Starting phenix.real_space_refine on Sun Aug 24 23:11:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cu5_45928/08_2025/9cu5_45928.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cu5_45928/08_2025/9cu5_45928.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9cu5_45928/08_2025/9cu5_45928.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cu5_45928/08_2025/9cu5_45928.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9cu5_45928/08_2025/9cu5_45928.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cu5_45928/08_2025/9cu5_45928.map" } resolution = 3.4 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= -0.000 sd= 0.020 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 152 5.16 5 C 14786 2.51 5 N 3954 2.21 5 O 4646 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23538 Number of models: 1 Model: "" Number of chains: 26 Chain: "D" Number of atoms: 1009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1009 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 6, 'TRANS': 122} Chain: "E" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 851 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 7, 'TRANS': 104} Chain: "F" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1003 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 6, 'TRANS': 121} Chain: "G" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 851 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 7, 'TRANS': 104} Chain: "J" Number of atoms: 1009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1009 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 6, 'TRANS': 122} Chain: "K" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 851 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 7, 'TRANS': 104} Chain: "H" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 947 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 7, 'TRANS': 113} Chain: "L" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 822 Classifications: {'peptide': 106} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 99} Chain: "I" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 947 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 7, 'TRANS': 113} Chain: "M" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 822 Classifications: {'peptide': 106} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 99} Chain: "C" Number of atoms: 4529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 569, 4529 Classifications: {'peptide': 569} Link IDs: {'PTRANS': 23, 'TRANS': 545} Chain breaks: 6 Chain: "B" Number of atoms: 4466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 561, 4466 Classifications: {'peptide': 561} Link IDs: {'PTRANS': 23, 'TRANS': 537} Chain breaks: 6 Chain: "A" Number of atoms: 4405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 554, 4405 Classifications: {'peptide': 554} Link IDs: {'PTRANS': 23, 'TRANS': 530} Chain breaks: 7 Chain: "N" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "Q" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 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: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "U" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 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: "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: "B" 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: "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 Time building chain proxies: 4.81, per 1000 atoms: 0.20 Number of scatterers: 23538 At special positions: 0 Unit cell: (156.932, 136.418, 133.341, 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 152 16.00 O 4646 8.00 N 3954 7.00 C 14786 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=46, symmetry=0 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.04 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=1.81 Simple disulfide: pdb=" SG CYS E 89 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.04 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=1.55 Simple disulfide: pdb=" SG CYS G 89 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.02 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Simple disulfide: pdb=" SG CYS K 89 " - pdb=" SG CYS K 96 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=1.95 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=1.80 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 B 662 " distance=2.03 Simple disulfide: pdb=" SG CYS C 598 " - pdb=" SG CYS C 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS A 501 " distance=2.04 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 74 " distance=2.04 Simple disulfide: pdb=" SG CYS B 119 " - pdb=" SG CYS B 205 " distance=2.03 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 196 " distance=1.91 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 157 " distance=2.03 Simple disulfide: pdb=" SG CYS B 218 " - pdb=" SG CYS B 247 " distance=2.03 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 239 " distance=2.03 Simple disulfide: pdb=" SG CYS B 296 " - pdb=" SG CYS B 331 " distance=2.01 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 445 " distance=2.03 Simple disulfide: pdb=" SG CYS B 385 " - pdb=" SG CYS B 418 " distance=2.03 Simple disulfide: pdb=" SG CYS B 501 " - pdb=" SG CYS A 662 " distance=1.53 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.02 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " 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 ALPHA1-2 " MAN P 4 " - " MAN P 5 " " MAN T 4 " - " MAN T 5 " " MAN T 5 " - " MAN T 6 " " MAN T 8 " - " MAN T 9 " ALPHA1-3 " BMA N 3 " - " MAN N 4 " " BMA P 3 " - " MAN P 4 " " BMA Q 3 " - " MAN Q 4 " " BMA T 3 " - " MAN T 4 " " MAN T 7 " - " MAN T 8 " " BMA U 3 " - " MAN U 4 " " BMA W 3 " - " MAN W 4 " ALPHA1-6 " BMA N 3 " - " MAN N 5 " " BMA Q 3 " - " MAN Q 5 " " BMA T 3 " - " MAN T 7 " " MAN T 7 " - " MAN T 10 " " BMA U 3 " - " MAN U 5 " BETA1-4 " 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 P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " NAG-ASN " NAG A 701 " - " ASN A 160 " " NAG A 702 " - " ASN A 241 " " NAG A 703 " - " ASN A 276 " " NAG A 704 " - " ASN A 295 " " NAG A 705 " - " ASN A 301 " " NAG A 706 " - " ASN A 332 " " NAG A 707 " - " ASN A 362 " " NAG A 708 " - " ASN A 386 " " NAG A 709 " - " ASN A 392 " " NAG A 710 " - " ASN A 448 " " NAG A 711 " - " ASN A 339 " " NAG A 712 " - " ASN A 625 " " NAG B 701 " - " ASN B 160 " " NAG B 702 " - " ASN B 276 " " NAG B 703 " - " ASN B 295 " " NAG B 704 " - " ASN B 301 " " NAG B 705 " - " ASN B 332 " " NAG B 706 " - " ASN B 362 " " NAG B 707 " - " ASN B 386 " " NAG B 708 " - " ASN B 392 " " NAG B 709 " - " ASN B 448 " " NAG B 710 " - " ASN B 339 " " NAG B 711 " - " ASN B 625 " " NAG B 712 " - " ASN B 637 " " NAG C 701 " - " ASN C 160 " " NAG C 702 " - " ASN C 241 " " NAG C 703 " - " ASN C 276 " " NAG C 704 " - " ASN C 295 " " NAG C 705 " - " ASN C 301 " " NAG C 706 " - " ASN C 332 " " NAG C 707 " - " ASN C 362 " " NAG C 708 " - " ASN C 386 " " NAG C 709 " - " ASN C 392 " " NAG C 710 " - " ASN C 448 " " NAG C 711 " - " ASN C 339 " " NAG C 712 " - " ASN C 625 " " NAG N 1 " - " ASN C 88 " " NAG O 1 " - " ASN C 156 " " NAG P 1 " - " ASN C 262 " " NAG Q 1 " - " ASN B 88 " " NAG R 1 " - " ASN B 156 " " NAG S 1 " - " ASN B 241 " " NAG T 1 " - " ASN B 262 " " NAG U 1 " - " ASN A 88 " " NAG V 1 " - " ASN A 156 " " NAG W 1 " - " ASN A 262 " Time building additional restraints: 1.80 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 476.8 nanoseconds 5592 Ramachandran restraints generated. 2796 Oldfield, 0 Emsley, 2796 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5282 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 56 sheets defined 16.9% alpha, 36.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.878A pdb=" N TYR D 32 " --> pdb=" O PHE D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 64 Processing helix chain 'D' and resid 83 through 86 Processing helix chain 'E' and resid 27C through 31 Processing helix chain 'E' and resid 79 through 83 Processing helix chain 'F' and resid 61 through 64 removed outlier: 3.692A pdb=" N GLN F 64 " --> pdb=" O PRO F 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 61 through 64' Processing helix chain 'G' and resid 79 through 83 Processing helix chain 'J' and resid 61 through 64 removed outlier: 4.219A pdb=" N GLN J 64 " --> pdb=" O PRO J 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 61 through 64' Processing helix chain 'J' and resid 83 through 86 Processing helix chain 'K' and resid 26 through 27C Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.880A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 83 through 87 Processing helix chain 'M' and resid 79 through 83 removed outlier: 3.914A pdb=" N PHE M 83 " --> pdb=" O PRO M 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 74 Processing helix chain 'C' and resid 98 through 117 removed outlier: 4.086A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 335 through 353 Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 377 through 381 removed outlier: 3.739A pdb=" N GLU C 381 " --> pdb=" O CYS C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 429 removed outlier: 3.863A pdb=" N ARG C 429 " --> pdb=" O MET C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 481 removed outlier: 3.745A pdb=" N TRP C 479 " --> pdb=" O MET C 475 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER C 481 " --> pdb=" O ASP C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 529 through 536 removed outlier: 3.728A pdb=" N MET C 535 " --> pdb=" O GLY C 531 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR C 536 " --> pdb=" O ALA C 532 " (cutoff:3.500A) Processing helix chain 'C' and resid 536 through 543 removed outlier: 3.818A pdb=" N GLN C 540 " --> pdb=" O THR C 536 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ASN C 543 " --> pdb=" O VAL C 539 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 596 Processing helix chain 'C' and resid 618 through 624 removed outlier: 3.559A pdb=" N ASN C 624 " --> pdb=" O ASP C 620 " (cutoff:3.500A) Processing helix chain 'C' and resid 627 through 635 Processing helix chain 'C' and resid 635 through 649 Processing helix chain 'C' and resid 649 through 661 removed outlier: 3.693A pdb=" N GLN C 658 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLU C 659 " --> pdb=" O LYS C 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 116 removed outlier: 3.958A pdb=" N GLU B 102 " --> pdb=" O ASN B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 126 removed outlier: 4.113A pdb=" N LEU B 125 " --> pdb=" O LEU B 122 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N CYS B 126 " --> pdb=" O THR B 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 122 through 126' Processing helix chain 'B' and resid 335 through 354 removed outlier: 4.367A pdb=" N LYS B 348 " --> pdb=" O GLN B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 373 Processing helix chain 'B' and resid 476 through 481 removed outlier: 3.893A pdb=" N SER B 481 " --> pdb=" O ASP B 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 545 removed outlier: 3.979A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N LEU B 545 " --> pdb=" O ALA B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 596 Processing helix chain 'B' and resid 618 through 623 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 649 Processing helix chain 'B' and resid 650 through 660 Processing helix chain 'A' and resid 98 through 117 removed outlier: 3.704A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 127 Processing helix chain 'A' and resid 334 through 353 removed outlier: 3.641A pdb=" N THR A 341 " --> pdb=" O LYS A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 474 through 481 removed outlier: 3.612A pdb=" N ASN A 478 " --> pdb=" O ASP A 474 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 534 Processing helix chain 'A' and resid 572 through 596 removed outlier: 3.544A pdb=" N LEU A 576 " --> pdb=" O GLY A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 623 Processing helix chain 'A' and resid 627 through 636 Processing helix chain 'A' and resid 638 through 656 Processing sheet with id=AA1, first strand: chain 'D' and resid 3 through 6 Processing sheet with id=AA2, first strand: chain 'D' and resid 3 through 6 Processing sheet with id=AA3, first strand: chain 'D' and resid 57 through 59 removed outlier: 6.873A pdb=" N TRP D 36 " --> pdb=" O MET D 48 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N TRP D 50 " --> pdb=" O ILE D 34 