Starting phenix.real_space_refine on Thu Mar 5 04:48:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6x98_22104/03_2026/6x98_22104.cif Found real_map, /net/cci-nas-00/data/ceres_data/6x98_22104/03_2026/6x98_22104.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6x98_22104/03_2026/6x98_22104.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6x98_22104/03_2026/6x98_22104.map" model { file = "/net/cci-nas-00/data/ceres_data/6x98_22104/03_2026/6x98_22104.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6x98_22104/03_2026/6x98_22104.cif" } resolution = 3.38 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.101 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 12078 2.51 5 N 3228 2.21 5 O 3828 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19269 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 3435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3435 Classifications: {'peptide': 436} Link IDs: {'PTRANS': 22, 'TRANS': 413} Chain breaks: 4 Chain: "B" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 971 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain breaks: 1 Chain: "L" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 823 Classifications: {'peptide': 112} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 107} Chain: "H" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 892 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "C" Number of atoms: 3435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3435 Classifications: {'peptide': 436} Link IDs: {'PTRANS': 22, 'TRANS': 413} Chain breaks: 4 Chain: "D" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 971 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain breaks: 1 Chain: "E" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 823 Classifications: {'peptide': 112} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 107} Chain: "F" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 892 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "G" Number of atoms: 3435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3435 Classifications: {'peptide': 436} Link IDs: {'PTRANS': 22, 'TRANS': 413} Chain breaks: 4 Chain: "I" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 971 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain breaks: 1 Chain: "J" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 823 Classifications: {'peptide': 112} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 107} Chain: "K" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 892 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "C" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "G" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Time building chain proxies: 4.70, per 1000 atoms: 0.24 Number of scatterers: 19269 At special positions: 0 Unit cell: (157.59, 143.17, 118.45, 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 3828 8.00 N 3228 7.00 C 12078 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.05 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.04 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.04 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.05 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.02 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.04 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.06 Simple disulfide: pdb=" SG CYS H 35A" - pdb=" SG CYS H 50 " distance=2.02 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.05 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.04 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.04 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.05 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.02 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS D 605 " distance=2.04 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.04 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.06 Simple disulfide: pdb=" SG CYS F 35A" - pdb=" SG CYS F 50 " distance=2.02 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 74 " distance=2.03 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.05 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.04 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.04 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.04 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.05 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.03 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.02 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.03 Simple disulfide: pdb=" SG CYS G 501 " - pdb=" SG CYS I 605 " distance=2.04 Simple disulfide: pdb=" SG CYS I 598 " - pdb=" SG CYS I 604 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.06 Simple disulfide: pdb=" SG CYS K 35A" - pdb=" SG CYS K 50 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA N 3 " - " MAN N 4 " " BMA R 3 " - " MAN R 4 " " BMA V 3 " - " MAN V 4 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " NAG-ASN " NAG A 607 " - " ASN A 448 " " NAG A 608 " - " ASN A 295 " " NAG A 609 " - " ASN A 301 " " NAG A 610 " - " ASN A 156 " " NAG A 611 " - " ASN A 160 " " NAG A 612 " - " ASN A 133 " " NAG A 615 " - " ASN A 276 " " NAG A 616 " - " ASN A 339 " " NAG A 619 " - " ASN A 363 " " NAG A 620 " - " ASN A 332 " " NAG A 621 " - " ASN A 234 " " NAG A 622 " - " ASN A 392 " " NAG C 607 " - " ASN C 448 " " NAG C 608 " - " ASN C 295 " " NAG C 609 " - " ASN C 301 " " NAG C 610 " - " ASN C 156 " " NAG C 611 " - " ASN C 160 " " NAG C 612 " - " ASN C 133 " " NAG C 615 " - " ASN C 276 " " NAG C 616 " - " ASN C 339 " " NAG C 619 " - " ASN C 363 " " NAG C 620 " - " ASN C 332 " " NAG C 621 " - " ASN C 234 " " NAG C 622 " - " ASN C 392 " " NAG G 607 " - " ASN G 448 " " NAG G 608 " - " ASN G 295 " " NAG G 609 " - " ASN G 301 " " NAG G 610 " - " ASN G 156 " " NAG G 611 " - " ASN G 160 " " NAG G 612 " - " ASN G 133 " " NAG G 615 " - " ASN G 276 " " NAG G 616 " - " ASN G 339 " " NAG G 619 " - " ASN G 363 " " NAG G 620 " - " ASN G 332 " " NAG G 621 " - " ASN G 234 " " NAG G 622 " - " ASN G 392 " " NAG M 1 " - " ASN A 88 " " NAG N 1 " - " ASN A 262 " " NAG O 1 " - " ASN A 197 " " NAG P 1 " - " ASN A 386 " " NAG Q 1 " - " ASN C 88 " " NAG R 1 " - " ASN C 262 " " NAG S 1 " - " ASN C 197 " " NAG T 1 " - " ASN C 386 " " NAG U 1 " - " ASN G 88 " " NAG V 1 " - " ASN G 262 " " NAG W 1 " - " ASN G 197 " " NAG X 1 " - " ASN G 386 " Time building additional restraints: 2.20 Conformation dependent library (CDL) restraints added in 831.3 milliseconds 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4356 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 48 sheets defined 20.8% alpha, 42.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'A' and resid 70 through 74 Processing helix chain 'A' and resid 99 through 117 removed outlier: 3.633A pdb=" N LEU A 116 " --> pdb=" O TRP A 112 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS A 117 " --> pdb=" O ASP A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 335 through 350 Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 387 through 391 Processing helix chain 'A' and resid 474 through 479 Processing helix chain 'A' and resid 482 through 484 No H-bonds generated for 'chain 'A' and resid 482 through 484' Processing helix chain 'B' and resid 523 through 528 removed outlier: 4.216A pdb=" N GLY B 527 " --> pdb=" O GLY B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 542 removed outlier: 4.245A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 596 removed outlier: 3.506A pdb=" N LEU B 576 " --> pdb=" O GLY B 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 626 removed outlier: 3.763A pdb=" N ASP B 624 " --> pdb=" O SER B 620 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N MET B 626 " --> pdb=" O ILE B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 662 Processing helix chain 'H' and resid 61 through 64 removed outlier: 3.720A pdb=" N GLU H 64 " --> pdb=" O ARG H 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 61 through 64' Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'C' and resid 70 through 74 Processing helix chain 'C' and resid 99 through 117 removed outlier: 3.632A pdb=" N LEU C 116 " --> pdb=" O TRP C 112 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS C 117 " --> pdb=" O ASP C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 335 through 350 Processing helix chain 'C' and resid 351 through 353 No H-bonds generated for 'chain 'C' and resid 351 through 353' Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 387 through 391 Processing helix chain 'C' and resid 474 through 479 Processing helix chain 'C' and resid 482 through 484 No H-bonds generated for 'chain 'C' and resid 482 through 484' Processing helix chain 'D' and resid 523 through 528 removed outlier: 4.216A pdb=" N GLY D 527 " --> pdb=" O GLY D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 536 through 542 removed outlier: 4.244A pdb=" N GLN D 540 " --> pdb=" O THR D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 596 removed outlier: 3.506A pdb=" N LEU D 576 " --> pdb=" O GLY D 572 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 626 removed outlier: 3.762A pdb=" N ASP D 624 " --> pdb=" O SER D 620 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N MET D 626 " --> pdb=" O ILE D 622 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 635 Processing helix chain 'D' and resid 638 through 662 Processing helix chain 'F' and resid 61 through 64 removed outlier: 3.720A pdb=" N GLU F 64 " --> pdb=" O ARG F 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 61 through 64' Processing helix chain 'F' and resid 83 through 87 Processing helix chain 'G' and resid 70 through 74 Processing helix chain 'G' and resid 99 through 117 removed outlier: 3.632A pdb=" N LEU G 116 " --> pdb=" O TRP G 112 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS G 117 " --> pdb=" O ASP G 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 