Starting phenix.real_space_refine on Fri Jun 20 08:36:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cu6_45929/06_2025/9cu6_45929.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cu6_45929/06_2025/9cu6_45929.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9cu6_45929/06_2025/9cu6_45929.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cu6_45929/06_2025/9cu6_45929.map" model { file = "/net/cci-nas-00/data/ceres_data/9cu6_45929/06_2025/9cu6_45929.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cu6_45929/06_2025/9cu6_45929.cif" } resolution = 3.3 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= 0.025 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 149 5.16 5 C 14848 2.51 5 N 3966 2.21 5 O 4668 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 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: 23631 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" 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: "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: "H" Number of atoms: 962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 962 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 116} 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: 1009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1009 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 6, 'TRANS': 122} Chain: "L" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 825 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} 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: "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: "I" Number of atoms: 962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 962 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 116} Chain: "M" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 825 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "C" Number of atoms: 4463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 561, 4463 Classifications: {'peptide': 561} Link IDs: {'PTRANS': 23, 'TRANS': 537} Chain breaks: 5 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: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 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: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 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: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "W" Number of atoms: 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: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" 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: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 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 Time building chain proxies: 15.75, per 1000 atoms: 0.67 Number of scatterers: 23631 At special positions: 0 Unit cell: (159.498, 138.784, 133.605, 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 149 16.00 O 4668 8.00 N 3966 7.00 C 14848 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.02 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=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.02 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 662 " distance=2.03 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS C 501 " distance=2.02 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=1.82 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 89 " - pdb=" SG CYS E 96 " distance=2.05 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.05 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.03 Simple disulfide: pdb=" SG CYS G 89 " - pdb=" SG CYS G 96 " distance=2.17 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.04 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.04 Simple disulfide: pdb=" SG CYS K 89 " - pdb=" SG CYS K 96 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 196 " distance=2.02 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=2.02 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 445 " distance=2.02 Simple disulfide: pdb=" SG CYS B 385 " - pdb=" SG CYS B 418 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 598 " - pdb=" SG CYS C 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 U 4 " - " MAN U 5 " ALPHA1-3 " BMA N 3 " - " MAN N 4 " " BMA P 3 " - " MAN P 4 " " BMA R 3 " - " MAN R 4 " " BMA U 3 " - " MAN U 4 " " BMA W 3 " - " MAN W 4 " " BMA Y 3 " - " MAN Y 4 " ALPHA1-6 " BMA N 3 " - " MAN N 5 " " BMA R 3 " - " MAN R 5 " " BMA W 3 " - " MAN W 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 R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " BETA1-6 " NAG Q 1 " - " FUC Q 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG V 1 " - " FUC V 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 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 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 A 88 " " NAG O 1 " - " ASN A 156 " " NAG P 1 " - " ASN A 262 " " NAG Q 1 " - " ASN A 625 " " NAG R 1 " - " ASN B 88 " " NAG S 1 " - " ASN B 156 " " NAG T 1 " - " ASN B 241 " " NAG U 1 " - " ASN B 262 " " NAG V 1 " - " ASN B 625 " " NAG W 1 " - " ASN C 88 " " NAG X 1 " - " ASN C 156 " " NAG Y 1 " - " ASN C 262 " Time building additional restraints: 6.64 Conformation dependent library (CDL) restraints added in 3.0 seconds 5628 Ramachandran restraints generated. 2814 Oldfield, 0 Emsley, 2814 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5310 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 44 sheets defined 18.7% alpha, 23.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.02 Creating SS restraints... Processing helix chain 'A' and resid 70 through 74 Processing helix chain 'A' and resid 98 through 117 removed outlier: 4.010A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 335 through 353 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 377 through 381 removed outlier: 3.503A pdb=" N GLU A 381 " --> pdb=" O CYS A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 391 Processing helix chain 'A' and resid 425 through 429 removed outlier: 3.515A pdb=" N GLN A 428 " --> pdb=" O ASN A 425 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ARG A 429 " --> pdb=" O MET A 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 425 through 429' Processing helix chain 'A' and resid 475 through 484 removed outlier: 3.735A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 534 Processing helix chain 'A' and resid 536 through 542 removed outlier: 3.978A pdb=" N GLN A 540 " --> pdb=" O THR A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 597 Processing helix chain 'A' and resid 618 through 624 Processing helix chain 'A' and resid 627 through 636 Processing helix chain 'A' and resid 638 through 651 Processing helix chain 'A' and resid 653 through 662 removed outlier: 3.559A pdb=" N GLU A 659 " --> pdb=" O LYS A 655 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 32 Processing helix chain 'D' and resid 61 through 64 Processing helix chain 'D' and resid 83 through 87 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'E' and resid 26 through 27C Processing helix chain 'E' and resid 79 through 83 Processing helix chain 'F' and resid 28 through 32 removed outlier: 3.542A pdb=" N TYR F 32 " --> pdb=" O PHE F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 61 through 64 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'G' and resid 26 through 27C Processing helix chain 'G' and resid 79 through 84 removed outlier: 