Starting phenix.real_space_refine on Thu Sep 18 13:26:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9axk_43968/09_2025/9axk_43968.cif Found real_map, /net/cci-nas-00/data/ceres_data/9axk_43968/09_2025/9axk_43968.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9axk_43968/09_2025/9axk_43968.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9axk_43968/09_2025/9axk_43968.map" model { file = "/net/cci-nas-00/data/ceres_data/9axk_43968/09_2025/9axk_43968.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9axk_43968/09_2025/9axk_43968.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 101 5.16 5 C 10606 2.51 5 N 2929 2.21 5 O 3403 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17039 Number of models: 1 Model: "" Number of chains: 32 Chain: "M" Number of atoms: 3561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3561 Classifications: {'peptide': 447} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 24, 'TRANS': 422} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 3540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3540 Classifications: {'peptide': 443} Link IDs: {'PTRANS': 24, 'TRANS': 418} Chain breaks: 3 Chain: "I" Number of atoms: 3567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3567 Classifications: {'peptide': 447} Link IDs: {'PTRANS': 24, 'TRANS': 422} Chain breaks: 2 Chain: "F" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 545 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 109} Link IDs: {'TRANS': 108} Unresolved non-hydrogen bonds: 218 Unresolved non-hydrogen angles: 327 Unresolved non-hydrogen dihedrals: 109 Planarities with less than four sites: {'UNK:plan-1': 109} Unresolved non-hydrogen planarities: 109 Chain: "H" Number of atoms: 620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 620 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 124} Link IDs: {'TRANS': 123} Unresolved non-hydrogen bonds: 248 Unresolved non-hydrogen angles: 372 Unresolved non-hydrogen dihedrals: 124 Planarities with less than four sites: {'UNK:plan-1': 124} Unresolved non-hydrogen planarities: 124 Chain: "A" Number of atoms: 520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 520 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 104} Link IDs: {'TRANS': 103} Unresolved non-hydrogen bonds: 208 Unresolved non-hydrogen angles: 312 Unresolved non-hydrogen dihedrals: 104 Planarities with less than four sites: {'UNK:plan-1': 104} Unresolved non-hydrogen planarities: 104 Chain: "B" Number of atoms: 560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 560 Classifications: {'peptide': 112} Incomplete info: {'truncation_to_alanine': 112} Link IDs: {'TRANS': 111} Unresolved non-hydrogen bonds: 224 Unresolved non-hydrogen angles: 336 Unresolved non-hydrogen dihedrals: 112 Planarities with less than four sites: {'UNK:plan-1': 112} Unresolved non-hydrogen planarities: 112 Chain: "N" Number of atoms: 1020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1020 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 1, 'TRANS': 125} Chain breaks: 1 Chain: "C" Number of atoms: 1015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1015 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 2, 'TRANS': 123} Chain breaks: 1 Chain: "J" Number of atoms: 1043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1043 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 1, 'TRANS': 129} Chain breaks: 1 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "L" 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" 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 dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "D" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "I" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 4.05, per 1000 atoms: 0.24 Number of scatterers: 17039 At special positions: 0 Unit cell: (126.637, 140.263, 145.072, 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 101 16.00 O 3403 8.00 N 2929 7.00 C 10606 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=28, symmetry=0 Simple disulfide: pdb=" SG CYS M 54 " - pdb=" SG CYS M 73 " distance=2.03 Simple disulfide: pdb=" SG CYS M 74 " - pdb=" SG CYS N 562 " distance=2.03 Simple disulfide: pdb=" SG CYS M 119 " - pdb=" SG CYS M 209 " distance=2.03 Simple disulfide: pdb=" SG CYS M 126 " - pdb=" SG CYS M 200 " distance=2.02 Simple disulfide: pdb=" SG CYS M 131 " - pdb=" SG CYS M 157 " distance=2.03 Simple disulfide: pdb=" SG CYS M 222 " - pdb=" SG CYS M 251 " distance=2.03 Simple disulfide: pdb=" SG CYS M 232 " - pdb=" SG CYS M 243 " distance=2.03 Simple disulfide: pdb=" SG CYS M 300 " - pdb=" SG CYS M 333 " distance=2.03 Simple disulfide: pdb=" SG CYS M 379 " - pdb=" SG CYS M 446 " distance=2.03 Simple disulfide: pdb=" SG CYS M 386 " - pdb=" SG CYS M 419 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 73 " distance=2.03 Simple disulfide: pdb=" SG CYS D 119 " - pdb=" SG CYS D 209 " distance=2.03 Simple disulfide: pdb=" SG CYS D 126 " - pdb=" SG CYS D 200 " distance=2.03 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 157 " distance=2.03 Simple disulfide: pdb=" SG CYS D 222 " - pdb=" SG CYS D 251 " distance=2.03 Simple disulfide: pdb=" SG CYS D 232 " - pdb=" SG CYS D 243 " distance=2.03 Simple disulfide: pdb=" SG CYS D 300 " - pdb=" SG CYS D 333 " distance=2.03 Simple disulfide: pdb=" SG CYS D 379 " - pdb=" SG CYS D 446 " distance=2.03 Simple disulfide: pdb=" SG CYS D 386 " - pdb=" SG CYS D 419 " distance=2.03 Simple disulfide: pdb=" SG CYS I 54 " - pdb=" SG CYS I 73 " distance=2.03 Simple disulfide: pdb=" SG CYS I 119 " - pdb=" SG CYS I 209 " distance=2.03 Simple disulfide: pdb=" SG CYS I 126 " - pdb=" SG CYS I 200 " distance=2.02 Simple disulfide: pdb=" SG CYS I 131 " - pdb=" SG CYS I 157 " distance=2.03 Simple disulfide: pdb=" SG CYS I 222 " - pdb=" SG CYS I 251 " distance=2.03 Simple disulfide: pdb=" SG CYS I 232 " - pdb=" SG CYS I 243 " distance=2.03 Simple disulfide: pdb=" SG CYS I 300 " - pdb=" SG CYS I 333 " distance=2.03 Simple disulfide: pdb=" SG CYS I 379 " - pdb=" SG CYS I 446 " distance=2.03 Simple disulfide: pdb=" SG CYS I 386 " - pdb=" SG CYS I 419 " 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 ALPHA1-3 " BMA K 3 " - " MAN K 4 " " BMA S 3 " - " MAN S 4 " " BMA W 3 " - " MAN W 4 " ALPHA1-6 " BMA K 3 " - " MAN K 5 " " BMA S 3 " - " MAN S 5 " " BMA W 3 " - " MAN W 5 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG G 1 " - " NAG G 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG O 1 " - " NAG O 2 " " 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 S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " 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-ASN " NAG D 601 " - " ASN D 156 " " NAG D 602 " - " ASN D 160 " " NAG D 603 " - " ASN D 234 " " NAG D 604 " - " ASN D 245 " " NAG D 605 " - " ASN D 280 " " NAG D 606 " - " ASN D 293 " " NAG D 607 " - " ASN D 393 " " NAG D 608 " - " ASN D 443 " " NAG D 609 " - " ASN D 449 " " NAG D 610 " - " ASN D 305 " " NAG D 611 " - " ASN D 361 " " NAG D 612 " - " ASN D 397 " " NAG E 1 " - " ASN M 201 " " NAG G 1 " - " ASN M 245 " " NAG I 601 " - " ASN I 234 " " NAG I 602 " - " ASN I 238 " " NAG I 603 " - " ASN I 280 " " NAG I 604 " - " ASN I 305 " " NAG I 605 " - " ASN I 443 " " NAG I 606 " - " ASN I 449 " " NAG I 607 " - " ASN I 88 " " NAG I 608 " - " ASN I 160 " " NAG J 701 " - " ASN J 612 " " NAG K 1 " - " ASN M 266 " " NAG L 1 " - " ASN M 293 " " NAG M 601 " - " ASN M 156 " " NAG M 602 " - " ASN M 160 " " NAG M 603 " - " ASN M 234 " " NAG M 604 " - " ASN M 238 " " NAG M 605 " - " ASN M 280 " " NAG M 606 " - " ASN M 305 " " NAG M 607 " - " ASN M 361 " " NAG M 608 " - " ASN M 387 " " NAG M 609 " - " ASN M 443 " " NAG O 1 " - " ASN M 393 " " NAG P 1 " - " ASN M 449 " " NAG Q 1 " - " ASN D 201 " " NAG R 1 " - " ASN D 238 " " NAG S 1 " - " ASN D 266 " " NAG T 1 " - " ASN D 387 " " NAG U 1 " - " ASN I 201 " " NAG V 1 " - " ASN I 245 " " NAG W 1 " - " ASN I 266 " " NAG X 1 " - " ASN I 293 " " NAG Y 1 " - " ASN I 387 " " NAG Z 1 " - " ASN I 393 " " NAG a 1 " - " ASN I 156 " " NAG b 1 " - " ASN N 612 " Time building additional restraints: 1.50 Conformation dependent library (CDL) restraints added in 664.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4132 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 31 sheets defined 28.4% alpha, 27.