Starting phenix.real_space_refine on Thu Mar 5 08:16:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6um7_20819/03_2026/6um7_20819.cif Found real_map, /net/cci-nas-00/data/ceres_data/6um7_20819/03_2026/6um7_20819.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6um7_20819/03_2026/6um7_20819.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6um7_20819/03_2026/6um7_20819.map" model { file = "/net/cci-nas-00/data/ceres_data/6um7_20819/03_2026/6um7_20819.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6um7_20819/03_2026/6um7_20819.cif" } resolution = 3.5 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= 0.009 sd= 0.141 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 135 5.16 5 C 12687 2.51 5 N 3375 2.21 5 O 4137 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 73 residue(s): 0.01s 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: 20334 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 3613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3613 Classifications: {'peptide': 462} Link IDs: {'CIS': 4, 'PTRANS': 23, 'TRANS': 434} Chain: "H" 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: "J" Number of atoms: 991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 991 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "K" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 800 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "D" 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: "E" Number of atoms: 3613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3613 Classifications: {'peptide': 462} Link IDs: {'CIS': 4, 'PTRANS': 23, 'TRANS': 434} Chain: "F" Number of atoms: 991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 991 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "G" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 800 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "1" 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: "B" Number of atoms: 991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 991 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "C" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 800 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "I" Number of atoms: 3613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3613 Classifications: {'peptide': 462} Link IDs: {'CIS': 4, 'PTRANS': 23, 'TRANS': 434} Chain: "L" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" 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: "N" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} 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: "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: 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: "Q" 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: "R" 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: "S" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} 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: "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: 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: "V" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "W" 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: "X" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} 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: "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: 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: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "E" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "I" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 4.65, per 1000 atoms: 0.23 Number of scatterers: 20334 At special positions: 0 Unit cell: (160.5, 161.57, 140.17, 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 135 16.00 O 4137 8.00 N 3375 7.00 C 12687 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, 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=2.20 Simple disulfide: pdb=" SG CYS A 201 " - pdb=" SG CYS A 433 " distance=2.00 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=1.98 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.08 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.20 Simple disulfide: pdb=" SG CYS H 598 " - pdb=" SG CYS H 604 " distance=2.07 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.09 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 90 " distance=2.02 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.07 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=2.20 Simple disulfide: pdb=" SG CYS E 201 " - pdb=" SG CYS E 433 " distance=2.00 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.02 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=1.98 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.08 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.19 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.08 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 90 " distance=2.02 Simple disulfide: pdb=" SG CYS 1 598 " - pdb=" SG CYS 1 604 " distance=2.07 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.08 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 90 " distance=2.02 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=2.20 Simple disulfide: pdb=" SG CYS I 201 " - pdb=" SG CYS I 433 " distance=2.00 Simple disulfide: pdb=" SG CYS I 218 " - pdb=" SG CYS I 247 " distance=2.03 Simple disulfide: pdb=" SG CYS I 228 " - pdb=" SG CYS I 239 " distance=2.03 Simple disulfide: pdb=" SG CYS I 296 " - pdb=" SG CYS I 331 " distance=1.98 Simple disulfide: pdb=" SG CYS I 378 " - pdb=" SG CYS I 445 " distance=2.08 Simple disulfide: pdb=" SG CYS I 385 " - pdb=" SG CYS I 418 " distance=2.19 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 ALPHA1-2 " MAN N 4 " - " MAN N 5 " " MAN S 4 " - " MAN S 5 " " MAN X 4 " - " MAN X 5 " ALPHA1-3 " BMA N 3 " - " MAN N 4 " " BMA S 3 " - " MAN S 4 " " BMA X 3 " - " MAN X 4 " ALPHA1-6 " BMA N 3 " - " MAN N 6 " " BMA S 3 " - " MAN S 6 " " BMA X 3 " - " MAN X 6 " BETA1-4 " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " 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 S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " 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 X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " NAG-ASN " NAG A 619 " - " ASN A 386 " " NAG A 620 " - " ASN A 362 " " NAG A 621 " - " ASN A 197 " " NAG A 622 " - " ASN A 158 " " NAG A 623 " - " ASN A 234 " " NAG A 624 " - " ASN A 88 " " NAG A 625 " - " ASN A 241 " " NAG A 626 " - " ASN A 339 " " NAG E 619 " - " ASN E 386 " " NAG E 620 " - " ASN E 362 " " NAG E 621 " - " ASN E 197 " " NAG E 622 " - " ASN E 158 " " NAG E 623 " - " ASN E 234 " " NAG E 624 " - " ASN E 88 " " NAG E 625 " - " ASN E 241 " " NAG E 626 " - " ASN E 339 " " NAG I 619 " - " ASN I 386 " " NAG I 620 " - " ASN I 362 " " NAG I 621 " - " ASN I 197 " " NAG I 622 " - " ASN I 158 " " NAG I 623 " - " ASN I 234 " " NAG I 624 " - " ASN I 88 " " NAG I 625 " - " ASN I 241 " " NAG I 626 " - " ASN I 339 " " NAG L 1 " - " ASN A 262 " " NAG M 1 " - " ASN A 301 " " NAG N 1 " - " ASN A 332 " " NAG O 1 " - " ASN A 154 " " NAG P 1 " - " ASN A 392 " " NAG Q 1 " - " ASN E 262 " " NAG R 1 " - " ASN E 301 " " NAG S 1 " - " ASN E 332 " " NAG T 1 " - " ASN E 154 " " NAG U 1 " - " ASN E 392 " " NAG V 1 " - " ASN I 262 " " NAG W 1 " - " ASN I 301 " " NAG X 1 " - " ASN I 332 " " NAG Y 1 " - " ASN I 154 " " NAG Z 1 " - " ASN I 392 " Time building additional restraints: 1.87 Conformation dependent library (CDL) restraints added in 1.0 seconds 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4590 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 42 sheets defined 25.5% alpha, 33.