Starting phenix.real_space_refine on Mon Oct 26 03:15:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6vo0_21256/10_2026/6vo0_21256.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vo0_21256/10_2026/6vo0_21256.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6vo0_21256/10_2026/6vo0_21256.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6vo0_21256/10_2026/6vo0_21256.cif" model { file = "/net/cci-nas-00/data/ceres_data/6vo0_21256/10_2026/6vo0_21256.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vo0_21256/10_2026/6vo0_21256.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6vo0_21256/10_2026/6vo0_21256.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vo0_21256/10_2026/6vo0_21256.map" } resolution = 3.52 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.082 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 132 5.16 5 C 12225 2.51 5 N 3267 2.21 5 O 3870 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 81 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19494 Number of models: 1 Model: "" Number of chains: 36 Chain: "L" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 848 Classifications: {'peptide': 113} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 107} Chain: "H" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 917 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 114} Chain: "A" Number of atoms: 3429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3429 Classifications: {'peptide': 433} Link IDs: {'PTRANS': 22, 'TRANS': 410} Chain breaks: 4 Chain: "B" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 971 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain breaks: 1 Chain: "J" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 848 Classifications: {'peptide': 113} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 107} Chain: "G" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 917 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 114} Chain: "C" Number of atoms: 3429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3429 Classifications: {'peptide': 433} Link IDs: {'PTRANS': 22, 'TRANS': 410} Chain breaks: 4 Chain: "E" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 971 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain breaks: 1 Chain: "K" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 848 Classifications: {'peptide': 113} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 107} Chain: "I" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 917 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 114} Chain: "D" Number of atoms: 3429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3429 Classifications: {'peptide': 433} Link IDs: {'PTRANS': 22, 'TRANS': 410} Chain breaks: 4 Chain: "F" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 971 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain breaks: 1 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: 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: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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: 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: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 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: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "D" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 3.90, per 1000 atoms: 0.20 Number of scatterers: 19494 At special positions: 0 Unit cell: (165.83, 162.74, 146.26, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 132 16.00 O 3870 8.00 N 3267 7.00 C 12225 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 35A" - pdb=" SG CYS H 50 " distance=2.03 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=2.10 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=2.04 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=2.04 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.04 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.04 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.02 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.04 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS G 35A" - pdb=" SG CYS G 50 " distance=2.03 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=2.10 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=2.04 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=2.04 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.04 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.04 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.02 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS E 605 " distance=2.03 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.04 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 35A" - pdb=" SG CYS I 50 " distance=2.02 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 74 " distance=2.03 Simple disulfide: pdb=" SG CYS D 119 " - pdb=" SG CYS D 205 " distance=2.10 Simple disulfide: pdb=" SG CYS D 126 " - pdb=" SG CYS D 196 " distance=2.03 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 157 " distance=2.04 Simple disulfide: pdb=" SG CYS D 218 " - pdb=" SG CYS D 247 " distance=2.03 Simple disulfide: pdb=" SG CYS D 228 " - pdb=" SG CYS D 239 " distance=2.04 Simple disulfide: pdb=" SG CYS D 296 " - pdb=" SG CYS D 331 " distance=2.04 Simple disulfide: pdb=" SG CYS D 378 " - pdb=" SG CYS D 445 " distance=2.04 Simple disulfide: pdb=" SG CYS D 385 " - pdb=" SG CYS D 418 " distance=2.02 Simple disulfide: pdb=" SG CYS D 501 " - pdb=" SG CYS F 605 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " NAG-ASN " NAG A 608 " - " ASN A 276 " " NAG A 611 " - " ASN A 301 " " NAG A 612 " - " ASN A 332 " " NAG A 613 " - " ASN A 386 " " NAG A 614 " - " ASN A 392 " " NAG A 617 " - " ASN A 363 " " NAG A 618 " - " ASN A 234 " " NAG A 619 " - " ASN A 197 " " NAG A 624 " - " ASN A 88 " " NAG C 608 " - " ASN C 276 " " NAG C 611 " - " ASN C 301 " " NAG C 612 " - " ASN C 332 " " NAG C 613 " - " ASN C 386 " " NAG C 614 " - " ASN C 392 " " NAG C 617 " - " ASN C 363 " " NAG C 618 " - " ASN C 234 " " NAG C 619 " - " ASN C 197 " " NAG C 624 " - " ASN C 88 " " NAG D 608 " - " ASN D 276 " " NAG D 611 " - " ASN D 301 " " NAG D 612 " - " ASN D 332 " " NAG D 613 " - " ASN D 386 " " NAG D 614 " - " ASN D 392 " " NAG D 617 " - " ASN D 363 " " NAG D 618 " - " ASN D 234 " " NAG D 619 " - " ASN D 197 " " NAG D 624 " - " ASN D 88 " " NAG M 1 " - " ASN A 133 " " NAG N 1 " - " ASN A 160 " " NAG O 1 " - " ASN A 262 " " NAG P 1 " - " ASN A 295 " " NAG Q 1 " - " ASN A 448 " " NAG R 1 " - " ASN A 156 " " NAG S 1 " - " ASN A 137 " " NAG T 1 " - " ASN C 133 " " NAG U 1 " - " ASN C 160 " " NAG V 1 " - " ASN C 262 " " NAG W 1 " - " ASN C 295 " " NAG X 1 " - " ASN C 448 " " NAG Y 1 " - " ASN C 156 " " NAG Z 1 " - " ASN C 137 " " NAG a 1 " - " ASN D 133 " " NAG b 1 " - " ASN D 160 " " NAG c 1 " - " ASN D 262 " " NAG d 1 " - " ASN D 295 " " NAG e 1 " - " ASN D 448 " " NAG f 1 " - " ASN D 156 " " NAG g 1 " - " ASN D 137 " Time building additional restraints: 1.87 Conformation dependent library (CDL) restraints added in 635.8 milliseconds 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4368 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 48 sheets defined 23.1% alpha, 36.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'L' and resid 59 through 62 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'A' and resid 98 through 115 removed outlier: 3.661A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 139 through 151 Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 334 through 354 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 377 through 381 Processing helix chain 'A' and resid 387 through 390 Processing helix chain 'A' and resid 476 through 481 Processing helix chain 'B' and resid 523 through 528 removed outlier: 4.229A pdb=" N GLY B 527 " --> pdb=" O GLY B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 543 Processing helix chain 'B' and resid 569 through 596 Processing helix chain 'B' and resid 618 through 626 removed outlier: 3.744A pdb=" N MET B 626 " --> pdb=" O ILE B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 639 through 662 removed outlier: 4.780A pdb=" N LEU B 645 " --> pdb=" O ILE B 641 " (cutoff:3.500A) Processing helix chain 'J' and resid 59 through 62 Processing helix chain 'J' and resid 79 through 83 Processing helix chain 'G' and resid 61 through 64 Processing helix chain 'G' and resid 83 through 87 Processing helix chain 'C' and resid 98 through 115 removed outlier: 3.661A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 139 through 151 Processing helix chain 'C' and resid 195 through 198 Processing helix chain 'C' and resid 334 through 354 Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 377 through 381 Processing helix chain 'C' and resid 387 through 390 Processing helix chain 'C' and resid 476 through 481 Processing helix chain 'E' and resid 523 through 528 removed outlier: 4.229A pdb=" N GLY E 527 " --> pdb=" O GLY E 524 " (cutoff:3.500A) Processing helix chain 'E' and resid 529 through 534 Processing helix chain 'E' and resid 536 through 543 Processing helix chain 'E' and resid 569 through 596 Processing helix chain 