Starting phenix.real_space_refine on Sun Sep 13 04:01:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6um7_20819/09_2026/6um7_20819.cif Found real_map, /net/cci-nas-00/data/ceres_data/6um7_20819/09_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_20819/09_2026/6um7_20819.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6um7_20819/09_2026/6um7_20819.map" model { file = "/net/cci-nas-00/data/ceres_data/6um7_20819/09_2026/6um7_20819.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6um7_20819/09_2026/6um7_20819.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6um7_20819/09_2026/6um7_20819.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6um7_20819/09_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 chiralities: 8 Time building chain proxies: 4.20, per 1000 atoms: 0.21 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: 1.92 Conformation dependent library (CDL) restraints added in 802.8 milliseconds 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: 0.69 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: 4.08 Time building geometry restraints manager: 2.48 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: 11453 23.43 - 46.85: 238 46.85 - 70.28: 85 70.28 - 93.70: 17 93.70 - 117.13: 3 Dihedral angle restraints: 11796 sinusoidal: 4626 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 11793 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: 0.06 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: 2.590 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: 0.250 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 19.320 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6595 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 : 11.263 117.128 7107 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/Z covalent geometry : bond 0.01832 / 1.05 (20748) covalent geometry : angle 2.06774 / 1.36 (28200) SS BOND : bond 0.10475 / 7.12 ( 33) SS BOND : angle 4.98638 / 3.34 ( 66) hydrogen bonds : bond 0.17454 / 11.58 ( 756) hydrogen bonds : angle 8.69583 / 6.03 ( 2025) link_ALPHA1-2 : bond 0.00193 / 0.10 ( 3) link_ALPHA1-2 : angle 2.90895 / 1.39 ( 9) link_ALPHA1-3 : bond 0.00944 / 0.48 ( 3) link_ALPHA1-3 : angle 5.25557 / 2.56 ( 9) link_ALPHA1-6 : bond 0.00096 / 0.05 ( 3) link_ALPHA1-6 : angle 1.55173 / 0.78 ( 9) link_BETA1-4 : bond 0.00468 / 0.27 ( 30) link_BETA1-4 : angle 2.07072 / 1.50 ( 90) link_NAG-ASN : bond 0.06756 / 4.30 ( 39) link_NAG-ASN : angle 5.66940 / 3.49 ( 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 : 0.712 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: 0.1722 time to fit residues: 50.8326 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 : 0.802 ------------------------------------------------------------------------------- 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... 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 = 0.3682 r_free = 0.3682 target = 0.045241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.039400 restraints weight = 182911.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.040597 restraints weight = 98350.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.040867 restraints weight = 64504.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.040960 restraints weight = 59062.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.041034 restraints weight = 53899.674| |-----------------------------------------------------------------------------| r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7055 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 20859 Z= 0.218 Angle : 0.964 17.068 28500 Z= 0.486 Chirality : 0.053 0.384 3396 Planarity : 0.006 0.073 3489 Dihedral : 6.630 90.254 2683 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.73 % Allowed : 3.25 % Favored : 96.02 % Rotamer: Outliers : 1.12 % Allowed : 4.57 % Favored : 94.31 % 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: -0.18 (0.17), residues: 2460 helix: 1.00 (0.28), residues: 402 sheet: 0.14 (0.18), residues: 714 loop : -0.57 (0.17), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 446 TYR 0.025 0.002 TYR K 51 PHE 0.031 0.002 PHE H 522 TRP 0.036 0.003 TRP F 101 HIS 0.012 0.002 HIS I 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.22 (20748) covalent geometry : angle 0.92327 / 0.48 (28200) SS BOND : bond 0.00565 / 0.37 ( 33) SS BOND : angle 1.29909 / 0.91 ( 66) hydrogen bonds : bond 0.04865 / 3.14 ( 756) hydrogen bonds : angle 6.82877 / 4.69 ( 2025) link_ALPHA1-2 : bond 0.00363 / 0.18 ( 3) link_ALPHA1-2 : angle 1.24343 / 0.59 ( 9) link_ALPHA1-3 : bond 0.02213 / 1.11 ( 3) link_ALPHA1-3 : angle 1.79783 / 0.92 ( 9) link_ALPHA1-6 : bond 0.00262 / 0.13 ( 3) link_ALPHA1-6 : angle 1.58675 / 0.77 ( 9) link_BETA1-4 : bond 0.00731 / 0.45 ( 30) link_BETA1-4 : angle 2.04461 / 1.42 ( 90) link_NAG-ASN : bond 0.00743 / 0.46 ( 39) link_NAG-ASN : angle 