Starting phenix.real_space_refine on Thu Mar 5 06:59:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6um6_20818/03_2026/6um6_20818_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6um6_20818/03_2026/6um6_20818.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6um6_20818/03_2026/6um6_20818.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6um6_20818/03_2026/6um6_20818.map" model { file = "/net/cci-nas-00/data/ceres_data/6um6_20818/03_2026/6um6_20818_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6um6_20818/03_2026/6um6_20818_neut.cif" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.083 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 141 5.16 5 C 12579 2.51 5 N 3363 2.21 5 O 4050 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 49 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20133 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 3612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3612 Classifications: {'peptide': 462} Link IDs: {'CIS': 4, 'PTRANS': 23, 'TRANS': 434} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'CIS': 3, 'PTRANS': 1, 'TRANS': 127} Chain breaks: 1 Chain: "C" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 996 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "D" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 790 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "E" Number of atoms: 3612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3612 Classifications: {'peptide': 462} Link IDs: {'CIS': 4, 'PTRANS': 23, 'TRANS': 434} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'CIS': 3, 'PTRANS': 1, 'TRANS': 127} Chain breaks: 1 Chain: "G" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 996 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "H" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 790 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "I" Number of atoms: 3612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3612 Classifications: {'peptide': 462} Link IDs: {'CIS': 4, 'PTRANS': 23, 'TRANS': 434} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "J" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'CIS': 3, 'PTRANS': 1, 'TRANS': 127} Chain breaks: 1 Chain: "K" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 996 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "L" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 790 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "M" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "R" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" 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: "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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "W" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 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: 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: "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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "E" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "I" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 4.40, per 1000 atoms: 0.22 Number of scatterers: 20133 At special positions: 0 Unit cell: (159.84, 160.92, 140.4, 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 141 16.00 O 4050 8.00 N 3363 7.00 C 12579 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.27 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.02 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.02 Simple disulfide: pdb=" SG CYS A 201 " - pdb=" SG CYS A 433 " distance=2.01 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.01 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.26 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.11 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.20 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.08 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.14 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=1.98 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 90 " distance=2.20 Simple disulfide: pdb=" SG CYS D 91 " - pdb=" SG CYS D 101 " distance=2.14 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.27 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.02 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.02 Simple disulfide: pdb=" SG CYS E 201 " - pdb=" SG CYS E 433 " distance=2.01 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.01 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.26 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.11 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.20 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.08 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.14 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=1.98 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 90 " distance=2.20 Simple disulfide: pdb=" SG CYS H 91 " - pdb=" SG CYS H 101 " distance=2.14 Simple disulfide: pdb=" SG CYS I 54 " - pdb=" SG CYS I 74 " distance=2.27 Simple disulfide: pdb=" SG CYS I 119 " - pdb=" SG CYS I 205 " distance=2.02 Simple disulfide: pdb=" SG CYS I 126 " - pdb=" SG CYS I 196 " distance=2.02 Simple disulfide: pdb=" SG CYS I 201 " - pdb=" SG CYS I 433 " distance=2.01 Simple disulfide: pdb=" SG CYS I 218 " - pdb=" SG CYS I 247 " distance=2.01 Simple disulfide: pdb=" SG CYS I 228 " - pdb=" SG CYS I 239 " distance=2.26 Simple disulfide: pdb=" SG CYS I 296 " - pdb=" SG CYS I 331 " distance=2.11 Simple disulfide: pdb=" SG CYS I 378 " - pdb=" SG CYS I 445 " distance=2.20 Simple disulfide: pdb=" SG CYS I 385 " - pdb=" SG CYS I 418 " distance=2.07 Simple disulfide: pdb=" SG CYS J 598 " - pdb=" SG CYS J 604 " distance=2.14 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=1.98 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " distance=2.20 Simple disulfide: pdb=" SG CYS L 91 " - pdb=" SG CYS L 101 " distance=2.14 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 Q 3 " - " MAN Q 4 " " BMA V 3 " - " MAN V 4 " " BMA a 3 " - " MAN a 4 " ALPHA1-6 " BMA M 3 " - " MAN M 4 " " BMA R 3 " - " MAN R 4 " " BMA W 3 " - " MAN W 4 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " BETA1-6 " NAG N 1 " - " NAG N 2 " " NAG S 1 " - " NAG S 2 " " NAG X 1 " - " NAG X 2 " NAG-ASN " NAG A 610 " - " ASN A 154 " " NAG A 613 " - " ASN A 386 " " NAG A 614 " - " ASN A 197 " " NAG A 615 " - " ASN A 355 " " NAG A 620 " - " ASN A 448 " " NAG A 621 " - " ASN A 234 " " NAG E 610 " - " ASN E 154 " " NAG E 613 " - " ASN E 386 " " NAG E 614 " - " ASN E 197 " " NAG E 615 " - " ASN E 355 " " NAG E 620 " - " ASN E 448 " " NAG E 621 " - " ASN E 234 " " NAG I 610 " - " ASN I 154 " " NAG I 613 " - " ASN I 386 " " NAG I 614 " - " ASN I 197 " " NAG I 615 " - " ASN I 355 " " NAG I 620 " - " ASN I 448 " " NAG I 621 " - " ASN I 234 " " NAG M 1 " - " ASN A 332 " " NAG N 1 " - " ASN A 442 " " NAG O 1 " - " ASN A 301 " " NAG P 1 " - " ASN A 362 " " NAG Q 1 " - " ASN A 262 " " NAG R 1 " - " ASN E 332 " " NAG S 1 " - " ASN E 442 " " NAG T 1 " - " ASN E 301 " " NAG U 1 " - " ASN E 362 " " NAG V 1 " - " ASN E 262 " " NAG W 1 " - " ASN I 332 " " NAG X 1 " - " ASN I 442 " " NAG Y 1 " - " ASN I 301 " " NAG Z 1 " - " ASN I 362 " " NAG a 1 " - " ASN I 262 " Time building additional restraints: 1.74 Conformation dependent library (CDL) restraints added in 921.8 milliseconds 4908 Ramachandran restraints generated. 2454 Oldfield, 0 Emsley, 2454 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4560 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 42 sheets defined 24.2% alpha, 32.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 62 through 68 removed outlier: 3.657A pdb=" N HIS A 66 " --> pdb=" O LYS A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 98 No H-bonds generated for 'chain 'A' and resid 96 through 98' Processing helix chain 'A' and resid 99 through 116 removed outlier: 3.668A pdb=" N GLN A 103 " --> pdb=" O ASP A 99 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU A 116 " --> pdb=" O TRP A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 138 through 151 removed outlier: 3.855A pdb=" N GLU A 151 " --> pdb=" O GLY A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 335 through 350 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 377 through 381 Processing helix chain 'A' and resid 474 through 484 removed outlier: 3.549A pdb=" N ASN A 478 " --> pdb=" O ASP A 474 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 520 Processing helix chain 'B' and resid 523 through 536 removed outlier: 3.787A pdb=" N GLY B 527 " --> pdb=" O GLY B 524 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N THR B 529 " --> pdb=" O ALA B 526 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N MET B 530 " --> pdb=" O GLY B 527 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N GLY B 531 " --> pdb=" O SER B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 543 removed outlier: 3.634A pdb=" N ARG B 542 " --> pdb=" O THR B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 597 removed outlier: 3.644A pdb=" N LYS B 574 " --> pdb=" O VAL B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 611 through 615 Processing helix chain 'B' and resid 618 through 625 Processing helix chain 'B' and resid 627 through 635 removed outlier: 3.555A pdb=" N LYS B 633 " --> pdb=" O LEU B 629 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N GLU B 634 " --> pdb=" O GLN B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 664 Processing helix chain 'C' and resid 62 through 65 removed outlier: 3.770A pdb=" N GLN C 65 " --> pdb=" O ARG C 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 62 through 65' Processing helix chain 'C' and resid 87 through 91 removed outlier: 4.029A pdb=" N THR C 91 " --> pdb=" O SER C 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 85 removed outlier: 4.016A pdb=" N GLU D 85 " --> pdb=" O ALA D 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 68 removed outlier: 3.658A pdb=" N HIS E 66 " --> pdb=" O LYS E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 98 No H-bonds generated for 'chain 'E' and resid 96 through 98' Processing helix chain 'E' and resid 99 through 116 removed outlier: 3.668A pdb=" N GLN E 103 " --> pdb=" O ASP E 99 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU E 116 " --> pdb=" O TRP E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 138 through 151 removed outlier: 3.856A pdb=" N GLU E 151 " --> pdb=" O GLY E 139 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 198 Processing helix chain 'E' and resid 335 through 350 Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 377 through 381 Processing helix chain 'E' and resid 474 through 484 removed outlier: 3.549A pdb=" N ASN E 478 " --> pdb=" O ASP E 474 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 513 through 520 Processing helix chain 'F' and resid 523 through 536 removed outlier: 3.787A pdb=" N GLY F 527 " --> pdb=" O GLY F 524 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N THR F 529 " --> pdb=" O ALA F 526 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N MET F 530 " --> pdb=" O GLY F 527 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N GLY F 531 " --> pdb=" O SER F 528 " (cutoff:3.500A) Processing helix chain 'F' and resid 538 through 543 removed outlier: 3.635A pdb=" N ARG F 542 " --> pdb=" O THR F 538 " (cutoff:3.500A) Processing helix chain 'F' and resid 570 through 597 removed outlier: 3.644A pdb=" N LYS F 574 " --> pdb=" O VAL F 570 " (cutoff:3.500A) Processing helix chain 'F' and resid 611 through 615 Processing helix chain 'F' and resid 618 through 625 Processing helix chain 'F' and resid 627 through 635 removed outlier: 3.556A pdb=" N LYS F 633 " --> pdb=" O LEU F 629 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N GLU F 634 " --> pdb=" O GLN F 630 " (cutoff:3.500A) Processing helix chain 'F' and resid 638 through 664 Processing helix chain 'G' and resid 62 through 65 removed outlier: 3.770A pdb=" N GLN G 65 " --> pdb=" O ARG G 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 62 through 65' Processing helix chain 'G' and resid 87 through 91 removed outlier: 4.028A pdb=" N THR G 91 " --> pdb=" O SER G 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 81 through 85 removed outlier: 4.016A pdb=" N GLU H 85 " --> pdb=" O ALA H 82 " (cutoff:3.500A) Processing helix chain 'I' and resid 62 through 68 removed outlier: 3.656A pdb=" N HIS I 66 " --> pdb=" O LYS I 63 " (cutoff:3.500A) Processing helix chain 'I' and resid 96 through 98 No H-bonds generated for 'chain 'I' and resid 96 through 98' Processing helix chain 'I' and resid 99 through 116 removed outlier: 3.668A pdb=" N GLN I 103 " --> pdb=" O ASP I 99 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU I 116 " --> pdb=" O TRP I 112 " (cutoff:3.500A) Processing helix chain 'I' and resid 122 through 126 Processing helix chain 'I' and resid 138 through 151 removed outlier: 3.856A pdb=" N GLU I 151 " --> pdb=" O GLY I 139 " (cutoff:3.500A) Processing helix chain 'I' and resid 195 through 198 Processing helix chain 'I' and resid 335 through 350 Processing helix chain 'I' and resid 368 through 373 Processing helix chain 'I' and resid 377 through 381 Processing helix chain 'I' and resid 474 through 484 removed outlier: 3.549A pdb=" N ASN I 478 " --> pdb=" O ASP I 474 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N GLU I 482 " --> pdb=" O ASN I 478 " (cutoff:3.500A) Processing helix chain 'J' and resid 513 through 520 Processing helix chain 'J' and resid 523 through 536 removed outlier: 3.786A pdb=" N GLY J 527 " --> pdb=" O GLY J 524 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N THR J 529 " --> pdb=" O ALA J 526 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N MET J 530 " --> pdb=" O GLY J 527 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N GLY J 531 " --> pdb=" O SER J 528 " (cutoff:3.500A) Processing helix chain 'J' and resid 538 through 543 removed outlier: 3.634A pdb=" N ARG J 542 " --> pdb=" O THR J 538 " (cutoff:3.500A) Processing helix chain 'J' and resid 570 through 597 removed outlier: 3.644A pdb=" N LYS J 574 " --> pdb=" O VAL J 570 " (cutoff:3.500A) Processing helix chain 'J' and resid 611 through 615 Processing helix chain 'J' and resid 618 through 625 Processing helix chain 'J' and resid 627 through 635 removed outlier: 3.555A pdb=" N LYS J 633 " --> pdb=" O LEU J 629 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N GLU J 634 " --> pdb=" O GLN J 630 " (cutoff:3.500A) Processing helix chain 'J' and resid 638 through 664 Processing helix chain 'K' and resid 62 through 65 removed outlier: 3.770A pdb=" N GLN K 65 " --> pdb=" O ARG K 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 62 through 65' Processing helix chain 'K' and resid 87 through 91 removed outlier: 4.029A pdb=" N THR K 91 " --> pdb=" O SER K 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 81 through 85 removed outlier: 4.016A pdb=" N GLU L 85 " --> pdb=" O ALA L 82 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 495 through 498 removed outlier: 5.145A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 9.041A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AA3, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA4, first strand: chain 'A' and resid 167 through 174 removed outlier: 3.658A pdb=" N PHE A 174 " --> pdb=" O LYS A 153 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 260 through 261 removed outlier: 3.561A pdb=" N ILE A 443 " --> pdb=" O ARG A 298 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 11.543A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 11.742A pdb=" N LEU A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 11.799A pdb=" N LEU A 288 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 11.144A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 10.487A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 11.591A pdb=" N ASP A 457 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 12.319A pdb=" N ILE A 284 " --> pdb=" O ASP A 457 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N GLU A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N SER A 334 " --> pdb=" O GLU A 293 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL A 295 " --> pdb=" O ASN A 332 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 271 through 273 removed outlier: 12.319A pdb=" N ILE A 284 " --> pdb=" O ASP A 457 " (cutoff:3.500A) removed outlier: 11.591A pdb=" N ASP A 457 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 10.487A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 11.144A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 11.799A pdb=" N LEU A 288 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 11.742A pdb=" N LEU A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 11.543A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE A 443 " --> pdb=" O ARG A 298 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N THR A 357 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N PHE A 468 " --> pdb=" O THR A 357 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N LYS A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLY A 393 " --> pdb=" O TYR A 361 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 304 through 308 Processing sheet with id=AA8, first strand: chain 'A' and resid 423 through 426 removed outlier: 4.788A pdb=" N MET A 426 " --> pdb=" O ARG A 432 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ARG A 432 " --> pdb=" O MET A 426 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 3 through 6 removed outlier: 3.515A pdb=" N VAL C 18 " --> pdb=" O LEU C 83 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 10 through 12 removed outlier: 4.292A pdb=" N GLN C 10 " --> pdb=" O LEU C 122 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA C 92 " --> pdb=" O LEU C 123 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N HIS C 35 " --> pdb=" O THR C 97 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ILE C 34 " --> pdb=" O TRP C 50 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N TRP C 50 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N TRP C 36 " --> pdb=" O MET C 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 10 through 12 removed outlier: 4.292A pdb=" N GLN C 10 " --> pdb=" O LEU C 122 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA C 92 " --> pdb=" O LEU C 123 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N THR C 98 " --> pdb=" O HIS C 116 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N HIS C 116 " --> pdb=" O THR C 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 9 through 12 removed outlier: 6.422A pdb=" N VAL D 10 " --> pdb=" O THR D 108 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 9 through 12 removed outlier: 6.422A pdb=" N VAL D 10 " --> pdb=" O THR D 108 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 17 through 23 Processing sheet with id=AB6, first strand: chain 'E' and resid 495 through 498 removed outlier: 5.144A pdb=" N VAL F 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 9.042A pdb=" N VAL E 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N THR F 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 45 through 47 Processing sheet with id=AB8, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AB9, first strand: chain 'E' and resid 167 through 174 removed outlier: 3.658A pdb=" N PHE E 174 " --> pdb=" O LYS E 153 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 260 through 261 removed outlier: 3.561A pdb=" N ILE E 443 " --> pdb=" O ARG E 298 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N GLY E 451 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 11.543A pdb=" N THR E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 11.742A pdb=" N LEU E 453 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 11.799A pdb=" N LEU E 288 " --> pdb=" O LEU E 453 " (cutoff:3.500A) removed outlier: 11.144A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 10.487A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 11.591A pdb=" N ASP E 457 " --> pdb=" O ILE E 284 " (cutoff:3.500A) removed outlier: 12.319A pdb=" N ILE E 284 " --> pdb=" O ASP E 457 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N GLU E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N SER E 334 " --> pdb=" O GLU E 293 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL E 295 " --> pdb=" O ASN E 332 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 271 through 273 removed outlier: 12.319A pdb=" N ILE E 284 " --> pdb=" O ASP E 457 " (cutoff:3.500A) removed outlier: 11.591A pdb=" N ASP E 457 " --> pdb=" O ILE E 284 " (cutoff:3.500A) removed outlier: 10.487A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 11.144A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 11.799A pdb=" N LEU E 288 " --> pdb=" O LEU E 453 " (cutoff:3.500A) removed outlier: 11.742A pdb=" N LEU E 453 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 11.543A pdb=" N THR E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N GLY E 451 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE E 443 " --> pdb=" O ARG E 298 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N THR E 357 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N PHE E 468 " --> pdb=" O THR E 357 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N LYS E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLY E 393 " --> pdb=" O TYR E 361 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 304 through 308 Processing sheet with id=AC4, first strand: chain 'E' and resid 423 through 426 removed outlier: 4.787A pdb=" N MET E 426 " --> pdb=" O ARG E 432 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ARG E 432 " --> pdb=" O MET E 426 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 3 through 6 removed outlier: 3.515A pdb=" N VAL G 18 " --> pdb=" O LEU G 83 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 10 through 12 removed outlier: 4.292A pdb=" N GLN G 10 " --> pdb=" O LEU G 122 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA G 92 " --> pdb=" O LEU G 123 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N HIS G 35 " --> pdb=" O THR G 97 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ILE G 34 " --> pdb=" O TRP G 50 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N TRP G 50 " --> pdb=" O ILE G 34 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N TRP G 36 " --> pdb=" O MET G 48 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 10 through 12 removed outlier: 4.292A pdb=" N GLN G 10 " --> pdb=" O LEU G 122 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA G 92 " --> pdb=" O LEU G 123 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N THR G 98 " --> pdb=" O HIS G 116 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N HIS G 116 " --> pdb=" O THR G 98 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 9 through 12 removed outlier: 6.422A pdb=" N VAL H 10 " --> pdb=" O THR H 108 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 9 through 12 removed outlier: 6.422A pdb=" N VAL H 10 " --> pdb=" O THR H 108 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 17 through 23 Processing sheet with id=AD2, first strand: chain 'I' and resid 495 through 498 removed outlier: 5.144A pdb=" N VAL J 608 " --> pdb=" O VAL I 36 " (cutoff:3.500A) removed outlier: 9.042A pdb=" N VAL I 38 " --> pdb=" O THR J 606 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N THR J 606 " --> pdb=" O VAL I 38 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 45 through 47 Processing sheet with id=AD4, first strand: chain 'I' and resid 91 through 94 Processing sheet with id=AD5, first strand: chain 'I' and resid 167 through 174 removed outlier: 3.658A pdb=" N PHE I 174 " --> pdb=" O LYS I 153 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 260 through 261 removed outlier: 3.561A pdb=" N ILE I 443 " --> pdb=" O ARG I 298 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N GLY I 451 " --> pdb=" O THR I 290 " (cutoff:3.500A) removed outlier: 11.543A pdb=" N THR I 290 " --> pdb=" O GLY I 451 " (cutoff:3.500A) removed outlier: 11.742A pdb=" N LEU I 453 " --> pdb=" O LEU I 288 " (cutoff:3.500A) removed outlier: 11.799A pdb=" N LEU I 288 " --> pdb=" O LEU I 453 " (cutoff:3.500A) removed outlier: 11.144A pdb=" N THR I 455 " --> pdb=" O VAL I 286 " (cutoff:3.500A) removed outlier: 10.487A pdb=" N VAL I 286 " --> pdb=" O THR I 455 " (cutoff:3.500A) removed outlier: 11.591A pdb=" N ASP I 457 " --> pdb=" O ILE I 284 " (cutoff:3.500A) removed outlier: 12.319A pdb=" N ILE I 284 " --> pdb=" O ASP I 457 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N GLU I 293 " --> pdb=" O SER I 334 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N SER I 334 " --> pdb=" O GLU I 293 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL I 295 " --> pdb=" O ASN I 332 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ALA I 329 " --> pdb=" O CYS I 418 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 271 through 273 removed outlier: 12.319A pdb=" N ILE I 284 " --> pdb=" O ASP I 457 " (cutoff:3.500A) removed outlier: 11.591A pdb=" N ASP I 457 " --> pdb=" O ILE I 284 " (cutoff:3.500A) removed outlier: 10.487A pdb=" N VAL I 286 " --> pdb=" O THR I 455 " (cutoff:3.500A) removed outlier: 11.144A pdb=" N THR I 455 " --> pdb=" O VAL I 286 " (cutoff:3.500A) removed outlier: 11.799A pdb=" N LEU I 288 " --> pdb=" O LEU I 453 " (cutoff:3.500A) removed outlier: 11.742A pdb=" N LEU I 453 " --> pdb=" O LEU I 288 " (cutoff:3.500A) removed outlier: 11.543A pdb=" N THR I 290 " --> pdb=" O GLY I 451 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N GLY I 451 " --> pdb=" O THR I 290 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE I 443 " --> pdb=" O ARG I 298 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N THR I 357 " --> pdb=" O GLU I 466 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N PHE I 468 " --> pdb=" O THR I 357 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N LYS I 360 " --> pdb=" O PHE I 468 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLY I 393 " --> pdb=" O TYR I 361 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 304 through 308 Processing sheet with id=AD9, first strand: chain 'I' and resid 423 through 426 removed outlier: 4.788A pdb=" N MET I 426 " --> pdb=" O ARG I 432 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ARG I 432 " --> pdb=" O MET I 426 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'K' and resid 3 through 6 removed outlier: 3.514A pdb=" N VAL K 18 " --> pdb=" O LEU K 83 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'K' and resid 10 through 12 removed outlier: 4.292A pdb=" N GLN K 10 " --> pdb=" O LEU K 122 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA K 92 " --> pdb=" O LEU K 123 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N HIS K 35 " --> pdb=" O THR K 97 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ILE K 34 " --> pdb=" O TRP K 50 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N TRP K 50 " --> pdb=" O ILE K 34 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N TRP K 36 " --> pdb=" O MET K 48 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'K' and resid 10 through 12 removed outlier: 4.292A pdb=" N GLN K 10 " --> pdb=" O LEU K 122 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA K 92 " --> pdb=" O LEU K 123 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N THR K 98 " --> pdb=" O HIS K 116 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N HIS K 116 " --> pdb=" O THR K 98 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.422A pdb=" N VAL L 10 " --> pdb=" O THR L 108 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.422A pdb=" N VAL L 10 " --> pdb=" O THR L 108 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'L' and resid 17 through 23 747 hydrogen bonds defined for protein. 1917 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.57 Time building geometry restraints manager: 2.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 4199 1.32 - 1.47: 7507 1.47 - 1.61: 8652 1.61 - 1.76: 9 1.76 - 1.90: 186 Bond restraints: 20553 Sorted by residual: bond pdb=" C ARG A 469 " pdb=" N PRO A 470 " ideal model delta sigma weight residual 1.332 1.522 -0.190 1.30e-02 5.92e+03 2.15e+02 bond pdb=" C ARG E 469 " pdb=" N PRO E 470 " ideal model delta sigma weight residual 1.332 1.522 -0.190 1.30e-02 5.92e+03 2.14e+02 bond pdb=" C ARG I 469 " pdb=" N PRO I 470 " ideal model delta sigma weight residual 1.332 1.522 -0.190 1.30e-02 5.92e+03 2.13e+02 bond pdb=" CB HIS I 374 " pdb=" CG HIS I 374 " ideal model delta sigma weight residual 1.497 1.384 0.113 1.40e-02 5.10e+03 6.46e+01 bond pdb=" CB HIS A 374 " pdb=" CG HIS A 374 " ideal model delta sigma weight residual 1.497 1.385 0.112 1.40e-02 5.10e+03 6.40e+01 ... (remaining 20548 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.65: 27408 6.65 - 13.30: 492 13.30 - 19.95: 30 19.95 - 26.60: 9 26.60 - 33.25: 6 Bond angle restraints: 27945 Sorted by residual: angle pdb=" C SER B 546 " pdb=" N GLY B 547 " pdb=" CA GLY B 547 " ideal model delta sigma weight residual 121.70 154.95 -33.25 1.80e+00 3.09e-01 3.41e+02 angle pdb=" C SER J 546 " pdb=" N GLY J 547 " pdb=" CA GLY J 547 " ideal model delta sigma weight residual 121.70 154.94 -33.24 1.80e+00 3.09e-01 3.41e+02 angle pdb=" C SER F 546 " pdb=" N GLY F 547 " pdb=" CA GLY F 547 " ideal model delta sigma weight residual 121.70 154.91 -33.21 1.80e+00 3.09e-01 3.40e+02 angle pdb=" O ALA A 440 " pdb=" C ALA A 440 " pdb=" N GLY A 441 " ideal model delta sigma weight residual 122.82 102.31 20.51 1.30e+00 5.92e-01 2.49e+02 angle pdb=" O ALA E 440 " pdb=" C ALA E 440 " pdb=" N GLY E 441 " ideal model delta sigma weight residual 122.82 102.31 20.51 1.30e+00 5.92e-01 2.49e+02 ... (remaining 27940 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.76: 12523 22.76 - 45.53: 359 45.53 - 68.29: 87 68.29 - 91.06: 63 91.06 - 113.82: 36 Dihedral angle restraints: 13068 sinusoidal: 5934 harmonic: 7134 Sorted by residual: dihedral pdb=" C ASN E 234 " pdb=" N ASN E 234 " pdb=" CA ASN E 234 " pdb=" CB ASN E 234 " ideal model delta harmonic sigma weight residual -122.60 -101.26 -21.34 0 2.50e+00 1.60e-01 7.28e+01 dihedral pdb=" C ASN I 234 " pdb=" N ASN I 234 " pdb=" CA ASN I 234 " pdb=" CB ASN I 234 " ideal model delta harmonic sigma weight residual -122.60 -101.27 -21.33 0 2.50e+00 1.60e-01 7.28e+01 dihedral pdb=" C ASN A 234 " pdb=" N ASN A 234 " pdb=" CA ASN A 234 " pdb=" CB ASN A 234 " ideal model delta harmonic sigma weight residual -122.60 -101.27 -21.33 0 2.50e+00 1.60e-01 7.28e+01 ... (remaining 13065 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.273: 3211 0.273 - 0.546: 86 0.546 - 0.819: 18 0.819 - 1.092: 0 1.092 - 1.365: 3 Chirality restraints: 3318 Sorted by residual: chirality pdb=" C1 NAG P 2 " pdb=" O4 NAG P 1 " pdb=" C2 NAG P 2 " pdb=" O5 NAG P 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.79 -0.61 2.00e-02 2.50e+03 9.39e+02 chirality pdb=" C1 NAG U 2 " pdb=" O4 NAG U 1 " pdb=" C2 NAG U 2 " pdb=" O5 NAG U 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.79 -0.61 2.00e-02 2.50e+03 9.35e+02 chirality pdb=" C1 NAG Z 2 " pdb=" O4 NAG Z 1 " pdb=" C2 NAG Z 2 " pdb=" O5 NAG Z 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.79 -0.61 2.00e-02 2.50e+03 9.33e+02 ... (remaining 3315 not shown) Planarity restraints: 3519 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG O 2 " 0.350 2.00e-02 2.50e+03 3.01e-01 1.13e+03 pdb=" C7 NAG O 2 " -0.099 2.00e-02 2.50e+03 pdb=" C8 NAG O 2 " 0.071 2.00e-02 2.50e+03 pdb=" N2 NAG O 2 " -0.524 2.00e-02 2.50e+03 pdb=" O7 NAG O 2 " 0.202 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG T 2 " 0.350 2.00e-02 2.50e+03 3.01e-01 1.13e+03 pdb=" C7 NAG T 2 " -0.099 2.00e-02 2.50e+03 pdb=" C8 NAG T 2 " 0.071 2.00e-02 2.50e+03 pdb=" N2 NAG T 2 " -0.524 2.00e-02 2.50e+03 pdb=" O7 NAG T 2 " 0.202 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG Y 2 " -0.350 2.00e-02 2.50e+03 3.01e-01 1.13e+03 pdb=" C7 NAG Y 2 " 0.099 2.00e-02 2.50e+03 pdb=" C8 NAG Y 2 " -0.071 2.00e-02 2.50e+03 pdb=" N2 NAG Y 2 " 0.524 2.00e-02 2.50e+03 pdb=" O7 NAG Y 2 " -0.202 2.00e-02 2.50e+03 ... (remaining 3516 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 270 2.57 - 3.15: 16689 3.15 - 3.73: 30034 3.73 - 4.32: 42322 4.32 - 4.90: 66764 Nonbonded interactions: 156079 Sorted by model distance: nonbonded pdb=" O3 NAG V 2 " pdb=" O7 NAG V 2 " model vdw 1.987 3.040 nonbonded pdb=" O3 NAG Q 2 " pdb=" O7 NAG Q 2 " model vdw 1.987 3.040 nonbonded pdb=" O3 NAG a 2 " pdb=" O7 NAG a 2 " model vdw 1.987 3.040 nonbonded pdb=" OD1 ASN I 442 " pdb=" C1 NAG X 1 " model vdw 2.030 2.776 nonbonded pdb=" OD1 ASN A 442 " pdb=" C1 NAG N 1 " model vdw 2.031 2.776 ... (remaining 156074 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'J' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'Q' selection = chain 'R' selection = chain 'V' selection = chain 'W' selection = chain 'a' } ncs_group { reference = chain 'N' selection = chain 'P' selection = chain 'S' selection = chain 'U' selection = chain 'X' selection = chain 'Z' } ncs_group { reference = chain 'O' selection = chain 'T' selection = chain 'Y' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 18.640 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6696 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 : 0.020 0.242 20655 Z= 1.100 Angle : 2.453 33.253 28212 Z= 1.382 Chirality : 0.128 1.365 3318 Planarity : 0.026 0.301 3486 Dihedral : 14.448 113.824 8391 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.98 % Allowed : 5.99 % Favored : 93.03 % Rotamer: Outliers : 0.28 % Allowed : 1.54 % Favored : 98.18 % Cbeta Deviations : 0.66 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.89 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.16), residues: 2454 helix: -0.55 (0.23), residues: 414 sheet: -0.51 (0.20), residues: 600 loop : -0.70 (0.16), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 67 TYR 0.076 0.008 TYR I 400 PHE 0.047 0.006 PHE K 32 TRP 0.034 0.008 TRP E 69 HIS 0.007 0.002 HIS L 32 Details of bonding type rmsd covalent geometry : bond 0.01818 (20553) covalent geometry : angle 2.20237 (27945) SS BOND : bond 0.12503 ( 39) SS BOND : angle 4.08615 ( 78) hydrogen bonds : bond 0.21576 ( 705) hydrogen bonds : angle 8.56350 ( 1917) link_ALPHA1-3 : bond 0.04362 ( 3) link_ALPHA1-3 : angle 8.70742 ( 9) link_ALPHA1-6 : bond 0.01881 ( 3) link_ALPHA1-6 : angle 1.92597 ( 9) link_BETA1-4 : bond 0.02485 ( 21) link_BETA1-4 : angle 6.41288 ( 63) link_BETA1-6 : bond 0.01988 ( 3) link_BETA1-6 : angle 3.08044 ( 9) link_NAG-ASN : bond 0.17723 ( 33) link_NAG-ASN : angle 17.25761 ( 99) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4908 Ramachandran restraints generated. 2454 Oldfield, 0 Emsley, 2454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4908 Ramachandran restraints generated. 2454 Oldfield, 0 Emsley, 2454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 653 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 647 time to evaluate : 0.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 491 ILE cc_start: 0.9066 (mp) cc_final: 0.8617 (mt) REVERT: B 534 SER cc_start: 0.7984 (p) cc_final: 0.7227 (t) REVERT: B 580 VAL cc_start: 0.9494 (t) cc_final: 0.9166 (p) REVERT: B 624 ASP cc_start: 0.9236 (m-30) cc_final: 0.8984 (m-30) REVERT: D 77 ILE cc_start: 0.8196 (mt) cc_final: 0.7850 (mt) REVERT: D 108 THR cc_start: 0.5435 (m) cc_final: 0.4742 (t) REVERT: E 217 TYR cc_start: 0.6717 (m-80) cc_final: 0.6479 (m-80) REVERT: E 491 ILE cc_start: 0.9038 (mp) cc_final: 0.8770 (mt) REVERT: F 534 SER cc_start: 0.8021 (p) cc_final: 0.7225 (t) REVERT: F 580 VAL cc_start: 0.9425 (t) cc_final: 0.9093 (p) REVERT: F 624 ASP cc_start: 0.9200 (m-30) cc_final: 0.8997 (m-30) REVERT: H 77 ILE cc_start: 0.7993 (mt) cc_final: 0.7667 (mt) REVERT: H 108 THR cc_start: 0.5242 (m) cc_final: 0.4865 (t) REVERT: I 217 TYR cc_start: 0.6718 (m-80) cc_final: 0.6359 (m-80) REVERT: I 300 ASN cc_start: 0.8668 (OUTLIER) cc_final: 0.8307 (p0) REVERT: I 491 ILE cc_start: 0.9042 (mp) cc_final: 0.8778 (mt) REVERT: J 534 SER cc_start: 0.8153 (p) cc_final: 0.7812 (t) REVERT: J 624 ASP cc_start: 0.9219 (m-30) cc_final: 0.8972 (m-30) REVERT: K 35 HIS cc_start: 0.4325 (m-70) cc_final: 0.4090 (m-70) REVERT: L 77 ILE cc_start: 0.8089 (mt) cc_final: 0.7711 (mt) REVERT: L 108 THR cc_start: 0.5053 (m) cc_final: 0.4801 (t) outliers start: 6 outliers final: 5 residues processed: 653 average time/residue: 0.1387 time to fit residues: 140.4183 Evaluate side-chains 329 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 323 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 216 optimal weight: 5.9990 chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 3.9990 chunk 227 optimal weight: 6.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 6.9990 chunk 235 optimal weight: 9.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 249 HIS A 328 GLN A 422 GLN B 540 GLN ** B 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 651 ASN E 103 GLN ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 328 GLN E 422 GLN F 540 GLN ** F 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 651 ASN G 46 GLN ** I 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 328 GLN I 422 GLN J 540 GLN ** J 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 46 GLN K 65 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.062237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.049358 restraints weight = 104495.