Starting phenix.real_space_refine on Sat Sep 12 23:24:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6olp_20118/09_2026/6olp_20118.cif Found real_map, /net/cci-nas-00/data/ceres_data/6olp_20118/09_2026/6olp_20118.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6olp_20118/09_2026/6olp_20118.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6olp_20118/09_2026/6olp_20118.map" model { file = "/net/cci-nas-00/data/ceres_data/6olp_20118/09_2026/6olp_20118.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6olp_20118/09_2026/6olp_20118.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6olp_20118/09_2026/6olp_20118.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6olp_20118/09_2026/6olp_20118.cif" } resolution = 4.2 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= 0.000 sd= 0.003 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 116 5.16 5 C 11840 2.51 5 N 3064 2.21 5 O 3848 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 18868 Number of models: 1 Model: "" Number of chains: 40 Chain: "A" Number of atoms: 3392 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 430, 3386 Classifications: {'peptide': 430} Link IDs: {'PTRANS': 22, 'TRANS': 407} Chain breaks: 5 Conformer: "B" Number of residues, atoms: 430, 3386 Classifications: {'peptide': 430} Link IDs: {'PTRANS': 22, 'TRANS': 407} Chain breaks: 5 bond proxies already assigned to first conformer: 3449 Chain: "B" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1152 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 1, 'TRANS': 141} Chain: "C" Number of atoms: 3454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3454 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 22, 'TRANS': 415} Chain breaks: 3 Chain: "D" Number of atoms: 1014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1014 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 1, 'TRANS': 127} Chain breaks: 1 Chain: "E" Number of atoms: 3298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3298 Classifications: {'peptide': 419} Link IDs: {'PTRANS': 22, 'TRANS': 396} Chain breaks: 6 Chain: "F" Number of atoms: 1063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1063 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 1, 'TRANS': 132} Chain breaks: 2 Chain: "G" Number of atoms: 1062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1062 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 6, 'TRANS': 127} Chain: "I" Number of atoms: 838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 838 Classifications: {'peptide': 109} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 102} Chain: "H" Number of atoms: 1073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1073 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 6, 'TRANS': 128} Chain: "L" Number of atoms: 854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 854 Classifications: {'peptide': 111} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 104} Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 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: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 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: 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: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 110 Unusual residues: {'BMA': 1, 'FUC': 1, 'GAL': 1, 'MAN': 2, 'NAG': 4} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "W" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 96 Unusual residues: {'BMA': 1, 'FUC': 1, 'GAL': 1, 'MAN': 2, 'NAG': 3} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "X" 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: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "c" 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: "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: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 110 Unusual residues: {'BMA': 1, 'FUC': 1, 'GAL': 1, 'MAN': 2, 'NAG': 4} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "f" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 121 Unusual residues: {'BMA': 1, 'FUC': 1, 'GAL': 2, 'MAN': 2, 'NAG': 4} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 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: 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: 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: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen chiralities: 13 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen chiralities: 15 Chain: "F" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ASER A 393 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER A 393 " occ=0.50 Time building chain proxies: 4.75, per 1000 atoms: 0.25 Number of scatterers: 18868 At special positions: 0 Unit cell: (127.72, 133.9, 147.29, 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 116 16.00 O 3848 8.00 N 3064 7.00 C 11840 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=34, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.02 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.02 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.02 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.02 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.04 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 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 P 3 " - " MAN P 4 " " BMA V 3 " - " MAN V 4 " " BMA W 3 " - " MAN W 7 " " BMA b 3 " - " MAN b 4 " " BMA e 3 " - " MAN e 4 " " BMA f 3 " - " MAN f 9 " ALPHA1-6 " BMA V 3 " - " MAN V 8 " " BMA W 3 " - " MAN W 4 " " BMA b 3 " - " MAN b 5 " " BMA e 3 " - " MAN e 7 " " BMA f 3 " - " MAN f 4 " BETA1-2 " MAN V 4 " - " NAG V 5 " " MAN e 4 " - " NAG e 5 " " MAN e 7 " - " NAG e 8 " " MAN f 4 " - " NAG f 5 " BETA1-4 " NAG J 1 " - " NAG J 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " MAN V 4 " - " NAG V 7 " " NAG V 5 " - " GAL V 6 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG W 5 " - " GAL W 6 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG e 5 " - " GAL e 6 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG f 5 " - " GAL f 6 " " NAG f 7 " - " GAL f 8 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " BETA1-6 " NAG K 1 " - " NAG K 2 " " NAG V 1 " - " FUC V 9 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG W 1 " - " FUC W 8 " " MAN W 4 " - " NAG W 5 " " NAG X 1 " - " FUC X 2 " " NAG c 1 " - " FUC c 2 " " NAG e 1 " - " FUC e 9 " " NAG f 1 " - " FUC f 10 " " MAN f 4 " - " NAG f 7 " NAG-ASN " NAG A 603 " - " ASN A 160 " " NAG A 604 " - " ASN A 197 " " NAG A 605 " - " ASN A 234 " " NAG A 618 " - " ASN A 332 " " NAG A 619 " - " ASN A 392 " " NAG A 629 " - " ASN A 188 " " NAG A 632 " - " ASN A 356 " " NAG A 633 " - " ASN A 362 " " NAG C 603 " - " ASN C 130 " " NAG C 606 " - " ASN C 234 " " NAG C 614 " - " ASN C 448 " " NAG C 615 " - " ASN C 276 " " NAG C 616 " - " ASN C 156 " " NAG C 617 " - " ASN C 188 " " NAG C 620 " - " ASN C 295 " " NAG C 621 " - " ASN C 301 " " NAG C 622 " - " ASN C 332 " " NAG C 623 " - " ASN C 289 " " NAG C 624 " - " ASN C 392 " " NAG C 627 " - " ASN C 356 " " NAG C 628 " - " ASN C 362 " " NAG D 901 " - " ASN D 625 " " NAG E 608 " - " ASN E 160 " " NAG E 609 " - " ASN E 156 " " NAG E 610 " - " ASN E 276 " " NAG E 611 " - " ASN E 289 " " NAG E 612 " - " ASN E 332 " " NAG E 613 " - " ASN E 295 " " NAG E 614 " - " ASN E 301 " " NAG E 615 " - " ASN E 392 " " NAG E 616 " - " ASN E 362 " " NAG E 617 " - " ASN E 234 " " NAG E 618 " - " ASN E 356 " " NAG E 619 " - " ASN E 188 " " NAG E 620 " - " ASN E 197 " " NAG E 621 " - " ASN E 130 " " NAG E 622 " - " ASN E 448 " " NAG F 901 " - " ASN F 616 " " NAG F 902 " - " ASN F 625 " " NAG F 903 " - " ASN F 637 " " NAG F 904 " - " ASN F 611 " " NAG J 1 " - " ASN A 130 " " NAG K 1 " - " ASN A 241 " " NAG M 1 " - " ASN A 276 " " NAG N 1 " - " ASN A 386 " " NAG O 1 " - " ASN A 295 " " NAG P 1 " - " ASN A 262 " " NAG Q 1 " - " ASN A 301 " " NAG R 1 " - " ASN A 448 " " NAG S 1 " - " ASN A 88 " " NAG T 1 " - " ASN A 156 " " NAG U 1 " - " ASN A 289 " " NAG V 1 " - " ASN B 637 " " NAG W 1 " - " ASN B 611 " " NAG X 1 " - " ASN B 625 " " NAG Y 1 " - " ASN C 88 " " NAG Z 1 " - " ASN C 160 " " NAG a 1 " - " ASN C 241 " " NAG b 1 " - " ASN C 262 " " NAG c 1 " - " ASN C 197 " " NAG d 1 " - " ASN C 386 " " NAG e 1 " - " ASN D 637 " " NAG f 1 " - " ASN D 611 " " NAG g 1 " - " ASN E 88 " " NAG h 1 " - " ASN E 241 " " NAG i 1 " - " ASN E 262 " Time building additional restraints: 1.79 Conformation dependent library (CDL) restraints added in 912.5 milliseconds 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4062 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 39 sheets defined 19.2% alpha, 23.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 98 through 106 removed outlier: 4.176A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N MET A 104 " --> pdb=" O MET A 100 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N HIS A 105 " --> pdb=" O VAL A 101 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU A 106 " --> pdb=" O GLU A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 115 Processing helix chain 'A' and resid 122 through 126 removed outlier: 3.519A pdb=" N CYS A 126 " --> pdb=" O THR A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 350 removed outlier: 3.704A pdb=" N ASN A 339 " --> pdb=" O GLY A 335 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LYS A 343 " --> pdb=" O ASN A 339 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLN A 344 " --> pdb=" O ASP A 340 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LYS A 348 " --> pdb=" O GLN A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 373 removed outlier: 3.815A pdb=" N MET A 373 " --> pdb=" O PRO A 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 369 through 373' Processing helix chain 'A' and resid 474 through 482 removed outlier: 3.524A pdb=" N TRP A 479 " --> pdb=" O ARG A 476 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG A 480 " --> pdb=" O ASP A 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 537 removed outlier: 3.921A pdb=" N SER B 534 " --> pdb=" O MET B 530 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N MET B 535 " --> pdb=" O GLY B 531 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N THR B 536 " --> pdb=" O ALA B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 556 removed outlier: 4.353A pdb=" N ASN B 554 " --> pdb=" O GLN B 550 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 596 removed outlier: 4.091A pdb=" N LEU B 581 " --> pdb=" O GLN B 577 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N TYR B 586 " --> pdb=" O ALA B 582 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASP B 589 " --> pdb=" O ARG B 585 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU B 592 " --> pdb=" O LYS B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 624 removed outlier: 3.806A pdb=" N ILE B 622 " --> pdb=" O SER B 618 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TRP B 623 " --> pdb=" O