Starting phenix.real_space_refine on Sun May 18 14:13:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9axk_43968/05_2025/9axk_43968.cif Found real_map, /net/cci-nas-00/data/ceres_data/9axk_43968/05_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_43968/05_2025/9axk_43968.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9axk_43968/05_2025/9axk_43968.map" model { file = "/net/cci-nas-00/data/ceres_data/9axk_43968/05_2025/9axk_43968.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9axk_43968/05_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-5687/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: 11.28, per 1000 atoms: 0.66 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: 5.30 Conformation dependent library (CDL) restraints added in 1.9 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: 1.97 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: 4.97 Time building geometry restraints manager: 5.89 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: 6.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.670 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 38.340 Find NCS groups from input model: 0.920 Set up NCS constraints: 0.110 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.840 ------------------------------------------------------------------------------- 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 : 1.585 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: 0.3378 time to fit residues: 179.0140 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 : 1.611 ------------------------------------------------------------------------------- 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 = 0.093930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.078844 restraints weight = 45050.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.080871 restraints weight = 26183.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.082227 restraints weight = 18398.211| |-----------------------------------------------------------------------------| r_work (final): 0.3111 ------------------------------------------------------------------------------- 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 1.79850 ( 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 : 1.630 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: 0.8363 (m100) cc_final: 0.7990 (m100) REVERT: M 135 ASN cc_start: 0.8609 (p0) cc_final: 0.8319 (p0) REVERT: M 180 ASP cc_start: 0.8555 (m-30) cc_final: 0.8305 (m-30) REVERT: M 268 SER cc_start: 0.8894 (m) cc_final: 0.8676 (p) REVERT: M 483 GLU cc_start: 0.8229 (mm-30) cc_final: 0.7675 (mm-30) REVERT: D 42 VAL cc_start: 0.9317 (t) cc_final: 0.9038 (p) REVERT: D 117 LYS cc_start: 0.8842 (tttt) cc_final: 0.8542 (ttmm) REVERT: D 428 TRP cc_start: 0.8015 (m-90) cc_final: 0.7651 (m-90) REVERT: I 307 THR cc_start: 0.8454 (m) cc_final: 0.8162 (p) REVERT: I 420 ARG cc_start: 0.8679 (OUTLIER) cc_final: 0.7294 (mpp80) REVERT: I 493 LYS cc_start: 0.9301 (mmtt) cc_final: 0.8968 (mmtp) REVERT: N 541 GLN cc_start: 0.8207 (mm110) cc_final: 0.7767 (mt0) REVERT: N 543 ARG cc_start: 0.8062 (mmt90) cc_final: 0.7703 (mmt90) REVERT: C 636 GLU cc_start: 0.8498 (tp30) cc_final: 0.8254 (tm-30) REVERT: C 648 LEU cc_start: 0.9354 (OUTLIER) cc_final: 0.9032 (mm) REVERT: J 622 GLU cc_start: 0.8600 (tp30) cc_final: 0.8253 (tp30) REVERT: J 635 GLU cc_start: 0.8395 (tp30) cc_final: 0.8105 (tm-30) REVERT: J 657 ASN cc_start: 0.8455 (m-40) cc_final: 0.7962 (t0) outliers start: 41 outliers final: 21 residues processed: 258 average time/residue: 0.3116 time to fit residues: 117.5466 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 : 1.567 ------------------------------------------------------------------------------- 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: 0.7980 chunk 139 optimal weight: 10.0000 chunk 182 optimal weight: 2.9990 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: 0.0570 chunk 52 optimal weight: 0.0170 chunk 169 optimal weight: 10.0000 chunk 68 optimal weight: 7.9990 overall best weight: 0.9138 ------------------------------------------------------------------------------- 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 = 0.3349 r_free = 0.3349 target = 0.094902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.079933 restraints weight = 44419.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.081968 restraints weight = 25695.