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.051164 restraints weight = 60093.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.052417 restraints weight = 41412.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.053306 restraints weight = 31930.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.053950 restraints weight = 26541.005| |-----------------------------------------------------------------------------| r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.3801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 20655 Z= 0.264 Angle : 1.021 12.686 28212 Z= 0.517 Chirality : 0.053 0.250 3318 Planarity : 0.005 0.088 3486 Dihedral : 12.477 73.265 3963 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.61 % Allowed : 4.65 % Favored : 94.74 % Rotamer: Outliers : 0.61 % Allowed : 3.55 % Favored : 95.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.89 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.17), residues: 2454 helix: 0.73 (0.26), residues: 387 sheet: -0.26 (0.19), residues: 600 loop : -0.94 (0.16), residues: 1467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG J 585 TYR 0.019 0.002 TYR A 395 PHE 0.027 0.003 PHE E 233 TRP 0.030 0.003 TRP K 36 HIS 0.008 0.002 HIS G 35 Details of bonding type rmsd covalent geometry : bond 0.00550 (20553) covalent geometry : angle 0.99205 (27945) SS BOND : bond 0.00376 ( 39) SS BOND : angle 1.28064 ( 78) hydrogen bonds : bond 0.05929 ( 705) hydrogen bonds : angle 6.80339 ( 1917) link_ALPHA1-3 : bond 0.00798 ( 3) link_ALPHA1-3 : angle 0.84913 ( 9) link_ALPHA1-6 : bond 0.00589 ( 3) link_ALPHA1-6 : angle 1.50517 ( 9) link_BETA1-4 : bond 0.00594 ( 21) link_BETA1-4 : angle 3.02274 ( 63) link_BETA1-6 : bond 0.00693 ( 3) link_BETA1-6 : angle 1.62446 ( 9) link_NAG-ASN : bond 0.00623 ( 33) link_NAG-ASN : angle 3.43245 ( 99) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4908 Ramachandran restraints generated. 2454 Oldfield, 0 Emsley, 2454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4908 Ramachandran restraints generated. 2454 Oldfield, 0 Emsley, 2454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 385 time to evaluate : 0.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 LEU cc_start: 0.9088 (mt) cc_final: 0.8767 (mt) REVERT: A 98 ASN cc_start: 0.8950 (t0) cc_final: 0.8592 (t0) REVERT: A 107 ASP cc_start: 0.8697 (p0) cc_final: 0.8117 (p0) REVERT: A 374 HIS cc_start: 0.7533 (t-90) cc_final: 0.6979 (t-90) REVERT: A 389 ASN cc_start: 0.8292 (p0) cc_final: 0.7993 (p0) REVERT: A 434 MET cc_start: 0.8736 (ptt) cc_final: 0.8365 (ptt) REVERT: A 450 THR cc_start: 0.7307 (OUTLIER) cc_final: 0.7074 (m) REVERT: B 530 MET cc_start: 0.8775 (mtt) cc_final: 0.8356 (mtt) REVERT: B 537 LEU cc_start: 0.9428 (mp) cc_final: 0.9086 (mp) REVERT: B 589 ASP cc_start: 0.8995 (m-30) cc_final: 0.8603 (p0) REVERT: B 624 ASP cc_start: 0.9342 (m-30) cc_final: 0.8602 (p0) REVERT: B 630 GLN cc_start: 0.9516 (tp40) cc_final: 0.9124 (tp40) REVERT: B 657 GLU cc_start: 0.9433 (tp30) cc_final: 0.9186 (tp30) REVERT: C 48 MET cc_start: 0.8663 (mmp) cc_final: 0.8211 (mmm) REVERT: C 107 ASP cc_start: 0.8501 (p0) cc_final: 0.7969 (p0) REVERT: C 111 TYR cc_start: 0.9200 (m-10) cc_final: 0.8668 (m-80) REVERT: C 114 PHE cc_start: 0.9236 (m-10) cc_final: 0.8848 (m-10) REVERT: D 33 ASP cc_start: 0.9222 (p0) cc_final: 0.8556 (p0) REVERT: D 77 ILE cc_start: 0.9160 (mt) cc_final: 0.8710 (mt) REVERT: D 84 ASP cc_start: 0.7717 (m-30) cc_final: 0.7273 (m-30) REVERT: D 93 PHE cc_start: 0.9425 (t80) cc_final: 0.9141 (t80) REVERT: E 52 LEU cc_start: 0.9094 (mt) cc_final: 0.8746 (mt) REVERT: E 98 ASN cc_start: 0.8947 (t0) cc_final: 0.8605 (t0) REVERT: E 103 GLN cc_start: 0.8752 (OUTLIER) cc_final: 0.8455 (tm-30) REVERT: E 483 LEU cc_start: 0.9308 (tp) cc_final: 0.8952 (tp) REVERT: F 530 MET cc_start: 0.8673 (mtt) cc_final: 0.8218 (mtt) REVERT: F 624 ASP cc_start: 0.9324 (m-30) cc_final: 0.8513 (p0) REVERT: F 630 GLN cc_start: 0.9578 (tp40) cc_final: 0.9246 (tp40) REVERT: F 632 ASP cc_start: 0.9284 (t0) cc_final: 0.8928 (p0) REVERT: F 633 LYS cc_start: 0.9625 (mmtt) cc_final: 0.9202 (mmmm) REVERT: F 657 GLU cc_start: 0.9399 (tp30) cc_final: 0.9002 (pt0) REVERT: G 48 MET cc_start: 0.8738 (mmp) cc_final: 0.8335 (mmm) REVERT: G 106 TYR cc_start: 0.8878 (p90) cc_final: 0.8489 (p90) REVERT: G 107 ASP cc_start: 0.8608 (p0) cc_final: 0.8198 (p0) REVERT: G 111 TYR cc_start: 0.9099 (m-80) cc_final: 0.8706 (m-80) REVERT: G 114 PHE cc_start: 0.9265 (m-10) cc_final: 0.8748 (m-10) REVERT: H 55 LYS cc_start: 0.9029 (tppt) cc_final: 0.8494 (tppt) REVERT: H 77 ILE cc_start: 0.9170 (mt) cc_final: 0.8794 (mt) REVERT: H 84 ASP cc_start: 0.7966 (m-30) cc_final: 0.7692 (m-30) REVERT: I 98 ASN cc_start: 0.9025 (t0) cc_final: 0.8618 (t0) REVERT: I 129 LEU cc_start: 0.9657 (mp) cc_final: 0.9005 (tt) REVERT: I 374 HIS cc_start: 0.7608 (t-90) cc_final: 0.7351 (t70) REVERT: I 426 MET cc_start: 0.8849 (tpp) cc_final: 0.8579 (tpp) REVERT: I 483 LEU cc_start: 0.9300 (tp) cc_final: 0.9010 (tp) REVERT: J 530 MET cc_start: 0.8831 (mtt) cc_final: 0.8415 (mtt) REVERT: J 574 LYS cc_start: 0.9568 (mmtt) cc_final: 0.9320 (mmmt) REVERT: J 591 GLN cc_start: 0.9439 (tp40) cc_final: 0.9236 (tp40) REVERT: J 595 ILE cc_start: 0.9635 (tp) cc_final: 0.9414 (tt) REVERT: J 630 GLN cc_start: 0.9530 (tp40) cc_final: 0.9304 (tp40) REVERT: J 652 GLN cc_start: 0.9148 (tm-30) cc_final: 0.8877 (tm-30) REVERT: J 657 GLU cc_start: 0.9441 (tp30) cc_final: 0.9062 (pt0) REVERT: K 37 LEU cc_start: 0.9232 (tt) cc_final: 0.8939 (tt) REVERT: K 48 MET cc_start: 0.8677 (mmp) cc_final: 0.8307 (mmm) REVERT: K 107 ASP cc_start: 0.8560 (p0) cc_final: 0.8106 (p0) REVERT: K 111 TYR cc_start: 0.9080 (m-80) cc_final: 0.8570 (m-80) REVERT: K 114 PHE cc_start: 0.9196 (m-10) cc_final: 0.8818 (m-10) REVERT: L 33 ASP cc_start: 0.9168 (p0) cc_final: 0.8569 (p0) REVERT: L 77 ILE cc_start: 0.9322 (mt) cc_final: 0.8875 (mt) REVERT: L 84 ASP cc_start: 0.7907 (m-30) cc_final: 0.7550 (m-30) outliers start: 13 outliers final: 0 residues processed: 393 average time/residue: 0.1202 time to fit residues: 76.6768 Evaluate side-chains 270 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 268 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 156 optimal weight: 9.9990 chunk 30 optimal weight: 9.9990 chunk 221 optimal weight: 20.0000 chunk 227 optimal weight: 3.9990 chunk 104 optimal weight: 9.9990 chunk 17 optimal weight: 6.9990 chunk 40 optimal weight: 1.9990 chunk 198 optimal weight: 5.9990 chunk 193 optimal weight: 10.0000 chunk 176 optimal weight: 0.0570 chunk 42 optimal weight: 1.9990 overall best weight: 2.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 46 GLN ** I 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 46 GLN ** K 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.060633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.047655 restraints weight = 105329.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.049388 restraints weight = 60901.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.050615 restraints weight = 41924.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.051474 restraints weight = 32341.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.052101 restraints weight = 26911.572| |-----------------------------------------------------------------------------| r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.4666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 20655 Z= 0.203 Angle : 0.869 13.072 28212 Z= 0.438 Chirality : 0.049 0.271 3318 Planarity : 0.005 0.059 3486 Dihedral : 9.728 58.030 3963 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.49 % Allowed : 5.95 % Favored : 93.56 % Rotamer: Outliers : 0.23 % Allowed : 2.52 % Favored : 97.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.89 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.17), residues: 2454 helix: 1.40 (0.27), residues: 375 sheet: 0.22 (0.20), residues: 543 loop : -0.93 (0.16), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 84 TYR 0.027 0.002 TYR H 51 PHE 0.017 0.002 PHE E 376 TRP 0.030 0.002 TRP E 427 HIS 0.005 0.001 HIS K 35 Details of bonding type rmsd covalent geometry : bond 0.00424 (20553) covalent geometry : angle 0.84208 (27945) SS BOND : bond 0.00302 ( 39) SS BOND : angle 0.91701 ( 78) hydrogen bonds : bond 0.04762 ( 705) hydrogen bonds : angle 6.20560 ( 1917) link_ALPHA1-3 : bond 0.00361 ( 3) link_ALPHA1-3 : angle 2.51155 ( 9) link_ALPHA1-6 : bond 0.00530 ( 3) link_ALPHA1-6 : angle 1.49843 ( 9) link_BETA1-4 : bond 0.00478 ( 21) link_BETA1-4 : angle 2.86689 ( 63) link_BETA1-6 : bond 0.00288 ( 3) link_BETA1-6 : angle 1.47491 ( 9) link_NAG-ASN : bond 0.00461 ( 33) link_NAG-ASN : angle 2.84034 ( 99) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4908 Ramachandran restraints generated. 2454 Oldfield, 0 Emsley, 2454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4908 Ramachandran restraints generated. 2454 Oldfield, 0 Emsley, 2454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 332 time to evaluate : 0.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 LEU cc_start: 0.9353 (mt) cc_final: 0.9015 (mt) REVERT: A 95 MET cc_start: 0.9161 (ttm) cc_final: 0.8761 (ttm) REVERT: A 98 ASN cc_start: 0.8875 (t0) cc_final: 0.8481 (t0) REVERT: A 374 HIS cc_start: 0.7307 (t-90) cc_final: 0.6862 (t-90) REVERT: A 389 ASN cc_start: 0.8351 (p0) cc_final: 0.8029 (p0) REVERT: B 530 MET cc_start: 0.8751 (mtt) cc_final: 0.8447 (mtt) REVERT: B 535 MET cc_start: 0.8560 (mmp) cc_final: 0.8271 (mmp) REVERT: B 537 LEU cc_start: 0.9427 (mp) cc_final: 0.9191 (tp) REVERT: B 601 LYS cc_start: 0.9155 (mppt) cc_final: 0.8927 (mmtm) REVERT: B 632 ASP cc_start: 0.9245 (t0) cc_final: 0.8887 (p0) REVERT: B 633 LYS cc_start: 0.9500 (mmtt) cc_final: 0.9123 (mmmm) REVERT: B 657 GLU cc_start: 0.9480 (tp30) cc_final: 0.9050 (pt0) REVERT: C 11 MET cc_start: 0.7587 (pmm) cc_final: 0.7110 (tpt) REVERT: C 33 TYR cc_start: 0.9447 (m-10) cc_final: 0.8989 (m-10) REVERT: C 35 HIS cc_start: 0.9196 (m-70) cc_final: 0.8977 (m-70) REVERT: C 48 MET cc_start: 0.8530 (mmp) cc_final: 0.8205 (mmm) REVERT: C 107 ASP cc_start: 0.8499 (p0) cc_final: 0.7972 (p0) REVERT: C 111 TYR cc_start: 0.9296 (m-10) cc_final: 0.8797 (m-80) REVERT: C 114 PHE cc_start: 0.9444 (m-10) cc_final: 0.8726 (m-10) REVERT: D 77 ILE cc_start: 0.9181 (mt) cc_final: 0.8902 (mt) REVERT: D 84 ASP cc_start: 0.7545 (m-30) cc_final: 0.7135 (m-30) REVERT: E 69 TRP cc_start: 0.7038 (t60) cc_final: 0.6567 (t60) REVERT: E 95 MET cc_start: 0.9195 (ttm) cc_final: 0.8898 (ttm) REVERT: E 98 ASN cc_start: 0.8981 (t0) cc_final: 0.8681 (t0) REVERT: E 152 MET cc_start: 0.8641 (mmp) cc_final: 0.8439 (mmp) REVERT: E 434 MET cc_start: 0.9140 (ptm) cc_final: 0.8653 (ptt) REVERT: E 483 LEU cc_start: 0.9444 (tp) cc_final: 0.9189 (tp) REVERT: F 523 LEU cc_start: 0.7902 (mt) cc_final: 0.7698 (mt) REVERT: F 530 MET cc_start: 0.8518 (mtt) cc_final: 0.8099 (mtt) REVERT: F 574 LYS cc_start: 0.9522 (mmmm) cc_final: 0.9187 (mmmm) REVERT: F 589 ASP cc_start: 0.9334 (m-30) cc_final: 0.9082 (m-30) REVERT: F 601 LYS cc_start: 0.9239 (mppt) cc_final: 0.9016 (mmtm) REVERT: F 632 ASP cc_start: 0.9284 (t0) cc_final: 0.8988 (p0) REVERT: F 633 LYS cc_start: 0.9598 (mmtt) cc_final: 0.9215 (mmmm) REVERT: F 657 GLU cc_start: 0.9438 (tp30) cc_final: 0.9047 (pt0) REVERT: G 11 MET cc_start: 0.7539 (pmm) cc_final: 0.6946 (tpt) REVERT: G 48 MET cc_start: 0.8604 (mmp) cc_final: 0.8237 (mmm) REVERT: G 107 ASP cc_start: 0.8579 (p0) cc_final: 0.7740 (p0) REVERT: G 111 TYR cc_start: 0.9150 (m-80) cc_final: 0.8449 (m-80) REVERT: G 114 PHE cc_start: 0.9399 (m-10) cc_final: 0.8739 (m-10) REVERT: H 34 LEU cc_start: 0.9595 (mm) cc_final: 0.9390 (mm) REVERT: H 84 ASP cc_start: 0.7619 (m-30) cc_final: 0.7248 (m-30) REVERT: I 98 ASN cc_start: 0.9061 (t0) cc_final: 0.8745 (t0) REVERT: I 104 MET cc_start: 0.9251 (mmp) cc_final: 0.8991 (mmp) REVERT: I 374 HIS cc_start: 0.7472 (t-90) cc_final: 0.6953 (t-90) REVERT: I 483 LEU cc_start: 0.9476 (tp) cc_final: 0.9265 (tp) REVERT: J 530 MET cc_start: 0.8696 (mtt) cc_final: 0.8320 (mtt) REVERT: J 535 MET cc_start: 0.8647 (mmp) cc_final: 0.8360 (mmp) REVERT: J 574 LYS cc_start: 0.9554 (mmtt) cc_final: 0.9335 (mmmt) REVERT: J 589 ASP cc_start: 0.9209 (m-30) cc_final: 0.8924 (m-30) REVERT: J 601 LYS cc_start: 0.9212 (mppt) cc_final: 0.9003 (mmtm) REVERT: J 632 ASP cc_start: 0.9265 (t0) cc_final: 0.8875 (p0) REVERT: J 633 LYS cc_start: 0.9525 (mmtt) cc_final: 0.9099 (mmmm) REVERT: J 657 GLU cc_start: 0.9472 (tp30) cc_final: 0.9103 (pt0) REVERT: K 11 MET cc_start: 0.7437 (tpt) cc_final: 0.7051 (tpt) REVERT: K 37 LEU cc_start: 0.9300 (tt) cc_final: 0.8982 (tt) REVERT: K 48 MET cc_start: 0.8566 (mmp) cc_final: 0.8320 (mmm) REVERT: K 107 ASP cc_start: 0.8686 (p0) cc_final: 0.8019 (p0) REVERT: K 111 TYR cc_start: 0.9135 (m-80) cc_final: 0.8476 (m-80) REVERT: K 114 PHE cc_start: 0.9430 (m-10) cc_final: 0.8650 (m-10) REVERT: L 55 LYS cc_start: 0.8949 (tptm) cc_final: 0.8693 (tppt) REVERT: L 84 ASP cc_start: 0.7619 (m-30) cc_final: 0.7397 (m-30) REVERT: L 106 LYS cc_start: 0.9626 (pptt) cc_final: 0.9346 (pptt) outliers start: 5 outliers final: 1 residues processed: 336 average time/residue: 0.1240 time to fit residues: 67.0215 Evaluate side-chains 246 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 245 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 217 optimal weight: 7.9990 chunk 100 optimal weight: 0.9980 chunk 115 optimal weight: 0.9980 chunk 164 optimal weight: 0.0670 chunk 163 optimal weight: 6.9990 chunk 3 optimal weight: 5.9990 chunk 183 optimal weight: 0.9980 chunk 87 optimal weight: 4.9990 chunk 242 optimal weight: 0.6980 chunk 74 optimal weight: 0.6980 chunk 216 optimal weight: 6.9990 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 543 ASN B 575 GLN B 651 ASN ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 543 ASN F 651 ASN G 46 GLN ** I 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 543 ASN J 651 ASN K 65 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.062199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.049043 restraints weight = 105904.