TYR B 619 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 636 removed outlier: 3.519A pdb=" N ARG B 633 " --> pdb=" O MET B 629 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE B 635 " --> pdb=" O TRP B 631 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 648 removed outlier: 3.648A pdb=" N GLU B 647 " --> pdb=" O TYR B 643 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 664 removed outlier: 3.947A pdb=" N ASN B 656 " --> pdb=" O GLN B 652 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ASP B 664 " --> pdb=" O LEU B 660 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 117 removed outlier: 3.523A pdb=" N HIS C 105 " --> pdb=" O VAL C 101 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ILE C 109 " --> pdb=" O HIS C 105 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLN C 114 " --> pdb=" O SER C 110 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER C 115 " --> pdb=" O LEU C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 removed outlier: 3.730A pdb=" N LEU C 125 " --> pdb=" O LEU C 122 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N CYS C 126 " --> pdb=" O THR C 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 122 through 126' Processing helix chain 'C' and resid 334 through 349 removed outlier: 3.575A pdb=" N TRP C 338 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N LYS C 343 " --> pdb=" O ASN C 339 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLN C 344 " --> pdb=" O ASP C 340 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL C 347 " --> pdb=" O LYS C 343 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LYS C 348 " --> pdb=" O GLN C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 387 through 391 removed outlier: 3.531A pdb=" N LEU C 390 " --> pdb=" O SER C 387 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE C 391 " --> pdb=" O THR C 388 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 387 through 391' Processing helix chain 'C' and resid 475 through 483 Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 536 through 543 removed outlier: 4.340A pdb=" N GLN D 540 " --> pdb=" O THR D 536 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU D 543 " --> pdb=" O VAL D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 576 removed outlier: 4.185A pdb=" N GLN D 575 " --> pdb=" O GLY D 572 " (cutoff:3.500A) Processing helix chain 'D' and resid 577 through 596 removed outlier: 3.841A pdb=" N LEU D 581 " --> pdb=" O GLN D 577 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N VAL D 583 " --> pdb=" O ARG D 579 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TYR D 586 " --> pdb=" O ALA D 582 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LYS D 588 " --> pdb=" O GLU D 584 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU D 593 " --> pdb=" O ASP D 589 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 625 Processing helix chain 'D' and resid 627 through 635 removed outlier: 3.886A pdb=" N ARG D 633 " --> pdb=" O MET D 629 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU D 634 " --> pdb=" O GLU D 630 " (cutoff:3.500A) Processing helix chain 'D' and resid 638 through 648 removed outlier: 3.572A pdb=" N GLU D 647 " --> pdb=" O TYR D 643 " (cutoff:3.500A) Processing helix chain 'D' and resid 652 through 660 removed outlier: 3.751A pdb=" N ASN D 656 " --> pdb=" O GLN D 652 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLN D 658 " --> pdb=" O GLU D 654 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU D 660 " --> pdb=" O ASN D 656 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 106 removed outlier: 3.514A pdb=" N MET E 104 " --> pdb=" O MET E 100 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N HIS E 105 " --> pdb=" O VAL E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 107 through 115 removed outlier: 3.707A pdb=" N ASP E 113 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N SER E 115 " --> pdb=" O LEU E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 334 through 352 removed outlier: 3.729A pdb=" N TRP E 338 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ASN E 339 " --> pdb=" O GLY E 335 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASP E 340 " --> pdb=" O THR E 336 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS E 343 " --> pdb=" O ASN E 339 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE E 345 " --> pdb=" O THR E 341 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL E 347 " --> pdb=" O LYS E 343 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS E 348 " --> pdb=" O GLN E 344 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 387 through 392 removed outlier: 4.099A pdb=" N ASN E 392 " --> pdb=" O THR E 388 " (cutoff:3.500A) Processing helix chain 'E' and resid 427 through 429 No H-bonds generated for 'chain 'E' and resid 427 through 429' Processing helix chain 'E' and resid 475 through 480 removed outlier: 3.978A pdb=" N TRP E 479 " --> pdb=" O MET E 475 " (cutoff:3.500A) Processing helix chain 'F' and resid 523 through 528 removed outlier: 4.575A pdb=" N GLY F 527 " --> pdb=" O GLY F 524 " (cutoff:3.500A) Processing helix chain 'F' and resid 532 through 535 removed outlier: 3.523A pdb=" N MET F 535 " --> pdb=" O ALA F 532 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 532 through 535' Processing helix chain 'F' and resid 536 through 543 removed outlier: 3.618A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU F 543 " --> pdb=" O VAL F 539 " (cutoff:3.500A) Processing helix chain 'F' and resid 572 through 574 No H-bonds generated for 'chain 'F' and resid 572 through 574' Processing helix chain 'F' and resid 577 through 596 removed outlier: 3.523A pdb=" N ALA F 582 " --> pdb=" O ALA F 578 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL F 583 " --> pdb=" O ARG F 579 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASP F 589 " --> pdb=" O ARG F 585 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 623 removed outlier: 3.904A pdb=" N ILE F 622 " --> pdb=" O SER F 618 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 636 removed outlier: 3.692A pdb=" N TRP F 631 " --> pdb=" O THR F 627 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE F 635 " --> pdb=" O TRP F 631 " (cutoff:3.500A) Processing helix chain 'F' and resid 638 through 649 removed outlier: 3.514A pdb=" N THR F 644 " --> pdb=" O SER F 640 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU F 645 " --> pdb=" O LEU F 641 " (cutoff:3.500A) Processing helix chain 'F' and resid 653 through 658 removed outlier: 3.595A pdb=" N GLN F 658 " --> pdb=" O LYS F 655 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 32 Processing helix chain 'G' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.551A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 8.533A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.562A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.545A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ALA A 224 " --> pdb=" O VAL A 489 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 131 through 132 Processing sheet with id=AA4, first strand: chain 'A' and resid 181 through 183 Processing sheet with id=AA5, first strand: chain 'A' and resid 201 through 203 Processing sheet with id=AA6, first strand: chain 'A' and resid 256 through 257 removed outlier: 3.544A pdb=" N HIS A 330 " --> pdb=" O THR A 297 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N SER A 334 " --> pdb=" O GLU A 293 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N GLU A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 10.706A pdb=" N VAL A 286 " --> pdb=" O ILE A 455 " (cutoff:3.500A) removed outlier: 10.525A pdb=" N ILE A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 11.727A pdb=" N LEU A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 11.939A pdb=" N ILE A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 11.783A pdb=" N LYS A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 8.287A pdb=" N GLY A 451 " --> pdb=" O LYS A 290 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ILE A 443 " --> pdb=" O ARG A 298 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 261 removed outlier: 3.770A pdb=" N GLY A 451 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ILE A 443 " --> pdb=" O ARG A 298 " (cutoff:3.500A) removed outlier: 8.287A pdb=" N GLY A 451 " --> pdb=" O LYS A 290 " (cutoff:3.500A) removed outlier: 11.783A pdb=" N LYS A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 11.939A pdb=" N ILE A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 11.727A pdb=" N LEU A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 10.525A pdb=" N ILE A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 10.706A pdb=" N VAL A 286 " --> pdb=" O ILE A 455 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 284 through 298 current: chain 'A' and resid 360 through 361 Processing sheet with id=AA8, first strand: chain 'A' and resid 303 through 312 removed outlier: 6.976A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE A 309 " --> pdb=" O ARG A 315 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ARG A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 495 through 499 removed outlier: 5.647A pdb=" N VAL D 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N VAL C 38 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N THR D 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.517A pdb=" N LYS C 46 " --> pdb=" O LYS C 490 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL C 489 " --> pdb=" O ALA C 224 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 66 through 67 removed outlier: 6.578A pdb=" N HIS C 66 " --> pdb=" O SER C 209 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 93 through 94 Processing sheet with id=AB4, first strand: chain 'C' and resid 132 through 133 removed outlier: 3.532A pdb=" N ASN C 156 " --> pdb=" O THR C 132 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 181 through 183 Processing sheet with id=AB6, first strand: chain 'C' and resid 271 through 273 Processing sheet with id=AB7, first strand: chain 'C' and resid 374 through 377 removed outlier: 8.309A pdb=" N CYS C 296 " --> pdb=" O SER C 447 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N SER C 447 " --> pdb=" O CYS C 296 " (cutoff:3.500A) removed outlier: 8.489A pdb=" N ARG C 298 " --> pdb=" O CYS C 445 " (cutoff:3.500A) removed outlier: 8.888A pdb=" N CYS C 445 " --> pdb=" O ARG C 298 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N ASN C 300 " --> pdb=" O ILE C 443 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N ILE C 443 " --> pdb=" O ASN C 300 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ASN C 302 " --> pdb=" O GLY C 441 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 307 through 312 removed outlier: 4.328A pdb=" N HIS C 308 " --> pdb=" O PHE C 317 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE C 317 " --> pdb=" O HIS C 308 