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.083338 restraints weight = 17999.738| |-----------------------------------------------------------------------------| r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17431 Z= 0.119 Angle : 0.582 9.713 23885 Z= 0.276 Chirality : 0.043 0.270 2952 Planarity : 0.003 0.038 2957 Dihedral : 8.504 80.967 3888 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.02 % Allowed : 11.45 % Favored : 86.53 % 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: 0.42 (0.21), residues: 1689 helix: 2.40 (0.26), residues: 399 sheet: -0.18 (0.23), residues: 467 loop : -0.46 (0.22), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP N 624 HIS 0.003 0.001 HIS M 105 PHE 0.015 0.001 PHE I 362 TYR 0.016 0.001 TYR M 39 ARG 0.003 0.000 ARG N 543 Details of bonding type rmsd link_NAG-ASN : bond 0.00369 ( 48) link_NAG-ASN : angle 1.64790 ( 144) link_ALPHA1-6 : bond 0.00260 ( 3) link_ALPHA1-6 : angle 1.69802 ( 9) link_BETA1-4 : bond 0.00533 ( 22) link_BETA1-4 : angle 2.04033 ( 66) link_ALPHA1-3 : bond 0.00951 ( 3) link_ALPHA1-3 : angle 1.83837 ( 9) hydrogen bonds : bond 0.03627 ( 526) hydrogen bonds : angle 4.96678 ( 1410) SS BOND : bond 0.00572 ( 28) SS BOND : angle 1.32649 ( 56) covalent geometry : bond 0.00265 (17327) covalent geometry : angle 0.55540 (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 247 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 216 time to evaluate : 1.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 35 TRP cc_start: 0.8256 (m100) cc_final: 0.7961 (m100) REVERT: M 268 SER cc_start: 0.8861 (m) cc_final: 0.8601 (p) REVERT: M 483 GLU cc_start: 0.8177 (mm-30) cc_final: 0.7710 (mm-30) REVERT: D 42 VAL cc_start: 0.9280 (t) cc_final: 0.9020 (p) REVERT: D 117 LYS cc_start: 0.8850 (tttt) cc_final: 0.8547 (ttmm) REVERT: D 202 THR cc_start: 0.9291 (m) cc_final: 0.8984 (p) REVERT: D 428 TRP cc_start: 0.8003 (m-90) cc_final: 0.7697 (m-90) REVERT: D 480 TRP cc_start: 0.8668 (m-90) cc_final: 0.8369 (m-10) REVERT: D 501 ARG cc_start: 0.7360 (mtp180) cc_final: 0.7155 (ptt-90) REVERT: I 420 ARG cc_start: 0.8679 (OUTLIER) cc_final: 0.7277 (mpp80) REVERT: N 541 GLN cc_start: 0.8184 (mm110) cc_final: 0.7692 (mt0) REVERT: N 630 MET cc_start: 0.7858 (mmm) cc_final: 0.7510 (mmm) REVERT: N 659 LYS cc_start: 0.6323 (tttt) cc_final: 0.5192 (tttt) REVERT: C 619 LYS cc_start: 0.8986 (mttp) cc_final: 0.8488 (mtpp) REVERT: C 628 MET cc_start: 0.7873 (mtm) cc_final: 0.7371 (mtm) REVERT: C 648 LEU cc_start: 0.9405 (OUTLIER) cc_final: 0.9113 (mm) REVERT: J 585 GLU cc_start: 0.8265 (mt-10) cc_final: 0.7908 (mt-10) REVERT: J 622 GLU cc_start: 0.8627 (tp30) cc_final: 0.8251 (tp30) REVERT: J 657 ASN cc_start: 0.8413 (m-40) cc_final: 0.7958 (t0) outliers start: 31 outliers final: 12 residues processed: 235 average time/residue: 0.3077 time to fit residues: 105.2612 Evaluate side-chains 207 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 193 time to evaluate : 1.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 42 VAL Chi-restraints excluded: chain M residue 125 LEU Chi-restraints excluded: chain M residue 338 ASP Chi-restraints excluded: chain M residue 431 VAL Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 189 LYS Chi-restraints excluded: chain I residue 420 ARG Chi-restraints excluded: chain I residue 483 GLU Chi-restraints excluded: chain N residue 537 THR Chi-restraints excluded: chain N residue 590 ASP Chi-restraints excluded: chain C residue 614 SER Chi-restraints excluded: chain C residue 648 LEU Chi-restraints excluded: chain J residue 638 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 105 optimal weight: 0.9980 chunk 129 optimal weight: 10.0000 chunk 9 optimal weight: 3.9990 chunk 67 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 chunk 157 optimal weight: 20.0000 chunk 142 optimal weight: 10.0000 chunk 162 optimal weight: 10.0000 chunk 16 optimal weight: 9.9990 chunk 134 optimal weight: 9.9990 chunk 8 optimal weight: 3.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- 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 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.090364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.075556 restraints weight = 45310.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.077499 restraints weight = 26313.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.078795 restraints weight = 18543.957| |-----------------------------------------------------------------------------| r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 17431 Z= 0.298 Angle : 0.760 10.378 23885 Z= 0.357 Chirality : 0.047 0.241 2952 Planarity : 0.004 0.045 2957 Dihedral : 8.721 82.169 3888 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.93 % Allowed : 12.88 % Favored : 84.19 % 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: 2.27 (0.27), residues: 388 sheet: -0.33 (0.23), residues: 471 loop : -0.62 (0.22), residues: 830 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 0.021 0.002 PHE I 176 TYR 0.015 0.002 TYR M 396 ARG 0.005 0.001 ARG I 196 Details of bonding type rmsd link_NAG-ASN : bond 0.00428 ( 48) link_NAG-ASN : angle 2.00280 ( 144) link_ALPHA1-6 : bond 0.00118 ( 3) link_ALPHA1-6 : angle 1.77844 ( 9) link_BETA1-4 : bond 0.00388 ( 22) link_BETA1-4 : angle 2.18135 ( 66) link_ALPHA1-3 : bond 0.00937 ( 3) link_ALPHA1-3 : angle 2.62458 ( 9) hydrogen bonds : bond 0.04360 ( 526) hydrogen bonds : angle 5.06028 ( 1410) SS BOND : bond 0.00724 ( 28) SS BOND : angle 1.20198 ( 56) covalent geometry : bond 0.00685 (17327) covalent geometry : angle 0.73451 (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 245 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 200 time to evaluate : 1.