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.050825 restraints weight = 60749.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.052066 restraints weight = 42036.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.052925 restraints weight = 32570.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.053534 restraints weight = 27300.327| |-----------------------------------------------------------------------------| r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.5006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 20655 Z= 0.132 Angle : 0.804 14.094 28212 Z= 0.393 Chirality : 0.047 0.248 3318 Planarity : 0.004 0.062 3486 Dihedral : 8.697 59.954 3963 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.49 % Allowed : 5.26 % Favored : 94.25 % Rotamer: Outliers : 0.23 % Allowed : 2.43 % Favored : 97.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.89 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.17), residues: 2454 helix: 1.76 (0.27), residues: 372 sheet: 0.45 (0.21), residues: 540 loop : -0.82 (0.16), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 84 TYR 0.018 0.002 TYR K 27 PHE 0.018 0.001 PHE G 29 TRP 0.033 0.002 TRP E 427 HIS 0.005 0.001 HIS I 249 Details of bonding type rmsd covalent geometry : bond 0.00267 (20553) covalent geometry : angle 0.76862 (27945) SS BOND : bond 0.00276 ( 39) SS BOND : angle 1.03032 ( 78) hydrogen bonds : bond 0.04070 ( 705) hydrogen bonds : angle 5.85516 ( 1917) link_ALPHA1-3 : bond 0.00966 ( 3) link_ALPHA1-3 : angle 1.18778 ( 9) link_ALPHA1-6 : bond 0.00509 ( 3) link_ALPHA1-6 : angle 1.73347 ( 9) link_BETA1-4 : bond 0.00387 ( 21) link_BETA1-4 : angle 2.38902 ( 63) link_BETA1-6 : bond 0.00350 ( 3) link_BETA1-6 : angle 2.15602 ( 9) link_NAG-ASN : bond 0.00475 ( 33) link_NAG-ASN : angle 3.49565 ( 99) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4908 Ramachandran restraints generated. 2454 Oldfield, 0 Emsley, 2454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4908 Ramachandran restraints generated. 2454 Oldfield, 0 Emsley, 2454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 336 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 LEU cc_start: 0.9230 (mt) cc_final: 0.8943 (mt) REVERT: A 95 MET cc_start: 0.9176 (ttm) cc_final: 0.8846 (ttm) REVERT: A 98 ASN cc_start: 0.8894 (t0) cc_final: 0.8478 (t0) REVERT: A 374 HIS cc_start: 0.6895 (t-90) cc_final: 0.6535 (t-90) REVERT: A 389 ASN cc_start: 0.8236 (p0) cc_final: 0.7941 (p0) REVERT: B 530 MET cc_start: 0.8730 (mtm) cc_final: 0.8276 (mtt) REVERT: B 537 LEU cc_start: 0.9346 (mp) cc_final: 0.9122 (tp) REVERT: B 543 ASN cc_start: 0.8966 (OUTLIER) cc_final: 0.8475 (p0) REVERT: B 589 ASP cc_start: 0.9151 (m-30) cc_final: 0.8936 (m-30) REVERT: B 657 GLU cc_start: 0.9487 (tp30) cc_final: 0.9029 (pt0) REVERT: C 11 MET cc_start: 0.7504 (pmm) cc_final: 0.7007 (tpt) REVERT: C 33 TYR cc_start: 0.9427 (m-10) cc_final: 0.8988 (m-10) REVERT: C 48 MET cc_start: 0.8542 (mmp) cc_final: 0.8200 (mmm) REVERT: C 107 ASP cc_start: 0.8459 (p0) cc_final: 0.7777 (p0) REVERT: C 111 TYR cc_start: 0.9257 (m-10) cc_final: 0.8515 (m-80) REVERT: C 114 PHE cc_start: 0.9504 (m-10) cc_final: 0.8894 (m-10) REVERT: D 34 LEU cc_start: 0.9495 (mm) cc_final: 0.9276 (mm) REVERT: D 84 ASP cc_start: 0.7122 (m-30) cc_final: 0.6869 (m-30) REVERT: E 69 TRP cc_start: 0.7029 (t60) cc_final: 0.6592 (t60) REVERT: E 95 MET cc_start: 0.9207 (ttm) cc_final: 0.8969 (ttm) REVERT: E 98 ASN cc_start: 0.8941 (t0) cc_final: 0.8532 (t0) REVERT: E 178 ASP cc_start: 0.9245 (m-30) cc_final: 0.9025 (m-30) REVERT: E 434 MET cc_start: 0.8923 (ptm) cc_final: 0.8645 (ptm) REVERT: E 483 LEU cc_start: 0.9446 (tp) cc_final: 0.9009 (tt) REVERT: F 530 MET cc_start: 0.8555 (mtm) cc_final: 0.7996 (mtt) REVERT: F 535 MET cc_start: 0.8569 (mmp) cc_final: 0.8342 (mmm) REVERT: F 543 ASN cc_start: 0.8960 (OUTLIER) cc_final: 0.8436 (p0) REVERT: F 574 LYS cc_start: 0.9464 (mmmm) cc_final: 0.9121 (mmmm) REVERT: F 589 ASP cc_start: 0.9199 (m-30) cc_final: 0.8990 (m-30) REVERT: F 633 LYS cc_start: 0.9556 (mmtt) cc_final: 0.9355 (mmmm) REVERT: F 657 GLU cc_start: 0.9480 (tp30) cc_final: 0.9063 (pt0) REVERT: G 11 MET cc_start: 0.7528 (pmm) cc_final: 0.7032 (tpt) REVERT: G 48 MET cc_start: 0.8553 (mmp) cc_final: 0.8271 (mmm) REVERT: G 81 MET cc_start: 0.9206 (mtm) cc_final: 0.8699 (mtp) REVERT: G 107 ASP cc_start: 0.8562 (p0) cc_final: 0.7682 (p0) REVERT: G 111 TYR cc_start: 0.9096 (m-80) cc_final: 0.8361 (m-80) REVERT: G 114 PHE cc_start: 0.9450 (m-10) cc_final: 0.8793 (m-10) REVERT: I 98 ASN cc_start: 0.8928 (t0) cc_final: 0.8586 (t0) REVERT: I 217 TYR cc_start: 0.7415 (m-80) cc_final: 0.6855 (m-10) REVERT: I 374 HIS cc_start: 0.7222 (t-90) cc_final: 0.6811 (t-90) REVERT: I 475 MET cc_start: 0.9092 (mpp) cc_final: 0.8805 (mpp) REVERT: I 483 LEU cc_start: 0.9440 (tp) cc_final: 0.9218 (tp) REVERT: J 530 MET cc_start: 0.8781 (mtm) cc_final: 0.8303 (mtt) REVERT: J 543 ASN cc_start: 0.9309 (OUTLIER) cc_final: 0.8694 (p0) REVERT: J 574 LYS cc_start: 0.9492 (mmtt) cc_final: 0.9267 (mmmt) REVERT: J 589 ASP cc_start: 0.9105 (m-30) cc_final: 0.8896 (m-30) REVERT: J 601 LYS cc_start: 0.9211 (mppt) cc_final: 0.9003 (mmtm) REVERT: J 624 ASP cc_start: 0.9351 (m-30) cc_final: 0.8549 (p0) REVERT: J 633 LYS cc_start: 0.9499 (mmtt) cc_final: 0.9260 (mmmm) REVERT: J 657 GLU cc_start: 0.9473 (tp30) cc_final: 0.8946 (pt0) REVERT: K 11 MET cc_start: 0.7422 (tpt) cc_final: 0.7080 (tpt) REVERT: K 46 GLN cc_start: 0.8790 (mt0) cc_final: 0.8545 (pt0) REVERT: K 48 MET cc_start: 0.8527 (mmp) cc_final: 0.7998 (mmm) REVERT: K 107 ASP cc_start: 0.8520 (p0) cc_final: 0.7910 (p0) REVERT: K 111 TYR cc_start: 0.9150 (m-80) cc_final: 0.8486 (m-80) REVERT: K 114 PHE cc_start: 0.9488 (m-10) cc_final: 0.8877 (m-10) REVERT: L 33 ASP cc_start: 0.9067 (p0) cc_final: 0.8841 (p0) REVERT: L 106 LYS cc_start: 0.9600 (pptt) cc_final: 0.9367 (pptt) outliers start: 5 outliers final: 0 residues processed: 341 average time/residue: 0.1223 time to fit residues: 67.0997 Evaluate side-chains 252 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 249 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 164 optimal weight: 0.4980 chunk 39 optimal weight: 5.9990 chunk 59 optimal weight: 20.0000 chunk 213 optimal weight: 7.9990 chunk 232 optimal weight: 0.5980 chunk 88 optimal weight: 8.9990 chunk 165 optimal weight: 0.9990 chunk 236 optimal weight: 1.9990 chunk 125 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 137 optimal weight: 0.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 575 GLN G 46 GLN ** I 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 575 GLN K 65 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.062199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.048905 restraints weight = 104777.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.050675 restraints weight = 60478.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.051907 restraints weight = 41946.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.052770 restraints weight = 32524.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.053396 restraints weight = 27197.425| |-----------------------------------------------------------------------------| r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.5282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 20655 Z= 0.135 Angle : 0.792 13.851 28212 Z= 0.390 Chirality : 0.047 0.226 3318 Planarity : 0.004 0.061 3486 Dihedral : 8.159 57.476 3963 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.49 % Allowed : 5.54 % Favored : 93.97 % Rotamer: Outliers : 0.05 % Allowed : 1.82 % Favored : 98.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.89 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.17), residues: 2454 helix: 1.47 (0.27), residues: 375 sheet: 0.19 (0.20), residues: 585 loop : -0.73 (0.16), residues: 1494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 617 TYR 0.026 0.002 TYR L 41 PHE 0.011 0.001 PHE A 376 TRP 0.045 0.002 TRP I 479 HIS 0.004 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00284 (20553) covalent geometry : angle 0.75841 (27945) SS BOND : bond 0.00345 ( 39) SS BOND : angle 0.94835 ( 78) hydrogen bonds : bond 0.04047 ( 705) hydrogen bonds : angle 5.81244 ( 1917) link_ALPHA1-3 : bond 0.00946 ( 3) link_ALPHA1-3 : angle 1.20736 ( 9) link_ALPHA1-6 : bond 0.00453 ( 3) link_ALPHA1-6 : angle 1.75778 ( 9) link_BETA1-4 : bond 0.00335 ( 21) link_BETA1-4 : angle 2.34911 ( 63) link_BETA1-6 : bond 0.00286 ( 3) link_BETA1-6 : angle 1.57298 ( 9) link_NAG-ASN : bond 0.00420 ( 33) link_NAG-ASN : angle 3.37953 ( 99) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4908 Ramachandran restraints generated. 2454 Oldfield, 0 Emsley, 2454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4908 Ramachandran restraints generated. 2454 Oldfield, 0 Emsley, 2454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 330 time to evaluate : 0.