Starting phenix.real_space_refine on Fri Jun 20 09:59:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cu5_45928/06_2025/9cu5_45928.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cu5_45928/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9cu5_45928/06_2025/9cu5_45928.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cu5_45928/06_2025/9cu5_45928.map" model { file = "/net/cci-nas-00/data/ceres_data/9cu5_45928/06_2025/9cu5_45928.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cu5_45928/06_2025/9cu5_45928.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 14.16, per 1000 atoms: 0.60 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: 5.93 Conformation dependent library (CDL) restraints added in 2.6 seconds 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: 3.37 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: 8.87 Time building geometry restraints manager: 7.09 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 663 or resid 701 through 712)) selection = (chain 'B' and (resid 32 through 57 or resid 66 through 161 or resid 169 through \ 663 or resid 701 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 663 or resid 701 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: 7.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.810 Check model and map are aligned: 0.160 Set scattering table: 0.180 Process input model: 53.050 Find NCS groups from input model: 1.410 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.720 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.024 0.002 TRP F 36 HIS 0.012 0.002 HIS A 374 PHE 0.061 0.003 PHE B 522 TYR 0.054 0.003 TYR A 39 ARG 0.035 0.003 ARG E 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00597 ( 46) link_NAG-ASN : angle 2.69751 ( 138) 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_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) hydrogen bonds : bond 0.14500 ( 785) hydrogen bonds : angle 7.44580 ( 2256) SS BOND : bond 0.11486 ( 46) SS BOND : angle 6.58790 ( 92) covalent geometry : bond 0.00599 (24049) covalent geometry : angle 1.05726 (32654) *********************** 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 : 2.929 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: 0.6867 (t0) REVERT: I 111 VAL cc_start: 0.7987 (t) cc_final: 0.7699 (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: 0.3779 time to fit residues: 304.2021 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 : 2.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 236 optimal weight: 4.9990 chunk 212 optimal weight: 0.3980 chunk 117 optimal weight: 0.0370 chunk 72 optimal weight: 2.9990 chunk 143 optimal weight: 4.9990 chunk 113 optimal weight: 1.9990 chunk 219 optimal weight: 5.9990 chunk 84 optimal weight: 1.9990 chunk 133 optimal weight: 0.5980 chunk 163 optimal weight: 2.9990 chunk 254 optimal weight: 5.9990 overall best weight: 1.0062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 39 GLN J 82BASN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 45 GLN M 55 HIS C 103 GLN C 396 ASN ** C 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 114 GLN A 66 HIS ** A 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.121251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.094402 restraints weight = 42078.164| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 3.37 r_work: 0.3098 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.1324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 24173 Z= 0.162 Angle : 0.696 10.079 32980 Z= 0.347 Chirality : 0.047 0.389 3843 Planarity : 0.004 0.054 4050 Dihedral : 8.558 81.520 4676 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.20 % Allowed : 15.07 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.16), residues: 2796 helix: 0.78 (0.26), residues: 377 sheet: 0.16 (0.17), residues: 913 loop : -0.98 (0.15), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP F 100D HIS 0.010 0.001 HIS G 93 PHE 0.023 0.002 PHE F 31 TYR 0.018 0.002 TYR F 27 ARG 0.010 0.001 ARG F 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00644 ( 46) link_NAG-ASN : angle 2.77928 ( 138) link_ALPHA1-6 : bond 0.00700 ( 5) link_ALPHA1-6 : angle 1.64593 ( 15) link_BETA1-4 : bond 0.00597 ( 16) link_BETA1-4 : angle 2.37606 ( 48) link_ALPHA1-2 : bond 0.01760 ( 4) link_ALPHA1-2 : angle 3.23971 ( 12) link_ALPHA1-3 : bond 0.00957 ( 7) link_ALPHA1-3 : angle 1.72923 ( 21) hydrogen bonds : bond 0.04368 ( 785) hydrogen bonds : angle 5.91827 ( 2256) SS BOND : bond 0.00522 ( 46) SS BOND : angle 1.12877 ( 92) covalent geometry : bond 0.00371 (24049) covalent geometry : angle 0.66150 (32654) *********************** 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 543 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 488 time to evaluate : 2.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 46 GLU cc_start: 0.7008 (mp0) cc_final: 0.6642 (pm20) REVERT: D 65 ASP cc_start: 0.8454 (p0) cc_final: 0.8131 (p0) REVERT: D 72 ASP cc_start: 0.8933 (m-30) cc_final: 0.8606 (m-30) REVERT: D 83 LYS cc_start: 0.8392 (mttp) cc_final: 0.8179 (mmmt) REVERT: E 29 SER cc_start: 0.8513 (t) cc_final: 0.8300 (m) REVERT: E 79 ARG cc_start: 0.8650 (mtt180) cc_final: 0.8281 (ttm110) REVERT: E 81 GLU cc_start: 0.8302 (pm20) cc_final: 0.7622 (pm20) REVERT: F 6 GLN cc_start: 0.7888 (mp10) cc_final: 0.7219 (mp10) REVERT: F 81 GLU cc_start: 0.7273 (tp30) cc_final: 0.6747 (tp30) REVERT: G 17 GLN cc_start: 0.8724 (mp10) cc_final: 0.7946 (mp10) REVERT: G 37 GLN cc_start: 0.7364 (tt0) cc_final: 0.6801 (tt0) REVERT: J 91 PHE cc_start: 0.7564 (m-80) cc_final: 0.7244 (m-80) REVERT: K 61 ARG cc_start: 0.6612 (ttp80) cc_final: 0.6264 (ttp80) REVERT: K 77 ASP cc_start: 0.7253 (t70) cc_final: 0.6942 (t0) REVERT: H 105 ARG cc_start: 0.8122 (mtp-110) cc_final: 0.7446 (mtm110) REVERT: L 4 MET cc_start: 0.8449 (mmm) cc_final: 0.8106 (mmm) REVERT: L 26 ARG cc_start: 0.8456 (tpt90) cc_final: 0.7836 (tpp80) REVERT: L 89 GLN cc_start: 0.8904 (OUTLIER) cc_final: 0.8438 (tt0) REVERT: C 50 THR cc_start: 0.8889 (t) cc_final: 0.8649 (t) REVERT: C 127 VAL cc_start: 0.8762 (t) cc_final: 0.8502 (m) REVERT: C 280 ASN cc_start: 0.8894 (p0) cc_final: 0.8662 (p0) REVERT: C 322 GLU cc_start: 0.8277 (mm-30) cc_final: 0.7935 (pm20) REVERT: C 502 LYS cc_start: 0.8546 (OUTLIER) cc_final: 0.7847 (tptm) REVERT: C 650 GLN cc_start: 0.7452 (mm-40) cc_final: 0.6942 (mm-40) REVERT: B 164 GLU cc_start: 0.7653 (mm-30) cc_final: 0.6387 (pm20) REVERT: B 490 LYS cc_start: 0.8522 (tttp) cc_final: 0.8302 (tttp) REVERT: B 585 ARG cc_start: 0.8186 (mtp-110) cc_final: 0.7588 (ptm-80) REVERT: A 330 HIS cc_start: 0.8248 (p-80) cc_final: 0.7821 (p-80) REVERT: A 373 MET cc_start: 0.8237 (mmt) cc_final: 0.7349 (mmp) REVERT: A 377 ASN cc_start: 0.8380 (t0) cc_final: 0.8165 (t0) REVERT: A 434 MET cc_start: 0.8674 (ttp) cc_final: 0.8297 (ttt) REVERT: A 484 TYR cc_start: 0.9042 (p90) cc_final: 0.8305 (p90) REVERT: A 530 MET cc_start: 0.8842 (mtp) cc_final: 0.8594 (mtp) REVERT: A 577 GLN cc_start: 0.8360 (tp40) cc_final: 0.7992 (mm110) REVERT: A 584 GLU cc_start: 0.8618 (tm-30) cc_final: 0.8333 (tm-30) REVERT: A 654 GLU cc_start: 0.8491 (tp30) cc_final: 0.8263 (pt0) REVERT: A 655 LYS cc_start: 0.7977 (pttt) cc_final: 0.7631 (ptpp) outliers start: 55 outliers final: 37 residues processed: 511 average time/residue: 0.3770 time to fit residues: 297.8683 Evaluate side-chains 478 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 439 time to evaluate : 2.518 ------------------------------------------------------------------------------- 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 538 THR 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 32 optimal weight: 9.9990 chunk 279 optimal weight: 9.9990 chunk 98 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 198 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 148 optimal weight: 6.9990 chunk 58 optimal weight: 10.0000 chunk 208 optimal weight: 3.9990 chunk 225 optimal weight: 3.9990 chunk 150 optimal weight: 0.7980 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 