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 35 TRP cc_start: 0.8434 (m100) cc_final: 0.8022 (m100) REVERT: M 255 ILE cc_start: 0.9389 (mm) cc_final: 0.9164 (mt) REVERT: M 435 MET cc_start: 0.9122 (ptm) cc_final: 0.8783 (ptp) REVERT: M 483 GLU cc_start: 0.8151 (mm-30) cc_final: 0.7558 (tp30) REVERT: D 42 VAL cc_start: 0.9317 (t) cc_final: 0.9052 (p) REVERT: D 117 LYS cc_start: 0.8911 (tttt) cc_final: 0.8585 (ttmm) REVERT: I 420 ARG cc_start: 0.8740 (OUTLIER) cc_final: 0.7428 (mpp80) REVERT: N 541 GLN cc_start: 0.8295 (mm110) cc_final: 0.7835 (mt0) REVERT: N 572 TRP cc_start: 0.7654 (m-10) cc_final: 0.7428 (m-10) REVERT: C 648 LEU cc_start: 0.9423 (OUTLIER) cc_final: 0.9216 (mm) REVERT: J 585 GLU cc_start: 0.8349 (mt-10) cc_final: 0.7988 (mt-10) REVERT: J 622 GLU cc_start: 0.8813 (tp30) cc_final: 0.8444 (tp30) REVERT: J 635 GLU cc_start: 0.8014 (tm-30) cc_final: 0.7772 (tm-30) REVERT: J 653 GLN cc_start: 0.7984 (tp40) cc_final: 0.7612 (tp40) REVERT: J 657 ASN cc_start: 0.8469 (m-40) cc_final: 0.8193 (t0) outliers start: 45 outliers final: 32 residues processed: 230 average time/residue: 0.3229 time to fit residues: 109.4564 Evaluate side-chains 215 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 181 time to evaluate : 1.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 42 VAL Chi-restraints excluded: chain M residue 95 MET Chi-restraints excluded: chain M residue 125 LEU Chi-restraints excluded: chain M residue 172 VAL Chi-restraints excluded: chain M residue 181 ILE Chi-restraints excluded: chain M residue 338 ASP Chi-restraints excluded: chain M residue 374 THR Chi-restraints excluded: chain M residue 394 SER Chi-restraints excluded: chain M residue 431 VAL Chi-restraints excluded: chain D residue 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 327 ASN Chi-restraints excluded: chain D residue 379 CYS Chi-restraints excluded: chain D residue 435 MET 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 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 C residue 648 LEU Chi-restraints excluded: chain J residue 519 VAL 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: 1.9990 chunk 7 optimal weight: 0.0970 chunk 56 optimal weight: 5.9990 chunk 13 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 152 optimal weight: 5.9990 chunk 185 optimal weight: 0.8980 chunk 139 optimal weight: 10.0000 chunk 157 optimal weight: 20.0000 chunk 149 optimal weight: 9.9990 chunk 106 optimal weight: 3.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- 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 103 GLN 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 = 0.3296 r_free = 0.3296 target = 0.091792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.077089 restraints weight = 45321.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.079075 restraints weight = 25889.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.080402 restraints weight = 18051.781| |-----------------------------------------------------------------------------| r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.2989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 17431 Z= 0.171 Angle : 0.632 10.164 23885 Z= 0.299 Chirality : 0.043 0.249 2952 Planarity : 0.003 0.041 2957 Dihedral : 8.243 79.744 3888 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.99 % Allowed : 13.40 % Favored : 83.60 % 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: 0.28 (0.21), residues: 1689 helix: 2.36 (0.27), residues: 389 sheet: -0.25 (0.24), residues: 457 loop : -0.56 (0.22), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP M 96 HIS 0.007 0.001 HIS C 566 PHE 0.018 0.002 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 0.00323 ( 48) link_NAG-ASN : angle 1.78721 ( 144) link_ALPHA1-6 : bond 0.00184 ( 3) link_ALPHA1-6 : angle 1.66776 ( 9) link_BETA1-4 : bond 0.00435 ( 22) link_BETA1-4 : angle 2.10857 ( 66) link_ALPHA1-3 : bond 0.00973 ( 3) link_ALPHA1-3 : angle 2.16679 ( 9) hydrogen bonds : bond 0.03804 ( 526) hydrogen bonds : angle 4.85525 ( 1410) SS BOND : bond 0.00501 ( 28) SS BOND : angle 0.92941 ( 56) covalent geometry : bond 0.00399 (17327) covalent geometry : angle 0.60651 (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 239 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 193 time to evaluate : 1.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 35 TRP cc_start: 0.8314 (m100) cc_final: 0.8036 (m100) REVERT: M 255 ILE cc_start: 0.9387 (mm) cc_final: 0.9149 (mt) REVERT: M 483 GLU cc_start: 0.8021 (mm-30) cc_final: 0.7545 (tp30) REVERT: D 42 VAL cc_start: 0.9312 (t) cc_final: 0.9024 (p) REVERT: D 117 LYS cc_start: 0.8876 (tttt) cc_final: 0.8564 (ttmm) REVERT: D 428 TRP cc_start: 0.8117 (m-90) cc_final: 0.7645 (m-90) REVERT: I 420 ARG cc_start: 0.8700 (OUTLIER) cc_final: 0.7407 (mpp80) REVERT: N 541 GLN cc_start: 0.8246 (mm110) cc_final: 0.7714 (mt0) REVERT: N 630 MET cc_start: 0.7848 (mmm) cc_final: 0.7529 (tmm) REVERT: C 648 LEU cc_start: 0.9375 (OUTLIER) cc_final: 0.9169 (mm) REVERT: J 585 GLU cc_start: 0.8320 (mt-10) cc_final: 0.8097 (mt-10) REVERT: J 622 GLU cc_start: 0.8756 (tp30) cc_final: 0.8377 (tp30) REVERT: J 635 GLU cc_start: 0.8055 (tm-30) cc_final: 0.7797 (tm-30) REVERT: J 657 ASN cc_start: 0.8586 (m-40) cc_final: 0.8129 (t0) outliers start: 46 outliers final: 28 residues processed: 219 average time/residue: 0.3109 time to fit residues: 99.1427 Evaluate side-chains 207 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 177 time to evaluate : 1.