Starting phenix.real_space_refine on Sun Jun 15 08:07:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9axk_43968/06_2025/9axk_43968.cif Found real_map, /net/cci-nas-00/data/ceres_data/9axk_43968/06_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_43968/06_2025/9axk_43968.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9axk_43968/06_2025/9axk_43968.map" model { file = "/net/cci-nas-00/data/ceres_data/9axk_43968/06_2025/9axk_43968.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9axk_43968/06_2025/9axk_43968.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 13.39, per 1000 atoms: 0.79 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: 6.12 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 2.02 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: 6.40 Time building geometry restraints manager: 6.95 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 505 or \ resid 601 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 505 or resid 601 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 505 or resid 601 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: 8.800 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: 0.020 Extract box with map and model: 0.710 Check model and map are aligned: 0.110 Set scattering table: 0.160 Process input model: 44.970 Find NCS groups from input model: 1.120 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.230 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.013 0.001 TRP M 96 HIS 0.005 0.001 HIS I 72 PHE 0.014 0.002 PHE I 362 TYR 0.015 0.001 TYR M 195 ARG 0.003 0.000 ARG I 196 Details of bonding type rmsd link_NAG-ASN : bond 0.00567 ( 48) link_NAG-ASN : angle 2.42112 ( 144) 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_ALPHA1-3 : bond 0.00360 ( 3) link_ALPHA1-3 : angle 1.78348 ( 9) hydrogen bonds : bond 0.18707 ( 526) hydrogen bonds : angle 7.00802 ( 1410) SS BOND : bond 0.00307 ( 28) SS BOND : angle 0.61493 ( 56) covalent geometry : bond 0.00554 (17327) covalent geometry : angle 0.76411 (23601) *********************** 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 : 1.740 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: M 35 TRP cc_start: 0.8420 (m100) cc_final: 0.7911 (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: 0.8477 (m-30) REVERT: M 214 PHE cc_start: 0.8295 (m-80) cc_final: 0.7967 (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: 0.7921 (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: 0.8602 (ttmm) REVERT: D 202 THR cc_start: 0.9208 (m) cc_final: 0.8908 (p) REVERT: D 231 LYS cc_start: 0.8557 (ttpt) cc_final: 0.8335 (tttt) REVERT: D 428 TRP cc_start: 0.8243 (m-90) cc_final: 0.7840 (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: 0.9230 (p) REVERT: I 49 GLU cc_start: 0.7620 (mt-10) cc_final: 0.6904 (mt-10) REVERT: I 493 LYS cc_start: 0.9300 (mmtt) cc_final: 0.9012 (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: 0.6300 (t70) REVERT: C 663 LEU cc_start: 0.7357 (mt) cc_final: 0.6771 (mt) REVERT: J 589 LYS cc_start: 0.9100 (tptt) cc_final: 0.8886 (tppt) REVERT: J 637 SER cc_start: 0.9146 (p) cc_final: 0.8936 (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: 0.3503 time to fit residues: 187.3595 Evaluate side-chains 207 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 207 time to evaluate : 1.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 179 optimal weight: 3.9990 chunk 160 optimal weight: 20.0000 chunk 89 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 108 optimal weight: 0.6980 chunk 85 optimal weight: 4.9990 chunk 166 optimal weight: 20.0000 chunk 64 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 chunk 123 optimal weight: 5.9990 chunk 192 optimal weight: 4.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- 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 = 0.3332 r_free = 0.3332 target = 0.093933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.078845 restraints weight = 45048.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.080870 restraints weight = 26154.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.082223 restraints weight = 18413.170| |-----------------------------------------------------------------------------| r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17431 Z= 0.187 Angle : 0.673 10.635 23885 Z= 0.314 Chirality : 0.045 0.266 2952 Planarity : 0.003 0.034 2957 Dihedral : 9.533 86.441 3888 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.67 % Allowed : 9.30 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.21), residues: 1689 helix: 2.38 (0.26), residues: 400 sheet: -0.31 (0.24), residues: 452 loop : -0.60 (0.21), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 624 HIS 0.011 0.001 HIS M 105 PHE 0.020 0.002 PHE I 362 TYR 0.015 0.001 TYR D 195 ARG 0.005 0.001 ARG M 477 Details of bonding type rmsd link_NAG-ASN : bond 0.00441 ( 48) link_NAG-ASN : angle 1.82244 ( 144) link_ALPHA1-6 : bond 0.00458 ( 3) link_ALPHA1-6 : angle 1.79849 ( 9) link_BETA1-4 : bond 0.00554 ( 22) link_BETA1-4 : angle 2.33552 ( 66) link_ALPHA1-3 : bond 0.00842 ( 3) link_ALPHA1-3 : angle 2.22425 ( 9) hydrogen bonds : bond 0.04463 ( 526) hydrogen bonds : angle 5.32847 ( 1410) SS BOND : bond 0.00402 ( 