6 GLN ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 55 HIS I 96 ASN M 90 GLN C 103 GLN C 422 GLN C 656 ASN A 66 HIS A 352 GLN ** A 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 651 ASN A 656 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.112466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.084904 restraints weight = 42980.016| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 3.36 r_work: 0.2953 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 24173 Z= 0.291 Angle : 0.766 10.280 32980 Z= 0.383 Chirality : 0.050 0.364 3843 Planarity : 0.005 0.051 4050 Dihedral : 7.941 68.674 4676 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 4.16 % Allowed : 14.95 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.16), residues: 2796 helix: 0.55 (0.26), residues: 379 sheet: 0.00 (0.17), residues: 912 loop : -1.02 (0.15), residues: 1505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP F 50 HIS 0.007 0.002 HIS G 93 PHE 0.030 0.003 PHE F 31 TYR 0.025 0.002 TYR C 302 ARG 0.009 0.001 ARG H 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00697 ( 46) link_NAG-ASN : angle 2.82352 ( 138) link_ALPHA1-6 : bond 0.00574 ( 5) link_ALPHA1-6 : angle 1.73511 ( 15) link_BETA1-4 : bond 0.00676 ( 16) link_BETA1-4 : angle 2.31399 ( 48) link_ALPHA1-2 : bond 0.01660 ( 4) link_ALPHA1-2 : angle 3.17569 ( 12) link_ALPHA1-3 : bond 0.00923 ( 7) link_ALPHA1-3 : angle 1.81658 ( 21) hydrogen bonds : bond 0.04625 ( 785) hydrogen bonds : angle 5.75026 ( 2256) SS BOND : bond 0.00736 ( 46) SS BOND : angle 1.47499 ( 92) covalent geometry : bond 0.00679 (24049) covalent geometry : angle 0.73318 (32654) *********************** 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 557 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 453 time to evaluate : 2.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 36 TRP cc_start: 0.8199 (m100) cc_final: 0.7948 (m100) REVERT: D 46 GLU cc_start: 0.7183 (mp0) cc_final: 0.6932 (mp0) REVERT: D 82 ARG cc_start: 0.6948 (mtm-85) cc_final: 0.6497 (mpp80) REVERT: D 108 LEU cc_start: 0.8896 (mm) cc_final: 0.8010 (pt) REVERT: E 38 TRP cc_start: 0.8882 (t60) cc_final: 0.8679 (t60) REVERT: E 79 ARG cc_start: 0.8660 (mtt180) cc_final: 0.8307 (ttm110) REVERT: E 81 GLU cc_start: 0.8312 (pm20) cc_final: 0.7607 (pm20) REVERT: F 43 ARG cc_start: 0.7969 (mmm160) cc_final: 0.7399 (ttt-90) REVERT: F 48 MET cc_start: 0.8063 (mmt) cc_final: 0.7811 (mmt) REVERT: F 50 TRP cc_start: 0.3855 (m-90) cc_final: 0.3129 (m-90) REVERT: F 81 GLU cc_start: 0.7159 (tp30) cc_final: 0.6583 (tp30) REVERT: F 82 ILE cc_start: 0.6852 (tp) cc_final: 0.6399 (tp) REVERT: G 17 GLN cc_start: 0.8754 (mp10) cc_final: 0.7929 (mp10) REVERT: G 37 GLN cc_start: 0.7622 (tt0) cc_final: 0.7161 (tt0) REVERT: G 58 ILE cc_start: 0.8091 (mm) cc_final: 0.7859 (mt) REVERT: G 77 ASP cc_start: 0.7686 (t0) cc_final: 0.7033 (t0) REVERT: J 36 TRP cc_start: 0.8544 (m100) cc_final: 0.8200 (m100) REVERT: J 66 ARG cc_start: 0.7164 (tpp80) cc_final: 0.6961 (tpp80) REVERT: J 91 PHE cc_start: 0.7615 (m-80) cc_final: 0.7414 (m-80) REVERT: K 42 ARG cc_start: 0.6756 (mtt90) cc_final: 0.6399 (mtm-85) REVERT: L 4 MET cc_start: 0.8880 (mmm) cc_final: 0.8538 (mmt) REVERT: L 26 ARG cc_start: 0.8687 (tpt90) cc_final: 0.8092 (tpp80) REVERT: L 48 ILE cc_start: 0.9051 (mm) cc_final: 0.8735 (mm) REVERT: L 89 GLN cc_start: 0.8961 (tt0) cc_final: 0.8459 (tt0) REVERT: I 105 ARG cc_start: 0.8614 (mtp85) cc_final: 0.8409 (mtp85) REVERT: M 69 ARG cc_start: 0.8995 (OUTLIER) cc_final: 0.8696 (ptm160) REVERT: C 127 VAL cc_start: 0.8764 (t) cc_final: 0.8528 (m) REVERT: C 173 TYR cc_start: 0.8027 (p90) cc_final: 0.7810 (p90) REVERT: C 280 ASN cc_start: 0.8920 (p0) cc_final: 0.8676 (p0) REVERT: C 322 GLU cc_start: 0.8351 (mm-30) cc_final: 0.8084 (pm20) REVERT: C 377 ASN cc_start: 0.8681 (t0) cc_final: 0.8442 (t0) REVERT: C 475 MET cc_start: 0.8553 (tpp) cc_final: 0.8206 (tpp) REVERT: C 629 MET cc_start: 0.8351 (mmm) cc_final: 0.7821 (mmm) REVERT: C 650 GLN cc_start: 0.7677 (mm-40) cc_final: 0.6862 (mm-40) REVERT: B 164 GLU cc_start: 0.7804 (mm-30) cc_final: 0.6534 (pm20) REVERT: B 530 MET cc_start: 0.8926 (mmm) cc_final: 0.8465 (mtp) REVERT: B 585 ARG cc_start: 0.8254 (mtp-110) cc_final: 0.7925 (ptm-80) REVERT: A 116 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7750 (mp) REVERT: A 373 MET cc_start: 0.8522 (mmt) cc_final: 0.7601 (mmp) REVERT: A 377 ASN cc_start: 0.8674 (t0) cc_final: 0.8432 (t0) REVERT: A 482 GLU cc_start: 0.8629 (tt0) cc_final: 0.8258 (tt0) REVERT: A 584 GLU cc_start: 0.8684 (tm-30) cc_final: 0.8313 (tm-30) REVERT: A 606 THR cc_start: 0.9210 (OUTLIER) cc_final: 0.9006 (p) REVERT: A 654 GLU cc_start: 0.8494 (tp30) cc_final: 0.8217 (pt0) REVERT: A 655 LYS cc_start: 0.8042 (pttt) cc_final: 0.7650 (ptpp) outliers start: 104 outliers final: 65 residues processed: 513 average time/residue: 0.4417 time to fit residues: 349.8812 Evaluate side-chains 486 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 418 time to evaluate : 2.621 ------------------------------------------------------------------------------- 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 34 ILE 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 82 ILE Chi-restraints excluded: chain J residue 82 LEU 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 64 ASP Chi-restraints excluded: chain H residue 68 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 33 LEU 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 58 VAL Chi-restraints excluded: chain M residue 69 ARG Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 244 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 68 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 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 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 529 THR 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 176 optimal weight: 1.9990 chunk 251 optimal weight: 8.9990 chunk 18 optimal weight: 6.9990 chunk 179 optimal weight: 1.9990 chunk 178 optimal weight: 0.5980 chunk 75 optimal weight: 1.9990 chunk 242 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 279 optimal weight: 10.0000 chunk 165 optimal weight: 1.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 65 ASN L 24 GLN M 45 GLN M 76 ASN C 103 GLN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 651 ASN A 66 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.113329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.085899 restraints weight = 42961.396| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 3.36 r_work: 0.2968 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 24173 Z= 0.208 Angle : 0.678 10.065 32980 Z= 0.337 Chirality : 0.047 0.354 3843 Planarity : 0.004 0.052 4050 Dihedral : 7.411 60.192 4676 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 3.44 % Allowed : 17.23 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.16), residues: 2796 helix: 0.62 (0.27), residues: 381 sheet: 0.02 (0.17), residues: 928 loop : -0.95 (0.16), residues: 1487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 69 HIS 0.006 0.001 HIS G 93 PHE 0.021 0.002 PHE F 31 TYR 0.023 0.002 TYR D 27 ARG 0.005 0.001 ARG E 42 Details of bonding type rmsd link_NAG-ASN : bond 0.00645 ( 46) link_NAG-ASN : angle 2.61281 ( 138) link_ALPHA1-6 : bond 0.00770 ( 5) link_ALPHA1-6 : angle 1.62809 ( 15) link_BETA1-4 : bond 0.00583 ( 16) link_BETA1-4 : angle 2.05553 ( 48) link_ALPHA1-2 : bond 0.01613 ( 4) link_ALPHA1-2 : angle 3.21911 ( 12) link_ALPHA1-3 : bond 0.00966 ( 7) link_ALPHA1-3 : angle 1.68196 ( 21) hydrogen bonds : bond 0.04089 ( 785) hydrogen bonds : angle 5.52514 ( 2256) SS BOND : bond 0.00453 ( 46) SS BOND : angle 1.48562 ( 92) covalent geometry : bond 0.00484 (24049) covalent geometry : angle 0.64531 (32654) *********************** 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: 86 poor density : 444 time to evaluate : 2.