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 42 VAL Chi-restraints excluded: chain M residue 74 CYS Chi-restraints excluded: chain M residue 125 LEU Chi-restraints excluded: chain M residue 180 ASP Chi-restraints excluded: chain M residue 338 ASP Chi-restraints excluded: chain M residue 394 SER Chi-restraints excluded: chain M residue 431 VAL Chi-restraints excluded: chain D residue 97 LYS 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 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 307 THR Chi-restraints excluded: chain I residue 420 ARG Chi-restraints excluded: chain I residue 483 GLU Chi-restraints excluded: chain N residue 537 THR Chi-restraints excluded: chain N residue 605 CYS Chi-restraints excluded: chain C residue 523 PHE Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 585 ILE 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=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: 4.9990 chunk 107 optimal weight: 0.7980 chunk 161 optimal weight: 30.0000 chunk 170 optimal weight: 10.0000 chunk 42 optimal weight: 5.9990 chunk 60 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 85 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- 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 C 566 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.091340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.076634 restraints weight = 45213.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.078605 restraints weight = 25936.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.079936 restraints weight = 18119.255| |-----------------------------------------------------------------------------| r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.3175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 17431 Z= 0.179 Angle : 0.628 10.055 23885 Z= 0.296 Chirality : 0.043 0.246 2952 Planarity : 0.003 0.042 2957 Dihedral : 7.983 77.388 3888 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.12 % Allowed : 13.86 % Favored : 83.02 % 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: 0.32 (0.21), residues: 1689 helix: 2.51 (0.27), residues: 383 sheet: -0.20 (0.24), residues: 447 loop : -0.60 (0.21), residues: 859 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP N 572 HIS 0.006 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 0.00393 ( 48) link_NAG-ASN : angle 1.77896 ( 144) link_ALPHA1-6 : bond 0.00283 ( 3) link_ALPHA1-6 : angle 1.67194 ( 9) link_BETA1-4 : bond 0.00448 ( 22) link_BETA1-4 : angle 2.09414 ( 66) link_ALPHA1-3 : bond 0.01054 ( 3) link_ALPHA1-3 : angle 2.27973 ( 9) hydrogen bonds : bond 0.03714 ( 526) hydrogen bonds : angle 4.77213 ( 1410) SS BOND : bond 0.00482 ( 28) SS BOND : angle 0.89037 ( 56) covalent geometry : bond 0.00413 (17327) covalent geometry : angle 0.60240 (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 237 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 189 time to evaluate : 1.787 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: 0.8321 (m100) cc_final: 0.8047 (m100) REVERT: M 483 GLU cc_start: 0.8038 (mm-30) cc_final: 0.7667 (mm-30) REVERT: D 117 LYS cc_start: 0.8906 (tttt) cc_final: 0.8583 (ttmm) REVERT: D 202 THR cc_start: 0.9292 (m) cc_final: 0.9002 (p) REVERT: D 301 THR cc_start: 0.9159 (OUTLIER) cc_final: 0.8876 (p) REVERT: D 428 TRP cc_start: 0.8084 (m-90) cc_final: 0.7675 (m-90) REVERT: I 378 ASN cc_start: 0.8885 (t0) cc_final: 0.7894 (p0) REVERT: I 420 ARG cc_start: 0.8715 (OUTLIER) cc_final: 0.7427 (mpp80) REVERT: N 541 GLN cc_start: 0.8280 (mm110) cc_final: 0.7749 (mt0) REVERT: N 630 MET cc_start: 0.7867 (mmm) cc_final: 0.7531 (tmm) REVERT: C 648 LEU cc_start: 0.9391 (OUTLIER) cc_final: 0.9191 (mm) REVERT: J 585 GLU cc_start: 0.8315 (mt-10) cc_final: 0.8072 (mt-10) REVERT: J 622 GLU cc_start: 0.8694 (tp30) cc_final: 0.8328 (tp30) REVERT: J 635 GLU cc_start: 0.8078 (tm-30) cc_final: 0.7700 (tm-30) REVERT: J 657 ASN cc_start: 0.8461 (m-40) cc_final: 0.7906 (t0) outliers start: 48 outliers final: 31 residues processed: 220 average time/residue: 0.3107 time to fit residues: 101.6052 Evaluate side-chains 215 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 181 time to evaluate : 1.