126 Processing helix chain 'G' and resid 335 through 350 Processing helix chain 'G' and resid 351 through 353 No H-bonds generated for 'chain 'G' and resid 351 through 353' Processing helix chain 'G' and resid 368 through 373 Processing helix chain 'G' and resid 387 through 391 Processing helix chain 'G' and resid 474 through 479 Processing helix chain 'G' and resid 482 through 484 No H-bonds generated for 'chain 'G' and resid 482 through 484' Processing helix chain 'I' and resid 523 through 528 removed outlier: 4.216A pdb=" N GLY I 527 " --> pdb=" O GLY I 524 " (cutoff:3.500A) Processing helix chain 'I' and resid 529 through 534 Processing helix chain 'I' and resid 536 through 542 removed outlier: 4.245A pdb=" N GLN I 540 " --> pdb=" O THR I 536 " (cutoff:3.500A) Processing helix chain 'I' and resid 572 through 596 removed outlier: 3.506A pdb=" N LEU I 576 " --> pdb=" O GLY I 572 " (cutoff:3.500A) Processing helix chain 'I' and resid 618 through 626 removed outlier: 3.762A pdb=" N ASP I 624 " --> pdb=" O SER I 620 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N MET I 626 " --> pdb=" O ILE I 622 " (cutoff:3.500A) Processing helix chain 'I' and resid 627 through 635 Processing helix chain 'I' and resid 638 through 662 Processing helix chain 'K' and resid 61 through 64 removed outlier: 3.720A pdb=" N GLU K 64 " --> pdb=" O ARG K 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 61 through 64' Processing helix chain 'K' and resid 83 through 87 Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 498 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 75 through 76 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AA6, first strand: chain 'A' and resid 200 through 203 removed outlier: 6.166A pdb=" N ALA A 200 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N TYR A 435 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 393 through 395 removed outlier: 6.288A pdb=" N ILE A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N PHE A 468 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N GLY A 441 " --> pdb=" O ASN A 300 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N ASN A 300 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE A 443 " --> pdb=" O ARG A 298 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.655A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 11.905A pdb=" N ILE A 453 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 11.987A pdb=" N PHE A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 10.801A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 10.652A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 259 through 260 removed outlier: 6.617A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 271 through 274 Processing sheet with id=AB1, first strand: chain 'A' and resid 315 through 323A removed outlier: 7.135A pdb=" N ALA A 316 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ILE A 309 " --> pdb=" O ALA A 316 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N TYR A 318 " --> pdb=" O ILE A 307 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ILE A 307 " --> pdb=" O TYR A 318 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N THR A 320 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N LYS A 305 " --> pdb=" O THR A 320 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ASP A 322 " --> pdb=" O THR A 303 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ASN A 301 " --> pdb=" O ILE A 323A" (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AB3, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.752A pdb=" N VAL L 11 " --> pdb=" O VAL L 105 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.752A pdb=" N VAL L 11 " --> pdb=" O VAL L 105 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AB6, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.949A pdb=" N TYR H 33 " --> pdb=" O PHE H 52 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N PHE H 52 " --> pdb=" O TYR H 33 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N MET H 35 " --> pdb=" O CYS H 50 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N CYS H 50 " --> pdb=" O MET H 35 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 10 through 11 removed outlier: 3.505A pdb=" N LEU H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N ASP H 96 " --> pdb=" O ALA H 100E" (cutoff:3.500A) removed outlier: 6.846A pdb=" N ALA H 100E" --> pdb=" O ASP H 96 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 494 through 498 Processing sheet with id=AB9, first strand: chain 'C' and resid 45 through 47 Processing sheet with id=AC1, first strand: chain 'C' and resid 75 through 76 Processing sheet with id=AC2, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AC3, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AC4, first strand: chain 'C' and resid 200 through 203 removed outlier: 6.167A pdb=" N ALA C 200 " --> pdb=" O ALA C 433 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N TYR C 435 " --> pdb=" O ALA C 200 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 393 through 395 removed outlier: 6.288A pdb=" N ILE C 358 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N PHE C 468 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N GLY C 441 " --> pdb=" O ASN C 300 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N ASN C 300 " --> pdb=" O GLY C 441 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE C 443 " --> pdb=" O ARG C 298 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N GLY C 451 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.655A pdb=" N THR C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 11.905A pdb=" N ILE C 453 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 11.988A pdb=" N PHE C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 10.801A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 10.652A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 259 through 260 removed outlier: 6.617A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 271 through 274 Processing sheet with id=AC8, first strand: chain 'C' and resid 315 through 323A removed outlier: 7.135A pdb=" N ALA C 316 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ILE C 309 " --> pdb=" O ALA C 316 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N TYR C 318 " --> pdb=" O ILE C 307 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ILE C 307 " --> pdb=" O TYR C 318 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N THR C 320 " --> pdb=" O LYS C 305 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N LYS C 305 " --> pdb=" O THR C 320 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ASP C 322 " --> pdb=" O THR C 303 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ASN C 301 " --> pdb=" O ILE C 323A" (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 4 through 7 Processing sheet with id=AD1, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.752A pdb=" N VAL E 11 " --> pdb=" O VAL E 105 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N GLN E 37 " --> pdb=" O LEU E 46 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N LEU E 46 " --> pdb=" O GLN E 37 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.752A pdb=" N VAL E 11 " --> pdb=" O VAL E 105 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 4 through 7 Processing sheet with id=AD4, first strand: chain 'F' and resid 10 through 11 removed outlier: 6.950A pdb=" N TYR F 33 " --> pdb=" O PHE F 52 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N PHE F 52 " --> pdb=" O TYR F 33 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N MET F 35 " --> pdb=" O CYS F 50 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N CYS F 50 " --> pdb=" O MET F 35 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 10 through 11 removed outlier: 3.504A pdb=" N LEU F 102 " --> pdb=" O ARG F 94 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N ASP F 96 " --> pdb=" O ALA F 100E" (cutoff:3.500A) removed outlier: 6.846A pdb=" N ALA F 100E" --> pdb=" O ASP F 96 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 494 through 498 Processing sheet with id=AD7, first strand: chain 'G' and resid 45 through 47 Processing sheet with id=AD8, first strand: chain 'G' and resid 75 through 76 Processing sheet with id=AD9, first strand: chain 'G' and resid 91 through 94 Processing sheet with id=AE1, first strand: chain 'G' and resid 169 through 177 Processing sheet with id=AE2, first strand: chain 'G' and resid 200 through 203 removed outlier: 6.167A pdb=" N ALA G 200 " --> pdb=" O ALA G 433 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N TYR G 435 " --> pdb=" O ALA G 200 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N THR G 202 " --> pdb=" O TYR G 435 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 393 through 395 removed outlier: 6.288A pdb=" N ILE G 358 " --> pdb=" O GLU G 466 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N PHE G 468 " --> pdb=" O ILE G 358 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ARG G 360 " --> pdb=" O PHE G 468 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N GLY G 441 " --> pdb=" O ASN G 300 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N ASN G 300 " --> pdb=" O GLY G 441 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE G 443 " --> pdb=" O ARG G 298 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N GLY G 451 " --> pdb=" O THR G 290 " (cutoff:3.500A) removed outlier: 10.655A pdb=" N THR G 290 " --> pdb=" O GLY G 451 " (cutoff:3.500A) removed outlier: 11.905A pdb=" N ILE G 453 " --> pdb=" O PHE G 288 " (cutoff:3.500A) removed outlier: 11.987A pdb=" N PHE G 288 " --> pdb=" O ILE G 453 " (cutoff:3.500A) removed outlier: 10.800A pdb=" N THR G 455 " --> pdb=" O VAL G 286 " (cutoff:3.500A) removed outlier: 10.651A pdb=" N VAL G 286 " --> pdb=" O THR G 455 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N