'E' and resid 618 through 626 removed outlier: 3.745A pdb=" N MET E 626 " --> pdb=" O ILE E 622 " (cutoff:3.500A) Processing helix chain 'E' and resid 627 through 635 Processing helix chain 'E' and resid 639 through 662 removed outlier: 4.781A pdb=" N LEU E 645 " --> pdb=" O ILE E 641 " (cutoff:3.500A) Processing helix chain 'K' and resid 59 through 62 Processing helix chain 'K' and resid 79 through 83 Processing helix chain 'I' and resid 61 through 64 Processing helix chain 'I' and resid 83 through 87 Processing helix chain 'D' and resid 98 through 115 removed outlier: 3.661A pdb=" N GLU D 102 " --> pdb=" O ASN D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 126 Processing helix chain 'D' and resid 139 through 151 Processing helix chain 'D' and resid 195 through 198 Processing helix chain 'D' and resid 334 through 354 Processing helix chain 'D' and resid 368 through 373 Processing helix chain 'D' and resid 377 through 381 Processing helix chain 'D' and resid 387 through 390 Processing helix chain 'D' and resid 476 through 481 Processing helix chain 'F' and resid 523 through 528 removed outlier: 4.228A pdb=" N GLY F 527 " --> pdb=" O GLY F 524 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 536 through 543 Processing helix chain 'F' and resid 569 through 596 Processing helix chain 'F' and resid 618 through 626 removed outlier: 3.744A pdb=" N MET F 626 " --> pdb=" O ILE F 622 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 639 through 662 removed outlier: 4.780A pdb=" N LEU F 645 " --> pdb=" O ILE F 641 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AA2, first strand: chain 'L' and resid 10 through 14 removed outlier: 4.675A pdb=" N GLY L 100 " --> pdb=" O CYS L 88 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ASN L 53 " --> pdb=" O TYR L 49 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA4, first strand: chain 'H' and resid 57 through 59 removed outlier: 5.393A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N SER H 96 " --> pdb=" O VAL H 100H" (cutoff:3.500A) removed outlier: 6.019A pdb=" N VAL H 100H" --> pdb=" O SER H 96 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 57 through 59 removed outlier: 5.393A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 494 through 499 Processing sheet with id=AA7, first strand: chain 'A' and resid 45 through 47 removed outlier: 7.466A pdb=" N VAL A 242 " --> pdb=" O HIS A 85 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N HIS A 85 " --> pdb=" O VAL A 242 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA9, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AB1, first strand: chain 'A' and resid 129 through 130 Processing sheet with id=AB2, first strand: chain 'A' and resid 154 through 155 Processing sheet with id=AB3, first strand: chain 'A' and resid 158 through 162 Processing sheet with id=AB4, first strand: chain 'A' and resid 200 through 203 removed outlier: 6.116A pdb=" N ALA A 200 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N TYR A 435 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 315 through 323A removed outlier: 6.425A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N ILE A 323 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ASN A 301 " --> pdb=" O ILE A 323 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.459A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ILE A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N PHE A 468 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 271 through 274 removed outlier: 6.906A pdb=" N THR A 450 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 9.738A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.279A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.562A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.792A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.772A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 10.193A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.363A pdb=" N CYS A 296 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 10.576A pdb=" N VAL A 442 " --> pdb=" O CYS A 296 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'J' and resid 4 through 7 Processing sheet with id=AB9, first strand: chain 'J' and resid 10 through 14 removed outlier: 4.674A pdb=" N GLY J 100 " --> pdb=" O CYS J 88 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ASN J 53 " --> pdb=" O TYR J 49 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AC2, first strand: chain 'G' and resid 57 through 59 removed outlier: 5.392A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N SER G 96 " --> pdb=" O VAL G 100H" (cutoff:3.500A) removed outlier: 6.019A pdb=" N VAL G 100H" --> pdb=" O SER G 96 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 57 through 59 removed outlier: 5.392A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 494 through 499 Processing sheet with id=AC5, first strand: chain 'C' and resid 45 through 47 removed outlier: 7.466A pdb=" N VAL C 242 " --> pdb=" O HIS C 85 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N HIS C 85 " --> pdb=" O VAL C 242 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AC7, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AC8, first strand: chain 'C' and resid 129 through 130 Processing sheet with id=AC9, first strand: chain 'C' and resid 154 through 155 Processing sheet with id=AD1, first strand: chain 'C' and resid 158 through 162 Processing sheet with id=AD2, first strand: chain 'C' and resid 200 through 203 removed outlier: 6.116A pdb=" N ALA C 200 " --> pdb=" O ALA C 433 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N TYR C 435 " --> pdb=" O ALA C 200 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 315 through 323A removed outlier: 6.425A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N ILE C 323 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ASN C 301 " --> pdb=" O ILE C 323 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 259 through 261 removed outlier: 6.459A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ILE C 358 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N PHE C 468 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 271 through 274 removed outlier: 6.906A pdb=" N THR C 450 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 9.738A pdb=" N THR C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 9.279A pdb=" N ASN C 448 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.562A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.792A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 11.772A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 10.193A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 11.363A pdb=" N CYS C 296 " --> pdb=" O VAL C 442 " (cutoff:3.500A) removed outlier: 10.575A pdb=" N VAL C 442 " --> pdb=" O CYS C 296 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'K' and resid 4 through 7 Processing sheet with id=AD7, first strand: chain 'K' and resid 10 through 14 removed outlier: 4.675A pdb=" N GLY K 100 " --> pdb=" O CYS K 88 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ASN K 53 " --> pdb=" O TYR K 49 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AD9, first strand: chain 'I' and resid 57 through 59 removed outlier: 5.393A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N SER I 96 " --> pdb=" O VAL I 100H" (cutoff:3.500A) removed outlier: 6.019A pdb=" N VAL I 100H" --> pdb=" O SER I 96 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 57 through 59 removed outlier: 5.393A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 494 through 499 Processing sheet with id=AE3, first strand: chain 'D' and resid 45 through 47 removed outlier: 7.466A pdb=" N VAL D 242 " --> pdb=" O HIS D 85 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N HIS D 85 " --> pdb=" O VAL D 242 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 53 through 55 Processing sheet with id=AE5, first strand: chain 'D' and resid 91 through 94 Processing sheet with id=AE6, first strand: chain 'D' and resid 129 through 130 Processing sheet with id=AE7, first strand: chain 'D' and resid 154 through 155 Processing sheet with id=AE8, first strand: chain 'D' and resid 158 through 162 Processing sheet with id=AE9, first strand: chain 'D' and resid 200 through 203 removed outlier: 6.117A pdb=" N ALA D 200 " --> pdb=" O ALA D 433 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N TYR D 435 " --> pdb=" O ALA D 200 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N THR D 202 " --> pdb=" O TYR D 435 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 315 through 323A removed outlier: 6.425A pdb=" N GLN D 315 " --> pdb=" O ILE D 309 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N THR D 303 " --> pdb=" O GLY D 321 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N ILE D 323 " --> pdb=" O ASN D 301 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ASN D 301 " --> pdb=" O ILE D 323 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ALA D 329 " --> pdb=" O CYS D 418 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N PHE D 382 " --> pdb=" O LYS D 421 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 259 through 261 removed outlier: 6.460A pdb=" N LEU D 260 " --> pdb=" O THR D 450 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ILE D 358 " --> pdb=" O GLU D 466 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N PHE D 468 " --> pdb=" O ILE D 358 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ARG D 360 " --> pdb=" O PHE D 468 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 271 through 274 removed outlier: 6.906A pdb=" N THR D 450 " --> pdb=" O PHE D 288 " (cutoff:3.500A) removed outlier: 9.738A pdb=" N THR D 290 " --> pdb=" O ASN D 448 " (cutoff:3.500A) removed outlier: 9.279A pdb=" N ASN D 448 " --> pdb=" O THR D 290 " (cutoff:3.500A) removed outlier: 10.562A pdb=" N VAL D 292 " --> pdb=" O VAL D 446 " (cutoff:3.500A) removed outlier: 9.792A pdb=" N VAL D 446 " --> pdb=" O VAL D 292 " (cutoff:3.500A) removed outlier: 11.772A pdb=" N ILE D 294 " --> pdb=" O ARG D 444 " (cutoff:3.500A) removed outlier: 10.193A pdb=" N ARG D 444 " --> pdb=" O ILE D 294 " (cutoff:3.500A) removed outlier: 11.363A pdb=" N CYS D 296 " --> pdb=" O VAL D 442 " (cutoff:3.500A) removed outlier: 10.575A pdb=" N VAL D 442 " --> pdb=" O CYS D 296 " (cutoff:3.500A) 783 hydrogen bonds defined for protein. 