28) SS BOND : angle 0.99545 ( 56) covalent geometry : bond 0.00427 (17327) covalent geometry : angle 0.64572 (23601) *********************** 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 267 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 226 time to evaluate : 1.693 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: M 35 TRP cc_start: 0.8365 (m100) cc_final: 0.7990 (m100) REVERT: M 135 ASN cc_start: 0.8610 (p0) cc_final: 0.8320 (p0) REVERT: M 180 ASP cc_start: 0.8558 (m-30) cc_final: 0.8308 (m-30) REVERT: M 268 SER cc_start: 0.8893 (m) cc_final: 0.8676 (p) REVERT: M 483 GLU cc_start: 0.8232 (mm-30) cc_final: 0.7677 (mm-30) REVERT: D 42 VAL cc_start: 0.9317 (t) cc_final: 0.9038 (p) REVERT: D 117 LYS cc_start: 0.8844 (tttt) cc_final: 0.8543 (ttmm) REVERT: D 428 TRP cc_start: 0.8016 (m-90) cc_final: 0.7651 (m-90) REVERT: I 307 THR cc_start: 0.8455 (m) cc_final: 0.8162 (p) REVERT: I 420 ARG cc_start: 0.8681 (OUTLIER) cc_final: 0.7293 (mpp80) REVERT: I 493 LYS cc_start: 0.9302 (mmtt) cc_final: 0.8968 (mmtp) REVERT: N 541 GLN cc_start: 0.8209 (mm110) cc_final: 0.7768 (mt0) REVERT: N 543 ARG cc_start: 0.8063 (mmt90) cc_final: 0.7703 (mmt90) REVERT: C 636 GLU cc_start: 0.8503 (tp30) cc_final: 0.8258 (tm-30) REVERT: C 648 LEU cc_start: 0.9353 (OUTLIER) cc_final: 0.9031 (mm) REVERT: J 622 GLU cc_start: 0.8604 (tp30) cc_final: 0.8254 (tp30) REVERT: J 635 GLU cc_start: 0.8399 (tp30) cc_final: 0.8106 (tm-30) REVERT: J 657 ASN cc_start: 0.8454 (m-40) cc_final: 0.7961 (t0) outliers start: 41 outliers final: 21 residues processed: 258 average time/residue: 0.3041 time to fit residues: 116.4857 Evaluate side-chains 212 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 189 time to evaluate : 1.608 ------------------------------------------------------------------------------- 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 252 THR Chi-restraints excluded: chain M residue 338 ASP Chi-restraints excluded: chain M residue 394 SER Chi-restraints excluded: chain M residue 417 ILE 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 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 101 optimal weight: 0.8980 chunk 139 optimal weight: 10.0000 chunk 182 optimal weight: 3.9990 chunk 191 optimal weight: 0.6980 chunk 86 optimal weight: 6.9990 chunk 158 optimal weight: 10.0000 chunk 51 optimal weight: 3.9990 chunk 206 optimal weight: 5.9990 chunk 52 optimal weight: 0.9980 chunk 169 optimal weight: 9.9990 chunk 68 optimal weight: 7.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- 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** N 654 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.092982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.077905 restraints weight = 45034.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.079898 restraints weight = 26250.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.081237 restraints weight = 18553.711| |-----------------------------------------------------------------------------| r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17431 Z= 0.180 Angle : 0.631 10.319 23885 Z= 0.298 Chirality : 0.044 0.275 2952 Planarity : 0.003 0.041 2957 Dihedral : 8.715 82.689 3888 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.60 % Allowed : 11.26 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.21), residues: 1689 helix: 2.40 (0.26), residues: 394 sheet: -0.27 (0.23), residues: 469 loop : -0.54 (0.22), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP N 624 HIS 0.004 0.001 HIS M 220 PHE 0.017 0.002 PHE I 362 TYR 0.013 0.001 TYR D 195 ARG 0.004 0.000 ARG I 196 Details of bonding type rmsd link_NAG-ASN : bond 0.00363 ( 48) link_NAG-ASN : angle 1.75907 ( 144) link_ALPHA1-6 : bond 0.00211 ( 3) link_ALPHA1-6 : angle 1.75159 ( 9) link_BETA1-4 : bond 0.00448 ( 22) link_BETA1-4 : angle 2.07578 ( 66) link_ALPHA1-3 : bond 0.00916 ( 3) link_ALPHA1-3 : angle 2.05013 ( 9) hydrogen bonds : bond 0.03941 ( 526) hydrogen bonds : angle 5.02605 ( 1410) SS BOND : bond 0.00551 ( 28) SS BOND : angle 1.29869 ( 56) covalent geometry : bond 0.00413 (17327) covalent geometry : angle 0.60417 (23601) *********************** 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 243 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 203 time to evaluate : 1.849 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: 0.8328 (m100) cc_final: 0.7997 (m100) REVERT: M 180 ASP cc_start: 0.8552 (m-30) cc_final: 0.8317 (m-30) REVERT: M 268 SER cc_start: 0.8857 (m) cc_final: 0.8616 (p) REVERT: M 483 GLU cc_start: 0.8168 (mm-30) cc_final: 0.7734 (mm-30) REVERT: D 42 VAL cc_start: 0.9301 (t) cc_final: 0.9021 (p) REVERT: D 117 LYS cc_start: 0.8873 (tttt) cc_final: 0.8550 (ttmm) REVERT: D 428 TRP cc_start: 0.8052 (m-90) cc_final: 0.7679 (m-90) REVERT: I 420 ARG cc_start: 0.8703 (OUTLIER) cc_final: 0.7397 (mpp80) REVERT: N 541 GLN cc_start: 0.8258 (mm110) cc_final: 0.7739 (mt0) REVERT: N 590 ASP cc_start: 0.8115 (OUTLIER) cc_final: 0.7822 (t0) REVERT: N 630 MET cc_start: 0.7868 (mmm) cc_final: 0.7490 (tmm) REVERT: N 659 LYS cc_start: 0.6444 (tttt) cc_final: 0.5150 (tttt) REVERT: C 628 MET cc_start: 0.7942 (mtm) cc_final: 0.7595 (mtp) REVERT: C 648 LEU cc_start: 