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'M' and resid 67 through 72 Processing helix chain 'M' and resid 98 through 117 removed outlier: 3.854A pdb=" N GLU M 102 " --> pdb=" O ASN M 98 " (cutoff:3.500A) Processing helix chain 'M' and resid 122 through 126 Processing helix chain 'M' and resid 337 through 355 Processing helix chain 'M' and resid 388 through 391 Processing helix chain 'M' and resid 426 through 430 removed outlier: 3.861A pdb=" N GLN M 429 " --> pdb=" O ASN M 426 " (cutoff:3.500A) Processing helix chain 'M' and resid 476 through 485 removed outlier: 3.612A pdb=" N TRP M 480 " --> pdb=" O MET M 476 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLU M 483 " --> pdb=" O ASN M 479 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 72 Processing helix chain 'D' and resid 98 through 117 removed outlier: 3.981A 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 337 through 355 Processing helix chain 'D' and resid 369 through 374 removed outlier: 3.602A pdb=" N THR D 374 " --> pdb=" O LEU D 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 426 through 430 removed outlier: 3.853A pdb=" N GLN D 429 " --> pdb=" O ASN D 426 " (cutoff:3.500A) Processing helix chain 'D' and resid 476 through 485 removed outlier: 3.863A pdb=" N TRP D 480 " --> pdb=" O MET D 476 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLU D 483 " --> pdb=" O ASN D 479 " (cutoff:3.500A) Processing helix chain 'I' and resid 67 through 72 Processing helix chain 'I' and resid 98 through 117 removed outlier: 3.918A pdb=" N GLU I 102 " --> pdb=" O ASN I 98 " (cutoff:3.500A) Processing helix chain 'I' and resid 337 through 355 Processing helix chain 'I' and resid 388 through 391 Processing helix chain 'I' and resid 426 through 430 removed outlier: 4.250A pdb=" N GLN I 429 " --> pdb=" O ASN I 426 " (cutoff:3.500A) Processing helix chain 'I' and resid 476 through 484 removed outlier: 3.964A pdb=" N TRP I 480 " --> pdb=" O MET I 476 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 33 Processing helix chain 'F' and resid 80 through 84 removed outlier: 3.587A pdb=" N UNK F 84 " --> pdb=" O UNK F 81 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 64 removed outlier: 3.570A pdb=" N UNK H 64 " --> pdb=" O UNK H 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 61 through 64' Processing helix chain 'H' and resid 85 through 89 Processing helix chain 'A' and resid 78 through 82 removed outlier: 3.928A pdb=" N UNK A 82 " --> pdb=" O UNK A 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 62 Processing helix chain 'B' and resid 82 through 86 removed outlier: 3.592A pdb=" N UNK B 86 " --> pdb=" O UNK B 83 " (cutoff:3.500A) Processing helix chain 'N' and resid 530 through 542 removed outlier: 4.142A pdb=" N VAL N 540 " --> pdb=" O ILE N 536 " (cutoff:3.500A) Processing helix chain 'N' and resid 543 through 545 No H-bonds generated for 'chain 'N' and resid 543 through 545' Processing helix chain 'N' and resid 561 through 565 Processing helix chain 'N' and resid 571 through 597 removed outlier: 3.565A pdb=" N TRP N 597 " --> pdb=" O LEU N 593 " (cutoff:3.500A) Processing helix chain 'N' and resid 612 through 616 Processing helix chain 'N' and resid 628 through 636 Processing helix chain 'N' and resid 639 through 662 Processing helix chain 'C' and resid 536 through 538 No H-bonds generated for 'chain 'C' and resid 536 through 538' Processing helix chain 'C' and resid 539 through 544 Processing helix chain 'C' and resid 564 through 569 removed outlier: 4.063A pdb=" N LEU C 568 " --> pdb=" O GLN C 564 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLN C 569 " --> pdb=" O GLN C 565 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 564 through 569' Processing helix chain 'C' and resid 572 through 598 removed outlier: 3.565A pdb=" N TRP C 598 " --> pdb=" O LEU C 594 " (cutoff:3.500A) Processing helix chain 'C' and resid 620 through 625 Processing helix chain 'C' and resid 629 through 637 Processing helix chain 'C' and resid 640 through 663 Processing helix chain 'J' and resid 520 through 524 Processing helix chain 'J' and resid 530 through 538 Processing helix chain 'J' and resid 541 through 547 Processing helix chain 'J' and resid 571 through 597 Processing helix chain 'J' and resid 619 through 626 Processing helix chain 'J' and resid 628 through 636 Processing helix chain 'J' and resid 639 through 659 Processing sheet with id=AA1, first strand: chain 'M' and resid 496 through 500 removed outlier: 5.423A pdb=" N VAL N 609 " --> pdb=" O VAL M 36 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N VAL M 38 " --> pdb=" O THR N 607 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N THR N 607 " --> pdb=" O VAL M 38 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'M' and resid 45 through 47 Processing sheet with id=AA3, first strand: chain 'M' and resid 53 through 56 Processing sheet with id=AA4, first strand: chain 'M' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'M' and resid 169 through 177 Processing sheet with id=AA6, first strand: chain 'M' and resid 205 through 207 Processing sheet with id=AA7, first strand: chain 'M' and resid 263 through 265 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 263 through 265 current: chain 'M' and resid 288 through 302 removed outlier: 6.671A pdb=" N GLU M 297 " --> pdb=" O LYS M 336 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LYS M 336 " --> pdb=" O GLU M 297 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 331 through 336 current: chain 'M' and resid 382 through 386 removed outlier: 4.253A pdb=" N PHE M 383 " --> pdb=" O LYS M 422 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 414 through 422 current: chain 'M' and resid 466 through 471 Processing sheet with id=AA8, first strand: chain 'M' and resid 305 through 314 removed outlier: 4.112A pdb=" N ASN M 305 " --> pdb=" O ILE M 325A" (cutoff:3.500A) removed outlier: 6.018A pdb=" N LYS M 309 " --> pdb=" O THR M 322 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N THR M 322 " --> pdb=" O LYS M 309 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N ILE M 311 " --> pdb=" O TYR M 320 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N TYR M 320 " --> pdb=" O ILE M 311 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N ILE M 313 " --> pdb=" O TRP M 318 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N TRP M 318 " --> pdb=" O ILE M 313 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 496 through 500 removed outlier: 5.559A pdb=" N VAL C 610 " --> pdb=" O VAL D 36 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N VAL D 38 " --> pdb=" O THR C 608 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N THR C 608 " --> pdb=" O VAL D 38 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 45 through 47 Processing sheet with id=AB2, first strand: chain 'D' and resid 53 through 55 Processing sheet with id=AB3, first strand: chain 'D' and resid 91 through 93 removed outlier: 3.506A pdb=" N PHE D 93 " --> pdb=" O GLY D 241 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY D 241 " --> pdb=" O PHE D 93 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 169 through 177 Processing sheet with id=AB5, first strand: chain 'D' and resid 206 through 207 removed outlier: 6.391A pdb=" N THR D 206 " --> pdb=" O TYR D 436 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 263 through 264 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 263 through 264 current: chain 'D' and resid 288 through 302 removed outlier: 6.614A pdb=" N GLU D 297 " --> pdb=" O LYS D 336 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS D 336 " --> pdb=" O GLU D 297 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 331 through 336 current: chain 'D' and resid 382 through 386 removed outlier: 4.001A pdb=" N PHE D 383 " --> pdb=" O LYS D 422 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 414 through 422 current: chain 'D' and resid 466 through 471 Processing sheet with id=AB7, first strand: chain 'D' and resid 309 through 314 removed outlier: 6.710A pdb=" N GLN D 317 " --> pdb=" O ILE D 313 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 496 through 500 removed outlier: 5.383A pdb=" N VAL J 609 " --> pdb=" O VAL I 36 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N VAL I 38 " --> pdb=" O THR J 607 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N THR J 607 " --> pdb=" O VAL I 38 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 45 through 47 removed outlier: 3.527A pdb=" N ILE I 229 " --> pdb=" O VAL I 249 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N VAL I 246 " --> pdb=" O LEU I 86 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 75 through 76 removed outlier: 4.295A pdb=" N VAL I 75 " --> pdb=" O CYS I 54 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 91 through 94 removed outlier: 3.571A pdb=" N GLU I 91 " --> pdb=" O CYS I 243 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 169 through 177 Processing sheet with id=AC4, first strand: chain 'I' and resid 206 through 207 removed outlier: 6.762A pdb=" N THR I 206 " --> pdb=" O TYR I 436 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 263 through 265 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 263 through 265 current: chain 'I' and resid 288 through 314 removed outlier: 4.143A pdb=" N ASN I 305 " --> pdb=" O ILE I 325A" (cutoff:3.500A) removed outlier: 6.099A pdb=" N LYS I 309 " --> pdb=" O THR I 322 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N THR I 322 " --> pdb=" O LYS I 309 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N ILE I 311 " --> pdb=" O TYR I 320 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N TYR I 320 " --> pdb=" O ILE I 311 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N ILE I 313 " --> pdb=" O TRP I 318 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N TRP I 318 " --> pdb=" O ILE I 313 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 317 through 325A current: chain 'I' and resid 382 through 386 removed outlier: 4.083A pdb=" N PHE I 383 " --> pdb=" O LYS I 422 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 414 through 422 current: chain 'I' and resid 469 through 471 Processing sheet with id=AC6, first strand: chain 'I' and resid 359 through 360 removed outlier: 5.915A pdb=" N ILE I 359 " --> pdb=" O GLU I 467 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'F' and resid 4 through 6 removed outlier: 3.802A pdb=" N UNK F 72 " --> pdb=" O UNK F 23 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 10 through 11 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 10 through 11 current: chain 'F' and resid 47 through 50 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 47 through 50 current: chain 'F' and resid 98 through 100 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 98 through 100 current: chain 'B' and resid 45 through 46 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 54 through 57 current: chain 'B' and resid 107 through 108 Processing sheet with id=AC9, first strand: chain 'H' and resid 2 through 6 removed outlier: 5.735A pdb=" N UNK H 15 " --> pdb=" O UNK H 83 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N UNK H 83 " --> pdb=" O UNK H 15 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N UNK H 76 " --> pdb=" O UNK H 72 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 10 through 12 current: chain 'H' and resid 45 through 50 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 57 through 59 current: chain 'H' and resid 106 through 112 Processing sheet with id=AD2, first strand: chain 'A' and resid 5 through 6 Processing sheet with id=AD3, first strand: chain 'A' and resid 44 through 47 removed outlier: 6.262A pdb=" N UNK A 34 " --> pdb=" O UNK A 46 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 4 through 6 removed outlier: 3.862A pdb=" N UNK B 21 " --> pdb=" O UNK B 4 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N UNK B 19 " --> pdb=" O UNK B 6 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N UNK B 14 " --> pdb=" O UNK B 80 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N UNK B 80 " --> pdb=" O UNK B 14 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N UNK B 74 " --> pdb=" O UNK B 20 " (cutoff:3.500A) 526 hydrogen bonds defined for protein. 