1989 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: 3.81 Time building geometry restraints manager: 2.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 4876 1.32 - 1.46: 6261 1.46 - 1.60: 8579 1.60 - 1.73: 15 1.73 - 1.87: 159 Bond restraints: 19890 Sorted by residual: bond pdb=" C1 NAG a 2 " pdb=" O5 NAG a 2 " ideal model delta sigma weight residual 1.406 1.549 -0.143 2.00e-02 2.50e+03 5.08e+01 bond pdb=" C1 NAG T 2 " pdb=" O5 NAG T 2 " ideal model delta sigma weight residual 1.406 1.548 -0.142 2.00e-02 2.50e+03 5.05e+01 bond pdb=" C1 NAG M 2 " pdb=" O5 NAG M 2 " ideal model delta sigma weight residual 1.406 1.548 -0.142 2.00e-02 2.50e+03 5.01e+01 bond pdb=" C1 NAG b 2 " pdb=" O5 NAG b 2 " ideal model delta sigma weight residual 1.406 1.544 -0.138 2.00e-02 2.50e+03 4.79e+01 bond pdb=" C1 NAG e 2 " pdb=" O5 NAG e 2 " ideal model delta sigma weight residual 1.406 1.544 -0.138 2.00e-02 2.50e+03 4.77e+01 ... (remaining 19885 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.54: 23410 2.54 - 5.09: 3048 5.09 - 7.63: 515 7.63 - 10.17: 26 10.17 - 12.71: 10 Bond angle restraints: 27009 Sorted by residual: angle pdb=" N SER J 90 " pdb=" CA SER J 90 " pdb=" C SER J 90 " ideal model delta sigma weight residual 111.07 121.28 -10.21 1.07e+00 8.73e-01 9.11e+01 angle pdb=" N SER K 90 " pdb=" CA SER K 90 " pdb=" C SER K 90 " ideal model delta sigma weight residual 111.07 121.27 -10.20 1.07e+00 8.73e-01 9.09e+01 angle pdb=" N SER L 90 " pdb=" CA SER L 90 " pdb=" C SER L 90 " ideal model delta sigma weight residual 111.07 121.25 -10.18 1.07e+00 8.73e-01 9.04e+01 angle pdb=" C ILE I 48 " pdb=" CA ILE I 48 " pdb=" CB ILE I 48 " ideal model delta sigma weight residual 111.71 104.26 7.45 8.50e-01 1.38e+00 7.67e+01 angle pdb=" C ILE G 48 " pdb=" CA ILE G 48 " pdb=" CB ILE G 48 " ideal model delta sigma weight residual 111.71 104.27 7.44 8.50e-01 1.38e+00 7.65e+01 ... (remaining 27004 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.66: 10842 16.66 - 33.31: 339 33.31 - 49.97: 84 49.97 - 66.63: 42 66.63 - 83.29: 12 Dihedral angle restraints: 11319 sinusoidal: 4533 harmonic: 6786 Sorted by residual: dihedral pdb=" C PHE G 98 " pdb=" N PHE G 98 " pdb=" CA PHE G 98 " pdb=" CB PHE G 98 " ideal model delta harmonic sigma weight residual -122.60 -113.59 -9.01 0 2.50e+00 1.60e-01 1.30e+01 dihedral pdb=" C PHE H 98 " pdb=" N PHE H 98 " pdb=" CA PHE H 98 " pdb=" CB PHE H 98 " ideal model delta harmonic sigma weight residual -122.60 -113.61 -8.99 0 2.50e+00 1.60e-01 1.29e+01 dihedral pdb=" C PHE I 98 " pdb=" N PHE I 98 " pdb=" CA PHE I 98 " pdb=" CB PHE I 98 " ideal model delta harmonic sigma weight residual -122.60 -113.62 -8.98 0 2.50e+00 1.60e-01 1.29e+01 ... (remaining 11316 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 2230 0.098 - 0.195: 810 0.195 - 0.293: 182 0.293 - 0.390: 18 0.390 - 0.488: 3 Chirality restraints: 3243 Sorted by residual: chirality pdb=" C1 NAG a 2 " pdb=" O4 NAG a 1 " pdb=" C2 NAG a 2 " pdb=" O5 NAG a 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.57 0.17 2.00e-02 2.50e+03 6.84e+01 chirality pdb=" C1 NAG e 2 " pdb=" O4 NAG e 1 " pdb=" C2 NAG e 2 " pdb=" O5 NAG e 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.57 0.17 2.00e-02 2.50e+03 6.82e+01 chirality pdb=" C1 NAG Q 2 " pdb=" O4 NAG Q 1 " pdb=" C2 NAG Q 2 " pdb=" O5 NAG Q 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.57 0.17 2.00e-02 2.50e+03 6.81e+01 ... (remaining 3240 not shown) Planarity restraints: 3387 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL H 109 " 0.047 2.00e-02 2.50e+03 9.68e-02 9.37e+01 pdb=" C VAL H 109 " -0.167 2.00e-02 2.50e+03 pdb=" O VAL H 109 " 0.062 2.00e-02 2.50e+03 pdb=" OXT VAL H 109 " 0.058 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL G 109 " -0.047 2.00e-02 2.50e+03 9.67e-02 9.36e+01 pdb=" C VAL G 109 " 0.167 2.00e-02 2.50e+03 pdb=" O VAL G 109 " -0.062 2.00e-02 2.50e+03 pdb=" OXT VAL G 109 " -0.058 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL I 109 " 0.047 2.00e-02 2.50e+03 9.67e-02 9.35e+01 pdb=" C VAL I 109 " -0.167 2.00e-02 2.50e+03 pdb=" O VAL I 109 " 0.062 2.00e-02 2.50e+03 pdb=" OXT VAL I 109 " 0.058 2.00e-02 2.50e+03 ... (remaining 3384 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.88: 8036 2.88 - 3.39: 17290 3.39 - 3.89: 33084 3.89 - 4.40: 37992 4.40 - 4.90: 61141 Nonbonded interactions: 157543 Sorted by model distance: nonbonded pdb=" OG1 THR H 72 " pdb=" OG1 THR H 76 " model vdw 2.380 3.040 nonbonded pdb=" OG1 THR I 72 " pdb=" OG1 THR I 76 " model vdw 2.380 3.040 nonbonded pdb=" OG1 THR G 72 " pdb=" OG1 THR G 76 " model vdw 2.380 3.040 nonbonded pdb=" OD2 ASP A 57 " pdb=" NZ LYS A 59 " model vdw 2.404 3.120 nonbonded pdb=" OD2 ASP D 57 " pdb=" NZ LYS D 59 " model vdw 2.405 3.120 ... (remaining 157538 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' } ncs_group { reference = chain 'O' selection = chain 'V' selection = chain 'c' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.400 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 17.580 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.022 0.147 20004 Z= 1.161 Angle : 1.824 12.713 27309 Z= 1.184 Chirality : 0.104 0.488 3243 Planarity : 0.010 0.097 3339 Dihedral : 10.048 83.285 6825 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 1.72 Ramachandran Plot: Outliers : 0.78 % Allowed : 3.64 % Favored : 95.58 % Rotamer: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.17), residues: 2310 helix: -0.48 (0.23), residues: 447 sheet: 0.49 (0.18), residues: 708 loop : 0.36 (0.18), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG K 95C TYR 0.067 0.008 TYR B 638 PHE 0.027 0.005 PHE A 53 TRP 0.061 0.010 TRP J 35 HIS 0.013 0.003 HIS H 100F Details of bonding type rmsd/Z covalent geometry : bond 0.02186 / 1.16 (19890) covalent geometry : angle 1.79611 / 1.18 (27009) SS BOND : bond 0.02012 / 1.54 ( 42) SS BOND : angle 3.63762 / 2.36 ( 84) hydrogen bonds : bond 0.17194 / 11.76 ( 741) hydrogen bonds : angle 7.82075 / 5.38 ( 1989) link_BETA1-4 : bond 0.02845 / 1.94 ( 24) link_BETA1-4 : angle 3.79808 / 2.47 ( 72) link_NAG-ASN : bond 0.03088 / 1.98 ( 48) link_NAG-ASN : angle 3.31612 / 2.32 ( 144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 539 time to evaluate : 0.679 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: L 62 PHE cc_start: 0.8541 (m-80) cc_final: 0.8228 (m-80) REVERT: H 82 LEU cc_start: 0.8814 (mt) cc_final: 0.8563 (mp) REVERT: A 481 SER cc_start: 0.8662 (p) cc_final: 0.8400 (t) REVERT: B 543 ASN cc_start: 0.8300 (t0) cc_final: 0.8087 (t0) REVERT: G 82 LEU cc_start: 0.8803 (mt) cc_final: 0.8548 (mp) REVERT: C 481 SER cc_start: 0.8745 (p) cc_final: 0.8510 (t) REVERT: E 658 GLN cc_start: 0.7587 (tt0) cc_final: 0.7349 (tm-30) REVERT: K 39 LYS cc_start: 0.8735 (mmmt) cc_final: 0.8189 (mmmm) REVERT: K 73 LEU cc_start: 0.8841 (mt) cc_final: 0.8533 (tp) REVERT: D 180 ASP cc_start: 0.7790 (m-30) cc_final: 0.7527 (m-30) REVERT: D 481 SER cc_start: 0.8680 (p) cc_final: 0.8445 (t) REVERT: F 543 ASN cc_start: 0.8246 (t0) cc_final: 0.7995 (t0) REVERT: F 658 GLN cc_start: 0.7644 (tt0) cc_final: 0.7331 (tm-30) outliers start: 0 outliers final: 0 residues processed: 539 average time/residue: 0.1513 time to fit residues: 121.8425 Evaluate side-chains 266 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 266 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: [216, 98, 194, 227, 107, 10, 66, 130, 124, 103, 200] chunk 216 optimal weight: 2.9990 chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 0.9990 chunk 227 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 10.0000 chunk 200 optimal weight: 0.