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 LEU cc_start: 0.9265 (mt) cc_final: 0.8906 (mt) REVERT: A 95 MET cc_start: 0.9186 (ttm) cc_final: 0.8883 (ttm) REVERT: A 98 ASN cc_start: 0.8842 (t0) cc_final: 0.8436 (t0) REVERT: A 176 LYS cc_start: 0.9156 (tptp) cc_final: 0.8820 (tmtt) REVERT: A 374 HIS cc_start: 0.6496 (t-90) cc_final: 0.6118 (t-90) REVERT: A 389 ASN cc_start: 0.8248 (p0) cc_final: 0.7974 (p0) REVERT: B 530 MET cc_start: 0.8784 (mtm) cc_final: 0.8472 (mtt) REVERT: B 589 ASP cc_start: 0.9199 (m-30) cc_final: 0.8963 (m-30) REVERT: B 601 LYS cc_start: 0.9196 (mppt) cc_final: 0.8953 (mmtm) REVERT: B 633 LYS cc_start: 0.9448 (mmtt) cc_final: 0.9167 (mmmm) REVERT: B 657 GLU cc_start: 0.9480 (tp30) cc_final: 0.9026 (pt0) REVERT: C 11 MET cc_start: 0.7474 (pmm) cc_final: 0.6918 (mtt) REVERT: C 33 TYR cc_start: 0.9444 (m-10) cc_final: 0.8972 (m-10) REVERT: C 48 MET cc_start: 0.8542 (mmp) cc_final: 0.8121 (mmm) REVERT: C 81 MET cc_start: 0.9262 (mtp) cc_final: 0.9013 (mtp) REVERT: D 77 ILE cc_start: 0.8956 (mm) cc_final: 0.8568 (mm) REVERT: D 84 ASP cc_start: 0.7151 (m-30) cc_final: 0.6854 (m-30) REVERT: E 69 TRP cc_start: 0.7053 (t60) cc_final: 0.6509 (t60) REVERT: E 95 MET cc_start: 0.9215 (ttm) cc_final: 0.8989 (ttm) REVERT: E 98 ASN cc_start: 0.8898 (t0) cc_final: 0.8691 (t0) REVERT: E 369 MET cc_start: 0.6973 (mtm) cc_final: 0.6618 (mtm) REVERT: E 434 MET cc_start: 0.8845 (ptm) cc_final: 0.8609 (ptm) REVERT: E 483 LEU cc_start: 0.9471 (tp) cc_final: 0.9225 (tp) REVERT: F 530 MET cc_start: 0.8608 (mtm) cc_final: 0.8234 (mtt) REVERT: F 535 MET cc_start: 0.8529 (mmp) cc_final: 0.8296 (mmm) REVERT: F 574 LYS cc_start: 0.9441 (mmmm) cc_final: 0.9178 (mmmm) REVERT: F 589 ASP cc_start: 0.9201 (m-30) cc_final: 0.8990 (m-30) REVERT: F 633 LYS cc_start: 0.9537 (mmtt) cc_final: 0.9311 (mmmm) REVERT: F 657 GLU cc_start: 0.9507 (tp30) cc_final: 0.9088 (pt0) REVERT: G 11 MET cc_start: 0.7444 (pmm) cc_final: 0.6928 (tpt) REVERT: G 48 MET cc_start: 0.8542 (mmp) cc_final: 0.8243 (mmm) REVERT: G 107 ASP cc_start: 0.8564 (p0) cc_final: 0.7739 (p0) REVERT: G 111 TYR cc_start: 0.9085 (m-80) cc_final: 0.8362 (m-80) REVERT: G 114 PHE cc_start: 0.9446 (m-10) cc_final: 0.8845 (m-10) REVERT: H 77 ILE cc_start: 0.8983 (mm) cc_final: 0.8674 (mm) REVERT: H 84 ASP cc_start: 0.7115 (m-30) cc_final: 0.6855 (m-30) REVERT: I 98 ASN cc_start: 0.8900 (t0) cc_final: 0.8649 (t0) REVERT: I 374 HIS cc_start: 0.7166 (t-90) cc_final: 0.6718 (t-90) REVERT: I 483 LEU cc_start: 0.9513 (tp) cc_final: 0.9264 (tp) REVERT: J 530 MET cc_start: 0.8691 (mtm) cc_final: 0.8377 (mtt) REVERT: J 535 MET cc_start: 0.8506 (mmp) cc_final: 0.8238 (mmp) REVERT: J 574 LYS cc_start: 0.9505 (mmtt) cc_final: 0.9266 (mmmt) REVERT: J 589 ASP cc_start: 0.9104 (m-30) cc_final: 0.8895 (m-30) REVERT: J 601 LYS cc_start: 0.9178 (mppt) cc_final: 0.8943 (mmtm) REVERT: J 624 ASP cc_start: 0.9328 (m-30) cc_final: 0.8491 (p0) REVERT: J 633 LYS cc_start: 0.9487 (mmtt) cc_final: 0.9241 (mmmm) REVERT: J 657 GLU cc_start: 0.9456 (tp30) cc_final: 0.8948 (pt0) REVERT: K 11 MET cc_start: 0.7391 (tpt) cc_final: 0.7011 (tpt) REVERT: K 46 GLN cc_start: 0.8761 (mt0) cc_final: 0.8478 (pt0) REVERT: K 48 MET cc_start: 0.8511 (mmp) cc_final: 0.7933 (mmm) REVERT: K 82 GLU cc_start: 0.8724 (mm-30) cc_final: 0.8470 (mm-30) REVERT: K 107 ASP cc_start: 0.8538 (p0) cc_final: 0.7895 (p0) REVERT: K 111 TYR cc_start: 0.9114 (m-80) cc_final: 0.8462 (m-80) REVERT: L 33 ASP cc_start: 0.9077 (p0) cc_final: 0.8852 (p0) REVERT: L 77 ILE cc_start: 0.9052 (mm) cc_final: 0.8659 (mm) REVERT: L 106 LYS cc_start: 0.9576 (pptt) cc_final: 0.9276 (pptt) outliers start: 1 outliers final: 0 residues processed: 331 average time/residue: 0.1191 time to fit residues: 64.1022 Evaluate side-chains 237 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 237 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 192 optimal weight: 3.9990 chunk 103 optimal weight: 0.3980 chunk 227 optimal weight: 10.0000 chunk 196 optimal weight: 0.8980 chunk 22 optimal weight: 9.9990 chunk 154 optimal weight: 10.0000 chunk 17 optimal weight: 0.9990 chunk 130 optimal weight: 0.9980 chunk 75 optimal weight: 8.9990 chunk 148 optimal weight: 9.9990 chunk 41 optimal weight: 20.0000 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 65 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.061506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.048180 restraints weight = 105450.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.049915 restraints weight = 61234.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.051116 restraints weight = 42641.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.051950 restraints weight = 33229.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.052551 restraints weight = 27926.556| |-----------------------------------------------------------------------------| r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.5575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20655 Z= 0.142 Angle : 0.776 12.925 28212 Z= 0.384 Chirality : 0.046 0.221 3318 Planarity : 0.004 0.066 3486 Dihedral : 7.750 56.834 3963 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.49 % Allowed : 5.62 % Favored : 93.89 % Rotamer: Outliers : 0.09 % Allowed : 1.45 % Favored : 98.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.89 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.17), residues: 2454 helix: 1.50 (0.27), residues: 378 sheet: 0.21 (0.20), residues: 624 loop : -0.64 (0.17), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 617 TYR 0.017 0.002 TYR K 27 PHE 0.019 0.001 PHE G 29 TRP 0.043 0.002 TRP I 427 HIS 0.005 0.001 HIS G 35 Details of bonding type rmsd covalent geometry : bond 0.00300 (20553) covalent geometry : angle 0.74561 (27945) SS BOND : bond 0.00276 ( 39) SS BOND : angle 0.89792 ( 78) hydrogen bonds : bond 0.03896 ( 705) hydrogen bonds : angle 5.72991 ( 1917) link_ALPHA1-3 : bond 0.01140 ( 3) link_ALPHA1-3 : angle 1.40257 ( 9) link_ALPHA1-6 : bond 0.00495 ( 3) link_ALPHA1-6 : angle 1.66809 ( 9) link_BETA1-4 : bond 0.00254 ( 21) link_BETA1-4 : angle 2.20404 ( 63) link_BETA1-6 : bond 0.00228 ( 3) link_BETA1-6 : angle 1.52071 ( 9) link_NAG-ASN : bond 0.00380 ( 33) link_NAG-ASN : angle 3.20805 ( 99) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4908 Ramachandran restraints generated. 2454 Oldfield, 0 Emsley, 2454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4908 Ramachandran restraints generated. 2454 Oldfield, 0 Emsley, 2454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 315 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.9146 (ttm) cc_final: 0.8834 (ttm) REVERT: A 98 ASN cc_start: 0.8835 (t0) cc_final: 0.8320 (t0) REVERT: A 389 ASN cc_start: 0.8335 (p0) cc_final: 0.8045 (p0) REVERT: A 434 MET cc_start: 0.8385 (ptt) cc_final: 0.8108 (ptt) REVERT: B 530 MET cc_start: 0.8711 (mtm) cc_final: 0.8494 (mtt) REVERT: B 589 ASP cc_start: 0.9140 (m-30) cc_final: 0.8924 (m-30) REVERT: B 601 LYS cc_start: 0.9295 (mppt) cc_final: 0.9074 (mmtm) REVERT: B 626 MET cc_start: 0.8208 (tpp) cc_final: 0.7746 (tpp) REVERT: B 633 LYS cc_start: 0.9431 (mmtt) cc_final: 0.9114 (mmmm) REVERT: B 657 GLU cc_start: 0.9475 (tp30) cc_final: 0.9007 (pt0) REVERT: C 11 MET cc_start: 0.7440 (pmm) cc_final: 0.6883 (mtt) REVERT: C 13 ASN cc_start: 0.9257 (t0) cc_final: 0.8937 (t0) REVERT: C 33 TYR cc_start: 0.9481 (m-10) cc_final: 0.9021 (m-10) REVERT: C 48 MET cc_start: 0.8628 (mmp) cc_final: 0.8247 (mmm) REVERT: D 4 LEU cc_start: 0.8608 (mt) cc_final: 0.8332 (mt) REVERT: D 77 ILE cc_start: 0.8934 (mm) cc_final: 0.8556 (mm) REVERT: D 84 ASP cc_start: 0.6992 (m-30) cc_final: 0.6703 (m-30) REVERT: E 69 TRP cc_start: 0.7129 (t60) cc_final: 0.6555 (t60) REVERT: E 95 MET cc_start: 0.9245 (ttm) cc_final: 0.9042 (ttm) REVERT: E 369 MET cc_start: 0.7014 (mtm) cc_final: 0.6701 (mtm) REVERT: E 374 HIS cc_start: 0.7625 (t70) cc_final: 0.7337 (t-90) REVERT: E 434 MET cc_start: 0.8700 (ptm) cc_final: 0.8465 (ptm) REVERT: E 483 LEU cc_start: 0.9503 (tp) cc_final: 0.9218 (tp) REVERT: F 530 MET cc_start: 0.8615 (mtm) cc_final: 0.8249 (mtt) REVERT: F 535 MET cc_start: 0.8480 (mmp) cc_final: 0.8277 (mmm) REVERT: F 574 LYS cc_start: 0.9440 (mmmm) cc_final: 0.9171 (mmmm) REVERT: F 589 ASP cc_start: 0.9190 (m-30) cc_final: 0.8954 (m-30) REVERT: F 633 LYS cc_start: 0.9564 (mmtt) cc_final: 0.9339 (mmmm) REVERT: F 657 GLU cc_start: 0.9511 (tp30) cc_final: 0.9089 (pt0) REVERT: G 11 MET cc_start: 0.7501 (pmm) cc_final: 0.6996 (tpt) REVERT: G 48 MET cc_start: 0.8555 (mmp) cc_final: 0.8248 (mmm) REVERT: G 107 ASP cc_start: 0.8588 (p0) cc_final: 0.7717 (p0) REVERT: G 111 TYR cc_start: 0.9128 (m-80) cc_final: 0.8384 (m-80) REVERT: G 114 PHE cc_start: 0.9500 (m-10) cc_final: 0.8919 (m-10) REVERT: H 77 ILE cc_start: 0.9011 (mm) cc_final: 0.8682 (mm) REVERT: H 84 ASP cc_start: 0.6998 (m-30) cc_final: 0.6699 (m-30) REVERT: I 98 ASN cc_start: 0.8933 (t0) cc_final: 0.8702 (t0) REVERT: I 374 HIS cc_start: 0.7331 (t-90) cc_final: 0.6909 (t-90) REVERT: I 483 LEU cc_start: 0.9541 (tp) cc_final: 0.9311 (tp) REVERT: J 535 MET cc_start: 0.8496 (mmp) cc_final: 0.8214 (mmp) REVERT: J 574 LYS cc_start: 0.9501 (mmtt) cc_final: 0.9257 (mmmt) REVERT: J 589 ASP cc_start: 0.9089 (m-30) cc_final: 0.8833 (m-30) REVERT: J 601 LYS cc_start: 0.9229 (mppt) cc_final: 0.8967 (mmtm) REVERT: J 633 LYS cc_start: 0.9407 (mmtt) cc_final: 0.9053 (mmmm) REVERT: J 657 GLU cc_start: 0.9461 (tp30) cc_final: 0.8931 (pt0) REVERT: K 11 MET cc_start: 0.7389 (tpt) cc_final: 0.6984 (tpt) REVERT: K 35 HIS cc_start: 0.9105 (m-70) cc_final: 0.8863 (m-70) REVERT: K 46 GLN cc_start: 0.8826 (mt0) cc_final: 0.8541 (pt0) REVERT: K 48 MET cc_start: 0.8541 (mmp) cc_final: 0.7867 (mmm) REVERT: K 81 MET cc_start: 0.9184 (mtp) cc_final: 0.8759 (mtp) REVERT: K 82 GLU cc_start: 0.8580 (mm-30) cc_final: 0.8261 (mm-30) REVERT: K 107 ASP cc_start: 0.8591 (p0) cc_final: 0.7972 (p0) REVERT: K 111 TYR cc_start: 0.9087 (m-80) cc_final: 0.8431 (m-80) REVERT: L 4 LEU cc_start: 0.8437 (mt) cc_final: 0.8210 (mt) REVERT: L 33 ASP cc_start: 0.9092 (p0) cc_final: 0.8809 (p0) REVERT: L 77 ILE cc_start: 0.9053 (mm) cc_final: 0.8711 (mm) REVERT: L 106 LYS cc_start: 0.9573 (pptt) cc_final: 0.9302 (pptt) outliers start: 2 outliers final: 0 residues processed: 317 average time/residue: 0.1262 time to fit residues: 64.9071 Evaluate side-chains 234 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 234 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 200 optimal weight: 0.4980 chunk 103 optimal weight: 0.8980 chunk 139 optimal weight: 7.9990 chunk 86 optimal weight: 8.9990 chunk 62 optimal weight: 1.9990 chunk 45 optimal weight: 6.9990 chunk 90 optimal weight: 2.9990 chunk 120 optimal weight: 5.9990 chunk 239 optimal weight: 8.9990 chunk 233 optimal weight: 10.0000 chunk 56 optimal weight: 0.1980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 65 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.061703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.048305 restraints weight = 106987.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.050032 restraints weight = 62660.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.051229 restraints weight = 43959.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.052062 restraints weight = 34425.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.052662 restraints weight = 29043.641| |-----------------------------------------------------------------------------| r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.5742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 20655 Z= 0.136 Angle : 0.771 12.820 28212 Z= 0.382 Chirality : 0.046 0.224 3318 Planarity : 0.004 0.080 3486 Dihedral : 7.559 57.003 3963 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.49 % Allowed : 5.42 % Favored : 94.09 % Rotamer: Outliers : 0.05 % Allowed : 1.40 % Favored : 98.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.89 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.17), residues: 2454 helix: 1.57 (0.27), residues: 375 sheet: 0.20 (0.20), residues: 624 loop : -0.61 (0.17), residues: 1455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 419 TYR 0.017 0.001 TYR K 80 PHE 0.008 0.001 PHE I 233 TRP 0.051 0.002 TRP I 427 HIS 0.004 0.001 HIS G 35 Details of bonding type rmsd covalent geometry : bond 0.00283 (20553) covalent geometry : angle 0.74222 (27945) SS BOND : bond 0.00336 ( 39) SS BOND : angle 1.03986 ( 78) hydrogen bonds : bond 0.03841 ( 705) hydrogen bonds : angle 5.65703 ( 1917) link_ALPHA1-3 : bond 0.00727 ( 3) link_ALPHA1-3 : angle 1.24102 ( 9) link_ALPHA1-6 : bond 0.00517 ( 3) link_ALPHA1-6 : angle 1.60786 ( 9) link_BETA1-4 : bond 0.00339 ( 21) link_BETA1-4 : angle 2.05028 ( 63) link_BETA1-6 : bond 0.00281 ( 3) link_BETA1-6 : angle 1.49955 ( 9) link_NAG-ASN : bond 0.00400 ( 33) link_NAG-ASN : angle 3.10894 ( 99) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4908 Ramachandran restraints generated. 2454 Oldfield, 0 Emsley, 2454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4908 Ramachandran restraints generated. 