4.04502 / 2.61 ( 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 113 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 89 time to evaluate : 0.970 Fit side-chains revert: symmetry clash REVERT: H 626 MET cc_start: 0.5348 (tpp) cc_final: 0.5098 (tpp) REVERT: E 125 LEU cc_start: 0.8317 (mm) cc_final: 0.7904 (mt) REVERT: E 369 MET cc_start: 0.4695 (OUTLIER) cc_final: 0.4471 (ptm) REVERT: F 48 MET cc_start: 0.4382 (mpp) cc_final: 0.4135 (mtm) REVERT: 1 642 ILE cc_start: 0.6697 (mm) cc_final: 0.6337 (mm) outliers start: 24 outliers final: 6 residues processed: 106 average time/residue: 0.1279 time to fit residues: 22.6167 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 : 0.755 ------------------------------------------------------------------------------- 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: 9.9990 chunk 81 optimal weight: 8.9990 chunk 39 optimal weight: 0.9990 chunk 167 optimal weight: 9.9990 chunk 219 optimal weight: 4.9990 chunk 107 optimal weight: 8.9990 chunk 80 optimal weight: 2.9990 chunk 48 optimal weight: 7.9990 chunk 16 optimal weight: 0.0370 chunk 113 optimal weight: 8.9990 chunk 127 optimal weight: 4.9990 overall best weight: 2.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 330 HIS H 658 GLN J 115 ASN ** K 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 40 GLN ** E 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 115 ASN G 40 GLN 1 543 ASN B 65 GLN B 115 ASN I 422 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.043242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.036605 restraints weight = 188958.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.037535 restraints weight = 107918.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.038154 restraints weight = 76853.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.038553 restraints weight = 61906.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.038788 restraints weight = 53771.122| |-----------------------------------------------------------------------------| r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.5526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 20859 Z= 0.224 Angle : 0.907 13.885 28500 Z= 0.457 Chirality : 0.051 0.273 3396 Planarity : 0.006 0.071 3489 Dihedral : 5.888 32.394 2676 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.61 % Allowed : 4.47 % Favored : 94.92 % Rotamer: Outliers : 1.35 % Allowed : 6.15 % Favored : 92.49 % 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: 0.02 (0.17), residues: 2460 helix: 1.46 (0.27), residues: 399 sheet: 0.31 (0.19), residues: 681 loop : -0.55 (0.17), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 122 TYR 0.029 0.002 TYR K 51 PHE 0.027 0.003 PHE I 382 TRP 0.021 0.002 TRP H 623 HIS 0.008 0.002 HIS E 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00494 / 0.22 (20748) covalent geometry : angle 0.88007 / 0.45 (28200) SS BOND : bond 0.00375 / 0.26 ( 33) SS BOND : angle 1.16652 / 0.79 ( 66) hydrogen bonds : bond 0.04641 / 3.06 ( 756) hydrogen bonds : angle 6.17850 / 4.25 ( 2025) link_ALPHA1-2 : bond 0.00365 / 0.19 ( 3) link_ALPHA1-2 : angle 2.05259 / 0.95 ( 9) link_ALPHA1-3 : bond 0.01509 / 0.75 ( 3) link_ALPHA1-3 : angle 1.65173 / 0.82 ( 9) link_ALPHA1-6 : bond 0.00347 / 0.17 ( 3) link_ALPHA1-6 : angle 1.53249 / 0.78 ( 9) link_BETA1-4 : bond 0.00805 / 0.47 ( 30) link_BETA1-4 : angle 1.96138 / 1.37 ( 90) link_NAG-ASN : bond 0.00606 / 0.35 ( 39) link_NAG-ASN : angle 3.01691 / 2.06 ( 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 109 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 80 time to evaluate : 0.684 Fit side-chains revert: symmetry clash REVERT: E 125 LEU cc_start: 0.8688 (mm) cc_final: 0.8281 (mt) REVERT: E 369 MET cc_start: 0.5614 (OUTLIER) cc_final: 0.5408 (ptm) REVERT: C 100 ILE cc_start: 0.8116 (OUTLIER) cc_final: 0.7495 (pt) REVERT: I 434 MET cc_start: 0.8851 (ptm) cc_final: 0.8507 (ptt) outliers start: 29 outliers final: 15 residues processed: 99 average time/residue: 0.1194 time to fit residues: 20.0765 Evaluate side-chains 84 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 67 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 81 MET Chi-restraints excluded: chain J residue 89 ASP Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 657 GLU Chi-restraints excluded: chain E residue 184 GLU Chi-restraints excluded: chain E residue 369 MET Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain 1 residue 573 ILE Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 91 optimal weight: 9.9990 chunk 26 optimal weight: 9.9990 chunk 45 optimal weight: 8.9990 chunk 49 optimal weight: 10.0000 chunk 3 optimal weight: 8.9990 chunk 165 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 209 optimal weight: 2.9990 chunk 222 optimal weight: 4.9990 chunk 177 optimal weight: 8.9990 chunk 65 optimal weight: 2.