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 62 through 68 removed outlier: 3.711A 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: 3.550A pdb=" N GLN A 103 " --> pdb=" O ASP A 99 " (cutoff:3.500A) removed outlier: 3.622A 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: 3.915A 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 389 through 392 Processing helix chain 'A' and resid 474 through 484 removed outlier: 3.669A pdb=" N ASN A 478 " --> pdb=" O ASP A 474 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'H' and resid 513 through 520 Processing helix chain 'H' and resid 523 through 528 removed outlier: 4.062A pdb=" N GLY H 527 " --> pdb=" O GLY H 524 " (cutoff:3.500A) Processing helix chain 'H' and resid 529 through 536 Processing helix chain 'H' and resid 538 through 543 removed outlier: 3.562A pdb=" N ARG H 542 " --> pdb=" O THR H 538 " (cutoff:3.500A) Processing helix chain 'H' and resid 570 through 597 removed outlier: 3.593A pdb=" N LYS H 574 " --> pdb=" O VAL H 570 " (cutoff:3.500A) Processing helix chain 'H' and resid 611 through 615 Processing helix chain 'H' and resid 618 through 625 Processing helix chain 'H' and resid 627 through 635 removed outlier: 3.545A pdb=" N LYS H 633 " --> pdb=" O LEU H 629 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLU H 634 " --> pdb=" O GLN H 630 " (cutoff:3.500A) Processing helix chain 'H' and resid 638 through 664 Processing helix chain 'J' and resid 28 through 30 No H-bonds generated for 'chain 'J' and resid 28 through 30' Processing helix chain 'J' and resid 74 through 76 No H-bonds generated for 'chain 'J' and resid 74 through 76' Processing helix chain 'J' and resid 87 through 91 Processing helix chain 'K' and resid 25 through 30 Processing helix chain 'K' and resid 81 through 85 Processing helix chain 'D' and resid 513 through 520 Processing helix chain 'D' and resid 523 through 528 removed outlier: 4.061A pdb=" N GLY D 527 " --> pdb=" O GLY D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 536 Processing helix chain 'D' and resid 538 through 543 removed outlier: 3.561A pdb=" N ARG D 542 " --> pdb=" O THR D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 570 through 597 removed outlier: 3.592A pdb=" N LYS D 574 " --> pdb=" O VAL D 570 " (cutoff:3.500A) Processing helix chain 'D' and resid 611 through 615 Processing helix chain 'D' and resid 618 through 625 Processing helix chain 'D' and resid 627 through 635 removed outlier: 3.546A pdb=" N LYS D 633 " --> pdb=" O LEU D 629 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLU D 634 " --> pdb=" O GLN D 630 " (cutoff:3.500A) Processing helix chain 'D' and resid 638 through 664 Processing helix chain 'E' and resid 62 through 68 removed outlier: 3.710A 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: 3.552A pdb=" N GLN E 103 " --> pdb=" O ASP E 99 " (cutoff:3.500A) removed outlier: 3.621A 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: 3.915A 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 389 through 392 Processing helix chain 'E' and resid 474 through 484 removed outlier: 3.671A pdb=" N ASN E 478 " --> pdb=" O ASP E 474 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 30 No H-bonds generated for 'chain 'F' and resid 28 through 30' Processing helix chain 'F' and resid 74 through 76 No H-bonds generated for 'chain 'F' and resid 74 through 76' Processing helix chain 'F' and resid 87 through 91 Processing helix chain 'G' and resid 25 through 30 Processing helix chain 'G' and resid 81 through 85 Processing helix chain '1' and resid 513 through 520 Processing helix chain '1' and resid 523 through 528 removed outlier: 4.061A pdb=" N GLY 1 527 " --> pdb=" O GLY 1 524 " (cutoff:3.500A) Processing helix chain '1' and resid 529 through 536 Processing helix chain '1' and resid 538 through 543 removed outlier: 3.561A pdb=" N ARG 1 542 " --> pdb=" O THR 1 538 " (cutoff:3.500A) Processing helix chain '1' and resid 570 through 597 removed outlier: 3.591A pdb=" N LYS 1 574 " --> pdb=" O VAL 1 570 " (cutoff:3.500A) Processing helix chain '1' and resid 611 through 615 Processing helix chain '1' and resid 618 through 625 Processing helix chain '1' and resid 627 through 635 removed outlier: 3.547A pdb=" N LYS 1 633 " --> pdb=" O LEU 1 629 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLU 1 634 " --> pdb=" O GLN 1 630 " (cutoff:3.500A) Processing helix chain '1' and resid 638 through 664 Processing helix chain 'B' and resid 28 through 30 No H-bonds generated for 'chain 'B' and resid 28 through 30' Processing helix chain 'B' and resid 74 through 76 No H-bonds generated for 'chain 'B' and resid 74 through 76' Processing helix chain 'B' and resid 87 through 91 Processing helix chain 'C' and resid 25 through 30 Processing helix chain 'C' and resid 81 through 85 Processing helix chain 'I' and resid 62 through 68 removed outlier: 3.710A 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: 3.552A pdb=" N GLN I 103 " --> pdb=" O ASP I 99 " (cutoff:3.500A) removed outlier: 3.623A 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: 3.914A 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 389 through 392 Processing helix chain 'I' and resid 474 through 484 removed outlier: 3.670A pdb=" N ASN I 478 " --> pdb=" O ASP I 474 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N GLU I 482 " --> pdb=" O ASN I 478 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 495 through 498 removed outlier: 5.009A pdb=" N VAL H 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 8.837A pdb=" N VAL A 38 " --> pdb=" O THR H 606 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N THR H 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 175 Processing sheet with id=AA5, first strand: chain 'A' and resid 260 through 261 removed outlier: 8.030A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 11.716A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 12.000A pdb=" N LEU A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 12.023A pdb=" N LEU A 288 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 11.326A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 10.604A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 11.610A pdb=" N ASP A 457 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 12.254A pdb=" N ILE A 284 " --> pdb=" O ASP A 457 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N GLU A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N SER A 334 " --> pdb=" O GLU A 293 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 271 through 273 removed outlier: 12.254A pdb=" N ILE A 284 " --> pdb=" O ASP A 457 " (cutoff:3.500A) removed outlier: 11.610A pdb=" N ASP A 457 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 10.604A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 11.326A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 12.023A pdb=" N LEU A 288 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 12.000A pdb=" N LEU A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 11.716A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N THR A 357 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N PHE A 468 " --> pdb=" O THR A 357 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LYS A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILE A 358 " --> pdb=" O TYR A 395 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TYR A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 302 through 308 removed outlier: 7.085A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 423 through 426 removed outlier: 4.866A pdb=" N MET A 426 " --> pdb=" O ARG A 432 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ARG A 432 " --> pdb=" O MET A 426 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'J' and resid 3 through 6 Processing sheet with id=AB1, first strand: chain 'J' and resid 10 through 12 removed outlier: 4.847A pdb=" N TYR J 33 " --> pdb=" O GLY J 99 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ILE J 34 " --> pdb=" O TRP J 50 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N TRP J 50 " --> pdb=" O ILE J 34 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'J' and resid 10 through 12 removed outlier: 4.217A pdb=" N TYR J 116 " --> pdb=" O ARG J 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 9 through 10 removed outlier: 6.364A pdb=" N TRP K 37 " --> pdb=" O MET K 49 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 9 through 10 removed outlier: 6.249A pdb=" N THR K 98 " --> pdb=" O ALA K 94 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'K' and resid 18 through 23 Processing sheet with id=AB6, first strand: chain 'D' and resid 603 through 609 removed outlier: 7.842A pdb=" N THR D 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 8.838A pdb=" N VAL E 38 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N VAL D 608 " --> pdb=" O VAL E 36 " (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 175 Processing sheet with id=AC1, first strand: chain 'E' and resid 260 through 261 removed outlier: 8.032A pdb=" N GLY E 451 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 11.716A pdb=" N THR E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 12.000A pdb=" N LEU E 453 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 12.021A pdb=" N