GLN G 293 " --> pdb=" O SER G 334 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER G 334 " --> pdb=" O GLN G 293 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N PHE G 382 " --> pdb=" O LYS G 421 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 259 through 260 removed outlier: 6.617A pdb=" N LEU G 260 " --> pdb=" O THR G 450 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 271 through 274 Processing sheet with id=AE6, first strand: chain 'G' and resid 315 through 323A removed outlier: 7.135A pdb=" N ALA G 316 " --> pdb=" O ILE G 309 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ILE G 309 " --> pdb=" O ALA G 316 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N TYR G 318 " --> pdb=" O ILE G 307 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ILE G 307 " --> pdb=" O TYR G 318 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N THR G 320 " --> pdb=" O LYS G 305 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N LYS G 305 " --> pdb=" O THR G 320 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ASP G 322 " --> pdb=" O THR G 303 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ASN G 301 " --> pdb=" O ILE G 323A" (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 4 through 7 Processing sheet with id=AE8, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.752A pdb=" N VAL J 11 " --> pdb=" O VAL J 105 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N GLN J 37 " --> pdb=" O LEU J 46 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N LEU J 46 " --> pdb=" O GLN J 37 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.752A pdb=" N VAL J 11 " --> pdb=" O VAL J 105 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'K' and resid 4 through 7 Processing sheet with id=AF2, first strand: chain 'K' and resid 10 through 11 removed outlier: 6.949A pdb=" N TYR K 33 " --> pdb=" O PHE K 52 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N PHE K 52 " --> pdb=" O TYR K 33 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N MET K 35 " --> pdb=" O CYS K 50 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N CYS K 50 " --> pdb=" O MET K 35 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N TRP K 36 " --> pdb=" O VAL K 48 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'K' and resid 10 through 11 removed outlier: 3.504A pdb=" N LEU K 102 " --> pdb=" O ARG K 94 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N ASP K 96 " --> pdb=" O ALA K 100E" (cutoff:3.500A) removed outlier: 6.845A pdb=" N ALA K 100E" --> pdb=" O ASP K 96 " (cutoff:3.500A) 756 hydrogen bonds defined for protein. 1908 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: 4.53 Time building geometry restraints manager: 2.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 4334 1.32 - 1.45: 5735 1.45 - 1.58: 9392 1.58 - 1.72: 9 1.72 - 1.85: 180 Bond restraints: 19650 Sorted by residual: bond pdb=" CB HIS C 374 " pdb=" CG HIS C 374 " ideal model delta sigma weight residual 1.497 1.426 0.071 1.40e-02 5.10e+03 2.54e+01 bond pdb=" CB HIS G 374 " pdb=" CG HIS G 374 " ideal model delta sigma weight residual 1.497 1.427 0.070 1.40e-02 5.10e+03 2.50e+01 bond pdb=" CB HIS A 374 " pdb=" CG HIS A 374 " ideal model delta sigma weight residual 1.497 1.427 0.070 1.40e-02 5.10e+03 2.49e+01 bond pdb=" N PRO G 470 " pdb=" CA PRO G 470 " ideal model delta sigma weight residual 1.465 1.414 0.052 1.19e-02 7.06e+03 1.88e+01 bond pdb=" N PRO A 470 " pdb=" CA PRO A 470 " ideal model delta sigma weight residual 1.465 1.414 0.051 1.19e-02 7.06e+03 1.87e+01 ... (remaining 19645 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.26: 22595 2.26 - 4.52: 3457 4.52 - 6.78: 560 6.78 - 9.04: 70 9.04 - 11.30: 21 Bond angle restraints: 26703 Sorted by residual: angle pdb=" N LEU A 261 " pdb=" CA LEU A 261 " pdb=" C LEU A 261 " ideal model delta sigma weight residual 113.28 123.89 -10.61 1.22e+00 6.72e-01 7.57e+01 angle pdb=" N LEU C 261 " pdb=" CA LEU C 261 " pdb=" C LEU C 261 " ideal model delta sigma weight residual 113.28 123.89 -10.61 1.22e+00 6.72e-01 7.56e+01 angle pdb=" N LEU G 261 " pdb=" CA LEU G 261 " pdb=" C LEU G 261 " ideal model delta sigma weight residual 113.28 123.87 -10.59 1.22e+00 6.72e-01 7.53e+01 angle pdb=" C CYS G 239 " pdb=" N PRO G 240 " pdb=" CA PRO G 240 " ideal model delta sigma weight residual 119.56 127.82 -8.26 1.02e+00 9.61e-01 6.55e+01 angle pdb=" C CYS C 239 " pdb=" N PRO C 240 " pdb=" CA PRO C 240 " ideal model delta sigma weight residual 119.56 127.79 -8.23 1.02e+00 9.61e-01 6.51e+01 ... (remaining 26698 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.85: 12114 21.85 - 43.71: 330 43.71 - 65.56: 75 65.56 - 87.41: 30 87.41 - 109.27: 18 Dihedral angle restraints: 12567 sinusoidal: 5793 harmonic: 6774 Sorted by residual: dihedral pdb=" CB CYS A 228 " pdb=" SG CYS A 228 " pdb=" SG CYS A 239 " pdb=" CB CYS A 239 " ideal model delta sinusoidal sigma weight residual -86.00 -174.45 88.45 1 1.00e+01 1.00e-02 9.34e+01 dihedral pdb=" CB CYS C 228 " pdb=" SG CYS C 228 " pdb=" SG CYS C 239 " pdb=" CB CYS C 239 " ideal model delta sinusoidal sigma weight residual -86.00 -174.44 88.44 1 1.00e+01 1.00e-02 9.34e+01 dihedral pdb=" CB CYS G 228 " pdb=" SG CYS G 228 " pdb=" SG CYS G 239 " pdb=" CB CYS G 239 " ideal model delta sinusoidal sigma weight residual -86.00 -174.43 88.43 1 1.00e+01 1.00e-02 9.34e+01 ... (remaining 12564 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 2400 0.103 - 0.206: 719 0.206 - 0.308: 97 0.308 - 0.411: 0 0.411 - 0.514: 3 Chirality restraints: 3219 Sorted by residual: chirality pdb=" C1 NAG T 2 " pdb=" O4 NAG T 1 " pdb=" C2 NAG T 2 " pdb=" O5 NAG T 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.55 0.15 2.00e-02 2.50e+03 5.38e+01 chirality pdb=" C1 NAG P 2 " pdb=" O4 NAG P 1 " pdb=" C2 NAG P 2 " pdb=" O5 NAG P 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.55 0.15 2.00e-02 2.50e+03 5.37e+01 chirality pdb=" C1 NAG X 2 " pdb=" O4 NAG X 1 " pdb=" C2 NAG X 2 " pdb=" O5 NAG X 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.55 0.15 2.00e-02 2.50e+03 5.30e+01 ... (remaining 3216 not shown) Planarity restraints: 3351 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 620 " -0.055 2.00e-02 2.50e+03 4.48e-02 2.50e+01 pdb=" C7 NAG A 620 " 0.012 2.00e-02 2.50e+03 pdb=" C8 NAG A 620 " -0.041 2.00e-02 2.50e+03 pdb=" N2 NAG A 620 " 0.071 2.00e-02 2.50e+03 pdb=" O7 NAG A 620 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG G 620 " -0.055 2.00e-02 2.50e+03 4.47e-02 2.49e+01 pdb=" C7 NAG G 620 " 0.012 2.00e-02 2.50e+03 pdb=" C8 NAG G 620 " -0.041 2.00e-02 2.50e+03 pdb=" N2 NAG G 620 " 0.071 2.00e-02 2.50e+03 pdb=" O7 NAG G 620 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 620 " 0.054 2.00e-02 2.50e+03 4.44e-02 2.46e+01 pdb=" C7 NAG C 620 " -0.012 2.00e-02 2.50e+03 pdb=" C8 NAG C 620 " 0.040 2.00e-02 2.50e+03 pdb=" N2 NAG C 620 " -0.071 2.00e-02 2.50e+03 pdb=" O7 NAG C 620 " -0.012 2.00e-02 2.50e+03 ... (remaining 3348 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 7360 2.87 - 3.38: 16296 3.38 - 3.89: 32071 3.89 - 4.39: 36098 4.39 - 4.90: 60324 Nonbonded interactions: 152149 Sorted by model distance: nonbonded pdb=" OG1 THR G 37 " pdb=" OG1 THR G 499 " model vdw 2.363 3.040 nonbonded pdb=" OG1 THR C 37 " pdb=" OG1 THR C 499 " model vdw 2.364 3.040 nonbonded pdb=" OG1 THR A 37 " pdb=" OG1 THR A 499 " model vdw 2.364 3.040 nonbonded pdb=" N ASN G 133 " pdb=" OD1 ASN G 133 " model vdw 2.368 3.120 nonbonded pdb=" N ASN A 133 " pdb=" OD1 ASN A 133 " model vdw 2.368 3.120 ... (remaining 152144 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'I' } ncs_group { reference = chain 'E' selection = chain 'J' selection = chain 'L' } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'K' } ncs_group { reference = chain 'M' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'W' selection = chain 'X' } ncs_group { reference = chain 'N' selection = chain 'R' selection = chain 'V' } 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 individual isotropic 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: 1.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 20.730 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.070 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:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.020 0.126 19758 Z= 1.043 Angle : 1.726 11.300 26985 Z= 1.116 Chirality : 0.093 0.514 3219 Planarity : 0.009 0.045 3303 Dihedral : 11.484 109.268 8085 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 1.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.15 % Allowed : 0.30 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % 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: 1.15 (0.17), residues: 2313 helix: 0.54 (0.26), residues: 354 sheet: 0.85 (0.19), residues: 708 loop : 0.98 (0.18), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 298 TYR 0.050 0.008 TYR A 40 PHE 0.027 0.006 PHE F 67 TRP 0.052 0.009 TRP B 571 HIS 0.008 0.002 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.01967 (19650) covalent geometry : angle 1.71144 (26703) SS BOND : bond 0.01209 ( 42) SS BOND : angle 2.80689 ( 84) hydrogen bonds : bond 0.17909 ( 732) hydrogen bonds : angle 6.89014 ( 1908) link_ALPHA1-3 : bond 0.03519 ( 3) link_ALPHA1-3 : angle 1.92749 ( 9) link_BETA1-4 : bond 0.02682 ( 15) link_BETA1-4 : angle 3.89926 ( 45) link_NAG-ASN : bond 0.02800 ( 48) link_NAG-ASN : angle 2.34003 ( 144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 2031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 529 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 HIS cc_start: 0.6820 (p-80) cc_final: 0.6505 (m170) REVERT: C 72 HIS cc_start: 0.7000 (p-80) cc_final: 0.6443 (m170) REVERT: G 72 HIS cc_start: 0.6797 (p-80) cc_final: 0.6446 (m170) REVERT: G 95 MET cc_start: 0.9027 (ptm) cc_final: 0.8701 (ptm) REVERT: G 424 ILE cc_start: 0.9129 (mm) cc_final: 0.8866 (mm) REVERT: I 632 ASP cc_start: 0.8405 (t70) cc_final: 0.8134 (t0) outliers start: 3 outliers final: 3 residues processed: 532 average time/residue: 0.1387 time to fit residues: 109.4953 Evaluate side-chains 256 residues out of total 2031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 253 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 ASN Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain G residue 133 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 216 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 0.8980 chunk 227 optimal weight: 0.