Starting phenix.real_space_refine on Thu Aug 6 17:13:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9yih_72990/08_2026/9yih_72990.cif Found real_map, /net/cci-nas-00/data/ceres_data/9yih_72990/08_2026/9yih_72990.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9yih_72990/08_2026/9yih_72990.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9yih_72990/08_2026/9yih_72990.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9yih_72990/08_2026/9yih_72990.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9yih_72990/08_2026/9yih_72990.map" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 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 112 5.16 5 C 9988 2.51 5 N 2672 2.21 5 O 3190 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15962 Number of models: 1 Model: "" Number of chains: 29 Chain: "A" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 956 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Chain: "B" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 956 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Chain: "C" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 956 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Chain: "E" Number of atoms: 3423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3423 Classifications: {'peptide': 433} Link IDs: {'PTRANS': 22, 'TRANS': 410} Chain breaks: 4 Chain: "F" Number of atoms: 3423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3423 Classifications: {'peptide': 433} Link IDs: {'PTRANS': 22, 'TRANS': 410} Chain breaks: 4 Chain: "G" Number of atoms: 3423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3423 Classifications: {'peptide': 433} Link IDs: {'PTRANS': 22, 'TRANS': 410} Chain breaks: 4 Chain: "H" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 990 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "L" Number of atoms: 854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 854 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 10, 'TRANS': 100} Chain: "D" 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: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" 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: "K" 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: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 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: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "F" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "G" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 2.75, per 1000 atoms: 0.17 Number of scatterers: 15962 At special positions: 0 Unit cell: (144.768, 129.792, 136.448, 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 112 16.00 O 3190 8.00 N 2672 7.00 C 9988 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.03 Simple disulfide: pdb=" SG CYS A 605 " - pdb=" SG CYS E 501 " distance=2.02 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS B 605 " - pdb=" SG CYS F 501 " distance=2.03 Simple disulfide: pdb=" SG CYS C 598 " - pdb=" SG CYS C 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 605 " - pdb=" SG CYS G 501 " distance=2.04 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 201 " - pdb=" SG CYS E 433 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 74 " distance=2.03 Simple disulfide: pdb=" SG CYS F 119 " - pdb=" SG CYS F 205 " distance=2.03 Simple disulfide: pdb=" SG CYS F 126 " - pdb=" SG CYS F 196 " distance=2.03 Simple disulfide: pdb=" SG CYS F 131 " - pdb=" SG CYS F 157 " distance=2.03 Simple disulfide: pdb=" SG CYS F 201 " - pdb=" SG CYS F 433 " distance=2.03 Simple disulfide: pdb=" SG CYS F 218 " - pdb=" SG CYS F 247 " distance=2.03 Simple disulfide: pdb=" SG CYS F 228 " - pdb=" SG CYS F 239 " distance=2.03 Simple disulfide: pdb=" SG CYS F 296 " - pdb=" SG CYS F 331 " distance=2.03 Simple disulfide: pdb=" SG CYS F 378 " - pdb=" SG CYS F 445 " distance=2.03 Simple disulfide: pdb=" SG CYS F 385 " - pdb=" SG CYS F 418 " distance=2.03 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 74 " distance=2.03 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.03 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.03 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.03 Simple disulfide: pdb=" SG CYS G 201 " - pdb=" SG CYS G 433 " distance=2.03 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.03 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.03 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.03 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.03 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.03 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 V 5 " - " MAN V 6 " ALPHA1-3 " BMA V 3 " - " MAN V 8 " " MAN V 4 " - " MAN V 5 " ALPHA1-6 " BMA V 3 " - " MAN V 4 " " MAN V 4 " - " MAN V 7 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " NAG-ASN " NAG A 701 " - " ASN A 611 " " NAG B 701 " - " ASN B 611 " " NAG C 701 " - " ASN C 611 " " NAG D 1 " - " ASN E 156 " " NAG E 601 " - " ASN E 88 " " NAG E 602 " - " ASN E 133 " " NAG E 603 " - " ASN E 160 " " NAG E 604 " - " ASN E 197 " " NAG E 605 " - " ASN E 234 " " NAG E 606 " - " ASN E 276 " " NAG E 607 " - " ASN E 301 " " NAG E 608 " - " ASN E 339 " " NAG E 609 " - " ASN E 392 " " NAG E 610 " - " ASN E 448 " " NAG F 601 " - " ASN F 88 " " NAG F 602 " - " ASN F 