LEU E 288 " --> pdb=" O LEU E 453 " (cutoff:3.500A) removed outlier: 11.327A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 10.603A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 11.610A pdb=" N ASP E 457 " --> pdb=" O ILE E 284 " (cutoff:3.500A) removed outlier: 12.253A pdb=" N ILE E 284 " --> pdb=" O ASP E 457 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N GLU E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N SER E 334 " --> pdb=" O GLU E 293 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 271 through 273 removed outlier: 12.253A pdb=" N ILE E 284 " --> pdb=" O ASP E 457 " (cutoff:3.500A) removed outlier: 11.610A pdb=" N ASP E 457 " --> pdb=" O ILE E 284 " (cutoff:3.500A) removed outlier: 10.603A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 11.327A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 12.021A pdb=" N LEU E 288 " --> pdb=" O LEU E 453 " (cutoff:3.500A) removed outlier: 12.000A pdb=" N LEU E 453 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 11.716A pdb=" N THR E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N GLY E 451 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N THR E 357 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N PHE E 468 " --> pdb=" O THR E 357 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LYS E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE E 358 " --> pdb=" O TYR E 395 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TYR E 395 " --> pdb=" O ILE E 358 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 302 through 308 removed outlier: 7.085A pdb=" N THR E 303 " --> pdb=" O GLY E 321 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 423 through 426 removed outlier: 4.868A pdb=" N MET E 426 " --> pdb=" O ARG E 432 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ARG E 432 " --> pdb=" O MET E 426 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 3 through 6 Processing sheet with id=AC6, first strand: chain 'F' and resid 10 through 12 removed outlier: 4.847A pdb=" N TYR F 33 " --> pdb=" O GLY F 99 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ILE F 34 " --> pdb=" O TRP F 50 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N TRP F 50 " --> pdb=" O ILE F 34 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 10 through 12 removed outlier: 4.215A pdb=" N TYR F 116 " --> pdb=" O ARG F 98 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 9 through 10 removed outlier: 6.364A pdb=" N TRP G 37 " --> pdb=" O MET G 49 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 9 through 10 removed outlier: 6.251A pdb=" N THR G 98 " --> pdb=" O ALA G 94 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 18 through 23 Processing sheet with id=AD2, first strand: chain '1' and resid 603 through 609 removed outlier: 7.842A pdb=" N THR 1 606 " --> pdb=" O VAL I 38 " (cutoff:3.500A) removed outlier: 8.838A pdb=" N VAL I 38 " --> pdb=" O THR 1 606 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N VAL 1 608 " --> pdb=" O VAL I 36 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 3 through 6 Processing sheet with id=AD4, first strand: chain 'B' and resid 10 through 12 removed outlier: 4.847A pdb=" N TYR B 33 " --> pdb=" O GLY B 99 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ILE B 34 " --> pdb=" O TRP B 50 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N TRP B 50 " --> pdb=" O ILE B 34 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 10 through 12 removed outlier: 4.216A pdb=" N TYR B 116 " --> pdb=" O ARG B 98 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 9 through 10 removed outlier: 6.363A pdb=" N TRP C 37 " --> pdb=" O MET C 49 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 9 through 10 removed outlier: 6.249A pdb=" N THR C 98 " --> pdb=" O ALA C 94 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 18 through 23 Processing sheet with id=AD9, first strand: chain 'I' and resid 45 through 47 Processing sheet with id=AE1, first strand: chain 'I' and resid 91 through 94 Processing sheet with id=AE2, first strand: chain 'I' and resid 167 through 175 Processing sheet with id=AE3, first strand: chain 'I' and resid 260 through 261 removed outlier: 8.031A pdb=" N GLY I 451 " --> pdb=" O THR I 290 " (cutoff:3.500A) removed outlier: 11.717A pdb=" N THR I 290 " --> pdb=" O GLY I 451 " (cutoff:3.500A) removed outlier: 12.002A pdb=" N LEU I 453 " --> pdb=" O LEU I 288 " (cutoff:3.500A) removed outlier: 12.025A pdb=" N LEU I 288 " --> pdb=" O LEU I 453 " (cutoff:3.500A) removed outlier: 11.326A pdb=" N THR I 455 " --> pdb=" O VAL I 286 " (cutoff:3.500A) removed outlier: 10.603A pdb=" N VAL I 286 " --> pdb=" O THR I 455 " (cutoff:3.500A) removed outlier: 11.610A pdb=" N ASP I 457 " --> pdb=" O ILE I 284 " (cutoff:3.500A) removed outlier: 12.254A pdb=" N ILE I 284 " --> pdb=" O ASP I 457 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N GLU I 293 " --> pdb=" O SER I 334 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N SER I 334 " --> pdb=" O GLU I 293 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ALA I 329 " --> pdb=" O CYS I 418 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N PHE I 382 " --> pdb=" O LYS I 421 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'I' and resid 271 through 273 removed outlier: 12.254A pdb=" N ILE I 284 " --> pdb=" O ASP I 457 " (cutoff:3.500A) removed outlier: 11.610A pdb=" N ASP I 457 " --> pdb=" O ILE I 284 " (cutoff:3.500A) removed outlier: 10.603A pdb=" N VAL I 286 " --> pdb=" O THR I 455 " (cutoff:3.500A) removed outlier: 11.326A pdb=" N THR I 455 " --> pdb=" O VAL I 286 " (cutoff:3.500A) removed outlier: 12.025A pdb=" N LEU I 288 " --> pdb=" O LEU I 453 " (cutoff:3.500A) removed outlier: 12.002A pdb=" N LEU I 453 " --> pdb=" O LEU I 288 " (cutoff:3.500A) removed outlier: 11.717A pdb=" N THR I 290 " --> pdb=" O GLY I 451 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N GLY I 451 " --> pdb=" O THR I 290 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N THR I 357 " --> pdb=" O GLU I 466 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N PHE I 468 " --> pdb=" O THR I 357 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LYS I 360 " --> pdb=" O PHE I 468 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE I 358 " --> pdb=" O TYR I 395 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TYR I 395 " --> pdb=" O ILE I 358 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'I' and resid 302 through 308 removed outlier: 7.085A pdb=" N THR I 303 " --> pdb=" O GLY I 321 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'I' and resid 423 through 426 removed outlier: 4.867A pdb=" N MET I 426 " --> pdb=" O ARG I 432 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ARG I 432 " --> pdb=" O MET I 426 " (cutoff:3.500A) 810 hydrogen bonds defined for protein. 2025 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: 3.89 Time building geometry restraints manager: 2.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.33: 5203 1.33 - 1.47: 6467 1.47 - 1.62: 8892 1.62 - 1.76: 21 1.76 - 1.90: 165 Bond restraints: 20748 Sorted by residual: bond pdb=" N PRO I 177 " pdb=" CD PRO I 177 " ideal model delta sigma weight residual 1.473 1.689 -0.216 1.40e-02 5.10e+03 2.38e+02 bond pdb=" N PRO A 177 " pdb=" CD PRO A 177 " ideal model delta sigma weight residual 1.473 1.689 -0.216 1.40e-02 5.10e+03 2.38e+02 bond pdb=" N PRO E 177 " pdb=" CD PRO E 177 " ideal model delta sigma weight residual 1.473 1.689 -0.216 1.40e-02 5.10e+03 2.38e+02 bond pdb=" CB HIS A 374 " pdb=" CG HIS A 374 " ideal model delta sigma weight residual 1.497 1.384 0.113 1.40e-02 5.10e+03 6.50e+01 bond pdb=" CB HIS E 374 " pdb=" CG HIS E 374 " ideal model delta sigma weight residual 1.497 1.386 0.111 1.40e-02 5.10e+03 6.29e+01 ... (remaining 20743 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.69: 27911 6.69 - 13.38: 271 13.38 - 20.07: 9 20.07 - 26.76: 0 26.76 - 33.44: 9 Bond angle restraints: 28200 Sorted by residual: angle pdb=" C SER F 84 " pdb=" N ARG F 85 " pdb=" CA ARG F 85 " ideal model delta sigma weight residual 122.68 152.73 -30.05 1.47e+00 4.63e-01 4.18e+02 angle pdb=" C SER B 84 " pdb=" N ARG B 85 " pdb=" CA ARG B 85 " ideal model delta sigma weight residual 122.68 152.62 -29.94 1.47e+00 4.63e-01 4.15e+02 angle pdb=" C SER J 84 " pdb=" N ARG J 85 " pdb=" CA ARG J 85 " ideal model delta sigma weight residual 122.68 152.62 -29.94 1.47e+00 4.63e-01 4.15e+02 