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 517 through 521 removed outlier: 7.401A pdb=" N GLY G 113 " --> pdb=" O VAL D 518 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 84 through 85 removed outlier: 4.009A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LYS E 487 " --> pdb=" O LEU E 226 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N VAL E 489 " --> pdb=" O TRP E 45 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N TRP E 45 " --> pdb=" O VAL E 489 " (cutoff:3.500A) removed outlier: 8.671A pdb=" N ILE E 491 " --> pdb=" O PRO E 43 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 53 through 56 removed outlier: 4.038A pdb=" N PHE E 53 " --> pdb=" O CYS E 218 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N CYS E 218 " --> pdb=" O PHE E 53 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AC4, first strand: chain 'E' and resid 130 through 133 removed outlier: 3.546A pdb=" N PHE E 176 " --> pdb=" O LYS E 155 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 181 through 183 Processing sheet with id=AC6, first strand: chain 'E' and resid 201 through 203 removed outlier: 6.560A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 259 through 261 removed outlier: 6.802A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 374 through 377 removed outlier: 3.861A pdb=" N HIS E 330 " --> pdb=" O THR E 297 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N CYS E 296 " --> pdb=" O SER E 447 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N SER E 447 " --> pdb=" O CYS E 296 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N ARG E 298 " --> pdb=" O CYS E 445 " (cutoff:3.500A) removed outlier: 8.464A pdb=" N CYS E 445 " --> pdb=" O ARG E 298 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ASN E 300 " --> pdb=" O ILE E 443 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N ILE E 443 " --> pdb=" O ASN E 300 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 304 through 308 Processing sheet with id=AD1, first strand: chain 'G' and resid 4 through 5 removed outlier: 3.886A pdb=" N VAL G 5 " --> pdb=" O VAL G 23 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ASP G 73 " --> pdb=" O THR G 78 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 10 through 12 removed outlier: 3.621A pdb=" N VAL G 131 " --> pdb=" O ALA G 92 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA G 92 " --> pdb=" O VAL G 131 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA G 97 " --> pdb=" O TYR G 35 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N MET G 34 " --> pdb=" O ALA G 50 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N ALA G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 10 through 12 removed outlier: 3.621A pdb=" N VAL G 131 " --> pdb=" O ALA G 92 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA G 92 " --> pdb=" O VAL G 131 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N CYS G 96 " --> pdb=" O TRP G 125 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N TRP G 125 " --> pdb=" O CYS G 96 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ARG G 98 " --> pdb=" O ASP G 123 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 4 through 7 removed outlier: 3.654A pdb=" N SER I 22 " --> pdb=" O THR I 7 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 10 through 12 Processing sheet with id=AD6, first strand: chain 'I' and resid 45 through 48 removed outlier: 7.461A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLN I 38 " --> pdb=" O PHE I 85 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'H' and resid 5 through 7 removed outlier: 3.606A pdb=" N VAL H 18 " --> pdb=" O MET H 83 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 5 through 7 Processing sheet with id=AD9, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.722A pdb=" N THR H 132 " --> pdb=" O GLY H 10 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL H 131 " --> pdb=" O ALA H 92 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA H 92 " --> pdb=" O VAL H 131 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL H 37 " --> pdb=" O ARG H 95 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA H 97 " --> pdb=" O TYR H 35 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N MET H 34 " --> pdb=" O ALA H 50 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ALA H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.722A pdb=" N THR H 132 " --> pdb=" O GLY H 10 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL H 131 " --> pdb=" O ALA H 92 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA H 92 " --> pdb=" O VAL H 131 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N VAL H 124 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'L' and resid 19 through 22 removed outlier: 3.579A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'L' and resid 53 through 54 removed outlier: 3.856A pdb=" N GLU L 50 " --> pdb=" O ASN L 53 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N LEU L 46 " --> pdb=" O ARG L 37 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N ARG L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) 438 hydrogen bonds defined for protein. 1122 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: 3.61 Time building geometry restraints manager: 2.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5740 1.34 - 1.46: 4898 1.46 - 1.59: 8425 1.59 - 1.71: 1 1.71 - 1.83: 164 Bond restraints: 19228 Sorted by residual: bond pdb=" C ASP I 93 " pdb=" N PHE I 94 " ideal model delta sigma weight residual 1.331 1.222 0.109 2.07e-02 2.33e+03 2.77e+01 bond pdb=" C1 NAG C 615 " pdb=" O5 NAG C 615 " ideal model delta sigma weight residual 1.406 1.507 -0.101 2.00e-02 2.50e+03 2.54e+01 bond pdb=" C1 MAN b 4 " pdb=" C2 MAN b 4 " ideal model delta sigma weight residual 1.526 1.597 -0.071 2.00e-02 2.50e+03 1.27e+01 bond pdb=" C1 NAG g 1 " pdb=" O5 NAG g 1 " ideal model delta sigma weight residual 1.406 1.477 -0.071 2.00e-02 2.50e+03 1.26e+01 bond pdb=" C5 MAN f 4 " pdb=" O5 MAN f 4 " ideal model delta sigma weight residual 1.418 1.480 -0.062 2.00e-02 2.50e+03 9.48e+00 ... (remaining 19223 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.46: 24970 2.46 - 4.92: 947 4.92 - 7.38: 137 7.38 - 9.85: 31 9.85 - 12.31: 5 Bond angle restraints: 26090 Sorted by residual: angle pdb=" C LEU B 565 " pdb=" N LEU B 566 " pdb=" CA LEU B 566 " ideal model delta sigma weight residual 121.54 132.80 -11.26 1.91e+00 2.74e-01 3.47e+01 angle pdb=" C GLY A 354 " pdb=" N ASN A 356 " pdb=" CA ASN A 356 " ideal model delta sigma weight residual 121.54 132.18 -10.64 1.91e+00 2.74e-01 3.11e+01 angle pdb=" C PHE C 353 " pdb=" N GLY C 354 " pdb=" CA GLY C 354 " ideal model delta sigma weight residual 121.41 131.10 -9.69 1.96e+00 2.60e-01 2.45e+01 angle pdb=" C PHE A 159 " pdb=" N ASN A 160 " pdb=" CA ASN A 160 " ideal model delta sigma weight residual 122.14 114.50 7.64 1.67e+00 3.59e-01 2.09e+01 angle pdb=" N ASN E 289 " pdb=" CA ASN E 289 " pdb=" C ASN E 289 " ideal model delta sigma weight residual 110.55 104.40 6.15 1.35e+00 5.49e-01 2.07e+01 ... (remaining 26085 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.67: 9873 15.67 - 31.34: 530 31.34 - 47.02: 132 47.02 - 62.69: 26 62.69 - 78.36: 8 Dihedral angle restraints: 10569 sinusoidal: 4278 harmonic: 6291 Sorted by residual: dihedral pdb=" CB CYS C 378 " pdb=" SG CYS C 378 " pdb=" SG CYS C 445 " pdb=" CB CYS C 445 " ideal model delta sinusoidal sigma weight residual -86.00 -148.37 62.37 1 1.00e+01 1.00e-02 5.15e+01 dihedral pdb=" CB CYS A 54 " pdb=" SG CYS A 54 " pdb=" SG CYS A 74 " pdb=" CB CYS A 74 " ideal model delta sinusoidal sigma weight residual 93.00 152.37 -59.37 1 1.00e+01 1.00e-02 4.71e+01 dihedral pdb=" CB CYS C 119 " pdb=" SG CYS C 119 " pdb=" SG CYS C 205 " pdb=" CB CYS C 205 " ideal model delta sinusoidal sigma weight residual -86.00 -137.52 51.52 1 1.00e+01 1.00e-02 3.63e+01 ... (remaining 10566 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.160: 3243 0.160 - 0.321: 52 0.321 - 0.481: 9 0.481 - 0.641: 2 0.641 - 0.801: 2 Chirality restraints: 3308 Sorted by residual: chirality pdb=" C1 NAG X 1 " pdb=" ND2 ASN B 625 " pdb=" C2 NAG X 1 " pdb=" O5 NAG X 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.60 -0.80 2.00e-01 2.50e+01 1.60e+01 chirality pdb=" C1 NAG S 1 " pdb=" ND2 ASN A 88 " pdb=" C2 NAG S 1 " pdb=" O5 NAG S 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.73 -0.67 2.00e-01 2.50e+01 1.12e+01 chirality pdb=" C1 NAG C 623 " pdb=" ND2 ASN C 289 " pdb=" C2 NAG C 623 " pdb=" O5 NAG C 623 " both_signs ideal model delta sigma weight residual False -2.40 -1.84 -0.56 2.00e-01 2.50e+01 7.98e+00 ... (remaining 3305 not shown) Planarity restraints: 3198 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 88 " -0.033 2.00e-02 2.50e+03 3.11e-02 1.21e+01 pdb=" CG ASN A 88 " 0.034 2.00e-02 2.50e+03 pdb=" OD1 ASN A 88 " -0.004 2.00e-02 2.50e+03 pdb=" ND2 ASN A 88 " 0.037 2.00e-02 2.50e+03 pdb=" C1 NAG S 1 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 625 " 0.014 2.00e-02 2.50e+03 2.91e-02 8.47e+00 pdb=" C ASN B 625 " -0.050 2.00e-02 2.50e+03 pdb=" O ASN B 625 " 0.019 2.00e-02 2.50e+03 pdb=" N MET B 626 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 651 " 0.015 2.00e-02 2.50e+03 2.90e-02 8.43e+00 pdb=" CG ASN B 651 " -0.050 2.00e-02 2.50e+03 pdb=" OD1 ASN B 651 " 0.019 2.00e-02 2.50e+03 pdb=" ND2 ASN B 651 " 0.017 2.00e-02 2.50e+03 ... (remaining 3195 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 3097 2.76 - 3.29: 17425 3.29 - 3.83: 30751 3.83 - 4.36: 34347 4.36 - 4.90: 57830 Nonbonded interactions: 143450 Sorted by model distance: nonbonded pdb=" OG SER A 209 " pdb=" OE1 GLU A 211 " model vdw 2.224 3.040 nonbonded pdb=" OG SER I 25 " pdb=" O GLU I 27 " model vdw 2.239 3.040 nonbonded pdb=" OG1 THR A 303 " pdb=" O GLU A 322 " model vdw 2.263 3.040 nonbonded pdb=" OG SER G 120 " pdb=" OH TYR I 34 " model vdw 2.268 3.040 nonbonded pdb=" O MET H 122 " pdb=" OH TYR L 36 " model vdw 2.286 3.040 ... (remaining 143445 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 58 or resid 65 through 134 or resid 152 through \ 165 or resid 170 through 353 or resid 356 through 392 or resid 413 through 457 \ or resid 467 through 633)) selection = (chain 'C' and (resid 33 through 58 or resid 65 through 134 or resid 152 through \ 165 or resid 170 through 353 or resid 356 through 364 or resid 368 through 392 \ or resid 413 through 457 or resid 467 through 505 or resid 617 through 628)) selection = (chain 'E' and (resid 33 through 134 or resid 152 through 364 or resid 368 throu \ gh 392 or resid 413 through 505 or resid 615 through 622)) } ncs_group { reference = (chain 'B' and (resid 522 through 557 or resid 571 through 574 or resid 576 thro \ ugh 659)) selection = (chain 'F' and resid 522 through 659) } ncs_group { reference = chain 'G' selection = (chain 'H' and resid 2 through 135) } ncs_group { reference = chain 'I' selection = (chain 'L' and resid 2 through 105) } ncs_group { reference = (chain 'J' and resid 1) selection = (chain 'K' and resid 1) selection = (chain 'M' and resid 1) selection = (chain 'N' and resid 1) selection = (chain 'O' and resid 1) selection = (chain 'Q' and resid 1) selection = (chain 'S' and resid 1) selection = (chain 'T' and resid 1) selection = (chain 'U' and resid 1) selection = (chain 'X' and resid 1) selection = (chain 'Y' and resid 1) selection = (chain 'Z' and resid 1) selection = (chain 'a' and resid 1) selection = (chain 'c' and resid 1) selection = (chain 'd' and resid 1) selection = (chain 'g' and resid 1) selection = (chain 'h' and resid 1) } ncs_group { reference = chain 'R' selection = chain 'i' } ncs_group { reference = (chain 'V' and resid 9) selection = (chain 'W' and resid 8) selection = (chain 'e' and resid 9) selection = (chain 'f' and resid 10) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 18.550 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 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 : 0.009 0.109 19388 Z= 0.414 Angle : 1.223 18.235 26536 Z= 0.577 Chirality : 0.070 0.801 3308 Planarity : 0.007 0.059 3132 Dihedral : 10.496 78.359 6405 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.75 % Favored : 88.25 % Rotamer: Outliers : 0.57 % Allowed : 3.22 % Favored : 96.