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain M residue 42 VAL Chi-restraints excluded: chain M residue 74 CYS Chi-restraints excluded: chain M residue 125 LEU Chi-restraints excluded: chain M residue 172 VAL Chi-restraints excluded: chain M residue 180 ASP Chi-restraints excluded: chain M residue 252 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 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 D residue 448 SER Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 173 TYR Chi-restraints excluded: chain I residue 307 THR Chi-restraints excluded: chain I residue 420 ARG Chi-restraints excluded: chain I residue 483 GLU Chi-restraints excluded: chain N residue 523 PHE Chi-restraints excluded: chain N residue 537 THR Chi-restraints excluded: chain N residue 605 CYS Chi-restraints excluded: chain C residue 523 PHE Chi-restraints excluded: chain C residue 537 THR Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 614 SER Chi-restraints excluded: chain C residue 639 ASN Chi-restraints excluded: chain C residue 648 LEU Chi-restraints excluded: chain J residue 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: 0.9990 chunk 70 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 95 optimal weight: 4.9990 chunk 113 optimal weight: 10.0000 chunk 22 optimal weight: 0.6980 chunk 157 optimal weight: 20.0000 chunk 194 optimal weight: 4.9990 chunk 163 optimal weight: 10.0000 chunk 196 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.090383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.075737 restraints weight = 45387.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.077692 restraints weight = 26117.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.079011 restraints weight = 18270.378| |-----------------------------------------------------------------------------| r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.3404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 17431 Z= 0.219 Angle : 0.679 11.402 23885 Z= 0.319 Chirality : 0.044 0.246 2952 Planarity : 0.003 0.042 2957 Dihedral : 7.988 75.604 3888 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 3.06 % Allowed : 14.77 % Favored : 82.17 % 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: 0.25 (0.21), residues: 1689 helix: 2.39 (0.27), residues: 383 sheet: -0.23 (0.24), residues: 453 loop : -0.62 (0.22), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 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 0.007 0.001 ARG C 635 Details of bonding type rmsd link_NAG-ASN : bond 0.00313 ( 48) link_NAG-ASN : angle 1.87358 ( 144) link_ALPHA1-6 : bond 0.00365 ( 3) link_ALPHA1-6 : angle 1.63816 ( 9) link_BETA1-4 : bond 0.00397 ( 22) link_BETA1-4 : angle 2.10827 ( 66) link_ALPHA1-3 : bond 0.01252 ( 3) link_ALPHA1-3 : angle 2.64631 ( 9) hydrogen bonds : bond 0.03883 ( 526) hydrogen bonds : angle 4.81509 ( 1410) SS BOND : bond 0.00560 ( 28) SS BOND : angle 0.90642 ( 56) covalent geometry : bond 0.00507 (17327) covalent geometry : angle 0.65372 (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: 47 poor density : 191 time to evaluate : 1.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 35 TRP cc_start: 0.8339 (m100) cc_final: 0.8060 (m100) REVERT: M 427 MET cc_start: 0.7266 (mtm) cc_final: 0.7020 (mtp) REVERT: M 483 GLU cc_start: 0.8009 (mm-30) cc_final: 0.7495 (tp30) REVERT: D 117 LYS cc_start: 0.8943 (tttt) cc_final: 0.8622 (ttmm) REVERT: D 202 THR cc_start: 0.9313 (m) cc_final: 0.9021 (p) REVERT: D 301 THR cc_start: 0.9165 (OUTLIER) cc_final: 0.8895 (p) REVERT: I 378 ASN cc_start: 0.8897 (t0) cc_final: 0.7925 (p0) REVERT: I 420 ARG cc_start: 0.8701 (OUTLIER) cc_final: 0.7398 (mpp80) REVERT: N 523 PHE cc_start: 0.6714 (OUTLIER) cc_final: 0.6468 (p90) REVERT: N 541 GLN cc_start: 0.8279 (mm110) cc_final: 0.7790 (mt0) REVERT: N 630 MET cc_start: 0.7879 (mmm) cc_final: 0.7493 (tmm) REVERT: C 566 HIS cc_start: 0.7064 (OUTLIER) cc_final: 0.6584 (p90) REVERT: C 648 LEU cc_start: 0.9387 (OUTLIER) cc_final: 0.9186 (mm) REVERT: J 622 GLU cc_start: 0.8749 (tp30) cc_final: 0.8367 (tp30) REVERT: J 635 GLU cc_start: 0.8088 (tm-30) cc_final: 0.7678 (tm-30) REVERT: J 657 ASN cc_start: 0.8449 (m-40) cc_final: 0.7898 (t0) outliers start: 47 outliers final: 32 residues processed: 222 average time/residue: 0.3043 time to fit residues: 99.8155 Evaluate side-chains 217 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 180 time to evaluate : 1.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain M residue 42 VAL Chi-restraints excluded: chain M residue 74 CYS Chi-restraints excluded: chain M residue 125 LEU Chi-restraints excluded: chain M residue 172 VAL Chi-restraints excluded: chain M residue 180 ASP Chi-restraints excluded: chain M residue 181 ILE Chi-restraints excluded: chain M residue 252 THR Chi-restraints excluded: chain M residue 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 268 SER Chi-restraints excluded: chain D residue 301 THR 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 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 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 566 HIS Chi-restraints excluded: chain C residue 614 SER Chi-restraints excluded: chain C residue 631 MET Chi-restraints excluded: chain C residue 639 ASN Chi-restraints excluded: chain C residue 648 LEU Chi-restraints excluded: chain J residue 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: 4.9990 chunk 158 optimal weight: 10.0000 chunk 13 optimal weight: 4.9990 chunk 84 optimal weight: 6.9990 chunk 151 optimal weight: 9.9990 chunk 149 optimal weight: 10.0000 chunk 55 optimal weight: 1.9990 chunk 178 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 chunk 128 optimal weight: 0.0770 chunk 80 optimal weight: 2.9990 overall best weight: 3.