angle pdb=" C SER 1 546 " pdb=" N GLY 1 547 " pdb=" CA GLY 1 547 " ideal model delta sigma weight residual 121.70 155.14 -33.44 1.80e+00 3.09e-01 3.45e+02 angle pdb=" C SER D 546 " pdb=" N GLY D 547 " pdb=" CA GLY D 547 " ideal model delta sigma weight residual 121.70 155.07 -33.37 1.80e+00 3.09e-01 3.44e+02 ... (remaining 28195 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.43: 12770 23.43 - 46.85: 355 46.85 - 70.28: 100 70.28 - 93.70: 98 93.70 - 117.13: 63 Dihedral angle restraints: 13386 sinusoidal: 6216 harmonic: 7170 Sorted by residual: dihedral pdb=" CA ARG I 446 " pdb=" C ARG I 446 " pdb=" N SER I 447 " pdb=" CA SER I 447 " ideal model delta harmonic sigma weight residual 180.00 62.87 117.13 0 5.00e+00 4.00e-02 5.49e+02 dihedral pdb=" CA ARG A 446 " pdb=" C ARG A 446 " pdb=" N SER A 447 " pdb=" CA SER A 447 " ideal model delta harmonic sigma weight residual 180.00 62.93 117.07 0 5.00e+00 4.00e-02 5.48e+02 dihedral pdb=" CA ARG E 446 " pdb=" C ARG E 446 " pdb=" N SER E 447 " pdb=" CA SER E 447 " ideal model delta harmonic sigma weight residual 180.00 63.16 116.84 0 5.00e+00 4.00e-02 5.46e+02 ... (remaining 13383 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.940: 3393 0.940 - 1.879: 0 1.879 - 2.819: 0 2.819 - 3.759: 0 3.759 - 4.699: 3 Chirality restraints: 3396 Sorted by residual: chirality pdb=" C1 MAN S 4 " pdb=" O3 BMA S 3 " pdb=" C2 MAN S 4 " pdb=" O5 MAN S 4 " both_signs ideal model delta sigma weight residual False 2.40 1.70 0.70 2.00e-02 2.50e+03 1.22e+03 chirality pdb=" C1 MAN N 4 " pdb=" O3 BMA N 3 " pdb=" C2 MAN N 4 " pdb=" O5 MAN N 4 " both_signs ideal model delta sigma weight residual False 2.40 1.70 0.70 2.00e-02 2.50e+03 1.22e+03 chirality pdb=" C1 MAN X 4 " pdb=" O3 BMA X 3 " pdb=" C2 MAN X 4 " pdb=" O5 MAN X 4 " both_signs ideal model delta sigma weight residual False 2.40 1.71 0.69 2.00e-02 2.50e+03 1.19e+03 ... (remaining 3393 not shown) Planarity restraints: 3528 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG R 2 " -0.344 2.00e-02 2.50e+03 2.97e-01 1.10e+03 pdb=" C7 NAG R 2 " 0.081 2.00e-02 2.50e+03 pdb=" C8 NAG R 2 " -0.057 2.00e-02 2.50e+03 pdb=" N2 NAG R 2 " 0.522 2.00e-02 2.50e+03 pdb=" O7 NAG R 2 " -0.201 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG M 2 " -0.344 2.00e-02 2.50e+03 2.97e-01 1.10e+03 pdb=" C7 NAG M 2 " 0.081 2.00e-02 2.50e+03 pdb=" C8 NAG M 2 " -0.057 2.00e-02 2.50e+03 pdb=" N2 NAG M 2 " 0.521 2.00e-02 2.50e+03 pdb=" O7 NAG M 2 " -0.201 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG W 2 " 0.344 2.00e-02 2.50e+03 2.97e-01 1.10e+03 pdb=" C7 NAG W 2 " -0.081 2.00e-02 2.50e+03 pdb=" C8 NAG W 2 " 0.057 2.00e-02 2.50e+03 pdb=" N2 NAG W 2 " -0.521 2.00e-02 2.50e+03 pdb=" O7 NAG W 2 " 0.201 2.00e-02 2.50e+03 ... (remaining 3525 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 1321 2.69 - 3.24: 20028 3.24 - 3.79: 32047 3.79 - 4.35: 41984 4.35 - 4.90: 66859 Nonbonded interactions: 162239 Sorted by model distance: nonbonded pdb=" OG1 THR E 297 " pdb=" O ILE E 443 " model vdw 2.132 3.040 nonbonded pdb=" OG1 THR I 297 " pdb=" O ILE I 443 " model vdw 2.132 3.040 nonbonded pdb=" OG1 THR A 297 " pdb=" O ILE A 443 " model vdw 2.133 3.040 nonbonded pdb=" OD1 ASN E 339 " pdb=" C1 NAG E 626 " model vdw 2.165 2.776 nonbonded pdb=" OD1 ASN I 339 " pdb=" C1 NAG I 626 " model vdw 2.165 2.776 ... (remaining 162234 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.05 Found NCS groups: ncs_group { reference = chain '1' selection = chain 'D' selection = chain 'H' } 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 'L' selection = chain 'M' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'Y' selection = chain 'Z' } ncs_group { reference = chain 'N' selection = chain 'S' selection = chain 'X' } 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: 3.140 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: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 18.540 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6512 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 : 0.019 0.239 20859 Z= 1.073 Angle : 2.108 33.444 28500 Z= 1.363 Chirality : 0.177 4.699 3396 Planarity : 0.027 0.297 3489 Dihedral : 16.468 117.128 8697 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.85 % Allowed : 4.96 % Favored : 94.19 % Rotamer: Outliers : 0.89 % Allowed : 1.26 % Favored : 97.86 % Cbeta Deviations : 0.52 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.88 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.17), residues: 2460 helix: -0.60 (0.23), residues: 399 sheet: 0.62 (0.21), residues: 546 loop : 0.05 (0.17), residues: 1515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG J 57 TYR 0.079 0.009 TYR F 105 PHE 0.033 0.007 PHE G 101 TRP 0.053 0.010 TRP C 37 HIS 0.008 0.003 HIS J 35 Details of bonding type rmsd covalent geometry : bond 0.01832 (20748) covalent geometry : angle 2.06774 (28200) SS BOND : bond 0.10475 ( 33) SS BOND : angle 4.98638 ( 66) hydrogen bonds : bond 0.17454 ( 756) hydrogen bonds : angle 8.69583 ( 2025) link_ALPHA1-2 : bond 0.00193 ( 3) link_ALPHA1-2 : angle 2.90895 ( 9) link_ALPHA1-3 : bond 0.00944 ( 3) link_ALPHA1-3 : angle 5.25557 ( 9) link_ALPHA1-6 : bond 0.00096 ( 3) link_ALPHA1-6 : angle 1.55173 ( 9) link_BETA1-4 : bond 0.00468 ( 30) link_BETA1-4 : angle 2.07072 ( 90) link_NAG-ASN : bond 0.06756 ( 39) link_NAG-ASN : angle 5.66940 ( 117) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 185 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 518 VAL cc_start: 0.4024 (t) cc_final: 0.3691 (p) REVERT: J 89 ASP cc_start: 0.8254 (m-30) cc_final: 0.8004 (m-30) REVERT: E 125 LEU cc_start: 0.7985 (mm) cc_final: 0.7611 (mt) REVERT: 1 535 MET cc_start: 0.4424 (mmp) cc_final: 0.4209 (mpp) REVERT: B 70 MET cc_start: 0.5300 (mtm) cc_final: 0.4996 (mtm) outliers start: 19 outliers final: 3 residues processed: 203 average time/residue: 0.1771 time to fit residues: 51.6504 Evaluate side-chains 77 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 74 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain E residue 241 ASN Chi-restraints excluded: chain G residue 52 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 216 optimal weight: 10.0000 chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 0.6980 chunk 227 optimal weight: 5.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 4.9990 chunk 235 optimal weight: 8.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 GLN A 287 HIS A 363 GLN H 575 GLN J 3 GLN D 575 GLN D 591 GLN E 203 GLN E 287 HIS E 300 ASN E 363 GLN F 1 GLN F 113 ASN 1 658 GLN B 65 GLN I 203 GLN I 287 HIS I 363 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.045088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.039096 restraints weight = 186532.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.040021 restraints weight = 104804.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.040634 restraints weight = 73870.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.041022 restraints weight = 58971.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.041239 restraints weight = 50877.670| |-----------------------------------------------------------------------------| r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6934 moved from start: 0.3042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 20859 Z= 0.221 Angle : 1.004 17.319 28500 Z= 0.497 Chirality : 0.054 0.397 3396 Planarity : 0.006 0.074 3489 Dihedral : 12.681 91.090 4273 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.57 % Allowed : 3.46 % Favored : 95.98 % Rotamer: Outliers : 1.12 % Allowed : 4.52 % Favored : 94.