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 203 GLN ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 417 GLN J 3 GLN ** K 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 40 GLN E 287 HIS E 300 ASN 1 575 GLN 1 591 GLN ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 417 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.041396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.034453 restraints weight = 188405.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.035317 restraints weight = 111934.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.035900 restraints weight = 82074.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.036267 restraints weight = 67477.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.036499 restraints weight = 59565.589| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.7735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 20859 Z= 0.270 Angle : 0.941 14.770 28500 Z= 0.469 Chirality : 0.052 0.305 3396 Planarity : 0.006 0.068 3489 Dihedral : 6.135 33.408 2676 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.57 % Allowed : 5.37 % Favored : 94.07 % Rotamer: Outliers : 1.72 % Allowed : 7.37 % Favored : 90.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.88 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: 0.84 (0.26), residues: 426 sheet: 0.05 (0.20), residues: 630 loop : -0.96 (0.17), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 308 TYR 0.031 0.003 TYR I 217 PHE 0.026 0.003 PHE A 174 TRP 0.033 0.003 TRP E 112 HIS 0.006 0.002 HIS J 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00612 / 0.27 (20748) covalent geometry : angle 0.91306 / 0.46 (28200) SS BOND : bond 0.00461 / 0.30 ( 33) SS BOND : angle 1.35168 / 0.90 ( 66) hydrogen bonds : bond 0.04744 / 3.07 ( 756) hydrogen bonds : angle 6.42405 / 4.42 ( 2025) link_ALPHA1-2 : bond 0.00233 / 0.12 ( 3) link_ALPHA1-2 : angle 1.50701 / 0.71 ( 9) link_ALPHA1-3 : bond 0.01324 / 0.68 ( 3) link_ALPHA1-3 : angle 1.85640 / 0.89 ( 9) link_ALPHA1-6 : bond 0.00291 / 0.15 ( 3) link_ALPHA1-6 : angle 1.47803 / 0.74 ( 9) link_BETA1-4 : bond 0.00624 / 0.38 ( 30) link_BETA1-4 : angle 2.10359 / 1.45 ( 90) link_NAG-ASN : bond 0.00627 / 0.39 ( 39) link_NAG-ASN : angle 3.12583 / 2.14 ( 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 103 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 66 time to evaluate : 0.733 Fit side-chains REVERT: A 152 MET cc_start: 0.8327 (mmt) cc_final: 0.8094 (mmt) REVERT: J 48 MET cc_start: 0.6330 (mpp) cc_final: 0.5930 (mtm) REVERT: D 626 MET cc_start: 0.8232 (ttm) cc_final: 0.7833 (ttm) REVERT: E 175 TYR cc_start: 0.6904 (OUTLIER) cc_final: 0.5060 (p90) REVERT: F 102 ILE cc_start: 0.8815 (OUTLIER) cc_final: 0.8406 (pt) REVERT: G 100 ILE cc_start: 0.8072 (OUTLIER) cc_final: 0.7708 (mt) REVERT: G 107 MET cc_start: 0.7718 (tpp) cc_final: 0.7122 (tpp) REVERT: 1 626 MET cc_start: 0.7772 (tpp) cc_final: 0.7506 (tpp) REVERT: I 104 MET cc_start: 0.9046 (ttm) cc_final: 0.8845 (ttm) REVERT: I 434 MET cc_start: 0.8620 (ptm) cc_final: 0.7785 (ptm) REVERT: I 503 ARG cc_start: 0.6769 (OUTLIER) cc_final: 0.5708 (ptp-170) outliers start: 37 outliers final: 14 residues processed: 95 average time/residue: 0.1300 time to fit residues: 20.3156 Evaluate side-chains 77 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 59 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 121 LYS Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 175 TYR 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 23 LYS 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 323 ILE Chi-restraints excluded: chain I residue 475 MET Chi-restraints excluded: chain I residue 503 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 9 optimal weight: 3.9990 chunk 141 optimal weight: 0.9990 chunk 147 optimal weight: 9.9990 chunk 161 optimal weight: 4.9990 chunk 96 optimal weight: 3.9990 chunk 120 optimal weight: 7.9990 chunk 38 optimal weight: 5.9990 chunk 167 optimal weight: 6.9990 chunk 186 optimal weight: 9.9990 chunk 88 optimal weight: 1.9990 chunk 164 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 229 ASN ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 1 GLN E 300 ASN E 422 GLN B 3 GLN ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.041576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.034700 restraints weight = 186928.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.035569 restraints weight = 109890.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.036153 restraints weight = 80438.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.036521 restraints weight = 66119.