1410 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: 2.46 Time building geometry restraints manager: 1.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2811 1.32 - 1.44: 4631 1.44 - 1.57: 9754 1.57 - 1.69: 0 1.69 - 1.82: 131 Bond restraints: 17327 Sorted by residual: bond pdb=" C PRO D 365 " pdb=" O PRO D 365 " ideal model delta sigma weight residual 1.233 1.195 0.038 1.10e-02 8.26e+03 1.20e+01 bond pdb=" N GLY J 570 " pdb=" CA GLY J 570 " ideal model delta sigma weight residual 1.445 1.476 -0.032 9.90e-03 1.02e+04 1.02e+01 bond pdb=" N ILE J 623 " pdb=" CA ILE J 623 " ideal model delta sigma weight residual 1.461 1.496 -0.035 1.17e-02 7.31e+03 8.85e+00 bond pdb=" N THR D 363 " pdb=" CA THR D 363 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.23e-02 6.61e+03 7.76e+00 bond pdb=" N GLN J 568 " pdb=" CA GLN J 568 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.15e-02 7.56e+03 6.98e+00 ... (remaining 17322 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.40: 22019 1.40 - 2.81: 1307 2.81 - 4.21: 210 4.21 - 5.61: 58 5.61 - 7.02: 7 Bond angle restraints: 23601 Sorted by residual: angle pdb=" N GLN J 568 " pdb=" CA GLN J 568 " pdb=" C GLN J 568 " ideal model delta sigma weight residual 113.38 109.07 4.31 1.17e+00 7.31e-01 1.36e+01 angle pdb=" N ASP J 569 " pdb=" CA ASP J 569 " pdb=" C ASP J 569 " ideal model delta sigma weight residual 113.12 108.77 4.35 1.25e+00 6.40e-01 1.21e+01 angle pdb=" CA ILE J 623 " pdb=" C ILE J 623 " pdb=" O ILE J 623 " ideal model delta sigma weight residual 121.17 117.72 3.45 1.06e+00 8.90e-01 1.06e+01 angle pdb=" C UNK B 97 " pdb=" CA UNK B 97 " pdb=" CB UNK B 97 " ideal model delta sigma weight residual 110.08 116.22 -6.14 1.90e+00 2.77e-01 1.04e+01 angle pdb=" CA GLY J 570 " pdb=" C GLY J 570 " pdb=" O GLY J 570 " ideal model delta sigma weight residual 121.57 118.16 3.41 1.07e+00 8.73e-01 1.02e+01 ... (remaining 23596 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.30: 11048 21.30 - 42.59: 324 42.59 - 63.89: 35 63.89 - 85.18: 30 85.18 - 106.48: 17 Dihedral angle restraints: 11454 sinusoidal: 5115 harmonic: 6339 Sorted by residual: dihedral pdb=" CB CYS D 119 " pdb=" SG CYS D 119 " pdb=" SG CYS D 209 " pdb=" CB CYS D 209 " ideal model delta sinusoidal sigma weight residual -86.00 -119.17 33.17 1 1.00e+01 1.00e-02 1.56e+01 dihedral pdb=" CB CYS M 74 " pdb=" SG CYS M 74 " pdb=" SG CYS N 562 " pdb=" CB CYS N 562 " ideal model delta sinusoidal sigma weight residual 93.00 126.02 -33.02 1 1.00e+01 1.00e-02 1.55e+01 dihedral pdb=" CB CYS I 119 " pdb=" SG CYS I 119 " pdb=" SG CYS I 209 " pdb=" CB CYS I 209 " ideal model delta sinusoidal sigma weight residual -86.00 -117.71 31.71 1 1.00e+01 1.00e-02 1.43e+01 ... (remaining 11451 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.204: 2923 0.204 - 0.407: 22 0.407 - 0.611: 5 0.611 - 0.814: 0 0.814 - 1.018: 2 Chirality restraints: 2952 Sorted by residual: chirality pdb=" C1 NAG K 2 " pdb=" O4 NAG K 1 " pdb=" C2 NAG K 2 " pdb=" O5 NAG K 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-02 2.50e+03 2.36e+02 chirality pdb=" C1 NAG W 2 " pdb=" O4 NAG W 1 " pdb=" C2 NAG W 2 " pdb=" O5 NAG W 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-02 2.50e+03 2.02e+02 chirality pdb=" C1 MAN W 5 " pdb=" O6 BMA W 3 " pdb=" C2 MAN W 5 " pdb=" O5 MAN W 5 " both_signs ideal model delta sigma weight residual False 2.40 2.17 0.23 2.00e-02 2.50e+03 1.37e+02 ... (remaining 2949 not shown) Planarity restraints: 3005 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG S 1 " 0.334 2.00e-02 2.50e+03 2.86e-01 1.02e+03 pdb=" C7 NAG S 1 " -0.084 2.00e-02 2.50e+03 pdb=" C8 NAG S 1 " 0.169 2.00e-02 2.50e+03 pdb=" N2 NAG S 1 " -0.504 2.00e-02 2.50e+03 pdb=" O7 NAG S 1 " 0.086 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG b 2 " -0.327 2.00e-02 2.50e+03 2.84e-01 1.01e+03 pdb=" C7 NAG b 2 " 0.073 2.00e-02 2.50e+03 pdb=" C8 NAG b 2 " -0.054 2.00e-02 2.50e+03 pdb=" N2 NAG b 2 " 0.501 2.00e-02 2.50e+03 pdb=" O7 NAG b 2 " -0.193 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 2 " 0.317 2.00e-02 2.50e+03 2.68e-01 8.99e+02 pdb=" C7 NAG E 2 " -0.082 2.00e-02 2.50e+03 pdb=" C8 NAG E 2 " 0.187 2.00e-02 2.50e+03 pdb=" N2 NAG E 2 " -0.464 2.00e-02 2.50e+03 pdb=" O7 NAG E 2 " 0.042 2.00e-02 2.50e+03 ... (remaining 3002 not shown) Histogram of nonbonded interaction distances: 1.12 - 1.87: 4 1.87 - 2.63: 194 2.63 - 3.39: 22158 3.39 - 4.14: 38081 4.14 - 4.90: 67878 Nonbonded interactions: 128315 Sorted by model distance: nonbonded pdb=" CG ASN D 387 " pdb=" O7 NAG T 1 " model vdw 1.118 3.270 nonbonded pdb=" OD1 ASN D 387 " pdb=" O7 NAG T 1 " model vdw 1.517 3.040 nonbonded pdb=" ND2 ASN D 387 " pdb=" O7 NAG T 1 " model vdw 1.618 3.120 nonbonded pdb=" O3 NAG J 702 " pdb=" O7 NAG J 702 " model vdw 1.840 3.040 nonbonded pdb=" OD1 ASN D 387 " pdb=" C7 NAG T 1 " model vdw 1.977 3.270 ... (remaining 128310 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 9 through 112) selection = (chain 'F' and resid 6 through 109) } ncs_group { reference = (chain 'C' and (resid 523 through 545 or resid 565 through 663)) selection = (chain 'J' and (resid 523 through 545 or resid 564 through 662)) selection = (chain 'N' and (resid 523 through 545 or resid 564 through 662)) } ncs_group { reference = (chain 'D' and (resid 34 through 135 or (resid 152 and (name N or name CA or nam \ e C or name O or name CB )) or resid 153 through 399 or resid 413 through 608)) selection = (chain 'I' and (resid 34 through 135 or (resid 152 and (name N or name CA or nam \ e C or name O or name CB )) or resid 153 through 399 or resid 413 through 459 or \ resid 462 through 608)) selection = (chain 'M' and (resid 34 through 135 or resid 152 through 399 or resid 413 throu \ gh 459 or resid 462 through 608)) } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' } ncs_group { reference = chain 'K' selection = chain 'S' selection = chain 'W' } 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: 11.100 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: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 14.520 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 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 : 0.006 0.044 17431 Z= 0.279 Angle : 0.795 9.817 23885 Z= 0.381 Chirality : 0.062 1.018 2952 Planarity : 0.022 0.286 2957 Dihedral : 11.634 106.475 7238 Min Nonbonded Distance : 1.118 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.13 (0.21), residues: 1689 helix: 2.44 (0.26), residues: 397 sheet: -0.37 (0.24), residues: 442 loop : -0.79 (0.21), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 196 TYR 0.015 0.001 TYR M 195 PHE 0.014 0.002 PHE I 362 TRP 0.013 0.001 TRP M 96 HIS 0.005 0.001 HIS I 72 Details of bonding type rmsd covalent geometry : bond 0.00554 (17327) covalent geometry : angle 0.76411 (23601) SS BOND : bond 0.00307 ( 28) SS BOND : angle 0.61493 ( 56) hydrogen bonds : bond 0.18707 ( 526) hydrogen bonds : angle 7.00802 ( 1410) link_ALPHA1-3 : bond 0.00360 ( 3) link_ALPHA1-3 : angle 1.78348 ( 9) link_ALPHA1-6 : bond 0.00442 ( 3) link_ALPHA1-6 : angle 2.14857 ( 9) link_BETA1-4 : bond 0.01124 ( 22) link_BETA1-4 : angle 2.38131 ( 66) link_NAG-ASN : bond 0.00567 ( 48) link_NAG-ASN : angle 2.42112 ( 144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 377 time to evaluate : 0.432 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: M 35 TRP cc_start: 0.8420 (m100) cc_final: 0.7910 (m100) REVERT: M 135 ASN cc_start: 0.8610 (p0) cc_final: 0.8240 (p0) REVERT: M 180 ASP cc_start: 0.8694 (m-30) cc_final: 0.8478 (m-30) REVERT: M 214 PHE cc_start: 0.8295 (m-80) cc_final: 0.7971 (m-80) REVERT: M 235 LYS cc_start: 0.9162 (mtpt) cc_final: 0.8903 (mttm) REVERT: M 268 SER cc_start: 0.8940 (m) cc_final: 0.8684 (p) REVERT: M 483 GLU cc_start: 0.8491 (mm-30) cc_final: 0.7915 (mm-30) REVERT: D 42 VAL cc_start: 0.9280 (t) cc_final: 0.8801 (p) REVERT: D 117 LYS cc_start: 0.8898 (tttt) cc_final: 0.8600 (ttmm) REVERT: D 202 THR cc_start: 0.9208 (m) cc_final: 0.8909 (p) REVERT: D 231 LYS cc_start: 0.8557 (ttpt) cc_final: 0.8336 (tttt) REVERT: D 428 TRP cc_start: 0.8243 (m-90) cc_final: 0.7841 (m-90) REVERT: D 480 TRP cc_start: 0.8733 (m-90) cc_final: 0.8382 (m-10) REVERT: I 44 VAL cc_start: 0.9454 (t) cc_final: 0.9231 (p) REVERT: I 49 GLU cc_start: 0.7620 (mt-10) cc_final: 0.6903 (mt-10) REVERT: I 493 LYS cc_start: 0.9300 (mmtt) cc_final: 0.9013 (mmtp) REVERT: N 585 GLU cc_start: 0.9134 (mt-10) cc_final: 0.8731 (mt-10) REVERT: C 566 HIS cc_start: 0.6712 (t70) cc_final: 0.6301 (t70) REVERT: C 663 LEU cc_start: 0.7357 (mt) cc_final: 0.6769 (mt) REVERT: J 589 LYS cc_start: 0.9100 (tptt) cc_final: 0.8887 (tppt) REVERT: J 637 SER cc_start: 0.9146 (p) cc_final: 0.8935 (t) REVERT: J 650 SER cc_start: 0.8938 (t) cc_final: 0.8646 (p) outliers start: 0 outliers final: 0 residues processed: 377 average time/residue: 0.1430 time to fit residues: 76.8664 Evaluate side-chains 206 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 206 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 7.9990 chunk 200 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 8.