4.018A pdb=" N THR G 84 " --> pdb=" O GLU G 81 " (cutoff:3.500A) Processing helix chain 'J' and resid 28 through 32 removed outlier: 3.580A pdb=" N TYR J 32 " --> pdb=" O PHE J 29 " (cutoff:3.500A) Processing helix 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 'K' and resid 79 through 83 Processing helix chain 'B' and resid 70 through 74 Processing helix chain 'B' and resid 98 through 117 removed outlier: 4.071A pdb=" N GLU B 102 " --> pdb=" O ASN B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 354 removed outlier: 3.951A pdb=" N GLN B 352 " --> pdb=" O LYS B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 373 Processing helix chain 'B' and resid 377 through 381 removed outlier: 3.527A pdb=" N GLY B 380 " --> pdb=" O ASN B 377 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU B 381 " --> pdb=" O CYS B 378 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 377 through 381' Processing helix chain 'B' and resid 475 through 484 removed outlier: 3.596A pdb=" N TRP B 479 " --> pdb=" O MET B 475 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU B 482 " --> pdb=" O ASN B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 535 No H-bonds generated for 'chain 'B' and resid 533 through 535' Processing helix chain 'B' and resid 536 through 543 removed outlier: 3.894A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 596 Processing helix chain 'B' and resid 618 through 624 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 649 removed outlier: 3.511A pdb=" N THR B 644 " --> pdb=" O SER B 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 660 removed outlier: 3.600A pdb=" N LEU B 660 " --> pdb=" O ASN B 656 " (cutoff:3.500A) Processing helix chain 'I' and resid 60 through 65 removed outlier: 4.638A pdb=" N ASN I 65 " --> pdb=" O PRO I 61 " (cutoff:3.500A) Processing helix chain 'I' and resid 83 through 87 Processing helix chain 'C' and resid 70 through 74 Processing helix chain 'C' and resid 98 through 117 removed outlier: 3.861A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 removed outlier: 3.604A pdb=" N LEU C 125 " --> pdb=" O LEU C 122 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N CYS C 126 " --> pdb=" O THR C 123 " (cutoff:3.500A) No H-bonds generated for '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 475 through 484 removed outlier: 3.766A pdb=" N SER C 481 " --> pdb=" O ASP C 477 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 529 through 534 Processing helix chain 'C' and resid 536 through 542 removed outlier: 3.694A pdb=" N GLN C 540 " --> pdb=" O THR C 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 597 removed outlier: 3.588A pdb=" N LYS C 574 " --> pdb=" O VAL C 570 " (cutoff:3.500A) Processing helix chain 'C' and resid 618 through 624 removed outlier: 3.532A 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 removed outlier: 4.659A pdb=" N SER C 640 " --> pdb=" O ASP C 636 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N GLU C 641 " --> pdb=" O ASN C 637 " (cutoff:3.500A) Processing helix chain 'C' and resid 650 through 655 Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.148A pdb=" N VAL A 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N VAL A 38 " --> pdb=" O THR A 606 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N THR A 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N TYR A 40 " --> pdb=" O CYS A 604 " (cutoff:3.500A) removed outlier: 8.155A pdb=" N CYS A 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.700A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 76 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 168 through 177 removed outlier: 4.289A pdb=" N LYS A 168 " --> pdb=" O THR A 163 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 200 through 203 removed outlier: 3.543A pdb=" N ALA A 433 " --> pdb=" O VAL A 200 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 259 through 261 current: chain 'A' and resid 284 through 298 removed outlier: 7.131A pdb=" N GLU A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N SER A 334 " --> pdb=" O GLU A 293 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 330 through 334 current: chain 'A' and resid 383 through 385 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 383 through 385 current: chain 'A' and resid 465 through 470 Processing sheet with id=AA8, first strand: chain 'A' and resid 304 through 312 removed outlier: 6.956A pdb=" N ARG A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 3 through 6 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 18 through 27 current: chain 'D' and resid 74 through 82 Processing sheet with id=AB1, first strand: chain 'D' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 10 through 12 current: chain 'D' and resid 44 through 51 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 57 through 59 current: chain 'D' and resid 100F through 103 Processing sheet with id=AB2, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AB3, first strand: chain 'H' and resid 11 through 12 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 11 through 12 current: chain 'H' and resid 46 through 52 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 57 through 59 current: chain 'H' and resid 100F through 103 Processing sheet with id=AB4, first strand: chain 'E' and resid 5 through 6 Processing sheet with id=AB5, first strand: chain 'E' and resid 11 through 14 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 11 through 14 current: chain 'E' and resid 45 through 48 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 45 through 48 current: chain 'E' and resid 97 through 98 No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'F' and resid 5 through 6 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 18 through 27 current: chain 'F' and resid 73 through 82 Processing sheet with id=AB7, first strand: chain 'F' and resid 34 through 40 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 44 through 45 current: chain 'F' and resid 57 through 59 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 57 through 59 current: chain 'F' and resid 100F through 103 Processing sheet with id=AB8, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.758A pdb=" N GLU L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N SER L 67 " --> pdb=" O GLU L 70 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.402A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 5 through 6 Processing sheet with id=AC2, first strand: chain 'G' and resid 9 through 14 removed outlier: 5.257A pdb=" N GLY G 95A" --> pdb=" O THR G 92 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N THR G 92 " --> pdb=" O GLY G 95A" (cutoff:3.500A) removed outlier: 5.691A pdb=" N CYS G 88 " --> pdb=" O GLY G 99 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N GLY G 101 " --> pdb=" O TYR G 86 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N TYR G 86 " --> pdb=" O GLY G 101 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N ILE G 33 " --> pdb=" O TYR G 49 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N TYR G 49 " --> pdb=" O ILE G 33 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N TRP G 35 " --> pdb=" O ILE G 47 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N GLU G 53 " --> pdb=" O TYR G 49 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'J' and resid 3 through 6 