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.88 % Twisted Proline : 3.03 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.17), residues: 2460 helix: 0.95 (0.28), residues: 402 sheet: 0.32 (0.18), residues: 693 loop : -0.62 (0.17), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 446 TYR 0.025 0.002 TYR K 51 PHE 0.032 0.003 PHE H 522 TRP 0.041 0.003 TRP F 101 HIS 0.012 0.002 HIS I 105 Details of bonding type rmsd covalent geometry : bond 0.00470 (20748) covalent geometry : angle 0.95740 (28200) SS BOND : bond 0.00536 ( 33) SS BOND : angle 1.33308 ( 66) hydrogen bonds : bond 0.04886 ( 756) hydrogen bonds : angle 6.82036 ( 2025) link_ALPHA1-2 : bond 0.00462 ( 3) link_ALPHA1-2 : angle 1.12699 ( 9) link_ALPHA1-3 : bond 0.02148 ( 3) link_ALPHA1-3 : angle 1.12283 ( 9) link_ALPHA1-6 : bond 0.00653 ( 3) link_ALPHA1-6 : angle 1.44508 ( 9) link_BETA1-4 : bond 0.00808 ( 30) link_BETA1-4 : angle 2.66919 ( 90) link_NAG-ASN : bond 0.00811 ( 39) link_NAG-ASN : angle 4.23944 ( 117) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 88 time to evaluate : 0.762 Fit side-chains revert: symmetry clash REVERT: E 125 LEU cc_start: 0.8312 (mm) cc_final: 0.7895 (mt) REVERT: E 369 MET cc_start: 0.4691 (OUTLIER) cc_final: 0.4485 (ptm) REVERT: F 48 MET cc_start: 0.4392 (mpp) cc_final: 0.4179 (mtm) REVERT: 1 642 ILE cc_start: 0.6711 (mm) cc_final: 0.6358 (mm) outliers start: 24 outliers final: 6 residues processed: 105 average time/residue: 0.1330 time to fit residues: 23.0298 Evaluate side-chains 77 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain E residue 184 GLU Chi-restraints excluded: chain E residue 369 MET Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain I residue 95 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 165 optimal weight: 8.9990 chunk 81 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 167 optimal weight: 10.0000 chunk 219 optimal weight: 5.9990 chunk 107 optimal weight: 7.9990 chunk 80 optimal weight: 8.9990 chunk 48 optimal weight: 0.9980 chunk 16 optimal weight: 10.0000 chunk 113 optimal weight: 9.9990 chunk 127 optimal weight: 5.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 115 ASN K 39 GLN E 203 GLN E 300 ASN F 115 ASN 1 543 ASN ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 ASN I 422 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.042573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.035816 restraints weight = 189068.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.036735 restraints weight = 108579.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.037343 restraints weight = 77772.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.037736 restraints weight = 62936.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.037979 restraints weight = 54860.421| |-----------------------------------------------------------------------------| r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.6336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.101 20859 Z= 0.289 Angle : 0.989 19.061 28500 Z= 0.502 Chirality : 0.056 0.432 3396 Planarity : 0.006 0.073 3489 Dihedral : 10.731 88.118 4266 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.57 % Allowed : 5.04 % Favored : 94.39 % Rotamer: Outliers : 1.68 % Allowed : 5.97 % Favored : 92.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.88 % Twisted Proline : 1.01 % Twisted General : 0.25 % 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: -0.56 (0.17), residues: 2460 helix: 0.51 (0.26), residues: 426 sheet: 0.02 (0.19), residues: 678 loop : -0.84 (0.17), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 308 TYR 0.024 0.003 TYR I 175 PHE 0.023 0.003 PHE I 382 TRP 0.037 0.003 TRP A 112 HIS 0.011 0.002 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00639 (20748) covalent geometry : angle 0.95425 (28200) SS BOND : bond 0.00531 ( 33) SS BOND : angle 1.37468 ( 66) hydrogen bonds : bond 0.05167 ( 756) hydrogen bonds : angle 6.51670 ( 2025) link_ALPHA1-2 : bond 0.00363 ( 3) link_ALPHA1-2 : angle 2.34848 ( 9) link_ALPHA1-3 : bond 0.01158 ( 3) link_ALPHA1-3 : angle 0.89030 ( 9) link_ALPHA1-6 : bond 0.00551 ( 3) link_ALPHA1-6 : angle 1.74443 ( 9) link_BETA1-4 : bond 0.00916 ( 30) link_BETA1-4 : angle 2.44623 ( 90) link_NAG-ASN : bond 0.00723 ( 39) link_NAG-ASN : angle 3.54529 ( 117) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 77 time to evaluate : 0.707 Fit side-chains revert: symmetry clash REVERT: D 626 MET cc_start: 0.8029 (ttm) cc_final: 0.7751 (ttm) REVERT: G 107 MET cc_start: 0.7662 (tpp) cc_final: 0.7252 (tpp) REVERT: C 100 ILE cc_start: 0.8278 (OUTLIER) cc_final: 0.7488 (pt) outliers start: 36 outliers final: 18 residues processed: 100 average time/residue: 0.1455 time to fit residues: 23.1751 Evaluate side-chains 81 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 62 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 89 ASP Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain E residue 184 GLU Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 23 LYS Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain 1 residue 573 ILE Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain C residue 51 TYR Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 95 MET Chi-restraints excluded: chain I residue 184 GLU Chi-restraints excluded: chain I residue 503 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 91 optimal weight: 8.9990 chunk 26 optimal weight: 7.9990 chunk 45 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 3 optimal weight: 9.9990 chunk 165 optimal weight: 7.9990 chunk 66 optimal weight: 7.9990 chunk 209 optimal weight: 5.9990 chunk 222 optimal weight: 10.0000 chunk 177 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 GLN H 658 GLN E 203 GLN E 287 HIS 1 575 GLN B 3 GLN B 65 GLN I 417 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.042054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.035212 restraints weight = 188061.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.036104 restraints weight = 110366.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.036700 restraints weight = 80051.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.037078 restraints weight = 65435.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.037326 restraints weight = 57404.784| |-----------------------------------------------------------------------------| r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.7186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 20859 Z= 0.197 Angle : 0.814 13.287 28500 Z= 0.407 Chirality : 0.049 0.274 3396 Planarity : 0.005 0.068 3489 Dihedral : 9.786 80.073 4266 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.57 % Allowed : 4.80 % Favored : 94.63 % Rotamer: Outliers : 1.26 % Allowed : 7.60 % Favored : 91.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.88 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.17), residues: 2460 helix: 1.22 (0.27), residues: 426 sheet: -0.17 (0.18), residues: 723 loop : -0.80 (0.18), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 432 TYR 0.026 0.002 TYR C 51 PHE 0.017 0.002 PHE I 383 TRP 0.026 0.002 TRP I 112 HIS 0.006 0.001 HIS F 35 Details of bonding type rmsd covalent geometry : bond 0.00440 (20748) covalent geometry : angle 0.78332 (28200) SS BOND : bond 0.00327 ( 33) SS BOND : angle 1.06909 ( 66) hydrogen bonds : bond 0.04151 ( 756) hydrogen bonds : angle 6.14425 ( 2025) link_ALPHA1-2 : bond 0.00590 ( 3) link_ALPHA1-2 : angle 1.23214 ( 9) link_ALPHA1-3 : bond 0.01735 ( 3) link_ALPHA1-3 : angle 0.99021 ( 9) link_ALPHA1-6 : bond 0.00695 ( 3) link_ALPHA1-6 : angle 1.50737 ( 9) link_BETA1-4 : bond 0.00748 ( 30) link_BETA1-4 : angle 2.12414 ( 90) link_NAG-ASN : bond 0.00409 ( 39) link_NAG-ASN : angle 3.02321 ( 117) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 66 time to evaluate : 0.718 Fit side-chains REVERT: A 152 MET cc_start: 0.8326 (mmt) cc_final: 0.7965 (mmt) REVERT: H 626 MET cc_start: 0.6717 (ttm) cc_final: 0.6295 (ttm) REVERT: D 626 MET cc_start: 0.8142 (ttm) cc_final: 0.7546 (ttm) REVERT: E 175 TYR cc_start: 0.6724 (OUTLIER) cc_final: 0.4908 (p90) REVERT: F 102 ILE cc_start: 0.8931 (OUTLIER) cc_final: 0.8586 (pt) REVERT: G 100 ILE cc_start: 0.8048 (OUTLIER) cc_final: 0.7711 (mt) REVERT: C 49 MET cc_start: 0.8185 (mmp) cc_final: 0.7939 (mmp) REVERT: I 434 MET cc_start: 0.8985 (ptm) cc_final: 0.8320 (ptm) outliers start: 27 outliers final: 13 residues processed: 86 average time/residue: 0.1190 time to fit residues: 17.4493 Evaluate side-chains 76 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 60 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain K residue 75 LEU Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 175 TYR Chi-restraints excluded: chain E residue 184 GLU Chi-restraints excluded: chain E residue 369 MET Chi-restraints excluded: chain E residue 414 ILE Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain I residue 95 MET Chi-restraints excluded: chain I residue 184 GLU Chi-restraints excluded: chain I residue 403 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 9 optimal weight: 5.9990 chunk 141 optimal weight: 7.9990 chunk 147 optimal weight: 10.0000 chunk 161 optimal weight: 9.9990 chunk 96 optimal weight: 1.9990 chunk 120 optimal weight: 8.9990 chunk 38 optimal weight: 0.7980 chunk 167 optimal weight: 10.0000 chunk 186 optimal weight: 9.9990 chunk 88 optimal weight: 0.9980 chunk 164 optimal weight: 6.9990 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 3 GLN J 113 ASN K 39 GLN D 658 GLN E 422 GLN C 1 GLN I 229 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.041359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.034455 restraints weight = 186857.