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 38 GLN L 89 GLN L 91 ASN H 39 GLN H 100FHIS A 72 HIS A 195 ASN A 216 HIS A 374 HIS A 478 ASN B 625 ASN B 653 GLN J 38 GLN ** J 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 89 GLN J 91 ASN G 100FHIS C 72 HIS C 94 ASN ** C 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 ASN C 216 HIS C 300 ASN E 625 ASN E 653 GLN K 38 GLN ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 39 GLN I 100FHIS D 72 HIS ** D 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 195 ASN D 216 HIS D 352 HIS F 591 GLN F 625 ASN F 653 GLN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.089628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.071010 restraints weight = 57839.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.073569 restraints weight = 29304.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.075181 restraints weight = 19685.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.076171 restraints weight = 15441.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.076794 restraints weight = 13312.821| |-----------------------------------------------------------------------------| r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.3028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 20004 Z= 0.189 Angle : 0.811 9.834 27309 Z= 0.420 Chirality : 0.048 0.250 3243 Planarity : 0.005 0.048 3339 Dihedral : 5.753 26.048 2529 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.52 % Allowed : 3.85 % Favored : 95.63 % Rotamer: Outliers : 2.43 % Allowed : 9.64 % Favored : 87.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.17), residues: 2310 helix: 0.66 (0.26), residues: 417 sheet: 0.21 (0.18), residues: 699 loop : -0.52 (0.17), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG I 66 TYR 0.024 0.002 TYR H 100C PHE 0.016 0.002 PHE I 98 TRP 0.021 0.002 TRP E 614 HIS 0.008 0.001 HIS I 100F Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.19 (19890) covalent geometry : angle 0.78607 / 0.42 (27009) SS BOND : bond 0.00378 / 0.24 ( 42) SS BOND : angle 1.14801 / 0.79 ( 84) hydrogen bonds : bond 0.05965 / 3.98 ( 741) hydrogen bonds : angle 6.01738 / 4.16 ( 1989) link_BETA1-4 : bond 0.00671 / 0.50 ( 24) link_BETA1-4 : angle 2.11159 / 1.44 ( 72) link_NAG-ASN : bond 0.00566 / 0.41 ( 48) link_NAG-ASN : angle 2.42773 / 1.60 ( 144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 361 time to evaluate : 0.769 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: L 94 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8794 (mt) REVERT: L 107 LYS cc_start: 0.8366 (OUTLIER) cc_final: 0.7042 (tptt) REVERT: H 45 LEU cc_start: 0.9043 (mt) cc_final: 0.8816 (mt) REVERT: A 150 MET cc_start: 0.8443 (tpt) cc_final: 0.8212 (tpp) REVERT: A 243 SER cc_start: 0.8510 (OUTLIER) cc_final: 0.8119 (t) REVERT: B 543 ASN cc_start: 0.8622 (t0) cc_final: 0.8137 (t0) REVERT: J 24 GLN cc_start: 0.8342 (tp40) cc_final: 0.8054 (tp40) REVERT: G 38 ARG cc_start: 0.8388 (ptt180) cc_final: 0.8087 (ptt180) REVERT: G 39 GLN cc_start: 0.8338 (tt0) cc_final: 0.7917 (tt0) REVERT: G 86 ASP cc_start: 0.8342 (m-30) cc_final: 0.8112 (m-30) REVERT: E 543 ASN cc_start: 0.8251 (t0) cc_final: 0.7935 (t0) REVERT: K 4 MET cc_start: 0.6952 (OUTLIER) cc_final: 0.6719 (mtp) REVERT: I 4 LEU cc_start: 0.8718 (mm) cc_final: 0.8508 (mm) REVERT: I 82 LEU cc_start: 0.9014 (mt) cc_final: 0.8613 (mp) REVERT: D 99 ASN cc_start: 0.8347 (p0) cc_final: 0.8106 (t0) REVERT: D 180 ASP cc_start: 0.8011 (m-30) cc_final: 0.7768 (m-30) REVERT: D 243 SER cc_start: 0.8534 (OUTLIER) cc_final: 0.8257 (t) REVERT: D 434 MET cc_start: 0.7858 (OUTLIER) cc_final: 0.7617 (ttp) REVERT: F 543 ASN cc_start: 0.8640 (t0) cc_final: 0.8127 (t0) REVERT: F 601 LYS cc_start: 0.8378 (OUTLIER) cc_final: 0.7975 (ptmt) REVERT: F 659 ASP cc_start: 0.8704 (m-30) cc_final: 0.8426 (m-30) outliers start: 50 outliers final: 24 residues processed: 385 average time/residue: 0.1339 time to fit residues: 81.4217 Evaluate side-chains 294 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 263 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 79 GLU Chi-restraints excluded: chain L residue 94 LEU Chi-restraints excluded: chain L residue 107 LYS Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain J residue 7 THR Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 79 GLU Chi-restraints excluded: chain G residue 55 ASP Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 195 ASN Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain E residue 612 SER Chi-restraints excluded: chain K residue 4 MET Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain D residue 434 MET Chi-restraints excluded: chain F residue 601 LYS Chi-restraints excluded: chain F residue 612 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: [158, 72, 155, 62, 169, 121, 179, 232, 154, 40, 56] chunk 158 optimal weight: 8.9990 chunk 72 optimal weight: 5.9990 chunk 155 optimal weight: 10.0000 chunk 62 optimal weight: 8.9990 chunk 169 optimal weight: 2.9990 chunk 121 optimal weight: 0.1980 chunk 179 optimal weight: 5.9990 chunk 232 optimal weight: 10.0000 chunk 154 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 chunk 56 optimal weight: 5.9990 overall best weight: 3.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 38 GLN L 91 ASN A 105 HIS A 352 HIS B 625 ASN B 653 GLN ** G 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 HIS ** C 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 ASN C 352 HIS C 478 ASN K 42 GLN I 39 GLN D 105 HIS ** D 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 195 ASN ** D 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 478 ASN F 625 ASN F 653 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.082983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.062586 restraints weight = 58950.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.065054 restraints weight = 30407.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.066608 restraints weight = 20740.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.067605 restraints weight = 16525.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.068199 restraints weight = 14333.933| |-----------------------------------------------------------------------------| r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.3859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.100 20004 Z= 0.286 Angle : 0.799 8.528 27309 Z= 0.414 Chirality : 0.050 0.249 3243 Planarity : 0.005 0.051 3339 Dihedral : 5.607 27.495 2529 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.52 % Allowed : 5.41 % Favored : 94.07 % Rotamer: Outliers : 3.31 % Allowed : 11.73 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.17), residues: 2310 helix: 0.67 (0.26), residues: 417 sheet: -0.00 (0.18), residues: 726 loop : -0.90 (0.17), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 429 TYR 0.021 0.002 TYR E 586 PHE 0.022 0.003 PHE G 98 TRP 0.023 0.002 TRP C 96 HIS 0.007 0.002 HIS C 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00664 / 0.29 (19890) covalent geometry : angle 0.77596 / 0.41 (27009) SS BOND : bond 0.00587 / 0.30 ( 42) SS BOND : angle 1.22313 / 0.80 ( 84) hydrogen bonds : bond 0.05597 / 3.72 ( 741) hydrogen bonds : angle 5.76410 / 4.00 ( 1989) link_BETA1-4 : bond 0.00485 / 0.37 ( 24) link_BETA1-4 : angle 1.77437 / 1.19 ( 72) link_NAG-ASN : bond 0.00620 / 0.41 ( 48) link_NAG-ASN : angle 2.37414 / 1.57 ( 144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 275 time to evaluate : 0.815 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: L 107 LYS cc_start: 0.8701 (OUTLIER) cc_final: 0.7488 (tptt) REVERT: H 53 ASP cc_start: 0.9067 (OUTLIER) cc_final: 0.8744 (t0) REVERT: H 80 ARG cc_start: 0.7933 (tpp80) cc_final: 0.7563 (tpp80) REVERT: A 150 MET cc_start: 0.8651 (tpt) cc_final: 0.8317 (tpp) REVERT: A 234 ASN cc_start: 0.7250 (OUTLIER) cc_final: 0.6868 (t0) REVERT: A 243 SER cc_start: 0.8474 (OUTLIER) cc_final: 0.8102 (t) REVERT: A 271 MET cc_start: 0.8029 (tpp) cc_final: 0.7378 (tpp) REVERT: B 543 ASN cc_start: 0.8931 (t0) cc_final: 0.8255 (t0) REVERT: B 624 ASP cc_start: 0.8225 (t0) cc_final: 0.7569 (p0) REVERT: J 22 LYS cc_start: 0.8715 (tppt) cc_final: 0.8411 (tptt) REVERT: J 77 ASP cc_start: 0.9019 (t0) cc_final: 0.8540 (t0) REVERT: J 78 LEU cc_start: 0.8934 (tp) cc_final: 0.8687 (tt) REVERT: G 4 LEU cc_start: 0.8642 (mm) cc_final: 0.8169 (mm) REVERT: G 80 ARG cc_start: 0.8017 (tpp80) cc_final: 0.7699 (tpp80) REVERT: C 234 ASN cc_start: 0.7122 (OUTLIER) cc_final: 0.6888 (t0) REVERT: E 530 MET cc_start: 0.8354 (mtp) cc_final: 0.8149 (mtp) REVERT: E 543 ASN cc_start: 0.8613 (t0) cc_final: 0.8144 (t0) REVERT: K 38 GLN cc_start: 0.9124 (OUTLIER) cc_final: 0.8436 (tt0) REVERT: I 4 LEU cc_start: 0.8701 (mm) cc_final: 0.8454 (mm) REVERT: I 39 GLN cc_start: 0.9013 (tt0) cc_final: 0.8259 (tt0) REVERT: D 234 ASN cc_start: 0.7142 (OUTLIER) cc_final: 0.6772 (t0) REVERT: F 543 ASN cc_start: 0.8957 (t0) cc_final: 0.8342 (t0) REVERT: F 624 ASP cc_start: 0.8470 (t0) cc_final: 0.7681 (p0) REVERT: F 626 MET cc_start: 0.7200 (mmt) cc_final: 0.6814 (tpp) outliers start: 68 outliers final: 36 residues processed: 309 average time/residue: 0.1306 time to fit residues: 63.9131 Evaluate side-chains 285 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 242 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 79 GLU Chi-restraints excluded: chain L residue 107 LYS Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 34 TYR Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain J residue 7 THR Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 79 GLU Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain G residue 34 TYR Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain C residue 475 MET Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 38 GLN Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 34 TYR Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain D residue 234 ASN Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain D residue 434 MET Chi-restraints excluded: chain D residue 475 MET Chi-restraints excluded: chain F residue 538 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: [71, 92, 173, 160, 11, 74, 178, 177, 195, 141, 22] chunk 71 optimal weight: 0.6980 chunk 92 optimal weight: 4.9990 chunk 173 optimal weight: 7.9990 chunk 160 optimal weight: 9.9990 chunk 11 optimal weight: 5.9990 chunk 74 optimal weight: 10.0000 chunk 178 optimal weight: 6.9990 chunk 177 optimal weight: 2.9990 chunk 195 optimal weight: 6.9990 chunk 141 optimal weight: 4.9990 chunk 22 optimal weight: 0.6980 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 39 GLN ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 195 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.083064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.062626 restraints weight = 59067.