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 170 GLN D 114 GLN ** D 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 378 ASN D 399 ASN D 426 ASN I 191 ASN I 199 ASN I 426 ASN N 654 GLN C 541 GLN C 658 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.093518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.078452 restraints weight = 44943.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.080462 restraints weight = 26137.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.081819 restraints weight = 18433.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.082715 restraints weight = 14593.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.083263 restraints weight = 12453.741| |-----------------------------------------------------------------------------| r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 17431 Z= 0.207 Angle : 0.703 11.139 23885 Z= 0.327 Chirality : 0.046 0.259 2952 Planarity : 0.004 0.036 2957 Dihedral : 9.409 85.784 3888 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.73 % Allowed : 9.17 % Favored : 88.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.22 (0.21), residues: 1689 helix: 2.31 (0.26), residues: 400 sheet: -0.32 (0.24), residues: 454 loop : -0.61 (0.21), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 543 TYR 0.018 0.001 TYR M 39 PHE 0.020 0.002 PHE I 362 TRP 0.014 0.001 TRP J 624 HIS 0.010 0.001 HIS M 105 Details of bonding type rmsd covalent geometry : bond 0.00471 (17327) covalent geometry : angle 0.67777 (23601) SS BOND : bond 0.00462 ( 28) SS BOND : angle 0.81930 ( 56) hydrogen bonds : bond 0.04256 ( 526) hydrogen bonds : angle 5.29957 ( 1410) link_ALPHA1-3 : bond 0.00919 ( 3) link_ALPHA1-3 : angle 2.54906 ( 9) link_ALPHA1-6 : bond 0.00248 ( 3) link_ALPHA1-6 : angle 1.76595 ( 9) link_BETA1-4 : bond 0.00580 ( 22) link_BETA1-4 : angle 2.35502 ( 66) link_NAG-ASN : bond 0.00505 ( 48) link_NAG-ASN : angle 1.82875 ( 144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 224 time to evaluate : 0.431 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: M 35 TRP cc_start: 0.8371 (m100) cc_final: 0.7954 (m100) REVERT: M 135 ASN cc_start: 0.8593 (p0) cc_final: 0.8304 (p0) REVERT: M 180 ASP cc_start: 0.8562 (m-30) cc_final: 0.8305 (m-30) REVERT: M 268 SER cc_start: 0.8916 (m) cc_final: 0.8690 (p) REVERT: M 483 GLU cc_start: 0.8218 (mm-30) cc_final: 0.7788 (mm-30) REVERT: D 42 VAL cc_start: 0.9290 (t) cc_final: 0.9018 (p) REVERT: D 117 LYS cc_start: 0.8839 (tttt) cc_final: 0.8536 (ttmm) REVERT: D 428 TRP cc_start: 0.7999 (m-90) cc_final: 0.7629 (m-90) REVERT: I 307 THR cc_start: 0.8447 (m) cc_final: 0.8170 (p) REVERT: I 420 ARG cc_start: 0.8688 (OUTLIER) cc_final: 0.7302 (mpp80) REVERT: N 541 GLN cc_start: 0.8192 (mm110) cc_final: 0.7735 (mt0) REVERT: N 590 ASP cc_start: 0.8108 (OUTLIER) cc_final: 0.7806 (t0) REVERT: N 659 LYS cc_start: 0.6529 (tttt) cc_final: 0.5365 (tttt) REVERT: N 660 ASP cc_start: 0.8205 (OUTLIER) cc_final: 0.7999 (m-30) REVERT: C 628 MET cc_start: 0.7936 (mtm) cc_final: 0.7478 (mtm) REVERT: C 636 GLU cc_start: 0.8487 (tp30) cc_final: 0.8269 (tm-30) REVERT: C 648 LEU cc_start: 0.9326 (OUTLIER) cc_final: 0.9088 (mm) REVERT: J 622 GLU cc_start: 0.8636 (tp30) cc_final: 0.8290 (tp30) REVERT: J 635 GLU cc_start: 0.8374 (tp30) cc_final: 0.8117 (tm-30) REVERT: J 657 ASN cc_start: 0.8440 (m-40) cc_final: 0.7975 (t0) outliers start: 42 outliers final: 19 residues processed: 258 average time/residue: 0.1234 time to fit residues: 46.9776 Evaluate side-chains 204 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 181 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 42 VAL Chi-restraints excluded: chain M residue 125 LEU Chi-restraints excluded: chain M residue 338 ASP Chi-restraints excluded: chain M residue 394 SER Chi-restraints excluded: chain M residue 431 VAL Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 189 LYS Chi-restraints excluded: chain D residue 203 SER Chi-restraints excluded: chain D residue 209 CYS Chi-restraints excluded: chain D residue 327 ASN Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 199 ASN Chi-restraints excluded: chain I residue 420 ARG Chi-restraints excluded: chain I residue 483 GLU Chi-restraints excluded: chain N residue 590 ASP Chi-restraints excluded: chain N residue 616 SER Chi-restraints excluded: chain N residue 660 ASP Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 648 LEU Chi-restraints excluded: chain J residue 638 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 55 optimal weight: 1.9990 chunk 136 optimal weight: 9.9990 chunk 163 optimal weight: 9.9990 chunk 102 optimal weight: 0.2980 chunk 48 optimal weight: 9.9990 chunk 3 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 181 optimal weight: 0.9990 chunk 180 optimal weight: 0.8980 chunk 50 optimal weight: 5.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 170 GLN ** D 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 199 ASN N 654 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.093834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.078899 restraints weight = 45036.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.080926 restraints weight = 25846.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.082292 restraints weight = 18036.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.083208 restraints weight = 14200.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.083820 restraints weight = 12054.683| |-----------------------------------------------------------------------------| r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 17431 Z= 0.140 Angle : 0.599 10.002 23885 Z= 0.283 Chirality : 0.043 0.232 2952 Planarity : 0.003 0.040 2957 Dihedral : 8.545 81.795 3888 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.67 % Allowed : 11.52 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.35 (0.21), residues: 1689 helix: 2.43 (0.26), residues: 394 sheet: -0.23 (0.23), residues: 469 loop : -0.53 (0.22), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 477 TYR 0.013 0.001 TYR D 195 PHE 0.016 0.002 PHE I 362 TRP 0.014 0.001 TRP D 45 HIS 0.004 0.001 HIS M 105 Details of bonding type rmsd covalent geometry : bond 0.00320 (17327) covalent geometry : angle 0.57230 (23601) SS BOND : bond 0.00403 ( 28) SS BOND : angle 1.39463 ( 56) hydrogen bonds : bond 0.03738 ( 526) hydrogen bonds : angle 4.99581 ( 1410) link_ALPHA1-3 : bond 0.00942 ( 3) link_ALPHA1-3 : angle 1.90228 ( 9) link_ALPHA1-6 : bond 0.00233 ( 3) link_ALPHA1-6 : angle 1.72160 ( 9) link_BETA1-4 : bond 0.00487 ( 22) link_BETA1-4 : angle 2.06011 ( 66) link_NAG-ASN : bond 0.00348 ( 48) link_NAG-ASN : angle 1.67339 ( 144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 210 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 35 TRP cc_start: 0.8242 (m100) cc_final: 0.7944 (m100) REVERT: M 268 SER cc_start: 0.8860 (m) cc_final: 0.8652 (p) REVERT: M 483 GLU cc_start: 0.8196 (mm-30) cc_final: 0.7631 (mm-30) REVERT: D 42 VAL cc_start: 0.9278 (t) cc_final: 0.9014 (p) REVERT: D 117 LYS cc_start: 0.8844 (tttt) cc_final: 0.8543 (ttmm) REVERT: D 202 THR cc_start: 0.9260 (m) cc_final: 0.8962 (p) REVERT: D 428 TRP cc_start: 0.7977 (m-90) cc_final: 0.7668 (m-90) REVERT: D 480 TRP cc_start: 0.8707 (m-10) cc_final: 0.8487 (m-10) REVERT: I 307 THR cc_start: 0.8383 (m) cc_final: 0.8078 (p) REVERT: I 420 ARG cc_start: 0.8653 (OUTLIER) cc_final: 0.7353 (mpp80) REVERT: N 541 GLN cc_start: 0.8129 (mm110) cc_final: 0.7708 (mt0) REVERT: N 590 ASP cc_start: 0.8071 (OUTLIER) cc_final: 0.7778 (t0) REVERT: N 630 MET cc_start: 0.7798 (mmm) cc_final: 0.7461 (mmm) REVERT: N 659 LYS cc_start: 0.6439 (tttt) cc_final: 0.5304 (tttt) REVERT: C 644 ILE cc_start: 0.9285 (mm) cc_final: 0.8921 (mm) REVERT: C 648 LEU cc_start: 0.9420 (OUTLIER) cc_final: 0.9139 (mm) REVERT: J 622 GLU cc_start: 0.8633 (tp30) cc_final: 0.8255 (tp30) REVERT: J 657 ASN cc_start: 0.8434 (m-40) cc_final: 0.7979 (t0) outliers start: 41 outliers final: 17 residues processed: 232 average time/residue: 0.1212 time to fit residues: 41.8822 Evaluate side-chains 203 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 183 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 42 VAL Chi-restraints excluded: chain M residue 125 LEU Chi-restraints excluded: chain M residue 338 ASP Chi-restraints excluded: chain M residue 431 VAL Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 189 LYS Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 199 ASN Chi-restraints excluded: chain I residue 420 ARG Chi-restraints excluded: chain I residue 483 GLU Chi-restraints excluded: chain N residue 537 THR Chi-restraints excluded: chain N residue 590 ASP Chi-restraints excluded: chain C residue 566 HIS Chi-restraints excluded: chain C residue 614 SER Chi-restraints excluded: chain C residue 639 ASN Chi-restraints excluded: chain C residue 648 LEU Chi-restraints excluded: chain J residue 638 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 201 optimal weight: 4.9990 chunk 202 optimal weight: 0.5980 chunk 101 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 18 optimal weight: 7.9990 chunk 85 optimal weight: 6.9990 chunk 139 optimal weight: 10.0000 chunk 192 optimal weight: 5.9990 chunk 200 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 135 ASN ** D 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 199 ASN N 654 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.093628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.078717 restraints weight = 44781.