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -4.54 (0.15), residues: 2131 helix: -3.53 (0.18), residues: 342 sheet: -2.65 (0.19), residues: 537 loop : -3.12 (0.15), residues: 1252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 585 TYR 0.036 0.003 TYR A 217 PHE 0.030 0.004 PHE I 49 TRP 0.033 0.004 TRP F 614 HIS 0.012 0.002 HIS E 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00888 / 0.41 (19228) covalent geometry : angle 1.13074 / 0.56 (26090) SS BOND : bond 0.00557 / 0.31 ( 34) SS BOND : angle 1.53555 / 1.05 ( 68) hydrogen bonds : bond 0.30925 / 20.48 ( 418) hydrogen bonds : angle 10.98581 / 7.57 ( 1122) link_ALPHA1-3 : bond 0.00722 / 0.39 ( 6) link_ALPHA1-3 : angle 1.88907 / 1.07 ( 18) link_ALPHA1-6 : bond 0.00505 / 0.22 ( 5) link_ALPHA1-6 : angle 1.98480 / 1.18 ( 15) link_BETA1-2 : bond 0.01175 / 0.58 ( 4) link_BETA1-2 : angle 2.15059 / 1.28 ( 12) link_BETA1-4 : bond 0.01061 / 0.67 ( 36) link_BETA1-4 : angle 3.48835 / 2.06 ( 108) link_BETA1-6 : bond 0.00807 / 0.55 ( 9) link_BETA1-6 : angle 2.67492 / 1.62 ( 27) link_NAG-ASN : bond 0.00942 / 0.54 ( 66) link_NAG-ASN : angle 4.77478 / 3.25 ( 198) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 377 time to evaluate : 0.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 TRP cc_start: 0.8308 (m-90) cc_final: 0.7987 (m-90) REVERT: A 106 GLU cc_start: 0.8410 (mm-30) cc_final: 0.7836 (pt0) REVERT: A 211 GLU cc_start: 0.8395 (mp0) cc_final: 0.8162 (mp0) REVERT: A 434 MET cc_start: 0.8873 (tmm) cc_final: 0.8473 (tmm) REVERT: B 638 TYR cc_start: 0.8994 (m-80) cc_final: 0.8763 (m-10) REVERT: B 645 LEU cc_start: 0.9481 (mt) cc_final: 0.9029 (tp) REVERT: B 656 ASN cc_start: 0.8931 (t0) cc_final: 0.8724 (t0) REVERT: B 657 GLU cc_start: 0.9191 (mt-10) cc_final: 0.8822 (tm-30) REVERT: B 659 GLU cc_start: 0.9474 (tt0) cc_final: 0.9103 (tm-30) REVERT: C 42 VAL cc_start: 0.9409 (t) cc_final: 0.9150 (p) REVERT: C 260 LEU cc_start: 0.8864 (pp) cc_final: 0.8583 (pp) REVERT: C 304 ARG cc_start: 0.8363 (tpm170) cc_final: 0.8152 (mmm160) REVERT: D 626 MET cc_start: 0.8925 (mtp) cc_final: 0.8543 (ttm) REVERT: D 632 GLU cc_start: 0.8980 (mm-30) cc_final: 0.8213 (tm-30) REVERT: D 651 ASN cc_start: 0.8850 (m-40) cc_final: 0.8618 (t0) REVERT: E 69 TRP cc_start: 0.7950 (m-90) cc_final: 0.7259 (m-90) REVERT: E 104 MET cc_start: 0.8105 (mmm) cc_final: 0.7898 (tpp) REVERT: E 111 LEU cc_start: 0.9031 (mt) cc_final: 0.8798 (tp) REVERT: E 293 GLU cc_start: 0.8128 (tt0) cc_final: 0.7856 (tm-30) REVERT: E 373 MET cc_start: 0.9044 (mmp) cc_final: 0.8598 (mmt) REVERT: E 426 MET cc_start: 0.6995 (mmm) cc_final: 0.6748 (mmm) REVERT: E 427 TRP cc_start: 0.7661 (m-90) cc_final: 0.7252 (m-90) REVERT: F 539 VAL cc_start: 0.9689 (t) cc_final: 0.9452 (p) REVERT: F 640 SER cc_start: 0.9276 (m) cc_final: 0.9012 (p) REVERT: G 35 TYR cc_start: 0.8853 (m-80) cc_final: 0.8564 (m-10) REVERT: I 27 GLU cc_start: 0.8645 (tp30) cc_final: 0.8431 (tp30) REVERT: I 89 MET cc_start: 0.8562 (ttt) cc_final: 0.7691 (ttt) REVERT: H 1 ARG cc_start: 0.7130 (ttp80) cc_final: 0.5677 (ttm-80) REVERT: H 45 LEU cc_start: 0.8797 (tp) cc_final: 0.8574 (tp) REVERT: H 90 ASP cc_start: 0.9140 (m-30) cc_final: 0.8879 (m-30) REVERT: L 17 GLN cc_start: 0.8420 (tt0) cc_final: 0.8164 (tm-30) REVERT: L 92 LYS cc_start: 0.9203 (tptp) cc_final: 0.8459 (tppp) REVERT: L 103 LYS cc_start: 0.8453 (tttt) cc_final: 0.8181 (tmtt) outliers start: 9 outliers final: 1 residues processed: 384 average time/residue: 0.1513 time to fit residues: 85.3109 Evaluate side-chains 191 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 190 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 5.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.6980 chunk 200 optimal weight: 0.9980 chunk 212 optimal weight: 8.9990 chunk 77 optimal weight: 0.6980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 103 GLN A 105 HIS A 216 HIS A 300 ASN C 82 GLN C 229 ASN C 287 GLN C 300 ASN ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 105 HIS E 344 GLN ** F 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 115 ASN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 101 GLN H 115 ASN L 53 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.061398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.050449 restraints weight = 94970.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.051890 restraints weight = 54026.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.052839 restraints weight = 36997.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.053537 restraints weight = 28659.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.054021 restraints weight = 23820.972| |-----------------------------------------------------------------------------| r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3058 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3058 r_free = 0.3058 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3058 r_free = 0.3058 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3058 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 19388 Z= 0.148 Angle : 0.825 13.537 26536 Z= 0.387 Chirality : 0.052 0.450 3308 Planarity : 0.005 0.058 3132 Dihedral : 6.469 25.645 2324 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.46 % Favored : 91.54 % Rotamer: Outliers : 0.10 % Allowed : 2.18 % Favored : 97.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -3.73 (0.16), residues: 2131 helix: -2.21 (0.23), residues: 347 sheet: -2.34 (0.20), residues: 535 loop : -2.70 (0.16), residues: 1249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 585 TYR 0.020 0.002 TYR I 36 PHE 0.027 0.002 PHE A 277 TRP 0.019 0.002 TRP C 479 HIS 0.005 0.001 HIS C 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.15 (19228) covalent geometry : angle 0.75502 / 0.37 (26090) SS BOND : bond 0.00335 / 0.23 ( 34) SS BOND : angle 1.02765 / 0.69 ( 68) hydrogen bonds : bond 0.05830 / 3.74 ( 418) hydrogen bonds : angle 7.34916 / 5.10 ( 1122) link_ALPHA1-3 : bond 0.01065 / 0.63 ( 6) link_ALPHA1-3 : angle 1.78112 / 1.13 ( 18) link_ALPHA1-6 : bond 0.00782 / 0.37 ( 5) link_ALPHA1-6 : angle 1.46399 / 0.83 ( 15) link_BETA1-2 : bond 0.00453 / 0.21 ( 4) link_BETA1-2 : angle 1.58058 / 0.93 ( 12) link_BETA1-4 : bond 0.00744 / 0.48 ( 36) link_BETA1-4 : angle 2.28855 / 1.27 ( 108) link_BETA1-6 : bond 0.00457 / 0.31 ( 9) link_BETA1-6 : angle 1.46103 / 0.89 ( 27) link_NAG-ASN : bond 0.00663 / 0.38 ( 66) link_NAG-ASN : angle 3.46520 / 2.40 ( 198) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 294 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.8096 (m90) cc_final: 0.7668 (m90) REVERT: A 69 TRP cc_start: 0.8233 (m-90) cc_final: 0.7850 (m-90) REVERT: A 106 GLU cc_start: 0.8282 (mm-30) cc_final: 0.7828 (pt0) REVERT: A 211 GLU cc_start: 0.8369 (mp0) cc_final: 0.7975 (mp0) REVERT: A 434 MET cc_start: 0.8892 (tmm) cc_final: 0.8592 (tmm) REVERT: A 477 ASP cc_start: 0.8876 (m-30) cc_final: 0.8625 (m-30) REVERT: B 638 TYR cc_start: 0.9117 (m-80) cc_final: 0.8880 (m-10) REVERT: B 651 ASN cc_start: 0.8704 (m110) cc_final: 0.8411 (t0) REVERT: C 42 VAL cc_start: 0.9520 (t) cc_final: 0.9274 (p) REVERT: C 304 ARG cc_start: 0.8115 (tpm170) cc_final: 0.7787 (mmm160) REVERT: C 427 TRP cc_start: 0.4461 (t60) cc_final: 0.3632 (t60) REVERT: D 584 GLU cc_start: 0.7922 (tm-30) cc_final: 0.7718 (tm-30) REVERT: D 620 ASN cc_start: 0.8818 (m-40) cc_final: 0.8515 (t0) REVERT: D 640 SER cc_start: 0.9073 (p) cc_final: 0.8851 (p) REVERT: D 645 LEU cc_start: 0.9602 (tp) cc_final: 0.9354 (tp) REVERT: D 650 GLN cc_start: 0.7862 (tt0) cc_final: 0.7377 (tt0) REVERT: E 69 TRP cc_start: 0.7938 (m-90) cc_final: 0.7292 (m-90) REVERT: E 95 MET cc_start: 0.9329 (ptm) cc_final: 0.8973 (ptt) REVERT: E 210 PHE cc_start: 0.8647 (m-80) cc_final: 0.8416 (m-10) REVERT: E 373 MET cc_start: 0.9055 (mmp) cc_final: 0.8670 (mmt) REVERT: E 427 TRP cc_start: 0.7701 (m-90) cc_final: 0.7404 (m-90) REVERT: F 586 TYR cc_start: 0.8893 (t80) cc_final: 0.8294 (t80) REVERT: F 646 ILE cc_start: 0.9642 (mm) cc_final: 0.9383 (tp) REVERT: I 4 MET cc_start: 0.6442 (tmm) cc_final: 0.6144 (ppp) REVERT: I 27 ARG cc_start: 0.7818 (tpt90) cc_final: 0.7554 (mmm160) REVERT: I 89 MET cc_start: 0.8366 (ttt) cc_final: 0.6662 (ttt) REVERT: H 108 LEU cc_start: 0.9162 (tp) cc_final: 0.8916 (tt) REVERT: L 17 GLN cc_start: 0.8807 (tt0) cc_final: 0.8447 (tm-30) REVERT: L 24 LYS cc_start: 0.9445 (tttt) cc_final: 0.9245 (tttp) REVERT: L 27 GLU cc_start: 0.7949 (tp30) cc_final: 0.7626 (tm-30) REVERT: L 92 LYS cc_start: 0.9161 (tptp) cc_final: 0.8585 (tppp) REVERT: L 103 LYS cc_start: 0.8483 (tttt) cc_final: 0.8000 (tmtt) outliers start: 0 outliers final: 0 residues processed: 294 average time/residue: 0.1347 time to fit residues: 60.9261 Evaluate side-chains 198 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 198 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 197 optimal weight: 9.9990 chunk 50 optimal weight: 0.7980 chunk 69 optimal weight: 0.4980 chunk 104 optimal weight: 0.7980 chunk 67 optimal weight: 20.0000 chunk 212 optimal weight: 4.9990 chunk 187 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 84 optimal weight: 9.9990 chunk 57 optimal weight: 6.9990 chunk 117 optimal weight: 0.8980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 103 GLN D 590 GLN ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 249 HIS ** F 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.061177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.049954 restraints weight = 97867.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.051475 restraints weight = 53336.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.052504 restraints weight = 35782.