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ILE D 34 " --> pdb=" O TRP D 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 5 through 6 Processing sheet with id=AA5, first strand: chain 'E' and resid 9 through 14 removed outlier: 6.722A pdb=" N VAL E 11 " --> pdb=" O SER E 105 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N LEU E 107 " --> pdb=" O VAL E 11 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N GLY E 13 " --> pdb=" O LEU E 107 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 9 through 14 removed outlier: 6.722A pdb=" N VAL E 11 " --> pdb=" O SER E 105 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N LEU E 107 " --> pdb=" O VAL E 11 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N GLY E 13 " --> pdb=" O LEU E 107 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N SER E 90 " --> pdb=" O VAL E 97 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 5 through 6 Processing sheet with id=AA8, first strand: chain 'F' and resid 57 through 59 removed outlier: 6.511A pdb=" N THR F 40 " --> pdb=" O PRO F 45 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N CYS F 92 " --> pdb=" O TRP F 103 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N TRP F 103 " --> pdb=" O CYS F 92 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N LYS F 94 " --> pdb=" O TYR F 101 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 57 through 59 removed outlier: 6.511A pdb=" N THR F 40 " --> pdb=" O PRO F 45 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 73B through 73E removed outlier: 4.011A pdb=" N VAL F 73D" --> pdb=" O THR F 73H" (cutoff:3.500A) removed outlier: 7.348A pdb=" N THR F 73H" --> pdb=" O VAL F 73D" (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 5 through 6 Processing sheet with id=AB3, first strand: chain 'G' and resid 11 through 14 removed outlier: 3.793A pdb=" N TYR G 36 " --> pdb=" O TYR G 87 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N TRP G 35 " --> pdb=" O ILE G 47 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 11 through 14 removed outlier: 3.696A pdb=" N SER G 90 " --> pdb=" O VAL G 97 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'J' and resid 3 through 6 removed outlier: 4.072A pdb=" N GLY J 26 " --> pdb=" O SER J 74 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N SER J 74 " --> pdb=" O GLY J 26 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'J' and resid 3 through 6 removed outlier: 4.072A pdb=" N GLY J 26 " --> pdb=" O SER J 74 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N SER J 74 " --> pdb=" O GLY J 26 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.505A pdb=" N GLU J 10 " --> pdb=" O THR J 110 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLY J 49 " --> pdb=" O TRP J 36 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N TRP J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N THR J 40 " --> pdb=" O PRO J 45 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.505A pdb=" N GLU J 10 " --> pdb=" O THR J 110 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N CYS J 92 " --> pdb=" O TRP J 103 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N TRP J 103 " --> pdb=" O CYS J 92 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N LYS J 94 " --> pdb=" O TYR J 101 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'K' and resid 5 through 6 Processing sheet with id=AC1, first strand: chain 'K' and resid 9 through 13 removed outlier: 6.814A pdb=" N TRP K 35 " --> pdb=" O ILE K 47 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILE K 47 " --> pdb=" O TRP K 35 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'K' and resid 9 through 13 Processing sheet with id=AC3, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AC4, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.536A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N TYR H 50 " --> pdb=" O TRP H 34 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N TRP H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.536A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N TYR H 50 " --> pdb=" O TRP H 34 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N TRP H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AC7, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.964A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 3 through 7 removed outlier: 3.536A pdb=" N GLN I 3 " --> pdb=" O SER I 25 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N GLN I 77 " --> pdb=" O ASP I 72 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 57 through 59 removed outlier: 6.514A pdb=" N TRP I 36 " --> pdb=" O ILE I 48 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N TYR I 50 " --> pdb=" O TRP I 34 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N TRP I 34 " --> pdb=" O TYR I 50 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N VAL I 102 " --> pdb=" O ARG I 94 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 57 through 59 removed outlier: 6.514A pdb=" N TRP I 36 " --> pdb=" O ILE I 48 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N TYR I 50 " --> pdb=" O TRP I 34 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N TRP I 34 " --> pdb=" O TYR I 50 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'M' and resid 4 through 7 Processing sheet with id=AD3, first strand: chain 'M' and resid 10 through 12 removed outlier: 6.968A pdb=" N LEU M 11 " --> pdb=" O GLU M 105 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N LEU M 33 " --> pdb=" O TYR M 49 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N TYR M 49 " --> pdb=" O LEU M 33 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N TRP M 35 " --> pdb=" O LEU M 47 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 494 through 499 removed outlier: 4.518A pdb=" N VAL C 36 " --> pdb=" O THR C 606 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 45 through 47 removed outlier: 4.494A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 75 through 76 Processing sheet with id=AD7, first strand: chain 'C' and resid 91 through 94 removed outlier: 3.689A pdb=" N GLU C 91 " --> pdb=" O CYS C 239 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AD9, first strand: chain 'C' and resid 200 through 203 removed outlier: 5.766A pdb=" N VAL C 200 " --> pdb=" O ALA C 433 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N TYR C 435 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 259 through 261 removed outlier: 3.846A pdb=" N ILE C 443 " --> pdb=" O ARG C 298 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N GLY C 451 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 10.692A pdb=" N GLU C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 12.164A pdb=" N LEU C 453 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 12.225A pdb=" N LEU C 288 " --> pdb=" O LEU C 453 " (cutoff:3.500A) removed outlier: 10.839A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 11.014A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N GLU C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N SER C 334 " --> pdb=" O GLU C 293 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS C 421 " --> pdb=" O PHE C 382 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 271 through 273 removed outlier: 11.014A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 10.839A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 12.225A pdb=" N LEU C 288 " --> pdb=" O LEU C 453 " (cutoff:3.500A) removed outlier: 12.164A pdb=" N LEU C 453 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 10.692A pdb=" N GLU C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N GLY C 451 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE C 443 " --> pdb=" O ARG C 298 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N THR C 357 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N PHE C 468 " --> pdb=" O THR C 357 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N VAL C 359 " --> pdb=" O PHE C 468 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE C 361 " --> pdb=" O SER C 393 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER C 393 " --> pdb=" O PHE C 361 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 301 through 312 removed outlier: 7.178A pdb=" N ASN C 301 " --> pdb=" O ILE C 323 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N ILE C 323 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ARG C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 494 through 499 removed outlier: 6.791A pdb=" N VAL B 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 45 through 47 removed outlier: 3.809A pdb=" N ILE B 225 " --> pdb=" O VAL B 245 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 75 through 76 Processing sheet with id=AE7, first strand: chain 'B' and resid 92 through 94 Processing sheet with id=AE8, first strand: chain 'B' and resid 170 through 177 Processing sheet with id=AE9, first strand: chain 'B' and resid 200 through 203 removed outlier: 3.584A pdb=" N ALA B 433 " --> pdb=" O VAL B 200 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'B' and resid 259 through 261 removed outlier: 3.818A pdb=" N ILE B 443 " --> pdb=" O ARG B 298 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N CYS B 296 " --> pdb=" O CYS B 445 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'B' and resid 271 through 273 removed outlier: 3.535A pdb=" N LEU B 454 " --> pdb=" O ILE B 284 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N THR B 357 " --> pdb=" O GLU B 466 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N PHE B 468 " --> pdb=" O THR B 357 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N VAL B 359 " --> pdb=" O PHE B 468 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'B' and resid 301 through 312 removed outlier: 7.611A pdb=" N ASN B 301 " --> pdb=" O ILE B 323 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N ILE B 323 " --> pdb=" O ASN B 301 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N THR B 303 " --> pdb=" O GLY B 321 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ARG B 315 " --> pdb=" O ILE B 309 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'B' and resid 329 through 334 removed outlier: 4.043A pdb=" N ALA B 329 " --> pdb=" O CYS B 418 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N PHE B 382 " --> pdb=" O LYS B 421 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'A' and resid 494 through 499 removed outlier: 4.132A pdb=" N VAL A 36 " --> pdb=" O THR A 606 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.719A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'A' and resid 91 through 94 removed outlier: 3.647A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'A' and resid 172 through 177 removed outlier: 3.668A pdb=" N ASN A 156 " --> pdb=" O LYS A 132 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'A' and resid 200 through 203 Processing sheet with id=AG1, first strand: chain 'A' and resid 259 through 261 removed outlier: 3.684A pdb=" N GLY A 451 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N GLY A 451 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 10.896A pdb=" N GLU A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 11.975A pdb=" N LEU A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 12.486A pdb=" N LEU A 288 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 10.439A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 10.707A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 284 through 297 current: chain 'A' and resid 357 through 361 Processing sheet with id=AG2, first strand: chain 'A' and resid 271 through 273 removed outlier: 10.707A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 10.439A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 12.486A pdb=" N LEU A 288 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 11.975A pdb=" N LEU A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 10.896A pdb=" N GLU A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N GLY A 451 " --> pdb=" O GLU A 290 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 447 through 456 current: chain 'A' and resid 416 through 418 875 hydrogen bonds defined for protein. 2256 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: 4.59 Time building geometry restraints manager: 2.