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 46 GLU cc_start: 0.6961 (mp0) cc_final: 0.6701 (mp0) REVERT: D 79 TYR cc_start: 0.8223 (m-80) cc_final: 0.8002 (m-80) REVERT: D 82 ARG cc_start: 0.6818 (mtm-85) cc_final: 0.6463 (mpp80) REVERT: D 82 ASN cc_start: 0.7785 (p0) cc_final: 0.6948 (p0) REVERT: D 83 LYS cc_start: 0.8400 (mtmm) cc_final: 0.7879 (mmtt) REVERT: D 108 LEU cc_start: 0.8908 (mm) cc_final: 0.8024 (pt) REVERT: E 54 ARG cc_start: 0.7904 (OUTLIER) cc_final: 0.7582 (mtm180) REVERT: E 79 ARG cc_start: 0.8649 (mtt180) cc_final: 0.8313 (ttm110) REVERT: E 81 GLU cc_start: 0.8401 (pm20) cc_final: 0.7870 (pm20) REVERT: F 43 ARG cc_start: 0.7929 (mmm160) cc_final: 0.7492 (ttt-90) REVERT: F 50 TRP cc_start: 0.3354 (m-90) cc_final: 0.2857 (m-90) REVERT: F 58 ASN cc_start: 0.7830 (t0) cc_final: 0.6631 (t0) REVERT: F 81 GLU cc_start: 0.7127 (tp30) cc_final: 0.6542 (tp30) REVERT: F 82 ILE cc_start: 0.6959 (tp) cc_final: 0.6556 (tp) REVERT: F 100 TRP cc_start: 0.5046 (t-100) cc_final: 0.4768 (t-100) REVERT: G 17 GLN cc_start: 0.8732 (mp10) cc_final: 0.7873 (mp10) REVERT: G 37 GLN cc_start: 0.7518 (tt0) cc_final: 0.6883 (tt0) REVERT: J 36 TRP cc_start: 0.8463 (m100) cc_final: 0.8042 (m100) REVERT: J 66 ARG cc_start: 0.7344 (tpp80) cc_final: 0.7114 (tpp80) REVERT: K 42 ARG cc_start: 0.6907 (mtt90) cc_final: 0.6451 (mtm-85) REVERT: H 80 LEU cc_start: 0.9257 (OUTLIER) cc_final: 0.9032 (tp) REVERT: L 26 ARG cc_start: 0.8601 (tpt90) cc_final: 0.7781 (tpp80) REVERT: L 36 TYR cc_start: 0.8979 (m-80) cc_final: 0.8272 (m-10) REVERT: L 48 ILE cc_start: 0.8912 (mm) cc_final: 0.8590 (mm) REVERT: L 89 GLN cc_start: 0.8956 (tt0) cc_final: 0.8370 (tt0) REVERT: M 65 SER cc_start: 0.8908 (p) cc_final: 0.8512 (m) REVERT: M 69 ARG cc_start: 0.8853 (OUTLIER) cc_final: 0.8534 (ptm160) REVERT: C 173 TYR cc_start: 0.7992 (p90) cc_final: 0.7759 (p90) REVERT: C 280 ASN cc_start: 0.8927 (p0) cc_final: 0.8718 (p0) REVERT: C 322 GLU cc_start: 0.8322 (mm-30) cc_final: 0.8071 (mm-30) REVERT: C 377 ASN cc_start: 0.8532 (t0) cc_final: 0.8300 (t0) REVERT: C 629 MET cc_start: 0.8132 (mmm) cc_final: 0.7696 (mmm) REVERT: B 164 GLU cc_start: 0.7873 (mm-30) cc_final: 0.6259 (pm20) REVERT: B 475 MET cc_start: 0.7821 (mmt) cc_final: 0.7545 (mmp) REVERT: B 530 MET cc_start: 0.8876 (mmm) cc_final: 0.8339 (mtp) REVERT: B 585 ARG cc_start: 0.8424 (mtp-110) cc_final: 0.7791 (ptm-80) REVERT: A 116 LEU cc_start: 0.7992 (OUTLIER) cc_final: 0.7724 (mp) REVERT: A 373 MET cc_start: 0.8512 (mmt) cc_final: 0.7577 (mmp) REVERT: A 584 GLU cc_start: 0.8677 (tm-30) cc_final: 0.8261 (tm-30) REVERT: A 606 THR cc_start: 0.9224 (p) cc_final: 0.9019 (p) REVERT: A 655 LYS cc_start: 0.8042 (pttt) cc_final: 0.7609 (ptmm) outliers start: 86 outliers final: 57 residues processed: 490 average time/residue: 0.3678 time to fit residues: 278.3206 Evaluate side-chains 474 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 413 time to evaluate : 2.468 ------------------------------------------------------------------------------- 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 54 ARG 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 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 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 24 THR Chi-restraints excluded: chain J residue 63 PHE Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 107 THR Chi-restraints excluded: chain K residue 11 VAL 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 7 SER Chi-restraints excluded: chain H residue 57 THR 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 80 LEU 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 65 SER 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 45 GLN Chi-restraints excluded: chain M residue 69 ARG 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 180 ASP 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 68 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 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 A residue 114 GLN Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 374 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 1 optimal weight: 5.9990 chunk 256 optimal weight: 0.0770 chunk 240 optimal weight: 4.9990 chunk 181 optimal weight: 0.9990 chunk 232 optimal weight: 0.6980 chunk 22 optimal weight: 10.0000 chunk 16 optimal weight: 2.9990 chunk 36 optimal weight: 7.9990 chunk 200 optimal weight: 0.9980 chunk 28 optimal weight: 6.9990 chunk 270 optimal weight: 4.9990 overall best weight: 1.1542 ------------------------------------------------------------------------------- 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** E 37 GLN ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 79 GLN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 651 ASN A 66 HIS A 363 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 = 0.3541 r_free = 0.3541 target = 0.114487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.087174 restraints weight = 42663.200| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 3.35 r_work: 0.2986 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 24173 Z= 0.161 Angle : 0.643 9.518 32980 Z= 0.318 Chirality : 0.046 0.348 3843 Planarity : 0.004 0.054 4050 Dihedral : 7.072 57.781 4676 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 3.76 % Allowed : 17.51 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.16), residues: 2796 helix: 0.66 (0.27), residues: 386 sheet: 0.18 (0.17), residues: 903 loop : -0.94 (0.16), residues: 1507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP F 36 HIS 0.005 0.001 HIS G 93 PHE 0.032 0.002 PHE B 522 TYR 0.022 0.001 TYR G 49 ARG 0.006 0.000 ARG E 42 Details of bonding type rmsd link_NAG-ASN : bond 0.00553 ( 46) link_NAG-ASN : angle 2.50602 ( 138) link_ALPHA1-6 : bond 0.00789 ( 5) link_ALPHA1-6 : angle 1.58549 ( 15) link_BETA1-4 : bond 0.00575 ( 16) link_BETA1-4 : angle 1.96165 ( 48) link_ALPHA1-2 : bond 0.01651 ( 4) link_ALPHA1-2 : angle 3.16982 ( 12) link_ALPHA1-3 : bond 0.00981 ( 7) link_ALPHA1-3 : angle 1.58732 ( 21) hydrogen bonds : bond 0.03877 ( 785) hydrogen bonds : angle 5.41124 ( 2256) SS BOND : bond 0.00412 ( 46) SS BOND : angle 1.19966 ( 92) covalent geometry : bond 0.00371 (24049) covalent geometry : angle 0.61217 (32654) *********************** 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 536 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 442 time to evaluate : 2.798 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 46 GLU cc_start: 0.6927 (mp0) cc_final: 0.6595 (mp0) REVERT: D 72 ASP cc_start: 0.8914 (m-30) cc_final: 0.8413 (m-30) REVERT: D 79 TYR cc_start: 0.8277 (m-80) cc_final: 0.8047 (m-80) REVERT: D 82 ARG cc_start: 0.6660 (mtm-85) cc_final: 0.6372 (mpp80) REVERT: D 82 ASN cc_start: 0.7775 (p0) cc_final: 0.6813 (p0) REVERT: D 83 LYS cc_start: 0.8414 (mtmm) cc_final: 0.7852 (mmtt) REVERT: D 94 LYS cc_start: 0.7902 (OUTLIER) cc_final: 0.7347 (ptmm) REVERT: D 108 LEU cc_start: 0.8896 (mm) cc_final: 0.8013 (pt) REVERT: E 6 GLN cc_start: 0.7097 (pm20) cc_final: 0.5868 (pp30) REVERT: E 79 ARG cc_start: 0.8568 (mtt180) cc_final: 0.8179 (ttm110) REVERT: E 81 GLU cc_start: 0.8440 (pm20) cc_final: 0.7917 (pm20) REVERT: F 36 TRP cc_start: 0.8670 (m100) cc_final: 0.8197 (m100) REVERT: F 43 ARG cc_start: 0.8001 (mmm160) cc_final: 0.7532 (ttt-90) REVERT: F 58 ASN cc_start: 0.7770 (t0) cc_final: 0.6653 (t0) REVERT: F 59 LEU cc_start: 0.7661 (tp) cc_final: 0.7405 (tp) REVERT: F 81 GLU cc_start: 0.7094 (OUTLIER) cc_final: 0.6464 (tp30) REVERT: F 82 ILE cc_start: 0.6902 (tp) cc_final: 0.6438 (tp) REVERT: F 100 TRP cc_start: 0.4914 (t-100) cc_final: 0.4088 (t-100) REVERT: G 17 GLN cc_start: 0.8743 (mp10) cc_final: 0.7914 (mp10) REVERT: G 37 GLN cc_start: 0.7501 (tt0) cc_final: 0.6869 (tt0) REVERT: G 49 TYR cc_start: 0.8043 (p90) cc_final: 0.7616 (p90) REVERT: J 36 TRP cc_start: 0.8521 (m100) cc_final: 0.8154 (m100) REVERT: J 66 ARG cc_start: 0.7373 (tpp80) cc_final: 0.7162 (tpp80) REVERT: K 42 ARG cc_start: 0.6855 (mtt90) cc_final: 0.6483 (mtm-85) REVERT: H 80 LEU cc_start: 0.9253 (OUTLIER) cc_final: 0.9012 (tp) REVERT: L 26 ARG cc_start: 0.8526 (tpt90) cc_final: 0.7749 (tpp80) REVERT: L 36 TYR cc_start: 0.8967 (m-80) cc_final: 0.8242 (m-10) REVERT: L 89 GLN cc_start: 0.8911 (tt0) cc_final: 0.8294 (tt0) REVERT: I 59 TYR cc_start: 0.9020 (m-80) cc_final: 0.8755 (m-80) REVERT: I 64 ASP cc_start: 0.8075 (t0) cc_final: 0.7848 (t0) REVERT: M 65 SER cc_start: 0.8980 (p) cc_final: 0.8645 (m) REVERT: C 173 TYR cc_start: 0.7924 (p90) cc_final: 0.7633 (p90) REVERT: C 280 ASN cc_start: 0.8953 (p0) cc_final: 0.8737 (p0) REVERT: C 320 MET cc_start: 0.8546 (mmt) cc_final: 0.8110 (mmt) REVERT: C 467 ILE cc_start: 0.7778 (OUTLIER) cc_final: 0.7507 (mt) REVERT: C 519 ARG cc_start: 0.7757 (ptp-110) cc_final: 0.7237 (mtt90) REVERT: C 629 MET cc_start: 0.8069 (mmm) cc_final: 0.7605 (mmm) REVERT: B 164 GLU cc_start: 0.7677 (mm-30) cc_final: 0.6184 (pm20) REVERT: B 475 MET cc_start: 0.7814 (mmt) cc_final: 0.7549 (mmp) REVERT: B 530 MET cc_start: 0.8833 (mmm) cc_final: 0.8283 (mtp) REVERT: B 585 ARG cc_start: 0.8399 (mtp-110) cc_final: 0.7985 (ptm-80) REVERT: A 102 GLU cc_start: 0.8366 (mp0) cc_final: 0.7973 (mp0) REVERT: A 116 LEU cc_start: 0.7991 (OUTLIER) cc_final: 0.7721 (mp) REVERT: A 373 MET cc_start: 0.8496 (mmt) cc_final: 0.7573 (mmp) REVERT: A 426 MET cc_start: 0.7536 (mtm) cc_final: 0.7329 (mtm) REVERT: A 584 GLU cc_start: 0.8641 (tm-30) cc_final: 0.8197 (tm-30) REVERT: A 601 LYS cc_start: 0.8523 (mttp) cc_final: 0.8269 (mtpp) REVERT: A 655 LYS cc_start: 0.7980 (pttt) cc_final: 0.7520 (ptmm) outliers start: 94 outliers final: 61 residues processed: 495 average time/residue: 0.3578 time to fit residues: 274.5867 Evaluate side-chains 490 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 424 time to evaluate : 2.667 ------------------------------------------------------------------------------- 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 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 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 24 THR Chi-restraints excluded: chain J residue 63 PHE Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 91 PHE Chi-restraints excluded: chain J residue 100 SER Chi-restraints excluded: chain J residue 107 THR Chi-restraints excluded: chain K residue 11 VAL 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 73 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 20 THR 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 97 THR Chi-restraints excluded: chain I residue 28 SER Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain M residue 97 THR 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 445 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 B residue 68 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 426 MET Chi-restraints excluded: chain B residue 445 CYS Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 306 SER 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 576 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 88 optimal weight: 5.9990 chunk 124 optimal weight: 0.9980 chunk 60 optimal weight: 7.9990 chunk 89 optimal weight: 1.9990 chunk 235 optimal weight: 0.3980 chunk 28 optimal weight: 4.9990 chunk 119 optimal weight: 0.7980 chunk 156 optimal weight: 3.9990 chunk 61 optimal weight: 7.9990 chunk 226 optimal weight: 0.7980 chunk 36 optimal weight: 10.0000 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 C 103 GLN B 651 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 = 0.3550 r_free = 0.3550 target = 0.115115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.087826 restraints weight = 42254.326| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 3.35 r_work: 0.3000 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 24173 Z= 0.147 Angle : 0.624 11.281 32980 Z= 0.308 Chirality : 0.045 0.339 3843 Planarity : 0.004 0.055 4050 Dihedral : 6.746 55.710 4676 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 3.76 % Allowed : 18.15 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.16), residues: 2796 helix: 0.78 (0.27), residues: 386 sheet: 0.26 (0.18), residues: 901 loop : -0.90 (0.16), residues: 1509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 50 HIS 0.004 0.001 HIS G 93 PHE 0.023 0.001 PHE B 522 TYR 0.021 0.001 TYR G 49 ARG 0.005 0.000 ARG J 82A Details of bonding type rmsd link_NAG-ASN : bond 0.00535 ( 46) link_NAG-ASN : angle 2.40123 ( 138) link_ALPHA1-6 : bond 0.00817 ( 5) link_ALPHA1-6 : angle 1.54493 ( 15) link_BETA1-4 : bond 0.00585 ( 16) link_BETA1-4 : angle 1.88973 ( 48) link_ALPHA1-2 : bond 0.01733 ( 4) link_ALPHA1-2 : angle 3.10777 ( 12) link_ALPHA1-3 : bond 0.01007 ( 7) link_ALPHA1-3 : angle 1.51766 ( 21) hydrogen bonds : bond 0.03689 ( 785) hydrogen bonds : angle 5.27917 ( 2256) SS BOND : bond 0.00427 ( 46) SS BOND : angle 1.31814 ( 92) covalent geometry : bond 0.00338 (24049) covalent geometry : angle 0.59393 (32654) *********************** 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 549 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 455 time to evaluate : 2.605 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 32 TYR cc_start: 0.8779 (m-10) cc_final: 0.8338 (m-10) REVERT: D 46 GLU cc_start: 0.6904 (mp0) cc_final: 0.6680 (mp0) REVERT: D 72 ASP cc_start: 0.8577 (m-30) cc_final: 0.8255 (m-30) REVERT: D 79 TYR cc_start: 0.8233 (m-80) cc_final: 0.7976 (m-80) REVERT: D 82 ASN cc_start: 0.7876 (p0) cc_final: 0.7273 (p0) REVERT: D 83 LYS cc_start: 0.8429 (mtmm) cc_final: 0.8019 (mmtt) REVERT: D 108 LEU cc_start: 0.8913 (mm) cc_final: 0.8013 (pt) REVERT: E 6 GLN cc_start: 0.7161 (pm20) cc_final: 0.5886 (pp30) REVERT: E 79 ARG cc_start: 0.8592 (mtt180) cc_final: 0.8202 (ttm110) REVERT: E 81 GLU cc_start: 0.8440 (pm20) cc_final: 0.7920 (pm20) REVERT: F 36 TRP cc_start: 0.8703 (m100) cc_final: 0.8241 (m100) REVERT: F 43 ARG cc_start: 0.7892 (mmm160) cc_final: 0.7423 (ttt-90) REVERT: F 59 LEU cc_start: 0.7756 (tp) cc_final: 0.7299 (tp) REVERT: F 81 GLU cc_start: 0.7066 (OUTLIER) cc_final: 0.6426 (tp30) REVERT: F 100 TRP cc_start: 0.4701 (t-100) cc_final: 0.3951 (t-100) REVERT: G 17 GLN cc_start: 0.8766 (mp10) cc_final: 0.7890 (mp10) REVERT: G 37 GLN cc_start: 0.7469 (tt0) cc_final: 0.6863 (tt0) REVERT: G 49 TYR cc_start: 0.8006 (p90) cc_final: 0.7682 (p90) REVERT: J 36 TRP cc_start: 0.8544 (m100) cc_final: 0.8170 (m100) REVERT: J 38 ARG cc_start: 0.5957 (OUTLIER) cc_final: 0.5623 (ptp-170) REVERT: J 66 ARG cc_start: 0.7601 (tpp80) cc_final: 0.7383 (tpp80) REVERT: J 82 ARG cc_start: 0.8288 (ptp90) cc_final: 0.7755 (ptp90) REVERT: K 42 ARG cc_start: 0.6690 (mtt90) cc_final: 0.6355 (mtm-85) REVERT: H 80 LEU cc_start: 0.9258 (OUTLIER) cc_final: 0.9025 (tp) REVERT: L 26 ARG cc_start: 0.8481 (tpt90) cc_final: 0.7946 (tpp80) REVERT: L 89 GLN cc_start: 0.8814 (OUTLIER) cc_final: 0.8206 (tt0) REVERT: L 106 MET cc_start: 0.6128 (ttp) cc_final: 0.5793 (ttp) REVERT: I 59 TYR cc_start: 0.8890 (m-80) cc_final: 0.8684 (m-80) REVERT: I 64 ASP cc_start: 0.8108 (t0) cc_final: 0.7786 (t0) REVERT: M 24 GLN cc_start: 0.8488 (mm-40) cc_final: 0.8205 (mm-40) REVERT: M 65 SER cc_start: 0.8924 (p) cc_final: 0.8634 (m) REVERT: M 69 ARG cc_start: 0.8779 (OUTLIER) cc_final: 0.8363 (ptm160) REVERT: C 173 TYR cc_start: 0.7886 (p90) cc_final: 0.7597 (p90) REVERT: C 280 ASN cc_start: 0.8938 (p0) cc_final: 0.8695 (p0) REVERT: C 318 TYR cc_start: 0.8887 (m-80) cc_final: 0.8463 (m-80) REVERT: C 320 MET cc_start: 0.8818 (mmt) cc_final: 0.8543 (mmt) REVERT: C 475 MET cc_start: 0.8320 (tpp) cc_final: 0.8031 (tpp) REVERT: C 502 LYS cc_start: 0.8591 (OUTLIER) cc_final: 0.7881 (tptm) REVERT: C 519 ARG cc_start: 0.7799 (ptp-110) cc_final: 0.7289 (mtt90) REVERT: C 629 MET cc_start: 0.8111 (mmm) cc_final: 0.7492 (mmm) REVERT: C 633 ARG cc_start: 0.8745 (ptp-170) cc_final: 0.8493 (ptp-170) REVERT: B 133 ASP cc_start: 0.9022 (t0) cc_final: 0.8807 (t0) REVERT: B 164 GLU cc_start: 0.7687 (mm-30) cc_final: 0.6212 (pm20) REVERT: B 585 ARG cc_start: 0.8369 (mtp-110) cc_final: 0.8098 (ptm-80) REVERT: B 652 GLN cc_start: 0.8435 (mp10) cc_final: 0.7964 (mp10) REVERT: A 102 GLU cc_start: 0.8425 (mp0) cc_final: 