0.9411 (OUTLIER) cc_final: 0.9138 (mm) REVERT: J 585 GLU cc_start: 0.8283 (mt-10) cc_final: 0.7956 (mt-10) REVERT: J 622 GLU cc_start: 0.8673 (tp30) cc_final: 0.8278 (tp30) REVERT: J 635 GLU cc_start: 0.8320 (tp30) cc_final: 0.8118 (tm-30) REVERT: J 657 ASN cc_start: 0.8448 (m-40) cc_final: 0.7987 (t0) outliers start: 40 outliers final: 20 residues processed: 225 average time/residue: 0.2981 time to fit residues: 99.6549 Evaluate side-chains 209 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 186 time to evaluate : 1.579 ------------------------------------------------------------------------------- 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 172 VAL 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 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 327 ASN Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain I residue 115 SER 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 566 LEU Chi-restraints excluded: chain N residue 590 ASP Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 614 SER 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 105 optimal weight: 0.9990 chunk 129 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 chunk 67 optimal weight: 7.9990 chunk 1 optimal weight: 4.9990 chunk 157 optimal weight: 20.0000 chunk 142 optimal weight: 10.0000 chunk 162 optimal weight: 10.0000 chunk 16 optimal weight: 3.9990 chunk 134 optimal weight: 9.9990 chunk 8 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 135 ASN M 334 ASN ** D 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 199 ASN I 426 ASN C 566 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.089890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.075126 restraints weight = 45392.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.077062 restraints weight = 26379.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.078352 restraints weight = 18565.032| |-----------------------------------------------------------------------------| r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.2936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 17431 Z= 0.293 Angle : 0.764 10.438 23885 Z= 0.359 Chirality : 0.047 0.241 2952 Planarity : 0.004 0.045 2957 Dihedral : 8.869 82.840 3888 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 3.19 % Allowed : 12.75 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.21), residues: 1689 helix: 2.32 (0.27), residues: 382 sheet: -0.43 (0.23), residues: 463 loop : -0.75 (0.22), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP I 480 HIS 0.010 0.002 HIS N 565 PHE 0.022 0.002 PHE I 362 TYR 0.017 0.002 TYR I 195 ARG 0.005 0.001 ARG I 196 Details of bonding type rmsd link_NAG-ASN : bond 0.00465 ( 48) link_NAG-ASN : angle 2.04442 ( 144) link_ALPHA1-6 : bond 0.00123 ( 3) link_ALPHA1-6 : angle 1.75388 ( 9) link_BETA1-4 : bond 0.00387 ( 22) link_BETA1-4 : angle 2.23339 ( 66) link_ALPHA1-3 : bond 0.00792 ( 3) link_ALPHA1-3 : angle 2.57843 ( 9) hydrogen bonds : bond 0.04396 ( 526) hydrogen bonds : angle 5.09955 ( 1410) SS BOND : bond 0.00858 ( 28) SS BOND : angle 1.19492 ( 56) covalent geometry : bond 0.00668 (17327) covalent geometry : angle 0.73739 (23601) *********************** 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 244 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 195 time to evaluate : 1.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 35 TRP cc_start: 0.8395 (m100) cc_final: 0.8009 (m100) REVERT: M 180 ASP cc_start: 0.8607 (m-30) cc_final: 0.8367 (m-30) REVERT: M 255 ILE cc_start: 0.9407 (mm) cc_final: 0.9171 (mt) REVERT: M 435 MET cc_start: 0.9148 (ptm) cc_final: 0.8838 (ptp) REVERT: M 483 GLU cc_start: 0.8080 (mm-30) cc_final: 0.7525 (tp30) REVERT: D 42 VAL cc_start: 0.9317 (t) cc_final: 0.9054 (p) REVERT: D 117 LYS cc_start: 0.8883 (tttt) cc_final: 0.8573 (ttmm) REVERT: D 301 THR cc_start: 0.9225 (OUTLIER) cc_final: 0.8942 (p) REVERT: I 420 ARG cc_start: 0.8731 (OUTLIER) cc_final: 0.7450 (mpp80) REVERT: N 541 GLN cc_start: 0.8287 (mm110) cc_final: 0.7865 (mt0) REVERT: N 572 TRP cc_start: 0.7692 (m-10) cc_final: 0.7463 (m-10) REVERT: J 585 GLU cc_start: 0.8319 (mt-10) cc_final: 0.7979 (mt-10) REVERT: J 622 GLU cc_start: 0.8782 (tp30) cc_final: 0.8484 (tp30) REVERT: J 657 ASN cc_start: 0.8471 (m-40) cc_final: 0.8234 (t0) outliers start: 49 outliers final: 29 residues processed: 227 average time/residue: 0.3158 time to fit residues: 105.8003 Evaluate side-chains 211 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 180 time to evaluate : 1.629 ------------------------------------------------------------------------------- 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 172 VAL Chi-restraints excluded: chain M residue 335 ILE 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 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 301 THR 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 173 TYR Chi-restraints excluded: chain I residue 199 ASN Chi-restraints excluded: chain I residue 374 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 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 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 42 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 56 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 130 optimal weight: 0.9980 chunk 152 optimal weight: 6.9990 chunk 185 optimal weight: 0.8980 chunk 139 optimal weight: 9.9990 chunk 157 optimal weight: 20.0000 chunk 149 optimal weight: 10.0000 chunk 106 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 291 HIS ** D 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 199 ASN I 426 ASN N 654 GLN C 566 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.092335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.077696 restraints weight = 45091.