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.080741 restraints weight = 25816.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.082088 restraints weight = 18067.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.082994 restraints weight = 14262.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.083571 restraints weight = 12133.388| |-----------------------------------------------------------------------------| r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17431 Z= 0.139 Angle : 0.583 9.473 23885 Z= 0.276 Chirality : 0.043 0.239 2952 Planarity : 0.003 0.039 2957 Dihedral : 8.056 78.888 3888 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.41 % Allowed : 12.56 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.42 (0.21), residues: 1689 helix: 2.60 (0.26), residues: 386 sheet: -0.17 (0.24), residues: 458 loop : -0.53 (0.21), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 635 TYR 0.012 0.001 TYR D 195 PHE 0.016 0.001 PHE I 362 TRP 0.013 0.001 TRP D 45 HIS 0.009 0.001 HIS N 565 Details of bonding type rmsd covalent geometry : bond 0.00320 (17327) covalent geometry : angle 0.55790 (23601) SS BOND : bond 0.00428 ( 28) SS BOND : angle 0.84871 ( 56) hydrogen bonds : bond 0.03514 ( 526) hydrogen bonds : angle 4.83992 ( 1410) link_ALPHA1-3 : bond 0.00908 ( 3) link_ALPHA1-3 : angle 1.92334 ( 9) link_ALPHA1-6 : bond 0.00238 ( 3) link_ALPHA1-6 : angle 1.70157 ( 9) link_BETA1-4 : bond 0.00465 ( 22) link_BETA1-4 : angle 2.05360 ( 66) link_NAG-ASN : bond 0.00352 ( 48) link_NAG-ASN : angle 1.65598 ( 144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 205 time to evaluate : 0.599 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: M 35 TRP cc_start: 0.8253 (m100) cc_final: 0.7991 (m100) REVERT: M 268 SER cc_start: 0.8881 (m) cc_final: 0.8634 (p) REVERT: M 435 MET cc_start: 0.9099 (ptm) cc_final: 0.8798 (ptp) REVERT: M 483 GLU cc_start: 0.8182 (mm-30) cc_final: 0.7721 (mm-30) REVERT: D 42 VAL cc_start: 0.9269 (t) cc_final: 0.9002 (p) REVERT: D 117 LYS cc_start: 0.8891 (tttt) cc_final: 0.8568 (ttmm) REVERT: D 202 THR cc_start: 0.9268 (m) cc_final: 0.8967 (p) REVERT: D 428 TRP cc_start: 0.8047 (m-90) cc_final: 0.7679 (m-90) REVERT: D 480 TRP cc_start: 0.8727 (m-10) cc_final: 0.8478 (m-10) REVERT: I 199 ASN cc_start: 0.8533 (OUTLIER) cc_final: 0.8241 (t0) REVERT: I 420 ARG cc_start: 0.8670 (OUTLIER) cc_final: 0.7367 (mpp80) REVERT: N 541 GLN cc_start: 0.8198 (mm110) cc_final: 0.7778 (mt0) REVERT: N 630 MET cc_start: 0.7853 (mmm) cc_final: 0.7490 (mmm) REVERT: N 659 LYS cc_start: 0.6409 (tttt) cc_final: 0.5326 (tttt) REVERT: C 633 TRP cc_start: 0.9107 (t-100) cc_final: 0.8251 (t-100) REVERT: C 644 ILE cc_start: 0.9283 (mm) cc_final: 0.8900 (mm) REVERT: C 648 LEU cc_start: 0.9429 (OUTLIER) cc_final: 0.9186 (mm) REVERT: J 585 GLU cc_start: 0.8287 (mt-10) cc_final: 0.7906 (mt-10) REVERT: J 622 GLU cc_start: 0.8721 (tp30) cc_final: 0.8314 (tp30) REVERT: J 657 ASN cc_start: 0.8334 (m-40) cc_final: 0.7967 (t0) outliers start: 37 outliers final: 23 residues processed: 233 average time/residue: 0.1191 time to fit residues: 41.4081 Evaluate side-chains 216 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 190 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain M residue 42 VAL Chi-restraints excluded: chain M residue 74 CYS Chi-restraints excluded: chain M residue 125 LEU Chi-restraints excluded: chain M residue 181 ILE Chi-restraints excluded: chain M residue 338 ASP Chi-restraints excluded: chain M residue 394 SER Chi-restraints excluded: chain M residue 431 VAL Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 189 LYS Chi-restraints excluded: chain D residue 209 CYS Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 199 ASN Chi-restraints excluded: chain I residue 420 ARG Chi-restraints excluded: chain I residue 483 GLU Chi-restraints excluded: chain N residue 537 THR Chi-restraints excluded: chain C residue 523 PHE Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 566 HIS Chi-restraints excluded: chain C residue 614 SER Chi-restraints excluded: chain C residue 639 ASN Chi-restraints excluded: chain C residue 648 LEU Chi-restraints excluded: chain J residue 593 LEU Chi-restraints excluded: chain J residue 638 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 14 optimal weight: 6.9990 chunk 29 optimal weight: 0.0060 chunk 2 optimal weight: 4.9990 chunk 140 optimal weight: 10.0000 chunk 76 optimal weight: 0.4980 chunk 200 optimal weight: 5.9990 chunk 178 optimal weight: 4.9990 chunk 197 optimal weight: 2.9990 chunk 9 optimal weight: 10.0000 chunk 149 optimal weight: 10.0000 chunk 101 optimal weight: 3.9990 overall best weight: 2.5002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 334 ASN ** D 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 654 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.092130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.077265 restraints weight = 45230.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.079247 restraints weight = 26086.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.080580 restraints weight = 18280.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.081478 restraints weight = 14436.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.082081 restraints weight = 12264.029| |-----------------------------------------------------------------------------| r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 17431 Z= 0.200 Angle : 0.641 10.170 23885 Z= 0.302 Chirality : 0.044 0.241 2952 Planarity : 0.003 0.043 2957 Dihedral : 8.007 78.747 3888 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.93 % Allowed : 13.66 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.37 (0.21), residues: 1689 helix: 2.48 (0.26), residues: 387 sheet: -0.13 (0.24), residues: 452 loop : -0.57 (0.21), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 635 TYR 0.014 0.001 TYR C 588 PHE 0.017 0.002 PHE I 362 TRP 0.013 0.001 TRP I 480 HIS 0.007 0.001 HIS N 565 Details of bonding type rmsd covalent geometry : bond 0.00462 (17327) covalent geometry : angle 0.61473 (23601) SS BOND : bond 0.00557 ( 28) SS BOND : angle 1.01955 ( 56) hydrogen bonds : bond 0.03779 ( 526) hydrogen bonds : angle 4.79924 ( 1410) link_ALPHA1-3 : bond 0.01034 ( 3) link_ALPHA1-3 : angle 2.34631 ( 9) link_ALPHA1-6 : bond 0.00193 ( 3) link_ALPHA1-6 : angle 1.69244 ( 9) link_BETA1-4 : bond 0.00422 ( 22) link_BETA1-4 : angle 2.08127 ( 66) link_NAG-ASN : bond 0.00323 ( 48) link_NAG-ASN : angle 1.79268 ( 144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 202 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 35 TRP cc_start: 0.8358 (m100) cc_final: 0.8032 (m100) REVERT: M 255 ILE cc_start: 0.9369 (mm) cc_final: 0.9152 (mt) REVERT: M 483 GLU cc_start: 0.8114 (mm-30) cc_final: 0.7477 (tp30) REVERT: D 42 VAL cc_start: 0.9251 (t) cc_final: 0.8967 (p) REVERT: D 117 LYS cc_start: 0.8876 (tttt) cc_final: 0.8564 (ttmm) REVERT: D 202 THR cc_start: 0.9302 (m) cc_final: 0.8983 (p) REVERT: I 420 ARG cc_start: 0.8705 (OUTLIER) cc_final: 0.7411 (mpp80) REVERT: N 541 GLN cc_start: 0.8203 (mm110) cc_final: 0.7792 (mt0) REVERT: N 572 TRP cc_start: 0.7568 (m-10) cc_final: 0.7354 (m-10) REVERT: C 619 LYS cc_start: 0.8865 (OUTLIER) cc_final: 0.8627 (mtpp) REVERT: C 628 MET cc_start: 0.7723 (mtm) cc_final: 0.7429 (mtm) REVERT: C 644 ILE cc_start: 0.9318 (mm) cc_final: 0.8965 (mm) REVERT: C 648 LEU cc_start: 0.9435 (OUTLIER) cc_final: 0.9218 (mm) REVERT: J 585 GLU cc_start: 0.8319 (mt-10) cc_final: 0.7917 (mt-10) REVERT: J 622 GLU cc_start: 0.8774 (tp30) cc_final: 0.8394 (tp30) REVERT: J 635 GLU cc_start: 0.7954 (tm-30) cc_final: 0.7574 (tm-30) REVERT: J 657 ASN cc_start: 0.8296 (m-40) cc_final: 0.7915 (t0) outliers start: 45 outliers final: 29 residues processed: 231 average time/residue: 0.1247 time to fit residues: 42.6308 Evaluate side-chains 216 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 184 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 42 VAL Chi-restraints excluded: chain M residue 95 MET Chi-restraints excluded: chain M residue 125 LEU Chi-restraints excluded: chain M residue 172 VAL Chi-restraints excluded: chain M residue 180 ASP Chi-restraints excluded: chain M residue 338 ASP Chi-restraints excluded: chain M residue 374 THR Chi-restraints excluded: chain M residue 394 SER Chi-restraints excluded: chain M residue 431 VAL Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 189 LYS Chi-restraints excluded: chain D residue 209 CYS Chi-restraints excluded: chain D residue 327 ASN Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 173 TYR Chi-restraints excluded: chain I residue 420 ARG Chi-restraints excluded: chain I residue 483 GLU Chi-restraints excluded: chain N residue 523 PHE Chi-restraints excluded: chain N residue 537 THR Chi-restraints excluded: chain N residue 616 SER Chi-restraints excluded: chain C residue 523 PHE Chi-restraints excluded: chain C residue 535 SER Chi-restraints excluded: chain C residue 537 THR Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 566 HIS Chi-restraints excluded: chain C residue 614 SER Chi-restraints excluded: chain C residue 619 LYS Chi-restraints excluded: chain C residue 648 LEU Chi-restraints excluded: chain J residue 593 LEU Chi-restraints excluded: chain J residue 638 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 164 optimal weight: 30.0000 chunk 206 optimal weight: 0.4980 chunk 120 optimal weight: 3.9990 chunk 155 optimal weight: 20.0000 chunk 150 optimal weight: 10.0000 chunk 209 optimal weight: 0.9990 chunk 122 optimal weight: 8.9990 chunk 181 optimal weight: 0.0060 chunk 184 optimal weight: 6.9990 chunk 191 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 overall best weight: 1.2800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 199 ASN I 426 ASN ** N 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 654 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.093321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.078499 restraints weight = 44720.