0.8010 (mp0) REVERT: A 373 MET cc_start: 0.8502 (mmt) cc_final: 0.7616 (mmp) REVERT: A 377 ASN cc_start: 0.8442 (t0) cc_final: 0.8071 (t0) REVERT: A 584 GLU cc_start: 0.8650 (tm-30) cc_final: 0.8199 (tm-30) REVERT: A 655 LYS cc_start: 0.8003 (pttt) cc_final: 0.7595 (ptmm) outliers start: 94 outliers final: 69 residues processed: 498 average time/residue: 0.3675 time to fit residues: 281.8710 Evaluate side-chains 501 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 426 time to evaluate : 2.611 ------------------------------------------------------------------------------- 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 92 CYS 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 57 LYS 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 102 LEU Chi-restraints excluded: chain G residue 30 HIS Chi-restraints excluded: chain G residue 92 THR 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 46 GLU Chi-restraints excluded: chain J residue 63 PHE Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 91 PHE Chi-restraints excluded: chain J residue 100 SER Chi-restraints excluded: chain K residue 11 VAL 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 73 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 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 28 SER Chi-restraints excluded: chain I residue 35 ASN 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 69 ARG Chi-restraints excluded: chain M residue 97 THR 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 244 THR Chi-restraints excluded: chain C residue 306 SER 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 68 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 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 606 THR Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 529 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 225 optimal weight: 3.9990 chunk 123 optimal weight: 0.0980 chunk 23 optimal weight: 10.0000 chunk 218 optimal weight: 0.9980 chunk 165 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 chunk 161 optimal weight: 0.9980 chunk 104 optimal weight: 7.9990 chunk 198 optimal weight: 2.9990 chunk 245 optimal weight: 2.9990 chunk 265 optimal weight: 1.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- 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 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 651 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 = 0.3539 r_free = 0.3539 target = 0.114214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.086776 restraints weight = 42941.431| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 3.36 r_work: 0.2981 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.2979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 24173 Z= 0.180 Angle : 0.639 10.221 32980 Z= 0.317 Chirality : 0.046 0.339 3843 Planarity : 0.004 0.055 4050 Dihedral : 6.715 55.960 4676 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 3.88 % Allowed : 18.19 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.16), residues: 2796 helix: 0.79 (0.27), residues: 386 sheet: 0.20 (0.17), residues: 921 loop : -0.90 (0.16), residues: 1489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 50 HIS 0.006 0.001 HIS G 93 PHE 0.028 0.002 PHE F 31 TYR 0.022 0.001 TYR G 49 ARG 0.005 0.000 ARG F 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00549 ( 46) link_NAG-ASN : angle 2.41695 ( 138) link_ALPHA1-6 : bond 0.00796 ( 5) link_ALPHA1-6 : angle 1.56542 ( 15) link_BETA1-4 : bond 0.00568 ( 16) link_BETA1-4 : angle 1.93474 ( 48) link_ALPHA1-2 : bond 0.01658 ( 4) link_ALPHA1-2 : angle 3.02770 ( 12) link_ALPHA1-3 : bond 0.00957 ( 7) link_ALPHA1-3 : angle 1.53873 ( 21) hydrogen bonds : bond 0.03755 ( 785) hydrogen bonds : angle 5.28059 ( 2256) SS BOND : bond 0.00499 ( 46) SS BOND : angle 1.24553 ( 92) covalent geometry : bond 0.00418 (24049) covalent geometry : angle 0.60931 (32654) *********************** 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 537 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 440 time to evaluate : 2.822 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 32 TYR cc_start: 0.8825 (m-10) cc_final: 0.8461 (m-10) REVERT: D 46 GLU cc_start: 0.7078 (mp0) cc_final: 0.6732 (mp0) REVERT: D 72 ASP cc_start: 0.8499 (m-30) cc_final: 0.8098 (m-30) REVERT: D 79 TYR cc_start: 0.8251 (m-80) cc_final: 0.8006 (m-80) REVERT: D 82 ASN cc_start: 0.7748 (p0) cc_final: 0.7209 (p0) REVERT: D 83 LYS cc_start: 0.8549 (mtmm) cc_final: 0.8093 (mmtt) REVERT: D 108 LEU cc_start: 0.8848 (mm) cc_final: 0.7951 (pt) REVERT: E 35 TRP cc_start: 0.7212 (m100) cc_final: 0.6518 (m100) REVERT: E 79 ARG cc_start: 0.8617 (mtt180) cc_final: 0.8215 (ttm110) REVERT: E 81 GLU cc_start: 0.8447 (pm20) cc_final: 0.7910 (pm20) REVERT: F 36 TRP cc_start: 0.8747 (m100) cc_final: 0.8238 (m100) REVERT: F 43 ARG cc_start: 0.7961 (mmm160) cc_final: 0.7551 (ttt-90) REVERT: F 59 LEU cc_start: 0.7871 (tp) cc_final: 0.7382 (tp) REVERT: F 81 GLU cc_start: 0.7115 (OUTLIER) cc_final: 0.6460 (tp30) REVERT: F 82 ILE cc_start: 0.6681 (tp) cc_final: 0.6154 (tp) REVERT: F 100 TRP cc_start: 0.4566 (t-100) cc_final: 0.3916 (t-100) REVERT: G 17 GLN cc_start: 0.8781 (mp10) cc_final: 0.7919 (mp10) REVERT: G 37 GLN cc_start: 0.7502 (tt0) cc_final: 0.7037 (tt0) REVERT: G 42 ARG cc_start: 0.8097 (OUTLIER) cc_final: 0.7214 (ttp80) REVERT: G 49 TYR cc_start: 0.8138 (p90) cc_final: 0.7844 (p90) REVERT: G 77 ASP cc_start: 0.7765 (t0) cc_final: 0.7053 (t0) REVERT: G 79 ARG cc_start: 0.7655 (mmp80) cc_final: 0.7427 (mmp80) REVERT: J 38 ARG cc_start: 0.6028 (OUTLIER) cc_final: 0.5658 (ptp-170) REVERT: K 42 ARG cc_start: 0.6775 (mtt90) cc_final: 0.6391 (mtm-85) REVERT: H 24 VAL cc_start: 0.9174 (t) cc_final: 0.8962 (m) REVERT: H 80 LEU cc_start: 0.9290 (OUTLIER) cc_final: 0.9052 (tp) REVERT: L 26 ARG cc_start: 0.8527 (tpt90) cc_final: 0.7783 (tpp80) REVERT: L 89 GLN cc_start: 0.8839 (OUTLIER) cc_final: 0.8231 (tt0) REVERT: I 6 GLU cc_start: 0.8153 (mp0) cc_final: 0.7924 (mp0) REVERT: I 13 LYS cc_start: 0.5538 (tptt) cc_final: 0.5319 (tptt) REVERT: I 46 GLU cc_start: 0.8085 (mt-10) cc_final: 0.7631 (pt0) REVERT: I 59 TYR cc_start: 0.8926 (m-80) cc_final: 0.8715 (m-80) REVERT: I 64 ASP cc_start: 0.8074 (t0) cc_final: 0.7812 (t0) REVERT: M 65 SER cc_start: 0.8924 (p) cc_final: 0.8641 (m) REVERT: M 69 ARG cc_start: 0.8813 (OUTLIER) cc_final: 0.8456 (ptm160) REVERT: C 173 TYR cc_start: 0.7868 (p90) cc_final: 0.7623 (p90) REVERT: C 280 ASN cc_start: 0.8943 (p0) cc_final: 0.8699 (p0) REVERT: C 320 MET cc_start: 0.8917 (mmt) cc_final: 0.8670 (mmt) REVERT: C 381 GLU cc_start: 0.8195 (tt0) cc_final: 0.7975 (tt0) REVERT: C 467 ILE cc_start: 0.7800 (OUTLIER) cc_final: 0.7501 (mp) REVERT: C 519 ARG cc_start: 0.7826 (ptp-110) cc_final: 0.7303 (mtt90) REVERT: C 629 MET cc_start: 0.8136 (mmm) cc_final: 0.7513 (mmm) REVERT: C 633 ARG cc_start: 0.8763 (ptp-170) cc_final: 0.8493 (ptp-170) REVERT: B 164 GLU cc_start: 0.7700 (mm-30) cc_final: 0.6231 (pm20) REVERT: B 530 MET cc_start: 0.8844 (mmm) cc_final: 0.8373 (mtp) REVERT: B 585 ARG cc_start: 0.8368 (mtp-110) cc_final: 0.8101 (ptm-80) REVERT: B 652 GLN cc_start: 0.8438 (mp10) cc_final: 0.7957 (mp10) REVERT: A 102 GLU cc_start: 0.8466 (mp0) cc_final: 0.8039 (mp0) REVERT: A 373 MET cc_start: 0.8537 (mmt) cc_final: 0.7651 (mmp) REVERT: A 584 GLU cc_start: 0.8654 (tm-30) cc_final: 0.8188 (tm-30) REVERT: A 655 LYS cc_start: 0.8020 (pttt) cc_final: 0.7576 (ptmm) outliers start: 97 outliers final: 68 residues processed: 492 average time/residue: 0.4137 time to fit residues: 316.8253 Evaluate side-chains 505 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 430 time to evaluate : 2.