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 7288 1.34 - 1.47: 6204 1.47 - 1.59: 10353 1.59 - 1.72: 0 1.72 - 1.85: 204 Bond restraints: 24049 Sorted by residual: bond pdb=" N ILE A 309 " pdb=" CA ILE A 309 " ideal model delta sigma weight residual 1.461 1.502 -0.042 1.19e-02 7.06e+03 1.23e+01 bond pdb=" N CYS A 501 " pdb=" CA CYS A 501 " ideal model delta sigma weight residual 1.453 1.497 -0.044 1.31e-02 5.83e+03 1.11e+01 bond pdb=" N GLY A 312 " pdb=" CA GLY A 312 " ideal model delta sigma weight residual 1.443 1.487 -0.044 1.37e-02 5.33e+03 1.05e+01 bond pdb=" N VAL H 37 " pdb=" CA VAL H 37 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.15e-02 7.56e+03 9.91e+00 bond pdb=" N ILE J 37 " pdb=" CA ILE J 37 " ideal model delta sigma weight residual 1.458 1.493 -0.036 1.14e-02 7.69e+03 9.85e+00 ... (remaining 24044 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.35: 31151 2.35 - 4.70: 1268 4.70 - 7.05: 214 7.05 - 9.40: 16 9.40 - 11.75: 5 Bond angle restraints: 32654 Sorted by residual: angle pdb=" N ILE A 309 " pdb=" CA ILE A 309 " pdb=" C ILE A 309 " ideal model delta sigma weight residual 110.62 116.01 -5.39 1.02e+00 9.61e-01 2.80e+01 angle pdb=" CA ILE A 309 " pdb=" C ILE A 309 " pdb=" O ILE A 309 " ideal model delta sigma weight residual 120.95 116.42 4.53 1.04e+00 9.25e-01 1.90e+01 angle pdb=" CB MET B 629 " pdb=" CG MET B 629 " pdb=" SD MET B 629 " ideal model delta sigma weight residual 112.70 124.45 -11.75 3.00e+00 1.11e-01 1.53e+01 angle pdb=" O ILE A 307 " pdb=" C ILE A 307 " pdb=" N ARG A 308 " ideal model delta sigma weight residual 123.03 118.93 4.10 1.05e+00 9.07e-01 1.53e+01 angle pdb=" CA GLY M 64 " pdb=" C GLY M 64 " pdb=" O GLY M 64 " ideal model delta sigma weight residual 120.94 117.91 3.03 7.80e-01 1.64e+00 1.51e+01 ... (remaining 32649 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.19: 14181 21.19 - 42.37: 916 42.37 - 63.56: 205 63.56 - 84.75: 56 84.75 - 105.93: 15 Dihedral angle restraints: 15373 sinusoidal: 7152 harmonic: 8221 Sorted by residual: dihedral pdb=" CB CYS B 501 " pdb=" SG CYS B 501 " pdb=" SG CYS A 662 " pdb=" CB CYS A 662 " ideal model delta sinusoidal sigma weight residual -86.00 -173.83 87.83 1 1.00e+01 1.00e-02 9.24e+01 dihedral pdb=" CB CYS J 22 " pdb=" SG CYS J 22 " pdb=" SG CYS J 92 " pdb=" CB CYS J 92 " ideal model delta sinusoidal sigma weight residual 93.00 178.16 -85.16 1 1.00e+01 1.00e-02 8.79e+01 dihedral pdb=" CB CYS G 89 " pdb=" SG CYS G 89 " pdb=" SG CYS G 96 " pdb=" CB CYS G 96 " ideal model delta sinusoidal sigma weight residual -86.00 -169.95 83.95 1 1.00e+01 1.00e-02 8.59e+01 ... (remaining 15370 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 3365 0.084 - 0.168: 445 0.168 - 0.252: 25 0.252 - 0.336: 6 0.336 - 0.420: 2 Chirality restraints: 3843 Sorted by residual: chirality pdb=" C1 NAG B 710 " pdb=" ND2 ASN B 339 " pdb=" C2 NAG B 710 " pdb=" O5 NAG B 710 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-01 2.50e+01 4.40e+00 chirality pdb=" C1 NAG V 1 " pdb=" ND2 ASN A 156 " pdb=" C2 NAG V 1 " pdb=" O5 NAG V 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.63e+00 chirality pdb=" C1 NAG A 712 " pdb=" ND2 ASN A 625 " pdb=" C2 NAG A 712 " pdb=" O5 NAG A 712 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-01 2.50e+01 2.61e+00 ... (remaining 3840 not shown) Planarity restraints: 4096 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 522 " 0.037 2.00e-02 2.50e+03 2.75e-02 1.32e+01 pdb=" CG PHE B 522 " -0.061 2.00e-02 2.50e+03 pdb=" CD1 PHE B 522 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE B 522 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE B 522 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE B 522 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE B 522 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO E 39 " -0.053 5.00e-02 4.00e+02 8.06e-02 1.04e+01 pdb=" N PRO E 40 " 0.139 5.00e-02 4.00e+02 pdb=" CA PRO E 40 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO E 40 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 335 " 0.260 9.50e-02 1.11e+02 1.17e-01 1.03e+01 pdb=" NE ARG B 335 " -0.024 2.00e-02 2.50e+03 pdb=" CZ ARG B 335 " 0.021 2.00e-02 2.50e+03 pdb=" NH1 ARG B 335 " -0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG B 335 " 0.001 2.00e-02 2.50e+03 ... (remaining 4093 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 104 2.50 - 3.10: 16877 3.10 - 3.70: 34062 3.70 - 4.30: 49449 4.30 - 4.90: 83798 Nonbonded interactions: 184290 Sorted by model distance: nonbonded pdb=" NH2 ARG H 38 " pdb=" OE2 GLU H 46 " model vdw 1.903 3.120 nonbonded pdb=" NE ARG F 43 " pdb=" OD1 ASP F 85 " model vdw 1.954 3.120 nonbonded pdb=" NH2 ARG M 69 " pdb=" O GLY B 472 " model vdw 1.969 3.120 nonbonded pdb=" NH2 ARG L 42 " pdb=" NE2 GLN L 45 " model vdw 2.116 3.200 nonbonded pdb=" CD2 HIS G 93 " pdb=" OD1 ASN G 94 " model vdw 2.119 3.260 ... (remaining 184285 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 32 through 136 or resid 150 through 503 or resid 520 throu \ gh 712)) selection = (chain 'B' and (resid 32 through 57 or resid 66 through 161 or resid 169 through \ 712)) selection = (chain 'C' and (resid 32 through 57 or resid 66 through 136 or resid 150 through \ 161 or resid 169 through 503 or resid 520 through 712)) } ncs_group { reference = (chain 'D' and resid 2 through 111) selection = chain 'F' selection = (chain 'J' and resid 2 through 111) } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'K' } ncs_group { reference = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'L' selection = chain 'M' } ncs_group { reference = chain 'N' selection = chain 'P' selection = chain 'Q' selection = chain 'U' } ncs_group { reference = chain 'O' selection = chain 'R' selection = chain 'S' 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: 5.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 19.790 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.050 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:0.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 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 : 0.008 0.502 24173 Z= 0.378 Angle : 1.129 32.506 32980 Z= 0.585 Chirality : 0.056 0.420 3843 Planarity : 0.009 0.117 4050 Dihedral : 14.732 105.932 9953 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 0.12 % Allowed : 15.31 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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 aren not related in a simple way. whole: -1.07 (0.15), residues: 2796 helix: -0.11 (0.26), residues: 365 sheet: -0.09 (0.18), residues: 866 loop : -1.22 (0.15), residues: 1565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.035 0.003 ARG E 54 TYR 0.054 0.003 TYR A 39 PHE 0.061 0.003 PHE B 522 TRP 0.024 0.002 TRP F 36 HIS 0.012 0.002 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00599 (24049) covalent geometry : angle 1.05726 (32654) SS BOND : bond 0.11486 ( 46) SS BOND : angle 6.58790 ( 92) hydrogen bonds : bond 0.14500 ( 785) hydrogen bonds : angle 7.44580 ( 2256) link_ALPHA1-2 : bond 0.01160 ( 4) link_ALPHA1-2 : angle 2.87911 ( 12) link_ALPHA1-3 : bond 0.00485 ( 7) link_ALPHA1-3 : angle 1.59683 ( 21) link_ALPHA1-6 : bond 0.00686 ( 5) link_ALPHA1-6 : angle 1.79556 ( 15) link_BETA1-4 : bond 0.00665 ( 16) link_BETA1-4 : angle 2.69307 ( 48) link_NAG-ASN : bond 0.00597 ( 46) link_NAG-ASN : angle 2.69751 ( 138) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5592 Ramachandran restraints generated. 2796 Oldfield, 0 Emsley, 2796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5592 Ramachandran restraints generated. 2796 Oldfield, 0 Emsley, 2796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 529 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 38 ARG cc_start: 0.6890 (ttm-80) cc_final: 0.6323 (mtp-110) REVERT: D 48 MET cc_start: 0.8667 (mtm) cc_final: 0.7696 (mtm) REVERT: D 65 ASP cc_start: 0.8354 (p0) cc_final: 0.7840 (p0) REVERT: D 69 MET cc_start: 0.7754 (mtp) cc_final: 0.7316 (mtm) REVERT: F 58 ASN cc_start: 0.6901 (t0) cc_final: 0.6593 (t0) REVERT: F 63 PHE cc_start: 0.7009 (m-80) cc_final: 0.6770 (m-80) REVERT: F 64 GLN cc_start: 0.8484 (mm-40) cc_final: 0.8272 (mm-40) REVERT: F 80 MET cc_start: 0.8037 (ptm) cc_final: 0.7831 (ptm) REVERT: F 81 GLU cc_start: 0.7350 (tp30) cc_final: 0.6999 (tp30) REVERT: G 17 GLN cc_start: 0.8600 (mp10) cc_final: 0.7991 (mp10) REVERT: G 50 GLU cc_start: 0.8025 (tp30) cc_final: 0.7659 (tt0) REVERT: G 54 ARG cc_start: 0.8299 (ttm110) cc_final: 0.8026 (mtm-85) REVERT: J 36 TRP cc_start: 0.8359 (m100) cc_final: 0.7349 (m100) REVERT: J 82 ARG cc_start: 0.8624 (ptp90) cc_final: 0.8076 (ptp90) REVERT: K 77 ASP cc_start: 0.7312 (t70) cc_final: 0.6866 (t0) REVERT: I 111 VAL cc_start: 0.7987 (t) cc_final: 0.7700 (m) REVERT: C 107 ASP cc_start: 0.8274 (m-30) cc_final: 0.7829 (m-30) REVERT: C 127 VAL cc_start: 0.8661 (t) cc_final: 0.8420 (m) REVERT: C 280 ASN cc_start: 0.8856 (p0) cc_final: 0.8605 (p0) REVERT: C 650 GLN cc_start: 0.7375 (mm-40) cc_final: 0.6981 (mm-40) REVERT: B 91 GLU cc_start: 0.8598 (tp30) cc_final: 0.8219 (mm-30) REVERT: B 164 GLU cc_start: 0.7613 (mm-30) cc_final: 0.6411 (pm20) REVERT: B 330 HIS cc_start: 0.6710 (p-80) cc_final: 0.6482 (p90) REVERT: B 475 MET cc_start: 0.7514 (mmp) cc_final: 0.7246 (mmp) REVERT: B 490 LYS cc_start: 0.8159 (tttp) cc_final: 0.7955 (tttp) REVERT: B 539 VAL cc_start: 0.8554 (p) cc_final: 0.8325 (p) REVERT: B 630 GLU cc_start: 0.8807 (mt-10) cc_final: 0.8581 (mt-10) REVERT: A 330 HIS cc_start: 0.7770 (p-80) cc_final: 0.7254 (p-80) REVERT: A 337 LYS cc_start: 0.8578 (mmtt) cc_final: 0.8210 (mmtt) REVERT: A 373 MET cc_start: 0.7819 (mmt) cc_final: 0.7041 (mmp) REVERT: A 434 MET cc_start: 0.8568 (ttp) cc_final: 0.8146 (ttt) REVERT: A 484 TYR cc_start: 0.8971 (p90) cc_final: 0.8054 (p90) REVERT: A 655 LYS cc_start: 0.8084 (pttt) cc_final: 0.7701 (ptmm) outliers start: 3 outliers final: 0 residues processed: 530 average time/residue: 0.1525 time to fit residues: 124.2482 Evaluate side-chains 451 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 451 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 0.0020 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 0.0870 chunk 183 optimal weight: 1.9990 chunk 111 optimal weight: 5.9990 overall best weight: 0.5568 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 82BASN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 45 GLN M 55 HIS C 103 GLN C 396 ASN C 591 GLN ** C 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 114 GLN ** A 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.123431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.096642 restraints weight = 41884.076| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 3.38 r_work: 0.3136 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.1303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 24173 Z= 0.137 Angle : 0.684 9.912 32980 Z= 0.340 Chirality : 0.047 0.387 3843 Planarity : 0.004 0.053 4050 Dihedral : 8.516 80.639 4676 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.20 % Allowed : 14.75 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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 aren not related in a simple way. whole: -0.54 (0.16), residues: 2796 helix: 0.73 (0.26), residues: 382 sheet: 0.18 (0.17), residues: 908 loop : -0.98 (0.15), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 38 TYR 0.018 0.001 TYR F 27 PHE 0.024 0.002 PHE F 31 TRP 0.020 0.001 TRP D 50 HIS 0.009 0.001 HIS G 93 Details of bonding type rmsd covalent geometry : bond 0.00306 (24049) covalent geometry : angle 0.65070 (32654) SS BOND : bond 0.00341 ( 46) SS BOND : angle 1.06261 ( 92) hydrogen bonds : bond 0.04228 ( 785) hydrogen bonds : angle 5.89900 ( 2256) link_ALPHA1-2 : bond 0.01736 ( 4) link_ALPHA1-2 : angle 3.29168 ( 12) link_ALPHA1-3 : bond 0.00976 ( 7) link_ALPHA1-3 : angle 1.74116 ( 21) link_ALPHA1-6 : bond 0.00738 ( 5) link_ALPHA1-6 : angle 1.62349 ( 15) link_BETA1-4 : bond 0.00618 ( 16) link_BETA1-4 : angle 2.32121 ( 48) link_NAG-ASN : bond 0.00708 ( 46) link_NAG-ASN : angle 2.72392 ( 138) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5592 Ramachandran restraints generated. 2796 Oldfield, 0 Emsley, 2796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5592 Ramachandran restraints generated. 2796 Oldfield, 0 Emsley, 2796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 556 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 501 time to evaluate : 0.