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 640 GLN ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 411 ASN I 640 GLN ** J 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 81 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.115518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.091514 restraints weight = 33292.408| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 3.45 r_work: 0.3212 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 19758 Z= 0.161 Angle : 0.719 9.017 26985 Z= 0.373 Chirality : 0.047 0.161 3219 Planarity : 0.004 0.042 3303 Dihedral : 8.247 62.870 3897 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.05 % Allowed : 8.12 % Favored : 88.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % 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: 1.09 (0.17), residues: 2313 helix: 1.95 (0.28), residues: 336 sheet: 0.58 (0.18), residues: 717 loop : 0.62 (0.17), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 579 TYR 0.028 0.002 TYR D 638 PHE 0.015 0.002 PHE A 383 TRP 0.019 0.002 TRP G 479 HIS 0.005 0.001 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00351 (19650) covalent geometry : angle 0.68918 (26703) SS BOND : bond 0.00487 ( 42) SS BOND : angle 1.15573 ( 84) hydrogen bonds : bond 0.05957 ( 732) hydrogen bonds : angle 5.46829 ( 1908) link_ALPHA1-3 : bond 0.01102 ( 3) link_ALPHA1-3 : angle 2.56840 ( 9) link_BETA1-4 : bond 0.00530 ( 15) link_BETA1-4 : angle 2.22084 ( 45) link_NAG-ASN : bond 0.00292 ( 48) link_NAG-ASN : angle 2.45098 ( 144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 2031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 325 time to evaluate : 0.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 HIS cc_start: 0.6656 (p-80) cc_final: 0.5958 (m170) REVERT: B 535 MET cc_start: 0.8258 (mtp) cc_final: 0.7985 (mtt) REVERT: B 543 ASN cc_start: 0.8550 (m110) cc_final: 0.8227 (m110) REVERT: B 632 ASP cc_start: 0.8760 (t70) cc_final: 0.8337 (t0) REVERT: L 4 MET cc_start: 0.8089 (mmm) cc_final: 0.7843 (mmm) REVERT: L 48 ILE cc_start: 0.9075 (mt) cc_final: 0.8766 (mm) REVERT: L 54 LEU cc_start: 0.8006 (mp) cc_final: 0.7755 (tp) REVERT: C 72 HIS cc_start: 0.6757 (p-80) cc_final: 0.5802 (m170) REVERT: C 486 TYR cc_start: 0.8960 (m-80) cc_final: 0.8662 (m-10) REVERT: D 543 ASN cc_start: 0.8759 (m110) cc_final: 0.8273 (m110) REVERT: D 632 ASP cc_start: 0.8757 (t70) cc_final: 0.8323 (t0) REVERT: E 4 MET cc_start: 0.8019 (mmm) cc_final: 0.7810 (mmm) REVERT: E 23 CYS cc_start: 0.6906 (t) cc_final: 0.5156 (t) REVERT: E 48 ILE cc_start: 0.8870 (mt) cc_final: 0.8644 (mm) REVERT: E 89 GLN cc_start: 0.9031 (tt0) cc_final: 0.8589 (tt0) REVERT: F 82 LEU cc_start: 0.8574 (mt) cc_final: 0.8318 (mm) REVERT: G 72 HIS cc_start: 0.6552 (p-80) cc_final: 0.5803 (m170) REVERT: G 486 TYR cc_start: 0.9020 (m-80) cc_final: 0.8758 (m-80) REVERT: I 617 ARG cc_start: 0.8141 (ttm170) cc_final: 0.7439 (mtm180) REVERT: I 621 GLU cc_start: 0.7733 (mt-10) cc_final: 0.7187 (pt0) REVERT: I 632 ASP cc_start: 0.8931 (t70) cc_final: 0.8383 (t0) REVERT: I 634 GLU cc_start: 0.7925 (mm-30) cc_final: 0.7116 (mm-30) REVERT: J 4 MET cc_start: 0.8336 (mmt) cc_final: 0.8033 (mmm) outliers start: 62 outliers final: 43 residues processed: 372 average time/residue: 0.1298 time to fit residues: 74.5698 Evaluate side-chains 293 residues out of total 2031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 250 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain L residue 24 GLN Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 82 SER Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 661 LEU Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 88 CYS Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 74 SER Chi-restraints excluded: chain F residue 82 SER Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain G residue 167 ASP Chi-restraints excluded: chain G residue 199 SER Chi-restraints excluded: chain G residue 411 ASN Chi-restraints excluded: chain G residue 434 MET Chi-restraints excluded: chain G residue 474 ASP Chi-restraints excluded: chain G residue 499 THR Chi-restraints excluded: chain I residue 616 ASN Chi-restraints excluded: chain I residue 620 SER Chi-restraints excluded: chain I residue 661 LEU Chi-restraints excluded: chain J residue 24 GLN Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 88 CYS Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 82 MET Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain K residue 102 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 43 optimal weight: 5.9990 chunk 200 optimal weight: 7.9990 chunk 36 optimal weight: 0.8980 chunk 227 optimal weight: 8.9990 chunk 220 optimal weight: 7.9990 chunk 2 optimal weight: 9.9990 chunk 57 optimal weight: 8.9990 chunk 53 optimal weight: 1.9990 chunk 140 optimal weight: 0.0770 chunk 17 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 overall best weight: 1.7944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 658 GLN ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 478 ASN D 575 GLN ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 82 GLN I 658 GLN ** J 37 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 = 0.3656 r_free = 0.3656 target = 0.113090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.087852 restraints weight = 34794.843| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 3.64 r_work: 0.3141 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.3356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 19758 Z= 0.188 Angle : 0.657 9.394 26985 Z= 0.339 Chirality : 0.045 0.148 3219 Planarity : 0.004 0.045 3303 Dihedral : 6.980 57.170 3891 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.40 % Allowed : 8.91 % Favored : 87.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % 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: 0.85 (0.17), residues: 2313 helix: 1.97 (0.28), residues: 357 sheet: 0.69 (0.19), residues: 696 loop : 0.16 (0.17), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 61 TYR 0.018 0.002 TYR D 638 PHE 0.016 0.002 PHE C 383 TRP 0.011 0.002 TRP G 69 HIS 0.006 0.002 HIS C 105 Details of bonding type rmsd covalent geometry : bond 0.00436 (19650) covalent geometry : angle 0.62830 (26703) SS BOND : bond 0.00330 ( 42) SS BOND : angle 1.05910 ( 84) hydrogen bonds : bond 0.05252 ( 732) hydrogen bonds : angle 5.03431 ( 1908) link_ALPHA1-3 : bond 0.01266 ( 3) link_ALPHA1-3 : angle 1.29375 ( 9) link_BETA1-4 : bond 0.00537 ( 15) link_BETA1-4 : angle 1.72843 ( 45) link_NAG-ASN : bond 0.00373 ( 48) link_NAG-ASN : angle 2.46227 ( 144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 267 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 HIS cc_start: 0.6682 (p-80) cc_final: 0.6044 (m-70) REVERT: B 535 MET cc_start: 0.8337 (mtp) cc_final: 0.8077 (mtt) REVERT: B 543 ASN cc_start: 0.8523 (m110) cc_final: 0.8211 (m110) REVERT: B 621 GLU cc_start: 0.7918 (tm-30) cc_final: 0.7569 (tm-30) REVERT: B 626 MET cc_start: 0.7393 (ttm) cc_final: 0.7146 (mtp) REVERT: B 632 ASP cc_start: 0.8691 (t70) cc_final: 0.8362 (t0) REVERT: L 4 MET cc_start: 0.8182 (mmm) cc_final: 0.7593 (mmt) REVERT: L 48 ILE cc_start: 0.9131 (mt) cc_final: 0.8804 (mm) REVERT: L 63 LYS cc_start: 0.7283 (ttpp) cc_final: 0.6850 (mtpp) REVERT: H 59 TYR cc_start: 0.7595 (m-80) cc_final: 0.7226 (m-80) REVERT: C 72 HIS cc_start: 0.6699 (p-80) cc_final: 0.5752 (m170) REVERT: D 543 ASN cc_start: 0.8748 (m110) cc_final: 0.8260 (m110) REVERT: D 621 GLU cc_start: 0.8074 (tt0) cc_final: 0.7850 (pt0) REVERT: D 632 ASP cc_start: 0.8841 (t70) cc_final: 0.8413 (t0) REVERT: D 661 LEU cc_start: 0.6992 (OUTLIER) cc_final: 0.6740 (mm) REVERT: E 4 MET cc_start: 0.8235 (mmm) cc_final: 0.7377 (mmt) REVERT: E 23 CYS cc_start: 0.7245 (t) cc_final: 0.5465 (t) REVERT: E 48 ILE cc_start: 0.8936 (mt) cc_final: 0.8684 (mm) REVERT: E 89 GLN cc_start: 0.9117 (tt0) cc_final: 0.8793 (tt0) REVERT: G 72 HIS cc_start: 0.6539 (p-80) cc_final: 0.5839 (m170) REVERT: G 475 MET cc_start: 0.8030 (mmm) cc_final: 0.7774 (mmm) REVERT: G 486 TYR cc_start: 0.9098 (m-80) cc_final: 0.8675 (m-80) REVERT: I 617 ARG cc_start: 0.8171 (ttm170) cc_final: 0.7648 (mtm180) REVERT: I 621 GLU cc_start: 0.7625 (mt-10) cc_final: 0.7407 (mp0) REVERT: I 632 ASP cc_start: 0.8887 (t70) cc_final: 0.8377 (t0) REVERT: I 654 GLU cc_start: 0.8337 (mm-30) cc_final: 0.7766 (mt-10) REVERT: J 63 LYS cc_start: 0.7727 (ttmm) cc_final: 0.7262 (mtpp) outliers start: 69 outliers final: 47 residues processed: 316 average time/residue: 0.1299 time to fit residues: 63.8088 Evaluate side-chains 284 residues out of total 2031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 236 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 ASN Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 652 GLN Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 24 GLN Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 82 SER Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 615 SER Chi-restraints excluded: chain D residue 652 GLN Chi-restraints excluded: chain D residue 661 LEU Chi-restraints excluded: chain E residue 24 GLN Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 82 SER Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 167 ASP Chi-restraints excluded: chain G residue 213 ILE Chi-restraints excluded: chain G residue 474 ASP Chi-restraints excluded: chain G residue 499 THR Chi-restraints excluded: chain I residue 615 SER Chi-restraints excluded: chain I residue 616 ASN Chi-restraints excluded: chain I residue 627 THR Chi-restraints excluded: chain I residue 661 LEU Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 24 GLN Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 82 MET Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain K residue 100 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 184 optimal weight: 9.9990 chunk 36 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 chunk 102 optimal weight: 0.8980 chunk 199 optimal weight: 6.9990 chunk 120 optimal weight: 0.6980 chunk 146 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 9 optimal weight: 8.9990 chunk 163 optimal weight: 6.9990 chunk 151 optimal weight: 10.0000 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 54 ASN C 478 ASN E 37 GLN ** J 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.112562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.086752 restraints weight = 34980.905| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 3.72 r_work: 0.3110 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.3830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 19758 Z= 0.179 Angle : 0.617 8.026 26985 Z= 0.317 Chirality : 0.045 0.156 3219 Planarity : 0.004 0.047 3303 Dihedral : 6.112 46.461 3891 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.69 % Allowed : 9.85 % Favored : 86.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % 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: 0.70 (0.17), residues: 2313 helix: 2.05 (0.29), residues: 357 sheet: 0.78 (0.19), residues: 702 loop : -0.15 (0.17), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 61 TYR 0.023 0.002 TYR E 30 PHE 0.017 0.002 PHE G 53 TRP 0.012 0.002 TRP G 69 HIS 0.006 0.002 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00422 (19650) covalent geometry : angle 0.59136 (26703) SS BOND : bond 0.00348 ( 42) SS BOND : angle 1.13808 ( 84) hydrogen bonds : bond 0.04724 ( 732) hydrogen bonds : angle 4.87791 ( 1908) link_ALPHA1-3 : bond 0.01443 ( 3) link_ALPHA1-3 : angle 1.61095 ( 9) link_BETA1-4 : bond 0.00430 ( 15) link_BETA1-4 : angle 1.51221 ( 45) link_NAG-ASN : bond 0.00279 ( 48) link_NAG-ASN : angle 2.17761 ( 144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 249 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 HIS cc_start: 0.6689 (p-80) cc_final: 0.6035 (m-70) REVERT: A 97 LYS cc_start: 0.9133 (tptt) cc_final: 0.8663 (tppp) REVERT: B 535 MET cc_start: 0.8554 (mtp) cc_final: 0.8238 (mtt) REVERT: B 543 ASN cc_start: 0.8579 (m110) cc_final: 0.8280 (m110) REVERT: B 621 GLU cc_start: 0.7935 (tm-30) cc_final: 0.7703 (tm-30) REVERT: B 632 ASP cc_start: 0.8765 (t70) cc_final: 0.8436 (t0) REVERT: B 638 TYR cc_start: 0.8012 (m-80) cc_final: 0.7789 (m-10) REVERT: B 654 GLU cc_start: 0.8257 (mm-30) cc_final: 0.7854 (mt-10) REVERT: L 63 LYS cc_start: 0.7278 (ttpp) cc_final: 0.6798 (mtpp) REVERT: H 31 ASP cc_start: 0.8004 (m-30) cc_final: 0.7647 (m-30) REVERT: H 38 ARG cc_start: 0.7625 (ptt180) cc_final: 0.7199 (ptt180) REVERT: C 46 LYS cc_start: 0.8171 (mmtt) cc_final: 0.7883 (mmtt) REVERT: C 72 HIS cc_start: 0.6700 (p-80) cc_final: 0.5824 (m170) REVERT: D 543 ASN cc_start: 0.8816 (m110) cc_final: 0.8440 (m110) REVERT: D 632 ASP cc_start: 0.8894 (t70) cc_final: 0.8283 (t0) REVERT: D 661 LEU cc_start: 0.7012 (OUTLIER) cc_final: 0.6720 (mm) REVERT: E 48 ILE cc_start: 0.8968 (mt) cc_final: 0.8740 (mm) REVERT: E 63 LYS cc_start: 0.7196 (ttmm) cc_final: 0.6794 (mtmm) REVERT: E 89 GLN cc_start: 0.9108 (OUTLIER) cc_final: 0.8873 (tt0) REVERT: F 100 VAL cc_start: 0.8820 (t) cc_final: 0.8581 (p) REVERT: G 46 LYS cc_start: 0.8237 (mmmt) cc_final: 0.7867 (mmtt) REVERT: G 72 HIS cc_start: 0.6547 (p-80) cc_final: 0.5856 (m-70) REVERT: G 486 TYR cc_start: 0.9159 (m-80) cc_final: 0.8865 (m-80) REVERT: I 621 GLU cc_start: 0.7576 (mt-10) cc_final: 0.7196 (tt0) REVERT: I 632 ASP cc_start: 0.8819 (t70) cc_final: 0.8270 (t0) REVERT: J 63 LYS cc_start: 0.7787 (ttmm) cc_final: 0.7345 (mtpp) REVERT: K 31 ASP cc_start: 0.7951 (m-30) cc_final: 0.7537 (m-30) outliers start: 75 outliers final: 53 residues processed: 306 average time/residue: 0.1299 time to fit residues: 61.8186 Evaluate side-chains 282 residues out of total 2031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 227 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 398 ASN Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 652 GLN Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 24 GLN Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 79 THR Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 82 SER Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 652 GLN Chi-restraints excluded: chain D residue 661 LEU Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 24 GLN Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 89 GLN Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 79 THR Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 213 ILE Chi-restraints excluded: chain G residue 434 MET Chi-restraints excluded: chain G residue 474 ASP Chi-restraints excluded: chain G residue 499 THR Chi-restraints excluded: chain I residue 616 ASN Chi-restraints excluded: chain I residue 661 LEU Chi-restraints excluded: chain J residue 24 GLN Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 47 LEU Chi-restraints excluded: chain J residue 106 VAL Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 82 MET Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain K residue 102 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 9 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 chunk 130 optimal weight: 9.9990 chunk 112 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 134 optimal weight: 7.9990 chunk 185 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 131 optimal weight: 10.0000 chunk 36 optimal weight: 4.9990 chunk 18 optimal weight: 0.7980 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 398 ASN A 478 ASN ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 ASN C 478 ASN G 478 ASN I 637 ASN ** J 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.108957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.083808 restraints weight = 35194.066| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 3.67 r_work: 0.3073 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.4148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 19758 Z= 0.238 Angle : 0.655 8.301 26985 Z= 0.339 Chirality : 0.046 0.145 3219 Planarity : 0.004 0.049 3303 Dihedral : 6.163 45.749 3891 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.50 % Allowed : 11.96 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % 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: 0.40 (0.17), residues: 2313 helix: 1.72 (0.29), residues: 375 sheet: 0.51 (0.19), residues: 672 loop : -0.26 (0.17), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 61 TYR 0.030 0.002 TYR D 638 PHE 0.018 0.002 PHE C 383 TRP 0.015 0.002 TRP A 69 HIS 0.007 0.002 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00565 (19650) covalent geometry : angle 0.63046 (26703) SS BOND : bond 0.00523 ( 42) SS BOND : angle 1.37076 ( 84) hydrogen bonds : bond 0.05148 ( 732) hydrogen bonds : angle 4.96096 ( 1908) link_ALPHA1-3 : bond 0.01219 ( 3) link_ALPHA1-3 : angle 1.23964 ( 9) link_BETA1-4 : bond 0.00494 ( 15) link_BETA1-4 : angle 1.66945 ( 45) link_NAG-ASN : bond 0.00383 ( 48) link_NAG-ASN : angle 2.16496 ( 144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 238 time to evaluate : 0.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8190 (mmmt) cc_final: 0.7473 (mmtt) REVERT: A 72 HIS cc_start: 0.6751 (p-80) cc_final: 0.6103 (m-70) REVERT: A 114 GLN cc_start: 0.8769 (tt0) cc_final: 0.8382 (tt0) REVERT: B 535 MET cc_start: 0.8717 (mtp) cc_final: 0.8400 (mtt) REVERT: B 543 ASN cc_start: 0.8633 (m110) cc_final: 0.8347 (m110) REVERT: B 621 GLU cc_start: 0.8138 (tm-30) cc_final: 0.7782 (tm-30) REVERT: B 632 ASP cc_start: 0.8871 (t70) cc_final: 0.8563 (t0) REVERT: B 654 GLU cc_start: 0.8255 (mm-30) cc_final: 0.7770 (mt-10) REVERT: L 3 VAL cc_start: 0.8562 (t) cc_final: 0.8223 (m) REVERT: L 4 MET cc_start: 0.8209 (mmm) cc_final: 0.7955 (mmm) REVERT: L 48 ILE cc_start: 0.9093 (mt) cc_final: 0.8831 (mm) REVERT: H 38 ARG cc_start: 0.7769 (ptt180) cc_final: 0.7283 (ptt180) REVERT: H 59 TYR cc_start: 0.7840 (m-80) cc_final: 0.7566 (m-80) REVERT: C 46 LYS cc_start: 0.8270 (mmtt) cc_final: 0.8007 (mmtt) REVERT: C 72 HIS cc_start: 0.6740 (p-80) cc_final: 0.5849 (m170) REVERT: C 323 ILE cc_start: 0.7941 (mm) cc_final: 0.7732 (mm) REVERT: D 543 ASN cc_start: 0.8830 (m110) cc_final: 0.8412 (m110) REVERT: D 632 ASP cc_start: 0.9024 (t70) cc_final: 0.8519 (t0) REVERT: D 661 LEU cc_start: 0.7094 (OUTLIER) cc_final: 0.6807 (mm) REVERT: E 3 VAL cc_start: 0.8602 (t) cc_final: 0.8241 (m) REVERT: E 63 LYS cc_start: 0.7334 (ttmm) cc_final: 0.6762 (mtmm) REVERT: E 89 GLN cc_start: 0.9037 (tt0) cc_final: 0.8734 (tt0) REVERT: F 31 ASP cc_start: 0.8034 (m-30) cc_final: 0.7576 (m-30) REVERT: F 100 VAL cc_start: 0.8861 (t) cc_final: 0.8571 (p) REVERT: G 46 LYS cc_start: 0.8184 (mmmt) cc_final: 0.7919 (mmtt) REVERT: G 72 HIS cc_start: 0.6620 (p-80) cc_final: 0.5939 (m-70) REVERT: I 621 GLU cc_start: 0.7640 (mt-10) cc_final: 0.7432 (mp0) REVERT: I 626 MET cc_start: 0.8119 (ttm) cc_final: 0.7565 (ttp) REVERT: I 632 ASP cc_start: 0.8893 (t70) cc_final: 0.8375 (t0) REVERT: I 637 ASN cc_start: 0.8624 (OUTLIER) cc_final: 0.8335 (p0) REVERT: J 4 MET cc_start: 0.8650 (tpt) cc_final: 0.8023 (tpt) REVERT: J 30 TYR cc_start: 0.8342 (m-80) cc_final: 0.8129 (m-10) REVERT: J 63 LYS cc_start: 0.7918 (ttmm) cc_final: 0.7498 (mtpp) REVERT: K 31 ASP cc_start: 0.8124 (m-30) cc_final: 0.7587 (m-30) outliers start: 71 