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 24 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 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 57 LYS 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 42 ARG 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 82 LEU Chi-restraints excluded: chain J residue 91 PHE Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 73 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 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 28 SER Chi-restraints excluded: chain I residue 35 ASN Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 89 ILE Chi-restraints excluded: chain M residue 69 ARG Chi-restraints excluded: chain M residue 97 THR 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 244 THR Chi-restraints excluded: chain C residue 306 SER Chi-restraints excluded: chain C residue 349 LEU 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 68 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 306 SER 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 539 VAL Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 529 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 199 optimal weight: 3.9990 chunk 118 optimal weight: 3.9990 chunk 227 optimal weight: 0.5980 chunk 111 optimal weight: 3.9990 chunk 251 optimal weight: 9.9990 chunk 254 optimal weight: 6.9990 chunk 117 optimal weight: 7.9990 chunk 121 optimal weight: 0.8980 chunk 8 optimal weight: 8.9990 chunk 60 optimal weight: 10.0000 chunk 57 optimal weight: 5.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- 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** ** K 93 HIS ** 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 79 GLN ** B 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 377 ASN ** B 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 651 ASN A 66 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.110566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.082699 restraints weight = 43399.456| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 3.36 r_work: 0.2921 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.3282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.083 24173 Z= 0.297 Angle : 0.741 9.735 32980 Z= 0.367 Chirality : 0.049 0.352 3843 Planarity : 0.004 0.055 4050 Dihedral : 7.188 58.951 4676 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 3.76 % Allowed : 18.63 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.16), residues: 2796 helix: 0.62 (0.27), residues: 382 sheet: 0.01 (0.17), residues: 926 loop : -0.98 (0.16), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP J 36 HIS 0.007 0.001 HIS K 93 PHE 0.040 0.002 PHE F 31 TYR 0.025 0.002 TYR G 49 ARG 0.006 0.001 ARG J 66 Details of bonding type rmsd link_NAG-ASN : bond 0.00689 ( 46) link_NAG-ASN : angle 2.64248 ( 138) link_ALPHA1-6 : bond 0.00731 ( 5) link_ALPHA1-6 : angle 1.65646 ( 15) link_BETA1-4 : bond 0.00594 ( 16) link_BETA1-4 : angle 2.15655 ( 48) link_ALPHA1-2 : bond 0.01581 ( 4) link_ALPHA1-2 : angle 3.00747 ( 12) link_ALPHA1-3 : bond 0.00865 ( 7) link_ALPHA1-3 : angle 1.66495 ( 21) hydrogen bonds : bond 0.04260 ( 785) hydrogen bonds : angle 5.52878 ( 2256) SS BOND : bond 0.00620 ( 46) SS BOND : angle 1.48456 ( 92) covalent geometry : bond 0.00691 (24049) covalent geometry : angle 0.71058 (32654) *********************** 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 523 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 429 time to evaluate : 3.190 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: D 32 TYR cc_start: 0.8955 (m-10) cc_final: 0.8732 (m-10) REVERT: D 46 GLU cc_start: 0.7166 (mp0) cc_final: 0.6782 (mp0) REVERT: D 72 ASP cc_start: 0.8436 (m-30) cc_final: 0.8027 (m-30) REVERT: D 82 ARG cc_start: 0.7537 (mpp80) cc_final: 0.7270 (mpp80) REVERT: D 82 ASN cc_start: 0.7797 (p0) cc_final: 0.7352 (p0) REVERT: D 83 LYS cc_start: 0.8593 (mtmm) cc_final: 0.8141 (mmtt) REVERT: D 108 LEU cc_start: 0.8851 (mm) cc_final: 0.7940 (pt) REVERT: E 35 TRP cc_start: 0.7212 (m100) cc_final: 0.6526 (m100) REVERT: E 54 ARG cc_start: 0.7887 (ptp-170) cc_final: 0.7199 (mtm180) REVERT: E 79 ARG cc_start: 0.8694 (mtt180) cc_final: 0.8294 (ttm110) REVERT: F 36 TRP cc_start: 0.8822 (m100) cc_final: 0.8389 (m100) REVERT: F 43 ARG cc_start: 0.8066 (mmm160) cc_final: 0.7599 (ttt-90) REVERT: F 59 LEU cc_start: 0.7832 (tp) cc_final: 0.7340 (tp) REVERT: F 81 GLU cc_start: 0.7172 (OUTLIER) cc_final: 0.6505 (tp30) REVERT: F 82 ILE cc_start: 0.6705 (tp) cc_final: 0.6193 (tp) REVERT: F 100 TRP cc_start: 0.4960 (t-100) cc_final: 0.4197 (t-100) REVERT: G 17 GLN cc_start: 0.8748 (mp10) cc_final: 0.7885 (mp10) REVERT: G 37 GLN cc_start: 0.7599 (tt0) cc_final: 0.6941 (tt0) REVERT: G 42 ARG cc_start: 0.8152 (OUTLIER) cc_final: 0.7250 (ttp80) REVERT: G 49 TYR cc_start: 0.8492 (p90) cc_final: 0.8171 (p90) REVERT: G 58 ILE cc_start: 0.8248 (mm) cc_final: 0.8047 (mt) REVERT: G 77 ASP cc_start: 0.7852 (t0) cc_final: 0.7051 (t0) REVERT: J 30 ASN cc_start: 0.8404 (t0) cc_final: 0.8187 (t0) REVERT: J 38 ARG cc_start: 0.5974 (OUTLIER) cc_final: 0.5614 (ptp-170) REVERT: J 66 ARG cc_start: 0.7077 (tpp80) cc_final: 0.6568 (tpp80) REVERT: H 80 LEU cc_start: 0.9292 (OUTLIER) cc_final: 0.9040 (tp) REVERT: H 96 ASN cc_start: 0.8549 (t0) cc_final: 0.8274 (t0) REVERT: L 26 ARG cc_start: 0.8720 (tpt90) cc_final: 0.7984 (tpp80) REVERT: I 46 GLU cc_start: 0.8141 (mt-10) cc_final: 0.7676 (mt-10) REVERT: I 59 TYR cc_start: 0.9021 (m-80) cc_final: 0.8747 (m-80) REVERT: I 64 ASP cc_start: 0.8263 (t0) cc_final: 0.8035 (t0) REVERT: M 65 SER cc_start: 0.9036 (p) cc_final: 0.8681 (m) REVERT: C 173 TYR cc_start: 0.7930 (p90) cc_final: 0.7679 (p90) REVERT: C 280 ASN cc_start: 0.9014 (p0) cc_final: 0.8772 (p0) REVERT: C 318 TYR cc_start: 0.8987 (m-80) cc_final: 0.8648 (m-80) REVERT: C 320 MET cc_start: 0.9035 (mmt) cc_final: 0.8799 (mmt) REVERT: C 381 GLU cc_start: 0.8346 (tt0) cc_final: 0.8139 (tt0) REVERT: C 467 ILE cc_start: 0.7795 (OUTLIER) cc_final: 0.7496 (mp) REVERT: C 519 ARG cc_start: 0.7901 (ptp-110) cc_final: 0.7271 (mtt90) REVERT: B 164 GLU cc_start: 0.7804 (mm-30) cc_final: 0.6349 (pm20) REVERT: B 467 ILE cc_start: 0.9181 (mm) cc_final: 0.8855 (mm) REVERT: B 530 MET cc_start: 0.8925 (mmm) cc_final: 0.8529 (mtp) REVERT: B 585 ARG cc_start: 0.8399 (mtp-110) cc_final: 0.8150 (ptm-80) REVERT: B 591 GLN cc_start: 0.7480 (tt0) cc_final: 0.6866 (mt0) REVERT: B 652 GLN cc_start: 0.8423 (mp10) cc_final: 0.7811 (mp10) REVERT: B 656 ASN cc_start: 0.8253 (m-40) cc_final: 0.8027 (m-40) REVERT: A 102 GLU cc_start: 0.8500 (mp0) cc_final: 0.8072 (mp0) REVERT: A 373 MET cc_start: 0.8655 (mmt) cc_final: 0.7744 (mmp) REVERT: A 584 GLU cc_start: 0.8677 (tm-30) cc_final: 0.8210 (tm-30) REVERT: A 655 LYS cc_start: 0.8070 (pttt) cc_final: 0.7648 (ptmm) outliers start: 94 outliers final: 79 residues processed: 480 average time/residue: 0.4036 time to fit residues: 300.6052 Evaluate side-chains 499 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 415 time to evaluate : 2.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 24 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 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 57 LYS 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 42 ARG 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 82 ILE Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 91 PHE Chi-restraints excluded: chain J residue 100 SER Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 47 ILE Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 20 THR 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 28 SER Chi-restraints excluded: chain I residue 35 ASN Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 89 ILE 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 123 THR Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 306 SER Chi-restraints excluded: chain C residue 349 LEU 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 68 VAL Chi-restraints excluded: chain B residue 95 MET Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 184 ILE 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 306 SER 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 539 VAL 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 196 CYS Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain A residue 434 MET 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 