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 18 through 27 current: chain 'J' and resid 74 through 82 Processing sheet with id=AC4, first strand: chain 'J' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 10 through 12 current: chain 'J' and resid 44 through 51 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 57 through 59 current: chain 'J' and resid 100F through 103 Processing sheet with id=AC5, first strand: chain 'K' and resid 9 through 14 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 9 through 14 current: chain 'K' and resid 45 through 48 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 45 through 48 current: chain 'K' and resid 96 through 98 No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'K' and resid 19 through 23 Processing sheet with id=AC7, first strand: chain 'B' and resid 494 through 499 removed outlier: 4.819A pdb=" N VAL B 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 45 through 47 removed outlier: 3.887A pdb=" N ILE B 225 " --> pdb=" O VAL B 245 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N VAL B 242 " --> pdb=" O LEU B 86 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 75 through 76 removed outlier: 6.714A pdb=" N CYS B 54 " --> pdb=" O VAL B 75 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 91 through 94 Processing sheet with id=AD2, first strand: chain 'B' and resid 121 through 122 removed outlier: 4.419A pdb=" N ILE B 201 " --> pdb=" O LEU B 122 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N THR B 202 " --> pdb=" O TYR B 435 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 170 through 177 Processing sheet with id=AD4, first strand: chain 'B' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 259 through 261 current: chain 'B' and resid 284 through 287 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 284 through 287 current: chain 'B' and resid 330 through 334 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 330 through 334 current: chain 'B' and resid 383 through 385 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 383 through 385 current: chain 'B' and resid 465 through 470 No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'B' and resid 304 through 312 removed outlier: 7.009A pdb=" N ARG B 315 " --> pdb=" O ILE B 309 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 4 through 7 removed outlier: 6.621A pdb=" N GLN I 77 " --> pdb=" O ASP I 72 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 11 through 12 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 11 through 12 current: chain 'I' and resid 46 through 51 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 57 through 59 current: chain 'I' and resid 100F through 103 Processing sheet with id=AD8, first strand: chain 'M' and resid 4 through 7 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 19 through 25 current: chain 'M' and resid 70 through 75 Processing sheet with id=AD9, first strand: chain 'M' and resid 10 through 13 removed outlier: 6.348A pdb=" N TRP M 35 " --> pdb=" O LEU M 47 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 494 through 499 removed outlier: 4.971A pdb=" N VAL C 36 " --> pdb=" O THR C 606 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 45 through 47 removed outlier: 4.633A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 75 through 76 removed outlier: 6.950A pdb=" N CYS C 54 " --> pdb=" O VAL C 75 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AE5, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AE6, first strand: chain 'C' and resid 200 through 203 removed outlier: 3.928A pdb=" N ALA C 433 " --> pdb=" O VAL C 200 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 259 through 261 current: chain 'C' and resid 284 through 298 removed outlier: 7.274A pdb=" N GLU C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N SER C 334 " --> pdb=" O GLU C 293 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 330 through 334 current: chain 'C' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 381 through 385 current: chain 'C' and resid 465 through 470 Processing sheet with id=AE8, first strand: chain 'C' and resid 301 through 312 removed outlier: 7.203A pdb=" N ASN C 301 " --> pdb=" O ILE C 322 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N ILE C 322 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY C 321 " --> pdb=" O THR C 303 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ARG C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) 616 hydrogen bonds defined for protein. 1596 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: 8.29 Time building geometry restraints manager: 7.83 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: 7130 1.34 - 1.47: 6398 1.47 - 1.59: 10420 1.59 - 1.72: 0 1.72 - 1.85: 201 Bond restraints: 24149 Sorted by residual: bond pdb=" CA TYR I 100D" pdb=" C TYR I 100D" ideal model delta sigma weight residual 1.523 1.476 0.047 1.35e-02 5.49e+03 1.21e+01 bond pdb=" N GLY A 441 " pdb=" CA GLY A 441 " ideal model delta sigma weight residual 1.444 1.478 -0.034 1.02e-02 9.61e+03 1.11e+01 bond pdb=" N ILE K 48 " pdb=" CA ILE K 48 " ideal model delta sigma weight residual 1.464 1.501 -0.038 1.13e-02 7.83e+03 1.10e+01 bond pdb=" N SER G 90 " pdb=" CA SER G 90 " ideal model delta sigma weight residual 1.454 1.492 -0.038 1.21e-02 6.83e+03 9.96e+00 bond pdb=" N ILE D 51 " pdb=" CA ILE D 51 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.17e-02 7.31e+03 8.98e+00 ... (remaining 24144 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.86: 31721 2.86 - 5.72: 961 5.72 - 8.58: 98 8.58 - 11.44: 11 11.44 - 14.30: 2 Bond angle restraints: 32793 Sorted by residual: angle pdb=" C GLN A 650 " pdb=" N ASN A 651 " pdb=" CA ASN A 651 " ideal model delta sigma weight residual 122.24 108.89 13.35 1.57e+00 4.06e-01 7.23e+01 angle pdb=" C SER A 649 " pdb=" N GLN A 650 " pdb=" CA GLN A 650 " ideal model delta sigma weight residual 122.42 108.12 14.30 1.77e+00 3.19e-01 6.53e+01 angle pdb=" N TYR H 100D" pdb=" CA TYR H 100D" pdb=" C TYR H 100D" ideal model delta sigma weight residual 113.12 103.83 9.29 1.25e+00 6.40e-01 5.52e+01 angle pdb=" N TYR I 100D" pdb=" CA TYR I 100D" pdb=" CB TYR I 100D" ideal model delta sigma weight residual 110.28 119.95 -9.67 1.55e+00 4.16e-01 3.89e+01 angle pdb=" C GLU K 50 " pdb=" N ASP K 51 " pdb=" CA ASP K 51 " ideal model delta sigma weight residual 120.71 110.84 9.87 1.67e+00 3.59e-01 3.49e+01 ... (remaining 32788 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.41: 14433 22.41 - 44.82: 727 44.82 - 67.22: 167 67.22 - 89.63: 62 89.63 - 112.04: 24 Dihedral angle restraints: 15413 sinusoidal: 7143 harmonic: 8270 Sorted by residual: dihedral pdb=" CB CYS K 89 " pdb=" SG CYS K 89 " pdb=" SG CYS K 96 " pdb=" CB CYS K 96 " ideal model delta sinusoidal sigma weight residual -86.00 -170.53 84.53 1 1.00e+01 1.00e-02 8.68e+01 dihedral pdb=" CB CYS F 22 " pdb=" SG CYS F 22 " pdb=" SG CYS F 92 " pdb=" CB CYS F 92 " ideal model delta sinusoidal sigma weight residual 93.00 25.62 67.38 1 1.00e+01 1.00e-02 5.91e+01 dihedral pdb=" CB CYS E 89 " pdb=" SG CYS E 89 " pdb=" SG CYS E 96 " pdb=" CB CYS E 96 " ideal model delta sinusoidal sigma weight residual 93.00 38.01 54.99 1 1.00e+01 1.00e-02 4.09e+01 ... (remaining 15410 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.187: 3811 0.187 - 0.374: 36 0.374 - 0.561: 1 0.561 - 0.748: 