outliers final: 56 residues processed: 292 average time/residue: 0.1259 time to fit residues: 57.4570 Evaluate side-chains 284 residues out of total 2031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 226 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 398 ASN Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain L residue 24 GLN Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 79 THR Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 82 SER Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 188 ASN Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 615 SER Chi-restraints excluded: chain D residue 652 GLN Chi-restraints excluded: chain D residue 661 LEU Chi-restraints excluded: chain E residue 24 GLN Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 30 SER Chi-restraints excluded: chain F residue 79 THR Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 82 SER Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 213 ILE Chi-restraints excluded: chain G residue 434 MET Chi-restraints excluded: chain G residue 474 ASP Chi-restraints excluded: chain G residue 499 THR Chi-restraints excluded: chain I residue 616 ASN Chi-restraints excluded: chain I residue 637 ASN Chi-restraints excluded: chain I residue 661 LEU Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 47 LEU Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 106 VAL Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 79 THR Chi-restraints excluded: chain K residue 82 MET Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain K residue 108 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 87 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 110 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 194 optimal weight: 0.6980 chunk 27 optimal weight: 9.9990 chunk 148 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 178 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN A 478 ASN L 37 GLN G 478 ASN I 637 ASN J 37 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.110436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.085354 restraints weight = 34954.402| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 3.67 r_work: 0.3072 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.4298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 19758 Z= 0.156 Angle : 0.591 9.810 26985 Z= 0.305 Chirality : 0.043 0.140 3219 Planarity : 0.004 0.044 3303 Dihedral : 5.869 44.737 3891 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.40 % Allowed : 12.60 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % 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: 0.44 (0.17), residues: 2313 helix: 1.87 (0.29), residues: 375 sheet: 0.50 (0.19), residues: 684 loop : -0.27 (0.17), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 61 TYR 0.028 0.001 TYR I 638 PHE 0.013 0.001 PHE C 383 TRP 0.012 0.001 TRP G 69 HIS 0.005 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00364 (19650) covalent geometry : angle 0.56824 (26703) SS BOND : bond 0.00388 ( 42) SS BOND : angle 0.99748 ( 84) hydrogen bonds : bond 0.04592 ( 732) hydrogen bonds : angle 4.75990 ( 1908) link_ALPHA1-3 : bond 0.01340 ( 3) link_ALPHA1-3 : angle 1.31159 ( 9) link_BETA1-4 : bond 0.00424 ( 15) link_BETA1-4 : angle 1.50065 ( 45) link_NAG-ASN : bond 0.00259 ( 48) link_NAG-ASN : angle 2.05175 ( 144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 238 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8071 (mmmt) cc_final: 0.7402 (mmtt) REVERT: A 72 HIS cc_start: 0.6701 (p-80) cc_final: 0.6028 (m-70) REVERT: A 114 GLN cc_start: 0.8603 (tt0) cc_final: 0.8228 (tt0) REVERT: B 535 MET cc_start: 0.8631 (mtp) cc_final: 0.8317 (mtt) REVERT: B 543 ASN cc_start: 0.8445 (m110) cc_final: 0.8139 (m110) REVERT: B 621 GLU cc_start: 0.8030 (tm-30) cc_final: 0.7685 (tm-30) REVERT: B 632 ASP cc_start: 0.8770 (t70) cc_final: 0.8485 (t0) REVERT: B 654 GLU cc_start: 0.8140 (mm-30) cc_final: 0.7637 (mt-10) REVERT: L 3 VAL cc_start: 0.8322 (t) cc_final: 0.8028 (m) REVERT: L 4 MET cc_start: 0.7946 (mmm) cc_final: 0.7593 (mmm) REVERT: L 23 CYS cc_start: 0.6756 (t) cc_final: 0.5124 (t) REVERT: L 48 ILE cc_start: 0.8973 (mt) cc_final: 0.8729 (mm) REVERT: H 38 ARG cc_start: 0.7458 (ptt180) cc_final: 0.6989 (ptt180) REVERT: H 59 TYR cc_start: 0.7692 (m-80) cc_final: 0.7387 (m-80) REVERT: C 53 PHE cc_start: 0.7930 (p90) cc_final: 0.7726 (p90) REVERT: C 72 HIS cc_start: 0.6697 (p-80) cc_final: 0.5764 (m170) REVERT: D 543 ASN cc_start: 0.8770 (m110) cc_final: 0.8383 (m110) REVERT: D 621 GLU cc_start: 0.8280 (tt0) cc_final: 0.7823 (pt0) REVERT: D 632 ASP cc_start: 0.8930 (t70) cc_final: 0.8483 (t0) REVERT: D 661 LEU cc_start: 0.6883 (OUTLIER) cc_final: 0.6601 (mm) REVERT: E 63 LYS cc_start: 0.7190 (ttmm) cc_final: 0.6781 (mtpp) REVERT: E 89 GLN cc_start: 0.9107 (OUTLIER) cc_final: 0.8865 (tt0) REVERT: F 31 ASP cc_start: 0.7927 (m-30) cc_final: 0.7445 (m-30) REVERT: F 38 ARG cc_start: 0.7650 (ptt180) cc_final: 0.7133 (ptt180) REVERT: F 100 VAL cc_start: 0.8638 (t) cc_final: 0.8308 (p) REVERT: G 46 LYS cc_start: 0.8081 (mmmt) cc_final: 0.7753 (mmtt) REVERT: G 72 HIS cc_start: 0.6534 (p-80) cc_final: 0.5768 (m-70) REVERT: G 161 MET cc_start: 0.8478 (ttm) cc_final: 0.8186 (ttm) REVERT: I 621 GLU cc_start: 0.7612 (mt-10) cc_final: 0.7401 (mp0) REVERT: I 632 ASP cc_start: 0.8793 (t70) cc_final: 0.8268 (t0) REVERT: J 4 MET cc_start: 0.8645 (tpt) cc_final: 0.7791 (tpt) REVERT: J 63 LYS cc_start: 0.7762 (ttmm) cc_final: 0.7313 (mtpp) REVERT: K 100 VAL cc_start: 0.8661 (t) cc_final: 0.8325 (p) outliers start: 69 outliers final: 55 residues processed: 290 average time/residue: 0.1217 time to fit residues: 54.8943 Evaluate side-chains 280 residues out of total 2031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 223 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 652 GLN Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain L residue 24 GLN Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 82 SER Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 652 GLN Chi-restraints excluded: chain D residue 661 LEU Chi-restraints excluded: chain E residue 24 GLN Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 89 GLN Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 30 SER Chi-restraints excluded: chain F residue 79 THR Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 82 SER Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 474 ASP Chi-restraints excluded: chain G residue 488 VAL Chi-restraints excluded: chain G residue 499 THR Chi-restraints excluded: chain I residue 616 ASN Chi-restraints excluded: chain I residue 661 LEU Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 24 GLN Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 47 LEU Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 106 VAL Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 82 MET Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain K residue 108 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 83 optimal weight: 4.9990 chunk 177 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 85 optimal weight: 0.9980 chunk 27 optimal weight: 10.0000 chunk 176 optimal weight: 4.9990 chunk 49 optimal weight: 7.9990 chunk 143 optimal weight: 7.9990 chunk 153 optimal weight: 5.9990 chunk 215 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN A 398 ASN C 398 ASN I 575 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.108710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.081917 restraints weight = 36304.214| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 3.72 r_work: 0.3004 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.4505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.062 19758 Z= 0.337 Angle : 0.739 7.347 26985 Z= 0.382 Chirality : 0.048 0.182 3219 Planarity : 0.005 0.050 3303 Dihedral : 6.350 45.540 3891 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 3.79 % Allowed : 13.00 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.17), residues: 2313 helix: 1.26 (0.28), residues: 387 sheet: 0.41 (0.18), residues: 726 loop : -0.51 (0.17), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 61 TYR 0.034 0.002 TYR I 638 PHE 0.021 0.003 PHE A 383 TRP 0.016 0.002 TRP G 69 HIS 0.008 0.002 HIS G 374 Details of bonding type rmsd covalent geometry : bond 0.00807 (19650) covalent geometry : angle 0.71611 (26703) SS BOND : bond 0.00615 ( 42) SS BOND : angle 1.38632 ( 84) hydrogen bonds : bond 0.05587 ( 732) hydrogen bonds : angle 5.01281 ( 1908) link_ALPHA1-3 : bond 0.01211 ( 3) link_ALPHA1-3 : angle 1.41810 ( 9) link_BETA1-4 : bond 0.00524 ( 15) link_BETA1-4 : angle 1.91197 ( 45) link_NAG-ASN : bond 0.00530 ( 48) link_NAG-ASN : angle 2.22485 ( 144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 225 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8127 (mmmt) cc_final: 0.7541 (mmtt) REVERT: A 72 HIS cc_start: 0.6768 (p-80) cc_final: 0.6098 (m-70) REVERT: A 114 GLN cc_start: 0.8615 (tt0) cc_final: 0.8269 (tt0) REVERT: A 198 THR cc_start: 0.9443 (OUTLIER) cc_final: 0.9106 (p) REVERT: B 535 MET cc_start: 0.8680 (mtp) cc_final: 0.8375 (mtt) REVERT: B 543 ASN cc_start: 0.8628 (m110) cc_final: 0.8297 (m110) REVERT: B 621 GLU cc_start: 0.8065 (tm-30) cc_final: 0.7526 (tm-30) REVERT: B 632 ASP cc_start: 0.8815 (t70) cc_final: 0.8505 (t0) REVERT: L 3 VAL cc_start: 0.8370 (t) cc_final: 0.8047 (m) REVERT: L 4 MET cc_start: 0.8008 (mmm) cc_final: 0.7233 (ttm) REVERT: L 23 CYS cc_start: 0.6965 (t) cc_final: 0.6060 (t) REVERT: H 38 ARG cc_start: 0.7577 (ptt180) cc_final: 0.7109 (ptt180) REVERT: C 46 LYS cc_start: 0.8112 (mmtt) cc_final: 0.7868 (mmtt) REVERT: C 53 PHE cc_start: 0.8064 (p90) cc_final: 0.7822 (p90) REVERT: C 72 HIS cc_start: 0.6838 (p-80) cc_final: 0.6089 (m170) REVERT: D 535 MET cc_start: 0.8601 (mtp) cc_final: 0.8180 (mtt) REVERT: D 543 ASN cc_start: 0.8794 (m110) cc_final: 0.8316 (m110) REVERT: D 