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.080509 restraints weight = 25756.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.081868 restraints weight = 18012.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.082765 restraints weight = 14187.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.083369 restraints weight = 12065.047| |-----------------------------------------------------------------------------| r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.3127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17431 Z= 0.127 Angle : 0.579 9.584 23885 Z= 0.275 Chirality : 0.042 0.247 2952 Planarity : 0.003 0.039 2957 Dihedral : 7.526 75.959 3888 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.60 % Allowed : 14.51 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.46 (0.21), residues: 1689 helix: 2.49 (0.26), residues: 387 sheet: -0.02 (0.24), residues: 446 loop : -0.51 (0.21), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 635 TYR 0.012 0.001 TYR M 39 PHE 0.016 0.001 PHE I 362 TRP 0.016 0.001 TRP D 45 HIS 0.005 0.001 HIS N 565 Details of bonding type rmsd covalent geometry : bond 0.00291 (17327) covalent geometry : angle 0.55472 (23601) SS BOND : bond 0.00375 ( 28) SS BOND : angle 0.76080 ( 56) hydrogen bonds : bond 0.03360 ( 526) hydrogen bonds : angle 4.61121 ( 1410) link_ALPHA1-3 : bond 0.01053 ( 3) link_ALPHA1-3 : angle 2.00815 ( 9) link_ALPHA1-6 : bond 0.00294 ( 3) link_ALPHA1-6 : angle 1.64597 ( 9) link_BETA1-4 : bond 0.00481 ( 22) link_BETA1-4 : angle 2.02172 ( 66) link_NAG-ASN : bond 0.00335 ( 48) link_NAG-ASN : angle 1.61515 ( 144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 201 time to evaluate : 0.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 35 TRP cc_start: 0.8299 (m100) cc_final: 0.8071 (m100) REVERT: M 255 ILE cc_start: 0.9373 (mm) cc_final: 0.9113 (mt) REVERT: M 483 GLU cc_start: 0.8025 (mm-30) cc_final: 0.7546 (tp30) REVERT: D 42 VAL cc_start: 0.9221 (t) cc_final: 0.8939 (p) REVERT: D 117 LYS cc_start: 0.8887 (tttt) cc_final: 0.8585 (ttmm) REVERT: D 202 THR cc_start: 0.9268 (m) cc_final: 0.8965 (p) REVERT: I 103 GLN cc_start: 0.8366 (tm-30) cc_final: 0.7852 (tm-30) REVERT: I 420 ARG cc_start: 0.8683 (OUTLIER) cc_final: 0.7385 (mpp80) REVERT: N 541 GLN cc_start: 0.8189 (mm110) cc_final: 0.7700 (mt0) REVERT: N 630 MET cc_start: 0.7955 (mmm) cc_final: 0.7440 (tmm) REVERT: C 564 GLN cc_start: 0.8365 (tt0) cc_final: 0.7912 (tt0) REVERT: C 633 TRP cc_start: 0.8972 (t-100) cc_final: 0.8134 (t-100) REVERT: C 644 ILE cc_start: 0.9289 (mm) cc_final: 0.8962 (mm) REVERT: C 648 LEU cc_start: 0.9398 (OUTLIER) cc_final: 0.9186 (mm) REVERT: J 585 GLU cc_start: 0.8287 (mt-10) cc_final: 0.8069 (mt-10) REVERT: J 622 GLU cc_start: 0.8733 (tp30) cc_final: 0.8364 (tp30) REVERT: J 635 GLU cc_start: 0.7975 (tm-30) cc_final: 0.7586 (tm-30) REVERT: J 657 ASN cc_start: 0.8206 (m-40) cc_final: 0.7843 (t0) outliers start: 40 outliers final: 27 residues processed: 227 average time/residue: 0.1191 time to fit residues: 40.0463 Evaluate side-chains 214 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 185 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 42 VAL Chi-restraints excluded: chain M residue 74 CYS Chi-restraints excluded: chain M residue 125 LEU Chi-restraints excluded: chain M residue 180 ASP Chi-restraints excluded: chain M residue 394 SER Chi-restraints excluded: chain M residue 431 VAL Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 189 LYS Chi-restraints excluded: chain D residue 209 CYS Chi-restraints excluded: chain D residue 231 LYS Chi-restraints excluded: chain D residue 428 TRP Chi-restraints excluded: chain I residue 173 TYR Chi-restraints excluded: chain I residue 199 ASN Chi-restraints excluded: chain I residue 307 THR Chi-restraints excluded: chain I residue 420 ARG Chi-restraints excluded: chain I residue 483 GLU Chi-restraints excluded: chain N residue 537 THR Chi-restraints excluded: chain N residue 605 CYS Chi-restraints excluded: chain C residue 523 PHE Chi-restraints excluded: chain C residue 535 SER Chi-restraints excluded: chain C residue 537 THR Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 566 HIS Chi-restraints excluded: chain C residue 585 ILE Chi-restraints excluded: chain C residue 639 ASN Chi-restraints excluded: chain C residue 648 LEU Chi-restraints excluded: chain J residue 593 LEU Chi-restraints excluded: chain J residue 638 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 1 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 chunk 190 optimal weight: 8.9990 chunk 137 optimal weight: 8.9990 chunk 117 optimal weight: 0.6980 chunk 98 optimal weight: 3.9990 chunk 202 optimal weight: 9.9990 chunk 9 optimal weight: 0.9990 chunk 159 optimal weight: 20.0000 chunk 127 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 199 ASN I 426 ASN ** N 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 654 GLN C 566 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.091507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.076744 restraints weight = 45180.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.078713 restraints weight = 26027.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.080037 restraints weight = 18259.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.080912 restraints weight = 14433.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.081496 restraints weight = 12304.420| |-----------------------------------------------------------------------------| r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.3303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 17431 Z= 0.191 Angle : 0.645 10.415 23885 Z= 0.304 Chirality : 0.044 0.247 2952 Planarity : 0.003 0.043 2957 Dihedral : 7.592 74.748 3888 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.34 % Allowed : 15.35 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.37 (0.21), residues: 1689 helix: 2.28 (0.27), residues: 389 sheet: -0.02 (0.25), residues: 438 loop : -0.54 (0.21), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 635 TYR 0.016 0.001 TYR C 588 PHE 0.017 0.002 PHE I 362 TRP 0.026 0.001 TRP N 572 HIS 0.005 0.001 HIS M 72 Details of bonding type rmsd covalent geometry : bond 0.00442 (17327) covalent geometry : angle 0.61960 (23601) SS BOND : bond 0.00488 ( 28) SS BOND : angle 1.12594 ( 56) hydrogen bonds : bond 0.03701 ( 526) hydrogen bonds : angle 4.67605 ( 1410) link_ALPHA1-3 : bond 0.01113 ( 3) link_ALPHA1-3 : angle 2.49113 ( 9) link_ALPHA1-6 : bond 0.00320 ( 3) link_ALPHA1-6 : angle 1.62435 ( 9) link_BETA1-4 : bond 0.00422 ( 22) link_BETA1-4 : angle 2.07167 ( 66) link_NAG-ASN : bond 0.00293 ( 48) link_NAG-ASN : angle 1.78135 ( 144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 185 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 35 TRP cc_start: 0.8361 (m100) cc_final: 0.8107 (m100) REVERT: M 255 ILE cc_start: 0.9385 (mm) cc_final: 0.9151 (mt) REVERT: M 483 GLU cc_start: 0.8053 (mm-30) cc_final: 0.7591 (tp30) REVERT: D 42 VAL cc_start: 0.9249 (t) cc_final: 0.8954 (p) REVERT: D 117 LYS cc_start: 0.8907 (tttt) cc_final: 0.8594 (ttmm) REVERT: D 202 THR cc_start: 0.9258 (m) cc_final: 0.8951 (p) REVERT: I 103 GLN cc_start: 0.8486 (tm-30) cc_final: 0.8069 (tm-30) REVERT: I 420 ARG cc_start: 0.8700 (OUTLIER) cc_final: 0.7420 (mpp80) REVERT: N 541 GLN cc_start: 0.8216 (mm110) cc_final: 0.7748 (mt0) REVERT: N 630 MET cc_start: 0.8084 (mmm) cc_final: 0.7519 (tmm) REVERT: C 564 GLN cc_start: 0.8408 (tt0) cc_final: 0.7945 (tt0) REVERT: C 634 ASP cc_start: 0.8435 (m-30) cc_final: 0.8114 (m-30) REVERT: C 644 ILE cc_start: 0.9309 (mm) cc_final: 0.9005 (mm) REVERT: C 648 LEU cc_start: 0.9367 (OUTLIER) cc_final: 0.9166 (mm) REVERT: J 622 GLU cc_start: 0.8779 (tp30) cc_final: 0.8438 (tp30) REVERT: J 635 GLU cc_start: 0.7970 (tm-30) cc_final: 0.7630 (tm-30) REVERT: J 657 ASN cc_start: 0.8208 (m-40) cc_final: 0.7675 (t0) outliers start: 36 outliers final: 31 residues processed: 207 average time/residue: 0.1254 time to fit residues: 38.1754 Evaluate side-chains 213 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 180 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain M residue 42 VAL Chi-restraints excluded: chain M residue 74 CYS Chi-restraints excluded: chain M residue 125 LEU Chi-restraints excluded: chain M residue 180 ASP Chi-restraints excluded: chain M residue 431 VAL Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 189 LYS Chi-restraints excluded: chain D residue 209 CYS Chi-restraints excluded: chain D residue 231 LYS Chi-restraints excluded: chain D residue 327 ASN Chi-restraints excluded: chain D residue 426 ASN Chi-restraints excluded: chain D residue 427 MET Chi-restraints excluded: chain D residue 428 TRP Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 173 TYR Chi-restraints excluded: chain I residue 307 THR Chi-restraints excluded: chain I residue 420 ARG Chi-restraints excluded: chain I residue 483 GLU Chi-restraints excluded: chain N residue 523 PHE Chi-restraints excluded: chain N residue 537 THR Chi-restraints excluded: chain N residue 616 SER Chi-restraints excluded: chain C residue 523 PHE Chi-restraints excluded: chain C residue 535 SER Chi-restraints excluded: chain C residue 537 THR Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 566 HIS Chi-restraints excluded: chain C residue 639 ASN Chi-restraints excluded: chain C residue 648 LEU Chi-restraints excluded: chain J residue 593 LEU Chi-restraints excluded: chain J residue 638 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 188 optimal weight: 0.9990 chunk 184 optimal weight: 5.9990 chunk 177 optimal weight: 6.9990 chunk 182 optimal weight: 0.8980 chunk 167 optimal weight: 20.0000 chunk 7 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 58 optimal weight: 7.9990 chunk 39 optimal weight: 4.9990 chunk 98 optimal weight: 7.