0 0.748 - 0.936: 3 Chirality restraints: 3851 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 -1.46 -0.94 2.00e-01 2.50e+01 2.19e+01 chirality pdb=" C1 NAG O 1 " pdb=" ND2 ASN A 156 " pdb=" C2 NAG O 1 " pdb=" O5 NAG O 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.53 -0.87 2.00e-01 2.50e+01 1.91e+01 chirality pdb=" C1 NAG P 1 " pdb=" ND2 ASN A 262 " pdb=" C2 NAG P 1 " pdb=" O5 NAG P 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.63 -0.77 2.00e-01 2.50e+01 1.48e+01 ... (remaining 3848 not shown) Planarity restraints: 4110 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER M 14 " 0.020 2.00e-02 2.50e+03 3.97e-02 1.57e+01 pdb=" C SER M 14 " -0.069 2.00e-02 2.50e+03 pdb=" O SER M 14 " 0.026 2.00e-02 2.50e+03 pdb=" N VAL M 15 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR M 49 " -0.034 2.00e-02 2.50e+03 2.75e-02 1.51e+01 pdb=" CG TYR M 49 " 0.068 2.00e-02 2.50e+03 pdb=" CD1 TYR M 49 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR M 49 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR M 49 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR M 49 " -0.007 2.00e-02 2.50e+03 pdb=" CZ TYR M 49 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR M 49 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP C 636 " -0.019 2.00e-02 2.50e+03 3.72e-02 1.38e+01 pdb=" C ASP C 636 " 0.064 2.00e-02 2.50e+03 pdb=" O ASP C 636 " -0.024 2.00e-02 2.50e+03 pdb=" N ASN C 637 " -0.022 2.00e-02 2.50e+03 ... (remaining 4107 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.70: 791 2.70 - 3.25: 22397 3.25 - 3.80: 36849 3.80 - 4.35: 49012 4.35 - 4.90: 81228 Nonbonded interactions: 190277 Sorted by model distance: nonbonded pdb=" CG ARG A 503 " pdb=" O THR A 605 " model vdw 2.144 3.440 nonbonded pdb=" OH TYR J 53 " pdb=" OE1 GLU B 87 " model vdw 2.155 3.040 nonbonded pdb=" NE2 GLN A 652 " pdb=" O SER C 534 " model vdw 2.177 3.120 nonbonded pdb=" O GLU B 641 " pdb=" OG1 THR B 644 " model vdw 2.195 3.040 nonbonded pdb=" OD1 ASP K 82 " pdb=" OH TYR K 86 " model vdw 2.207 3.040 ... (remaining 190272 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 59 or resid 64 through 136 or resid 150 through \ 503 or resid 521 through 655 or resid 701 through 711)) selection = (chain 'B' and (resid 32 through 503 or resid 521 through 655 or resid 701 throu \ gh 711)) selection = (chain 'C' and (resid 32 through 59 or resid 64 through 136 or resid 150 through \ 503 or resid 521 through 655 or resid 702 through 712)) } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'J' } 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 'R' selection = chain 'U' selection = chain 'W' } ncs_group { reference = chain 'O' selection = chain 'S' selection = chain 'T' selection = chain 'X' } ncs_group { reference = chain 'Q' selection = chain 'V' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.930 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: 0.950 Check model and map are aligned: 0.170 Set scattering table: 0.220 Process input model: 56.360 Find NCS groups from input model: 1.300 Set up NCS constraints: 0.180 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:3.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 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 : 0.007 0.207 24271 Z= 0.306 Angle : 1.188 35.520 33114 Z= 0.630 Chirality : 0.067 0.936 3851 Planarity : 0.006 0.088 4064 Dihedral : 14.817 112.039 9968 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 0.20 % Allowed : 10.96 % Favored : 88.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.59 (0.15), residues: 2814 helix: 0.68 (0.26), residues: 356 sheet: 0.80 (0.16), residues: 970 loop : 0.15 (0.16), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.003 TRP J 36 HIS 0.010 0.002 HIS C 66 PHE 0.044 0.004 PHE L 98 TYR 0.068 0.004 TYR M 49 ARG 0.015 0.001 ARG B 440 Details of bonding type rmsd link_NAG-ASN : bond 0.00474 ( 46) link_NAG-ASN : angle 3.30329 ( 138) link_ALPHA1-6 : bond 0.00759 ( 3) link_ALPHA1-6 : angle 2.58523 ( 9) link_BETA1-4 : bond 0.01441 ( 18) link_BETA1-4 : angle 4.23731 ( 54) link_ALPHA1-2 : bond 0.00149 ( 2) link_ALPHA1-2 : angle 1.74694 ( 6) link_ALPHA1-3 : bond 0.00319 ( 6) link_ALPHA1-3 : angle 2.61480 ( 18) hydrogen bonds : bond 0.16626 ( 616) hydrogen bonds : angle 7.57347 ( 1596) link_BETA1-6 : bond 0.00716 ( 2) link_BETA1-6 : angle 2.53908 ( 6) SS BOND : bond 0.03747 ( 45) SS BOND : angle 4.92631 ( 90) covalent geometry : bond 0.00634 (24149) covalent geometry : angle 1.13002 (32793) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5628 Ramachandran restraints generated. 2814 Oldfield, 0 Emsley, 2814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5628 Ramachandran restraints generated. 2814 Oldfield, 0 Emsley, 2814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 573 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 568 time to evaluate : 2.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ASP cc_start: 0.7969 (t0) cc_final: 0.7644 (t0) REVERT: A 164 GLU cc_start: 0.5746 (tp30) cc_final: 0.5468 (tp30) REVERT: A 327 ARG cc_start: 0.7977 (mtp85) cc_final: 0.7675 (mtp85) REVERT: A 535 MET cc_start: 0.8678 (mpp) cc_final: 0.8464 (mpp) REVERT: A 616 ASN cc_start: 0.8695 (p0) cc_final: 0.8370 (p0) REVERT: A 632 GLU cc_start: 0.8626 (tp30) cc_final: 0.8354 (tp30) REVERT: A 655 LYS cc_start: 0.8952 (mmtt) cc_final: 0.8700 (mmmm) REVERT: D 3 GLN cc_start: 0.6683 (tm-30) cc_final: 0.6471 (tm-30) REVERT: D 19 LYS cc_start: 0.8399 (tttm) cc_final: 0.8100 (tttm) REVERT: D 31 PHE cc_start: 0.9003 (m-10) cc_final: 0.8773 (m-10) REVERT: D 39 GLN cc_start: 0.7502 (tp40) cc_final: 0.7249 (tp40) REVERT: D 58 ASN cc_start: 0.8137 (t0) cc_final: 0.7903 (t0) REVERT: D 79 TYR cc_start: 0.7910 (m-80) cc_final: 0.7483 (m-10) REVERT: D 82 ASN cc_start: 0.8100 (m-40) cc_final: 0.7888 (m110) REVERT: H 5 GLN cc_start: 0.8954 (tp40) cc_final: 0.8729 (tp40) REVERT: H 13 ARG cc_start: 0.7794 (mtt-85) cc_final: 0.7519 (mtt-85) REVERT: E 35 TRP cc_start: 0.8210 (m100) cc_final: 0.7676 (m100) REVERT: F 83 LYS cc_start: 0.7795 (mmtm) cc_final: 0.7106 (mptt) REVERT: L 83 PHE cc_start: 0.8628 (t80) cc_final: 0.8345 (t80) REVERT: G 42 ARG cc_start: 0.8448 (ttm110) cc_final: 0.7883 (mtp85) REVERT: G 66 LYS cc_start: 0.8367 (ttpp) cc_final: 0.8105 (ttpp) REVERT: G 68 TYR cc_start: 0.7963 (m-80) cc_final: 0.7335 (t80) REVERT: J 57 LYS cc_start: 0.8672 (mtpp) cc_final: 0.8431 (mtpt) REVERT: J 58 ASN cc_start: 0.8161 (m-40) cc_final: 0.7828 (m-40) REVERT: J 90 TYR cc_start: 0.7890 (m-80) cc_final: 0.7480 (m-80) REVERT: K 29 SER cc_start: 0.8624 (t) cc_final: 0.8345 (p) REVERT: K 53 GLU cc_start: 0.7133 (mt-10) cc_final: 0.6846 (mp0) REVERT: K 72 TYR cc_start: 0.6518 (m-10) cc_final: 0.6310 (m-10) REVERT: B 35 TRP cc_start: 0.8339 (m100) cc_final: 0.7984 (m100) REVERT: B 110 SER cc_start: 0.8975 (t) cc_final: 0.8368 (m) REVERT: B 160 ASN cc_start: 0.8130 (m-40) cc_final: 0.7718 (p0) REVERT: B 189 THR cc_start: 0.9044 (p) cc_final: 0.8517 (t) REVERT: B 327 ARG cc_start: 0.8151 (mtp85) cc_final: 0.7508 (mmp80) REVERT: B 446 SER cc_start: 0.9143 (t) cc_final: 0.8645 (p) REVERT: B 475 MET cc_start: 0.8784 (mmm) cc_final: 0.8506 (tpp) REVERT: B 579 ARG cc_start: 0.8221 (mtp85) cc_final: 0.8002 (mtm180) REVERT: I 53 TYR cc_start: 0.9333 (t80) cc_final: 0.9018 (t80) REVERT: M 36 TYR cc_start: 0.8739 (m-10) cc_final: 0.8482 (m-80) REVERT: M 42 LYS cc_start: 0.8043 (mmmm) cc_final: 0.7778 (mmmt) REVERT: M 79 GLN cc_start: 0.8975 (mm-40) cc_final: 0.8652 (mm110) REVERT: C 35 TRP cc_start: 0.8417 (m100) cc_final: 0.8199 (m100) REVERT: C 37 THR cc_start: 0.9147 (m) cc_final: 0.8825 (p) REVERT: C 46 LYS cc_start: 0.8229 (mtpp) cc_final: 0.7880 (mttm) REVERT: C 53 PHE cc_start: 0.7590 (p90) cc_final: 0.7370 (p90) REVERT: C 168 LYS cc_start: 0.8626 (ttmm) cc_final: 0.8090 (mmtm) REVERT: C 217 TYR cc_start: 0.7943 (m-80) cc_final: 0.7670 (m-80) REVERT: C 355 ASN cc_start: 0.6765 (m-40) cc_final: 0.5843 (p0) REVERT: C 492 GLU cc_start: 0.8766 (mt-10) cc_final: 0.8402 (mt-10) outliers start: 5 outliers final: 2 residues processed: 573 average time/residue: 0.4036 time to fit residues: 344.2938 Evaluate side-chains 482 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 480 time to evaluate : 2.