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.035330 restraints weight = 110391.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.035910 restraints weight = 80714.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.036283 restraints weight = 66271.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.036522 restraints weight = 58443.144| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.8184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 20859 Z= 0.205 Angle : 0.801 12.773 28500 Z= 0.401 Chirality : 0.049 0.328 3396 Planarity : 0.005 0.065 3489 Dihedral : 9.525 80.581 4266 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.65 % Allowed : 5.49 % Favored : 93.86 % Rotamer: Outliers : 1.54 % Allowed : 8.48 % Favored : 89.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.88 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.17), residues: 2460 helix: 1.54 (0.27), residues: 408 sheet: -0.10 (0.18), residues: 702 loop : -0.85 (0.17), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 67 TYR 0.020 0.002 TYR C 51 PHE 0.019 0.002 PHE E 382 TRP 0.017 0.002 TRP I 112 HIS 0.008 0.001 HIS F 35 Details of bonding type rmsd covalent geometry : bond 0.00461 (20748) covalent geometry : angle 0.77351 (28200) SS BOND : bond 0.00396 ( 33) SS BOND : angle 1.16975 ( 66) hydrogen bonds : bond 0.04185 ( 756) hydrogen bonds : angle 6.04471 ( 2025) link_ALPHA1-2 : bond 0.00317 ( 3) link_ALPHA1-2 : angle 1.78993 ( 9) link_ALPHA1-3 : bond 0.01332 ( 3) link_ALPHA1-3 : angle 1.05882 ( 9) link_ALPHA1-6 : bond 0.00539 ( 3) link_ALPHA1-6 : angle 1.55958 ( 9) link_BETA1-4 : bond 0.00783 ( 30) link_BETA1-4 : angle 2.23673 ( 90) link_NAG-ASN : bond 0.00443 ( 39) link_NAG-ASN : angle 2.62750 ( 117) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 64 time to evaluate : 0.740 Fit side-chains REVERT: A 152 MET cc_start: 0.8415 (mmt) cc_final: 0.7857 (mmt) REVERT: A 175 TYR cc_start: 0.7008 (OUTLIER) cc_final: 0.5081 (p90) REVERT: J 48 MET cc_start: 0.5894 (mpp) cc_final: 0.5578 (mtm) REVERT: D 626 MET cc_start: 0.8111 (ttm) cc_final: 0.7753 (ttm) REVERT: F 102 ILE cc_start: 0.8890 (OUTLIER) cc_final: 0.8558 (pt) REVERT: G 107 MET cc_start: 0.7607 (tpp) cc_final: 0.7194 (tpp) REVERT: I 434 MET cc_start: 0.8674 (ptm) cc_final: 0.8270 (ptm) outliers start: 33 outliers final: 16 residues processed: 88 average time/residue: 0.1201 time to fit residues: 18.1096 Evaluate side-chains 79 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 61 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 175 TYR Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 89 ASP Chi-restraints excluded: chain K residue 62 PHE Chi-restraints excluded: chain D residue 657 GLU Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 184 GLU Chi-restraints excluded: chain E residue 403 THR Chi-restraints excluded: chain E residue 475 MET Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain I residue 403 THR Chi-restraints excluded: chain I residue 414 ILE Chi-restraints excluded: chain I residue 475 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 192 optimal weight: 0.0670 chunk 115 optimal weight: 20.0000 chunk 183 optimal weight: 2.9990 chunk 221 optimal weight: 0.5980 chunk 62 optimal weight: 0.9990 chunk 196 optimal weight: 5.9990 chunk 217 optimal weight: 0.0770 chunk 40 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 chunk 180 optimal weight: 4.9990 chunk 39 optimal weight: 10.0000 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 39 GLN C 1 GLN C 40 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.042380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.035607 restraints weight = 185539.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.036506 restraints weight = 108891.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.037114 restraints weight = 78734.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.037500 restraints weight = 64087.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.037746 restraints weight = 56241.446| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.8279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20859 Z= 0.125 Angle : 0.717 12.620 28500 Z= 0.357 Chirality : 0.046 0.305 3396 Planarity : 0.004 0.061 3489 Dihedral : 8.553 70.565 4266 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.65 % Allowed : 4.19 % Favored : 95.16 % Rotamer: Outliers : 1.12 % Allowed : 9.18 % Favored : 89.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.88 % 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: -0.04 (0.17), residues: 2460 helix: 1.87 (0.27), residues: 417 sheet: 0.06 (0.19), residues: 714 loop : -0.66 (0.18), residues: 1329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 38 TYR 0.020 0.001 TYR C 51 PHE 0.011 0.001 PHE A 382 TRP 0.014 0.001 TRP F 101 HIS 0.010 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00253 (20748) covalent geometry : angle 0.69069 (28200) SS BOND : bond 0.00280 ( 33) SS BOND : angle 0.93555 ( 66) hydrogen bonds : bond 0.03436 ( 756) hydrogen bonds : angle 5.72375 ( 2025) link_ALPHA1-2 : bond 0.00640 ( 3) link_ALPHA1-2 : angle 1.18298 ( 9) link_ALPHA1-3 : bond 0.01430 ( 3) link_ALPHA1-3 : angle 1.12085 ( 9) link_ALPHA1-6 : bond 0.00949 ( 3) link_ALPHA1-6 : angle 1.22269 ( 9) link_BETA1-4 : bond 0.00803 ( 30) link_BETA1-4 : angle 1.97217 ( 90) link_NAG-ASN : bond 0.00433 ( 39) link_NAG-ASN : angle 2.51802 ( 117) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 64 time to evaluate : 0.735 Fit side-chains REVERT: A 95 MET cc_start: 0.7234 (mtm) cc_final: 0.7024 (mtp) REVERT: H 626 MET cc_start: 0.7231 (ttm) cc_final: 0.6923 (ttm) REVERT: J 10 GLU cc_start: 0.6959 (OUTLIER) cc_final: 0.6409 (pp20) REVERT: J 70 MET cc_start: 0.7981 (mmt) cc_final: 0.6066 (mmt) REVERT: K 83 GLU cc_start: 0.8203 (mp0) cc_final: 0.7769 (tm-30) REVERT: D 626 MET cc_start: 0.7939 (ttm) cc_final: 0.7594 (ttm) REVERT: I 434 MET cc_start: 0.8764 (ptm) cc_final: 0.8346 (ptm) outliers start: 24 outliers final: 17 residues processed: 83 average time/residue: 0.1145 time to fit residues: 16.4915 Evaluate side-chains 79 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 61 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain J residue 10 GLU Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain K residue 62 PHE Chi-restraints excluded: chain K residue 75 LEU Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 184 GLU Chi-restraints excluded: chain E residue 403 THR Chi-restraints excluded: chain E residue 475 MET Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain I residue 184 GLU Chi-restraints excluded: chain I residue 326 ILE Chi-restraints excluded: chain I residue 403 THR Chi-restraints excluded: chain I residue 475 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 24 optimal weight: 5.9990 chunk 153 optimal weight: 7.9990 chunk 160 optimal weight: 30.0000 chunk 163 optimal weight: 10.0000 chunk 14 optimal weight: 2.9990 chunk 64 optimal weight: 7.9990 chunk 195 optimal weight: 7.9990 chunk 128 optimal weight: 4.9990 chunk 216 optimal weight: 1.9990 chunk 49 optimal weight: 10.0000 chunk 111 optimal weight: 9.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 417 GLN D 658 GLN C 40 GLN I 82 GLN ** I 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 287 HIS I 350 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.040653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.033646 restraints weight = 186535.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.034507 restraints weight = 111007.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.035076 restraints weight = 81756.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.035435 restraints weight = 67491.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.035609 restraints weight = 59761.005| |-----------------------------------------------------------------------------| r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.9014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.087 20859 Z= 0.253 Angle : 0.834 12.700 28500 Z= 0.413 Chirality : 0.050 0.337 3396 Planarity : 0.005 0.064 3489 Dihedral : 9.344 78.594 4266 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.65 % Allowed : 6.18 % Favored : 93.17 % Rotamer: Outliers : 1.77 % Allowed : 9.37 % Favored : 88.