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.079676 restraints weight = 25625.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.081018 restraints weight = 17784.233| |-----------------------------------------------------------------------------| r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.3074 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= 0.128 Angle : 0.603 9.698 23885 Z= 0.287 Chirality : 0.043 0.249 2952 Planarity : 0.003 0.040 2957 Dihedral : 8.132 78.572 3888 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.28 % Allowed : 13.92 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.21), residues: 1689 helix: 2.52 (0.27), residues: 381 sheet: -0.23 (0.24), residues: 458 loop : -0.61 (0.22), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP J 624 HIS 0.009 0.001 HIS C 566 PHE 0.016 0.001 PHE I 362 TYR 0.012 0.001 TYR D 195 ARG 0.005 0.000 ARG C 635 Details of bonding type rmsd link_NAG-ASN : bond 0.00316 ( 48) link_NAG-ASN : angle 1.71762 ( 144) link_ALPHA1-6 : bond 0.00203 ( 3) link_ALPHA1-6 : angle 1.61556 ( 9) link_BETA1-4 : bond 0.00478 ( 22) link_BETA1-4 : angle 2.09604 ( 66) link_ALPHA1-3 : bond 0.01003 ( 3) link_ALPHA1-3 : angle 2.00913 ( 9) hydrogen bonds : bond 0.03602 ( 526) hydrogen bonds : angle 4.80550 ( 1410) SS BOND : bond 0.00523 ( 28) SS BOND : angle 0.97895 ( 56) covalent geometry : bond 0.00292 (17327) covalent geometry : angle 0.57664 (23601) *********************** 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 238 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 203 time to evaluate : 1.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 35 TRP cc_start: 0.8263 (m100) cc_final: 0.8015 (m100) REVERT: M 483 GLU cc_start: 0.7991 (mm-30) cc_final: 0.7637 (mm-30) REVERT: D 42 VAL cc_start: 0.9295 (t) cc_final: 0.9008 (p) REVERT: D 117 LYS cc_start: 0.8895 (tttt) cc_final: 0.8585 (ttmm) REVERT: D 202 THR cc_start: 0.9313 (m) cc_final: 0.9030 (p) REVERT: D 428 TRP cc_start: 0.8040 (m-90) cc_final: 0.7629 (m-90) REVERT: I 103 GLN cc_start: 0.8304 (tm-30) cc_final: 0.7735 (tm-30) REVERT: I 420 ARG cc_start: 0.8707 (OUTLIER) cc_final: 0.7433 (mpp80) REVERT: N 541 GLN cc_start: 0.8235 (mm110) cc_final: 0.7774 (mt0) REVERT: N 630 MET cc_start: 0.7848 (mmm) cc_final: 0.7519 (tmm) REVERT: J 585 GLU cc_start: 0.8318 (mt-10) cc_final: 0.8088 (mt-10) REVERT: J 622 GLU cc_start: 0.8772 (tp30) cc_final: 0.8404 (tp30) REVERT: J 635 GLU cc_start: 0.8485 (tp30) cc_final: 0.8268 (tp30) REVERT: J 657 ASN cc_start: 0.8537 (m-40) cc_final: 0.8105 (t0) outliers start: 35 outliers final: 20 residues processed: 227 average time/residue: 0.3198 time to fit residues: 106.7709 Evaluate side-chains 197 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 176 time to evaluate : 1.689 ------------------------------------------------------------------------------- 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 125 LEU Chi-restraints excluded: chain M residue 172 VAL 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 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 662 LEU Chi-restraints excluded: chain C residue 523 PHE Chi-restraints excluded: chain C residue 585 ILE 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 117 optimal weight: 2.9990 chunk 143 optimal weight: 10.0000 chunk 122 optimal weight: 6.9990 chunk 107 optimal weight: 0.8980 chunk 161 optimal weight: 30.0000 chunk 170 optimal weight: 10.0000 chunk 42 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 85 optimal weight: 6.9990 chunk 9 optimal weight: 8.9990 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 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 = 0.3266 r_free = 0.3266 target = 0.090113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.075538 restraints weight = 45482.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.077473 restraints weight = 26100.