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.036769 restraints weight = 58187.906| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.8074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 20859 Z= 0.167 Angle : 0.770 12.803 28500 Z= 0.384 Chirality : 0.047 0.294 3396 Planarity : 0.004 0.064 3489 Dihedral : 5.620 31.364 2676 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.65 % Allowed : 4.72 % Favored : 94.63 % Rotamer: Outliers : 1.21 % Allowed : 8.67 % Favored : 90.12 % 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: -0.30 (0.17), residues: 2460 helix: 1.38 (0.27), residues: 426 sheet: 0.07 (0.19), residues: 648 loop : -0.83 (0.17), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 38 TYR 0.020 0.002 TYR K 51 PHE 0.015 0.002 PHE A 382 TRP 0.013 0.001 TRP E 96 HIS 0.005 0.001 HIS E 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.17 (20748) covalent geometry : angle 0.74518 / 0.38 (28200) SS BOND : bond 0.00334 / 0.22 ( 33) SS BOND : angle 1.06027 / 0.70 ( 66) hydrogen bonds : bond 0.03972 / 2.58 ( 756) hydrogen bonds : angle 6.01601 / 4.11 ( 2025) link_ALPHA1-2 : bond 0.00271 / 0.14 ( 3) link_ALPHA1-2 : angle 1.48679 / 0.70 ( 9) link_ALPHA1-3 : bond 0.01289 / 0.65 ( 3) link_ALPHA1-3 : angle 1.59658 / 0.78 ( 9) link_ALPHA1-6 : bond 0.00241 / 0.12 ( 3) link_ALPHA1-6 : angle 1.48039 / 0.74 ( 9) link_BETA1-4 : bond 0.00669 / 0.37 ( 30) link_BETA1-4 : angle 1.85588 / 1.32 ( 90) link_NAG-ASN : bond 0.00402 / 0.27 ( 39) link_NAG-ASN : angle 2.58453 / 1.77 ( 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 92 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 66 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 626 MET cc_start: 0.6711 (ttm) cc_final: 0.6359 (ttm) REVERT: K 83 GLU cc_start: 0.8205 (mp0) cc_final: 0.7672 (tm-30) REVERT: D 626 MET cc_start: 0.8085 (ttm) cc_final: 0.7685 (ttm) REVERT: G 100 ILE cc_start: 0.8125 (OUTLIER) cc_final: 0.7836 (mt) outliers start: 26 outliers final: 13 residues processed: 86 average time/residue: 0.1244 time to fit residues: 17.7999 Evaluate side-chains 75 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 61 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 121 LYS Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 89 ASP Chi-restraints excluded: chain K residue 75 LEU Chi-restraints excluded: chain E residue 184 GLU Chi-restraints excluded: chain E residue 403 THR Chi-restraints excluded: chain G residue 34 LEU 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 414 ILE Chi-restraints excluded: chain I residue 503 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 192 optimal weight: 10.0000 chunk 115 optimal weight: 9.9990 chunk 183 optimal weight: 9.9990 chunk 221 optimal weight: 0.6980 chunk 62 optimal weight: 3.9990 chunk 196 optimal weight: 20.0000 chunk 217 optimal weight: 2.9990 chunk 40 optimal weight: 7.9990 chunk 59 optimal weight: 0.8980 chunk 180 optimal weight: 0.6980 chunk 39 optimal weight: 0.0370 overall best weight: 1.0660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 39 GLN D 658 GLN C 40 GLN I 287 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.042087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.035272 restraints weight = 186698.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.036171 restraints weight = 109643.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.036768 restraints weight = 79720.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.037149 restraints weight = 65114.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.037399 restraints weight = 57172.884| |-----------------------------------------------------------------------------| r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.8272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20859 Z= 0.124 Angle : 0.717 12.676 28500 Z= 0.355 Chirality : 0.046 0.291 3396 Planarity : 0.004 0.060 3489 Dihedral : 5.254 28.889 2676 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.69 % Allowed : 4.59 % Favored : 94.72 % Rotamer: Outliers : 1.21 % Allowed : 9.23 % Favored : 89.56 % 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: -0.08 (0.17), residues: 2460 helix: 1.84 (0.27), residues: 417 sheet: 0.12 (0.19), residues: 696 loop : -0.75 (0.18), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 67 TYR 0.020 0.001 TYR K 51 PHE 0.012 0.001 PHE A 382 TRP 0.013 0.001 TRP F 101 HIS 0.009 0.001 HIS A 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (20748) covalent geometry : angle 0.69513 / 0.35 (28200) SS BOND : bond 0.00290 / 0.19 ( 33) SS BOND : angle 0.96953 / 0.64 ( 66) hydrogen bonds : bond 0.03432 / 2.22 ( 756) hydrogen bonds : angle 5.72392 / 3.91 ( 2025) link_ALPHA1-2 : bond 0.00538 / 0.27 ( 3) link_ALPHA1-2 : angle 1.21430 / 0.57 ( 9) link_ALPHA1-3 : bond 0.01283 / 0.65 ( 3) link_ALPHA1-3 : angle 1.69711 / 0.86 ( 9) link_ALPHA1-6 : bond 0.00339 / 0.17 ( 3) link_ALPHA1-6 : angle 1.40518 / 0.70 ( 9) link_BETA1-4 : bond 0.00608 / 0.35 ( 30) link_BETA1-4 : angle 1.70586 / 1.20 ( 90) link_NAG-ASN : bond 0.00402 / 0.27 ( 39) link_NAG-ASN : angle 