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.88 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.17), residues: 2460 helix: 1.53 (0.27), residues: 405 sheet: -0.14 (0.19), residues: 669 loop : -0.89 (0.17), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 57 TYR 0.021 0.002 TYR I 175 PHE 0.020 0.002 PHE A 382 TRP 0.016 0.002 TRP J 36 HIS 0.008 0.001 HIS B 35 Details of bonding type rmsd covalent geometry : bond 0.00584 (20748) covalent geometry : angle 0.80583 (28200) SS BOND : bond 0.00404 ( 33) SS BOND : angle 1.32888 ( 66) hydrogen bonds : bond 0.04398 ( 756) hydrogen bonds : angle 6.10649 ( 2025) link_ALPHA1-2 : bond 0.00304 ( 3) link_ALPHA1-2 : angle 2.04426 ( 9) link_ALPHA1-3 : bond 0.01366 ( 3) link_ALPHA1-3 : angle 1.18775 ( 9) link_ALPHA1-6 : bond 0.00570 ( 3) link_ALPHA1-6 : angle 1.55831 ( 9) link_BETA1-4 : bond 0.00787 ( 30) link_BETA1-4 : angle 2.33638 ( 90) link_NAG-ASN : bond 0.00472 ( 39) link_NAG-ASN : angle 2.66910 ( 117) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 64 time to evaluate : 0.680 Fit side-chains REVERT: A 95 MET cc_start: 0.7623 (OUTLIER) cc_final: 0.7407 (mtp) REVERT: A 175 TYR cc_start: 0.7080 (OUTLIER) cc_final: 0.5140 (p90) REVERT: H 626 MET cc_start: 0.7813 (ttm) cc_final: 0.7569 (ttm) REVERT: J 10 GLU cc_start: 0.7010 (OUTLIER) cc_final: 0.5776 (pp20) REVERT: K 83 GLU cc_start: 0.8319 (mp0) cc_final: 0.7921 (tm-30) REVERT: K 107 MET cc_start: 0.7946 (tpp) cc_final: 0.7699 (tmm) REVERT: D 626 MET cc_start: 0.8216 (ttm) cc_final: 0.7882 (ttm) REVERT: E 175 TYR cc_start: 0.6970 (OUTLIER) cc_final: 0.4969 (p90) REVERT: F 102 ILE cc_start: 0.8966 (OUTLIER) cc_final: 0.8661 (pt) REVERT: B 29 PHE cc_start: 0.7137 (OUTLIER) cc_final: 0.6093 (p90) REVERT: I 175 TYR cc_start: 0.6924 (OUTLIER) cc_final: 0.5281 (p90) REVERT: I 434 MET cc_start: 0.8870 (ptm) cc_final: 0.8585 (ptm) outliers start: 38 outliers final: 17 residues processed: 90 average time/residue: 0.1220 time to fit residues: 18.3863 Evaluate side-chains 84 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 60 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 175 TYR Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain J residue 10 GLU Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 89 ASP Chi-restraints excluded: chain K residue 62 PHE Chi-restraints excluded: chain E residue 175 TYR Chi-restraints excluded: chain E residue 184 GLU Chi-restraints excluded: chain E residue 369 MET Chi-restraints excluded: chain E residue 403 THR Chi-restraints excluded: chain E residue 414 ILE Chi-restraints excluded: chain E residue 475 MET Chi-restraints excluded: chain F residue 66 ASP Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain B residue 29 PHE Chi-restraints excluded: chain I residue 104 MET Chi-restraints excluded: chain I residue 175 TYR Chi-restraints excluded: chain I residue 184 GLU Chi-restraints excluded: chain I residue 403 THR Chi-restraints excluded: chain I residue 475 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 130 optimal weight: 8.9990 chunk 229 optimal weight: 3.9990 chunk 213 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 chunk 64 optimal weight: 0.8980 chunk 72 optimal weight: 8.9990 chunk 202 optimal weight: 20.0000 chunk 193 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 115 ASN D 658 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.041106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.034164 restraints weight = 187336.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.035047 restraints weight = 109767.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.035630 restraints weight = 80139.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.035997 restraints weight = 65778.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.036227 restraints weight = 58050.722| |-----------------------------------------------------------------------------| r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.9161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20859 Z= 0.144 Angle : 0.736 12.464 28500 Z= 0.364 Chirality : 0.047 0.324 3396 Planarity : 0.004 0.056 3489 Dihedral : 8.696 72.349 4266 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.65 % Allowed : 4.55 % Favored : 94.80 % Rotamer: Outliers : 1.26 % Allowed : 9.93 % Favored : 88.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.88 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.17), residues: 2460 helix: 2.02 (0.27), residues: 396 sheet: -0.08 (0.19), residues: 684 loop : -0.86 (0.17), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG I 273 TYR 0.019 0.001 TYR C 51 PHE 0.014 0.001 PHE A 382 TRP 0.017 0.001 TRP 1 614 HIS 0.009 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00313 (20748) covalent geometry : angle 0.70868 (28200) SS BOND : bond 0.00310 ( 33) SS BOND : angle 1.03296 ( 66) hydrogen bonds : bond 0.03702 ( 756) hydrogen bonds : angle 5.84362 ( 2025) link_ALPHA1-2 : bond 0.00462 ( 3) link_ALPHA1-2 : angle 1.31185 ( 9) link_ALPHA1-3 : bond 0.01530 ( 3) link_ALPHA1-3 : angle 0.92297 ( 9) link_ALPHA1-6 : bond 0.00843 ( 3) link_ALPHA1-6 : angle 1.29915 ( 9) link_BETA1-4 : bond 0.00850 ( 30) link_BETA1-4 : angle 2.16428 ( 90) link_NAG-ASN : bond 0.00395 ( 39) link_NAG-ASN : angle 2.49480 ( 117) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 61 time to evaluate : 0.727 Fit side-chains REVERT: J 10 GLU cc_start: 0.7195 (OUTLIER) cc_final: 0.6222 (pp20) REVERT: J 70 MET cc_start: 0.8277 (mmt) cc_final: 0.6757 (mmt) REVERT: K 83 GLU cc_start: 0.8271 (mp0) cc_final: 0.7908 (tm-30) REVERT: D 626 MET cc_start: 0.8123 (ttm) cc_final: 0.7795 (ttm) REVERT: F 102 ILE cc_start: 0.8977 (OUTLIER) cc_final: 0.8615 (pt) REVERT: 1 626 MET cc_start: 0.7790 (tpp) cc_final: 0.7519 (tpp) REVERT: I 434 MET cc_start: 0.8870 (ptm) cc_final: 0.8350 (ptm) outliers start: 27 outliers final: 16 residues processed: 81 average time/residue: 0.1107 time to fit residues: 15.6863 Evaluate side-chains 79 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 61 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain J residue 10 GLU Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 184 GLU Chi-restraints excluded: chain E residue 403 THR Chi-restraints excluded: chain E residue 414 ILE Chi-restraints excluded: chain E residue 475 MET Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain 1 residue 614 TRP Chi-restraints excluded: chain I residue 184 GLU Chi-restraints excluded: chain I residue 403 THR Chi-restraints excluded: chain I residue 475 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 2 optimal weight: 0.7980 chunk 165 optimal weight: 4.9990 chunk 101 optimal weight: 7.9990 chunk 42 optimal weight: 5.9990 chunk 35 optimal weight: 9.9990 chunk 178 optimal weight: 0.5980 chunk 202 optimal weight: 7.9990 chunk 123 optimal weight: 8.9990 chunk 188 optimal weight: 7.9990 chunk 88 optimal weight: 0.8980 chunk 75 optimal weight: 8.9990 overall best weight: 2.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.040985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.034057 restraints weight = 186305.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.034932 restraints weight = 109573.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.035509 restraints weight = 80207.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.035865 restraints weight = 66116.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.036096 restraints weight = 58450.326| |-----------------------------------------------------------------------------| r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.9456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 20859 Z= 0.168 Angle : 0.744 12.495 28500 Z= 0.367 Chirality : 0.047 0.332 3396 Planarity : 0.004 0.056 3489 Dihedral : 8.565 71.808 4266 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.65 % Allowed : 5.73 % Favored : 93.62 % Rotamer: Outliers : 1.31 % Allowed : 10.12 % Favored : 88.