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.078783 restraints weight = 18237.223| |-----------------------------------------------------------------------------| r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.3338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 17431 Z= 0.238 Angle : 0.698 10.425 23885 Z= 0.328 Chirality : 0.045 0.252 2952 Planarity : 0.003 0.045 2957 Dihedral : 8.161 77.439 3888 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.93 % Allowed : 14.38 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.21), residues: 1689 helix: 2.36 (0.27), residues: 381 sheet: -0.19 (0.24), residues: 449 loop : -0.71 (0.22), residues: 859 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP N 572 HIS 0.006 0.001 HIS N 565 PHE 0.018 0.002 PHE I 362 TYR 0.015 0.001 TYR I 195 ARG 0.006 0.001 ARG C 635 Details of bonding type rmsd link_NAG-ASN : bond 0.00381 ( 48) link_NAG-ASN : angle 1.93057 ( 144) link_ALPHA1-6 : bond 0.00365 ( 3) link_ALPHA1-6 : angle 1.63144 ( 9) link_BETA1-4 : bond 0.00372 ( 22) link_BETA1-4 : angle 2.14446 ( 66) link_ALPHA1-3 : bond 0.00837 ( 3) link_ALPHA1-3 : angle 2.53975 ( 9) hydrogen bonds : bond 0.04010 ( 526) hydrogen bonds : angle 4.89283 ( 1410) SS BOND : bond 0.00562 ( 28) SS BOND : angle 0.93323 ( 56) covalent geometry : bond 0.00554 (17327) covalent geometry : angle 0.67269 (23601) *********************** 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 238 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 193 time to evaluate : 1.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 35 TRP cc_start: 0.8353 (m100) cc_final: 0.8026 (m100) REVERT: M 483 GLU cc_start: 0.7990 (mm-30) cc_final: 0.7460 (tp30) REVERT: D 117 LYS cc_start: 0.8943 (tttt) cc_final: 0.8621 (ttmm) REVERT: D 428 TRP cc_start: 0.8166 (m-90) cc_final: 0.7695 (m-90) REVERT: I 103 GLN cc_start: 0.8578 (tm-30) cc_final: 0.8149 (tm-30) REVERT: I 378 ASN cc_start: 0.8889 (t0) cc_final: 0.7877 (p0) REVERT: I 420 ARG cc_start: 0.8716 (OUTLIER) cc_final: 0.7413 (mpp80) REVERT: N 541 GLN cc_start: 0.8305 (mm110) cc_final: 0.7783 (mt0) REVERT: N 630 MET cc_start: 0.8011 (mmm) cc_final: 0.7547 (tmm) REVERT: C 607 CYS cc_start: 0.8058 (OUTLIER) cc_final: 0.7852 (m) REVERT: J 585 GLU cc_start: 0.8332 (mt-10) cc_final: 0.8077 (mt-10) REVERT: J 622 GLU cc_start: 0.8806 (tp30) cc_final: 0.8452 (tp30) REVERT: J 657 ASN cc_start: 0.8475 (m-40) cc_final: 0.7950 (t0) outliers start: 45 outliers final: 31 residues processed: 225 average time/residue: 0.3150 time to fit residues: 105.3186 Evaluate side-chains 218 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 185 time to evaluate : 1.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 37 THR 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 181 ILE 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 327 ASN Chi-restraints excluded: chain D residue 426 ASN 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 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 N residue 616 SER Chi-restraints excluded: chain C residue 523 PHE 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 639 ASN Chi-restraints excluded: chain J residue 567 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 178 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 113 optimal weight: 7.9990 chunk 22 optimal weight: 0.6980 chunk 157 optimal weight: 20.0000 chunk 194 optimal weight: 3.9990 chunk 163 optimal weight: 9.9990 chunk 196 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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 N 654 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.090873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.076331 restraints weight = 45203.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.078271 restraints weight = 25802.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.079575 restraints weight = 18020.067| |-----------------------------------------------------------------------------| r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.3446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 17431 Z= 0.178 Angle : 0.643 10.237 23885 Z= 0.303 Chirality : 0.043 0.250 2952 Planarity : 0.003 0.040 2957 Dihedral : 7.855 74.784 3888 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.86 % Allowed : 15.03 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.21), residues: 1689 helix: 2.41 (0.27), residues: 381 sheet: -0.14 (0.25), residues: 432 loop : -0.64 (0.21), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP N 572 HIS 0.011 0.001 HIS M 72 PHE 0.017 0.002 PHE I 362 TYR 0.014 0.001 TYR I 195 ARG 0.007 0.000 ARG C 635 Details of bonding type rmsd link_NAG-ASN : bond 0.00287 ( 48) link_NAG-ASN : angle 1.82192 ( 144) link_ALPHA1-6 : bond 0.00337 ( 3) link_ALPHA1-6 : angle 1.61581 ( 9) link_BETA1-4 : bond 0.00479 ( 22) link_BETA1-4 : angle 2.10686 ( 66) link_ALPHA1-3 : bond 0.00968 ( 3) link_ALPHA1-3 : angle 2.29343 ( 9) hydrogen bonds : bond 0.03746 ( 526) hydrogen bonds : angle 4.79867 ( 1410) SS BOND : bond 0.00480 ( 28) SS BOND : angle 1.02521 ( 56) covalent geometry : bond 0.00413 (17327) covalent geometry : angle 0.61687 (23601) *********************** 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 238 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 194 time to evaluate : 1.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 35 TRP cc_start: 0.8286 (m100) cc_final: 0.8035 (m100) REVERT: M 483 GLU cc_start: 0.7979 (mm-30) cc_final: 0.7481 (tp30) REVERT: D 42 VAL cc_start: 0.9261 (t) cc_final: 0.8999 (p) REVERT: D 117 LYS cc_start: 0.8960 (tttt) cc_final: 0.8644 (ttmm) REVERT: D 202 THR cc_start: 0.9312 (m) cc_final: 0.9027 (p) REVERT: I 378 ASN cc_start: 0.8881 (t0) cc_final: 0.7906 (p0) REVERT: I 420 ARG cc_start: 0.8709 (OUTLIER) cc_final: 0.7424 (mpp80) REVERT: N 541 GLN cc_start: 0.8275 (mm110) cc_final: 0.7819 (mt0) REVERT: N 630 MET cc_start: 0.8014 (mmm) cc_final: 0.7552 (tmm) REVERT: C 566 HIS cc_start: 0.7094 (OUTLIER) cc_final: 0.6665 (p90) REVERT: C 607 CYS cc_start: 0.8072 (OUTLIER) cc_final: 0.7835 (m) REVERT: J 585 GLU cc_start: 0.8315 (mt-10) cc_final: 0.8047 (mt-10) REVERT: J 622 GLU cc_start: 0.8792 (tp30) cc_final: 0.8438 (tp30) REVERT: J 657 ASN cc_start: 0.8364 (m-40) cc_final: 0.7846 (t0) outliers start: 44 outliers final: 34 residues processed: 221 average time/residue: 0.3111 time to fit residues: 101.3041 Evaluate side-chains 224 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 187 time to evaluate : 1.