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 199 ASN I 426 ASN ** N 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 566 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.090585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.075374 restraints weight = 45428.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.077506 restraints weight = 24739.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.078920 restraints weight = 16807.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.079851 restraints weight = 13058.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.080472 restraints weight = 11022.951| |-----------------------------------------------------------------------------| r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.3455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 17431 Z= 0.232 Angle : 0.683 10.873 23885 Z= 0.321 Chirality : 0.044 0.249 2952 Planarity : 0.003 0.042 2957 Dihedral : 7.772 74.391 3888 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.12 % Allowed : 15.09 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.29 (0.21), residues: 1689 helix: 2.29 (0.27), residues: 383 sheet: -0.09 (0.24), residues: 456 loop : -0.60 (0.22), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 635 TYR 0.015 0.001 TYR I 195 PHE 0.019 0.002 PHE I 362 TRP 0.024 0.002 TRP N 572 HIS 0.008 0.001 HIS C 566 Details of bonding type rmsd covalent geometry : bond 0.00536 (17327) covalent geometry : angle 0.65845 (23601) SS BOND : bond 0.00558 ( 28) SS BOND : angle 0.92013 ( 56) hydrogen bonds : bond 0.03889 ( 526) hydrogen bonds : angle 4.77394 ( 1410) link_ALPHA1-3 : bond 0.01018 ( 3) link_ALPHA1-3 : angle 2.56396 ( 9) link_ALPHA1-6 : bond 0.00352 ( 3) link_ALPHA1-6 : angle 1.65897 ( 9) link_BETA1-4 : bond 0.00410 ( 22) link_BETA1-4 : angle 2.09044 ( 66) link_NAG-ASN : bond 0.00318 ( 48) link_NAG-ASN : angle 1.86954 ( 144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 185 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 35 TRP cc_start: 0.8391 (m100) cc_final: 0.8045 (m100) REVERT: M 255 ILE cc_start: 0.9374 (mm) cc_final: 0.9172 (mt) REVERT: M 483 GLU cc_start: 0.8079 (mm-30) cc_final: 0.7628 (tp30) REVERT: D 42 VAL cc_start: 0.9251 (t) cc_final: 0.8948 (p) REVERT: D 117 LYS cc_start: 0.8940 (tttt) cc_final: 0.8607 (ttmm) REVERT: D 202 THR cc_start: 0.9308 (m) cc_final: 0.8981 (p) REVERT: I 420 ARG cc_start: 0.8720 (OUTLIER) cc_final: 0.7430 (mpp80) REVERT: N 541 GLN cc_start: 0.8291 (mm110) cc_final: 0.7793 (mt0) REVERT: N 630 MET cc_start: 0.8152 (mmm) cc_final: 0.7620 (tmm) REVERT: C 644 ILE cc_start: 0.9332 (mm) cc_final: 0.9028 (mm) REVERT: C 648 LEU cc_start: 0.9383 (OUTLIER) cc_final: 0.9173 (mm) REVERT: J 585 GLU cc_start: 0.8363 (mt-10) cc_final: 0.8150 (mt-10) REVERT: J 622 GLU cc_start: 0.8852 (tp30) cc_final: 0.8459 (tp30) REVERT: J 635 GLU cc_start: 0.8058 (tm-30) cc_final: 0.7704 (tm-30) REVERT: J 657 ASN cc_start: 0.8231 (m-40) cc_final: 0.7914 (t0) outliers start: 48 outliers final: 38 residues processed: 212 average time/residue: 0.1282 time to fit residues: 40.3715 Evaluate side-chains 217 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 177 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain M residue 42 VAL Chi-restraints excluded: chain M residue 74 CYS Chi-restraints excluded: chain M residue 125 LEU Chi-restraints excluded: chain M residue 172 VAL Chi-restraints excluded: chain M residue 180 ASP Chi-restraints excluded: chain M residue 181 ILE Chi-restraints excluded: chain M residue 252 THR Chi-restraints excluded: chain M residue 291 HIS Chi-restraints excluded: chain M residue 394 SER Chi-restraints excluded: chain M residue 431 VAL Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 189 LYS Chi-restraints excluded: chain D residue 209 CYS Chi-restraints excluded: chain D residue 231 LYS Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 327 ASN Chi-restraints excluded: chain D residue 426 ASN Chi-restraints excluded: chain D residue 428 TRP Chi-restraints excluded: chain D residue 435 MET Chi-restraints excluded: chain D residue 448 SER Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 173 TYR Chi-restraints excluded: chain I residue 307 THR Chi-restraints excluded: chain I residue 420 ARG Chi-restraints excluded: chain I residue 483 GLU Chi-restraints excluded: chain N residue 537 THR Chi-restraints excluded: chain N residue 616 SER Chi-restraints excluded: chain C residue 523 PHE Chi-restraints excluded: chain C residue 535 SER Chi-restraints excluded: chain C residue 536 ILE Chi-restraints excluded: chain C residue 537 THR Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 631 MET Chi-restraints excluded: chain C residue 648 LEU Chi-restraints excluded: chain J residue 593 LEU Chi-restraints excluded: chain J residue 638 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 18 optimal weight: 6.9990 chunk 148 optimal weight: 10.0000 chunk 22 optimal weight: 4.9990 chunk 113 optimal weight: 7.9990 chunk 93 optimal weight: 3.9990 chunk 191 optimal weight: 1.9990 chunk 4 optimal weight: 6.9990 chunk 183 optimal weight: 8.9990 chunk 159 optimal weight: 20.0000 chunk 174 optimal weight: 10.0000 chunk 79 optimal weight: 0.0040 overall best weight: 3.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 654 GLN C 566 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.089210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.074510 restraints weight = 45882.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.076425 restraints weight = 26578.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.077707 restraints weight = 18729.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.078563 restraints weight = 14884.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.079131 restraints weight = 12744.662| |-----------------------------------------------------------------------------| r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.3714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 17431 Z= 0.273 Angle : 0.750 11.017 23885 Z= 0.353 Chirality : 0.046 0.252 2952 Planarity : 0.004 0.044 2957 Dihedral : 8.111 71.897 3888 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 3.51 % Allowed : 15.16 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.00 (0.21), residues: 1689 helix: 2.17 (0.27), residues: 378 sheet: -0.22 (0.25), residues: 437 loop : -0.85 (0.21), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 635 TYR 0.020 0.002 TYR C 588 PHE 0.020 0.002 PHE I 362 TRP 0.045 0.002 TRP N 572 HIS 0.026 0.002 HIS C 566 Details of bonding type rmsd covalent geometry : bond 0.00630 (17327) covalent geometry : angle 0.72390 (23601) SS BOND : bond 0.00670 ( 28) SS BOND : angle 1.06469 ( 56) hydrogen bonds : bond 0.04238 ( 526) hydrogen bonds : angle 4.95944 ( 1410) link_ALPHA1-3 : bond 0.01088 ( 3) link_ALPHA1-3 : angle 2.74645 ( 9) link_ALPHA1-6 : bond 0.00418 ( 3) link_ALPHA1-6 : angle 1.61269 ( 9) link_BETA1-4 : bond 0.00399 ( 22) link_BETA1-4 : angle 2.17458 ( 66) link_NAG-ASN : bond 0.00391 ( 48) link_NAG-ASN : angle 2.04405 ( 144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 183 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 35 TRP cc_start: 0.8384 (m100) cc_final: 0.8040 (m100) REVERT: M 255 ILE cc_start: 0.9384 (mm) cc_final: 0.9148 (mt) REVERT: M 483 GLU cc_start: 0.8034 (mm-30) cc_final: 0.7605 (tp30) REVERT: D 104 MET cc_start: 0.9328 (ttm) cc_final: 0.8884 (ttt) REVERT: D 117 LYS cc_start: 0.8933 (tttt) cc_final: 0.8612 (ttmm) REVERT: I 420 ARG cc_start: 0.8722 (OUTLIER) cc_final: 0.7497 (mpp80) REVERT: N 630 MET cc_start: 0.8180 (mmm) cc_final: 0.7711 (tmm) REVERT: C 535 SER cc_start: 0.8634 (OUTLIER) cc_final: 0.8222 (t) REVERT: C 564 GLN cc_start: 0.8321 (tt0) cc_final: 0.7998 (tt0) REVERT: C 607 CYS cc_start: 0.7995 (OUTLIER) cc_final: 0.7719 (m) REVERT: C 644 ILE cc_start: 0.9384 (mm) cc_final: 0.9071 (mm) REVERT: C 648 LEU cc_start: 0.9428 (OUTLIER) cc_final: 0.9218 (mm) REVERT: J 589 LYS cc_start: 0.9072 (ttmt) cc_final: 0.8664 (tppt) REVERT: J 622 GLU cc_start: 0.8805 (tp30) cc_final: 0.8455 (tp30) REVERT: J 630 MET cc_start: 0.8304 (mmm) cc_final: 0.7876 (mmm) REVERT: J 635 GLU cc_start: 0.8081 (tm-30) cc_final: 0.7778 (tm-30) REVERT: J 657 ASN cc_start: 0.8495 (m-40) cc_final: 0.7955 (t0) outliers start: 54 outliers final: 38 residues processed: 218 average time/residue: 0.1225 time to fit residues: 39.5467 Evaluate