2.36894 / 1.61 ( 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 89 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 63 time to evaluate : 0.758 Fit side-chains REVERT: H 626 MET cc_start: 0.6407 (ttm) cc_final: 0.6057 (ttm) REVERT: J 48 MET cc_start: 0.6248 (mpp) cc_final: 0.5978 (mtm) REVERT: K 83 GLU cc_start: 0.8219 (mp0) cc_final: 0.7776 (tm-30) REVERT: D 626 MET cc_start: 0.7828 (ttm) cc_final: 0.7508 (ttm) REVERT: F 102 ILE cc_start: 0.8912 (OUTLIER) cc_final: 0.8572 (pt) REVERT: G 100 ILE cc_start: 0.8106 (OUTLIER) cc_final: 0.7237 (pt) REVERT: G 107 MET cc_start: 0.7493 (tpp) cc_final: 0.6995 (tpp) REVERT: I 95 MET cc_start: 0.7624 (OUTLIER) cc_final: 0.7297 (ttp) REVERT: I 152 MET cc_start: 0.7392 (OUTLIER) cc_final: 0.7155 (mmm) REVERT: I 434 MET cc_start: 0.9020 (ptm) cc_final: 0.8439 (ptm) outliers start: 26 outliers final: 14 residues processed: 83 average time/residue: 0.1225 time to fit residues: 17.2571 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 : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 403 THR 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 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 G residue 100 ILE Chi-restraints excluded: chain 1 residue 614 TRP Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain I residue 95 MET Chi-restraints excluded: chain I residue 152 MET 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 24 optimal weight: 0.9980 chunk 153 optimal weight: 10.0000 chunk 160 optimal weight: 20.0000 chunk 163 optimal weight: 8.9990 chunk 14 optimal weight: 0.4980 chunk 64 optimal weight: 0.7980 chunk 195 optimal weight: 3.9990 chunk 128 optimal weight: 9.9990 chunk 216 optimal weight: 20.0000 chunk 49 optimal weight: 2.9990 chunk 111 optimal weight: 9.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 65 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.041729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.034839 restraints weight = 186640.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.035729 restraints weight = 109920.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.036314 restraints weight = 80123.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.036692 restraints weight = 65676.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.036936 restraints weight = 57756.946| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.8575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20859 Z= 0.142 Angle : 0.710 12.648 28500 Z= 0.352 Chirality : 0.045 0.315 3396 Planarity : 0.004 0.058 3489 Dihedral : 5.111 29.992 2676 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.65 % Allowed : 4.55 % Favored : 94.80 % Rotamer: Outliers : 1.40 % Allowed : 9.18 % Favored : 89.42 % 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: -0.06 (0.17), residues: 2460 helix: 2.16 (0.27), residues: 399 sheet: 0.09 (0.19), residues: 714 loop : -0.78 (0.18), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 67 TYR 0.017 0.001 TYR G 51 PHE 0.015 0.001 PHE A 382 TRP 0.011 0.001 TRP 1 631 HIS 0.008 0.001 HIS A 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (20748) covalent geometry : angle 0.68793 / 0.35 (28200) SS BOND : bond 0.00315 / 0.21 ( 33) SS BOND : angle 0.98235 / 0.65 ( 66) hydrogen bonds : bond 0.03530 / 2.30 ( 756) hydrogen bonds : angle 5.64559 / 3.86 ( 2025) link_ALPHA1-2 : bond 0.00222 / 0.11 ( 3) link_ALPHA1-2 : angle 1.43468 / 0.68 ( 9) link_ALPHA1-3 : bond 0.01262 / 0.64 ( 3) link_ALPHA1-3 : angle 1.66736 / 0.83 ( 9) link_ALPHA1-6 : bond 0.00341 / 0.17 ( 3) link_ALPHA1-6 : angle 1.39932 / 0.69 ( 9) link_BETA1-4 : bond 0.00630 / 0.36 ( 30) link_BETA1-4 : angle 1.77324 / 1.27 ( 90) link_NAG-ASN : bond 0.00372 / 0.26 ( 39) link_NAG-ASN : angle 2.30450 / 1.58 ( 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 94 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 64 time to evaluate : 0.703 Fit side-chains revert: symmetry clash REVERT: H 626 MET cc_start: 0.6747 (ttm) cc_final: 0.6336 (ttm) REVERT: J 29 PHE cc_start: 0.7276 (OUTLIER) cc_final: 0.6624 (p90) REVERT: J 48 MET cc_start: 0.6304 (mpp) cc_final: 0.6102 (mtm) REVERT: K 83 GLU cc_start: 0.8203 (mp0) cc_final: 0.7718 (tm-30) REVERT: D 626 MET cc_start: 0.7935 (ttm) cc_final: 0.7564 (ttm) REVERT: F 102 ILE cc_start: 0.8941 (OUTLIER) cc_final: 0.8617 (pt) REVERT: I 95 MET cc_start: 0.7659 (OUTLIER) cc_final: 0.7322 (ttp) REVERT: I 434 MET cc_start: 0.9002 (ptm) cc_final: 0.8668 (ptm) outliers start: 30 outliers final: 20 residues processed: 85 average time/residue: 0.1255 time to fit residues: 18.9950 Evaluate side-chains 86 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 63 time to evaluate : 0.541 ------------------------------------------------------------------------------- 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 29 PHE 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 