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.065148 restraints weight = 29818.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.066762 restraints weight = 20178.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.067759 restraints weight = 15927.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.068367 restraints weight = 13816.878| |-----------------------------------------------------------------------------| r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.4258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 20004 Z= 0.219 Angle : 0.718 9.816 27309 Z= 0.368 Chirality : 0.047 0.269 3243 Planarity : 0.005 0.052 3339 Dihedral : 5.512 31.417 2529 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.52 % Allowed : 5.28 % Favored : 94.20 % Rotamer: Outliers : 3.45 % Allowed : 12.55 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.17), residues: 2310 helix: 0.76 (0.26), residues: 417 sheet: -0.01 (0.19), residues: 705 loop : -1.03 (0.17), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG J 61 TYR 0.021 0.002 TYR E 586 PHE 0.020 0.002 PHE G 98 TRP 0.018 0.002 TRP E 628 HIS 0.005 0.001 HIS D 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00507 / 0.22 (19890) covalent geometry : angle 0.69909 / 0.36 (27009) SS BOND : bond 0.00483 / 0.27 ( 42) SS BOND : angle 1.14697 / 0.78 ( 84) hydrogen bonds : bond 0.05032 / 3.33 ( 741) hydrogen bonds : angle 5.53622 / 3.85 ( 1989) link_BETA1-4 : bond 0.00414 / 0.31 ( 24) link_BETA1-4 : angle 1.42927 / 0.96 ( 72) link_NAG-ASN : bond 0.00438 / 0.31 ( 48) link_NAG-ASN : angle 2.09083 / 1.38 ( 144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 259 time to evaluate : 0.715 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: L 38 GLN cc_start: 0.9104 (OUTLIER) cc_final: 0.8849 (tp40) REVERT: H 53 ASP cc_start: 0.9097 (OUTLIER) cc_final: 0.8795 (t0) REVERT: H 80 ARG cc_start: 0.7971 (tpp80) cc_final: 0.7617 (tpp80) REVERT: A 150 MET cc_start: 0.8525 (tpt) cc_final: 0.8275 (tpp) REVERT: A 234 ASN cc_start: 0.7253 (OUTLIER) cc_final: 0.6882 (t0) REVERT: A 243 SER cc_start: 0.8467 (OUTLIER) cc_final: 0.8038 (t) REVERT: A 271 MET cc_start: 0.8060 (tpp) cc_final: 0.7371 (tpp) REVERT: B 543 ASN cc_start: 0.8988 (t0) cc_final: 0.8290 (t0) REVERT: B 624 ASP cc_start: 0.8035 (t0) cc_final: 0.7496 (p0) REVERT: J 4 MET cc_start: 0.7017 (mtp) cc_final: 0.6589 (mtm) REVERT: J 94 LEU cc_start: 0.9145 (mm) cc_final: 0.8716 (mt) REVERT: G 4 LEU cc_start: 0.8659 (mm) cc_final: 0.8258 (mm) REVERT: G 39 GLN cc_start: 0.8591 (tt0) cc_final: 0.7911 (tt0) REVERT: G 80 ARG cc_start: 0.8083 (tpp80) cc_final: 0.7827 (tpp80) REVERT: G 82 LEU cc_start: 0.8514 (mm) cc_final: 0.8113 (tt) REVERT: E 543 ASN cc_start: 0.8787 (t0) cc_final: 0.8189 (t0) REVERT: K 38 GLN cc_start: 0.9107 (OUTLIER) cc_final: 0.8382 (tt0) REVERT: I 4 LEU cc_start: 0.8785 (mm) cc_final: 0.8581 (mm) REVERT: I 39 GLN cc_start: 0.8856 (tt0) cc_final: 0.8094 (tt0) REVERT: I 80 ARG cc_start: 0.8126 (tpp80) cc_final: 0.7874 (tpp80) REVERT: D 234 ASN cc_start: 0.7326 (OUTLIER) cc_final: 0.6954 (t0) REVERT: D 271 MET cc_start: 0.7882 (mmm) cc_final: 0.6979 (tpp) REVERT: F 530 MET cc_start: 0.8099 (mtp) cc_final: 0.7882 (mmm) REVERT: F 543 ASN cc_start: 0.9064 (t0) cc_final: 0.8416 (t0) REVERT: F 624 ASP cc_start: 0.8368 (t0) cc_final: 0.7713 (p0) outliers start: 71 outliers final: 49 residues processed: 298 average time/residue: 0.1279 time to fit residues: 60.8919 Evaluate side-chains 294 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 239 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 79 GLU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 34 TYR Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain J residue 7 THR Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 79 GLU Chi-restraints excluded: chain J residue 88 CYS Chi-restraints excluded: chain J residue 106 VAL Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 34 TYR Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 475 MET Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 612 SER Chi-restraints excluded: chain E residue 616 ASN Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 38 GLN Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 34 TYR Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 234 ASN Chi-restraints excluded: chain D residue 322 ASP Chi-restraints excluded: chain D residue 378 CYS Chi-restraints excluded: chain D residue 434 MET Chi-restraints excluded: chain D residue 475 MET Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 616 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: [156, 48, 170, 202, 96, 92, 159, 205, 219, 8, 31] chunk 156 optimal weight: 8.9990 chunk 48 optimal weight: 3.9990 chunk 170 optimal weight: 3.9990 chunk 202 optimal weight: 9.9990 chunk 96 optimal weight: 7.9990 chunk 92 optimal weight: 5.9990 chunk 159 optimal weight: 5.9990 chunk 205 optimal weight: 3.9990 chunk 219 optimal weight: 4.9990 chunk 8 optimal weight: 9.9990 chunk 31 optimal weight: 0.0870 overall best weight: 3.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 195 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.082673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.063298 restraints weight = 58463.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.065560 restraints weight = 31320.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.067003 restraints weight = 21851.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.067885 restraints weight = 17587.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.068407 restraints weight = 15419.480| |-----------------------------------------------------------------------------| r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.4528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 20004 Z= 0.251 Angle : 0.731 11.960 27309 Z= 0.372 Chirality : 0.047 0.299 3243 Planarity : 0.005 0.054 3339 Dihedral : 5.495 31.358 2529 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.43 % Allowed : 5.71 % Favored : 93.85 % Rotamer: Outliers : 4.04 % Allowed : 12.90 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.17), residues: 2310 helix: 1.04 (0.27), residues: 396 sheet: -0.12 (0.19), residues: 690 loop : -1.21 (0.17), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG G 38 TYR 0.020 0.002 TYR E 586 PHE 0.019 0.002 PHE G 98 TRP 0.016 0.002 TRP E 628 HIS 0.005 0.001 HIS C 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00584 / 0.25 (19890) covalent geometry : angle 0.71133 / 0.37 (27009) SS BOND : bond 0.00417 / 0.24 ( 42) SS BOND : angle 1.17111 / 0.80 ( 84) hydrogen bonds : bond 0.05038 / 3.33 ( 741) hydrogen bonds : angle 5.49194 / 3.82 ( 1989) link_BETA1-4 : bond 0.00364 / 0.27 ( 24) link_BETA1-4 : angle 1.42325 / 0.97 ( 72) link_NAG-ASN : bond 0.00503 / 0.34 ( 48) link_NAG-ASN : angle 2.17863 / 1.45 ( 144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 254 time to evaluate : 0.674 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: L 77 ASP cc_start: 0.8677 (t0) cc_final: 0.8235 (t0) REVERT: H 53 ASP cc_start: 0.8927 (OUTLIER) cc_final: 0.8639 (t0) REVERT: A 234 ASN cc_start: 0.7773 (OUTLIER) cc_final: 0.7442 (t0) REVERT: A 243 SER cc_start: 0.8662 (OUTLIER) cc_final: 0.8298 (t) REVERT: A 271 MET cc_start: 0.8016 (tpp) cc_final: 0.7439 (tpp) REVERT: B 543 ASN cc_start: 0.8603 (t0) cc_final: 0.8021 (t0) REVERT: J 42 GLN cc_start: 0.8327 (mp-120) cc_final: 0.7948 (mp10) REVERT: J 103 GLU cc_start: 0.8275 (tp30) cc_final: 0.8034 (tp30) REVERT: G 39 GLN cc_start: 0.8519 (tt0) cc_final: 0.7995 (tt0) REVERT: G 82 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8335 (tt) REVERT: C 150 MET cc_start: 0.8542 (tpp) cc_final: 0.8261 (tpp) REVERT: E 543 ASN cc_start: 0.8551 (t0) cc_final: 0.8059 (t0) REVERT: E 624 ASP cc_start: 0.8061 (t0) cc_final: 0.7626 (p0) REVERT: K 38 GLN cc_start: 0.8900 (OUTLIER) cc_final: 0.8065 (tt0) REVERT: K 77 ASP cc_start: 0.8787 (t0) cc_final: 0.8513 (t0) REVERT: I 39 GLN cc_start: 0.8852 (tt0) cc_final: 0.8257 (tt0) REVERT: I 53 ASP cc_start: 0.8818 (m-30) cc_final: 0.8563 (t0) REVERT: D 234 ASN cc_start: 0.7728 (OUTLIER) cc_final: 0.7386 (t0) REVERT: D 243 SER cc_start: 0.8652 (OUTLIER) cc_final: 0.8249 (t) REVERT: F 543 ASN cc_start: 0.8760 (t0) cc_final: 0.8284 (t0) REVERT: F 624 ASP cc_start: 0.7922 (t0) cc_final: 0.7655 (p0) outliers start: 83 outliers final: 52 residues processed: 309 average time/residue: 0.1254 time to fit residues: 61.7723 Evaluate side-chains 296 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 237 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 34 TYR Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain J residue 7 THR Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 79 GLU Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 34 TYR Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 475 MET Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 612 SER Chi-restraints excluded: chain E residue 616 ASN Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 38 GLN Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain K residue 98 PHE Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 34 TYR Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 95 THR Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 234 ASN Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain D residue 320 THR Chi-restraints excluded: chain D residue 322 ASP Chi-restraints excluded: chain D residue 378 CYS Chi-restraints excluded: chain D residue 475 MET Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 616 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: [165, 18, 211, 168, 127, 27, 217, 193, 3, 107, 197] chunk 165 optimal weight: 4.9990 chunk 18 optimal weight: 10.0000 chunk 211 optimal weight: 5.9990 chunk 168 optimal weight: 10.0000 chunk 127 optimal weight: 3.9990 chunk 27 optimal weight: 7.9990 chunk 217 optimal weight: 5.9990 chunk 193 optimal weight: 0.7980 chunk 3 optimal weight: 6.9990 chunk 107 optimal weight: 8.9990 chunk 197 optimal weight: 0.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 ASN ** G 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 ASN ** D 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 136 ASN ** 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 = 0.3455 r_free = 0.3455 target = 0.082236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.062923 restraints weight = 58275.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.065155 restraints weight = 31590.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.066571 restraints weight = 22098.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.067429 restraints weight = 17822.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.067992 restraints weight = 15639.329| |-----------------------------------------------------------------------------| r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.4818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 20004 Z= 0.247 Angle : 0.741 9.519 27309 Z= 0.377 Chirality : 0.047 0.299 3243 Planarity : 0.005 0.056 3339 Dihedral : 5.573 29.360 2529 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.39 % Allowed : 6.41 % Favored : 93.20 % Rotamer: Outliers : 4.18 % Allowed : 13.04 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.17), residues: 2310 helix: 0.94 (0.27), residues: 399 sheet: -0.31 (0.19), residues: 711 loop : -1.33 (0.17), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 166 TYR 0.016 0.002 TYR E 586 PHE 0.020 0.002 PHE G 98 TRP 0.016 0.002 TRP E 628 HIS 0.005 0.001 HIS A 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00572 / 0.25 (19890) covalent geometry : angle 0.72167 / 0.37 (27009) SS BOND : bond 0.00427 / 0.26 ( 42) SS BOND : angle 1.31060 / 0.85 ( 84) hydrogen bonds : bond 0.04943 / 3.26 ( 741) hydrogen bonds : angle 5.48618 / 3.81 ( 1989) link_BETA1-4 : bond 0.00361 / 0.27 ( 24) link_BETA1-4 : angle 1.35152 / 0.91 ( 72) link_NAG-ASN : bond 0.00506 / 0.34 ( 48) link_NAG-ASN : angle 2.15138 / 1.43 ( 144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 244 time to evaluate : 0.781 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: H 53 ASP cc_start: 0.8931 (OUTLIER) cc_final: 0.8660 (t0) REVERT: A 234 ASN cc_start: 0.7789 (OUTLIER) cc_final: 0.7501 (t0) REVERT: A 243 SER cc_start: 0.8630 (OUTLIER) cc_final: 0.8247 (t) REVERT: A 271 MET cc_start: 0.7868 (tpp) cc_final: 0.7334 (tpp) REVERT: B 543 ASN cc_start: 0.8625 (t0) cc_final: 0.8054 (t0) REVERT: J 38 GLN cc_start: 0.8701 (OUTLIER) cc_final: 0.8077 (tt0) REVERT: J 42 GLN cc_start: 0.8415 (mp-120) cc_final: 0.8172 (mp10) REVERT: J 103 GLU cc_start: 0.8305 (tp30) cc_final: 0.8016 (tp30) REVERT: G 82 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8339 (tt) REVERT: E 540 GLN cc_start: 0.7474 (OUTLIER) cc_final: 0.7062 (mp10) REVERT: E 543 ASN cc_start: 0.8591 (t0) cc_final: 0.8204 (t0) REVERT: E 624 ASP cc_start: 0.7847 (t0) cc_final: 0.7561 (p0) REVERT: K 38 GLN cc_start: 0.8890 (OUTLIER) cc_final: 0.8156 (tt0) REVERT: I 53 ASP cc_start: 0.8810 (m-30) cc_final: 0.8569 (t0) REVERT: D 234 ASN cc_start: 0.7820 (OUTLIER) cc_final: 0.7524 (t0) REVERT: D 243 SER cc_start: 0.8649 (OUTLIER) cc_final: 0.8258 (t) REVERT: D 271 MET cc_start: 0.7212 (tpt) cc_final: 0.6764 (tpp) REVERT: F 543 ASN cc_start: 0.8805 (t0) cc_final: 0.8304 (t0) outliers start: 86 outliers final: 59 residues processed: 303 average time/residue: 0.1259 time to fit residues: 61.3730 Evaluate side-chains 296 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 228 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 79 GLU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 34 TYR Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 428 GLN Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain J residue 7 THR Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 38 GLN Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 79 GLU Chi-restraints excluded: chain J residue 94 LEU Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 34 TYR Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 195 ASN Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 475 MET Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 540 GLN Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 612 SER Chi-restraints excluded: chain E residue 616 ASN Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 38 GLN Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain K residue 98 PHE Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 34 TYR Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 95 THR Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 234 ASN Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain D residue 320 THR Chi-restraints excluded: chain D residue 322 ASP Chi-restraints excluded: chain D residue 378 CYS Chi-restraints excluded: chain D residue 428 GLN Chi-restraints excluded: chain D residue 475 MET Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 616 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: [41, 119, 48, 1, 99, 42, 71, 196, 26, 106, 163] chunk 41 optimal weight: 6.9990 chunk 119 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 1 optimal weight: 0.0980 chunk 99 optimal weight: 6.9990 chunk 42 optimal weight: 7.9990 chunk 71 optimal weight: 3.9990 chunk 196 optimal weight: 6.9990 chunk 26 optimal weight: 7.9990 chunk 106 optimal weight: 1.9990 chunk 163 optimal weight: 9.9990 overall best weight: 2.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 GLN ** C 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 ASN ** D 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 136 ASN ** 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 = 0.3475 r_free = 0.3475 target = 0.083185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.063940 restraints weight = 58559.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.066229 restraints weight = 31318.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.067676 restraints weight = 21748.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.068591 restraints weight = 17455.