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain M residue 74 CYS Chi-restraints excluded: chain M residue 125 LEU Chi-restraints excluded: chain M residue 170 GLN Chi-restraints excluded: chain M residue 172 VAL Chi-restraints excluded: chain M residue 180 ASP Chi-restraints excluded: chain M residue 252 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 D residue 426 ASN Chi-restraints excluded: chain D residue 448 SER Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain I residue 42 VAL 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 605 CYS Chi-restraints excluded: chain N residue 662 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 566 HIS Chi-restraints excluded: chain C residue 585 ILE Chi-restraints excluded: chain C residue 607 CYS Chi-restraints excluded: chain C residue 639 ASN Chi-restraints excluded: chain J residue 567 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 192 optimal weight: 0.5980 chunk 158 optimal weight: 20.0000 chunk 13 optimal weight: 1.9990 chunk 84 optimal weight: 0.4980 chunk 151 optimal weight: 9.9990 chunk 149 optimal weight: 9.9990 chunk 55 optimal weight: 3.9990 chunk 178 optimal weight: 0.8980 chunk 52 optimal weight: 6.9990 chunk 128 optimal weight: 0.0970 chunk 80 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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** D 426 ASN N 654 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.092726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.078199 restraints weight = 44744.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.080174 restraints weight = 25457.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.081490 restraints weight = 17725.873| |-----------------------------------------------------------------------------| r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.3584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 17431 Z= 0.108 Angle : 0.584 10.135 23885 Z= 0.278 Chirality : 0.042 0.248 2952 Planarity : 0.003 0.039 2957 Dihedral : 7.227 70.670 3888 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.80 % Allowed : 15.35 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.21), residues: 1689 helix: 2.57 (0.27), residues: 376 sheet: 0.02 (0.25), residues: 432 loop : -0.61 (0.21), residues: 881 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP N 572 HIS 0.009 0.001 HIS M 72 PHE 0.015 0.001 PHE I 362 TYR 0.012 0.001 TYR M 39 ARG 0.008 0.000 ARG C 635 Details of bonding type rmsd link_NAG-ASN : bond 0.00302 ( 48) link_NAG-ASN : angle 1.59334 ( 144) link_ALPHA1-6 : bond 0.00419 ( 3) link_ALPHA1-6 : angle 1.57274 ( 9) link_BETA1-4 : bond 0.00503 ( 22) link_BETA1-4 : angle 2.00450 ( 66) link_ALPHA1-3 : bond 0.01083 ( 3) link_ALPHA1-3 : angle 1.95990 ( 9) hydrogen bonds : bond 0.03264 ( 526) hydrogen bonds : angle 4.62844 ( 1410) SS BOND : bond 0.00361 ( 28) SS BOND : angle 0.82911 ( 56) covalent geometry : bond 0.00245 (17327) covalent geometry : angle 0.56081 (23601) *********************** 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 250 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 207 time to evaluate : 1.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 483 GLU cc_start: 0.7903 (mm-30) cc_final: 0.7415 (tp30) REVERT: D 117 LYS cc_start: 0.8939 (tttt) cc_final: 0.8637 (ttmm) REVERT: D 202 THR cc_start: 0.9277 (m) cc_final: 0.9012 (p) REVERT: I 378 ASN cc_start: 0.8812 (t0) cc_final: 0.7882 (p0) REVERT: I 420 ARG cc_start: 0.8678 (OUTLIER) cc_final: 0.7434 (mpp80) REVERT: N 541 GLN cc_start: 0.8235 (mm110) cc_final: 0.7445 (tp40) REVERT: N 630 MET cc_start: 0.8045 (mmm) cc_final: 0.7480 (tmm) REVERT: C 545 LEU cc_start: 0.7266 (OUTLIER) cc_final: 0.6833 (tt) REVERT: C 566 HIS cc_start: 0.6924 (p90) cc_final: 0.6490 (p90) REVERT: J 585 GLU cc_start: 0.8260 (mt-10) cc_final: 0.8045 (mt-10) REVERT: J 622 GLU cc_start: 0.8758 (tp30) cc_final: 0.8416 (tp30) REVERT: J 657 ASN cc_start: 0.8265 (m-40) cc_final: 0.7779 (t0) outliers start: 43 outliers final: 29 residues processed: 233 average time/residue: 0.2999 time to fit residues: 103.2347 Evaluate side-chains 222 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 191 time to evaluate : 1.