880.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.061646 restraints weight = 37658.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.062879 restraints weight = 26539.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.063571 restraints weight = 21417.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.064116 restraints weight = 18836.016| |-----------------------------------------------------------------------------| r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.4169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 22086 Z= 0.136 Angle : 0.565 9.992 30170 Z= 0.275 Chirality : 0.044 0.272 3601 Planarity : 0.003 0.054 3673 Dihedral : 4.139 28.550 2790 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.45 % Favored : 95.39 % Rotamer: Outliers : 1.16 % Allowed : 10.17 % Favored : 88.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.95 % 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: 0.16 (0.17), residues: 2538 helix: 2.32 (0.28), residues: 365 sheet: 0.57 (0.18), residues: 839 loop : -0.84 (0.17), residues: 1334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 617 TYR 0.019 0.001 TYR N 91 PHE 0.013 0.001 PHE C 53 TRP 0.044 0.001 TRP L 35 HIS 0.004 0.001 HIS C 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (21952) covalent geometry : angle 0.54948 / 0.27 (29806) SS BOND : bond 0.00221 / 0.13 ( 38) SS BOND : angle 0.90950 / 0.71 ( 76) hydrogen bonds : bond 0.03648 / 2.44 ( 566) hydrogen bonds : angle 4.25452 / 3.14 ( 1494) link_ALPHA1-3 : bond 0.00728 / 0.37 ( 5) link_ALPHA1-3 : angle 1.44099 / 0.93 ( 15) link_ALPHA1-6 : bond 0.01108 / 0.55 ( 2) link_ALPHA1-6 : angle 1.70269 / 1.39 ( 6) link_BETA1-4 : bond 0.00306 / 0.19 ( 20) link_BETA1-4 : angle 1.35486 / 0.90 ( 60) link_BETA1-6 : bond 0.00323 / 0.19 ( 6) link_BETA1-6 : angle 1.70707 / 1.00 ( 18) link_NAG-ASN : bond 0.00194 / 0.12 ( 63) link_NAG-ASN : angle 1.36730 / 0.96 ( 189) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3225.21 seconds wall clock time: 56 minutes 53.04 seconds (3413.04 seconds total)