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.069168 restraints weight = 15205.881| |-----------------------------------------------------------------------------| r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.4968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 20004 Z= 0.173 Angle : 0.700 11.956 27309 Z= 0.353 Chirality : 0.046 0.285 3243 Planarity : 0.004 0.054 3339 Dihedral : 5.386 29.522 2529 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.43 % Allowed : 5.71 % Favored : 93.85 % Rotamer: Outliers : 3.31 % Allowed : 14.50 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.17), residues: 2310 helix: 0.96 (0.26), residues: 408 sheet: -0.26 (0.19), residues: 696 loop : -1.35 (0.17), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 80 TYR 0.015 0.001 TYR H 100C PHE 0.018 0.002 PHE G 98 TRP 0.018 0.001 TRP B 631 HIS 0.003 0.001 HIS A 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.17 (19890) covalent geometry : angle 0.68192 / 0.35 (27009) SS BOND : bond 0.00510 / 0.33 ( 42) SS BOND : angle 1.30786 / 0.89 ( 84) hydrogen bonds : bond 0.04553 / 3.00 ( 741) hydrogen bonds : angle 5.35227 / 3.73 ( 1989) link_BETA1-4 : bond 0.00380 / 0.27 ( 24) link_BETA1-4 : angle 1.24301 / 0.85 ( 72) link_NAG-ASN : bond 0.00389 / 0.27 ( 48) link_NAG-ASN : angle 1.96052 / 1.30 ( 144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 248 time to evaluate : 0.613 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: H 31 ARG cc_start: 0.8140 (ptm-80) cc_final: 0.7868 (ptm-80) REVERT: H 53 ASP cc_start: 0.8892 (OUTLIER) cc_final: 0.8668 (t0) REVERT: A 234 ASN cc_start: 0.7824 (OUTLIER) cc_final: 0.7562 (t0) REVERT: A 243 SER cc_start: 0.8639 (OUTLIER) cc_final: 0.8233 (t) REVERT: A 271 MET cc_start: 0.7818 (tpp) cc_final: 0.7341 (tpp) REVERT: B 543 ASN cc_start: 0.8605 (t0) cc_final: 0.8136 (t0) REVERT: J 103 GLU cc_start: 0.8298 (tp30) cc_final: 0.8001 (tp30) REVERT: G 82 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8304 (tt) REVERT: E 543 ASN cc_start: 0.8580 (t0) cc_final: 0.8196 (t0) REVERT: K 38 GLN cc_start: 0.8766 (OUTLIER) cc_final: 0.8347 (tp40) REVERT: I 53 ASP cc_start: 0.8791 (m-30) cc_final: 0.8557 (t0) REVERT: D 234 ASN cc_start: 0.7848 (OUTLIER) cc_final: 0.7558 (t0) REVERT: D 243 SER cc_start: 0.8651 (OUTLIER) cc_final: 0.8226 (t) REVERT: D 271 MET cc_start: 0.7213 (tpt) cc_final: 0.6686 (tpp) REVERT: F 543 ASN cc_start: 0.8766 (t0) cc_final: 0.8286 (t0) outliers start: 68 outliers final: 48 residues processed: 295 average time/residue: 0.1258 time to fit residues: 59.4928 Evaluate side-chains 286 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 231 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain H residue 34 TYR Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain J residue 7 THR Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 34 TYR Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 428 GLN Chi-restraints excluded: chain C residue 475 MET Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 612 SER Chi-restraints excluded: chain E residue 616 ASN Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 38 GLN Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain K residue 98 PHE Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 34 TYR Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 95 THR Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 234 ASN Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain D residue 320 THR Chi-restraints excluded: chain D residue 322 ASP Chi-restraints excluded: chain D residue 378 CYS Chi-restraints excluded: chain D residue 475 MET Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain F residue 619 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: [53, 213, 164, 198, 5, 25, 4, 21, 52, 172, 77] chunk 53 optimal weight: 9.9990 chunk 213 optimal weight: 6.9990 chunk 164 optimal weight: 7.9990 chunk 198 optimal weight: 0.1980 chunk 5 optimal weight: 1.9990 chunk 25 optimal weight: 8.9990 chunk 4 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 52 optimal weight: 0.9980 chunk 172 optimal weight: 0.1980 chunk 77 optimal weight: 5.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 103 GLN ** C 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 103 GLN ** D 136 ASN ** 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 = 0.3512 r_free = 0.3512 target = 0.085098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.065814 restraints weight = 57806.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.068195 restraints weight = 29857.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.069734 restraints weight = 20364.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.070641 restraints weight = 16099.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.071257 restraints weight = 14029.694| |-----------------------------------------------------------------------------| r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.5137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20004 Z= 0.129 Angle : 0.666 9.770 27309 Z= 0.339 Chirality : 0.045 0.268 3243 Planarity : 0.005 0.058 3339 Dihedral : 5.221 34.077 2529 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.39 % Allowed : 6.06 % Favored : 93.55 % Rotamer: Outliers : 2.73 % Allowed : 15.52 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.17), residues: 2310 helix: 0.95 (0.26), residues: 426 sheet: -0.10 (0.20), residues: 666 loop : -1.40 (0.17), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 166 TYR 0.018 0.001 TYR G 100C PHE 0.016 0.001 PHE G 98 TRP 0.023 0.001 TRP F 631 HIS 0.002 0.001 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (19890) covalent geometry : angle 0.65200 / 0.34 (27009) SS BOND : bond 0.00349 / 0.18 ( 42) SS BOND : angle 1.10794 / 0.76 ( 84) hydrogen bonds : bond 0.04159 / 2.74 ( 741) hydrogen bonds : angle 5.18801 / 3.61 ( 1989) link_BETA1-4 : bond 0.00455 / 0.32 ( 24) link_BETA1-4 : angle 1.16125 / 0.80 ( 72) link_NAG-ASN : bond 0.00334 / 0.25 ( 48) link_NAG-ASN : angle 1.76570 / 1.16 ( 144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 264 time to evaluate : 0.788 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: H 31 ARG cc_start: 0.8155 (ptm-80) cc_final: 0.7928 (ptm-80) REVERT: H 53 ASP cc_start: 0.8858 (m-30) cc_final: 0.8635 (t0) REVERT: A 234 ASN cc_start: 0.7806 (OUTLIER) cc_final: 0.7566 (t0) REVERT: A 271 MET cc_start: 0.7708 (tpp) cc_final: 0.7156 (tpp) REVERT: B 543 ASN cc_start: 0.8587 (t0) cc_final: 0.8174 (t0) REVERT: B 657 GLU cc_start: 0.8677 (mm-30) cc_final: 0.8454 (mm-30) REVERT: J 103 GLU cc_start: 0.8270 (tp30) cc_final: 0.8003 (tp30) REVERT: G 82 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8286 (tt) REVERT: C 150 MET cc_start: 0.8079 (tpp) cc_final: 0.7653 (tpp) REVERT: E 543 ASN cc_start: 0.8575 (t0) cc_final: 0.8216 (t0) REVERT: K 38 GLN cc_start: 0.8405 (OUTLIER) cc_final: 0.8119 (tp40) REVERT: I 53 ASP cc_start: 0.8732 (m-30) cc_final: 0.8492 (t0) REVERT: D 234 ASN cc_start: 0.7953 (OUTLIER) cc_final: 0.7672 (t0) REVERT: D 271 MET cc_start: 0.7277 (tpt) cc_final: 0.6743 (tpp) REVERT: F 543 ASN cc_start: 0.8670 (t0) cc_final: 0.8257 (t0) outliers start: 56 outliers final: 38 residues processed: 300 average time/residue: 0.1253 time to fit residues: 60.2810 Evaluate side-chains 279 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 237 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 34 TYR Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain J residue 7 THR Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 34 TYR Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 428 GLN Chi-restraints excluded: chain C residue 475 MET Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 612 SER Chi-restraints excluded: chain E residue 616 ASN Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 38 GLN Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 34 TYR Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 95 THR Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 234 ASN Chi-restraints excluded: chain D residue 320 THR Chi-restraints excluded: chain D residue 322 ASP Chi-restraints excluded: chain D residue 378 CYS Chi-restraints excluded: chain D residue 428 GLN Chi-restraints excluded: chain D residue 475 MET Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain F residue 619 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: [207, 114, 124, 21, 72, 84, 147, 52, 113, 220, 77] chunk 207 optimal weight: 7.9990 chunk 114 optimal weight: 5.9990 chunk 124 optimal weight: 8.9990 chunk 21 optimal weight: 5.9990 chunk 72 optimal weight: 7.9990 chunk 84 optimal weight: 10.0000 chunk 147 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 113 optimal weight: 0.6980 chunk 220 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 ASN E 625 ASN ** D 136 ASN ** 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 = 0.3465 r_free = 0.3465 target = 0.082602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.063362 restraints weight = 57910.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.065607 restraints weight = 30989.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.067032 restraints weight = 21443.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.067949 restraints weight = 17212.