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 37 THR 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 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 426 ASN Chi-restraints excluded: chain D residue 428 TRP Chi-restraints excluded: chain D residue 448 SER Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain I residue 115 SER 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 523 PHE Chi-restraints excluded: chain N residue 537 THR Chi-restraints excluded: chain N residue 605 CYS Chi-restraints excluded: chain N residue 662 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 585 ILE Chi-restraints excluded: chain C residue 639 ASN 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 111 optimal weight: 10.0000 chunk 211 optimal weight: 7.9990 chunk 171 optimal weight: 20.0000 chunk 26 optimal weight: 0.0050 chunk 113 optimal weight: 3.9990 chunk 127 optimal weight: 4.9990 chunk 122 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 183 optimal weight: 4.9990 chunk 191 optimal weight: 2.9990 chunk 31 optimal weight: 9.9990 overall best weight: 3.4002 ------------------------------------------------------------------------------- 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** D 426 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 = 0.3257 r_free = 0.3257 target = 0.089637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.075088 restraints weight = 45879.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.077011 restraints weight = 26318.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.078295 restraints weight = 18419.475| |-----------------------------------------------------------------------------| r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.3730 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= 0.264 Angle : 0.728 10.947 23885 Z= 0.342 Chirality : 0.045 0.252 2952 Planarity : 0.004 0.046 2957 Dihedral : 7.731 70.406 3888 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.80 % Allowed : 14.83 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.21), residues: 1689 helix: 2.31 (0.27), residues: 381 sheet: -0.18 (0.25), residues: 446 loop : -0.70 (0.22), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP N 572 HIS 0.015 0.001 HIS M 72 PHE 0.017 0.002 PHE I 362 TYR 0.022 0.002 TYR C 588 ARG 0.007 0.001 ARG C 635 Details of bonding type rmsd link_NAG-ASN : bond 0.00382 ( 48) link_NAG-ASN : angle 1.96631 ( 144) link_ALPHA1-6 : bond 0.00396 ( 3) link_ALPHA1-6 : angle 1.58063 ( 9) link_BETA1-4 : bond 0.00371 ( 22) link_BETA1-4 : angle 2.14116 ( 66) link_ALPHA1-3 : bond 0.00980 ( 3) link_ALPHA1-3 : angle 2.67433 ( 9) hydrogen bonds : bond 0.04104 ( 526) hydrogen bonds : angle 4.86619 ( 1410) SS BOND : bond 0.00606 ( 28) SS BOND : angle 0.99225 ( 56) covalent geometry : bond 0.00607 (17327) covalent geometry : angle 0.70293 (23601) *********************** 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 225 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 182 time to evaluate : 1.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 483 GLU cc_start: 0.7991 (mm-30) cc_final: 0.7526 (tp30) REVERT: D 117 LYS cc_start: 0.8920 (tttt) cc_final: 0.8599 (ttmm) REVERT: I 420 ARG cc_start: 0.8703 (OUTLIER) cc_final: 0.7406 (mpp80) REVERT: N 630 MET cc_start: 0.8222 (mmm) cc_final: 0.7693 (tmm) REVERT: C 545 LEU cc_start: 0.7290 (OUTLIER) cc_final: 0.6848 (tt) REVERT: C 566 HIS cc_start: 0.6954 (OUTLIER) cc_final: 0.6558 (p90) REVERT: J 585 GLU cc_start: 0.8394 (mt-10) cc_final: 0.8092 (mt-10) REVERT: J 622 GLU cc_start: 0.8857 (tp30) cc_final: 0.8388 (tp30) REVERT: J 657 ASN cc_start: 0.8346 (m-40) cc_final: 0.7853 (t0) outliers start: 43 outliers final: 33 residues processed: 212 average time/residue: 0.3166 time to fit residues: 99.2292 Evaluate side-chains 209 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 173 time to evaluate : 1.755 ------------------------------------------------------------------------------- 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 170 GLN Chi-restraints excluded: chain M residue 180 ASP Chi-restraints excluded: chain M residue 181 ILE Chi-restraints excluded: chain M residue 431 VAL Chi-restraints excluded: chain D residue 99 ASP 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 268 SER Chi-restraints excluded: chain D residue 305 ASN Chi-restraints excluded: chain D residue 428 TRP Chi-restraints excluded: chain D residue 448 SER Chi-restraints excluded: chain I residue 42 VAL 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 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 537 THR Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 566 HIS Chi-restraints excluded: chain C residue 631 MET Chi-restraints excluded: chain C residue 639 ASN 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 145 optimal weight: 9.9990 chunk 30 optimal weight: 0.9980 chunk 204 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 119 optimal weight: 7.9990 chunk 201 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 135 optimal weight: 8.9990 chunk 12 optimal weight: 0.8980 chunk 122 optimal weight: 9.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- 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** D 426 ASN I 426 ASN ** N 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.091054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.076652 restraints weight = 45145.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.078588 restraints weight = 25709.