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 654 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.089841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.075318 restraints weight = 45319.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.077250 restraints weight = 26019.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.078551 restraints weight = 18182.651| |-----------------------------------------------------------------------------| r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.3658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 17431 Z= 0.233 Angle : 0.697 10.154 23885 Z= 0.327 Chirality : 0.045 0.251 2952 Planarity : 0.003 0.044 2957 Dihedral : 7.925 71.450 3888 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.19 % Allowed : 15.09 % Favored : 81.72 % 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: 0.12 (0.21), residues: 1689 helix: 2.27 (0.27), residues: 383 sheet: -0.24 (0.24), residues: 444 loop : -0.73 (0.22), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP N 572 HIS 0.005 0.001 HIS N 565 PHE 0.018 0.002 PHE I 362 TYR 0.026 0.001 TYR M 39 ARG 0.005 0.001 ARG C 635 Details of bonding type rmsd link_NAG-ASN : bond 0.00330 ( 48) link_NAG-ASN : angle 1.93705 ( 144) link_ALPHA1-6 : bond 0.00404 ( 3) link_ALPHA1-6 : angle 1.58262 ( 9) link_BETA1-4 : bond 0.00408 ( 22) link_BETA1-4 : angle 2.13661 ( 66) link_ALPHA1-3 : bond 0.01039 ( 3) link_ALPHA1-3 : angle 2.52846 ( 9) hydrogen bonds : bond 0.04034 ( 526) hydrogen bonds : angle 4.88099 ( 1410) SS BOND : bond 0.00575 ( 28) SS BOND : angle 1.04005 ( 56) covalent geometry : bond 0.00537 (17327) covalent geometry : angle 0.67100 (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 234 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 185 time to evaluate : 1.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 35 TRP cc_start: 0.8330 (m100) cc_final: 0.8017 (m100) REVERT: M 483 GLU cc_start: 0.8017 (mm-30) cc_final: 0.7526 (tp30) REVERT: D 117 LYS cc_start: 0.8979 (tttt) cc_final: 0.8669 (ttmm) REVERT: D 301 THR cc_start: 0.9187 (OUTLIER) cc_final: 0.8917 (p) REVERT: I 103 GLN cc_start: 0.8346 (OUTLIER) cc_final: 0.7807 (tm-30) REVERT: I 378 ASN cc_start: 0.8911 (t0) cc_final: 0.7910 (p0) REVERT: I 420 ARG cc_start: 0.8701 (OUTLIER) cc_final: 0.7412 (mpp80) REVERT: N 523 PHE cc_start: 0.6854 (OUTLIER) cc_final: 0.6631 (p90) REVERT: N 541 GLN cc_start: 0.8325 (mm110) cc_final: 0.7830 (mt0) REVERT: N 630 MET cc_start: 0.7862 (mmm) cc_final: 0.7536 (tmm) REVERT: C 566 HIS cc_start: 0.7029 (p90) cc_final: 0.6634 (p90) REVERT: C 608 THR cc_start: 0.9485 (OUTLIER) cc_final: 0.9116 (p) REVERT: J 622 GLU cc_start: 0.8745 (tp30) cc_final: 0.8290 (tp30) REVERT: J 635 GLU cc_start: 0.8062 (tm-30) cc_final: 0.7677 (tm-30) REVERT: J 657 ASN cc_start: 0.8410 (m-40) cc_final: 0.7880 (t0) outliers start: 49 outliers final: 32 residues processed: 218 average time/residue: 0.3083 time to fit residues: 98.8689 Evaluate side-chains 215 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 178 time to evaluate : 1.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain M residue 125 LEU Chi-restraints excluded: chain M residue 172 VAL Chi-restraints excluded: chain M residue 180 ASP Chi-restraints excluded: chain M residue 181 ILE Chi-restraints excluded: chain M residue 252 THR Chi-restraints excluded: chain M residue 374 THR Chi-restraints excluded: chain M residue 394 SER 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 301 THR Chi-restraints excluded: chain D residue 327 ASN Chi-restraints excluded: chain D residue 428 TRP Chi-restraints excluded: chain D residue 448 SER Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain I residue 103 GLN 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 369 ASP 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 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 608 THR Chi-restraints excluded: chain C residue 614 SER 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 111 optimal weight: 5.9990 chunk 211 optimal weight: 10.0000 chunk 171 optimal weight: 20.0000 chunk 26 optimal weight: 6.9990 chunk 113 optimal weight: 7.9990 chunk 127 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 183 optimal weight: 0.9990 chunk 191 optimal weight: 0.8980 chunk 31 optimal weight: 4.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- 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 654 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.090196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.075718 restraints weight = 45513.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.077656 restraints weight = 25995.