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 650 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 237 optimal weight: 0.7980 chunk 212 optimal weight: 1.9990 chunk 118 optimal weight: 0.5980 chunk 72 optimal weight: 0.1980 chunk 143 optimal weight: 3.9990 chunk 113 optimal weight: 0.8980 chunk 220 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 133 optimal weight: 0.8980 chunk 163 optimal weight: 1.9990 chunk 255 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 GLN ** A 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 58 ASN L 34 ASN J 105 GLN B 249 HIS B 422 GLN B 624 ASN ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 34 ASN C 66 HIS C 246 GLN C 249 HIS C 575 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.134277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.106504 restraints weight = 38752.387| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 3.07 r_work: 0.3287 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.1356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 24271 Z= 0.146 Angle : 0.691 13.419 33114 Z= 0.345 Chirality : 0.047 0.487 3851 Planarity : 0.004 0.037 4064 Dihedral : 9.543 79.811 4684 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.62 % Favored : 96.30 % Rotamer: Outliers : 2.11 % Allowed : 11.55 % Favored : 86.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.52 (0.15), residues: 2814 helix: 1.20 (0.27), residues: 360 sheet: 0.71 (0.15), residues: 1008 loop : -0.06 (0.17), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 50 HIS 0.004 0.001 HIS B 363 PHE 0.015 0.002 PHE C 277 TYR 0.030 0.002 TYR G 49 ARG 0.009 0.001 ARG K 42 Details of bonding type rmsd link_NAG-ASN : bond 0.00345 ( 46) link_NAG-ASN : angle 2.60086 ( 138) link_ALPHA1-6 : bond 0.01107 ( 3) link_ALPHA1-6 : angle 2.13624 ( 9) link_BETA1-4 : bond 0.00824 ( 18) link_BETA1-4 : angle 2.72121 ( 54) link_ALPHA1-2 : bond 0.00136 ( 2) link_ALPHA1-2 : angle 1.98859 ( 6) link_ALPHA1-3 : bond 0.00637 ( 6) link_ALPHA1-3 : angle 2.07244 ( 18) hydrogen bonds : bond 0.04435 ( 616) hydrogen bonds : angle 6.05241 ( 1596) link_BETA1-6 : bond 0.00528 ( 2) link_BETA1-6 : angle 2.06990 ( 6) SS BOND : bond 0.00351 ( 45) SS BOND : angle 1.34643 ( 90) covalent geometry : bond 0.00327 (24149) covalent geometry : angle 0.65727 (32793) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5628 Ramachandran restraints generated. 2814 Oldfield, 0 Emsley, 2814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5628 Ramachandran restraints generated. 2814 Oldfield, 0 Emsley, 2814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 578 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 525 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: A 57 ASP cc_start: 0.7972 (t0) cc_final: 0.7609 (t0) REVERT: A 616 ASN cc_start: 0.8717 (p0) cc_final: 0.8350 (p0) REVERT: A 632 GLU cc_start: 0.8757 (tp30) cc_final: 0.8464 (tp30) REVERT: A 652 GLN cc_start: 0.8737 (tp40) cc_final: 0.8525 (tp40) REVERT: D 58 ASN cc_start: 0.8152 (t0) cc_final: 0.7888 (t0) REVERT: D 79 TYR cc_start: 0.8214 (m-80) cc_final: 0.7889 (m-10) REVERT: D 80 MET cc_start: 0.8180 (tmm) cc_final: 0.7807 (tmm) REVERT: D 82 ASN cc_start: 0.8084 (m-40) cc_final: 0.7828 (m110) REVERT: H 81 LYS cc_start: 0.8975 (mmtt) cc_final: 0.8749 (mmmm) REVERT: F 19 LYS cc_start: 0.7480 (ttmt) cc_final: 0.7032 (ttmm) REVERT: F 57 LYS cc_start: 0.8657 (mtmt) cc_final: 0.8290 (mttt) REVERT: F 66 ARG cc_start: 0.6373 (ttm170) cc_final: 0.5580 (ttt180) REVERT: F 82 ARG cc_start: 0.6990 (mtp180) cc_final: 0.6736 (mtp-110) REVERT: F 82 LEU cc_start: 0.8319 (mp) cc_final: 0.8044 (mp) REVERT: F 83 LYS cc_start: 0.8093 (mmtm) cc_final: 0.7434 (mptt) REVERT: L 4 MET cc_start: 0.8742 (mmm) cc_final: 0.8349 (mmm) REVERT: G 12 SER cc_start: 0.8711 (t) cc_final: 0.8492 (m) REVERT: G 54 ARG cc_start: 0.8457 (mtm180) cc_final: 0.7954 (mtp180) REVERT: J 19 LYS cc_start: 0.8202 (tptt) cc_final: 0.6990 (tptp) REVERT: J 46 GLU cc_start: 0.8211 (tm-30) cc_final: 0.7725 (tm-30) REVERT: J 58 ASN cc_start: 0.8220 (m-40) cc_final: 0.7872 (m-40) REVERT: J 90 TYR cc_start: 0.7781 (m-80) cc_final: 0.7302 (m-80) REVERT: J 105 GLN cc_start: 0.8060 (OUTLIER) cc_final: 0.7835 (pm20) REVERT: K 29 SER cc_start: 0.8576 (t) cc_final: 0.8275 (p) REVERT: K 42 ARG cc_start: 0.7479 (mtm-85) cc_final: 0.7154 (mtm-85) REVERT: B 35 TRP cc_start: 0.8335 (m100) cc_final: 0.7774 (m100) REVERT: B 110 SER cc_start: 0.9114 (t) cc_final: 0.8518 (m) REVERT: B 126 CYS cc_start: 0.7847 (OUTLIER) cc_final: 0.7342 (t) REVERT: B 160 ASN cc_start: 0.8297 (m-40) cc_final: 0.7766 (p0) REVERT: B 189 THR cc_start: 0.9144 (p) cc_final: 0.8501 (t) REVERT: B 327 ARG cc_start: 0.8218 (mtp85) cc_final: 0.7737 (mmp80) REVERT: B 446 SER cc_start: 0.9093 (t) cc_final: 0.8580 (p) REVERT: B 490 LYS cc_start: 0.8872 (tttm) cc_final: 0.8565 (tttp) REVERT: B 579 ARG cc_start: 0.8219 (mtp85) cc_final: 0.7995 (mtm180) REVERT: B 624 ASN cc_start: 0.8060 (m-40) cc_final: 0.7836 (m-40) REVERT: I 81 LYS cc_start: 0.8920 (ttmm) cc_final: 0.8372 (ttpp) REVERT: M 48 ILE cc_start: 0.9581 (mm) cc_final: 0.9373 (mm) REVERT: M 79 GLN cc_start: 0.8833 (mm-40) cc_final: 0.8382 (mm110) REVERT: C 46 LYS cc_start: 0.8213 (mtpp) cc_final: 0.7946 (mttm) REVERT: C 103 GLN cc_start: 0.7992 (tt0) cc_final: 0.7670 (tm-30) REVERT: C 217 TYR cc_start: 0.8312 (m-80) cc_final: 0.8077 (m-80) REVERT: C 355 ASN cc_start: 0.6822 (m-40) cc_final: 0.5933 (p0) outliers start: 53 outliers final: 34 residues processed: 551 average time/residue: 0.3871 time to fit residues: 321.8074 Evaluate side-chains 496 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 460 time to evaluate : 2.