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 46 GLU cc_start: 0.6956 (mp0) cc_final: 0.6586 (pm20) REVERT: D 65 ASP cc_start: 0.8339 (p0) cc_final: 0.8020 (p0) REVERT: D 72 ASP cc_start: 0.8921 (m-30) cc_final: 0.8606 (m-30) REVERT: D 83 LYS cc_start: 0.8389 (mttp) cc_final: 0.8176 (mmmt) REVERT: E 29 SER cc_start: 0.8444 (t) cc_final: 0.8234 (m) REVERT: E 79 ARG cc_start: 0.8675 (mtt180) cc_final: 0.8287 (ttm110) REVERT: E 81 GLU cc_start: 0.8289 (pm20) cc_final: 0.7363 (pm20) REVERT: F 6 GLN cc_start: 0.7931 (mp10) cc_final: 0.7204 (mp10) REVERT: F 43 ARG cc_start: 0.7882 (mmm160) cc_final: 0.7639 (mmm160) REVERT: F 81 GLU cc_start: 0.7246 (tp30) cc_final: 0.6730 (tp30) REVERT: F 82 ILE cc_start: 0.7036 (tp) cc_final: 0.6743 (tp) REVERT: G 17 GLN cc_start: 0.8716 (mp10) cc_final: 0.7932 (mp10) REVERT: G 37 GLN cc_start: 0.7360 (tt0) cc_final: 0.6801 (tt0) REVERT: J 91 PHE cc_start: 0.7516 (m-80) cc_final: 0.7256 (m-80) REVERT: K 77 ASP cc_start: 0.7255 (t70) cc_final: 0.6950 (t0) REVERT: L 89 GLN cc_start: 0.8865 (OUTLIER) cc_final: 0.8439 (tt0) REVERT: C 50 THR cc_start: 0.8871 (t) cc_final: 0.8607 (t) REVERT: C 127 VAL cc_start: 0.8750 (t) cc_final: 0.8484 (m) REVERT: C 280 ASN cc_start: 0.8873 (p0) cc_final: 0.8637 (p0) REVERT: C 322 GLU cc_start: 0.8268 (mm-30) cc_final: 0.7925 (pm20) REVERT: C 502 LYS cc_start: 0.8562 (OUTLIER) cc_final: 0.7854 (tptm) REVERT: C 650 GLN cc_start: 0.7432 (mm-40) cc_final: 0.6916 (mm-40) REVERT: B 133 ASP cc_start: 0.8875 (t0) cc_final: 0.8575 (t0) REVERT: B 164 GLU cc_start: 0.7621 (mm-30) cc_final: 0.6370 (pm20) REVERT: B 300 ASN cc_start: 0.8253 (m-40) cc_final: 0.8023 (m-40) REVERT: B 490 LYS cc_start: 0.8488 (tttp) cc_final: 0.8263 (tttp) REVERT: B 492 GLU cc_start: 0.8207 (mt-10) cc_final: 0.7960 (mt-10) REVERT: B 585 ARG cc_start: 0.8155 (mtp-110) cc_final: 0.7701 (ptm-80) REVERT: A 111 LEU cc_start: 0.8761 (mp) cc_final: 0.8538 (mp) REVERT: A 330 HIS cc_start: 0.8217 (p-80) cc_final: 0.7666 (p-80) REVERT: A 373 MET cc_start: 0.8101 (mmt) cc_final: 0.7296 (mmp) REVERT: A 377 ASN cc_start: 0.8335 (t0) cc_final: 0.8067 (t0) REVERT: A 434 MET cc_start: 0.8612 (ttp) cc_final: 0.8213 (ttt) REVERT: A 482 GLU cc_start: 0.8648 (tt0) cc_final: 0.8356 (tt0) REVERT: A 484 TYR cc_start: 0.9006 (p90) cc_final: 0.8296 (p90) REVERT: A 577 GLN cc_start: 0.8336 (tp40) cc_final: 0.7959 (mm110) REVERT: A 584 GLU cc_start: 0.8609 (tm-30) cc_final: 0.8317 (tm-30) REVERT: A 654 GLU cc_start: 0.8481 (tp30) cc_final: 0.8261 (pt0) REVERT: A 655 LYS cc_start: 0.8006 (pttt) cc_final: 0.7662 (ptpp) outliers start: 55 outliers final: 37 residues processed: 523 average time/residue: 0.1514 time to fit residues: 123.5631 Evaluate side-chains 492 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 453 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 94 LYS Chi-restraints excluded: chain E residue 47 ILE Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 68 ILE Chi-restraints excluded: chain F residue 69 MET Chi-restraints excluded: chain F residue 79 TYR Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain G residue 30 HIS Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain J residue 73 SER Chi-restraints excluded: chain J residue 82 ILE Chi-restraints excluded: chain J residue 82 ASN Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 45 GLN Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain M residue 45 GLN Chi-restraints excluded: chain M residue 69 ARG Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 445 CYS Chi-restraints excluded: chain C residue 502 LYS Chi-restraints excluded: chain C residue 639 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 196 CYS Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 651 ASN Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 606 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 76 optimal weight: 1.9990 chunk 194 optimal weight: 3.9990 chunk 116 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 chunk 91 optimal weight: 4.9990 chunk 140 optimal weight: 2.9990 chunk 216 optimal weight: 4.9990 chunk 195 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 18 optimal weight: 10.0000 chunk 170 optimal weight: 0.9980 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 17 GLN ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 55 HIS M 38 GLN M 76 ASN M 90 GLN C 103 GLN ** C 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 66 HIS A 352 GLN ** A 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 651 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.113548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.086235 restraints weight = 43129.142| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 3.35 r_work: 0.2972 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 24173 Z= 0.288 Angle : 0.756 10.286 32980 Z= 0.377 Chirality : 0.050 0.366 3843 Planarity : 0.005 0.050 4050 Dihedral : 7.959 70.496 4676 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 3.96 % Allowed : 14.91 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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 aren not related in a simple way. whole: -0.64 (0.16), residues: 2796 helix: 0.63 (0.27), residues: 379 sheet: 0.04 (0.17), residues: 925 loop : -0.99 (0.15), residues: 1492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 38 TYR 0.024 0.002 TYR C 302 PHE 0.027 0.003 PHE F 31 TRP 0.023 0.002 TRP A 69 HIS 0.007 0.001 HIS G 93 Details of bonding type rmsd covalent geometry : bond 0.00674 (24049) covalent geometry : angle 0.72279 (32654) SS BOND : bond 0.00822 ( 46) SS BOND : angle 1.61598 ( 92) hydrogen bonds : bond 0.04564 ( 785) hydrogen bonds : angle 5.75385 ( 2256) link_ALPHA1-2 : bond 0.01609 ( 4) link_ALPHA1-2 : angle 3.12410 ( 12) link_ALPHA1-3 : bond 0.00928 ( 7) link_ALPHA1-3 : angle 1.82522 ( 21) link_ALPHA1-6 : bond 0.00571 ( 5) link_ALPHA1-6 : angle 1.75077 ( 15) link_BETA1-4 : bond 0.00698 ( 16) link_BETA1-4 : angle 2.34688 ( 48) link_NAG-ASN : bond 0.00831 ( 46) link_NAG-ASN : angle 2.77826 ( 138) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5592 Ramachandran restraints generated. 2796 Oldfield, 0 Emsley, 2796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5592 Ramachandran restraints generated. 2796 Oldfield, 0 Emsley, 2796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 548 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 449 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 36 TRP cc_start: 0.8205 (m100) cc_final: 0.7917 (m100) REVERT: D 46 GLU cc_start: 0.7077 (mp0) cc_final: 0.6864 (mp0) REVERT: D 82 ARG cc_start: 0.6838 (mtm-85) cc_final: 0.6337 (mpp80) REVERT: E 38 TRP cc_start: 0.8838 (t60) cc_final: 0.8605 (t60) REVERT: E 79 ARG cc_start: 0.8657 (mtt180) cc_final: 0.8364 (ttm110) REVERT: F 48 MET cc_start: 0.8061 (mmt) cc_final: 0.7766 (mmt) REVERT: F 50 TRP cc_start: 0.4167 (m-90) cc_final: 0.2882 (m-90) REVERT: F 81 GLU cc_start: 0.7142 (tp30) cc_final: 0.6648 (tp30) REVERT: G 17 GLN cc_start: 0.8749 (mp10) cc_final: 0.7916 (mp10) REVERT: G 37 GLN cc_start: 0.7518 (tt0) cc_final: 0.6932 (tt0) REVERT: G 58 ILE cc_start: 0.8070 (mm) cc_final: 0.7837 (mt) REVERT: G 77 ASP cc_start: 0.7654 (t0) cc_final: 0.7020 (t0) REVERT: J 36 TRP cc_start: 0.8504 (m100) cc_final: 0.8179 (m100) REVERT: J 66 ARG cc_start: 0.7157 (tpp80) cc_final: 0.6647 (tpp80) REVERT: J 82 ARG cc_start: 0.8649 (ptp90) cc_final: 0.7671 (ptp90) REVERT: J 91 PHE cc_start: 0.7678 (m-80) cc_final: 0.7463 (m-80) REVERT: L 4 MET cc_start: 0.8883 (mmm) cc_final: 0.8484 (mmm) REVERT: L 26 ARG cc_start: 0.8685 (tpt90) cc_final: 0.8041 (tpp80) REVERT: L 48 ILE cc_start: 0.9103 (mm) cc_final: 0.8805 (mm) REVERT: L 89 GLN cc_start: 0.8965 (tt0) cc_final: 0.8472 (tt0) REVERT: C 127 VAL cc_start: 0.8737 (t) cc_final: 0.8471 (m) REVERT: C 173 TYR cc_start: 0.8010 (p90) cc_final: 0.7762 (p90) REVERT: C 280 ASN cc_start: 0.8947 (p0) cc_final: 0.8738 (p0) REVERT: C 322 GLU cc_start: 0.8346 (mm-30) cc_final: 0.8054 (pm20) REVERT: C 377 ASN cc_start: 0.8701 (t0) cc_final: 0.8453 (t0) REVERT: C 475 MET cc_start: 0.8547 (tpp) cc_final: 0.8193 (tpp) REVERT: C 629 MET cc_start: 0.8254 (mmm) cc_final: 0.7693 (mmm) REVERT: C 650 GLN cc_start: 0.7621 (mm-40) cc_final: 0.6845 (mm-40) REVERT: B 164 GLU cc_start: 0.7750 (mm-30) cc_final: 0.6530 (pm20) REVERT: B 330 HIS cc_start: 0.7768 (p90) cc_final: 0.7405 (p-80) REVERT: B 475 MET cc_start: 0.7787 (mmt) cc_final: 0.7581 (mmp) REVERT: B 530 MET cc_start: 0.8882 (mmm) cc_final: 0.8396 (mtp) REVERT: B 585 ARG cc_start: 0.8244 (mtp-110) cc_final: 0.7894 (ptm-80) REVERT: A 116 LEU cc_start: 0.8066 (OUTLIER) cc_final: 0.7749 (mp) REVERT: A 320 MET cc_start: 0.8426 (mmm) cc_final: 0.8187 (mmm) REVERT: A 373 MET cc_start: 0.8446 (mmt) cc_final: 0.7509 (mmp) REVERT: A 377 ASN cc_start: 0.8666 (t0) cc_final: 0.8386 (t0) REVERT: A 381 GLU cc_start: 0.6718 (mm-30) cc_final: 0.6249 (tp30) REVERT: A 482 GLU cc_start: 0.8663 (tt0) cc_final: 0.8285 (tt0) REVERT: A 577 GLN cc_start: 0.8577 (tp40) cc_final: 0.8373 (tp40) REVERT: A 584 GLU cc_start: 0.8677 (tm-30) cc_final: 0.8309 (tm-30) REVERT: A 654 GLU cc_start: 0.8483 (tp30) cc_final: 0.8217 (pt0) REVERT: A 655 LYS cc_start: 0.8018 (pttt) cc_final: 0.7629 (ptpp) outliers start: 99 outliers final: 63 residues processed: 503 average time/residue: 0.1482 time to fit residues: 115.7068 Evaluate side-chains 483 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 419 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 94 LYS Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 28 CYS Chi-restraints excluded: chain E residue 88 CYS Chi-restraints excluded: chain E residue 89 CYS Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 68 ILE Chi-restraints excluded: chain F residue 69 MET Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 79 TYR Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain G residue 30 HIS Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain J residue 24 THR Chi-restraints excluded: chain J residue 63 PHE Chi-restraints excluded: chain J residue 68 ILE Chi-restraints excluded: chain J residue 81 GLU Chi-restraints excluded: chain J residue 82 ILE Chi-restraints excluded: chain J residue 107 THR Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 32 ASN Chi-restraints excluded: chain L residue 45 GLN Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain I residue 67 VAL Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain M residue 17 ASP Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 320 MET Chi-restraints excluded: chain C residue 445 CYS Chi-restraints excluded: chain C residue 502 LYS Chi-restraints excluded: chain C residue 639 THR Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 95 MET Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 196 CYS Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 606 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 252 optimal weight: 0.9990 chunk 227 optimal weight: 5.9990 chunk 76 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 177 optimal weight: 0.6980 chunk 40 optimal weight: 0.0020 chunk 147 optimal weight: 1.9990 chunk 103 optimal weight: 0.5980 chunk 155 optimal weight: 0.7980 chunk 29 optimal weight: 5.9990 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 37 GLN ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 GLN C 422 GLN C 656 ASN ** B 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 66 HIS A 363 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.118057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.090821 restraints weight = 42013.627| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 3.35 r_work: 0.3045 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 24173 Z= 0.127 Angle : 0.626 9.571 32980 Z= 0.311 Chirality : 0.046 0.345 3843 Planarity : 0.004 0.052 4050 Dihedral : 7.104 59.597 4676 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.76 % Allowed : 16.79 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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 aren not related in a simple way. whole: -0.46 (0.16), residues: 2796 helix: 0.77 (0.27), residues: 385 sheet: 0.20 (0.17), residues: 901 loop : -0.89 (0.16), residues: 1510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 42 TYR 0.019 0.001 TYR D 32 PHE 0.021 0.001 PHE F 31 TRP 0.021 0.001 TRP F 36 HIS 0.005 0.001 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00283 (24049) covalent geometry : angle 0.59577 (32654) SS BOND : bond 0.00325 ( 46) SS BOND : angle 1.24988 ( 92) hydrogen bonds : bond 0.03738 ( 785) hydrogen bonds : angle 5.37211 ( 2256) link_ALPHA1-2 : bond 0.01694 ( 4) link_ALPHA1-2 : angle 3.18715 ( 12) link_ALPHA1-3 : bond 0.01064 ( 7) link_ALPHA1-3 : angle 1.56925 ( 21) link_ALPHA1-6 : bond 0.00869 ( 5) link_ALPHA1-6 : angle 1.57457 ( 15) link_BETA1-4 : bond 0.00636 ( 16) link_BETA1-4 : angle 1.88496 ( 48) link_NAG-ASN : bond 0.00565 ( 46) link_NAG-ASN : angle 2.44498 ( 138) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5592 Ramachandran restraints generated. 