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.053209 restraints weight = 27196.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.053662 restraints weight = 22511.486| |-----------------------------------------------------------------------------| r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3055 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3055 r_free = 0.3055 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3055 r_free = 0.3055 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3055 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 19388 Z= 0.135 Angle : 0.748 12.911 26536 Z= 0.350 Chirality : 0.049 0.374 3308 Planarity : 0.004 0.048 3132 Dihedral : 5.904 25.286 2324 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.51 % Favored : 91.49 % Rotamer: Outliers : 0.10 % Allowed : 2.60 % Favored : 97.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -3.31 (0.16), residues: 2131 helix: -1.44 (0.25), residues: 353 sheet: -2.09 (0.20), residues: 535 loop : -2.55 (0.16), residues: 1243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 585 TYR 0.025 0.001 TYR A 217 PHE 0.017 0.001 PHE I 49 TRP 0.024 0.002 TRP G 125 HIS 0.004 0.001 HIS A 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (19228) covalent geometry : angle 0.68733 / 0.34 (26090) SS BOND : bond 0.00284 / 0.16 ( 34) SS BOND : angle 0.87953 / 0.60 ( 68) hydrogen bonds : bond 0.04492 / 2.90 ( 418) hydrogen bonds : angle 6.57146 / 4.58 ( 1122) link_ALPHA1-3 : bond 0.01011 / 0.57 ( 6) link_ALPHA1-3 : angle 1.57406 / 0.97 ( 18) link_ALPHA1-6 : bond 0.00700 / 0.32 ( 5) link_ALPHA1-6 : angle 1.48208 / 0.81 ( 15) link_BETA1-2 : bond 0.00410 / 0.18 ( 4) link_BETA1-2 : angle 1.35047 / 0.77 ( 12) link_BETA1-4 : bond 0.00712 / 0.48 ( 36) link_BETA1-4 : angle 2.11287 / 1.17 ( 108) link_BETA1-6 : bond 0.00380 / 0.26 ( 9) link_BETA1-6 : angle 1.29431 / 0.78 ( 27) link_NAG-ASN : bond 0.00599 / 0.33 ( 66) link_NAG-ASN : angle 3.05496 / 2.12 ( 198) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 267 time to evaluate : 0.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.8085 (m90) cc_final: 0.7522 (m90) REVERT: A 69 TRP cc_start: 0.8244 (m-90) cc_final: 0.7786 (m-90) REVERT: A 106 GLU cc_start: 0.8335 (mm-30) cc_final: 0.7833 (pt0) REVERT: A 176 PHE cc_start: 0.8776 (m-10) cc_final: 0.8439 (m-10) REVERT: A 211 GLU cc_start: 0.8375 (mp0) cc_final: 0.7977 (mp0) REVERT: A 434 MET cc_start: 0.8876 (tmm) cc_final: 0.8553 (tmm) REVERT: A 477 ASP cc_start: 0.8864 (m-30) cc_final: 0.8591 (m-30) REVERT: C 42 VAL cc_start: 0.9451 (t) cc_final: 0.9224 (p) REVERT: C 304 ARG cc_start: 0.8177 (tpm170) cc_final: 0.7770 (mmm160) REVERT: D 584 GLU cc_start: 0.8118 (tm-30) cc_final: 0.7838 (tm-30) REVERT: D 630 GLU cc_start: 0.8915 (pt0) cc_final: 0.8701 (pt0) REVERT: D 632 GLU cc_start: 0.8711 (mm-30) cc_final: 0.7960 (tm-30) REVERT: E 42 VAL cc_start: 0.9265 (t) cc_final: 0.8912 (p) REVERT: E 69 TRP cc_start: 0.7783 (m-90) cc_final: 0.7253 (m-90) REVERT: E 95 MET cc_start: 0.9357 (ptm) cc_final: 0.9126 (ptm) REVERT: E 210 PHE cc_start: 0.8652 (m-80) cc_final: 0.8416 (m-10) REVERT: E 293 GLU cc_start: 0.8415 (tt0) cc_final: 0.7911 (tm-30) REVERT: E 373 MET cc_start: 0.9095 (mmp) cc_final: 0.8657 (mmt) REVERT: F 586 TYR cc_start: 0.8941 (t80) cc_final: 0.8478 (t80) REVERT: G 35 TYR cc_start: 0.8232 (m-10) cc_final: 0.7939 (m-10) REVERT: G 99 MET cc_start: 0.7980 (ttt) cc_final: 0.7770 (tpp) REVERT: I 89 MET cc_start: 0.8674 (ttt) cc_final: 0.7237 (ttt) REVERT: L 27 GLU cc_start: 0.7956 (tp30) cc_final: 0.7647 (tm-30) REVERT: L 89 MET cc_start: 0.8731 (ttt) cc_final: 0.8432 (ttt) REVERT: L 92 LYS cc_start: 0.9232 (tptp) cc_final: 0.8587 (tppp) REVERT: L 103 LYS cc_start: 0.8498 (tttt) cc_final: 0.7984 (tmtt) outliers start: 0 outliers final: 0 residues processed: 267 average time/residue: 0.1325 time to fit residues: 54.6501 Evaluate side-chains 190 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 64 optimal weight: 7.9990 chunk 17 optimal weight: 7.9990 chunk 166 optimal weight: 10.0000 chunk 8 optimal weight: 1.9990 chunk 128 optimal weight: 6.9990 chunk 190 optimal weight: 0.0770 chunk 169 optimal weight: 0.7980 chunk 3 optimal weight: 7.9990 chunk 160 optimal weight: 0.0980 chunk 194 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 overall best weight: 1.3942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 66 HIS ** F 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 65 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 = 0.3272 r_free = 0.3272 target = 0.061105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.049909 restraints weight = 97964.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.051397 restraints weight = 54478.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.052399 restraints weight = 36811.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.053090 restraints weight = 28204.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.053559 restraints weight = 23445.495| |-----------------------------------------------------------------------------| r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3057 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3057 r_free = 0.3057 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3057 r_free = 0.3057 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3057 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.3078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19388 Z= 0.131 Angle : 0.730 12.860 26536 Z= 0.340 Chirality : 0.049 0.361 3308 Planarity : 0.004 0.048 3132 Dihedral : 5.557 25.363 2324 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 0.10 % Allowed : 2.39 % Favored : 97.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -2.95 (0.17), residues: 2131 helix: -0.89 (0.27), residues: 351 sheet: -1.91 (0.20), residues: 539 loop : -2.37 (0.17), residues: 1241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 98 TYR 0.021 0.001 TYR B 638 PHE 0.013 0.001 PHE I 49 TRP 0.016 0.001 TRP A 427 HIS 0.003 0.001 HIS E 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (19228) covalent geometry : angle 0.67442 / 0.33 (26090) SS BOND : bond 0.00253 / 0.15 ( 34) SS BOND : angle 0.83130 / 0.56 ( 68) hydrogen bonds : bond 0.03863 / 2.46 ( 418) hydrogen bonds : angle 6.14789 / 4.29 ( 1122) link_ALPHA1-3 : bond 0.00967 / 0.56 ( 6) link_ALPHA1-3 : angle 1.53606 / 0.95 ( 18) link_ALPHA1-6 : bond 0.00585 / 0.25 ( 5) link_ALPHA1-6 : angle 1.46604 / 0.79 ( 15) link_BETA1-2 : bond 0.00492 / 0.22 ( 4) link_BETA1-2 : angle 1.30010 / 0.74 ( 12) link_BETA1-4 : bond 0.00646 / 0.42 ( 36) link_BETA1-4 : angle 2.09209 / 1.17 ( 108) link_BETA1-6 : bond 0.00387 / 0.27 ( 9) link_BETA1-6 : angle 1.24802 / 0.75 ( 27) link_NAG-ASN : bond 0.00739 / 0.50 ( 66) link_NAG-ASN : angle 2.87161 / 1.97 ( 198) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 246 time to evaluate : 0.667 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: A 66 HIS cc_start: 0.8055 (m90) cc_final: 0.7501 (m90) REVERT: A 69 TRP cc_start: 0.8192 (m-90) cc_final: 0.7689 (m-90) REVERT: A 106 GLU cc_start: 0.8284 (mm-30) cc_final: 0.7808 (pt0) REVERT: A 176 PHE cc_start: 0.8760 (m-10) cc_final: 0.8461 (m-10) REVERT: A 211 GLU cc_start: 0.8351 (mp0) cc_final: 0.7958 (mp0) REVERT: A 434 MET cc_start: 0.8780 (tmm) cc_final: 0.8499 (tmm) REVERT: A 477 ASP cc_start: 0.8761 (m-30) cc_final: 0.8505 (m-30) REVERT: C 304 ARG cc_start: 0.8195 (tpm170) cc_final: 0.7693 (mmm160) REVERT: D 584 GLU cc_start: 0.8179 (tm-30) cc_final: 0.7904 (tm-30) REVERT: D 591 GLN cc_start: 0.8652 (tt0) cc_final: 0.8242 (tt0) REVERT: D 601 LYS cc_start: 0.8114 (mttp) cc_final: 0.7861 (mttp) REVERT: D 632 GLU cc_start: 0.8696 (mm-30) cc_final: 0.8094 (tm-30) REVERT: D 655 LYS cc_start: 0.9220 (mmtp) cc_final: 0.8837 (mmmt) REVERT: E 42 VAL cc_start: 0.9356 (t) cc_final: 0.9030 (p) REVERT: E 69 TRP cc_start: 0.7673 (m-90) cc_final: 0.7155 (m-90) REVERT: E 210 PHE cc_start: 0.8574 (m-80) cc_final: 0.8338 (m-10) REVERT: E 277 PHE cc_start: 0.8004 (p90) cc_final: 0.7719 (p90) REVERT: E 293 GLU cc_start: 0.8368 (tt0) cc_final: 0.7939 (tm-30) REVERT: E 373 MET cc_start: 0.9073 (mmp) cc_final: 0.8639 (mmt) REVERT: E 434 MET cc_start: 0.7822 (tmm) cc_final: 0.7621 (tmm) REVERT: F 586 TYR cc_start: 0.8966 (t80) cc_final: 0.8636 (t80) REVERT: F 601 LYS cc_start: 0.8921 (mtmm) cc_final: 0.8660 (mtmm) REVERT: G 35 TYR cc_start: 0.8316 (m-10) cc_final: 0.7892 (m-10) REVERT: I 4 MET cc_start: 0.6864 (tmm) cc_final: 0.6635 (tmm) REVERT: I 89 MET cc_start: 0.8636 (ttt) cc_final: 0.8139 (ttt) REVERT: H 35 TYR cc_start: 0.8880 (m-80) cc_final: 0.8638 (m-80) REVERT: H 99 MET cc_start: 0.7113 (ttt) cc_final: 0.6544 (mtp) REVERT: L 17 GLN cc_start: 0.8826 (tt0) cc_final: 0.8334 (tm-30) REVERT: L 27 GLU cc_start: 0.7887 (tp30) cc_final: 0.7563 (tm-30) REVERT: L 74 ARG cc_start: 0.7945 (tpp80) cc_final: 0.7637 (mmm160) REVERT: L 92 LYS cc_start: 0.9222 (tptp) cc_final: 0.8579 (tppp) REVERT: L 103 LYS cc_start: 0.8391 (tttt) cc_final: 0.7902 (tmtt) outliers start: 0 outliers final: 0 residues processed: 246 average time/residue: 0.1306 time to fit residues: 49.5894 Evaluate side-chains 183 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 99 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 113 optimal weight: 8.9990 chunk 56 optimal weight: 0.9980 chunk 116 optimal weight: 7.9990 chunk 158 optimal weight: 5.9990 chunk 31 optimal weight: 7.9990 chunk 57 optimal weight: 1.9990 chunk 38 optimal weight: 9.9990 chunk 153 optimal weight: 10.0000 chunk 151 optimal weight: 6.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 65 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.060000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.048677 restraints weight = 101000.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.050112 restraints weight = 57401.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.051081 restraints weight = 39468.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.051742 restraints weight = 30598.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.052194 restraints weight = 25738.226| |-----------------------------------------------------------------------------| r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3013 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3013 r_free = 0.3013 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3013 r_free = 0.3013 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3013 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.3203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 19388 Z= 0.177 Angle : 0.750 12.957 26536 Z= 0.349 Chirality : 0.049 0.324 3308 Planarity : 0.004 0.046 3132 Dihedral : 5.506 24.806 2324 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.54 % Favored : 90.46 % Rotamer: Outliers : 0.10 % Allowed : 2.13 % Favored : 97.