2454 Oldfield, 0 Emsley, 2454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 312 time to evaluate : 0.691 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: A 95 MET cc_start: 0.9107 (ttm) cc_final: 0.8774 (ttm) REVERT: A 374 HIS cc_start: 0.7020 (t-90) cc_final: 0.6004 (t-90) REVERT: A 389 ASN cc_start: 0.8295 (p0) cc_final: 0.8020 (p0) REVERT: B 530 MET cc_start: 0.8685 (mtm) cc_final: 0.8443 (mtt) REVERT: B 589 ASP cc_start: 0.9143 (m-30) cc_final: 0.8932 (m-30) REVERT: B 601 LYS cc_start: 0.9288 (mppt) cc_final: 0.9060 (mmtm) REVERT: B 633 LYS cc_start: 0.9414 (mmtt) cc_final: 0.9078 (mmmm) REVERT: B 657 GLU cc_start: 0.9489 (tp30) cc_final: 0.8994 (pt0) REVERT: C 11 MET cc_start: 0.7417 (pmm) cc_final: 0.6882 (mtt) REVERT: C 13 ASN cc_start: 0.9251 (t0) cc_final: 0.8871 (t0) REVERT: C 33 TYR cc_start: 0.9470 (m-10) cc_final: 0.9023 (m-10) REVERT: C 48 MET cc_start: 0.8564 (mmp) cc_final: 0.8216 (mmm) REVERT: D 84 ASP cc_start: 0.6745 (m-30) cc_final: 0.6481 (m-30) REVERT: D 106 LYS cc_start: 0.9535 (pptt) cc_final: 0.9327 (pptt) REVERT: E 69 TRP cc_start: 0.7201 (t60) cc_final: 0.6616 (t60) REVERT: E 95 MET cc_start: 0.9240 (ttm) cc_final: 0.9020 (ttm) REVERT: E 374 HIS cc_start: 0.7663 (t70) cc_final: 0.7328 (t-90) REVERT: E 475 MET cc_start: 0.9135 (mpp) cc_final: 0.8567 (mpp) REVERT: E 479 TRP cc_start: 0.8983 (m-10) cc_final: 0.8396 (m-90) REVERT: E 483 LEU cc_start: 0.9524 (tp) cc_final: 0.8991 (tt) REVERT: F 530 MET cc_start: 0.8622 (mtm) cc_final: 0.8232 (mtt) REVERT: F 535 MET cc_start: 0.8486 (mmp) cc_final: 0.8175 (mmm) REVERT: F 574 LYS cc_start: 0.9433 (mmmm) cc_final: 0.9158 (mmmm) REVERT: F 589 ASP cc_start: 0.9175 (m-30) cc_final: 0.8931 (m-30) REVERT: F 633 LYS cc_start: 0.9579 (mmtt) cc_final: 0.9264 (mmmm) REVERT: F 657 GLU cc_start: 0.9509 (tp30) cc_final: 0.9103 (pt0) REVERT: G 11 MET cc_start: 0.7407 (pmm) cc_final: 0.7036 (tpt) REVERT: G 48 MET cc_start: 0.8510 (mmp) cc_final: 0.8210 (mmm) REVERT: G 107 ASP cc_start: 0.8601 (p0) cc_final: 0.7735 (p0) REVERT: G 111 TYR cc_start: 0.9119 (m-80) cc_final: 0.8401 (m-80) REVERT: H 4 LEU cc_start: 0.8528 (mt) cc_final: 0.8251 (mt) REVERT: H 77 ILE cc_start: 0.9038 (mm) cc_final: 0.8714 (mm) REVERT: H 84 ASP cc_start: 0.6825 (m-30) cc_final: 0.6572 (m-30) REVERT: I 374 HIS cc_start: 0.7309 (t-90) cc_final: 0.6837 (t-90) REVERT: I 483 LEU cc_start: 0.9559 (tp) cc_final: 0.9314 (tp) REVERT: J 574 LYS cc_start: 0.9495 (mmtt) cc_final: 0.9244 (mmmt) REVERT: J 589 ASP cc_start: 0.9064 (m-30) cc_final: 0.8813 (m-30) REVERT: J 601 LYS cc_start: 0.9254 (mppt) cc_final: 0.9021 (mmtm) REVERT: J 633 LYS cc_start: 0.9433 (mmtt) cc_final: 0.9083 (mmmm) REVERT: J 657 GLU cc_start: 0.9461 (tp30) cc_final: 0.8952 (pt0) REVERT: K 11 MET cc_start: 0.7418 (tpt) cc_final: 0.6986 (tpt) REVERT: K 35 HIS cc_start: 0.9114 (m-70) cc_final: 0.8846 (m-70) REVERT: K 46 GLN cc_start: 0.8787 (mt0) cc_final: 0.8475 (pt0) REVERT: K 48 MET cc_start: 0.8495 (mmp) cc_final: 0.7879 (mmm) REVERT: K 81 MET cc_start: 0.9111 (mtp) cc_final: 0.8642 (mtp) REVERT: K 82 GLU cc_start: 0.8568 (mm-30) cc_final: 0.8260 (mm-30) REVERT: K 107 ASP cc_start: 0.8549 (p0) cc_final: 0.7817 (p0) REVERT: K 111 TYR cc_start: 0.9089 (m-80) cc_final: 0.8355 (m-80) REVERT: L 33 ASP cc_start: 0.9108 (p0) cc_final: 0.8842 (p0) REVERT: L 77 ILE cc_start: 0.9085 (mm) cc_final: 0.8739 (mm) outliers start: 1 outliers final: 0 residues processed: 313 average time/residue: 0.1281 time to fit residues: 64.9173 Evaluate side-chains 232 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 232 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 136 optimal weight: 5.9990 chunk 94 optimal weight: 3.9990 chunk 90 optimal weight: 0.7980 chunk 60 optimal weight: 7.9990 chunk 17 optimal weight: 4.9990 chunk 176 optimal weight: 1.9990 chunk 194 optimal weight: 9.9990 chunk 59 optimal weight: 20.0000 chunk 31 optimal weight: 20.0000 chunk 160 optimal weight: 0.0570 chunk 25 optimal weight: 6.9990 overall best weight: 2.3704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 65 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.058911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.045330 restraints weight = 107857.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.047020 restraints weight = 63700.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.048217 restraints weight = 44903.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.049049 restraints weight = 35263.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.049628 restraints weight = 29823.653| |-----------------------------------------------------------------------------| r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.6023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 20655 Z= 0.174 Angle : 0.783 12.704 28212 Z= 0.391 Chirality : 0.046 0.225 3318 Planarity : 0.005 0.070 3486 Dihedral : 7.514 57.502 3963 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.49 % Allowed : 6.15 % Favored : 93.36 % Rotamer: Outliers : 0.05 % Allowed : 1.07 % Favored : 98.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.89 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.17), residues: 2454 helix: 1.40 (0.27), residues: 372 sheet: 0.09 (0.20), residues: 630 loop : -0.65 (0.17), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 84 TYR 0.017 0.002 TYR F 638 PHE 0.012 0.001 PHE G 29 TRP 0.036 0.002 TRP E 427 HIS 0.004 0.001 HIS K 116 Details of bonding type rmsd covalent geometry : bond 0.00374 (20553) covalent geometry : angle 0.75611 (27945) SS BOND : bond 0.00322 ( 39) SS BOND : angle 1.14415 ( 78) hydrogen bonds : bond 0.03959 ( 705) hydrogen bonds : angle 5.79196 ( 1917) link_ALPHA1-3 : bond 0.00630 ( 3) link_ALPHA1-3 : angle 1.31521 ( 9) link_ALPHA1-6 : bond 0.00451 ( 3) link_ALPHA1-6 : angle 1.61839 ( 9) link_BETA1-4 : bond 0.00337 ( 21) link_BETA1-4 : angle 1.97466 ( 63) link_BETA1-6 : bond 0.00174 ( 3) link_BETA1-6 : angle 1.57944 ( 9) link_NAG-ASN : bond 0.00420 ( 33) link_NAG-ASN : angle 3.05562 ( 99) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4908 Ramachandran restraints generated. 2454 Oldfield, 0 Emsley, 2454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4908 Ramachandran restraints generated. 2454 Oldfield, 0 Emsley, 2454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 309 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.9116 (ttm) cc_final: 0.8752 (ttm) REVERT: A 374 HIS cc_start: 0.6978 (t-90) cc_final: 0.6242 (t-90) REVERT: A 389 ASN cc_start: 0.8475 (p0) cc_final: 0.8176 (p0) REVERT: A 434 MET cc_start: 0.8652 (ptp) cc_final: 0.8379 (ptt) REVERT: B 543 ASN cc_start: 0.8989 (t0) cc_final: 0.8778 (t0) REVERT: B 589 ASP cc_start: 0.9221 (m-30) cc_final: 0.8980 (m-30) REVERT: B 633 LYS cc_start: 0.9415 (mmtt) cc_final: 0.9056 (mmmm) REVERT: B 657 GLU cc_start: 0.9524 (tp30) cc_final: 0.9024 (pt0) REVERT: C 11 MET cc_start: 0.7341 (pmm) cc_final: 0.6831 (mtt) REVERT: C 13 ASN cc_start: 0.9289 (t0) cc_final: 0.8907 (t0) REVERT: C 33 TYR cc_start: 0.9525 (m-10) cc_final: 0.9137 (m-10) REVERT: C 34 ILE cc_start: 0.9419 (mm) cc_final: 0.9218 (mm) REVERT: C 48 MET cc_start: 0.8658 (mmp) cc_final: 0.8298 (mmm) REVERT: D 22 CYS cc_start: 0.6789 (t) cc_final: 0.4596 (t) REVERT: D 77 ILE cc_start: 0.8992 (mm) cc_final: 0.8560 (mm) REVERT: D 84 ASP cc_start: 0.6794 (m-30) cc_final: 0.6563 (m-30) REVERT: D 90 CYS cc_start: 0.3562 (p) cc_final: 0.0104 (p) REVERT: D 106 LYS cc_start: 0.9575 (pptt) cc_final: 0.9334 (pptt) REVERT: E 69 TRP cc_start: 0.7272 (t60) cc_final: 0.6667 (t60) REVERT: E 95 MET cc_start: 0.9247 (ttm) cc_final: 0.9001 (ttm) REVERT: E 369 MET cc_start: 0.7054 (mtm) cc_final: 0.6706 (mtm) REVERT: E 475 MET cc_start: 0.9267 (mpp) cc_final: 0.8671 (mpp) REVERT: E 479 TRP cc_start: 0.9056 (m-10) cc_final: 0.8426 (m-90) REVERT: E 483 LEU cc_start: 0.9550 (tp) cc_final: 0.9213 (tp) REVERT: F 530 MET cc_start: 0.8673 (mtm) cc_final: 0.8245 (mtt) REVERT: F 535 MET cc_start: 0.8563 (mmp) cc_final: 0.8247 (mmm) REVERT: F 574 LYS cc_start: 0.9488 (mmmm) cc_final: 0.9166 (mmmm) REVERT: F 589 ASP cc_start: 0.9286 (m-30) cc_final: 0.9063 (m-30) REVERT: F 626 MET cc_start: 0.7754 (tpp) cc_final: 0.7548 (mmm) REVERT: F 633 LYS cc_start: 0.9599 (mmtt) cc_final: 0.9305 (mmmm) REVERT: F 657 GLU cc_start: 0.9561 (tp30) cc_final: 0.9079 (pt0) REVERT: G 11 MET cc_start: 0.7414 (pmm) cc_final: 0.6982 (tpt) REVERT: G 48 MET cc_start: 0.8618 (mmp) cc_final: 0.8290 (mmm) REVERT: G 107 ASP cc_start: 0.8760 (p0) cc_final: 0.7938 (p0) REVERT: G 111 TYR cc_start: 0.9202 (m-80) cc_final: 0.8433 (m-80) REVERT: H 77 ILE cc_start: 0.9056 (mm) cc_final: 0.8704 (mm) REVERT: H 84 ASP cc_start: 0.6831 (m-30) cc_final: 0.6589 (m-30) REVERT: I 176 LYS cc_start: 0.9186 (tptt) cc_final: 0.8855 (tptp) REVERT: I 195 ASN cc_start: 0.8367 (p0) cc_final: 0.8123 (p0) REVERT: I 374 HIS cc_start: 0.7411 (t-90) cc_final: 0.6886 (t-90) REVERT: I 483 LEU cc_start: 0.9586 (tp) cc_final: 0.9332 (tp) REVERT: J 535 MET cc_start: 0.8562 (mmp) cc_final: 0.8346 (mmp) REVERT: J 543 ASN cc_start: 0.9087 (t0) cc_final: 0.8620 (p0) REVERT: J 574 LYS cc_start: 0.9549 (mmtt) cc_final: 0.9297 (mmmt) REVERT: J 589 ASP cc_start: 0.9158 (m-30) cc_final: 0.8908 (m-30) REVERT: J 601 LYS cc_start: 0.9214 (mppt) cc_final: 0.9013 (mmtm) REVERT: J 633 LYS cc_start: 0.9406 (mmtt) cc_final: 0.9043 (mmmm) REVERT: J 657 GLU cc_start: 0.9499 (tp30) cc_final: 0.8979 (pt0) REVERT: K 11 MET cc_start: 0.7402 (tpt) cc_final: 0.6965 (tpt) REVERT: K 35 HIS cc_start: 0.9221 (m-70) cc_final: 0.8942 (m-70) REVERT: K 48 MET cc_start: 0.8583 (mmp) cc_final: 0.7643 (mmm) REVERT: K 107 ASP cc_start: 0.8798 (p0) cc_final: 0.8027 (p0) REVERT: K 111 TYR cc_start: 0.9147 (m-80) cc_final: 0.8341 (m-80) REVERT: L 33 ASP cc_start: 0.9191 (p0) cc_final: 0.8906 (p0) REVERT: L 77 ILE cc_start: 0.9140 (mm) cc_final: 0.8829 (mm) outliers start: 1 outliers final: 0 residues processed: 310 average time/residue: 0.1271 time to fit residues: 63.2415 Evaluate side-chains 229 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 229 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 40 optimal weight: 5.9990 chunk 43 optimal weight: 0.9990 chunk 91 optimal weight: 20.0000 chunk 171 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 chunk 165 optimal weight: 5.9990 chunk 73 optimal weight: 6.9990 chunk 15 optimal weight: 0.9980 chunk 198 optimal weight: 10.0000 chunk 90 optimal weight: 0.8980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 113 ASN ** E 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 377 ASN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 65 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.059359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.045713 restraints weight = 106770.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.047414 restraints weight = 63365.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.048603 restraints weight = 44672.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.049439 restraints weight = 35099.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.050033 restraints weight = 29671.337| |-----------------------------------------------------------------------------| r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.6216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20655 Z= 0.141 Angle : 0.773 14.298 28212 Z= 0.385 Chirality : 0.046 0.226 3318 Planarity : 0.004 0.068 3486 Dihedral : 7.435 57.683 3963 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.49 % Allowed : 5.62 % Favored : 93.89 % Rotamer: Outliers : 0.14 % Allowed : 0.56 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.89 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.17), residues: 2454 helix: 1.44 (0.27), residues: 372 sheet: 0.19 (0.21), residues: 558 loop : -0.67 (0.17), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 84 TYR 0.046 0.002 TYR I 217 PHE 0.011 0.001 PHE C 29 TRP 0.040 0.002 TRP E 427 HIS 0.004 0.001 HIS I 216 Details of bonding type rmsd covalent geometry : bond 0.00297 (20553) covalent geometry : angle 0.74800 (27945) SS BOND : bond 0.00511 ( 39) SS BOND : angle 1.05776 ( 78) hydrogen bonds : bond 0.03832 ( 705) hydrogen bonds : angle 5.69056 ( 1917) link_ALPHA1-3 : bond 0.00836 ( 3) link_ALPHA1-3 : angle 1.41718 ( 9) link_ALPHA1-6 : bond 0.00518 ( 3) link_ALPHA1-6 : angle 1.52051 ( 9) link_BETA1-4 : bond 0.00312 ( 21) link_BETA1-4 : angle 1.83549 ( 63) link_BETA1-6 : bond 0.00268 ( 3) link_BETA1-6 : angle 1.53493 ( 9) link_NAG-ASN : bond 0.00377 ( 33) link_NAG-ASN : angle 2.95214 ( 99) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4908 Ramachandran restraints generated. 2454 Oldfield, 0 Emsley, 2454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4908 Ramachandran restraints generated. 