2796 Oldfield, 0 Emsley, 2796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5592 Ramachandran restraints generated. 2796 Oldfield, 0 Emsley, 2796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 461 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 72 ASP cc_start: 0.8860 (m-30) cc_final: 0.8654 (m-30) REVERT: D 82 ARG cc_start: 0.6785 (mtm-85) cc_final: 0.6510 (mpp80) REVERT: D 83 LYS cc_start: 0.8395 (mtmm) cc_final: 0.8174 (mttp) REVERT: E 38 TRP cc_start: 0.8813 (t60) cc_final: 0.8604 (t60) REVERT: F 43 ARG cc_start: 0.7987 (mmm160) cc_final: 0.7352 (ttt-90) REVERT: F 50 TRP cc_start: 0.3098 (m-90) cc_final: 0.2368 (m-90) REVERT: F 58 ASN cc_start: 0.7837 (t0) cc_final: 0.6568 (t0) REVERT: F 81 GLU cc_start: 0.7107 (tp30) cc_final: 0.6528 (tp30) REVERT: F 82 ILE cc_start: 0.6994 (tp) cc_final: 0.6523 (tp) REVERT: F 100 TRP cc_start: 0.4710 (t-100) cc_final: 0.3957 (t-100) REVERT: G 17 GLN cc_start: 0.8733 (mp10) cc_final: 0.8169 (mp10) REVERT: G 37 GLN cc_start: 0.7392 (tt0) cc_final: 0.6799 (tt0) REVERT: J 36 TRP cc_start: 0.8480 (m100) cc_final: 0.8111 (m100) REVERT: J 66 ARG cc_start: 0.7061 (tpp80) cc_final: 0.6641 (tpp80) REVERT: J 82 ARG cc_start: 0.8323 (ptp90) cc_final: 0.8044 (ptp90) REVERT: K 42 ARG cc_start: 0.6913 (mtt90) cc_final: 0.6497 (mtm-85) REVERT: H 80 LEU cc_start: 0.9225 (OUTLIER) cc_final: 0.8988 (tp) REVERT: L 4 MET cc_start: 0.8829 (mmm) cc_final: 0.8387 (mmm) REVERT: L 24 GLN cc_start: 0.8611 (mp10) cc_final: 0.7843 (mm-40) REVERT: L 26 ARG cc_start: 0.8487 (tpt90) cc_final: 0.7889 (tpp80) REVERT: L 89 GLN cc_start: 0.8797 (tt0) cc_final: 0.8269 (tt0) REVERT: I 59 TYR cc_start: 0.8976 (m-80) cc_final: 0.8697 (m-80) REVERT: I 64 ASP cc_start: 0.7977 (t0) cc_final: 0.7771 (t0) REVERT: I 76 ASN cc_start: 0.8656 (p0) cc_final: 0.8327 (p0) REVERT: M 24 GLN cc_start: 0.8422 (mm-40) cc_final: 0.8130 (mm-40) REVERT: M 65 SER cc_start: 0.8863 (p) cc_final: 0.8490 (m) REVERT: C 173 TYR cc_start: 0.7953 (p90) cc_final: 0.7716 (p90) REVERT: C 280 ASN cc_start: 0.8913 (p0) cc_final: 0.8686 (p0) REVERT: C 377 ASN cc_start: 0.8515 (t0) cc_final: 0.8285 (t0) REVERT: C 475 MET cc_start: 0.8270 (tpp) cc_final: 0.7920 (tpp) REVERT: C 502 LYS cc_start: 0.8535 (OUTLIER) cc_final: 0.7864 (tptm) REVERT: C 629 MET cc_start: 0.8068 (mmm) cc_final: 0.7561 (mmm) REVERT: C 650 GLN cc_start: 0.7546 (mm-40) cc_final: 0.6678 (mm-40) REVERT: B 164 GLU cc_start: 0.7725 (mm-30) cc_final: 0.6251 (pm20) REVERT: B 330 HIS cc_start: 0.7584 (p90) cc_final: 0.7277 (p-80) REVERT: A 320 MET cc_start: 0.8430 (mmm) cc_final: 0.8104 (mmm) REVERT: A 373 MET cc_start: 0.8350 (mmt) cc_final: 0.7485 (mmp) REVERT: A 377 ASN cc_start: 0.8426 (t0) cc_final: 0.8129 (t0) REVERT: A 381 GLU cc_start: 0.6791 (mm-30) cc_final: 0.6538 (tp30) REVERT: A 484 TYR cc_start: 0.9048 (p90) cc_final: 0.8304 (p90) REVERT: A 584 GLU cc_start: 0.8660 (tm-30) cc_final: 0.8237 (tm-30) REVERT: A 655 LYS cc_start: 0.8033 (pttt) cc_final: 0.7665 (ptpp) outliers start: 69 outliers final: 42 residues processed: 492 average time/residue: 0.1438 time to fit residues: 110.9480 Evaluate side-chains 471 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 427 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 69 MET Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 79 TYR Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain G residue 30 HIS Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain J residue 24 THR Chi-restraints excluded: chain J residue 63 PHE Chi-restraints excluded: chain J residue 82 ILE Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain K residue 47 ILE Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain I residue 89 ILE Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 320 MET Chi-restraints excluded: chain C residue 445 CYS Chi-restraints excluded: chain C residue 502 LYS Chi-restraints excluded: chain C residue 639 THR Chi-restraints excluded: chain B residue 95 MET Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 196 CYS Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 651 ASN Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 576 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 15 optimal weight: 5.9990 chunk 246 optimal weight: 0.9980 chunk 177 optimal weight: 2.9990 chunk 12 optimal weight: 9.9990 chunk 56 optimal weight: 6.9990 chunk 190 optimal weight: 2.9990 chunk 35 optimal weight: 9.9990 chunk 76 optimal weight: 0.8980 chunk 136 optimal weight: 0.5980 chunk 97 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 65 ASN ** L 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 45 GLN M 79 GLN C 103 GLN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 66 HIS A 656 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.114125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.086558 restraints weight = 42542.605| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 3.37 r_work: 0.2981 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.2632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 24173 Z= 0.211 Angle : 0.665 9.410 32980 Z= 0.329 Chirality : 0.047 0.350 3843 Planarity : 0.004 0.053 4050 Dihedral : 6.952 57.539 4676 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 3.68 % Allowed : 17.43 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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 aren not related in a simple way. whole: -0.48 (0.16), residues: 2796 helix: 0.74 (0.27), residues: 383 sheet: 0.13 (0.17), residues: 915 loop : -0.87 (0.16), residues: 1498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 42 TYR 0.024 0.002 TYR G 49 PHE 0.024 0.002 PHE B 522 TRP 0.019 0.002 TRP F 36 HIS 0.006 0.001 HIS G 93 Details of bonding type rmsd covalent geometry : bond 0.00489 (24049) covalent geometry : angle 0.63500 (32654) SS BOND : bond 0.00459 ( 46) SS BOND : angle 1.23174 ( 92) hydrogen bonds : bond 0.03985 ( 785) hydrogen bonds : angle 5.38810 ( 2256) link_ALPHA1-2 : bond 0.01715 ( 4) link_ALPHA1-2 : angle 3.10433 ( 12) link_ALPHA1-3 : bond 0.00915 ( 7) link_ALPHA1-3 : angle 1.66151 ( 21) link_ALPHA1-6 : bond 0.00716 ( 5) link_ALPHA1-6 : angle 1.61508 ( 15) link_BETA1-4 : bond 0.00562 ( 16) link_BETA1-4 : angle 2.06093 ( 48) link_NAG-ASN : bond 0.00619 ( 46) link_NAG-ASN : angle 2.50334 ( 138) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5592 Ramachandran restraints generated. 2796 Oldfield, 0 Emsley, 2796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5592 Ramachandran restraints generated. 2796 Oldfield, 0 Emsley, 2796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 448 time to evaluate : 0.597 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: D 72 ASP cc_start: 0.8746 (m-30) cc_final: 0.7949 (m-30) REVERT: D 79 TYR cc_start: 0.8222 (m-80) cc_final: 0.7910 (m-80) REVERT: D 82 ARG cc_start: 0.6659 (mtm-85) cc_final: 0.6387 (mpp80) REVERT: D 83 LYS cc_start: 0.8404 (mtmm) cc_final: 0.7990 (mmtt) REVERT: D 108 LEU cc_start: 0.8921 (mm) cc_final: 0.8037 (pt) REVERT: E 6 GLN cc_start: 0.7139 (pm20) cc_final: 0.5909 (pp30) REVERT: E 38 TRP cc_start: 0.8911 (t60) cc_final: 0.8665 (t60) REVERT: E 79 ARG cc_start: 0.8606 (mtt180) cc_final: 0.8313 (ttm110) REVERT: E 81 GLU cc_start: 0.8341 (pm20) cc_final: 0.7301 (pm20) REVERT: F 43 ARG cc_start: 0.8010 (mmm160) cc_final: 0.7370 (ttt-90) REVERT: F 81 GLU cc_start: 0.7077 (tp30) cc_final: 0.6443 (tp30) REVERT: F 82 ILE cc_start: 0.6565 (tp) cc_final: 0.6012 (tp) REVERT: F 100 TRP cc_start: 0.4848 (t-100) cc_final: 0.4019 (t-100) REVERT: G 17 GLN cc_start: 0.8762 (mp10) cc_final: 0.7910 (mp10) REVERT: G 37 GLN cc_start: 0.7491 (tt0) cc_final: 0.6892 (tt0) REVERT: G 49 TYR cc_start: 0.8133 (p90) cc_final: 0.7798 (p90) REVERT: G 77 ASP cc_start: 0.7682 (t0) cc_final: 0.6887 (t0) REVERT: J 36 TRP cc_start: 0.8462 (m100) cc_final: 0.8149 (m100) REVERT: J 38 ARG cc_start: 0.5951 (OUTLIER) cc_final: 0.5604 (ptp-170) REVERT: J 66 ARG cc_start: 0.7054 (tpp80) cc_final: 0.6618 (tpp80) REVERT: J 81 GLU cc_start: 0.8810 (OUTLIER) cc_final: 0.8373 (pp20) REVERT: K 42 ARG cc_start: 0.6639 (mtt90) cc_final: 0.6388 (mtm-85) REVERT: H 80 LEU cc_start: 0.9307 (OUTLIER) cc_final: 0.9096 (tp) REVERT: L 24 GLN cc_start: 0.8734 (mp10) cc_final: 0.8459 (mt0) REVERT: L 26 ARG cc_start: 0.8640 (tpt90) cc_final: 0.7840 (tpp80) REVERT: L 89 GLN cc_start: 0.8890 (OUTLIER) cc_final: 0.8323 (tt0) REVERT: I 46 GLU cc_start: 0.8104 (mt-10) cc_final: 0.7659 (pt0) REVERT: I 64 ASP cc_start: 0.8071 (t0) cc_final: 0.7810 (t0) REVERT: M 65 SER cc_start: 0.9026 (p) cc_final: 0.8686 (m) REVERT: C 173 TYR cc_start: 0.7970 (p90) cc_final: 0.7718 (p90) REVERT: C 280 ASN cc_start: 0.8906 (p0) cc_final: 0.8692 (p0) REVERT: C 318 TYR cc_start: 0.8914 (m-80) cc_final: 0.8567 (m-80) REVERT: C 629 MET cc_start: 0.8290 (mmm) cc_final: 0.7789 (mmm) REVERT: B 164 GLU cc_start: 0.7637 (mm-30) cc_final: 0.6291 (pm20) REVERT: B 475 MET cc_start: 0.7900 (mmt) cc_final: 0.7556 (mmp) REVERT: B 530 MET cc_start: 0.8877 (mmm) cc_final: 0.8370 (mtp) REVERT: B 585 ARG cc_start: 0.8411 (mtp-110) cc_final: 0.8006 (ptm-80) REVERT: B 652 GLN cc_start: 0.8472 (mp10) cc_final: 0.8253 (mp10) REVERT: A 102 GLU cc_start: 0.8554 (mp0) cc_final: 0.8136 (mp0) REVERT: A 116 LEU cc_start: 0.8029 (OUTLIER) cc_final: 0.7703 (mp) REVERT: A 320 MET cc_start: 0.8568 (mmm) cc_final: 0.8218 (mmm) REVERT: A 373 MET cc_start: 0.8555 (mmt) cc_final: 0.7663 (mmp) REVERT: A 381 GLU cc_start: 0.7021 (mm-30) cc_final: 0.6730 (tp30) REVERT: A 584 GLU cc_start: 0.8690 (tm-30) cc_final: 0.8245 (tm-30) REVERT: A 655 LYS cc_start: 0.8035 (pttt) cc_final: 0.7649 (ptpp) outliers start: 92 outliers final: 58 residues processed: 496 average time/residue: 0.1455 time to fit residues: 111.9875 Evaluate side-chains 491 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 428 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 94 LYS Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain E residue 28 CYS Chi-restraints excluded: chain E residue 89 CYS Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 69 MET Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 79 TYR Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain G residue 30 HIS Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain J residue 17 SER Chi-restraints excluded: chain J residue 22 CYS Chi-restraints excluded: chain J residue 24 THR Chi-restraints excluded: chain J residue 38 ARG Chi-restraints excluded: chain J residue 63 PHE Chi-restraints excluded: chain J residue 68 ILE Chi-restraints excluded: chain J residue 81 GLU Chi-restraints excluded: chain J residue 82 ILE Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 91 PHE Chi-restraints excluded: chain K residue 47 ILE Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 89 ILE Chi-restraints excluded: chain M residue 45 GLN Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 306 SER Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain C residue 445 CYS Chi-restraints excluded: chain C residue 502 LYS Chi-restraints excluded: chain C residue 639 THR Chi-restraints excluded: chain B residue 95 MET Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 196 CYS Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 426 MET Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 651 ASN Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 535 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 233 optimal weight: 0.9990 chunk 139 optimal weight: 0.9990 chunk 187 optimal weight: 0.9980 chunk 209 optimal weight: 0.0770 chunk 69 optimal weight: 2.9990 chunk 236 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 chunk 232 optimal weight: 0.8980 chunk 46 optimal weight: 9.9990 chunk 38 optimal weight: 6.9990 overall best weight: 0.7540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 45 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 66 HIS A 229 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.116167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.089090 restraints weight = 42473.559| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 3.36 r_work: 0.3017 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24173 Z= 0.132 Angle : 0.620 11.068 32980 Z= 0.307 Chirality : 0.045 0.337 3843 Planarity : 0.004 0.058 4050 Dihedral : 6.657 56.131 4676 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 3.24 % Allowed : 18.03 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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 aren not related in a simple way. whole: -0.39 (0.16), residues: 2796 helix: 0.78 (0.27), residues: 386 sheet: 0.26 (0.18), residues: 907 loop : -0.84 (0.16), residues: 1503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 42 TYR 0.021 0.001 TYR G 49 PHE 0.024 0.001 PHE B 522 TRP 0.022 0.001 TRP F 36 HIS 0.005 0.001 HIS G 93 Details of bonding type rmsd covalent geometry : bond 0.00299 (24049) covalent geometry : angle 0.59137 (32654) SS BOND : bond 0.00345 ( 46) SS BOND : angle 1.18396 ( 92) hydrogen bonds : bond 0.03687 ( 785) hydrogen bonds : angle 5.29394 ( 2256) link_ALPHA1-2 : bond 0.01723 ( 4) link_ALPHA1-2 : angle 3.12627 ( 12) link_ALPHA1-3 : bond 0.01009 ( 7) link_ALPHA1-3 : angle 1.49934 ( 21) link_ALPHA1-6 : bond 0.00842 ( 5) link_ALPHA1-6 : angle 1.54062 ( 15) link_BETA1-4 : bond 0.00587 ( 16) link_BETA1-4 : angle 1.87279 ( 48) link_NAG-ASN : bond 0.00527 ( 46) link_NAG-ASN : angle 2.36595 ( 138) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5592 Ramachandran restraints generated. 