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.078974 restraints weight = 18107.547| |-----------------------------------------------------------------------------| r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.3766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 17431 Z= 0.204 Angle : 0.668 11.084 23885 Z= 0.314 Chirality : 0.044 0.249 2952 Planarity : 0.003 0.040 2957 Dihedral : 7.686 67.192 3888 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.99 % Allowed : 15.09 % Favored : 81.91 % 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: 0.08 (0.21), residues: 1689 helix: 2.24 (0.27), residues: 384 sheet: -0.21 (0.25), residues: 432 loop : -0.79 (0.21), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP N 572 HIS 0.019 0.001 HIS M 72 PHE 0.018 0.002 PHE I 362 TYR 0.015 0.001 TYR M 396 ARG 0.006 0.000 ARG D 329 Details of bonding type rmsd link_NAG-ASN : bond 0.00303 ( 48) link_NAG-ASN : angle 1.86871 ( 144) link_ALPHA1-6 : bond 0.00375 ( 3) link_ALPHA1-6 : angle 1.53554 ( 9) link_BETA1-4 : bond 0.00419 ( 22) link_BETA1-4 : angle 2.08648 ( 66) link_ALPHA1-3 : bond 0.00985 ( 3) link_ALPHA1-3 : angle 2.35961 ( 9) hydrogen bonds : bond 0.03824 ( 526) hydrogen bonds : angle 4.85862 ( 1410) SS BOND : bond 0.00527 ( 28) SS BOND : angle 0.97754 ( 56) covalent geometry : bond 0.00472 (17327) covalent geometry : angle 0.64273 (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 228 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 182 time to evaluate : 1.659 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: 0.8266 (m100) cc_final: 0.8020 (m100) REVERT: M 483 GLU cc_start: 0.8010 (mm-30) cc_final: 0.7513 (tp30) REVERT: D 117 LYS cc_start: 0.8943 (tttt) cc_final: 0.8630 (ttmm) REVERT: D 202 THR cc_start: 0.9287 (m) cc_final: 0.9010 (p) REVERT: D 301 THR cc_start: 0.9181 (OUTLIER) cc_final: 0.8898 (p) REVERT: I 103 GLN cc_start: 0.8333 (OUTLIER) cc_final: 0.7778 (tm-30) REVERT: I 378 ASN cc_start: 0.8900 (t0) cc_final: 0.7921 (p0) REVERT: I 420 ARG cc_start: 0.8705 (OUTLIER) cc_final: 0.7430 (mpp80) REVERT: N 541 GLN cc_start: 0.8297 (mm110) cc_final: 0.7825 (mt0) REVERT: N 630 MET cc_start: 0.7880 (mmm) cc_final: 0.7509 (tmm) REVERT: C 545 LEU cc_start: 0.7330 (OUTLIER) cc_final: 0.6895 (tt) REVERT: C 566 HIS cc_start: 0.6934 (p90) cc_final: 0.6522 (p90) REVERT: J 622 GLU cc_start: 0.8713 (tp30) cc_final: 0.8262 (tp30) REVERT: J 635 GLU cc_start: 0.8100 (tm-30) cc_final: 0.7694 (tm-30) REVERT: J 657 ASN cc_start: 0.8405 (m-40) cc_final: 0.7879 (t0) outliers start: 46 outliers final: 37 residues processed: 213 average time/residue: 0.3152 time to fit residues: 99.0093 Evaluate side-chains 216 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 175 time to evaluate : 1.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain M residue 125 LEU Chi-restraints excluded: chain M residue 172 VAL Chi-restraints excluded: chain M residue 180 ASP Chi-restraints excluded: chain M residue 181 ILE Chi-restraints excluded: chain M residue 252 THR Chi-restraints excluded: chain M residue 374 THR 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 268 SER Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 305 ASN Chi-restraints excluded: chain D residue 327 ASN Chi-restraints excluded: chain D residue 426 ASN Chi-restraints excluded: chain D residue 427 MET Chi-restraints excluded: chain D residue 428 TRP Chi-restraints excluded: chain D residue 448 SER Chi-restraints excluded: chain I residue 42 VAL Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain I residue 103 GLN 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 431 VAL 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 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 614 SER 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: 10.0000 chunk 30 optimal weight: 2.9990 chunk 204 optimal weight: 0.9980 chunk 93 optimal weight: 0.4980 chunk 119 optimal weight: 7.9990 chunk 201 optimal weight: 0.8980 chunk 19 optimal weight: 0.5980 chunk 8 optimal weight: 3.9990 chunk 135 optimal weight: 9.9990 chunk 12 optimal weight: 1.9990 chunk 122 optimal weight: 8.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.092035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.077656 restraints weight = 44825.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.079638 restraints weight = 25371.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.080964 restraints weight = 17567.290| |-----------------------------------------------------------------------------| r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.3827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17431 Z= 0.119 Angle : 0.602 11.192 23885 Z= 0.286 Chirality : 0.042 0.247 2952 Planarity : 0.003 0.038 2957 Dihedral : 7.161 63.889 3888 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.02 % Allowed : 16.72 % Favored : 81.26 % 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: 0.30 (0.21), residues: 1689 helix: 2.37 (0.26), residues: 384 sheet: -0.06 (0.25), residues: 429 loop : -0.63 (0.21), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.002 TRP N 572 