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 230 ASP Chi-restraints excluded: chain A residue 650 GLN Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain H residue 65 ASN Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain F residue 79 TYR Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain G residue 83 GLU Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 105 GLN Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 85 THR Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain K residue 97 VAL Chi-restraints excluded: chain K residue 102 THR Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 378 CYS Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 67 SER Chi-restraints excluded: chain M residue 85 THR Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 545 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 173 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 187 optimal weight: 0.0470 chunk 226 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 102 optimal weight: 0.9990 chunk 208 optimal weight: 4.9990 chunk 59 optimal weight: 0.9980 chunk 114 optimal weight: 7.9990 chunk 113 optimal weight: 3.9990 chunk 191 optimal weight: 4.9990 overall best weight: 1.4084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 30 ASN ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 6 GLN C 575 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.137580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.109705 restraints weight = 39623.804| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 3.04 r_work: 0.3201 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 24271 Z= 0.187 Angle : 0.658 12.751 33114 Z= 0.329 Chirality : 0.047 0.442 3851 Planarity : 0.004 0.041 4064 Dihedral : 8.291 67.464 4684 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.12 % Favored : 95.74 % Rotamer: Outliers : 2.83 % Allowed : 12.91 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.31 (0.15), residues: 2814 helix: 1.13 (0.27), residues: 362 sheet: 0.60 (0.15), residues: 1016 loop : -0.25 (0.16), residues: 1436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP F 50 HIS 0.006 0.001 HIS G 93 PHE 0.020 0.002 PHE C 53 TYR 0.028 0.002 TYR K 49 ARG 0.007 0.001 ARG C 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00336 ( 46) link_NAG-ASN : angle 2.32026 ( 138) link_ALPHA1-6 : bond 0.01221 ( 3) link_ALPHA1-6 : angle 2.16794 ( 9) link_BETA1-4 : bond 0.00774 ( 18) link_BETA1-4 : angle 2.51276 ( 54) link_ALPHA1-2 : bond 0.00112 ( 2) link_ALPHA1-2 : angle 1.91596 ( 6) link_ALPHA1-3 : bond 0.00761 ( 6) link_ALPHA1-3 : angle 1.86950 ( 18) hydrogen bonds : bond 0.04058 ( 616) hydrogen bonds : angle 5.69344 ( 1596) link_BETA1-6 : bond 0.00359 ( 2) link_BETA1-6 : angle 2.03594 ( 6) SS BOND : bond 0.00400 ( 45) SS BOND : angle 1.20402 ( 90) covalent geometry : bond 0.00431 (24149) covalent geometry : angle 0.62906 (32793) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5628 Ramachandran restraints generated. 2814 Oldfield, 0 Emsley, 2814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5628 Ramachandran restraints generated. 2814 Oldfield, 0 Emsley, 2814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 547 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 476 time to evaluate : 2.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ASP cc_start: 0.8099 (t0) cc_final: 0.7843 (t0) REVERT: A 616 ASN cc_start: 0.8860 (p0) cc_final: 0.8461 (p0) REVERT: A 632 GLU cc_start: 0.8806 (tp30) cc_final: 0.8522 (tp30) REVERT: D 58 ASN cc_start: 0.8031 (t0) cc_final: 0.7686 (t0) REVERT: D 79 TYR cc_start: 0.8377 (m-80) cc_final: 0.8164 (m-10) REVERT: D 80 MET cc_start: 0.8348 (tmm) cc_final: 0.7827 (tmm) REVERT: H 13 ARG cc_start: 0.8288 (mtt-85) cc_final: 0.7736 (mtm-85) REVERT: H 81 LYS cc_start: 0.8986 (mmtt) cc_final: 0.8745 (mmmm) REVERT: F 19 LYS cc_start: 0.7464 (ttmt) cc_final: 0.7006 (ttmm) REVERT: F 32 TYR cc_start: 0.8567 (m-80) cc_final: 0.8366 (m-10) REVERT: F 57 LYS cc_start: 0.8771 (mtmt) cc_final: 0.8395 (mttt) REVERT: G 12 SER cc_start: 0.8750 (t) cc_final: 0.8490 (m) REVERT: G 54 ARG cc_start: 0.8467 (mtm-85) cc_final: 0.7899 (mtp180) REVERT: G 86 TYR cc_start: 0.8228 (m-10) cc_final: 0.7918 (m-10) REVERT: J 46 GLU cc_start: 0.8197 (tm-30) cc_final: 0.7459 (tm-30) REVERT: J 56 ASP cc_start: 0.7217 (m-30) cc_final: 0.7014 (m-30) REVERT: J 57 LYS cc_start: 0.8767 (mtpt) cc_final: 0.8510 (mtpt) REVERT: J 58 ASN cc_start: 0.8216 (m-40) cc_final: 0.7835 (m-40) REVERT: K 29 SER cc_start: 0.8541 (t) cc_final: 0.8232 (p) REVERT: B 35 TRP cc_start: 0.8225 (m100) cc_final: 0.7610 (m100) REVERT: B 110 SER cc_start: 0.9163 (t) cc_final: 0.8571 (m) REVERT: B 126 CYS cc_start: 0.7948 (OUTLIER) cc_final: 0.7374 (t) REVERT: B 160 ASN cc_start: 0.8316 (m-40) cc_final: 0.7705 (p0) REVERT: B 189 THR cc_start: 0.9140 (p) cc_final: 0.8456 (t) REVERT: B 217 TYR cc_start: 0.9141 (m-80) cc_final: 0.8254 (m-80) REVERT: B 446 SER cc_start: 0.9155 (t) cc_final: 0.8635 (p) REVERT: B 585 ARG cc_start: 0.8359 (ttt-90) cc_final: 0.8125 (ttp80) REVERT: I 81 LYS cc_start: 0.8888 (ttmm) cc_final: 0.8354 (ttpp) REVERT: M 42 LYS cc_start: 0.7988 (mmmm) cc_final: 0.7697 (mmmt) REVERT: M 79 GLN cc_start: 0.8911 (mm-40) cc_final: 0.8428 (mm110) REVERT: C 91 GLU cc_start: 0.8337 (tp30) cc_final: 0.7938 (tp30) REVERT: C 103 GLN cc_start: 0.8050 (tt0) cc_final: 0.7627 (tm-30) REVERT: C 168 LYS cc_start: 0.9073 (OUTLIER) cc_final: 0.8218 (mmtm) REVERT: C 217 TYR cc_start: 0.8542 (m-80) cc_final: 0.8296 (m-80) REVERT: C 355 ASN cc_start: 0.7049 (m-40) cc_final: 0.6061 (p0) outliers start: 71 outliers final: 56 residues processed: 514 average time/residue: 0.3776 time to fit residues: 292.9331 Evaluate side-chains 500 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 442 time to evaluate : 2.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 230 ASP Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain A residue 650 GLN Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain H residue 65 ASN Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 49 TYR Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 68 ILE Chi-restraints excluded: chain F residue 79 TYR Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain G residue 9 SER Chi-restraints excluded: chain G residue 83 GLU Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 89 CYS Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain K residue 97 VAL Chi-restraints excluded: chain K residue 102 THR Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 354 GLU Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain I residue 35 SER Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 67 SER Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 168 LYS Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 320 MET Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 626 MET Chi-restraints excluded: chain C residue 640 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 22 optimal weight: 4.9990 chunk 244 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 248 optimal weight: 2.9990 chunk 202 optimal weight: 3.9990 chunk 66 optimal weight: 8.9990 chunk 105 optimal weight: 4.9990 chunk 191 optimal weight: 3.9990 chunk 225 optimal weight: 5.9990 chunk 166 optimal weight: 0.8980 chunk 91 optimal weight: 6.