F residue 66 ASP Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain 1 residue 614 TRP Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain I residue 95 MET Chi-restraints excluded: chain I residue 184 GLU Chi-restraints excluded: chain I residue 403 THR Chi-restraints excluded: chain I residue 426 MET Chi-restraints excluded: chain I residue 475 MET Chi-restraints excluded: chain I residue 503 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 130 optimal weight: 5.9990 chunk 229 optimal weight: 0.9990 chunk 213 optimal weight: 7.9990 chunk 62 optimal weight: 7.9990 chunk 64 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 202 optimal weight: 20.0000 chunk 193 optimal weight: 0.9980 chunk 41 optimal weight: 9.9990 chunk 91 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 229 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.041351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.034398 restraints weight = 186953.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.035278 restraints weight = 111043.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.035865 restraints weight = 81058.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.036247 restraints weight = 66428.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.036485 restraints weight = 58446.635| |-----------------------------------------------------------------------------| r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.8983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 20859 Z= 0.159 Angle : 0.727 12.545 28500 Z= 0.360 Chirality : 0.046 0.316 3396 Planarity : 0.004 0.057 3489 Dihedral : 5.154 31.061 2676 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.65 % Allowed : 5.45 % Favored : 93.90 % Rotamer: Outliers : 1.40 % Allowed : 9.42 % Favored : 89.18 % 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: -0.05 (0.17), residues: 2460 helix: 2.13 (0.27), residues: 399 sheet: 0.26 (0.19), residues: 660 loop : -0.84 (0.17), residues: 1401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 67 TYR 0.016 0.001 TYR G 51 PHE 0.016 0.002 PHE A 382 TRP 0.011 0.001 TRP H 628 HIS 0.007 0.001 HIS A 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.16 (20748) covalent geometry : angle 0.70458 / 0.36 (28200) SS BOND : bond 0.00307 / 0.20 ( 33) SS BOND : angle 0.99685 / 0.67 ( 66) hydrogen bonds : bond 0.03650 / 2.36 ( 756) hydrogen bonds : angle 5.70013 / 3.88 ( 2025) link_ALPHA1-2 : bond 0.00181 / 0.09 ( 3) link_ALPHA1-2 : angle 1.43164 / 0.68 ( 9) link_ALPHA1-3 : bond 0.01150 / 0.58 ( 3) link_ALPHA1-3 : angle 1.58435 / 0.79 ( 9) link_ALPHA1-6 : bond 0.00295 / 0.15 ( 3) link_ALPHA1-6 : angle 1.39565 / 0.69 ( 9) link_BETA1-4 : bond 0.00663 / 0.38 ( 30) link_BETA1-4 : angle 1.81062 / 1.29 ( 90) link_NAG-ASN : bond 0.00428 / 0.28 ( 39) link_NAG-ASN : angle 2.31845 / 1.59 ( 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 94 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 64 time to evaluate : 0.680 Fit side-chains revert: symmetry clash REVERT: A 175 TYR cc_start: 0.6960 (OUTLIER) cc_final: 0.5045 (p90) REVERT: H 626 MET cc_start: 0.7145 (ttm) cc_final: 0.6886 (ttm) REVERT: J 29 PHE cc_start: 0.7399 (OUTLIER) cc_final: 0.6935 (p90) REVERT: K 83 GLU cc_start: 0.8339 (mp0) cc_final: 0.7867 (tm-30) REVERT: D 626 MET cc_start: 0.8037 (ttm) cc_final: 0.7693 (ttm) REVERT: F 102 ILE cc_start: 0.8955 (OUTLIER) cc_final: 0.8602 (pt) REVERT: 1 530 MET cc_start: 0.5495 (mtt) cc_final: 0.5162 (mtt) REVERT: B 29 PHE cc_start: 0.6913 (OUTLIER) cc_final: 0.5917 (p90) REVERT: I 95 MET cc_start: 0.7684 (OUTLIER) cc_final: 0.7328 (ttp) REVERT: I 434 MET cc_start: 0.8982 (ptm) cc_final: 0.8562 (ptm) outliers start: 30 outliers final: 21 residues processed: 85 average time/residue: 0.1305 time to fit residues: 18.6303 Evaluate side-chains 88 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 62 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 261 LEU Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain J residue 29 PHE Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 81 MET 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 F residue 102 ILE Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 29 PHE Chi-restraints excluded: chain I residue 95 MET Chi-restraints excluded: chain I residue 152 MET Chi-restraints excluded: chain I residue 184 GLU Chi-restraints excluded: chain I residue 403 THR Chi-restraints excluded: chain I residue 414 ILE Chi-restraints excluded: chain I residue 426 MET Chi-restraints excluded: chain I residue 475 MET Chi-restraints excluded: chain I residue 503 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 2 optimal weight: 5.9990 chunk 165 optimal weight: 8.9990 chunk 101 optimal weight: 9.9990 chunk 42 optimal weight: 0.9980 chunk 35 optimal weight: 7.9990 chunk 178 optimal weight: 2.9990 chunk 202 optimal weight: 6.9990 chunk 123 optimal weight: 4.9990 chunk 188 optimal weight: 0.8980 chunk 88 optimal weight: 0.0980 chunk 75 optimal weight: 0.