632 ASP cc_start: 0.9011 (t70) cc_final: 0.8381 (t0) REVERT: D 661 LEU cc_start: 0.7054 (OUTLIER) cc_final: 0.6777 (mm) REVERT: E 63 LYS cc_start: 0.7268 (ttmm) cc_final: 0.6823 (mtpp) REVERT: E 89 GLN cc_start: 0.9216 (OUTLIER) cc_final: 0.8812 (tt0) REVERT: F 31 ASP cc_start: 0.7999 (m-30) cc_final: 0.7495 (m-30) REVERT: F 100 VAL cc_start: 0.8735 (t) cc_final: 0.8373 (p) REVERT: G 46 LYS cc_start: 0.8166 (mmmt) cc_final: 0.7839 (mmtt) REVERT: G 72 HIS cc_start: 0.6713 (p-80) cc_final: 0.6012 (m-70) REVERT: G 161 MET cc_start: 0.8549 (ttm) cc_final: 0.8333 (ttm) REVERT: G 207 LYS cc_start: 0.9009 (tptt) cc_final: 0.8595 (pttm) REVERT: I 621 GLU cc_start: 0.7582 (mt-10) cc_final: 0.7346 (mp0) REVERT: I 632 ASP cc_start: 0.8778 (t70) cc_final: 0.8265 (t0) REVERT: J 4 MET cc_start: 0.8720 (tpt) cc_final: 0.8195 (tpt) REVERT: K 100 VAL cc_start: 0.8683 (t) cc_final: 0.8359 (p) outliers start: 77 outliers final: 67 residues processed: 287 average time/residue: 0.1249 time to fit residues: 55.8152 Evaluate side-chains 288 residues out of total 2031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 218 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 398 ASN Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 24 GLN Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 79 THR Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 82 SER Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 398 ASN Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 661 LEU Chi-restraints excluded: chain E residue 24 GLN Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 89 GLN Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 30 SER Chi-restraints excluded: chain F residue 79 THR Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 82 SER Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 377 ASN Chi-restraints excluded: chain G residue 443 ILE Chi-restraints excluded: chain G residue 488 VAL Chi-restraints excluded: chain G residue 499 THR Chi-restraints excluded: chain I residue 616 ASN Chi-restraints excluded: chain I residue 661 LEU Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 24 GLN Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 47 LEU Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 106 VAL Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 79 THR Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain K residue 108 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 150 optimal weight: 10.0000 chunk 218 optimal weight: 0.2980 chunk 3 optimal weight: 0.0470 chunk 64 optimal weight: 2.9990 chunk 223 optimal weight: 0.9990 chunk 164 optimal weight: 0.9980 chunk 117 optimal weight: 0.9990 chunk 138 optimal weight: 9.9990 chunk 43 optimal weight: 7.9990 chunk 123 optimal weight: 5.9990 chunk 90 optimal weight: 1.9990 overall best weight: 0.6682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 398 ASN C 398 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.111248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.086278 restraints weight = 34780.748| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 3.67 r_work: 0.3114 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.4619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19758 Z= 0.118 Angle : 0.574 8.253 26985 Z= 0.296 Chirality : 0.043 0.157 3219 Planarity : 0.004 0.041 3303 Dihedral : 5.734 43.165 3891 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.61 % Allowed : 14.08 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % 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: 0.28 (0.17), residues: 2313 helix: 1.66 (0.28), residues: 387 sheet: 0.40 (0.19), residues: 690 loop : -0.37 (0.17), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 61 TYR 0.020 0.001 TYR E 95D PHE 0.016 0.001 PHE G 53 TRP 0.018 0.001 TRP A 69 HIS 0.003 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00261 (19650) covalent geometry : angle 0.55190 (26703) SS BOND : bond 0.00250 ( 42) SS BOND : angle 0.88852 ( 84) hydrogen bonds : bond 0.04206 ( 732) hydrogen bonds : angle 4.64014 ( 1908) link_ALPHA1-3 : bond 0.01264 ( 3) link_ALPHA1-3 : angle 1.17564 ( 9) link_BETA1-4 : bond 0.00467 ( 15) link_BETA1-4 : angle 1.42916 ( 45) link_NAG-ASN : bond 0.00223 ( 48) link_NAG-ASN : angle 2.00944 ( 144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 251 time to evaluate : 0.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8088 (mmmt) cc_final: 0.7515 (mmtt) REVERT: A 72 HIS cc_start: 0.6736 (p-80) cc_final: 0.6058 (m-70) REVERT: A 114 GLN cc_start: 0.8600 (tt0) cc_final: 0.8279 (tt0) REVERT: A 198 THR cc_start: 0.9408 (OUTLIER) cc_final: 0.9089 (p) REVERT: B 535 MET cc_start: 0.8727 (mtp) cc_final: 0.8398 (mtt) REVERT: B 543 ASN cc_start: 0.8451 (m110) cc_final: 0.8147 (m110) REVERT: B 621 GLU cc_start: 0.8149 (tm-30) cc_final: 0.7644 (tm-30) REVERT: B 632 ASP cc_start: 0.8817 (t70) cc_final: 0.8533 (t0) REVERT: B 638 TYR cc_start: 0.8090 (m-80) cc_final: 0.7532 (m-10) REVERT: L 3 VAL cc_start: 0.8332 (t) cc_final: 0.8068 (m) REVERT: L 23 CYS cc_start: 0.6623 (t) cc_final: 0.5640 (t) REVERT: L 48 ILE cc_start: 0.8954 (mt) cc_final: 0.8752 (mm) REVERT: L 89 GLN cc_start: 0.8872 (tt0) cc_final: 0.8586 (pt0) REVERT: H 38 ARG cc_start: 0.7504 (ptt180) cc_final: 0.7077 (ptt180) REVERT: H 100 VAL cc_start: 0.8727 (t) cc_final: 0.8421 (p) REVERT: C 46 LYS cc_start: 0.8143 (mmtt) cc_final: 0.7901 (mmtt) REVERT: C 72 HIS cc_start: 0.6855 (p-80) cc_final: 0.6063 (m170) REVERT: C 198 THR cc_start: 0.9517 (OUTLIER) cc_final: 0.9248 (p) REVERT: D 535 MET cc_start: 0.8722 (mtp) cc_final: 0.8331 (mtt) REVERT: D 543 ASN cc_start: 0.8738 (m110) cc_final: 0.8390 (m110) REVERT: D 621 GLU cc_start: 0.8304 (tt0) cc_final: 0.7910 (tm-30) REVERT: D 632 ASP cc_start: 0.8979 (t70) cc_final: 0.8383 (t0) REVERT: D 661 LEU cc_start: 0.6867 (OUTLIER) cc_final: 0.6616 (mm) REVERT: E 63 LYS cc_start: 0.7220 (ttmm) cc_final: 0.6772 (mtpp) REVERT: F 31 ASP cc_start: 0.7988 (m-30) cc_final: 0.7480 (m-30) REVERT: F 38 ARG cc_start: 0.7682 (ptt180) cc_final: 0.7281 (ptt180) REVERT: F 100 VAL cc_start: 0.8661 (t) cc_final: 0.8367 (p) REVERT: G 46 LYS cc_start: 0.8125 (mmmt) cc_final: 0.7814 (mmtt) REVERT: G 53 PHE cc_start: 0.8107 (p90) cc_final: 0.7905 (p90) REVERT: G 72 HIS cc_start: 0.6671 (p-80) cc_final: 0.5901 (m-70) REVERT: G 161 MET cc_start: 0.8508 (ttm) cc_final: 0.8210 (ttm) REVERT: G 207 LYS cc_start: 0.8995 (tptt) cc_final: 0.8581 (pttm) REVERT: I 632 ASP cc_start: 0.8731 (t70) cc_final: 0.8226 (t0) REVERT: J 4 MET cc_start: 0.8684 (tpt) cc_final: 0.8162 (tpt) REVERT: J 63 LYS cc_start: 0.7768 (ttmm) cc_final: 0.7356 (mtpp) REVERT: K 100 VAL cc_start: 0.8689 (t) cc_final: 0.8408 (p) outliers start: 53 outliers final: 36 residues processed: 289 average time/residue: 0.1282 time to fit residues: 57.7730 Evaluate side-chains 274 residues out of total 2031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 235 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 398 ASN Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 652 GLN Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 24 GLN Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 398 ASN Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 652 GLN Chi-restraints excluded: chain D residue 661 LEU Chi-restraints excluded: chain E residue 24 GLN Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain G residue 199 SER Chi-restraints excluded: chain G residue 377 ASN Chi-restraints excluded: chain G residue 488 VAL Chi-restraints excluded: chain G residue 499 THR Chi-restraints excluded: chain I residue 616 ASN Chi-restraints excluded: chain I residue 661 LEU Chi-restraints excluded: chain J residue 47 LEU Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 108 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 120 optimal weight: 7.9990 chunk 0 optimal weight: 6.9990 chunk 113 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 185 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 195 optimal weight: 0.5980 chunk 225 optimal weight: 3.9990 chunk 172 optimal weight: 0.7980 chunk 46 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 478 ASN G 398 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.111643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.086673 restraints weight = 34897.862| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 3.68 r_work: 0.3095 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.4713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 19758 Z= 0.120 Angle : 0.577 9.125 26985 Z= 0.295 Chirality : 0.043 0.162 3219 Planarity : 0.004 0.046 3303 Dihedral : 5.463 41.930 3891 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.22 % Allowed : 14.67 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % 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: 0.39 (0.17), residues: 2313 helix: 1.78 (0.28), residues: 384 sheet: 0.56 (0.19), residues: 720 loop : -0.40 (0.17), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 61 TYR 0.016 0.001 TYR E 95D PHE 0.015 0.001 PHE A 53 TRP 0.015 0.001 TRP D 571 HIS 0.003 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00271 (19650) covalent geometry : angle 0.55467 (26703) SS BOND : bond 0.00306 ( 42) SS BOND : angle 0.96089 ( 84) hydrogen bonds : bond 0.04051 ( 732) hydrogen bonds : angle 4.52581 ( 1908) link_ALPHA1-3 : bond 0.01133 ( 3) link_ALPHA1-3 : angle 1.11917 ( 9) link_BETA1-4 : bond 0.00457 ( 15) link_BETA1-4 : angle 1.43026 ( 45) link_NAG-ASN : bond 0.00223 ( 48) link_NAG-ASN : angle 2.00730 ( 144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 248 time to evaluate : 0.