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.068518 restraints weight = 14994.483| |-----------------------------------------------------------------------------| r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.5235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 20004 Z= 0.237 Angle : 0.731 12.333 27309 Z= 0.372 Chirality : 0.047 0.281 3243 Planarity : 0.005 0.057 3339 Dihedral : 5.392 42.838 2529 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.43 % Allowed : 6.93 % Favored : 92.64 % Rotamer: Outliers : 2.77 % Allowed : 16.16 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.17), residues: 2310 helix: 1.17 (0.26), residues: 405 sheet: -0.25 (0.19), residues: 711 loop : -1.42 (0.17), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 166 TYR 0.018 0.002 TYR L 49 PHE 0.018 0.002 PHE G 98 TRP 0.040 0.002 TRP E 631 HIS 0.003 0.001 HIS C 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00552 / 0.24 (19890) covalent geometry : angle 0.71432 / 0.37 (27009) SS BOND : bond 0.00362 / 0.21 ( 42) SS BOND : angle 1.24137 / 0.83 ( 84) hydrogen bonds : bond 0.04633 / 3.04 ( 741) hydrogen bonds : angle 5.27575 / 3.68 ( 1989) link_BETA1-4 : bond 0.00326 / 0.25 ( 24) link_BETA1-4 : angle 1.31674 / 0.89 ( 72) link_NAG-ASN : bond 0.00463 / 0.31 ( 48) link_NAG-ASN : angle 1.98771 / 1.32 ( 144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 235 time to evaluate : 0.622 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: H 31 ARG cc_start: 0.8182 (ptm-80) cc_final: 0.7934 (ptm-80) REVERT: A 271 MET cc_start: 0.7765 (tpp) cc_final: 0.7288 (tpp) REVERT: B 543 ASN cc_start: 0.8560 (t0) cc_final: 0.8147 (t0) REVERT: B 657 GLU cc_start: 0.8677 (mm-30) cc_final: 0.8460 (mm-30) REVERT: J 103 GLU cc_start: 0.8238 (tp30) cc_final: 0.7936 (tp30) REVERT: C 150 MET cc_start: 0.8217 (tpp) cc_final: 0.7812 (tpp) REVERT: C 271 MET cc_start: 0.7824 (tpp) cc_final: 0.7484 (tpp) REVERT: E 543 ASN cc_start: 0.8584 (t0) cc_final: 0.8234 (t0) REVERT: K 38 GLN cc_start: 0.8552 (OUTLIER) cc_final: 0.8179 (tp40) REVERT: D 271 MET cc_start: 0.7148 (tpt) cc_final: 0.6740 (tpp) REVERT: F 543 ASN cc_start: 0.8665 (t0) cc_final: 0.8233 (t0) outliers start: 57 outliers final: 42 residues processed: 274 average time/residue: 0.1239 time to fit residues: 55.1376 Evaluate side-chains 270 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 227 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 34 TYR Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 428 GLN Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain J residue 7 THR Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain G residue 34 TYR Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 195 ASN Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 428 GLN Chi-restraints excluded: chain C residue 475 MET Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 612 SER Chi-restraints excluded: chain E residue 616 ASN Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 38 GLN Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain K residue 98 PHE Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 34 TYR Chi-restraints excluded: chain I residue 95 THR Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 320 THR Chi-restraints excluded: chain D residue 322 ASP Chi-restraints excluded: chain D residue 378 CYS Chi-restraints excluded: chain D residue 428 GLN Chi-restraints excluded: chain D residue 475 MET Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain F residue 619 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: [225, 104, 42, 96, 39, 163, 224, 47, 12, 43, 143] chunk 225 optimal weight: 6.9990 chunk 104 optimal weight: 4.9990 chunk 42 optimal weight: 0.8980 chunk 96 optimal weight: 7.9990 chunk 39 optimal weight: 1.9990 chunk 163 optimal weight: 7.9990 chunk 224 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 chunk 12 optimal weight: 6.9990 chunk 43 optimal weight: 0.8980 chunk 143 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 195 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.084781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.065508 restraints weight = 58019.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.067900 restraints weight = 29859.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.069427 restraints weight = 20297.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.070341 restraints weight = 16084.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.070961 restraints weight = 13995.021| |-----------------------------------------------------------------------------| r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.5332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20004 Z= 0.137 Angle : 0.695 13.174 27309 Z= 0.351 Chirality : 0.046 0.259 3243 Planarity : 0.004 0.057 3339 Dihedral : 5.302 41.720 2529 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.43 % Allowed : 6.06 % Favored : 93.51 % Rotamer: Outliers : 2.14 % Allowed : 16.74 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.17), residues: 2310 helix: 1.33 (0.26), residues: 405 sheet: -0.14 (0.19), residues: 711 loop : -1.43 (0.17), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 166 TYR 0.017 0.001 TYR H 100C PHE 0.017 0.001 PHE G 98 TRP 0.044 0.001 TRP E 631 HIS 0.003 0.001 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 (19890) covalent geometry : angle 0.67821 / 0.35 (27009) SS BOND : bond 0.00371 / 0.20 ( 42) SS BOND : angle 1.17788 / 0.87 ( 84) hydrogen bonds : bond 0.04276 / 2.80 ( 741) hydrogen bonds : angle 5.15005 / 3.59 ( 1989) link_BETA1-4 : bond 0.00423 / 0.29 ( 24) link_BETA1-4 : angle 1.14507 / 0.79 ( 72) link_NAG-ASN : bond 0.00341 / 0.24 ( 48) link_NAG-ASN : angle 1.95617 / 1.32 ( 144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 243 time to evaluate : 0.720 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 271 MET cc_start: 0.7732 (tpp) cc_final: 0.7210 (tpp) REVERT: B 543 ASN cc_start: 0.8605 (t0) cc_final: 0.8242 (t0) REVERT: B 657 GLU cc_start: 0.8667 (mm-30) cc_final: 0.8421 (mm-30) REVERT: J 103 GLU cc_start: 0.8161 (tp30) cc_final: 0.7942 (tp30) REVERT: C 150 MET cc_start: 0.8121 (tpp) cc_final: 0.7692 (mmm) REVERT: C 271 MET cc_start: 0.7765 (tpp) cc_final: 0.7375 (tpp) REVERT: E 543 ASN cc_start: 0.8555 (t0) cc_final: 0.8180 (t0) REVERT: K 38 GLN cc_start: 0.8383 (OUTLIER) cc_final: 0.8149 (tp40) REVERT: I 5 VAL cc_start: 0.8962 (t) cc_final: 0.8755 (m) REVERT: D 243 SER cc_start: 0.8630 (OUTLIER) cc_final: 0.8284 (t) REVERT: D 271 MET cc_start: 0.7163 (tpt) cc_final: 0.6663 (tpp) REVERT: F 543 ASN cc_start: 0.8681 (t0) cc_final: 0.8277 (t0) outliers start: 44 outliers final: 38 residues processed: 274 average time/residue: 0.1271 time to fit residues: 55.7678 Evaluate side-chains 272 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 232 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 79 GLU Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 34 TYR Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain G residue 34 TYR Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 428 GLN Chi-restraints excluded: chain C residue 475 MET Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 612 SER Chi-restraints excluded: chain E residue 619 LEU Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 38 GLN Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 34 TYR Chi-restraints excluded: chain I residue 95 THR Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain D residue 320 THR Chi-restraints excluded: chain D residue 322 ASP Chi-restraints excluded: chain D residue 378 CYS Chi-restraints excluded: chain D residue 428 GLN Chi-restraints excluded: chain D residue 475 MET Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain F residue 619 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: [52, 64, 1, 83, 228, 213, 182, 35, 202, 7, 124] chunk 52 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 228 optimal weight: 1.9990 chunk 213 optimal weight: 0.9980 chunk 182 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 202 optimal weight: 7.9990 chunk 7 optimal weight: 7.9990 chunk 124 optimal weight: 6.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 ASN ** D 136 ASN ** 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 = 0.3453 r_free = 0.3453 target = 0.082711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.062397 restraints weight = 58543.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.064952 restraints weight = 28473.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.066551 restraints weight = 18808.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.067579 restraints weight = 14720.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.068181 restraints weight = 12636.846| |-----------------------------------------------------------------------------| r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.5410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 20004 Z= 0.173 Angle : 0.702 13.396 27309 Z= 0.355 Chirality : 0.046 0.263 3243 Planarity : 0.004 0.058 3339 Dihedral : 5.288 41.235 2529 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.43 % Allowed : 6.62 % Favored : 92.94 % Rotamer: Outliers : 2.24 % Allowed : 17.03 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.17), residues: 2310 helix: 1.42 (0.26), residues: 405 sheet: -0.17 (0.19), residues: 711 loop : -1.44 (0.17), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 166 TYR 0.017 0.001 TYR H 100C PHE 0.017 0.002 PHE G 98 TRP 0.041 0.001 TRP F 631 HIS 0.002 0.001 HIS C 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.17 (19890) covalent geometry : angle 0.68613 / 0.35 (27009) SS BOND : bond 0.00371 / 0.19 ( 42) SS BOND : angle 1.20874 / 0.90 ( 84) hydrogen bonds : bond 0.04335 / 2.84 ( 741) hydrogen bonds : angle 5.14205 / 3.58 ( 1989) link_BETA1-4 : bond 0.00361 / 0.26 ( 24) link_BETA1-4 : angle 1.19862 / 0.82 ( 72) link_NAG-ASN : bond 0.00341 / 0.24 ( 48) link_NAG-ASN : angle 1.89277 / 1.27 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3497.30 seconds wall clock time: 61 minutes 28.56 seconds (3688.56 seconds total)