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.041911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.035050 restraints weight = 186224.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.035937 restraints weight = 109751.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.036537 restraints weight = 79836.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.036920 restraints weight = 65263.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.037158 restraints weight = 57391.154| |-----------------------------------------------------------------------------| r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.9103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20859 Z= 0.122 Angle : 0.701 12.452 28500 Z= 0.346 Chirality : 0.045 0.316 3396 Planarity : 0.004 0.056 3489 Dihedral : 4.998 29.001 2676 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.61 % Allowed : 4.47 % Favored : 94.92 % Rotamer: Outliers : 1.40 % Allowed : 9.37 % Favored : 89.23 % 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: 2.31 (0.28), residues: 399 sheet: 0.22 (0.19), residues: 699 loop : -0.78 (0.18), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 500 TYR 0.016 0.001 TYR K 51 PHE 0.013 0.001 PHE A 382 TRP 0.016 0.001 TRP 1 614 HIS 0.009 0.001 HIS A 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (20748) covalent geometry : angle 0.67979 / 0.34 (28200) SS BOND : bond 0.00276 / 0.18 ( 33) SS BOND : angle 0.94919 / 0.63 ( 66) hydrogen bonds : bond 0.03336 / 2.16 ( 756) hydrogen bonds : angle 5.56175 / 3.80 ( 2025) link_ALPHA1-2 : bond 0.00390 / 0.20 ( 3) link_ALPHA1-2 : angle 1.29409 / 0.61 ( 9) link_ALPHA1-3 : bond 0.01104 / 0.55 ( 3) link_ALPHA1-3 : angle 1.66099 / 0.83 ( 9) link_ALPHA1-6 : bond 0.00309 / 0.15 ( 3) link_ALPHA1-6 : angle 1.41914 / 0.70 ( 9) link_BETA1-4 : bond 0.00640 / 0.37 ( 30) link_BETA1-4 : angle 1.74915 / 1.25 ( 90) link_NAG-ASN : bond 0.00444 / 0.29 ( 39) link_NAG-ASN : angle 2.22280 / 1.53 ( 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 93 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 63 time to evaluate : 0.773 Fit side-chains REVERT: H 626 MET cc_start: 0.6924 (ttm) cc_final: 0.6360 (ttm) REVERT: K 83 GLU cc_start: 0.8318 (mp0) cc_final: 0.7876 (tm-30) REVERT: D 626 MET cc_start: 0.7998 (ttm) cc_final: 0.7677 (ttm) REVERT: F 102 ILE cc_start: 0.8950 (OUTLIER) cc_final: 0.8611 (pt) REVERT: I 95 MET cc_start: 0.7582 (OUTLIER) cc_final: 0.7255 (ttp) REVERT: I 434 MET cc_start: 0.8967 (ptm) cc_final: 0.8515 (ptm) outliers start: 30 outliers final: 21 residues processed: 82 average time/residue: 0.1216 time to fit residues: 17.5269 Evaluate side-chains 86 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 63 time to evaluate : 0.783 ------------------------------------------------------------------------------- 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 66 ASP 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 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 G residue 34 LEU Chi-restraints excluded: chain G residue 101 PHE Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain I residue 95 MET Chi-restraints excluded: chain I residue 152 MET Chi-restraints excluded: chain I residue 403 THR Chi-restraints excluded: chain I residue 414 ILE Chi-restraints excluded: chain I residue 426 MET 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: 9.9990 chunk 76 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 52 optimal weight: 0.8980 chunk 6 optimal weight: 9.9990 chunk 187 optimal weight: 4.9990 chunk 74 optimal weight: 10.0000 chunk 205 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3513 r_free = 0.3513 target = 0.041003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.034010 restraints weight = 187110.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.034891 restraints weight = 110630.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.035477 restraints weight = 80870.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.035846 restraints weight = 66363.