114 optimal weight: 0.8980 chunk 34 optimal weight: 0.5980 chunk 216 optimal weight: 0.8980 chunk 13 optimal weight: 10.0000 chunk 125 optimal weight: 4.9990 chunk 262 optimal weight: 4.9990 chunk 153 optimal weight: 1.9990 chunk 221 optimal weight: 0.9990 chunk 160 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 chunk 166 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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** ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 45 GLN B 279 ASN B 377 ASN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 651 ASN A 66 HIS A 229 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.114266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.086550 restraints weight = 42497.317| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 3.39 r_work: 0.2982 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.3275 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= 0.142 Angle : 0.650 11.198 32980 Z= 0.321 Chirality : 0.046 0.336 3843 Planarity : 0.004 0.057 4050 Dihedral : 6.738 54.989 4676 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 3.12 % Allowed : 19.54 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.16), residues: 2796 helix: 0.70 (0.27), residues: 386 sheet: 0.10 (0.17), residues: 943 loop : -0.90 (0.16), residues: 1467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP J 36 HIS 0.005 0.001 HIS K 93 PHE 0.029 0.002 PHE F 31 TYR 0.020 0.001 TYR G 49 ARG 0.005 0.000 ARG G 79 Details of bonding type rmsd link_NAG-ASN : bond 0.00559 ( 46) link_NAG-ASN : angle 2.43274 ( 138) link_ALPHA1-6 : bond 0.00896 ( 5) link_ALPHA1-6 : angle 1.51632 ( 15) link_BETA1-4 : bond 0.00578 ( 16) link_BETA1-4 : angle 1.85887 ( 48) link_ALPHA1-2 : bond 0.01688 ( 4) link_ALPHA1-2 : angle 3.17875 ( 12) link_ALPHA1-3 : bond 0.01004 ( 7) link_ALPHA1-3 : angle 1.42163 ( 21) hydrogen bonds : bond 0.03764 ( 785) hydrogen bonds : angle 5.32211 ( 2256) SS BOND : bond 0.00352 ( 46) SS BOND : angle 1.18587 ( 92) covalent geometry : bond 0.00324 (24049) covalent geometry : angle 0.62227 (32654) *********************** 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 521 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 443 time to evaluate : 2.763 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 32 TYR cc_start: 0.8887 (m-10) cc_final: 0.8537 (m-10) REVERT: D 46 GLU cc_start: 0.7099 (mp0) cc_final: 0.6732 (mp0) REVERT: D 79 TYR cc_start: 0.8292 (m-80) cc_final: 0.7946 (m-80) REVERT: D 82 ARG cc_start: 0.7568 (mpp80) cc_final: 0.7294 (mpp80) REVERT: D 82 ASN cc_start: 0.7629 (p0) cc_final: 0.7137 (p0) REVERT: D 83 LYS cc_start: 0.8532 (mtmm) cc_final: 0.8078 (mmtt) REVERT: D 108 LEU cc_start: 0.8846 (mm) cc_final: 0.7939 (pt) REVERT: E 6 GLN cc_start: 0.7227 (pm20) cc_final: 0.6986 (pp30) REVERT: E 35 TRP cc_start: 0.7149 (m100) cc_final: 0.6512 (m100) REVERT: E 54 ARG cc_start: 0.7680 (ptp-170) cc_final: 0.7136 (mtm180) REVERT: E 81 GLU cc_start: 0.8254 (pm20) cc_final: 0.7916 (pm20) REVERT: F 18 VAL cc_start: 0.7233 (m) cc_final: 0.6503 (m) REVERT: F 36 TRP cc_start: 0.8755 (m100) cc_final: 0.8288 (m100) REVERT: F 43 ARG cc_start: 0.7980 (mmm160) cc_final: 0.7454 (ttt-90) REVERT: F 59 LEU cc_start: 0.7964 (tp) cc_final: 0.7458 (tp) REVERT: F 81 GLU cc_start: 0.7115 (OUTLIER) cc_final: 0.6517 (tp30) REVERT: F 82 ILE cc_start: 0.6595 (tp) cc_final: 0.6128 (tp) REVERT: F 100 TRP cc_start: 0.4784 (t-100) cc_final: 0.4206 (t-100) REVERT: G 17 GLN cc_start: 0.8736 (mp10) cc_final: 0.7856 (mp10) REVERT: G 37 GLN cc_start: 0.7546 (tt0) cc_final: 0.6899 (tt0) REVERT: G 49 TYR cc_start: 0.8194 (p90) cc_final: 0.7948 (p90) REVERT: J 38 ARG cc_start: 0.5926 (OUTLIER) cc_final: 0.5551 (ptp-170) REVERT: J 66 ARG cc_start: 0.6963 (tpp80) cc_final: 0.6458 (tpp80) REVERT: K 91 TYR cc_start: 0.7321 (p90) cc_final: 0.7023 (p90) REVERT: K 102 THR cc_start: 0.7651 (m) cc_final: 0.7064 (p) REVERT: H 80 LEU cc_start: 0.9267 (OUTLIER) cc_final: 0.8998 (tp) REVERT: H 96 ASN cc_start: 0.8356 (t0) cc_final: 0.8056 (t0) REVERT: L 26 ARG cc_start: 0.8552 (tpt90) cc_final: 0.8031 (tpp80) REVERT: I 13 LYS cc_start: 0.5438 (tptt) cc_final: 0.5185 (tptt) REVERT: I 46 GLU cc_start: 0.8091 (mt-10) cc_final: 0.7595 (pt0) REVERT: I 64 ASP cc_start: 0.8277 (t0) cc_final: 0.8037 (t0) REVERT: M 65 SER cc_start: 0.8942 (p) cc_final: 0.8667 (m) REVERT: C 149 MET cc_start: 0.5835 (mmp) cc_final: 0.5593 (mmp) REVERT: C 173 TYR cc_start: 0.7819 (p90) cc_final: 0.7576 (p90) REVERT: C 280 ASN cc_start: 0.8953 (p0) cc_final: 0.8727 (p0) REVERT: C 318 TYR cc_start: 0.8901 (m-80) cc_final: 0.8520 (m-80) REVERT: C 320 MET cc_start: 0.8988 (mmt) cc_final: 0.8671 (mmt) REVERT: C 467 ILE cc_start: 0.7795 (OUTLIER) cc_final: 0.7496 (mt) REVERT: C 475 MET cc_start: 0.8338 (tpp) cc_final: 0.8064 (tpp) REVERT: C 519 ARG cc_start: 0.7872 (ptp-110) cc_final: 0.7260 (mtt90) REVERT: B 164 GLU cc_start: 0.7659 (mm-30) cc_final: 0.6266 (pm20) REVERT: B 467 ILE cc_start: 0.9144 (mm) cc_final: 0.8827 (mm) REVERT: B 585 ARG cc_start: 0.8329 (mtp-110) cc_final: 0.8095 (ptm-80) REVERT: B 591 GLN cc_start: 0.7436 (tt0) cc_final: 0.6789 (mt0) REVERT: B 652 GLN cc_start: 0.8521 (mp10) cc_final: 0.7888 (mp10) REVERT: A 102 GLU cc_start: 0.8401 (mp0) cc_final: 0.7996 (mp0) REVERT: A 320 MET cc_start: 0.8262 (mmm) cc_final: 0.7794 (mmm) REVERT: A 373 MET cc_start: 0.8523 (mmt) cc_final: 0.7615 (mmp) REVERT: A 584 GLU cc_start: 0.8650 (tm-30) cc_final: 0.8175 (tm-30) REVERT: A 601 LYS cc_start: 0.8607 (mttp) cc_final: 0.8335 (mtpp) REVERT: A 655 LYS cc_start: 0.8057 (pttt) cc_final: 0.7641 (ptmm) outliers start: 78 outliers final: 64 residues processed: 481 average time/residue: 0.4205 time to fit residues: 311.9383 Evaluate side-chains 493 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 425 time to evaluate : 2.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 73 LEU 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 57 LYS 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 92 THR 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 46 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 K residue 47 ILE Chi-restraints excluded: chain K residue 97 VAL 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 7 SER Chi-restraints excluded: chain L residue 33 LEU 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 28 SER Chi-restraints excluded: chain I residue 35 ASN 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 349 LEU 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 279 ASN Chi-restraints excluded: chain B residue 306 SER 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 539 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 434 MET Chi-restraints excluded: chain A residue 449 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 205 optimal weight: 0.0370 chunk 84 optimal weight: 1.9990 chunk 245 optimal weight: 2.9990 chunk 167 optimal weight: 2.9990 chunk 149 optimal weight: 4.9990 chunk 176 optimal weight: 2.9990 chunk 249 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 240 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 185 optimal weight: 0.0470 overall best weight: 1.4162 ------------------------------------------------------------------------------- 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 B 377 ASN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 651 ASN A 66 HIS A 344 GLN ** 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 = 0.3524 r_free = 0.3524 target = 0.113277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.085480 restraints weight = 42845.218| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 3.41 r_work: 0.2965 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.3328 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= 0.183 Angle : 0.669 12.321 32980 Z= 0.331 Chirality : 0.046 0.338 3843 Planarity : 0.004 0.056 4050 Dihedral : 6.674 55.910 4676 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 3.04 % Allowed : 19.58 % Favored : 77.