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -2.84 (0.17), residues: 2131 helix: -0.68 (0.28), residues: 362 sheet: -1.90 (0.20), residues: 551 loop : -2.31 (0.17), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 585 TYR 0.020 0.001 TYR I 34 PHE 0.015 0.002 PHE I 49 TRP 0.016 0.002 TRP E 338 HIS 0.004 0.001 HIS A 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.18 (19228) covalent geometry : angle 0.69607 / 0.34 (26090) SS BOND : bond 0.00297 / 0.16 ( 34) SS BOND : angle 0.85777 / 0.59 ( 68) hydrogen bonds : bond 0.03845 / 2.46 ( 418) hydrogen bonds : angle 6.05852 / 4.22 ( 1122) link_ALPHA1-3 : bond 0.00873 / 0.50 ( 6) link_ALPHA1-3 : angle 1.61615 / 0.97 ( 18) link_ALPHA1-6 : bond 0.00557 / 0.22 ( 5) link_ALPHA1-6 : angle 1.55169 / 0.84 ( 15) link_BETA1-2 : bond 0.00507 / 0.23 ( 4) link_BETA1-2 : angle 1.23806 / 0.70 ( 12) link_BETA1-4 : bond 0.00637 / 0.43 ( 36) link_BETA1-4 : angle 2.09650 / 1.17 ( 108) link_BETA1-6 : bond 0.00349 / 0.24 ( 9) link_BETA1-6 : angle 1.44324 / 0.87 ( 27) link_NAG-ASN : bond 0.00568 / 0.29 ( 66) link_NAG-ASN : angle 2.83620 / 1.94 ( 198) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 229 time to evaluate : 0.611 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: A 66 HIS cc_start: 0.8092 (m90) cc_final: 0.7883 (m90) REVERT: A 69 TRP cc_start: 0.8159 (m-90) cc_final: 0.7643 (m-90) REVERT: A 106 GLU cc_start: 0.8303 (mm-30) cc_final: 0.7864 (pt0) REVERT: A 107 ASP cc_start: 0.8581 (m-30) cc_final: 0.8364 (m-30) REVERT: A 211 GLU cc_start: 0.8442 (mp0) cc_final: 0.8087 (mp0) REVERT: A 434 MET cc_start: 0.8781 (tmm) cc_final: 0.8499 (tmm) REVERT: A 477 ASP cc_start: 0.8664 (m-30) cc_final: 0.8462 (m-30) REVERT: B 651 ASN cc_start: 0.8162 (m110) cc_final: 0.7786 (m110) REVERT: C 304 ARG cc_start: 0.8109 (tpm170) cc_final: 0.7622 (mmm160) REVERT: D 584 GLU cc_start: 0.8327 (tm-30) cc_final: 0.8029 (tm-30) REVERT: D 591 GLN cc_start: 0.8686 (tt0) cc_final: 0.8078 (tt0) REVERT: D 601 LYS cc_start: 0.8099 (mttp) cc_final: 0.7821 (mttp) REVERT: D 629 MET cc_start: 0.8398 (tpp) cc_final: 0.8176 (tpp) REVERT: D 632 GLU cc_start: 0.8723 (mm-30) cc_final: 0.8165 (tm-30) REVERT: D 655 LYS cc_start: 0.9253 (mmtp) cc_final: 0.8942 (mmmt) REVERT: E 42 VAL cc_start: 0.9406 (t) cc_final: 0.9098 (p) REVERT: E 69 TRP cc_start: 0.7573 (m-90) cc_final: 0.6965 (m-90) REVERT: E 277 PHE cc_start: 0.7991 (p90) cc_final: 0.7714 (p90) REVERT: E 293 GLU cc_start: 0.8280 (tt0) cc_final: 0.7948 (tm-30) REVERT: E 373 MET cc_start: 0.9035 (mmp) cc_final: 0.8594 (mmt) REVERT: F 586 TYR cc_start: 0.9116 (t80) cc_final: 0.8599 (t80) REVERT: F 626 MET cc_start: 0.7775 (tmm) cc_final: 0.6997 (tmm) REVERT: G 35 TYR cc_start: 0.8212 (m-10) cc_final: 0.7966 (m-10) REVERT: G 99 MET cc_start: 0.8484 (tpp) cc_final: 0.7043 (tpt) REVERT: I 89 MET cc_start: 0.8594 (ttt) cc_final: 0.7991 (ttt) REVERT: H 99 MET cc_start: 0.7438 (ttt) cc_final: 0.6612 (mtp) REVERT: L 27 GLU cc_start: 0.7944 (tp30) cc_final: 0.7561 (tm-30) REVERT: L 73 LEU cc_start: 0.8286 (tt) cc_final: 0.8031 (tp) REVERT: L 74 ARG cc_start: 0.8068 (tpp80) cc_final: 0.7718 (mmm160) REVERT: L 92 LYS cc_start: 0.9214 (tptp) cc_final: 0.8568 (tppp) REVERT: L 103 LYS cc_start: 0.8315 (tttt) cc_final: 0.7777 (tmtt) outliers start: 0 outliers final: 0 residues processed: 229 average time/residue: 0.1270 time to fit residues: 45.1392 Evaluate side-chains 179 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 205 optimal weight: 7.9990 chunk 187 optimal weight: 3.9990 chunk 104 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 199 optimal weight: 10.0000 chunk 115 optimal weight: 9.9990 chunk 40 optimal weight: 1.9990 chunk 119 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 178 optimal weight: 10.0000 chunk 172 optimal weight: 9.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 550 GLN ** F 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 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 = 0.3230 r_free = 0.3230 target = 0.059412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.048381 restraints weight = 100251.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.049718 restraints weight = 58888.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.050622 restraints weight = 41344.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.051242 restraints weight = 32603.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.051662 restraints weight = 27680.477| |-----------------------------------------------------------------------------| r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2997 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2997 r_free = 0.2997 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2997 r_free = 0.2997 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2997 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.3350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 19388 Z= 0.202 Angle : 0.775 13.090 26536 Z= 0.361 Chirality : 0.049 0.360 3308 Planarity : 0.004 0.047 3132 Dihedral : 5.575 24.380 2324 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.96 % Favored : 90.04 % Rotamer: Outliers : 0.10 % Allowed : 1.56 % Favored : 98.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -2.81 (0.17), residues: 2131 helix: -0.67 (0.28), residues: 368 sheet: -1.89 (0.21), residues: 543 loop : -2.29 (0.17), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 476 TYR 0.019 0.001 TYR I 34 PHE 0.014 0.002 PHE A 277 TRP 0.016 0.002 TRP E 427 HIS 0.004 0.001 HIS C 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.20 (19228) covalent geometry : angle 0.72346 / 0.35 (26090) SS BOND : bond 0.00372 / 0.19 ( 34) SS BOND : angle 0.96237 / 0.68 ( 68) hydrogen bonds : bond 0.03866 / 2.50 ( 418) hydrogen bonds : angle 6.02281 / 4.19 ( 1122) link_ALPHA1-3 : bond 0.00842 / 0.49 ( 6) link_ALPHA1-3 : angle 1.65279 / 0.98 ( 18) link_ALPHA1-6 : bond 0.00556 / 0.21 ( 5) link_ALPHA1-6 : angle 1.58538 / 0.86 ( 15) link_BETA1-2 : bond 0.00565 / 0.26 ( 4) link_BETA1-2 : angle 1.26305 / 0.70 ( 12) link_BETA1-4 : bond 0.00602 / 0.40 ( 36) link_BETA1-4 : angle 2.12490 / 1.19 ( 108) link_BETA1-6 : bond 0.00339 / 0.22 ( 9) link_BETA1-6 : angle 1.52701 / 0.92 ( 27) link_NAG-ASN : bond 0.00511 / 0.28 ( 66) link_NAG-ASN : angle 2.82597 / 1.93 ( 198) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 227 time to evaluate : 0.698 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: A 69 TRP cc_start: 0.8153 (m-90) cc_final: 0.7630 (m-90) REVERT: A 106 GLU cc_start: 0.8294 (mm-30) cc_final: 0.7874 (pt0) REVERT: A 211 GLU cc_start: 0.8434 (mp0) cc_final: 0.8110 (mp0) REVERT: A 434 MET cc_start: 0.8789 (tmm) cc_final: 0.8534 (tmm) REVERT: B 651 ASN cc_start: 0.8194 (m110) cc_final: 0.7852 (m110) REVERT: C 304 ARG cc_start: 0.8264 (tpm170) cc_final: 0.7756 (mmm160) REVERT: D 584 GLU cc_start: 0.8396 (tm-30) cc_final: 0.8169 (tm-30) REVERT: D 601 LYS cc_start: 0.8121 (mttp) cc_final: 0.7815 (mttp) REVERT: D 632 GLU cc_start: 0.8680 (mm-30) cc_final: 0.8175 (tm-30) REVERT: D 655 LYS cc_start: 0.9258 (mmtp) cc_final: 0.8968 (mmmt) REVERT: E 42 VAL cc_start: 0.9389 (t) cc_final: 0.9087 (p) REVERT: E 69 TRP cc_start: 0.7499 (m-90) cc_final: 0.6860 (m-90) REVERT: E 104 MET cc_start: 0.8400 (ttp) cc_final: 0.8174 (ttm) REVERT: E 210 PHE cc_start: 0.8649 (m-10) cc_final: 0.8324 (m-10) REVERT: E 277 PHE cc_start: 0.8022 (p90) cc_final: 0.7689 (p90) REVERT: E 373 MET cc_start: 0.8988 (mmp) cc_final: 0.8520 (mmt) REVERT: E 479 TRP cc_start: 0.8900 (m100) cc_final: 0.8636 (m100) REVERT: F 586 TYR cc_start: 0.9149 (t80) cc_final: 0.8612 (t80) REVERT: F 601 LYS cc_start: 0.8839 (pttm) cc_final: 0.8636 (pttp) REVERT: F 626 MET cc_start: 0.7334 (tmm) cc_final: 0.6996 (tmm) REVERT: G 99 MET cc_start: 0.8512 (tpp) cc_final: 0.7110 (tpt) REVERT: I 4 MET cc_start: 0.7152 (tmm) cc_final: 0.6871 (tmm) REVERT: I 98 PHE cc_start: 0.8634 (m-80) cc_final: 0.8019 (m-10) REVERT: H 99 MET cc_start: 0.7516 (ttt) cc_final: 0.6805 (mtp) REVERT: L 17 GLN cc_start: 0.8671 (tt0) cc_final: 0.8121 (tm-30) REVERT: L 27 GLU cc_start: 0.8008 (tp30) cc_final: 0.7674 (tm-30) REVERT: L 73 LEU cc_start: 0.8217 (tt) cc_final: 0.7989 (tp) REVERT: L 74 ARG cc_start: 0.8001 (tpp80) cc_final: 0.7649 (mmm160) REVERT: L 92 LYS cc_start: 0.9213 (tptp) cc_final: 0.8564 (tppp) REVERT: L 103 LYS cc_start: 0.8318 (tttt) cc_final: 0.7854 (tmtt) outliers start: 0 outliers final: 0 residues processed: 227 average time/residue: 0.1296 time to fit residues: 45.6113 Evaluate side-chains 175 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 76 optimal weight: 1.9990 chunk 134 optimal weight: 5.9990 chunk 6 optimal weight: 6.9990 chunk 125 optimal weight: 7.9990 chunk 155 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 170 optimal weight: 6.9990 chunk 150 optimal weight: 7.9990 chunk 52 optimal weight: 3.9990 chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 442 GLN ** F 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 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 = 0.3201 r_free = 0.3201 target = 0.058406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.047300 restraints weight = 100724.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.048664 restraints weight = 57816.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.049596 restraints weight = 40035.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.050200 restraints weight = 31250.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.050649 restraints weight = 26475.904| |-----------------------------------------------------------------------------| r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2970 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2970 r_free = 0.2970 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2970 r_free = 0.2970 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2970 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.3487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 19388 Z= 0.233 Angle : 0.811 13.308 26536 Z= 0.378 Chirality : 0.050 0.329 3308 Planarity : 0.004 0.046 3132 Dihedral : 5.684 24.880 2324 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.76 % Favored : 89.24 % Rotamer: Outliers : 0.10 % Allowed : 1.19 % Favored : 98.