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.036074 restraints weight = 58538.274| |-----------------------------------------------------------------------------| r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.9476 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= 0.177 Angle : 0.745 12.353 28500 Z= 0.368 Chirality : 0.047 0.324 3396 Planarity : 0.004 0.057 3489 Dihedral : 5.135 32.233 2676 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.61 % Allowed : 5.73 % Favored : 93.66 % Rotamer: Outliers : 1.26 % Allowed : 9.56 % Favored : 89.18 % 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: -0.12 (0.17), residues: 2460 helix: 2.08 (0.27), residues: 399 sheet: 0.17 (0.19), residues: 672 loop : -0.87 (0.17), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 57 TYR 0.017 0.001 TYR G 51 PHE 0.016 0.002 PHE A 382 TRP 0.014 0.002 TRP J 47 HIS 0.008 0.001 HIS A 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.18 (20748) covalent geometry : angle 0.72298 / 0.36 (28200) SS BOND : bond 0.00335 / 0.22 ( 33) SS BOND : angle 1.06529 / 0.71 ( 66) hydrogen bonds : bond 0.03829 / 2.48 ( 756) hydrogen bonds : angle 5.72890 / 3.91 ( 2025) link_ALPHA1-2 : bond 0.00015 / 0.01 ( 3) link_ALPHA1-2 : angle 1.58353 / 0.75 ( 9) link_ALPHA1-3 : bond 0.01155 / 0.58 ( 3) link_ALPHA1-3 : angle 1.56826 / 0.76 ( 9) link_ALPHA1-6 : bond 0.00335 / 0.17 ( 3) link_ALPHA1-6 : angle 1.34844 / 0.67 ( 9) link_BETA1-4 : bond 0.00622 / 0.35 ( 30) link_BETA1-4 : angle 1.89203 / 1.35 ( 90) link_NAG-ASN : bond 0.00432 / 0.27 ( 39) link_NAG-ASN : angle 2.28707 / 1.57 ( 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 89 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 62 time to evaluate : 0.762 Fit side-chains REVERT: K 83 GLU cc_start: 0.8370 (mp0) cc_final: 0.7987 (tm-30) REVERT: D 626 MET cc_start: 0.8171 (ttm) cc_final: 0.7851 (ttm) REVERT: F 102 ILE cc_start: 0.8981 (OUTLIER) cc_final: 0.8619 (pt) REVERT: G 107 MET cc_start: 0.7678 (tpp) cc_final: 0.7029 (tpp) REVERT: 1 614 TRP cc_start: 0.5619 (OUTLIER) cc_final: 0.4250 (m-90) REVERT: B 29 PHE cc_start: 0.7237 (OUTLIER) cc_final: 0.6227 (p90) REVERT: I 434 MET cc_start: 0.8965 (ptm) cc_final: 0.8584 (ptm) outliers start: 27 outliers final: 17 residues processed: 80 average time/residue: 0.1287 time to fit residues: 17.8293 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 : 0.769 ------------------------------------------------------------------------------- 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 66 ASP 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 475 MET Chi-restraints excluded: chain F residue 66 ASP Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain G residue 101 PHE Chi-restraints excluded: chain 1 residue 614 TRP Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 29 PHE Chi-restraints excluded: chain I residue 403 THR Chi-restraints excluded: chain I residue 414 ILE Chi-restraints excluded: chain I residue 426 MET 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: 0.8980 chunk 139 optimal weight: 4.9990 chunk 218 optimal weight: 7.9990 chunk 51 optimal weight: 10.0000 chunk 113 optimal weight: 2.9990 chunk 200 optimal weight: 4.9990 chunk 216 optimal weight: 7.9990 chunk 149 optimal weight: 1.9990 chunk 186 optimal weight: 5.9990 chunk 26 optimal weight: 9.9990 chunk 44 optimal weight: 1.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 113 ASN E 229 ASN ** I 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.041057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.034114 restraints weight = 186481.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.034991 restraints weight = 110042.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.035575 restraints weight = 80398.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.035942 restraints weight = 65993.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.036152 restraints weight = 58248.595| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.9725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20859 Z= 0.153 Angle : 0.724 12.260 28500 Z= 0.357 Chirality : 0.046 0.325 3396 Planarity : 0.004 0.056 3489 Dihedral : 5.104 30.738 2676 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.65 % Allowed : 4.55 % Favored : 94.80 % Rotamer: Outliers : 0.89 % Allowed : 9.98 % Favored : 89.14 % 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: -0.14 (0.17), residues: 2460 helix: 2.18 (0.27), residues: 396 sheet: 0.18 (0.20), residues: 642 loop : -0.91 (0.17), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 273 TYR 0.017 0.001 TYR G 51 PHE 0.014 0.001 PHE A 382 TRP 0.012 0.001 TRP 1 614 HIS 0.008 0.001 HIS A 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 (20748) covalent geometry : angle 0.70188 / 0.35 (28200) SS BOND : bond 0.00307 / 0.21 ( 33) SS BOND : angle 0.99937 / 0.67 ( 66) hydrogen bonds : bond 0.03590 / 2.33 ( 756) hydrogen bonds : angle 5.69412 / 3.88 ( 2025) link_ALPHA1-2 : bond 0.00277 / 0.14 ( 3) link_ALPHA1-2 : angle 1.36114 / 0.65 ( 9) link_ALPHA1-3 : bond 0.01187 / 0.59 ( 3) link_ALPHA1-3 : angle 1.61616 / 0.80 ( 9) link_ALPHA1-6 : bond 0.00258 / 0.13 ( 3) link_ALPHA1-6 : angle 1.41754 / 0.70 ( 9) link_BETA1-4 : bond 0.00673 / 0.38 ( 30) link_BETA1-4 : angle 1.84505 / 1.32 ( 90) link_NAG-ASN : bond 0.00430 / 0.28 ( 39) link_NAG-ASN : angle 2.28351 / 1.57 ( 117) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3168.33 seconds wall clock time: 56 minutes 4.04 seconds (3364.04 seconds total)