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8103 (mmmt) cc_final: 0.7514 (mmtt) REVERT: A 72 HIS cc_start: 0.6703 (p-80) cc_final: 0.6053 (m-70) REVERT: A 114 GLN cc_start: 0.8539 (tt0) cc_final: 0.8199 (tt0) REVERT: A 198 THR cc_start: 0.9353 (OUTLIER) cc_final: 0.9065 (p) REVERT: B 535 MET cc_start: 0.8608 (mtp) cc_final: 0.8275 (mtt) REVERT: B 543 ASN cc_start: 0.8414 (m110) cc_final: 0.8091 (m110) REVERT: B 621 GLU cc_start: 0.8172 (tm-30) cc_final: 0.7683 (tm-30) REVERT: B 632 ASP cc_start: 0.8751 (t70) cc_final: 0.8499 (t0) REVERT: L 3 VAL cc_start: 0.8324 (t) cc_final: 0.8056 (m) REVERT: L 4 MET cc_start: 0.8137 (mmm) cc_final: 0.7570 (tpp) REVERT: L 5 THR cc_start: 0.8178 (OUTLIER) cc_final: 0.7751 (p) REVERT: L 23 CYS cc_start: 0.6765 (t) cc_final: 0.6077 (t) REVERT: L 48 ILE cc_start: 0.8793 (mt) cc_final: 0.8560 (mm) REVERT: H 38 ARG cc_start: 0.7456 (ptt180) cc_final: 0.6987 (ptt180) REVERT: H 46 GLU cc_start: 0.7629 (tp30) cc_final: 0.7428 (tp30) REVERT: H 100 VAL cc_start: 0.8592 (t) cc_final: 0.8254 (p) REVERT: C 46 LYS cc_start: 0.8064 (mmtt) cc_final: 0.7834 (mmtt) REVERT: C 72 HIS cc_start: 0.6919 (p-80) cc_final: 0.6189 (m170) REVERT: C 198 THR cc_start: 0.9465 (OUTLIER) cc_final: 0.9255 (p) REVERT: D 535 MET cc_start: 0.8638 (mtp) cc_final: 0.8204 (mtt) REVERT: D 543 ASN cc_start: 0.8673 (m110) cc_final: 0.8306 (m110) REVERT: D 621 GLU cc_start: 0.8295 (tt0) cc_final: 0.8082 (tm-30) REVERT: D 632 ASP cc_start: 0.8937 (t70) cc_final: 0.8277 (t0) REVERT: E 48 ILE cc_start: 0.8839 (mt) cc_final: 0.8605 (mm) REVERT: E 63 LYS cc_start: 0.7142 (ttmm) cc_final: 0.6771 (mtpp) REVERT: F 31 ASP cc_start: 0.7922 (m-30) cc_final: 0.7417 (m-30) REVERT: F 38 ARG cc_start: 0.7521 (ptt180) cc_final: 0.7101 (ptt180) REVERT: F 100 VAL cc_start: 0.8691 (t) cc_final: 0.8396 (p) REVERT: G 46 LYS cc_start: 0.8054 (mmmt) cc_final: 0.7790 (mmtt) REVERT: G 72 HIS cc_start: 0.6701 (p-80) cc_final: 0.5955 (m-70) REVERT: G 161 MET cc_start: 0.8455 (ttm) cc_final: 0.8156 (ttm) REVERT: G 207 LYS cc_start: 0.8981 (tptt) cc_final: 0.8541 (pttm) REVERT: I 632 ASP cc_start: 0.8682 (t70) cc_final: 0.8223 (t0) REVERT: J 4 MET cc_start: 0.8582 (tpt) cc_final: 0.7960 (tpt) REVERT: J 63 LYS cc_start: 0.7706 (ttmm) cc_final: 0.7309 (mtpp) REVERT: K 100 VAL cc_start: 0.8534 (t) cc_final: 0.8199 (p) outliers start: 45 outliers final: 33 residues processed: 283 average time/residue: 0.1246 time to fit residues: 54.7225 Evaluate side-chains 275 residues out of total 2031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 239 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 652 GLN Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 24 GLN Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 478 ASN Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 652 GLN Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain G residue 377 ASN Chi-restraints excluded: chain G residue 474 ASP Chi-restraints excluded: chain G residue 488 VAL Chi-restraints excluded: chain G residue 499 THR Chi-restraints excluded: chain I residue 616 ASN Chi-restraints excluded: chain I residue 661 LEU Chi-restraints excluded: chain J residue 24 GLN Chi-restraints excluded: chain J residue 47 LEU Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 108 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 135 optimal weight: 0.7980 chunk 178 optimal weight: 0.3980 chunk 110 optimal weight: 3.9990 chunk 169 optimal weight: 0.8980 chunk 44 optimal weight: 9.9990 chunk 127 optimal weight: 9.9990 chunk 77 optimal weight: 5.9990 chunk 32 optimal weight: 0.5980 chunk 52 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 153 optimal weight: 6.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 478 ASN C 478 ASN G 398 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.111531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.086618 restraints weight = 35124.030| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 3.68 r_work: 0.3094 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.4780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19758 Z= 0.133 Angle : 0.583 9.629 26985 Z= 0.299 Chirality : 0.043 0.160 3219 Planarity : 0.004 0.045 3303 Dihedral : 5.349 41.599 3891 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.02 % Allowed : 15.16 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % 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: 0.36 (0.17), residues: 2313 helix: 1.83 (0.28), residues: 384 sheet: 0.46 (0.19), residues: 690 loop : -0.35 (0.17), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 61 TYR 0.028 0.002 TYR J 95D PHE 0.011 0.001 PHE C 383 TRP 0.023 0.001 TRP D 571 HIS 0.004 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00308 (19650) covalent geometry : angle 0.56068 (26703) SS BOND : bond 0.00360 ( 42) SS BOND : angle 1.12305 ( 84) hydrogen bonds : bond 0.04024 ( 732) hydrogen bonds : angle 4.46734 ( 1908) link_ALPHA1-3 : bond 0.01066 ( 3) link_ALPHA1-3 : angle 1.11265 ( 9) link_BETA1-4 : bond 0.00453 ( 15) link_BETA1-4 : angle 1.45371 ( 45) link_NAG-ASN : bond 0.00225 ( 48) link_NAG-ASN : angle 1.96515 ( 144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 248 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8080 (mmmt) cc_final: 0.7485 (mmtt) REVERT: A 72 HIS cc_start: 0.6743 (p-80) cc_final: 0.6019 (m-70) REVERT: A 114 GLN cc_start: 0.8548 (tt0) cc_final: 0.8215 (tt0) REVERT: A 198 THR cc_start: 0.9350 (OUTLIER) cc_final: 0.9114 (p) REVERT: B 535 MET cc_start: 0.8661 (mtp) cc_final: 0.8337 (mtt) REVERT: B 543 ASN cc_start: 0.8449 (m110) cc_final: 0.8123 (m110) REVERT: B 621 GLU cc_start: 0.8183 (tm-30) cc_final: 0.7696 (tm-30) REVERT: B 632 ASP cc_start: 0.8766 (t70) cc_final: 0.8508 (t0) REVERT: L 3 VAL cc_start: 0.8370 (t) cc_final: 0.8097 (m) REVERT: L 5 THR cc_start: 0.8128 (OUTLIER) cc_final: 0.7769 (p) REVERT: L 23 CYS cc_start: 0.6776 (t) cc_final: 0.5848 (t) REVERT: L 48 ILE cc_start: 0.8841 (mt) cc_final: 0.8632 (mm) REVERT: L 63 LYS cc_start: 0.7065 (ttmm) cc_final: 0.6709 (mtpp) REVERT: H 100 VAL cc_start: 0.8580 (t) cc_final: 0.8247 (p) REVERT: C 46 LYS cc_start: 0.8013 (mmtt) cc_final: 0.7775 (mmtt) REVERT: C 72 HIS cc_start: 0.6995 (p-80) cc_final: 0.6182 (m170) REVERT: C 198 THR cc_start: 0.9433 (OUTLIER) cc_final: 0.9231 (p) REVERT: D 535 MET cc_start: 0.8653 (mtp) cc_final: 0.8222 (mtt) REVERT: D 543 ASN cc_start: 0.8683 (m110) cc_final: 0.8310 (m110) REVERT: D 621 GLU cc_start: 0.8293 (tt0) cc_final: 0.7939 (tm-30) REVERT: D 632 ASP cc_start: 0.8925 (t70) cc_final: 0.8277 (t0) REVERT: E 48 ILE cc_start: 0.8936 (mt) cc_final: 0.8698 (mm) REVERT: E 63 LYS cc_start: 0.7242 (ttmm) cc_final: 0.6879 (mtpp) REVERT: F 31 ASP cc_start: 0.7888 (m-30) cc_final: 0.7389 (m-30) REVERT: F 38 ARG cc_start: 0.7581 (ptt180) cc_final: 0.7153 (ptt180) REVERT: F 100 VAL cc_start: 0.8710 (t) cc_final: 0.8440 (p) REVERT: G 46 LYS cc_start: 0.8049 (mmmt) cc_final: 0.7836 (mmtt) REVERT: G 72 HIS cc_start: 0.6678 (p-80) cc_final: 0.5923 (m-70) REVERT: G 161 MET cc_start: 0.8473 (ttm) cc_final: 0.8188 (ttm) REVERT: I 626 MET cc_start: 0.8537 (ttp) cc_final: 0.8328 (ttp) REVERT: I 632 ASP cc_start: 0.8675 (t70) cc_final: 0.8183 (t0) REVERT: J 4 MET cc_start: 0.8589 (tpt) cc_final: 0.7944 (tpt) REVERT: J 63 LYS cc_start: 0.7720 (ttmm) cc_final: 0.7330 (mtpp) REVERT: K 100 VAL cc_start: 0.8576 (t) cc_final: 0.8224 (p) outliers start: 41 outliers final: 32 residues processed: 280 average time/residue: 0.1196 time to fit residues: 52.4746 Evaluate side-chains 277 residues out of total 2031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 242 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 24 GLN Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 652 GLN Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain G residue 377 ASN Chi-restraints excluded: chain G residue 398 ASN Chi-restraints excluded: chain G residue 488 VAL Chi-restraints excluded: chain G residue 499 THR Chi-restraints excluded: chain I residue 616 ASN Chi-restraints excluded: chain I residue 661 LEU Chi-restraints excluded: chain J residue 24 GLN Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 47 LEU Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 29 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 147 optimal weight: 0.7980 chunk 44 optimal weight: 10.0000 chunk 198 optimal weight: 7.9990 chunk 187 optimal weight: 2.9990 chunk 126 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 139 optimal weight: 7.9990 chunk 161 optimal weight: 0.7980 chunk 192 optimal weight: 0.8980 chunk 116 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 478 ASN E 37 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.111639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.086841 restraints weight = 34910.530| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 3.67 r_work: 0.3098 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.4820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19758 Z= 0.132 Angle : 0.594 16.557 26985 Z= 0.302 Chirality : 0.043 0.158 3219 Planarity : 0.004 0.045 3303 Dihedral : 5.283 40.799 3891 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.02 % Allowed : 15.31 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % 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: 0.40 (0.17), residues: 2313 helix: 1.79 (0.28), residues: 387 sheet: 0.55 (0.19), residues: 720 loop : -0.38 (0.17), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 61 TYR 0.029 0.002 TYR J 95D PHE 0.014 0.001 PHE G 53 TRP 0.031 0.001 TRP D 571 HIS 0.004 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00305 (19650) covalent geometry : angle 0.57159 (26703) SS BOND : bond 0.00248 ( 42) SS BOND : angle 1.35702 ( 84) hydrogen bonds : bond 0.03971 ( 732) hydrogen bonds : angle 4.44261 ( 1908) link_ALPHA1-3 : bond 0.01043 ( 3) link_ALPHA1-3 : angle 1.12379 ( 9) link_BETA1-4 : bond 0.00463 ( 15) link_BETA1-4 : angle 1.45419 ( 45) link_NAG-ASN : bond 0.00219 ( 48) link_NAG-ASN : angle 1.93067 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3521.79 seconds wall clock time: 62 minutes 35.00 seconds (3755.00 seconds total)