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.88 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.17), residues: 2460 helix: 2.01 (0.27), residues: 396 sheet: -0.10 (0.19), residues: 702 loop : -0.96 (0.17), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 273 TYR 0.018 0.001 TYR C 51 PHE 0.015 0.002 PHE A 382 TRP 0.012 0.001 TRP I 96 HIS 0.008 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00377 (20748) covalent geometry : angle 0.71632 (28200) SS BOND : bond 0.00322 ( 33) SS BOND : angle 1.06155 ( 66) hydrogen bonds : bond 0.03805 ( 756) hydrogen bonds : angle 5.79255 ( 2025) link_ALPHA1-2 : bond 0.00098 ( 3) link_ALPHA1-2 : angle 1.63748 ( 9) link_ALPHA1-3 : bond 0.01456 ( 3) link_ALPHA1-3 : angle 0.89089 ( 9) link_ALPHA1-6 : bond 0.00823 ( 3) link_ALPHA1-6 : angle 1.34503 ( 9) link_BETA1-4 : bond 0.00864 ( 30) link_BETA1-4 : angle 2.23094 ( 90) link_NAG-ASN : bond 0.00378 ( 39) link_NAG-ASN : angle 2.47318 ( 117) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 61 time to evaluate : 0.756 Fit side-chains REVERT: J 10 GLU cc_start: 0.7380 (OUTLIER) cc_final: 0.6319 (pp20) REVERT: J 70 MET cc_start: 0.8289 (mmt) cc_final: 0.6849 (mmt) REVERT: K 83 GLU cc_start: 0.8242 (mp0) cc_final: 0.7882 (tm-30) REVERT: K 107 MET cc_start: 0.8088 (tpp) cc_final: 0.7568 (tpp) REVERT: D 626 MET cc_start: 0.8115 (ttm) cc_final: 0.7805 (ttm) REVERT: F 102 ILE cc_start: 0.8978 (OUTLIER) cc_final: 0.8614 (pt) REVERT: B 29 PHE cc_start: 0.7225 (OUTLIER) cc_final: 0.6183 (p90) REVERT: I 152 MET cc_start: 0.7169 (mmp) cc_final: 0.6879 (mmm) REVERT: I 434 MET cc_start: 0.8881 (ptm) cc_final: 0.8395 (ptm) outliers start: 28 outliers final: 19 residues processed: 82 average time/residue: 0.1140 time to fit residues: 16.5891 Evaluate side-chains 83 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 61 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain J residue 10 GLU Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain D residue 657 GLU Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 184 GLU Chi-restraints excluded: chain E residue 403 THR Chi-restraints excluded: chain E residue 414 ILE Chi-restraints excluded: chain E residue 475 MET Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain 1 residue 604 CYS Chi-restraints excluded: chain 1 residue 614 TRP Chi-restraints excluded: chain B residue 29 PHE Chi-restraints excluded: chain I residue 184 GLU Chi-restraints excluded: chain I residue 403 THR Chi-restraints excluded: chain I residue 475 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 191 optimal weight: 5.9990 chunk 128 optimal weight: 7.9990 chunk 76 optimal weight: 0.2980 chunk 3 optimal weight: 10.0000 chunk 52 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 187 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 205 optimal weight: 2.9990 chunk 80 optimal weight: 7.9990 chunk 39 optimal weight: 0.8980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.041378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.034514 restraints weight = 187400.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.035394 restraints weight = 109106.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.035982 restraints weight = 79504.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.036354 restraints weight = 65197.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.036561 restraints weight = 57466.813| |-----------------------------------------------------------------------------| r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.9543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20859 Z= 0.126 Angle : 0.710 12.367 28500 Z= 0.349 Chirality : 0.046 0.325 3396 Planarity : 0.004 0.054 3489 Dihedral : 8.159 66.552 4266 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.65 % Allowed : 4.19 % Favored : 95.16 % Rotamer: Outliers : 0.93 % Allowed : 10.30 % Favored : 88.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.88 % 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: -0.15 (0.17), residues: 2460 helix: 2.24 (0.27), residues: 396 sheet: -0.02 (0.19), residues: 699 loop : -0.84 (0.17), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 273 TYR 0.019 0.001 TYR C 51 PHE 0.013 0.001 PHE A 382 TRP 0.016 0.001 TRP E 96 HIS 0.009 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00269 (20748) covalent geometry : angle 0.68418 (28200) SS BOND : bond 0.00285 ( 33) SS BOND : angle 0.98986 ( 66) hydrogen bonds : bond 0.03444 ( 756) hydrogen bonds : angle 5.63193 ( 2025) link_ALPHA1-2 : bond 0.00372 ( 3) link_ALPHA1-2 : angle 1.35900 ( 9) link_ALPHA1-3 : bond 0.01494 ( 3) link_ALPHA1-3 : angle 1.01486 ( 9) link_ALPHA1-6 : bond 0.00983 ( 3) link_ALPHA1-6 : angle 1.18607 ( 9) link_BETA1-4 : bond 0.00889 ( 30) link_BETA1-4 : angle 2.12049 ( 90) link_NAG-ASN : bond 0.00406 ( 39) link_NAG-ASN : angle 2.37660 ( 117) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 62 time to evaluate : 0.689 Fit side-chains REVERT: A 95 MET cc_start: 0.7522 (OUTLIER) cc_final: 0.7169 (mtp) REVERT: A 434 MET cc_start: 0.8831 (ttt) cc_final: 0.8588 (ttm) REVERT: J 70 MET cc_start: 0.8178 (mmt) cc_final: 0.6924 (mmt) REVERT: K 83 GLU cc_start: 0.8339 (mp0) cc_final: 0.7993 (tm-30) REVERT: K 107 MET cc_start: 0.8169 (tpp) cc_final: 0.7923 (tpp) REVERT: D 626 MET cc_start: 0.8077 (ttm) cc_final: 0.7792 (ttm) REVERT: F 102 ILE cc_start: 0.9009 (OUTLIER) cc_final: 0.8651 (pt) REVERT: 1 614 TRP cc_start: 0.5791 (OUTLIER) cc_final: 0.4876 (m-90) REVERT: I 434 MET cc_start: 0.8868 (ptm) cc_final: 0.8380 (ptm) outliers start: 20 outliers final: 15 residues processed: 78 average time/residue: 0.1111 time to fit residues: 15.3605 Evaluate side-chains 79 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 61 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 184 GLU Chi-restraints excluded: chain E residue 403 THR Chi-restraints excluded: chain E residue 414 ILE Chi-restraints excluded: chain E residue 475 MET Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain 1 residue 604 CYS Chi-restraints excluded: chain 1 residue 614 TRP Chi-restraints excluded: chain I residue 184 GLU Chi-restraints excluded: chain I residue 403 THR Chi-restraints excluded: chain I residue 475 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 188 optimal weight: 3.9990 chunk 139 optimal weight: 8.9990 chunk 218 optimal weight: 6.9990 chunk 51 optimal weight: 6.9990 chunk 113 optimal weight: 0.9990 chunk 200 optimal weight: 8.9990 chunk 216 optimal weight: 6.9990 chunk 149 optimal weight: 9.9990 chunk 186 optimal weight: 10.0000 chunk 26 optimal weight: 9.9990 chunk 44 optimal weight: 1.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 658 GLN ** I 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.040429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.033442 restraints weight = 186817.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.034288 restraints weight = 110783.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.034856 restraints weight = 81497.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.035214 restraints weight = 67196.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.035391 restraints weight = 59518.368| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.9877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 20859 Z= 0.225 Angle : 0.789 12.417 28500 Z= 0.389 Chirality : 0.049 0.332 3396 Planarity : 0.004 0.055 3489 Dihedral : 8.717 71.819 4266 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.69 % Allowed : 6.02 % Favored : 93.29 % Rotamer: Outliers : 1.03 % Allowed : 10.21 % Favored : 88.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.88 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.17), residues: 2460 helix: 1.89 (0.27), residues: 396 sheet: -0.07 (0.19), residues: 702 loop : -0.99 (0.17), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 273 TYR 0.020 0.002 TYR C 51 PHE 0.017 0.002 PHE 1 519 TRP 0.014 0.002 TRP J 47 HIS 0.008 0.002 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00523 (20748) covalent geometry : angle 0.76115 (28200) SS BOND : bond 0.00353 ( 33) SS BOND : angle 1.14215 ( 66) hydrogen bonds : bond 0.04077 ( 756) hydrogen bonds : angle 5.91338 ( 2025) link_ALPHA1-2 : bond 0.00178 ( 3) link_ALPHA1-2 : angle 1.79565 ( 9) link_ALPHA1-3 : bond 0.01460 ( 3) link_ALPHA1-3 : angle 1.04728 ( 9) link_ALPHA1-6 : bond 0.00825 ( 3) link_ALPHA1-6 : angle 1.35343 ( 9) link_BETA1-4 : bond 0.00857 ( 30) link_BETA1-4 : angle 2.33365 ( 90) link_NAG-ASN : bond 0.00392 ( 39) link_NAG-ASN : angle 2.56244 ( 117) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3000.00 seconds wall clock time: 53 minutes 1.99 seconds (3181.99 seconds total)