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 130 ASN A 575 GLN ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN L 34 ASN G 6 GLN ** J 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 575 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.123648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.095043 restraints weight = 40043.083| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 3.10 r_work: 0.3051 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.2836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.077 24271 Z= 0.358 Angle : 0.799 13.490 33114 Z= 0.400 Chirality : 0.052 0.397 3851 Planarity : 0.005 0.054 4064 Dihedral : 7.776 59.801 4684 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.87 % Favored : 94.95 % Rotamer: Outliers : 4.02 % Allowed : 13.07 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.27 (0.15), residues: 2814 helix: 0.79 (0.27), residues: 359 sheet: 0.11 (0.15), residues: 1001 loop : -0.56 (0.16), residues: 1454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP F 50 HIS 0.009 0.002 HIS A 374 PHE 0.023 0.003 PHE C 53 TYR 0.047 0.002 TYR M 49 ARG 0.011 0.001 ARG J 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00548 ( 46) link_NAG-ASN : angle 2.55295 ( 138) link_ALPHA1-6 : bond 0.01071 ( 3) link_ALPHA1-6 : angle 2.19629 ( 9) link_BETA1-4 : bond 0.00772 ( 18) link_BETA1-4 : angle 2.74564 ( 54) link_ALPHA1-2 : bond 0.00315 ( 2) link_ALPHA1-2 : angle 2.14628 ( 6) link_ALPHA1-3 : bond 0.00616 ( 6) link_ALPHA1-3 : angle 2.05810 ( 18) hydrogen bonds : bond 0.04615 ( 616) hydrogen bonds : angle 5.83501 ( 1596) link_BETA1-6 : bond 0.00082 ( 2) link_BETA1-6 : angle 2.33890 ( 6) SS BOND : bond 0.00651 ( 45) SS BOND : angle 1.56624 ( 90) covalent geometry : bond 0.00835 (24149) covalent geometry : angle 0.76999 (32793) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5628 Ramachandran restraints generated. 2814 Oldfield, 0 Emsley, 2814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5628 Ramachandran restraints generated. 2814 Oldfield, 0 Emsley, 2814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 562 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 461 time to evaluate : 2.424 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: A 46 LYS cc_start: 0.8632 (mttm) cc_final: 0.7962 (mttm) REVERT: A 277 PHE cc_start: 0.8353 (OUTLIER) cc_final: 0.7274 (t80) REVERT: A 632 GLU cc_start: 0.8862 (tp30) cc_final: 0.8560 (tp30) REVERT: D 58 ASN cc_start: 0.8092 (t0) cc_final: 0.7736 (t0) REVERT: D 79 TYR cc_start: 0.8411 (m-80) cc_final: 0.8205 (m-10) REVERT: D 80 MET cc_start: 0.8385 (tmm) cc_final: 0.7903 (tmm) REVERT: D 81 GLU cc_start: 0.7428 (pt0) cc_final: 0.7180 (pt0) REVERT: H 13 ARG cc_start: 0.8378 (mtt-85) cc_final: 0.7820 (mtm-85) REVERT: F 3 GLN cc_start: 0.8796 (tp-100) cc_final: 0.8424 (tp-100) REVERT: F 19 LYS cc_start: 0.7458 (ttmt) cc_final: 0.6997 (ttmm) REVERT: F 46 GLU cc_start: 0.7253 (tp30) cc_final: 0.6998 (tp30) REVERT: F 57 LYS cc_start: 0.8875 (mtmt) cc_final: 0.8420 (ttmt) REVERT: F 80 MET cc_start: 0.8262 (ppp) cc_final: 0.7897 (ptt) REVERT: F 90 TYR cc_start: 0.8891 (m-80) cc_final: 0.8516 (m-80) REVERT: L 6 GLN cc_start: 0.8993 (tt0) cc_final: 0.8626 (tt0) REVERT: L 94 TYR cc_start: 0.8594 (t80) cc_final: 0.8278 (t80) REVERT: G 54 ARG cc_start: 0.8554 (mtm-85) cc_final: 0.8290 (mtp180) REVERT: G 86 TYR cc_start: 0.8363 (m-10) cc_final: 0.8016 (m-10) REVERT: J 43 ARG cc_start: 0.7840 (ttp80) cc_final: 0.7584 (mtm110) REVERT: J 57 LYS cc_start: 0.8859 (mtpt) cc_final: 0.8561 (mtpt) REVERT: J 80 MET cc_start: 0.7444 (OUTLIER) cc_final: 0.7178 (tpt) REVERT: J 82 ARG cc_start: 0.8131 (mmm-85) cc_final: 0.7909 (mmm-85) REVERT: J 90 TYR cc_start: 0.7834 (m-80) cc_final: 0.7478 (m-80) REVERT: K 42 ARG cc_start: 0.7573 (mtm-85) cc_final: 0.7338 (mtm-85) REVERT: B 126 CYS cc_start: 0.7914 (OUTLIER) cc_final: 0.7526 (t) REVERT: B 217 TYR cc_start: 0.9226 (m-80) cc_final: 0.8448 (m-80) REVERT: B 277 PHE cc_start: 0.9283 (OUTLIER) cc_final: 0.8559 (t80) REVERT: B 490 LYS cc_start: 0.8963 (tttm) cc_final: 0.8657 (tttp) REVERT: B 500 ARG cc_start: 0.7005 (mtm180) cc_final: 0.6708 (ptt90) REVERT: B 502 LYS cc_start: 0.7723 (tttt) cc_final: 0.7507 (tttt) REVERT: I 81 LYS cc_start: 0.8855 (ttmm) cc_final: 0.8322 (ttpp) REVERT: M 26 ARG cc_start: 0.8639 (tpt90) cc_final: 0.8369 (tpt90) REVERT: M 79 GLN cc_start: 0.8979 (mm-40) cc_final: 0.8714 (mm-40) REVERT: M 105 GLU cc_start: 0.8208 (mm-30) cc_final: 0.7914 (mt-10) REVERT: C 42 VAL cc_start: 0.9395 (t) cc_final: 0.9100 (m) REVERT: C 91 GLU cc_start: 0.8476 (tp30) cc_final: 0.7978 (tp30) REVERT: C 103 GLN cc_start: 0.8172 (tt0) cc_final: 0.7754 (tm-30) REVERT: C 168 LYS cc_start: 0.9224 (OUTLIER) cc_final: 0.8246 (mmtm) REVERT: C 217 TYR cc_start: 0.9092 (m-80) cc_final: 0.8463 (m-80) REVERT: C 573 ILE cc_start: 0.6862 (mm) cc_final: 0.6322 (mt) outliers start: 101 outliers final: 71 residues processed: 517 average time/residue: 0.4039 time to fit residues: 318.5922 Evaluate side-chains 504 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 428 time to evaluate : 2.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 230 ASP Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 277 PHE Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain A residue 650 GLN Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 42 ARG Chi-restraints excluded: chain E residue 49 TYR Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 50 TRP Chi-restraints excluded: chain F residue 68 ILE Chi-restraints excluded: chain F residue 79 TYR Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 83 PHE Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 45 THR Chi-restraints excluded: chain G residue 58 ILE Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 80 MET Chi-restraints excluded: chain J residue 82 ASN Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 85 THR Chi-restraints excluded: chain K residue 89 CYS Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain K residue 102 THR Chi-restraints excluded: chain B residue 112 TRP Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 194 ILE Chi-restraints excluded: chain B residue 277 PHE Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 354 GLU Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 378 CYS Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 620 ASP Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain I residue 35 SER Chi-restraints excluded: chain I residue 82 THR Chi-restraints excluded: chain I residue 107 ILE Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 22 THR Chi-restraints excluded: chain M residue 58 ILE Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 85 THR Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 168 LYS Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 320 MET Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain C residue 640 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 142 optimal weight: 6.9990 chunk 253 optimal weight: 0.6980 chunk 255 optimal weight: 0.6980 chunk 4 optimal weight: 3.9990 chunk 119 optimal weight: 6.9990 chunk 154 optimal weight: 0.5980 chunk 243 optimal weight: 0.7980 chunk 170 optimal weight: 0.9990 chunk 272 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 214 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 656 ASN D 6 GLN L 34 ASN ** B 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 543 ASN C 575 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.127571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.099638 restraints weight = 39044.583| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 3.05 r_work: 0.3150 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 24271 Z= 0.132 Angle : 0.627 13.155 33114 Z= 0.311 Chirality : 0.046 0.418 3851 Planarity : 0.004 0.055 4064 Dihedral : 6.988 58.968 4684 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.34 % Favored : 95.45 % Rotamer: Outliers : 2.87 % Allowed : 15.18 % Favored : 81.