2796 Oldfield, 0 Emsley, 2796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5592 Ramachandran restraints generated. 2796 Oldfield, 0 Emsley, 2796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 459 time to evaluate : 0.608 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: D 79 TYR cc_start: 0.8213 (m-80) cc_final: 0.7946 (m-80) REVERT: D 83 LYS cc_start: 0.8420 (mtmm) cc_final: 0.8005 (mmtt) REVERT: D 108 LEU cc_start: 0.8907 (mm) cc_final: 0.8026 (pt) REVERT: E 6 GLN cc_start: 0.7141 (pm20) cc_final: 0.5844 (pp30) REVERT: E 79 ARG cc_start: 0.8588 (mtt180) cc_final: 0.8297 (ttm110) REVERT: E 81 GLU cc_start: 0.8380 (pm20) cc_final: 0.7395 (pm20) REVERT: F 43 ARG cc_start: 0.7950 (mmm160) cc_final: 0.7323 (ttt-90) REVERT: F 59 LEU cc_start: 0.7706 (OUTLIER) cc_final: 0.7182 (tp) REVERT: F 81 GLU cc_start: 0.7020 (tp30) cc_final: 0.6403 (tp30) REVERT: F 82 ILE cc_start: 0.6620 (tp) cc_final: 0.6113 (tp) REVERT: F 100 TRP cc_start: 0.4724 (t-100) cc_final: 0.4216 (t-100) REVERT: G 17 GLN cc_start: 0.8744 (mp10) cc_final: 0.7882 (mp10) REVERT: G 37 GLN cc_start: 0.7398 (tt0) cc_final: 0.6813 (tt0) REVERT: G 49 TYR cc_start: 0.7934 (p90) cc_final: 0.7613 (p90) REVERT: J 38 ARG cc_start: 0.5959 (OUTLIER) cc_final: 0.5627 (ptp-170) REVERT: J 66 ARG cc_start: 0.7153 (tpp80) cc_final: 0.6694 (tpp80) REVERT: J 81 GLU cc_start: 0.8733 (OUTLIER) cc_final: 0.7994 (pp20) REVERT: J 82 ARG cc_start: 0.8489 (ptp90) cc_final: 0.7431 (ptp90) REVERT: K 42 ARG cc_start: 0.6700 (mtt90) cc_final: 0.6397 (mtm-85) REVERT: L 4 MET cc_start: 0.8860 (mmm) cc_final: 0.8338 (mmm) REVERT: L 26 ARG cc_start: 0.8503 (tpt90) cc_final: 0.7727 (tpp80) REVERT: I 64 ASP cc_start: 0.8092 (t0) cc_final: 0.7761 (t0) REVERT: I 76 ASN cc_start: 0.8724 (p0) cc_final: 0.8422 (p0) REVERT: M 65 SER cc_start: 0.8927 (p) cc_final: 0.8628 (m) REVERT: C 173 TYR cc_start: 0.7910 (p90) cc_final: 0.7669 (p90) REVERT: C 280 ASN cc_start: 0.8904 (p0) cc_final: 0.8684 (p0) REVERT: C 318 TYR cc_start: 0.8840 (m-80) cc_final: 0.8491 (m-80) REVERT: C 320 MET cc_start: 0.8624 (mmt) cc_final: 0.8309 (mmt) REVERT: C 475 MET cc_start: 0.7876 (tpp) cc_final: 0.7668 (tpp) REVERT: C 519 ARG cc_start: 0.7764 (ptp-110) cc_final: 0.7254 (mtt90) REVERT: C 629 MET cc_start: 0.8082 (mmm) cc_final: 0.7460 (mmm) REVERT: B 164 GLU cc_start: 0.7650 (mm-30) cc_final: 0.6221 (pm20) REVERT: B 377 ASN cc_start: 0.8179 (OUTLIER) cc_final: 0.7958 (t0) REVERT: B 475 MET cc_start: 0.7806 (mmt) cc_final: 0.7524 (mmp) REVERT: B 585 ARG cc_start: 0.8388 (mtp-110) cc_final: 0.8058 (ptm-80) REVERT: A 102 GLU cc_start: 0.8423 (mp0) cc_final: 0.8006 (mp0) REVERT: A 320 MET cc_start: 0.8483 (mmm) cc_final: 0.8082 (mmm) REVERT: A 373 MET cc_start: 0.8460 (mmt) cc_final: 0.7571 (mmp) REVERT: A 584 GLU cc_start: 0.8648 (tm-30) cc_final: 0.8190 (tm-30) REVERT: A 655 LYS cc_start: 0.8062 (pttt) cc_final: 0.7662 (ptpp) outliers start: 81 outliers final: 56 residues processed: 495 average time/residue: 0.1486 time to fit residues: 113.9955 Evaluate side-chains 488 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 428 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 94 LYS Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain E residue 28 CYS Chi-restraints excluded: chain E residue 89 CYS Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 50 TRP Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 69 MET Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 79 TYR Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain G residue 30 HIS Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain J residue 17 SER Chi-restraints excluded: chain J residue 22 CYS Chi-restraints excluded: chain J residue 24 THR Chi-restraints excluded: chain J residue 38 ARG Chi-restraints excluded: chain J residue 63 PHE Chi-restraints excluded: chain J residue 81 GLU Chi-restraints excluded: chain J residue 82 ILE Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 91 PHE Chi-restraints excluded: chain K residue 47 ILE Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain I residue 35 ASN Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 502 LYS Chi-restraints excluded: chain C residue 639 THR Chi-restraints excluded: chain B residue 95 MET Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 196 CYS Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 377 ASN Chi-restraints excluded: chain B residue 426 MET Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 651 ASN Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 535 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 85 optimal weight: 0.0970 chunk 52 optimal weight: 6.9990 chunk 272 optimal weight: 4.9990 chunk 55 optimal weight: 0.9980 chunk 90 optimal weight: 0.8980 chunk 153 optimal weight: 6.9990 chunk 198 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 170 optimal weight: 2.9990 chunk 120 optimal weight: 3.9990 chunk 8 optimal weight: 8.9990 overall best weight: 1.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 45 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 45 GLN A 66 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.113677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.086428 restraints weight = 42635.723| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 3.35 r_work: 0.2975 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 24173 Z= 0.199 Angle : 0.657 9.705 32980 Z= 0.327 Chirality : 0.047 0.340 3843 Planarity : 0.004 0.057 4050 Dihedral : 6.687 56.872 4676 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 3.76 % Allowed : 17.79 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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 aren not related in a simple way. whole: -0.44 (0.16), residues: 2796 helix: 0.74 (0.27), residues: 386 sheet: 0.18 (0.17), residues: 929 loop : -0.85 (0.16), residues: 1481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 82A TYR 0.023 0.002 TYR G 49 PHE 0.029 0.002 PHE F 31 TRP 0.025 0.002 TRP F 36 HIS 0.006 0.001 HIS G 93 Details of bonding type rmsd covalent geometry : bond 0.00463 (24049) covalent geometry : angle 0.62808 (32654) SS BOND : bond 0.00456 ( 46) SS BOND : angle 1.29912 ( 92) hydrogen bonds : bond 0.03859 ( 785) hydrogen bonds : angle 5.34261 ( 2256) link_ALPHA1-2 : bond 0.01624 ( 4) link_ALPHA1-2 : angle 2.99906 ( 12) link_ALPHA1-3 : bond 0.00937 ( 7) link_ALPHA1-3 : angle 1.56885 ( 21) link_ALPHA1-6 : bond 0.00759 ( 5) link_ALPHA1-6 : angle 1.58527 ( 15) link_BETA1-4 : bond 0.00553 ( 16) link_BETA1-4 : angle 1.96908 ( 48) link_NAG-ASN : bond 0.00564 ( 46) link_NAG-ASN : angle 2.42485 ( 138) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5592 Ramachandran restraints generated. 2796 Oldfield, 0 Emsley, 2796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5592 Ramachandran restraints generated. 2796 Oldfield, 0 Emsley, 2796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 441 time to evaluate : 0.923 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: D 72 ASP cc_start: 0.8490 (m-30) cc_final: 0.8252 (m-30) REVERT: D 79 TYR cc_start: 0.8272 (m-80) cc_final: 0.7903 (m-80) REVERT: D 83 LYS cc_start: 0.8504 (mtmm) cc_final: 0.8077 (mmtt) REVERT: D 94 LYS cc_start: 0.8387 (OUTLIER) cc_final: 0.8058 (pttp) REVERT: D 108 LEU cc_start: 0.8876 (mm) cc_final: 0.7987 (pt) REVERT: E 35 TRP cc_start: 0.7202 (m100) cc_final: 0.6504 (m100) REVERT: E 79 ARG cc_start: 0.8580 (mtt180) cc_final: 0.8188 (ttm110) REVERT: E 81 GLU cc_start: 0.8293 (pm20) cc_final: 0.7815 (pm20) REVERT: F 36 TRP cc_start: 0.8717 (m100) cc_final: 0.8282 (m100) REVERT: F 43 ARG cc_start: 0.8030 (mmm160) cc_final: 0.7413 (ttt-90) REVERT: F 59 LEU cc_start: 0.7808 (OUTLIER) cc_final: 0.7337 (tp) REVERT: F 81 GLU cc_start: 0.7085 (OUTLIER) cc_final: 0.6450 (tp30) REVERT: F 82 ILE cc_start: 0.6454 (tp) cc_final: 0.5932 (tp) REVERT: F 100 TRP cc_start: 0.4843 (t-100) cc_final: 0.4267 (t-100) REVERT: G 17 GLN cc_start: 0.8789 (mp10) cc_final: 0.7908 (mp10) REVERT: G 37 GLN cc_start: 0.7470 (tt0) cc_final: 0.6863 (tt0) REVERT: G 49 TYR cc_start: 0.8196 (p90) cc_final: 0.7887 (p90) REVERT: G 77 ASP cc_start: 0.7806 (t0) cc_final: 0.7134 (t0) REVERT: G 79 ARG cc_start: 0.7694 (mmp80) cc_final: 0.7458 (mmp80) REVERT: J 66 ARG cc_start: 0.7071 (tpp80) cc_final: 0.6621 (tpp80) REVERT: J 81 GLU cc_start: 0.8721 (OUTLIER) cc_final: 0.7886 (pp20) REVERT: J 82 ARG cc_start: 0.8534 (ptp90) cc_final: 0.7488 (ptp90) REVERT: K 42 ARG cc_start: 0.6777 (mtt90) cc_final: 0.6457 (mtm-85) REVERT: K 102 THR cc_start: 0.7721 (m) cc_final: 0.7136 (p) REVERT: L 26 ARG cc_start: 0.8593 (tpt90) cc_final: 0.7810 (tpp80) REVERT: L 89 GLN cc_start: 0.8832 (OUTLIER) cc_final: 0.8217 (tt0) REVERT: I 46 GLU cc_start: 0.8090 (mt-10) cc_final: 0.7640 (pt0) REVERT: I 64 ASP cc_start: 0.8200 (t0) cc_final: 0.7854 (t0) REVERT: M 65 SER cc_start: 0.8950 (p) cc_final: 0.8651 (m) REVERT: C 173 TYR cc_start: 0.7921 (p90) cc_final: 0.7682 (p90) REVERT: C 280 ASN cc_start: 0.8928 (p0) cc_final: 0.8705 (p0) REVERT: C 318 TYR cc_start: 0.8986 (m-80) cc_final: 0.8644 (m-80) REVERT: C 378 CYS cc_start: 0.7758 (OUTLIER) cc_final: 0.7545 (p) REVERT: C 467 ILE cc_start: 0.7800 (OUTLIER) cc_final: 0.7512 (mp) REVERT: C 519 ARG cc_start: 0.7798 (ptp-110) cc_final: 0.7294 (mtt90) REVERT: B 164 GLU cc_start: 0.7692 (mm-30) cc_final: 0.6247 (pm20) REVERT: B 475 MET cc_start: 0.7819 (mmt) cc_final: 0.7307 (mmp) REVERT: B 530 MET cc_start: 0.8894 (mmm) cc_final: 0.8426 (mtp) REVERT: B 585 ARG cc_start: 0.8373 (mtp-110) cc_final: 0.8058 (ptm-80) REVERT: B 652 GLN cc_start: 0.8378 (mp10) cc_final: 0.7889 (mp10) REVERT: A 69 TRP cc_start: 0.7887 (m-90) cc_final: 0.7569 (m-90) REVERT: A 102 GLU cc_start: 0.8479 (mp0) cc_final: 0.8047 (mp0) REVERT: A 320 MET cc_start: 0.8524 (mmm) cc_final: 0.8096 (mmm) REVERT: A 373 MET cc_start: 0.8548 (mmt) cc_final: 0.7655 (mmp) REVERT: A 584 GLU cc_start: 0.8666 (tm-30) cc_final: 0.8199 (tm-30) REVERT: A 655 LYS cc_start: 0.8104 (pttt) cc_final: 0.7687 (ptpp) outliers start: 94 outliers final: 71 residues processed: 484 average time/residue: 0.1856 time to fit residues: 137.9265 Evaluate side-chains 501 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 423 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 92 CYS Chi-restraints excluded: chain D residue 94 LYS Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 28 CYS Chi-restraints excluded: chain E residue 89 CYS Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 50 TRP Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 69 MET Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 79 TYR Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain G residue 30 HIS Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain J residue 17 SER Chi-restraints excluded: chain J residue 22 CYS Chi-restraints excluded: chain J residue 24 THR Chi-restraints excluded: chain J residue 63 PHE Chi-restraints excluded: chain J residue 81 GLU Chi-restraints excluded: chain J residue 82 ILE Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 91 PHE Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 64 ASP Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain I residue 35 ASN Chi-restraints excluded: chain I residue 80 LEU Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 89 ILE Chi-restraints excluded: chain M residue 45 GLN Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 306 SER Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 467 ILE Chi-restraints excluded: chain C residue 502 LYS Chi-restraints excluded: chain C residue 639 THR Chi-restraints excluded: chain C residue 660 LEU Chi-restraints excluded: chain B residue 95 MET Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 196 CYS Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 377 ASN Chi-restraints excluded: chain B residue 426 MET Chi-restraints excluded: chain B residue 445 CYS Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 651 ASN Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 535 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 174 optimal weight: 2.9990 chunk 264 optimal weight: 1.9990 chunk 238 optimal weight: 0.7980 chunk 33 optimal weight: 8.9990 chunk 64 optimal weight: 4.9990 chunk 271 optimal weight: 1.9990 chunk 68 optimal weight: 8.9990 chunk 11 optimal weight: 0.9990 chunk 246 optimal weight: 0.9990 chunk 139 optimal weight: 0.9980 chunk 89 optimal weight: 0.7980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 45 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 45 GLN B 279 ASN B 543 ASN A 66 HIS ** A 377 ASN ** 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 = 0.3549 r_free = 0.3549 target = 0.115209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.088138 restraints weight = 42217.080| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 3.34 r_work: 0.3006 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.3045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24173 Z= 0.144 Angle : 0.631 10.587 32980 Z= 0.313 Chirality : 0.046 0.329 3843 Planarity : 0.004 0.059 4050 Dihedral : 6.493 56.438 4676 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 3.36 % Allowed : 18.63 % Favored : 78.