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -2.82 (0.17), residues: 2131 helix: -0.67 (0.28), residues: 367 sheet: -1.89 (0.21), residues: 550 loop : -2.30 (0.17), residues: 1214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 95 TYR 0.022 0.002 TYR C 217 PHE 0.015 0.002 PHE A 277 TRP 0.020 0.002 TRP E 427 HIS 0.007 0.002 HIS C 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00515 / 0.23 (19228) covalent geometry : angle 0.76109 / 0.37 (26090) SS BOND : bond 0.00342 / 0.18 ( 34) SS BOND : angle 0.89983 / 0.62 ( 68) hydrogen bonds : bond 0.03904 / 2.51 ( 418) hydrogen bonds : angle 6.02396 / 4.18 ( 1122) link_ALPHA1-3 : bond 0.00852 / 0.50 ( 6) link_ALPHA1-3 : angle 1.68820 / 1.00 ( 18) link_ALPHA1-6 : bond 0.00571 / 0.22 ( 5) link_ALPHA1-6 : angle 1.64293 / 0.90 ( 15) link_BETA1-2 : bond 0.00623 / 0.29 ( 4) link_BETA1-2 : angle 1.33201 / 0.73 ( 12) link_BETA1-4 : bond 0.00631 / 0.42 ( 36) link_BETA1-4 : angle 2.16393 / 1.22 ( 108) link_BETA1-6 : bond 0.00374 / 0.24 ( 9) link_BETA1-6 : angle 1.61636 / 0.98 ( 27) link_NAG-ASN : bond 0.00528 / 0.30 ( 66) link_NAG-ASN : angle 2.84342 / 1.93 ( 198) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 221 time to evaluate : 0.667 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: A 69 TRP cc_start: 0.8181 (m-90) cc_final: 0.7785 (m-90) REVERT: A 106 GLU cc_start: 0.8338 (mm-30) cc_final: 0.7891 (pt0) REVERT: A 211 GLU cc_start: 0.8489 (mp0) cc_final: 0.8141 (mp0) REVERT: A 434 MET cc_start: 0.8755 (tmm) cc_final: 0.8042 (tmm) REVERT: D 584 GLU cc_start: 0.8529 (tm-30) cc_final: 0.8291 (tm-30) REVERT: D 601 LYS cc_start: 0.8226 (mttp) cc_final: 0.7813 (mttp) REVERT: D 629 MET cc_start: 0.8545 (tpp) cc_final: 0.8249 (tpp) REVERT: D 632 GLU cc_start: 0.8751 (mm-30) cc_final: 0.8207 (tm-30) REVERT: D 655 LYS cc_start: 0.9339 (mmtp) cc_final: 0.9073 (mmmm) REVERT: E 42 VAL cc_start: 0.9424 (t) cc_final: 0.9109 (p) REVERT: E 69 TRP cc_start: 0.7536 (m-90) cc_final: 0.6848 (m-90) REVERT: E 104 MET cc_start: 0.8642 (ttp) cc_final: 0.8091 (ttm) REVERT: E 210 PHE cc_start: 0.8662 (m-10) cc_final: 0.8333 (m-10) REVERT: E 277 PHE cc_start: 0.7910 (p90) cc_final: 0.7673 (p90) REVERT: E 373 MET cc_start: 0.8972 (mmp) cc_final: 0.8538 (mmt) REVERT: E 479 TRP cc_start: 0.9017 (m100) cc_final: 0.8398 (m100) REVERT: F 586 TYR cc_start: 0.9197 (t80) cc_final: 0.8612 (t80) REVERT: F 626 MET cc_start: 0.7350 (tmm) cc_final: 0.6839 (tmm) REVERT: G 35 TYR cc_start: 0.8393 (m-80) cc_final: 0.7894 (m-10) REVERT: G 99 MET cc_start: 0.8225 (tpp) cc_final: 0.7360 (tpt) REVERT: I 89 MET cc_start: 0.7926 (ppp) cc_final: 0.7271 (tmm) REVERT: I 98 PHE cc_start: 0.8700 (m-80) cc_final: 0.8129 (m-80) REVERT: H 99 MET cc_start: 0.7715 (ttt) cc_final: 0.6858 (mtp) REVERT: L 17 GLN cc_start: 0.8754 (tt0) cc_final: 0.8239 (tm-30) REVERT: L 27 GLU cc_start: 0.8126 (tp30) cc_final: 0.7695 (tm-30) REVERT: L 73 LEU cc_start: 0.8191 (tt) cc_final: 0.7980 (tp) REVERT: L 74 ARG cc_start: 0.8051 (tpp80) cc_final: 0.7653 (mmm160) REVERT: L 92 LYS cc_start: 0.9153 (tptp) cc_final: 0.8505 (tppp) REVERT: L 103 LYS cc_start: 0.8298 (tttt) cc_final: 0.7832 (tmtt) outliers start: 0 outliers final: 0 residues processed: 221 average time/residue: 0.1340 time to fit residues: 45.9773 Evaluate side-chains 166 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 203 optimal weight: 10.0000 chunk 23 optimal weight: 0.8980 chunk 90 optimal weight: 0.8980 chunk 3 optimal weight: 0.4980 chunk 1 optimal weight: 2.9990 chunk 10 optimal weight: 10.0000 chunk 63 optimal weight: 7.9990 chunk 68 optimal weight: 8.9990 chunk 98 optimal weight: 0.4980 chunk 205 optimal weight: 3.9990 chunk 201 optimal weight: 7.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 103 GLN ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 ASN ** F 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 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 = 0.3256 r_free = 0.3256 target = 0.060536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.049352 restraints weight = 100073.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.050739 restraints weight = 58346.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.051676 restraints weight = 40863.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.052308 restraints weight = 32067.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.052645 restraints weight = 27205.083| |-----------------------------------------------------------------------------| r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3022 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3022 r_free = 0.3022 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3022 r_free = 0.3022 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3022 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.3683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19388 Z= 0.124 Angle : 0.737 13.066 26536 Z= 0.341 Chirality : 0.049 0.554 3308 Planarity : 0.004 0.047 3132 Dihedral : 5.382 24.689 2324 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.22 % Favored : 91.78 % Rotamer: Outliers : 0.10 % Allowed : 0.52 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -2.65 (0.18), residues: 2131 helix: -0.53 (0.28), residues: 372 sheet: -1.69 (0.21), residues: 560 loop : -2.25 (0.17), residues: 1199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 72 TYR 0.029 0.001 TYR A 217 PHE 0.013 0.001 PHE I 49 TRP 0.012 0.001 TRP C 45 HIS 0.004 0.001 HIS C 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (19228) covalent geometry : angle 0.68439 / 0.33 (26090) SS BOND : bond 0.00251 / 0.14 ( 34) SS BOND : angle 0.81447 / 0.55 ( 68) hydrogen bonds : bond 0.03474 / 2.23 ( 418) hydrogen bonds : angle 5.78337 / 4.04 ( 1122) link_ALPHA1-3 : bond 0.00795 / 0.45 ( 6) link_ALPHA1-3 : angle 1.64117 / 0.98 ( 18) link_ALPHA1-6 : bond 0.00595 / 0.27 ( 5) link_ALPHA1-6 : angle 1.44022 / 0.78 ( 15) link_BETA1-2 : bond 0.00436 / 0.19 ( 4) link_BETA1-2 : angle 1.18221 / 0.67 ( 12) link_BETA1-4 : bond 0.00644 / 0.43 ( 36) link_BETA1-4 : angle 1.96817 / 1.10 ( 108) link_BETA1-6 : bond 0.00387 / 0.27 ( 9) link_BETA1-6 : angle 1.29036 / 0.77 ( 27) link_NAG-ASN : bond 0.00592 / 0.32 ( 66) link_NAG-ASN : angle 2.84173 / 1.93 ( 198) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 237 time to evaluate : 0.572 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 69 TRP cc_start: 0.8138 (m-90) cc_final: 0.7645 (m-90) REVERT: A 106 GLU cc_start: 0.8281 (mm-30) cc_final: 0.7869 (pt0) REVERT: A 165 MET cc_start: 0.8353 (mtm) cc_final: 0.8107 (mtp) REVERT: A 176 PHE cc_start: 0.8652 (m-10) cc_final: 0.8355 (m-10) REVERT: A 211 GLU cc_start: 0.8374 (mp0) cc_final: 0.8075 (mp0) REVERT: A 434 MET cc_start: 0.8778 (tmm) cc_final: 0.8518 (tmm) REVERT: B 585 ARG cc_start: 0.9098 (mtp-110) cc_final: 0.8811 (mmm-85) REVERT: C 475 MET cc_start: 0.7929 (mtm) cc_final: 0.7653 (mmm) REVERT: D 584 GLU cc_start: 0.8465 (tm-30) cc_final: 0.8193 (tm-30) REVERT: D 629 MET cc_start: 0.8492 (tpp) cc_final: 0.8111 (tpp) REVERT: D 632 GLU cc_start: 0.8725 (mm-30) cc_final: 0.8195 (tm-30) REVERT: D 655 LYS cc_start: 0.9283 (mmtp) cc_final: 0.8960 (mmmm) REVERT: E 42 VAL cc_start: 0.9370 (t) cc_final: 0.9103 (p) REVERT: E 69 TRP cc_start: 0.7485 (m-90) cc_final: 0.6838 (m-90) REVERT: E 210 PHE cc_start: 0.8618 (m-10) cc_final: 0.8313 (m-10) REVERT: E 277 PHE cc_start: 0.7799 (p90) cc_final: 0.7545 (p90) REVERT: E 373 MET cc_start: 0.8961 (mmp) cc_final: 0.8513 (mmt) REVERT: F 586 TYR cc_start: 0.9057 (t80) cc_final: 0.8609 (t80) REVERT: F 626 MET cc_start: 0.7302 (tmm) cc_final: 0.6954 (tmm) REVERT: I 4 MET cc_start: 0.7115 (tmm) cc_final: 0.6816 (tmm) REVERT: I 98 PHE cc_start: 0.8557 (m-80) cc_final: 0.8133 (m-10) REVERT: H 99 MET cc_start: 0.7668 (ttt) cc_final: 0.6987 (mtp) REVERT: L 17 GLN cc_start: 0.8688 (tt0) cc_final: 0.8214 (tm-30) REVERT: L 27 GLU cc_start: 0.7867 (tp30) cc_final: 0.7488 (tm-30) REVERT: L 73 LEU cc_start: 0.8200 (tt) cc_final: 0.7963 (tp) REVERT: L 74 ARG cc_start: 0.8053 (tpp80) cc_final: 0.7669 (mmm160) REVERT: L 77 ARG cc_start: 0.8372 (tpp-160) cc_final: 0.8049 (tpp-160) REVERT: L 92 LYS cc_start: 0.9160 (tptp) cc_final: 0.8509 (tppp) REVERT: L 103 LYS cc_start: 0.8239 (tttt) cc_final: 0.7763 (tmtt) outliers start: 0 outliers final: 0 residues processed: 237 average time/residue: 0.1347 time to fit residues: 49.2035 Evaluate side-chains 181 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 14 optimal weight: 7.9990 chunk 169 optimal weight: 7.9990 chunk 129 optimal weight: 2.9990 chunk 195 optimal weight: 4.9990 chunk 181 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 121 optimal weight: 20.0000 chunk 192 optimal weight: 3.9990 chunk 100 optimal weight: 0.6980 chunk 145 optimal weight: 20.0000 chunk 46 optimal weight: 0.8980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 103 GLN A 216 HIS ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 ASN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 650 GLN ** G 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 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 = 0.3251 r_free = 0.3251 target = 0.060336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.049241 restraints weight = 99668.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.050600 restraints weight = 58249.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.051528 restraints weight = 40806.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.052171 restraints weight = 32016.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.052562 restraints weight = 27113.183| |-----------------------------------------------------------------------------| r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3022 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3022 r_free = 0.3022 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3022 r_free = 0.3022 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3022 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.3789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 19388 Z= 0.142 Angle : 0.749 13.066 26536 Z= 0.347 Chirality : 0.049 0.457 3308 Planarity : 0.004 0.045 3132 Dihedral : 5.437 32.856 2324 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.98 % Favored : 91.02 % Rotamer: Outliers : 0.10 % Allowed : 0.47 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.54 (0.18), residues: 2131 helix: -0.46 (0.28), residues: 370 sheet: -1.62 (0.21), residues: 534 loop : -2.16 (0.17), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 419 TYR 0.020 0.001 TYR G 80 PHE 0.012 0.001 PHE I 49 TRP 0.012 0.001 TRP C 112 HIS 0.005 0.001 HIS C 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (19228) covalent geometry : angle 0.69563 / 0.34 (26090) SS BOND : bond 0.00372 / 0.20 ( 34) SS BOND : angle 1.60227 / 1.22 ( 68) hydrogen bonds : bond 0.03525 / 2.26 ( 418) hydrogen bonds : angle 5.81792 / 4.04 ( 1122) link_ALPHA1-3 : bond 0.00813 / 0.46 ( 6) link_ALPHA1-3 : angle 1.61583 / 0.97 ( 18) link_ALPHA1-6 : bond 0.00547 / 0.22 ( 5) link_ALPHA1-6 : angle 1.45349 / 0.79 ( 15) link_BETA1-2 : bond 0.00425 / 0.19 ( 4) link_BETA1-2 : angle 1.15420 / 0.65 ( 12) link_BETA1-4 : bond 0.00630 / 0.42 ( 36) link_BETA1-4 : angle 1.94631 / 1.10 ( 108) link_BETA1-6 : bond 0.00336 / 0.23 ( 9) link_BETA1-6 : angle 1.35634 / 0.81 ( 27) link_NAG-ASN : bond 0.00603 / 0.31 ( 66) link_NAG-ASN : angle 2.76888 / 1.89 ( 198) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 231 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8820 (mtmm) cc_final: 0.8606 (mttt) REVERT: A 66 HIS cc_start: 0.8168 (m90) cc_final: 0.7877 (m90) REVERT: A 69 TRP cc_start: 0.8115 (m-90) cc_final: 0.7701 (m-90) REVERT: A 106 GLU cc_start: 0.8271 (mm-30) cc_final: 0.7924 (pt0) REVERT: A 165 MET cc_start: 0.8352 (mtm) cc_final: 0.8085 (mtp) REVERT: A 176 PHE cc_start: 0.8688 (m-10) cc_final: 0.8392 (m-10) REVERT: A 211 GLU cc_start: 0.8393 (mp0) cc_final: 0.8065 (mp0) REVERT: A 434 MET cc_start: 0.8769 (tmm) cc_final: 0.8041 (tmm) REVERT: A 477 ASP cc_start: 0.8667 (m-30) cc_final: 0.8451 (m-30) REVERT: B 585 ARG cc_start: 0.9145 (mtp-110) cc_final: 0.8857 (mmm-85) REVERT: B 622 ILE cc_start: 0.9248 (pt) cc_final: 0.8589 (pt) REVERT: C 373 MET cc_start: 0.7339 (ttt) cc_final: 0.7025 (ttt) REVERT: C 426 MET cc_start: 0.8101 (tpp) cc_final: 0.7886 (tpt) REVERT: C 475 MET cc_start: 0.7974 (mtm) cc_final: 0.7747 (mmm) REVERT: D 584 GLU cc_start: 0.8498 (tm-30) cc_final: 0.8229 (tm-30) REVERT: D 591 GLN cc_start: 0.8723 (tt0) cc_final: 0.8136 (tt0) REVERT: D 629 MET cc_start: 0.8506 (tpp) cc_final: 0.8134 (tpp) REVERT: D 632 GLU cc_start: 0.8753 (mm-30) cc_final: 0.8213 (tm-30) REVERT: D 648 ASP cc_start: 0.8465 (t70) cc_final: 0.8113 (t0) REVERT: D 655 LYS cc_start: 0.9290 (mmtp) cc_final: 0.9019 (mmmm) REVERT: E 42 VAL cc_start: 0.9377 (t) cc_final: 0.9020 (p) REVERT: E 69 TRP cc_start: 0.7520 (m-90) cc_final: 0.6898 (m-90) REVERT: E 104 MET cc_start: 0.8181 (ttp) cc_final: 0.7738 (tmm) REVERT: E 210 PHE cc_start: 0.8617 (m-10) cc_final: 0.8317 (m-10) REVERT: E 277 PHE cc_start: 0.7812 (p90) cc_final: 0.7490 (p90) REVERT: E 373 MET cc_start: 0.8927 (mmp) cc_final: 0.8495 (mmt) REVERT: E 434 MET cc_start: 0.7613 (tmm) cc_final: 0.7127 (tmm) REVERT: E 479 TRP cc_start: 0.8721 (m100) cc_final: 0.8229 (m100) REVERT: F 586 TYR cc_start: 0.9095 (t80) cc_final: 0.8627 (t80) REVERT: G 35 TYR cc_start: 0.8175 (m-80) cc_final: 0.7295 (m-80) REVERT: G 99 MET cc_start: 0.8008 (tpp) cc_final: 0.7374 (tpt) REVERT: I 4 MET cc_start: 0.7068 (tmm) cc_final: 0.6788 (tmm) REVERT: I 98 PHE cc_start: 0.8487 (m-80) cc_final: 0.8154 (m-80) REVERT: H 45 LEU cc_start: 0.9080 (tp) cc_final: 0.8778 (tp) REVERT: H 46 GLU cc_start: 0.8357 (mm-30) cc_final: 0.8059 (mm-30) REVERT: L 17 GLN cc_start: 0.8666 (tt0) cc_final: 0.8242 (tm-30) REVERT: L 27 GLU cc_start: 0.7852 (tp30) cc_final: 0.7468 (tm-30) REVERT: L 73 LEU cc_start: 0.8180 (tt) cc_final: 0.7954 (tp) REVERT: L 74 ARG cc_start: 0.8056 (tpp80) cc_final: 0.7649 (mmm160) REVERT: L 77 ARG cc_start: 0.8371 (tpp-160) cc_final: 0.8065 (tpp-160) REVERT: L 92 LYS cc_start: 0.9188 (tptp) cc_final: 0.8711 (tppt) REVERT: L 103 LYS cc_start: 0.8170 (tttt) cc_final: 0.7600 (tmtt) outliers start: 0 outliers final: 0 residues processed: 231 average time/residue: 0.1363 time to fit residues: 48.4744 Evaluate side-chains 178 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 207 optimal weight: 9.9990 chunk 79 optimal weight: 5.9990 chunk 184 optimal weight: 9.9990 chunk 128 optimal weight: 0.9990 chunk 108 optimal weight: 5.9990 chunk 60 optimal weight: 0.9990 chunk 189 optimal weight: 9.9990 chunk 23 optimal weight: 7.9990 chunk 177 optimal weight: 4.9990 chunk 194 optimal weight: 3.9990 chunk 134 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 216 HIS ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 77 ASN ** I 6 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 = 0.3221 r_free = 0.3221 target = 0.059135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.048133 restraints weight = 100920.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.049467 restraints weight = 59065.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.050368 restraints weight = 41557.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.050998 restraints weight = 32685.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.051395 restraints weight = 27732.387| |-----------------------------------------------------------------------------| r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2988 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2988 r_free = 0.2988 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2988 r_free = 0.2988 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2988 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.3826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 19388 Z= 0.205 Angle : 0.797 13.229 26536 Z= 0.372 Chirality : 0.050 0.391 3308 Planarity : 0.004 0.046 3132 Dihedral : 5.607 28.198 2324 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.43 % Favored : 89.57 % Rotamer: Outliers : 0.10 % Allowed : 0.26 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -2.57 (0.18), residues: 2131 helix: -0.42 (0.28), residues: 364 sheet: -1.69 (0.21), residues: 544 loop : -2.17 (0.17), residues: 1223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 72 TYR 0.021 0.002 TYR C 217 PHE 0.014 0.002 PHE A 277 TRP 0.015 0.002 TRP E 427 HIS 0.005 0.001 HIS C 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.20 (19228) covalent geometry : angle 0.74504 / 0.36 (26090) SS BOND : bond 0.00343 / 0.19 ( 34) SS BOND : angle 1.47528 / 1.10 ( 68) hydrogen bonds : bond 0.03715 / 2.39 ( 418) hydrogen bonds : angle 5.93515 / 4.11 ( 1122) link_ALPHA1-3 : bond 0.00830 / 0.47 ( 6) link_ALPHA1-3 : angle 1.65659 / 0.97 ( 18) link_ALPHA1-6 : bond 0.00549 / 0.21 ( 5) link_ALPHA1-6 : angle 1.57322 / 0.86 ( 15) link_BETA1-2 : bond 0.00555 / 0.26 ( 4) link_BETA1-2 : angle 1.25237 / 0.69 ( 12) link_BETA1-4 : bond 0.00634 / 0.43 ( 36) link_BETA1-4 : angle 2.04269 / 1.17 ( 108) link_BETA1-6 : bond 0.00338 / 0.22 ( 9) link_BETA1-6 : angle 1.58372 / 0.95 ( 27) link_NAG-ASN : bond 0.00563 / 0.30 ( 66) link_NAG-ASN : angle 2.85673 / 1.93 ( 198) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 218 time to evaluate : 0.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 TRP cc_start: 0.8172 (m-90) cc_final: 0.7809 (m-90) REVERT: A 106 GLU cc_start: 0.8307 (mm-30) cc_final: 0.7967 (pt0) REVERT: A 165 MET cc_start: 0.8283 (mtm) cc_final: 0.8009 (mtp) REVERT: A 211 GLU cc_start: 0.8452 (mp0) cc_final: 0.8132 (mp0) REVERT: A 434 MET cc_start: 0.8735 (tmm) cc_final: 0.8015 (tmm) REVERT: B 585 ARG cc_start: 0.9182 (mtp-110) cc_final: 0.8852 (mmm-85) REVERT: C 373 MET cc_start: 0.7306 (ttt) cc_final: 0.6976 (ttt) REVERT: D 584 GLU cc_start: 0.8499 (tm-30) cc_final: 0.8228 (tm-30) REVERT: D 591 GLN cc_start: 0.8719 (tt0) cc_final: 0.7981 (tt0) REVERT: D 629 MET cc_start: 0.8542 (tpp) cc_final: 0.8174 (tpp) REVERT: D 632 GLU cc_start: 0.8813 (mm-30) cc_final: 0.8261 (tm-30) REVERT: D 648 ASP cc_start: 0.8485 (t70) cc_final: 0.8267 (t0) REVERT: D 655 LYS cc_start: 0.9283 (mmtp) cc_final: 0.8966 (mmmm) REVERT: E 42 VAL cc_start: 0.9422 (t) cc_final: 0.9132 (p) REVERT: E 69 TRP cc_start: 0.7497 (m-90) cc_final: 0.6902 (m-90) REVERT: E 210 PHE cc_start: 0.8658 (m-10) cc_final: 0.8364 (m-10) REVERT: E 277 PHE cc_start: 0.7776 (p90) cc_final: 0.7446 (p90) REVERT: E 434 MET cc_start: 0.7704 (tmm) cc_final: 0.7364 (tmm) REVERT: E 475 MET cc_start: 0.8005 (tpt) cc_final: 0.7538 (tpt) REVERT: E 479 TRP cc_start: 0.8863 (m100) cc_final: 0.8556 (m100) REVERT: F 586 TYR cc_start: 0.9165 (t80) cc_final: 0.8573 (t80) REVERT: G 35 TYR cc_start: 0.8270 (m-80) cc_final: 0.7171 (m-80) REVERT: G 99 MET cc_start: 0.8087 (tpp) cc_final: 0.7252 (tpt) REVERT: I 4 MET cc_start: 0.7187 (tmm) cc_final: 0.6881 (tmm) REVERT: I 98 PHE cc_start: 0.8528 (m-80) cc_final: 0.8157 (m-80) REVERT: H 45 LEU cc_start: 0.9070 (tp) cc_final: 0.8773 (tp) REVERT: H 46 GLU cc_start: 0.8300 (mm-30) cc_final: 0.8044 (mm-30) REVERT: H 99 MET cc_start: 0.7009 (ttt) cc_final: 0.6111 (mtp) REVERT: L 17 GLN cc_start: 0.8699 (tt0) cc_final: 0.8320 (tm-30) REVERT: L 27 GLU cc_start: 0.8032 (tp30) cc_final: 0.7615 (tm-30) REVERT: L 74 ARG cc_start: 0.8081 (tpp80) cc_final: 0.7787 (mmm160) REVERT: L 77 ARG cc_start: 0.8364 (tpp-160) cc_final: 0.8161 (tpp-160) REVERT: L 92 LYS cc_start: 0.9214 (tptp) cc_final: 0.8769 (tppt) REVERT: L 103 LYS cc_start: 0.8155 (tttt) cc_final: 0.7640 (tmtt) outliers start: 0 outliers final: 0 residues processed: 218 average time/residue: 0.1360 time to fit residues: 46.0156 Evaluate side-chains 175 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 151 optimal weight: 0.7980 chunk 52 optimal weight: 0.7980 chunk 11 optimal weight: 20.0000 chunk 171 optimal weight: 7.9990 chunk 144 optimal weight: 0.9990 chunk 184 optimal weight: 10.0000 chunk 123 optimal weight: 20.0000 chunk 158 optimal weight: 4.9990 chunk 195 optimal weight: 5.9990 chunk 39 optimal weight: 9.9990 chunk 124 optimal weight: 4.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 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 = 0.3233 r_free = 0.3233 target = 0.059658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.048566 restraints weight = 101024.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.049924 restraints weight = 58851.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.050858 restraints weight = 41213.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.051491 restraints weight = 32374.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.051890 restraints weight = 27439.889| |-----------------------------------------------------------------------------| r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3001 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3001 r_free = 0.3001 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3001 r_free = 0.3001 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3001 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.3898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 19388 Z= 0.172 Angle : 0.776 13.214 26536 Z= 0.362 Chirality : 0.050 0.461 3308 Planarity : 0.004 0.046 3132 Dihedral : 5.540 28.846 2324 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.30 % Favored : 90.70 % Rotamer: Outliers : 0.10 % Allowed : 0.26 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -2.55 (0.18), residues: 2131 helix: -0.45 (0.28), residues: 359 sheet: -1.71 (0.21), residues: 527 loop : -2.12 (0.17), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 72 TYR 0.022 0.001 TYR G 80 PHE 0.013 0.001 PHE C 382 TRP 0.018 0.002 TRP C 112 HIS 0.005 0.001 HIS C 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.17 (19228) covalent geometry : angle 0.72315 / 0.35 (26090) SS BOND : bond 0.00312 / 0.16 ( 34) SS BOND : angle 1.39609 / 1.03 ( 68) hydrogen bonds : bond 0.03734 / 2.42 ( 418) hydrogen bonds : angle 5.94016 / 4.11 ( 1122) link_ALPHA1-3 : bond 0.00807 / 0.46 ( 6) link_ALPHA1-3 : angle 1.65320 / 0.98 ( 18) link_ALPHA1-6 : bond 0.00535 / 0.21 ( 5) link_ALPHA1-6 : angle 1.52190 / 0.83 ( 15) link_BETA1-2 : bond 0.00485 / 0.22 ( 4) link_BETA1-2 : angle 1.20762 / 0.67 ( 12) link_BETA1-4 : bond 0.00619 / 0.42 ( 36) link_BETA1-4 : angle 1.97115 / 1.12 ( 108) link_BETA1-6 : bond 0.00342 / 0.23 ( 9) link_BETA1-6 : angle 1.47754 / 0.88 ( 27) link_NAG-ASN : bond 0.00589 / 0.32 ( 66) link_NAG-ASN : angle 2.85422 / 1.91 ( 198) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2954.76 seconds wall clock time: 52 minutes 13.19 seconds (3133.19 seconds total)