HIS 0.027 0.001 HIS M 72 PHE 0.017 0.001 PHE I 362 TYR 0.012 0.001 TYR M 195 ARG 0.006 0.000 ARG N 634 Details of bonding type rmsd link_NAG-ASN : bond 0.00299 ( 48) link_NAG-ASN : angle 1.63528 ( 144) link_ALPHA1-6 : bond 0.00475 ( 3) link_ALPHA1-6 : angle 1.55735 ( 9) link_BETA1-4 : bond 0.00494 ( 22) link_BETA1-4 : angle 2.00504 ( 66) link_ALPHA1-3 : bond 0.01095 ( 3) link_ALPHA1-3 : angle 2.07490 ( 9) hydrogen bonds : bond 0.03360 ( 526) hydrogen bonds : angle 4.69510 ( 1410) SS BOND : bond 0.00397 ( 28) SS BOND : angle 0.82209 ( 56) covalent geometry : bond 0.00272 (17327) covalent geometry : angle 0.57905 (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 218 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 187 time to evaluate : 1.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 483 GLU cc_start: 0.7939 (mm-30) cc_final: 0.7443 (tp30) REVERT: D 42 VAL cc_start: 0.9239 (t) cc_final: 0.9000 (p) REVERT: D 62 GLU cc_start: 0.6940 (mp0) cc_final: 0.6717 (mp0) REVERT: D 117 LYS cc_start: 0.8901 (tttt) cc_final: 0.8593 (ttmm) REVERT: D 202 THR cc_start: 0.9267 (m) cc_final: 0.9029 (p) REVERT: D 301 THR cc_start: 0.9138 (OUTLIER) cc_final: 0.8879 (p) REVERT: I 103 GLN cc_start: 0.8290 (OUTLIER) cc_final: 0.7975 (tt0) REVERT: I 221 TYR cc_start: 0.8944 (m-10) cc_final: 0.8370 (m-10) REVERT: I 378 ASN cc_start: 0.8867 (t0) cc_final: 0.7996 (p0) REVERT: I 420 ARG cc_start: 0.8676 (OUTLIER) cc_final: 0.7435 (mpp80) REVERT: N 630 MET cc_start: 0.7890 (mmm) cc_final: 0.7461 (tmm) REVERT: C 545 LEU cc_start: 0.7243 (OUTLIER) cc_final: 0.6776 (tt) REVERT: C 566 HIS cc_start: 0.6929 (p90) cc_final: 0.6588 (p90) REVERT: J 622 GLU cc_start: 0.8634 (tp30) cc_final: 0.8299 (tp30) REVERT: J 635 GLU cc_start: 0.8040 (tm-30) cc_final: 0.7643 (tm-30) REVERT: J 657 ASN cc_start: 0.8330 (m-40) cc_final: 0.7825 (t0) outliers start: 31 outliers final: 24 residues processed: 205 average time/residue: 0.2965 time to fit residues: 90.3122 Evaluate side-chains 208 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 180 time to evaluate : 1.823 ------------------------------------------------------------------------------- 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 180 ASP Chi-restraints excluded: chain M residue 181 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 209 CYS Chi-restraints excluded: chain D residue 231 LYS Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 428 TRP Chi-restraints excluded: chain D residue 435 MET Chi-restraints excluded: chain D residue 448 SER Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain I residue 103 GLN 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 566 LEU Chi-restraints excluded: chain N residue 605 CYS 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 631 MET 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: 0.8980 chunk 24 optimal weight: 5.9990 chunk 92 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 200 optimal weight: 9.9990 chunk 190 optimal weight: 9.9990 chunk 111 optimal weight: 10.0000 chunk 2 optimal weight: 10.0000 chunk 119 optimal weight: 5.9990 chunk 29 optimal weight: 0.6980 chunk 56 optimal weight: 6.9990 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 199 ASN ** D 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 426 ASN N 654 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.089546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.075144 restraints weight = 45603.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.077072 restraints weight = 26069.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.078370 restraints weight = 18172.759| |-----------------------------------------------------------------------------| r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.3923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 17431 Z= 0.253 Angle : 0.720 10.783 23885 Z= 0.337 Chirality : 0.045 0.255 2952 Planarity : 0.004 0.042 2957 Dihedral : 7.580 62.266 3888 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.41 % Allowed : 16.59 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.09 (0.21), residues: 1689 helix: 2.25 (0.27), residues: 384 sheet: -0.24 (0.25), residues: 446 loop : -0.78 (0.22), residues: 859 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.084 0.002 TRP N 572 HIS 0.027 0.002 HIS M 72 PHE 0.018 0.002 PHE I 362 TYR 0.021 0.002 TYR C 588 ARG 0.010 0.001 ARG D 329 Details of bonding type rmsd link_NAG-ASN : bond 0.00361 ( 48) link_NAG-ASN : angle 1.97333 ( 144) link_ALPHA1-6 : bond 0.00398 ( 3) link_ALPHA1-6 : angle 1.56093 ( 9) link_BETA1-4 : bond 0.00397 ( 22) link_BETA1-4 : angle 2.10984 ( 66) link_ALPHA1-3 : bond 0.00980 ( 3) link_ALPHA1-3 : angle 2.50194 ( 9) hydrogen bonds : bond 0.04019 ( 526) hydrogen bonds : angle 4.92665 ( 1410) SS BOND : bond 0.00610 ( 28) SS BOND : angle 0.97358 ( 56) covalent geometry : bond 0.00586 (17327) covalent geometry : angle 0.69459 (23601) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5129.94 seconds wall clock time: 91 minutes 4.62 seconds (5464.62 seconds total)