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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 aren not related in a simple way. whole: -0.39 (0.16), residues: 2796 helix: 0.79 (0.27), residues: 386 sheet: 0.21 (0.17), residues: 924 loop : -0.83 (0.16), residues: 1486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG M 42 TYR 0.027 0.001 TYR D 27 PHE 0.025 0.002 PHE F 31 TRP 0.029 0.002 TRP J 36 HIS 0.005 0.001 HIS G 93 Details of bonding type rmsd covalent geometry : bond 0.00330 (24049) covalent geometry : angle 0.60434 (32654) SS BOND : bond 0.00354 ( 46) SS BOND : angle 1.16546 ( 92) hydrogen bonds : bond 0.03670 ( 785) hydrogen bonds : angle 5.24687 ( 2256) link_ALPHA1-2 : bond 0.01724 ( 4) link_ALPHA1-2 : angle 3.00638 ( 12) link_ALPHA1-3 : bond 0.00994 ( 7) link_ALPHA1-3 : angle 1.45391 ( 21) link_ALPHA1-6 : bond 0.00846 ( 5) link_ALPHA1-6 : angle 1.53168 ( 15) link_BETA1-4 : bond 0.00586 ( 16) link_BETA1-4 : angle 1.85188 ( 48) link_NAG-ASN : bond 0.00505 ( 46) link_NAG-ASN : angle 2.32705 ( 138) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5592 Ramachandran restraints generated. 2796 Oldfield, 0 Emsley, 2796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5592 Ramachandran restraints generated. 2796 Oldfield, 0 Emsley, 2796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 441 time to evaluate : 0.971 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: D 72 ASP cc_start: 0.8438 (m-30) cc_final: 0.8104 (m-30) REVERT: D 79 TYR cc_start: 0.8204 (m-80) cc_final: 0.7818 (m-80) REVERT: D 82 ARG cc_start: 0.7734 (mpp80) cc_final: 0.7491 (mpp80) REVERT: D 83 LYS cc_start: 0.8467 (mtmm) cc_final: 0.8041 (mmtt) REVERT: D 108 LEU cc_start: 0.8863 (mm) cc_final: 0.7973 (pt) REVERT: E 6 GLN cc_start: 0.7088 (pm20) cc_final: 0.5726 (pp30) REVERT: E 35 TRP cc_start: 0.7124 (m100) cc_final: 0.6474 (m100) REVERT: E 79 ARG cc_start: 0.8553 (mtt180) cc_final: 0.8248 (ttm110) REVERT: F 36 TRP cc_start: 0.8692 (m100) cc_final: 0.8327 (m100) REVERT: F 43 ARG cc_start: 0.7979 (mmm160) cc_final: 0.7410 (ttt-90) REVERT: F 59 LEU cc_start: 0.7873 (OUTLIER) cc_final: 0.7390 (tp) REVERT: F 81 GLU cc_start: 0.7047 (OUTLIER) cc_final: 0.6399 (tp30) REVERT: F 82 ILE cc_start: 0.6419 (tp) cc_final: 0.5928 (tp) REVERT: F 100 TRP cc_start: 0.4700 (t-100) cc_final: 0.4217 (t-100) REVERT: G 17 GLN cc_start: 0.8783 (mp10) cc_final: 0.7910 (mp10) REVERT: G 37 GLN cc_start: 0.7454 (tt0) cc_final: 0.6854 (tt0) REVERT: G 49 TYR cc_start: 0.8014 (p90) cc_final: 0.7788 (p90) REVERT: J 50 TRP cc_start: 0.7577 (p-90) cc_final: 0.7167 (p-90) REVERT: J 66 ARG cc_start: 0.7104 (tpp80) cc_final: 0.6666 (tpp80) REVERT: J 81 GLU cc_start: 0.8683 (OUTLIER) cc_final: 0.7862 (pp20) REVERT: J 82 ARG cc_start: 0.8524 (ptp90) cc_final: 0.7498 (ptp90) REVERT: K 42 ARG cc_start: 0.6812 (mtt90) cc_final: 0.6433 (mtm-85) REVERT: L 26 ARG cc_start: 0.8506 (tpt90) cc_final: 0.7745 (tpp80) REVERT: L 89 GLN cc_start: 0.8700 (OUTLIER) cc_final: 0.8031 (tt0) REVERT: I 13 LYS cc_start: 0.5462 (tptt) cc_final: 0.5182 (tptt) REVERT: I 64 ASP cc_start: 0.8103 (t0) cc_final: 0.7814 (t0) REVERT: I 76 ASN cc_start: 0.8733 (p0) cc_final: 0.8439 (p0) REVERT: M 24 GLN cc_start: 0.8566 (mm-40) cc_final: 0.8203 (mm-40) REVERT: M 65 SER cc_start: 0.8897 (p) cc_final: 0.8643 (m) REVERT: C 173 TYR cc_start: 0.7859 (p90) cc_final: 0.7580 (p90) REVERT: C 280 ASN cc_start: 0.8899 (p0) cc_final: 0.8695 (p0) REVERT: C 318 TYR cc_start: 0.8950 (m-80) cc_final: 0.8501 (m-80) REVERT: C 381 GLU cc_start: 0.8264 (tt0) cc_final: 0.7946 (tt0) REVERT: C 475 MET cc_start: 0.8321 (tpp) cc_final: 0.8082 (tpp) REVERT: C 519 ARG cc_start: 0.7809 (ptp-110) cc_final: 0.7297 (mtt90) REVERT: B 133 ASP cc_start: 0.8983 (t0) cc_final: 0.8737 (t0) REVERT: B 164 GLU cc_start: 0.7558 (mm-30) cc_final: 0.6263 (pm20) REVERT: B 377 ASN cc_start: 0.8299 (OUTLIER) cc_final: 0.8071 (t0) REVERT: B 585 ARG cc_start: 0.8339 (mtp-110) cc_final: 0.8025 (ptm-80) REVERT: B 652 GLN cc_start: 0.8410 (mp10) cc_final: 0.7967 (mp10) REVERT: A 69 TRP cc_start: 0.7837 (m-90) cc_final: 0.7395 (m-90) REVERT: A 102 GLU cc_start: 0.8425 (mp0) cc_final: 0.7999 (mp0) REVERT: A 320 MET cc_start: 0.8498 (mmm) cc_final: 0.8085 (mmm) REVERT: A 373 MET cc_start: 0.8485 (mmt) cc_final: 0.7624 (mmp) REVERT: A 584 GLU cc_start: 0.8644 (tm-30) cc_final: 0.8164 (tm-30) REVERT: A 655 LYS cc_start: 0.8148 (pttt) cc_final: 0.7733 (ptpp) outliers start: 84 outliers final: 62 residues processed: 484 average time/residue: 0.1881 time to fit residues: 141.2070 Evaluate side-chains 492 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 425 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 92 CYS Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain E residue 89 CYS Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 50 TRP Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 69 MET Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 79 TYR Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain G residue 30 HIS Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain J residue 17 SER Chi-restraints excluded: chain J residue 22 CYS Chi-restraints excluded: chain J residue 24 THR Chi-restraints excluded: chain J residue 63 PHE Chi-restraints excluded: chain J residue 81 GLU Chi-restraints excluded: chain J residue 82 ILE Chi-restraints excluded: chain J residue 82 ASN Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 91 PHE Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain I residue 35 ASN Chi-restraints excluded: chain I residue 80 LEU Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 89 ILE Chi-restraints excluded: chain M residue 45 GLN Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 306 SER Chi-restraints excluded: chain C residue 502 LYS Chi-restraints excluded: chain C residue 660 LEU Chi-restraints excluded: chain B residue 95 MET Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 196 CYS Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 279 ASN Chi-restraints excluded: chain B residue 377 ASN Chi-restraints excluded: chain B residue 426 MET Chi-restraints excluded: chain B residue 445 CYS Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 651 ASN Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 535 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 227 optimal weight: 8.9990 chunk 130 optimal weight: 0.5980 chunk 89 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 119 optimal weight: 3.9990 chunk 51 optimal weight: 6.9990 chunk 253 optimal weight: 4.9990 chunk 57 optimal weight: 4.9990 chunk 234 optimal weight: 4.9990 chunk 92 optimal weight: 0.0170 chunk 40 optimal weight: 7.9990 overall best weight: 2.3224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 45 GLN ** B 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 66 HIS ** A 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.111867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.084722 restraints weight = 43089.000| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 3.29 r_work: 0.2947 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.3278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 24173 Z= 0.263 Angle : 0.718 10.568 32980 Z= 0.358 Chirality : 0.048 0.343 3843 Planarity : 0.004 0.058 4050 Dihedral : 6.851 58.135 4676 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 3.44 % Allowed : 18.43 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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 aren not related in a simple way. whole: -0.53 (0.16), residues: 2796 helix: 0.61 (0.27), residues: 386 sheet: 0.08 (0.17), residues: 957 loop : -0.89 (0.16), residues: 1453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 98 TYR 0.032 0.002 TYR H 100D PHE 0.038 0.002 PHE F 31 TRP 0.034 0.002 TRP J 36 HIS 0.007 0.001 HIS G 93 Details of bonding type rmsd covalent geometry : bond 0.00614 (24049) covalent geometry : angle 0.68995 (32654) SS BOND : bond 0.00524 ( 46) SS BOND : angle 1.41430 ( 92) hydrogen bonds : bond 0.04115 ( 785) hydrogen bonds : angle 5.48235 ( 2256) link_ALPHA1-2 : bond 0.01761 ( 4) link_ALPHA1-2 : angle 2.90935 ( 12) link_ALPHA1-3 : bond 0.00918 ( 7) link_ALPHA1-3 : angle 1.61546 ( 21) link_ALPHA1-6 : bond 0.00716 ( 5) link_ALPHA1-6 : angle 1.61273 ( 15) link_BETA1-4 : bond 0.00565 ( 16) link_BETA1-4 : angle 2.07759 ( 48) link_NAG-ASN : bond 0.00629 ( 46) link_NAG-ASN : angle 2.52774 ( 138) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5592 Ramachandran restraints generated. 2796 Oldfield, 0 Emsley, 2796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5592 Ramachandran restraints generated. 2796 Oldfield, 0 Emsley, 2796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 429 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 72 ASP cc_start: 0.8475 (m-30) cc_final: 0.8102 (m-30) REVERT: D 79 TYR cc_start: 0.8220 (m-80) cc_final: 0.7819 (m-80) REVERT: D 82 ARG cc_start: 0.7787 (mpp80) cc_final: 0.7572 (mpp80) REVERT: D 83 LYS cc_start: 0.8513 (mtmm) cc_final: 0.8066 (mmtt) REVERT: D 108 LEU cc_start: 0.8816 (mm) cc_final: 0.7949 (pt) REVERT: E 35 TRP cc_start: 0.7227 (m100) cc_final: 0.6506 (m100) REVERT: E 36 TYR cc_start: 0.8302 (m-80) cc_final: 0.8050 (m-80) REVERT: E 79 ARG cc_start: 0.8609 (mtt180) cc_final: 0.8243 (ttm110) REVERT: F 36 TRP cc_start: 0.8788 (m100) cc_final: 0.8442 (m100) REVERT: F 43 ARG cc_start: 0.8066 (mmm160) cc_final: 0.7479 (ttt-90) REVERT: F 59 LEU cc_start: 0.7872 (OUTLIER) cc_final: 0.7398 (tp) REVERT: F 81 GLU cc_start: 0.7121 (OUTLIER) cc_final: 0.6443 (tp30) REVERT: F 82 ILE cc_start: 0.6440 (tp) cc_final: 0.5869 (tp) REVERT: F 100 TRP cc_start: 0.4992 (t-100) cc_final: 0.4354 (t-100) REVERT: G 17 GLN cc_start: 0.8755 (mp10) cc_final: 0.7868 (mp10) REVERT: G 30 HIS cc_start: 0.7725 (OUTLIER) cc_final: 0.7506 (t70) REVERT: G 37 GLN cc_start: 0.7557 (tt0) cc_final: 0.6917 (tt0) REVERT: G 49 TYR cc_start: 0.8372 (p90) cc_final: 0.8075 (p90) REVERT: G 77 ASP cc_start: 0.7915 (t0) cc_final: 0.7165 (t0) REVERT: J 66 ARG cc_start: 0.7096 (tpp80) cc_final: 0.6686 (tpp80) REVERT: J 81 GLU cc_start: 0.8705 (OUTLIER) cc_final: 0.7861 (pp20) REVERT: J 82 ARG cc_start: 0.8564 (ptp90) cc_final: 0.7475 (ptp90) REVERT: K 42 ARG cc_start: 0.6844 (mtt90) cc_final: 0.6483 (mtm-85) REVERT: L 26 ARG cc_start: 0.8684 (tpt90) cc_final: 0.7937 (tpp80) REVERT: I 46 GLU cc_start: 0.8069 (mt-10) cc_final: 0.7577 (mt-10) REVERT: I 64 ASP cc_start: 0.8346 (t0) cc_final: 0.8031 (t0) REVERT: M 65 SER cc_start: 0.9011 (p) cc_final: 0.8686 (m) REVERT: C 173 TYR cc_start: 0.7918 (p90) cc_final: 0.7676 (p90) REVERT: C 280 ASN cc_start: 0.8967 (p0) cc_final: 0.8711 (p0) REVERT: C 381 GLU cc_start: 0.8297 (tt0) cc_final: 0.7999 (tt0) REVERT: C 467 ILE cc_start: 0.7768 (OUTLIER) cc_final: 0.7476 (mp) REVERT: C 519 ARG cc_start: 0.7904 (ptp-110) cc_final: 0.7286 (mtt90) REVERT: B 164 GLU cc_start: 0.7762 (mm-30) cc_final: 0.6281 (pm20) REVERT: B 475 MET cc_start: 0.7904 (mmt) cc_final: 0.7459 (mmp) REVERT: B 530 MET cc_start: 0.8935 (mmm) cc_final: 0.8516 (mtp) REVERT: B 585 ARG cc_start: 0.8396 (mtp-110) cc_final: 0.8126 (ptm-80) REVERT: B 591 GLN cc_start: 0.7453 (tt0) cc_final: 0.6901 (mt0) REVERT: B 652 GLN cc_start: 0.8474 (mp10) cc_final: 0.7999 (mp10) REVERT: A 102 GLU cc_start: 0.8535 (mp0) cc_final: 0.8095 (mp0) REVERT: A 107 ASP cc_start: 0.8104 (m-30) cc_final: 0.7606 (m-30) REVERT: A 320 MET cc_start: 0.8549 (mmm) cc_final: 0.8094 (mmm) REVERT: A 373 MET cc_start: 0.8635 (mmt) cc_final: 0.7734 (mmp) REVERT: A 584 GLU cc_start: 0.8679 (tm-30) cc_final: 0.8210 (tm-30) REVERT: A 655 LYS cc_start: 0.8200 (pttt) cc_final: 0.7743 (ptpp) outliers start: 86 outliers final: 71 residues processed: 471 average time/residue: 0.1874 time to fit residues: 135.4209 Evaluate side-chains 498 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 422 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 92 CYS Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 89 CYS Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 50 TRP Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 68 ILE Chi-restraints excluded: chain F residue 69 MET Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 79 TYR Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain G residue 30 HIS Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain J residue 17 SER Chi-restraints excluded: chain J residue 22 CYS Chi-restraints excluded: chain J residue 24 THR Chi-restraints excluded: chain J residue 63 PHE Chi-restraints excluded: chain J residue 81 GLU Chi-restraints excluded: chain J residue 82 ILE Chi-restraints excluded: chain J residue 82 ASN Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 91 PHE Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 64 ASP Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain I residue 35 ASN Chi-restraints excluded: chain I residue 80 LEU Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 89 ILE Chi-restraints excluded: chain M residue 45 GLN Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 467 ILE Chi-restraints excluded: chain C residue 502 LYS Chi-restraints excluded: chain C residue 639 THR Chi-restraints excluded: chain C residue 660 LEU Chi-restraints excluded: chain B residue 95 MET Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 196 CYS Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 426 MET Chi-restraints excluded: chain B residue 445 CYS Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 651 ASN Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 535 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 72 optimal weight: 1.9990 chunk 194 optimal weight: 3.9990 chunk 233 optimal weight: 1.9990 chunk 261 optimal weight: 0.5980 chunk 157 optimal weight: 6.9990 chunk 15 optimal weight: 6.9990 chunk 204 optimal weight: 2.9990 chunk 215 optimal weight: 3.9990 chunk 270 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 254 optimal weight: 3.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN L 45 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 45 GLN ** B 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 66 HIS ** A 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.113348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.086235 restraints weight = 42854.202| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 3.35 r_work: 0.2967 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.3318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 24173 Z= 0.192 Angle : 0.676 12.431 32980 Z= 0.336 Chirality : 0.047 0.333 3843 Planarity : 0.004 0.060 4050 Dihedral : 6.748 56.254 4676 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 3.12 % Allowed : 18.94 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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 aren not related in a simple way. whole: -0.51 (0.16), residues: 2796 helix: 0.68 (0.27), residues: 386 sheet: 0.08 (0.17), residues: 957 loop : -0.87 (0.16), residues: 1453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 42 TYR 0.044 0.002 TYR H 100D PHE 0.035 0.002 PHE F 31 TRP 0.033 0.002 TRP J 36 HIS 0.006 0.001 HIS G 93 Details of bonding type rmsd covalent geometry : bond 0.00444 (24049) covalent geometry : angle 0.64844 (32654) SS BOND : bond 0.00436 ( 46) SS BOND : angle 1.22477 ( 92) hydrogen bonds : bond 0.03876 ( 785) hydrogen bonds : angle 5.40471 ( 2256) link_ALPHA1-2 : bond 0.01672 ( 4) link_ALPHA1-2 : angle 3.00477 ( 12) link_ALPHA1-3 : bond 0.00929 ( 7) link_ALPHA1-3 : angle 1.47372 ( 21) link_ALPHA1-6 : bond 0.00837 ( 5) link_ALPHA1-6 : angle 1.55332 ( 15) link_BETA1-4 : bond 0.00564 ( 16) link_BETA1-4 : angle 1.92371 ( 48) link_NAG-ASN : bond 0.00538 ( 46) link_NAG-ASN : angle 2.43398 ( 138) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5592 Ramachandran restraints generated. 2796 Oldfield, 0 Emsley, 2796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5592 Ramachandran restraints generated. 2796 Oldfield, 0 Emsley, 2796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 438 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 82 ARG cc_start: 0.7792 (mpp80) cc_final: 0.7583 (mpp80) REVERT: D 83 LYS cc_start: 0.8447 (mtmm) cc_final: 0.8022 (mmtt) REVERT: D 108 LEU cc_start: 0.8792 (mm) cc_final: 0.7928 (pt) REVERT: E 6 GLN cc_start: 0.7271 (pm20) cc_final: 0.7060 (pm20) REVERT: E 35 TRP cc_start: 0.7143 (m100) cc_final: 0.6463 (m100) REVERT: E 38 TRP cc_start: 0.8894 (t60) cc_final: 0.8553 (t60) REVERT: E 81 GLU cc_start: 0.8278 (pm20) cc_final: 0.7464 (pm20) REVERT: E 102 THR cc_start: 0.7842 (OUTLIER) cc_final: 0.7481 (m) REVERT: F 36 TRP cc_start: 0.8744 (m100) cc_final: 0.8340 (m100) REVERT: F 43 ARG cc_start: 0.8065 (mmm160) cc_final: 0.7511 (ttt-90) REVERT: F 59 LEU cc_start: 0.7913 (OUTLIER) cc_final: 0.7471 (tp) REVERT: F 81 GLU cc_start: 0.7062 (OUTLIER) cc_final: 0.6389 (tp30) REVERT: F 82 ILE cc_start: 0.6463 (tp) cc_final: 0.5931 (tp) REVERT: F 100 TRP cc_start: 0.4887 (t-100) cc_final: 0.4301 (t-100) REVERT: G 17 GLN cc_start: 0.8734 (mp10) cc_final: 0.7888 (mp10) REVERT: G 37 GLN cc_start: 0.7533 (tt0) cc_final: 0.6906 (tt0) REVERT: G 49 TYR cc_start: 0.8251 (p90) cc_final: 0.7985 (p90) REVERT: G 77 ASP cc_start: 0.7830 (t0) cc_final: 0.7198 (t0) REVERT: G 79 ARG cc_start: 0.7644 (mmp80) cc_final: 0.7428 (mmp80) REVERT: J 66 ARG cc_start: 0.7119 (tpp80) cc_final: 0.6728 (tpp80) REVERT: J 81 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.7891 (pp20) REVERT: J 82 ARG cc_start: 0.8554 (ptp90) cc_final: 0.7472 (ptp90) REVERT: L 26 ARG cc_start: 0.8597 (tpt90) cc_final: 0.7854 (tpp80) REVERT: I 13 LYS cc_start: 0.5476 (tptt) cc_final: 0.5204 (tptt) REVERT: I 46 GLU cc_start: 0.8094 (mt-10) cc_final: 0.7591 (pt0) REVERT: I 64 ASP cc_start: 0.8215 (t0) cc_final: 0.7894 (t0) REVERT: M 45 GLN cc_start: 0.8461 (OUTLIER) cc_final: 0.8099 (mt0) REVERT: M 65 SER cc_start: 0.8965 (p) cc_final: 0.8667 (m) REVERT: C 173 TYR cc_start: 0.7883 (p90) cc_final: 0.7643 (p90) REVERT: C 280 ASN cc_start: 0.8955 (p0) cc_final: 0.8737 (p0) REVERT: C 381 GLU cc_start: 0.8288 (tt0) cc_final: 0.8022 (tt0) REVERT: C 467 ILE cc_start: 0.7785 (OUTLIER) cc_final: 0.7490 (mp) REVERT: C 475 MET cc_start: 0.8369 (tpp) cc_final: 0.8117 (tpp) REVERT: C 519 ARG cc_start: 0.7915 (ptp-110) cc_final: 0.7293 (mtt90) REVERT: B 164 GLU cc_start: 0.7643 (mm-30) cc_final: 0.6285 (pm20) REVERT: B 467 ILE cc_start: 0.9130 (mm) cc_final: 0.8803 (mm) REVERT: B 475 MET cc_start: 0.7865 (mmt) cc_final: 0.7394 (mmp) REVERT: B 530 MET cc_start: 0.8845 (mmm) cc_final: 0.8327 (mtp) REVERT: B 585 ARG cc_start: 0.8371 (mtp-110) cc_final: 0.8115 (ptm-80) REVERT: B 591 GLN cc_start: 0.7429 (tt0) cc_final: 0.6829 (mt0) REVERT: B 652 GLN cc_start: 0.8418 (mp10) cc_final: 0.7813 (mp10) REVERT: B 656 ASN cc_start: 0.8171 (m-40) cc_final: 0.7964 (m-40) REVERT: A 69 TRP cc_start: 0.7919 (m-90) cc_final: 0.7464 (m-90) REVERT: A 102 GLU cc_start: 0.8439 (mp0) cc_final: 0.8012 (mp0) REVERT: A 107 ASP cc_start: 0.8180 (m-30) cc_final: 0.7688 (m-30) REVERT: A 320 MET cc_start: 0.8499 (mmm) cc_final: 0.8044 (mmm) REVERT: A 373 MET cc_start: 0.8525 (mmt) cc_final: 0.7652 (mmp) REVERT: A 488 VAL cc_start: 0.8761 (t) cc_final: 0.8538 (p) REVERT: A 584 GLU cc_start: 0.8674 (tm-30) cc_final: 0.8183 (tm-30) REVERT: A 655 LYS cc_start: 0.8194 (pttt) cc_final: 0.7738 (ptpp) outliers start: 78 outliers final: 64 residues processed: 478 average time/residue: 0.1823 time to fit residues: 134.2622 Evaluate side-chains 498 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 428 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 92 CYS Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 89 CYS Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 50 TRP Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 69 MET Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 79 TYR Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain J residue 17 SER Chi-restraints excluded: chain J residue 22 CYS Chi-restraints excluded: chain J residue 24 THR Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 81 GLU Chi-restraints excluded: chain J residue 82 ILE Chi-restraints excluded: chain J residue 82 ASN Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 91 PHE Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 64 ASP Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain I residue 80 LEU Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 89 ILE Chi-restraints excluded: chain M residue 45 GLN Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 467 ILE Chi-restraints excluded: chain C residue 502 LYS Chi-restraints excluded: chain C residue 639 THR Chi-restraints excluded: chain B residue 95 MET Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 196 CYS Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 426 MET Chi-restraints excluded: chain B residue 445 CYS Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 651 ASN Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 351 GLU Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 535 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 197 optimal weight: 0.6980 chunk 169 optimal weight: 0.9990 chunk 146 optimal weight: 0.9980 chunk 148 optimal weight: 5.9990 chunk 260 optimal weight: 2.9990 chunk 240 optimal weight: 4.9990 chunk 113 optimal weight: 0.9990 chunk 206 optimal weight: 3.9990 chunk 277 optimal weight: 3.9990 chunk 264 optimal weight: 4.9990 chunk 182 optimal weight: 0.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 45 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 45 GLN B 279 ASN B 377 ASN B 543 ASN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 66 HIS ** A 377 ASN ** 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 = 0.3546 r_free = 0.3546 target = 0.114850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.087777 restraints weight = 42403.358| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 3.34 r_work: 0.2997 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.3352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24173 Z= 0.150 Angle : 0.652 12.970 32980 Z= 0.326 Chirality : 0.046 0.330 3843 Planarity : 0.004 0.058 4050 Dihedral : 6.564 57.169 4676 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 3.08 % Allowed : 19.46 % Favored : 77.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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 aren not related in a simple way. whole: -0.42 (0.16), residues: 2796 helix: 0.71 (0.27), residues: 386 sheet: 0.14 (0.17), residues: 955 loop : -0.80 (0.16), residues: 1455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG M 42 TYR 0.040 0.002 TYR H 100D PHE 0.026 0.002 PHE F 31 TRP 0.060 0.002 TRP F 47 HIS 0.006 0.001 HIS G 93 Details of bonding type rmsd covalent geometry : bond 0.00343 (24049) covalent geometry : angle 0.62624 (32654) SS BOND : bond 0.00369 ( 46) SS BOND : angle 1.14502 ( 92) hydrogen bonds : bond 0.03698 ( 785) hydrogen bonds : angle 5.33917 ( 2256) link_ALPHA1-2 : bond 0.01732 ( 4) link_ALPHA1-2 : angle 2.98506 ( 12) link_ALPHA1-3 : bond 0.00943 ( 7) link_ALPHA1-3 : angle 1.40879 ( 21) link_ALPHA1-6 : bond 0.00852 ( 5) link_ALPHA1-6 : angle 1.50730 ( 15) link_BETA1-4 : bond 0.00578 ( 16) link_BETA1-4 : angle 1.86467 ( 48) link_NAG-ASN : bond 0.00501 ( 46) link_NAG-ASN : angle 2.34476 ( 138) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4821.86 seconds wall clock time: 84 minutes 5.79 seconds (5045.79 seconds total)