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.11 (0.15), residues: 2814 helix: 1.13 (0.28), residues: 357 sheet: 0.22 (0.16), residues: 994 loop : -0.53 (0.16), residues: 1463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP F 50 HIS 0.008 0.001 HIS B 72 PHE 0.017 0.002 PHE C 53 TYR 0.026 0.002 TYR M 49 ARG 0.008 0.000 ARG D 82A Details of bonding type rmsd link_NAG-ASN : bond 0.00332 ( 46) link_NAG-ASN : angle 2.22689 ( 138) link_ALPHA1-6 : bond 0.01278 ( 3) link_ALPHA1-6 : angle 2.28414 ( 9) link_BETA1-4 : bond 0.00731 ( 18) link_BETA1-4 : angle 2.19809 ( 54) link_ALPHA1-2 : bond 0.00104 ( 2) link_ALPHA1-2 : angle 1.93812 ( 6) link_ALPHA1-3 : bond 0.01025 ( 6) link_ALPHA1-3 : angle 1.67422 ( 18) hydrogen bonds : bond 0.03766 ( 616) hydrogen bonds : angle 5.58755 ( 1596) link_BETA1-6 : bond 0.00421 ( 2) link_BETA1-6 : angle 2.02041 ( 6) SS BOND : bond 0.00468 ( 45) SS BOND : angle 1.09334 ( 90) covalent geometry : bond 0.00295 (24149) covalent geometry : angle 0.60088 (32793) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5628 Ramachandran restraints generated. 2814 Oldfield, 0 Emsley, 2814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5628 Ramachandran restraints generated. 2814 Oldfield, 0 Emsley, 2814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 546 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 474 time to evaluate : 2.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 277 PHE cc_start: 0.8017 (OUTLIER) cc_final: 0.7131 (t80) REVERT: A 632 GLU cc_start: 0.8823 (tp30) cc_final: 0.8539 (tp30) REVERT: D 58 ASN cc_start: 0.7874 (t0) cc_final: 0.7508 (t0) REVERT: D 66 ARG cc_start: 0.7962 (mtp180) cc_final: 0.7458 (ttp-170) REVERT: D 80 MET cc_start: 0.8372 (tmm) cc_final: 0.7841 (tmm) REVERT: D 81 GLU cc_start: 0.7310 (pt0) cc_final: 0.6994 (pt0) REVERT: H 13 ARG cc_start: 0.8159 (mtt-85) cc_final: 0.7595 (mtp-110) REVERT: F 3 GLN cc_start: 0.8693 (tp-100) cc_final: 0.8352 (tp-100) REVERT: F 19 LYS cc_start: 0.7411 (ttmt) cc_final: 0.6948 (ttmm) REVERT: F 32 TYR cc_start: 0.8498 (m-10) cc_final: 0.8176 (m-10) REVERT: F 46 GLU cc_start: 0.7163 (tp30) cc_final: 0.6824 (tp30) REVERT: F 80 MET cc_start: 0.8107 (ppp) cc_final: 0.7852 (ptt) REVERT: L 6 GLN cc_start: 0.8948 (tt0) cc_final: 0.8576 (tt0) REVERT: L 94 TYR cc_start: 0.8426 (t80) cc_final: 0.8168 (t80) REVERT: G 34 SER cc_start: 0.9103 (p) cc_final: 0.8401 (m) REVERT: G 52 ASN cc_start: 0.8763 (OUTLIER) cc_final: 0.8471 (p0) REVERT: G 86 TYR cc_start: 0.8362 (m-10) cc_final: 0.8031 (m-10) REVERT: G 91 TYR cc_start: 0.8788 (p90) cc_final: 0.8383 (p90) REVERT: J 58 ASN cc_start: 0.7288 (m-40) cc_final: 0.6986 (m-40) REVERT: J 80 MET cc_start: 0.7531 (OUTLIER) cc_final: 0.7069 (tpt) REVERT: J 82 ARG cc_start: 0.8093 (mmm-85) cc_final: 0.7854 (mmm-85) REVERT: J 90 TYR cc_start: 0.7671 (m-80) cc_final: 0.7380 (m-80) REVERT: K 29 SER cc_start: 0.8551 (t) cc_final: 0.8260 (p) REVERT: K 79 ARG cc_start: 0.7273 (mtt-85) cc_final: 0.7035 (mtt-85) REVERT: B 126 CYS cc_start: 0.7866 (OUTLIER) cc_final: 0.7417 (t) REVERT: B 151 ARG cc_start: 0.7676 (tpt170) cc_final: 0.7294 (tpm170) REVERT: B 217 TYR cc_start: 0.9163 (m-80) cc_final: 0.8266 (m-80) REVERT: B 232 THR cc_start: 0.8728 (OUTLIER) cc_final: 0.8470 (t) REVERT: B 277 PHE cc_start: 0.9137 (OUTLIER) cc_final: 0.8557 (t80) REVERT: B 352 GLN cc_start: 0.8520 (tt0) cc_final: 0.7947 (mt0) REVERT: B 446 SER cc_start: 0.9196 (t) cc_final: 0.8677 (p) REVERT: B 490 LYS cc_start: 0.8862 (tttm) cc_final: 0.8606 (tttp) REVERT: B 500 ARG cc_start: 0.7019 (mtm180) cc_final: 0.6636 (ptt90) REVERT: I 81 LYS cc_start: 0.8827 (ttmm) cc_final: 0.8269 (ttpp) REVERT: M 22 THR cc_start: 0.9455 (m) cc_final: 0.9206 (t) REVERT: M 79 GLN cc_start: 0.8803 (mm-40) cc_final: 0.8591 (mm-40) REVERT: M 105 GLU cc_start: 0.8106 (mm-30) cc_final: 0.7891 (mt-10) REVERT: C 91 GLU cc_start: 0.8301 (tp30) cc_final: 0.7965 (tp30) REVERT: C 103 GLN cc_start: 0.8057 (tt0) cc_final: 0.7622 (tm-30) REVERT: C 168 LYS cc_start: 0.9070 (OUTLIER) cc_final: 0.8272 (mmtm) REVERT: C 355 ASN cc_start: 0.7067 (m-40) cc_final: 0.6059 (p0) REVERT: C 573 ILE cc_start: 0.6654 (mm) cc_final: 0.6113 (mt) outliers start: 72 outliers final: 46 residues processed: 512 average time/residue: 0.3944 time to fit residues: 304.0331 Evaluate side-chains 485 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 432 time to evaluate : 2.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 230 ASP Chi-restraints excluded: chain A residue 277 PHE Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain A residue 650 GLN Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 42 ARG Chi-restraints excluded: chain E residue 49 TYR Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 68 ILE Chi-restraints excluded: chain F residue 79 TYR Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain F residue 92 CYS Chi-restraints excluded: chain F residue 100 TRP Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 83 PHE Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain G residue 52 ASN Chi-restraints excluded: chain G residue 83 GLU Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 68 ILE Chi-restraints excluded: chain J residue 80 MET Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 89 CYS Chi-restraints excluded: chain K residue 102 THR Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 277 PHE Chi-restraints excluded: chain B residue 354 GLU Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 620 ASP Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 168 LYS Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 545 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.2199 > 50: distance: 158 - 160: 25.912 distance: 160 - 161: 30.839 distance: 161 - 162: 28.450 distance: 161 - 164: 24.963 distance: 164 - 165: 13.355 distance: 164 - 166: 17.738 distance: 167 - 168: 40.649 distance: 168 - 169: 14.628 distance: 168 - 171: 20.450 distance: 169 - 170: 21.270 distance: 169 - 176: 12.062 distance: 171 - 172: 30.508 distance: 172 - 173: 16.255 distance: 173 - 174: 23.448 distance: 173 - 175: 33.384 distance: 176 - 177: 26.884 distance: 177 - 178: 10.545 distance: 177 - 180: 47.662 distance: 178 - 179: 30.091 distance: 180 - 182: 3.668 distance: 181 - 183: 41.371 distance: 185 - 186: 27.117 distance: 186 - 187: 26.954 distance: 186 - 195: 29.799 distance: 189 - 190: 5.465 distance: 189 - 191: 46.083 distance: 190 - 192: 40.116 distance: 191 - 193: 33.907 distance: 192 - 194: 19.892 distance: 193 - 194: 38.816 distance: 195 - 196: 20.569 distance: 196 - 197: 17.040 distance: 196 - 199: 18.345 distance: 197 - 198: 15.341 distance: 197 - 206: 35.005 distance: 199 - 200: 28.184 distance: 201 - 202: 25.918 distance: 202 - 203: 12.261 distance: 203 - 204: 3.516 distance: 203 - 205: 3.205 distance: 206 - 207: 18.245 distance: 206 - 212: 27.089 distance: 207 - 208: 4.760 distance: 207 - 210: 16.386 distance: 208 - 209: 34.858 distance: 208 - 213: 23.818 distance: 210 - 211: 17.918 distance: 211 - 212: 35.794 distance: 213 - 214: 10.751 distance: 214 - 215: 31.671 distance: 215 - 216: 41.487 distance: 215 - 217: 12.627 distance: 217 - 218: 30.793 distance: 218 - 219: 41.367 distance: 219 - 221: 24.528 distance: 221 - 222: 15.893 distance: 222 - 223: 18.742 distance: 223 - 224: 27.422 distance: 223 - 225: 5.400 distance: 225 - 226: 12.566 distance: 226 - 227: 12.556 distance: 226 - 229: 24.833 distance: 227 - 228: 9.701 distance: 227 - 233: 19.869 distance: 229 - 230: 36.889 distance: 230 - 231: 13.084 distance: 230 - 232: 32.334