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.16), residues: 2796 helix: 0.71 (0.27), residues: 386 sheet: 0.08 (0.17), residues: 945 loop : -0.88 (0.16), residues: 1465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP J 36 HIS 0.006 0.001 HIS G 93 PHE 0.034 0.002 PHE F 31 TYR 0.021 0.002 TYR G 49 ARG 0.011 0.000 ARG E 79 Details of bonding type rmsd link_NAG-ASN : bond 0.00546 ( 46) link_NAG-ASN : angle 2.44800 ( 138) link_ALPHA1-6 : bond 0.00846 ( 5) link_ALPHA1-6 : angle 1.55406 ( 15) link_BETA1-4 : bond 0.00554 ( 16) link_BETA1-4 : angle 1.91263 ( 48) link_ALPHA1-2 : bond 0.01615 ( 4) link_ALPHA1-2 : angle 2.99045 ( 12) link_ALPHA1-3 : bond 0.00940 ( 7) link_ALPHA1-3 : angle 1.47641 ( 21) hydrogen bonds : bond 0.03772 ( 785) hydrogen bonds : angle 5.32648 ( 2256) SS BOND : bond 0.00458 ( 46) SS BOND : angle 1.26040 ( 92) covalent geometry : bond 0.00425 (24049) covalent geometry : angle 0.64133 (32654) ********************** 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 506 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 430 time to evaluate : 4.679 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: D 32 TYR cc_start: 0.8929 (m-10) cc_final: 0.8665 (m-10) REVERT: D 46 GLU cc_start: 0.7227 (mp0) cc_final: 0.6858 (mp0) REVERT: D 82 ARG cc_start: 0.7636 (mpp80) cc_final: 0.7429 (mpp80) REVERT: D 82 ASN cc_start: 0.7621 (p0) cc_final: 0.7124 (p0) REVERT: D 83 LYS cc_start: 0.8542 (mtmm) cc_final: 0.8098 (mmtt) REVERT: D 94 LYS cc_start: 0.7882 (OUTLIER) cc_final: 0.7633 (pttp) REVERT: D 108 LEU cc_start: 0.8834 (mm) cc_final: 0.7928 (pt) REVERT: E 6 GLN cc_start: 0.7242 (pm20) cc_final: 0.5699 (pp30) REVERT: E 35 TRP cc_start: 0.7177 (m100) cc_final: 0.6570 (m100) REVERT: E 54 ARG cc_start: 0.7763 (ptp-170) cc_final: 0.7116 (mtm180) REVERT: F 18 VAL cc_start: 0.7267 (m) cc_final: 0.6759 (m) REVERT: F 36 TRP cc_start: 0.8796 (m100) cc_final: 0.8327 (m100) REVERT: F 43 ARG cc_start: 0.8037 (mmm160) cc_final: 0.7517 (ttt-90) REVERT: F 59 LEU cc_start: 0.7926 (tp) cc_final: 0.7442 (tp) REVERT: F 81 GLU cc_start: 0.7121 (OUTLIER) cc_final: 0.6528 (tp30) REVERT: F 100 TRP cc_start: 0.4879 (t-100) cc_final: 0.4307 (t-100) REVERT: G 17 GLN cc_start: 0.8763 (mp10) cc_final: 0.7910 (mp10) REVERT: G 37 GLN cc_start: 0.7613 (tt0) cc_final: 0.6973 (tt0) REVERT: G 42 ARG cc_start: 0.8180 (OUTLIER) cc_final: 0.7254 (ttp80) REVERT: G 49 TYR cc_start: 0.8286 (p90) cc_final: 0.8030 (p90) REVERT: G 77 ASP cc_start: 0.7815 (t0) cc_final: 0.7229 (t0) REVERT: J 38 ARG cc_start: 0.5962 (OUTLIER) cc_final: 0.5611 (ptp-170) REVERT: J 66 ARG cc_start: 0.7098 (tpp80) cc_final: 0.6588 (tpp80) REVERT: K 91 TYR cc_start: 0.7372 (p90) cc_final: 0.7065 (p90) REVERT: K 102 THR cc_start: 0.7693 (m) cc_final: 0.7110 (p) REVERT: H 80 LEU cc_start: 0.9322 (OUTLIER) cc_final: 0.9079 (tp) REVERT: H 96 ASN cc_start: 0.8472 (t0) cc_final: 0.8208 (t0) REVERT: L 26 ARG cc_start: 0.8597 (tpt90) cc_final: 0.7889 (tpp80) REVERT: I 13 LYS cc_start: 0.5552 (tptt) cc_final: 0.5283 (tptt) REVERT: I 46 GLU cc_start: 0.8136 (mt-10) cc_final: 0.7667 (pt0) REVERT: I 64 ASP cc_start: 0.8331 (t0) cc_final: 0.8093 (t0) REVERT: M 45 GLN cc_start: 0.8560 (OUTLIER) cc_final: 0.8094 (mt0) REVERT: M 65 SER cc_start: 0.8983 (p) cc_final: 0.8695 (m) REVERT: C 149 MET cc_start: 0.5743 (mmp) cc_final: 0.5490 (mmp) REVERT: C 173 TYR cc_start: 0.7875 (p90) cc_final: 0.7632 (p90) REVERT: C 280 ASN cc_start: 0.8962 (p0) cc_final: 0.8755 (p0) REVERT: C 318 TYR cc_start: 0.9020 (m-80) cc_final: 0.8607 (m-80) REVERT: C 320 MET cc_start: 0.9038 (mmt) cc_final: 0.8800 (mmt) REVERT: C 467 ILE cc_start: 0.7771 (OUTLIER) cc_final: 0.7476 (mp) REVERT: C 519 ARG cc_start: 0.7912 (ptp-110) cc_final: 0.7279 (mtt90) REVERT: B 164 GLU cc_start: 0.7685 (mm-30) cc_final: 0.6311 (pm20) REVERT: B 320 MET cc_start: 0.7836 (mmm) cc_final: 0.7489 (mtp) REVERT: B 467 ILE cc_start: 0.9193 (mm) cc_final: 0.8884 (mm) REVERT: B 530 MET cc_start: 0.8853 (mmm) cc_final: 0.8324 (mmt) REVERT: B 585 ARG cc_start: 0.8369 (mtp-110) cc_final: 0.8163 (ptm-80) REVERT: B 591 GLN cc_start: 0.7475 (tt0) cc_final: 0.6843 (mt0) REVERT: B 652 GLN cc_start: 0.8295 (mp10) cc_final: 0.7832 (mp10) REVERT: A 102 GLU cc_start: 0.8504 (mp0) cc_final: 0.8093 (mp0) REVERT: A 320 MET cc_start: 0.8459 (mmm) cc_final: 0.7968 (mmm) REVERT: A 373 MET cc_start: 0.8579 (mmt) cc_final: 0.7724 (mmp) REVERT: A 584 GLU cc_start: 0.8665 (tm-30) cc_final: 0.8190 (tm-30) REVERT: A 601 LYS cc_start: 0.8622 (mttp) cc_final: 0.8368 (mtpp) REVERT: A 655 LYS cc_start: 0.8098 (pttt) cc_final: 0.7680 (ptmm) outliers start: 76 outliers final: 66 residues processed: 468 average time/residue: 0.5686 time to fit residues: 421.8715 Evaluate side-chains 496 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 423 time to evaluate : 6.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 24 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 73 LEU 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 57 LYS 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 42 ARG Chi-restraints excluded: chain G residue 92 THR 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 46 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 K residue 47 ILE Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 57 THR 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 7 SER Chi-restraints excluded: chain L residue 33 LEU 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 28 SER 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 123 THR Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 306 SER Chi-restraints excluded: chain C residue 349 LEU 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 306 SER 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 539 VAL 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 434 MET Chi-restraints excluded: chain A residue 449 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 188 optimal weight: 0.0270 chunk 18 optimal weight: 10.0000 chunk 112 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 80 optimal weight: 2.9990 chunk 133 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 40 optimal weight: 0.0070 chunk 243 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 overall best weight: 0.8062 ------------------------------------------------------------------------------- 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** ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.113446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.086243 restraints weight = 42520.116| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 3.34 r_work: 0.2973 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.3343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.277 24173 Z= 0.271 Angle : 0.925 59.199 32980 Z= 0.520 Chirality : 0.050 0.885 3843 Planarity : 0.005 0.160 4050 Dihedral : 6.681 55.857 4676 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 2.96 % Allowed : 19.58 % Favored : 77.46 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.16), residues: 2796 helix: 0.70 (0.27), residues: 386 sheet: 0.08 (0.17), residues: 945 loop : -0.88 (0.16), residues: 1465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP J 36 HIS 0.006 0.001 HIS G 93 PHE 0.033 0.002 PHE F 31 TYR 0.031 0.002 TYR H 100D ARG 0.016 0.000 ARG E 79 Details of bonding type rmsd link_NAG-ASN : bond 0.00536 ( 46) link_NAG-ASN : angle 2.44331 ( 138) link_ALPHA1-6 : bond 0.00710 ( 5) link_ALPHA1-6 : angle 1.54590 ( 15) link_BETA1-4 : bond 0.00544 ( 16) link_BETA1-4 : angle 1.91279 ( 48) link_ALPHA1-2 : bond 0.01277 ( 4) link_ALPHA1-2 : angle 3.08598 ( 12) link_ALPHA1-3 : bond 0.00928 ( 7) link_ALPHA1-3 : angle 1.48871 ( 21) hydrogen bonds : bond 0.03754 ( 785) hydrogen bonds : angle 5.32874 ( 2256) SS BOND : bond 0.00453 ( 46) SS BOND : angle 1.25923 ( 92) covalent geometry : bond 0.00583 (24049) covalent geometry : angle 0.90716 (32654) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11442.07 seconds wall clock time: 202 minutes 16.50 seconds (12136.50 seconds total)