2454 Oldfield, 0 Emsley, 2454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 313 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.9128 (ttm) cc_final: 0.8737 (ttm) REVERT: A 374 HIS cc_start: 0.6904 (t-90) cc_final: 0.6093 (t-90) REVERT: A 389 ASN cc_start: 0.8432 (p0) cc_final: 0.8136 (p0) REVERT: A 434 MET cc_start: 0.8485 (ptp) cc_final: 0.8160 (ptt) REVERT: B 543 ASN cc_start: 0.8914 (t0) cc_final: 0.8713 (t0) REVERT: B 589 ASP cc_start: 0.9213 (m-30) cc_final: 0.8979 (m-30) REVERT: B 601 LYS cc_start: 0.9242 (mppt) cc_final: 0.8964 (mmtp) REVERT: B 633 LYS cc_start: 0.9419 (mmtt) cc_final: 0.9046 (mmmm) REVERT: B 657 GLU cc_start: 0.9530 (tp30) cc_final: 0.9051 (pt0) REVERT: C 11 MET cc_start: 0.7351 (pmm) cc_final: 0.6836 (mtt) REVERT: C 13 ASN cc_start: 0.9303 (t0) cc_final: 0.8901 (t0) REVERT: D 77 ILE cc_start: 0.8979 (mm) cc_final: 0.8590 (mm) REVERT: D 106 LYS cc_start: 0.9555 (pptt) cc_final: 0.9347 (pptt) REVERT: E 69 TRP cc_start: 0.7302 (t60) cc_final: 0.6707 (t60) REVERT: E 95 MET cc_start: 0.9265 (ttm) cc_final: 0.9018 (ttm) REVERT: E 369 MET cc_start: 0.6994 (mtm) cc_final: 0.6646 (mtm) REVERT: E 475 MET cc_start: 0.9200 (mpp) cc_final: 0.8602 (mpp) REVERT: E 479 TRP cc_start: 0.9021 (m-10) cc_final: 0.8325 (m-90) REVERT: E 483 LEU cc_start: 0.9546 (tp) cc_final: 0.9340 (tp) REVERT: F 530 MET cc_start: 0.8657 (mtm) cc_final: 0.8195 (mtt) REVERT: F 535 MET cc_start: 0.8564 (mmp) cc_final: 0.8251 (mmm) REVERT: F 574 LYS cc_start: 0.9451 (mmmm) cc_final: 0.9108 (mmmm) REVERT: F 589 ASP cc_start: 0.9257 (m-30) cc_final: 0.9013 (m-30) REVERT: F 633 LYS cc_start: 0.9605 (mmtt) cc_final: 0.9320 (mmmm) REVERT: F 657 GLU cc_start: 0.9519 (tp30) cc_final: 0.9096 (pt0) REVERT: G 11 MET cc_start: 0.7352 (pmm) cc_final: 0.6943 (tpt) REVERT: G 48 MET cc_start: 0.8583 (mmp) cc_final: 0.8259 (mmm) REVERT: G 80 TYR cc_start: 0.8839 (m-80) cc_final: 0.8566 (m-10) REVERT: G 107 ASP cc_start: 0.8762 (p0) cc_final: 0.7924 (p0) REVERT: G 111 TYR cc_start: 0.9185 (m-80) cc_final: 0.8396 (m-80) REVERT: H 38 TYR cc_start: 0.8016 (m-10) cc_final: 0.7407 (m-10) REVERT: H 77 ILE cc_start: 0.9088 (mm) cc_final: 0.8734 (mm) REVERT: H 84 ASP cc_start: 0.6548 (m-30) cc_final: 0.6320 (m-30) REVERT: I 374 HIS cc_start: 0.7411 (t-90) cc_final: 0.6900 (t-90) REVERT: I 483 LEU cc_start: 0.9625 (tp) cc_final: 0.9341 (tp) REVERT: J 543 ASN cc_start: 0.8925 (t0) cc_final: 0.8468 (p0) REVERT: J 574 LYS cc_start: 0.9489 (mmtt) cc_final: 0.9237 (mmmt) REVERT: J 589 ASP cc_start: 0.9149 (m-30) cc_final: 0.8895 (m-30) REVERT: J 624 ASP cc_start: 0.9411 (m-30) cc_final: 0.8553 (p0) REVERT: J 626 MET cc_start: 0.7787 (tpp) cc_final: 0.7572 (tpp) REVERT: J 633 LYS cc_start: 0.9412 (mmtt) cc_final: 0.9039 (mmmm) REVERT: J 657 GLU cc_start: 0.9501 (tp30) cc_final: 0.8973 (pt0) REVERT: K 11 MET cc_start: 0.7635 (tpt) cc_final: 0.7160 (pmm) REVERT: K 35 HIS cc_start: 0.9264 (m-70) cc_final: 0.8954 (m-70) REVERT: K 48 MET cc_start: 0.8617 (mmp) cc_final: 0.8174 (mmm) REVERT: K 82 GLU cc_start: 0.8594 (mm-30) cc_final: 0.8236 (mm-30) REVERT: K 107 ASP cc_start: 0.8825 (p0) cc_final: 0.8045 (p0) REVERT: K 111 TYR cc_start: 0.9157 (m-80) cc_final: 0.8378 (m-80) REVERT: L 33 ASP cc_start: 0.9193 (p0) cc_final: 0.8922 (p0) REVERT: L 106 LYS cc_start: 0.9591 (pptt) cc_final: 0.9305 (pptt) outliers start: 3 outliers final: 1 residues processed: 314 average time/residue: 0.1258 time to fit residues: 63.5411 Evaluate side-chains 237 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 236 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 2 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 188 optimal weight: 7.9990 chunk 201 optimal weight: 5.9990 chunk 181 optimal weight: 0.8980 chunk 9 optimal weight: 0.3980 chunk 137 optimal weight: 0.7980 chunk 23 optimal weight: 0.5980 chunk 142 optimal weight: 9.9990 chunk 82 optimal weight: 5.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 377 ASN ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 113 ASN ** E 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 113 ASN ** I 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 377 ASN ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 65 GLN K 113 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.060091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.046423 restraints weight = 105933.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.048155 restraints weight = 62288.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.049378 restraints weight = 43791.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.050234 restraints weight = 34270.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.050810 restraints weight = 28879.899| |-----------------------------------------------------------------------------| r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.6332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 20655 Z= 0.128 Angle : 0.764 14.004 28212 Z= 0.378 Chirality : 0.046 0.228 3318 Planarity : 0.005 0.076 3486 Dihedral : 7.317 57.623 3963 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.49 % Allowed : 5.66 % Favored : 93.85 % Rotamer: Outliers : 0.28 % Allowed : 0.14 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.89 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.17), residues: 2454 helix: 1.50 (0.27), residues: 372 sheet: 0.24 (0.20), residues: 609 loop : -0.70 (0.17), residues: 1473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 84 TYR 0.019 0.001 TYR K 27 PHE 0.008 0.001 PHE I 233 TRP 0.040 0.002 TRP E 427 HIS 0.004 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00266 (20553) covalent geometry : angle 0.74077 (27945) SS BOND : bond 0.00299 ( 39) SS BOND : angle 0.96665 ( 78) hydrogen bonds : bond 0.03680 ( 705) hydrogen bonds : angle 5.62194 ( 1917) link_ALPHA1-3 : bond 0.00900 ( 3) link_ALPHA1-3 : angle 1.49437 ( 9) link_ALPHA1-6 : bond 0.00551 ( 3) link_ALPHA1-6 : angle 1.46558 ( 9) link_BETA1-4 : bond 0.00354 ( 21) link_BETA1-4 : angle 1.70675 ( 63) link_BETA1-6 : bond 0.00331 ( 3) link_BETA1-6 : angle 1.56080 ( 9) link_NAG-ASN : bond 0.00376 ( 33) link_NAG-ASN : angle 2.86308 ( 99) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4908 Ramachandran restraints generated. 2454 Oldfield, 0 Emsley, 2454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4908 Ramachandran restraints generated. 2454 Oldfield, 0 Emsley, 2454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 315 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.9119 (ttm) cc_final: 0.8736 (ttm) REVERT: A 374 HIS cc_start: 0.6676 (t-90) cc_final: 0.5959 (t-90) REVERT: A 389 ASN cc_start: 0.8355 (p0) cc_final: 0.8083 (p0) REVERT: B 535 MET cc_start: 0.8704 (mmp) cc_final: 0.8474 (mmp) REVERT: B 538 THR cc_start: 0.9552 (p) cc_final: 0.9243 (p) REVERT: B 589 ASP cc_start: 0.9212 (m-30) cc_final: 0.8984 (m-30) REVERT: B 601 LYS cc_start: 0.9222 (mppt) cc_final: 0.8935 (mtmm) REVERT: B 633 LYS cc_start: 0.9385 (mmtt) cc_final: 0.9007 (mmmm) REVERT: B 657 GLU cc_start: 0.9537 (tp30) cc_final: 0.9060 (pt0) REVERT: C 11 MET cc_start: 0.7381 (pmm) cc_final: 0.6776 (mtt) REVERT: C 13 ASN cc_start: 0.9313 (t0) cc_final: 0.8900 (t0) REVERT: C 48 MET cc_start: 0.9404 (mmt) cc_final: 0.8737 (mmm) REVERT: D 84 ASP cc_start: 0.6891 (m-30) cc_final: 0.6656 (m-30) REVERT: D 106 LYS cc_start: 0.9571 (pptt) cc_final: 0.9327 (pptt) REVERT: E 69 TRP cc_start: 0.7276 (t60) cc_final: 0.6633 (t60) REVERT: E 95 MET cc_start: 0.9260 (ttm) cc_final: 0.9019 (ttm) REVERT: E 369 MET cc_start: 0.6751 (mtm) cc_final: 0.6392 (mtm) REVERT: E 475 MET cc_start: 0.9219 (mpp) cc_final: 0.8644 (mpp) REVERT: E 479 TRP cc_start: 0.8917 (m-10) cc_final: 0.8160 (m-90) REVERT: E 483 LEU cc_start: 0.9524 (tp) cc_final: 0.9236 (tp) REVERT: F 530 MET cc_start: 0.8640 (mtm) cc_final: 0.8254 (mtt) REVERT: F 535 MET cc_start: 0.8553 (mmp) cc_final: 0.8241 (mmm) REVERT: F 543 ASN cc_start: 0.8965 (t0) cc_final: 0.8574 (p0) REVERT: F 574 LYS cc_start: 0.9459 (mmmm) cc_final: 0.9113 (mmmm) REVERT: F 589 ASP cc_start: 0.9221 (m-30) cc_final: 0.8979 (m-30) REVERT: F 633 LYS cc_start: 0.9541 (mmtt) cc_final: 0.9221 (mmmm) REVERT: F 657 GLU cc_start: 0.9526 (tp30) cc_final: 0.9096 (pt0) REVERT: G 11 MET cc_start: 0.7339 (pmm) cc_final: 0.6962 (tpt) REVERT: G 48 MET cc_start: 0.8556 (mmp) cc_final: 0.8233 (mmm) REVERT: G 107 ASP cc_start: 0.8721 (p0) cc_final: 0.7840 (p0) REVERT: G 111 TYR cc_start: 0.9183 (m-80) cc_final: 0.8438 (m-80) REVERT: H 34 LEU cc_start: 0.9633 (mm) cc_final: 0.9300 (mm) REVERT: H 38 TYR cc_start: 0.7953 (m-10) cc_final: 0.7324 (m-10) REVERT: H 77 ILE cc_start: 0.9089 (mm) cc_final: 0.8871 (mm) REVERT: H 84 ASP cc_start: 0.6470 (m-30) cc_final: 0.6249 (m-30) REVERT: H 110 LEU cc_start: 0.5943 (mt) cc_final: 0.5690 (pp) REVERT: I 176 LYS cc_start: 0.8971 (tmtt) cc_final: 0.8344 (tmtt) REVERT: I 178 ASP cc_start: 0.9144 (m-30) cc_final: 0.8155 (m-30) REVERT: I 374 HIS cc_start: 0.7336 (t-90) cc_final: 0.6802 (t-90) REVERT: I 483 LEU cc_start: 0.9598 (tp) cc_final: 0.9338 (tp) REVERT: J 543 ASN cc_start: 0.8925 (t0) cc_final: 0.8502 (p0) REVERT: J 574 LYS cc_start: 0.9483 (mmtt) cc_final: 0.9224 (mmmt) REVERT: J 589 ASP cc_start: 0.9129 (m-30) cc_final: 0.8878 (m-30) REVERT: J 633 LYS cc_start: 0.9405 (mmtt) cc_final: 0.9035 (mmmm) REVERT: J 647 GLU cc_start: 0.9515 (tt0) cc_final: 0.9118 (tp30) REVERT: J 657 GLU cc_start: 0.9502 (tp30) cc_final: 0.8951 (pt0) REVERT: K 11 MET cc_start: 0.7630 (tpt) cc_final: 0.7090 (pmm) REVERT: K 35 HIS cc_start: 0.9254 (m-70) cc_final: 0.8988 (m-70) REVERT: K 48 MET cc_start: 0.8853 (mmp) cc_final: 0.8281 (mmm) REVERT: K 81 MET cc_start: 0.8996 (mtm) cc_final: 0.8563 (mtm) REVERT: K 82 GLU cc_start: 0.8467 (mm-30) cc_final: 0.8095 (mm-30) REVERT: K 107 ASP cc_start: 0.8744 (p0) cc_final: 0.7898 (p0) REVERT: K 111 TYR cc_start: 0.9166 (m-80) cc_final: 0.8406 (m-80) REVERT: L 33 ASP cc_start: 0.9184 (p0) cc_final: 0.8941 (p0) REVERT: L 77 ILE cc_start: 0.9211 (mm) cc_final: 0.9006 (mm) REVERT: L 106 LYS cc_start: 0.9571 (pptt) cc_final: 0.9282 (pptt) outliers start: 6 outliers final: 2 residues processed: 316 average time/residue: 0.1284 time to fit residues: 65.4153 Evaluate side-chains 246 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 244 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 17 optimal weight: 6.9990 chunk 18 optimal weight: 6.9990 chunk 234 optimal weight: 0.9980 chunk 91 optimal weight: 20.0000 chunk 77 optimal weight: 20.0000 chunk 206 optimal weight: 10.0000 chunk 47 optimal weight: 0.0170 chunk 238 optimal weight: 0.0370 chunk 101 optimal weight: 9.9990 chunk 220 optimal weight: 0.9980 chunk 114 optimal weight: 2.9990 overall best weight: 1.0098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 543 ASN ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 113 ASN ** E 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 377 ASN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 113 ASN ** I 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 65 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.060180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.046675 restraints weight = 105203.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.048389 restraints weight = 61678.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.049621 restraints weight = 43079.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.050475 restraints weight = 33574.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.051076 restraints weight = 28181.642| |-----------------------------------------------------------------------------| r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.6432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 20655 Z= 0.130 Angle : 0.763 13.853 28212 Z= 0.378 Chirality : 0.046 0.228 3318 Planarity : 0.004 0.069 3486 Dihedral : 7.287 57.433 3963 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.49 % Allowed : 5.58 % Favored : 93.93 % Rotamer: Outliers : 0.19 % Allowed : 0.33 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.89 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.17), residues: 2454 helix: 1.45 (0.27), residues: 372 sheet: 0.24 (0.20), residues: 612 loop : -0.74 (0.17), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 84 TYR 0.039 0.001 TYR I 217 PHE 0.007 0.001 PHE E 383 TRP 0.038 0.002 TRP E 427 HIS 0.004 0.001 HIS I 216 Details of bonding type rmsd covalent geometry : bond 0.00274 (20553) covalent geometry : angle 0.74083 (27945) SS BOND : bond 0.00318 ( 39) SS BOND : angle 1.06080 ( 78) hydrogen bonds : bond 0.03598 ( 705) hydrogen bonds : angle 5.56955 ( 1917) link_ALPHA1-3 : bond 0.00794 ( 3) link_ALPHA1-3 : angle 1.47058 ( 9) link_ALPHA1-6 : bond 0.00541 ( 3) link_ALPHA1-6 : angle 1.45055 ( 9) link_BETA1-4 : bond 0.00347 ( 21) link_BETA1-4 : angle 1.65035 ( 63) link_BETA1-6 : bond 0.00329 ( 3) link_BETA1-6 : angle 1.58444 ( 9) link_NAG-ASN : bond 0.00367 ( 33) link_NAG-ASN : angle 2.80441 ( 99) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3080.15 seconds wall clock time: 54 minutes 21.40 seconds (3261.40 seconds total)