side-chains 222 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 180 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain M residue 125 LEU Chi-restraints excluded: chain M residue 172 VAL Chi-restraints excluded: chain M residue 180 ASP Chi-restraints excluded: chain M residue 181 ILE Chi-restraints excluded: chain M residue 252 THR Chi-restraints excluded: chain M residue 291 HIS Chi-restraints excluded: chain M residue 394 SER Chi-restraints excluded: chain M residue 431 VAL Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 189 LYS Chi-restraints excluded: chain D residue 209 CYS Chi-restraints excluded: chain D residue 231 LYS Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 268 SER Chi-restraints excluded: chain D residue 327 ASN Chi-restraints excluded: chain D residue 427 MET Chi-restraints excluded: chain D residue 435 MET Chi-restraints excluded: chain D residue 448 SER Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 307 THR Chi-restraints excluded: chain I residue 420 ARG Chi-restraints excluded: chain I residue 483 GLU Chi-restraints excluded: chain N residue 523 PHE Chi-restraints excluded: chain N residue 537 THR Chi-restraints excluded: chain N residue 566 LEU Chi-restraints excluded: chain N residue 605 CYS Chi-restraints excluded: chain N residue 616 SER Chi-restraints excluded: chain C residue 523 PHE Chi-restraints excluded: chain C residue 535 SER Chi-restraints excluded: chain C residue 536 ILE Chi-restraints excluded: chain C residue 537 THR Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 607 CYS Chi-restraints excluded: chain C residue 614 SER Chi-restraints excluded: chain C residue 631 MET Chi-restraints excluded: chain C residue 648 LEU Chi-restraints excluded: chain J residue 593 LEU Chi-restraints excluded: chain J residue 638 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 161 optimal weight: 30.0000 chunk 16 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 207 optimal weight: 0.7980 chunk 93 optimal weight: 2.9990 chunk 40 optimal weight: 0.0050 chunk 90 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 154 optimal weight: 30.0000 overall best weight: 1.5600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 199 ASN ** D 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 426 ASN I 426 ASN ** N 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.091248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.076837 restraints weight = 44376.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.078792 restraints weight = 25352.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.080098 restraints weight = 17683.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.080974 restraints weight = 13911.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.081546 restraints weight = 11818.287| |-----------------------------------------------------------------------------| r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.3778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17431 Z= 0.143 Angle : 0.636 10.384 23885 Z= 0.302 Chirality : 0.043 0.249 2952 Planarity : 0.003 0.039 2957 Dihedral : 7.579 67.963 3888 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.54 % Allowed : 16.46 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.15 (0.21), residues: 1689 helix: 2.26 (0.27), residues: 378 sheet: -0.19 (0.24), residues: 454 loop : -0.70 (0.22), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 635 TYR 0.019 0.001 TYR C 588 PHE 0.017 0.001 PHE I 362 TRP 0.062 0.002 TRP N 572 HIS 0.013 0.001 HIS M 72 Details of bonding type rmsd covalent geometry : bond 0.00332 (17327) covalent geometry : angle 0.61232 (23601) SS BOND : bond 0.00446 ( 28) SS BOND : angle 0.80272 ( 56) hydrogen bonds : bond 0.03685 ( 526) hydrogen bonds : angle 4.82572 ( 1410) link_ALPHA1-3 : bond 0.01066 ( 3) link_ALPHA1-3 : angle 2.19534 ( 9) link_ALPHA1-6 : bond 0.00408 ( 3) link_ALPHA1-6 : angle 1.55238 ( 9) link_BETA1-4 : bond 0.00465 ( 22) link_BETA1-4 : angle 2.05521 ( 66) link_NAG-ASN : bond 0.00289 ( 48) link_NAG-ASN : angle 1.74666 ( 144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 183 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 35 TRP cc_start: 0.8254 (m100) cc_final: 0.8031 (m100) REVERT: M 255 ILE cc_start: 0.9380 (mm) cc_final: 0.9125 (mt) REVERT: M 483 GLU cc_start: 0.8007 (mm-30) cc_final: 0.7559 (tp30) REVERT: D 42 VAL cc_start: 0.9208 (t) cc_final: 0.8962 (p) REVERT: D 117 LYS cc_start: 0.8901 (tttt) cc_final: 0.8584 (ttmm) REVERT: D 202 THR cc_start: 0.9301 (m) cc_final: 0.9031 (p) REVERT: I 378 ASN cc_start: 0.8846 (t0) cc_final: 0.7922 (p0) REVERT: I 420 ARG cc_start: 0.8686 (OUTLIER) cc_final: 0.7503 (mpp80) REVERT: N 541 GLN cc_start: 0.8102 (mm110) cc_final: 0.7657 (mt0) REVERT: N 630 MET cc_start: 0.8157 (mmm) cc_final: 0.7607 (tmm) REVERT: C 535 SER cc_start: 0.8540 (OUTLIER) cc_final: 0.8138 (t) REVERT: C 545 LEU cc_start: 0.7318 (OUTLIER) cc_final: 0.6866 (tt) REVERT: C 564 GLN cc_start: 0.8236 (tt0) cc_final: 0.7977 (tt0) REVERT: C 608 THR cc_start: 0.9498 (OUTLIER) cc_final: 0.9104 (p) REVERT: C 644 ILE cc_start: 0.9333 (mm) cc_final: 0.9017 (mm) REVERT: C 648 LEU cc_start: 0.9423 (OUTLIER) cc_final: 0.9219 (mm) REVERT: J 622 GLU cc_start: 0.8775 (tp30) cc_final: 0.8419 (tp30) REVERT: J 635 GLU cc_start: 0.8088 (tm-30) cc_final: 0.7755 (tm-30) REVERT: J 657 ASN cc_start: 0.8352 (m-40) cc_final: 0.7880 (t0) outliers start: 39 outliers final: 32 residues processed: 208 average time/residue: 0.1188 time to fit residues: 36.7750 Evaluate side-chains 211 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 174 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain M residue 125 LEU Chi-restraints excluded: chain M residue 172 VAL Chi-restraints excluded: chain M residue 180 ASP Chi-restraints excluded: chain M residue 181 ILE Chi-restraints excluded: chain M residue 252 THR Chi-restraints excluded: chain M residue 291 HIS Chi-restraints excluded: chain M residue 394 SER Chi-restraints excluded: chain M residue 431 VAL Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 189 LYS Chi-restraints excluded: chain D residue 209 CYS Chi-restraints excluded: chain D residue 231 LYS Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 327 ASN Chi-restraints excluded: chain D residue 426 ASN Chi-restraints excluded: chain D residue 428 TRP Chi-restraints excluded: chain D residue 435 MET Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 199 ASN Chi-restraints excluded: chain I residue 307 THR Chi-restraints excluded: chain I residue 420 ARG Chi-restraints excluded: chain I residue 483 GLU Chi-restraints excluded: chain N residue 523 PHE Chi-restraints excluded: chain N residue 537 THR Chi-restraints excluded: chain N residue 566 LEU Chi-restraints excluded: chain C residue 523 PHE Chi-restraints excluded: chain C residue 535 SER Chi-restraints excluded: chain C residue 537 THR Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 608 THR Chi-restraints excluded: chain C residue 631 MET Chi-restraints excluded: chain C residue 639 ASN Chi-restraints excluded: chain C residue 648 LEU Chi-restraints excluded: chain J residue 593 LEU Chi-restraints excluded: chain J residue 638 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 151 optimal weight: 10.0000 chunk 86 optimal weight: 3.9990 chunk 201 optimal weight: 0.3980 chunk 205 optimal weight: 0.6980 chunk 113 optimal weight: 0.8980 chunk 115 optimal weight: 2.9990 chunk 185 optimal weight: 4.9990 chunk 146 optimal weight: 10.0000 chunk 59 optimal weight: 3.9990 chunk 156 optimal weight: 20.0000 chunk 30 optimal weight: 0.7980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 426 ASN ** N 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 654 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.091228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.076803 restraints weight = 44710.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.078767 restraints weight = 25466.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.080056 restraints weight = 17755.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.080954 restraints weight = 13971.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.081539 restraints weight = 11840.788| |-----------------------------------------------------------------------------| r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.3783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.110 17431 Z= 0.175 Angle : 0.815 59.199 23885 Z= 0.432 Chirality : 0.043 0.396 2952 Planarity : 0.003 0.039 2957 Dihedral : 7.600 67.941 3888 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.67 % Allowed : 16.46 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.15 (0.21), residues: 1689 helix: 2.26 (0.26), residues: 378 sheet: -0.19 (0.24), residues: 454 loop : -0.69 (0.22), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 635 TYR 0.014 0.001 TYR M 396 PHE 0.017 0.002 PHE D 159 TRP 0.055 0.002 TRP N 572 HIS 0.039 0.002 HIS M 72 Details of bonding type rmsd covalent geometry : bond 0.00376 (17327) covalent geometry : angle 0.78656 (23601) SS BOND : bond 0.00710 ( 28) SS BOND : angle 2.80346 ( 56) hydrogen bonds : bond 0.03727 ( 526) hydrogen bonds : angle 4.82944 ( 1410) link_ALPHA1-3 : bond 0.00938 ( 3) link_ALPHA1-3 : angle 2.18570 ( 9) link_ALPHA1-6 : bond 0.00399 ( 3) link_ALPHA1-6 : angle 1.55148 ( 9) link_BETA1-4 : bond 0.00461 ( 22) link_BETA1-4 : angle 2.05390 ( 66) link_NAG-ASN : bond 0.00342 ( 48) link_NAG-ASN : angle 1.79311 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2529.89 seconds wall clock time: 44 minutes 29.29 seconds (2669.29 seconds total)