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.079905 restraints weight = 17869.040| |-----------------------------------------------------------------------------| r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.3804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 17431 Z= 0.168 Angle : 0.650 10.359 23885 Z= 0.309 Chirality : 0.043 0.250 2952 Planarity : 0.003 0.042 2957 Dihedral : 7.444 67.439 3888 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.15 % Allowed : 15.61 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.21), residues: 1689 helix: 2.32 (0.27), residues: 382 sheet: -0.11 (0.24), residues: 444 loop : -0.67 (0.22), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.075 0.002 TRP N 572 HIS 0.028 0.001 HIS M 72 PHE 0.015 0.002 PHE I 362 TYR 0.019 0.001 TYR C 588 ARG 0.008 0.001 ARG C 635 Details of bonding type rmsd link_NAG-ASN : bond 0.00290 ( 48) link_NAG-ASN : angle 1.73357 ( 144) link_ALPHA1-6 : bond 0.00407 ( 3) link_ALPHA1-6 : angle 1.54860 ( 9) link_BETA1-4 : bond 0.00439 ( 22) link_BETA1-4 : angle 2.04610 ( 66) link_ALPHA1-3 : bond 0.01033 ( 3) link_ALPHA1-3 : angle 2.25455 ( 9) hydrogen bonds : bond 0.03700 ( 526) hydrogen bonds : angle 4.78519 ( 1410) SS BOND : bond 0.00440 ( 28) SS BOND : angle 1.00444 ( 56) covalent geometry : bond 0.00391 (17327) covalent geometry : angle 0.62658 (23601) ********************** 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 216 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 183 time to evaluate : 1.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 483 GLU cc_start: 0.7944 (mm-30) cc_final: 0.7471 (tp30) REVERT: D 117 LYS cc_start: 0.8901 (tttt) cc_final: 0.8609 (ttmm) REVERT: D 202 THR cc_start: 0.9271 (m) cc_final: 0.9017 (p) REVERT: I 378 ASN cc_start: 0.8894 (t0) cc_final: 0.8049 (p0) REVERT: I 420 ARG cc_start: 0.8688 (OUTLIER) cc_final: 0.7397 (mpp80) REVERT: N 541 GLN cc_start: 0.8157 (mm110) cc_final: 0.7599 (tp40) REVERT: N 630 MET cc_start: 0.8216 (mmm) cc_final: 0.7656 (tmm) REVERT: C 545 LEU cc_start: 0.7342 (OUTLIER) cc_final: 0.6856 (tt) REVERT: C 566 HIS cc_start: 0.6945 (p90) cc_final: 0.6515 (p90) REVERT: J 585 GLU cc_start: 0.8299 (mt-10) cc_final: 0.8079 (mt-10) REVERT: J 657 ASN cc_start: 0.8317 (m-40) cc_final: 0.7832 (t0) outliers start: 33 outliers final: 27 residues processed: 203 average time/residue: 0.2999 time to fit residues: 91.2481 Evaluate side-chains 205 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 176 time to evaluate : 1.681 ------------------------------------------------------------------------------- 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 170 GLN Chi-restraints excluded: chain M residue 180 ASP Chi-restraints excluded: chain M residue 431 VAL 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 448 SER Chi-restraints excluded: chain I residue 115 SER 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 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 537 THR Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 631 MET 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 33 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 92 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 200 optimal weight: 8.9990 chunk 190 optimal weight: 6.9990 chunk 111 optimal weight: 9.9990 chunk 2 optimal weight: 4.9990 chunk 119 optimal weight: 8.9990 chunk 29 optimal weight: 0.9990 chunk 56 optimal weight: 0.7980 overall best weight: 2.3186 ------------------------------------------------------------------------------- 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 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 = 0.3271 r_free = 0.3271 target = 0.090479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.075780 restraints weight = 45308.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.077827 restraints weight = 24794.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.079199 restraints weight = 16870.397| |-----------------------------------------------------------------------------| r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.3927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 17431 Z= 0.194 Angle : 0.665 10.481 23885 Z= 0.315 Chirality : 0.044 0.245 2952 Planarity : 0.003 0.044 2957 Dihedral : 7.365 63.692 3888 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.41 % Allowed : 15.55 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.21), residues: 1689 helix: 2.32 (0.27), residues: 382 sheet: -0.21 (0.24), residues: 449 loop : -0.71 (0.22), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.078 0.002 TRP N 572 HIS 0.026 0.001 HIS M 72 PHE 0.019 0.002 PHE I 362 TYR 0.021 0.001 TYR M 39 ARG 0.007 0.001 ARG M 166 Details of bonding type rmsd link_NAG-ASN : bond 0.00290 ( 48) link_NAG-ASN : angle 1.81831 ( 144) link_ALPHA1-6 : bond 0.00421 ( 3) link_ALPHA1-6 : angle 1.52119 ( 9) link_BETA1-4 : bond 0.00421 ( 22) link_BETA1-4 : angle 2.06453 ( 66) link_ALPHA1-3 : bond 0.01034 ( 3) link_ALPHA1-3 : angle 2.34479 ( 9) hydrogen bonds : bond 0.03819 ( 526) hydrogen bonds : angle 4.79013 ( 1410) SS BOND : bond 0.00521 ( 28) SS BOND : angle 1.10260 ( 56) covalent geometry : bond 0.00450 (17327) covalent geometry : angle 0.64013 (23601) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5388.32 seconds wall clock time: 94 minutes 32.38 seconds (5672.38 seconds total)