133 " " NAG F 603 " - " ASN F 160 " " NAG F 604 " - " ASN F 197 " " NAG F 605 " - " ASN F 234 " " NAG F 606 " - " ASN F 276 " " NAG F 607 " - " ASN F 301 " " NAG F 608 " - " ASN F 339 " " NAG F 609 " - " ASN F 392 " " NAG F 610 " - " ASN F 448 " " NAG G 601 " - " ASN G 88 " " NAG G 602 " - " ASN G 133 " " NAG G 603 " - " ASN G 160 " " NAG G 604 " - " ASN G 197 " " NAG G 605 " - " ASN G 234 " " NAG G 606 " - " ASN G 276 " " NAG G 607 " - " ASN G 301 " " NAG G 608 " - " ASN G 339 " " NAG G 609 " - " ASN G 392 " " NAG G 610 " - " ASN G 448 " " NAG I 1 " - " ASN E 262 " " NAG J 1 " - " ASN E 295 " " NAG K 1 " - " ASN E 332 " " NAG M 1 " - " ASN E 386 " " NAG N 1 " - " ASN F 156 " " NAG O 1 " - " ASN F 262 " " NAG P 1 " - " ASN F 295 " " NAG Q 1 " - " ASN F 332 " " NAG R 1 " - " ASN F 386 " " NAG S 1 " - " ASN G 156 " " NAG T 1 " - " ASN G 262 " " NAG U 1 " - " ASN G 295 " " NAG V 1 " - " ASN G 332 " " NAG W 1 " - " ASN G 386 " Time building additional restraints: 1.32 Conformation dependent library (CDL) restraints added in 423.7 milliseconds 3706 Ramachandran restraints generated. 1853 Oldfield, 0 Emsley, 1853 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3540 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 31 sheets defined 23.7% alpha, 19.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 529 through 534 Processing helix chain 'A' and resid 536 through 543 removed outlier: 3.892A pdb=" N GLN A 540 " --> pdb=" O THR A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 596 removed outlier: 3.625A pdb=" N TRP A 596 " --> pdb=" O LEU A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 625 Processing helix chain 'A' and resid 627 through 635 Processing helix chain 'A' and resid 638 through 651 removed outlier: 4.260A pdb=" N ASN A 651 " --> pdb=" O GLU A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 664 removed outlier: 3.928A pdb=" N ASP A 664 " --> pdb=" O LEU A 660 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 543 removed outlier: 3.893A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 596 removed outlier: 3.625A pdb=" N TRP B 596 " --> pdb=" O LEU B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 625 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 651 removed outlier: 4.259A pdb=" N ASN B 651 " --> pdb=" O GLU B 647 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 664 removed outlier: 3.928A pdb=" N ASP B 664 " --> pdb=" O LEU B 660 " (cutoff:3.500A) Processing helix chain 'C' and resid 529 through 534 Processing helix chain 'C' and resid 536 through 543 removed outlier: 3.892A pdb=" N GLN C 540 " --> pdb=" O THR C 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 596 removed outlier: 3.625A pdb=" N TRP C 596 " --> pdb=" O LEU C 592 " (cutoff:3.500A) Processing helix chain 'C' and resid 618 through 625 Processing helix chain 'C' and resid 627 through 635 Processing helix chain 'C' and resid 638 through 651 removed outlier: 4.259A pdb=" N ASN C 651 " --> pdb=" O GLU C 647 " (cutoff:3.500A) Processing helix chain 'C' and resid 652 through 664 removed outlier: 3.928A pdb=" N ASP C 664 " --> pdb=" O LEU C 660 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 117 Processing helix chain 'E' and resid 122 through 126 removed outlier: 3.507A pdb=" N LEU E 125 " --> pdb=" O LEU E 122 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N CYS E 126 " --> pdb=" O THR E 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 122 through 126' Processing helix chain 'E' and resid 177 through 179 No H-bonds generated for 'chain 'E' and resid 177 through 179' Processing helix chain 'E' and resid 335 through 353 Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 425 through 429 removed outlier: 3.635A pdb=" N ARG E 429 " --> pdb=" O MET E 426 " (cutoff:3.500A) Processing helix chain 'E' and resid 474 through 483 removed outlier: 3.842A pdb=" N ASN E 478 " --> pdb=" O ASP E 474 " (cutoff:3.500A) Processing helix chain 'F' and resid 99 through 117 Processing helix chain 'F' and resid 122 through 126 removed outlier: 3.506A pdb=" N LEU F 125 " --> pdb=" O LEU F 122 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N CYS F 126 " --> pdb=" O THR F 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 122 through 126' Processing helix chain 'F' and resid 177 through 179 No H-bonds generated for 'chain 'F' and resid 177 through 179' Processing helix chain 'F' and resid 335 through 353 Processing helix chain 'F' and resid 368 through 373 Processing helix chain 'F' and resid 425 through 429 removed outlier: 3.635A pdb=" N ARG F 429 " --> pdb=" O MET F 426 " (cutoff:3.500A) Processing helix chain 'F' and resid 474 through 483 removed outlier: 3.842A pdb=" N ASN F 478 " --> pdb=" O ASP F 474 " (cutoff:3.500A) Processing helix chain 'G' and resid 99 through 117 Processing helix chain 'G' and resid 122 through 126 removed outlier: 3.507A pdb=" N LEU G 125 " --> pdb=" O LEU G 122 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N CYS G 126 " --> pdb=" O THR G 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 122 through 126' Processing helix chain 'G' and resid 177 through 179 No H-bonds generated for 'chain 'G' and resid 177 through 179' Processing helix chain 'G' and resid 335 through 353 Processing helix chain 'G' and resid 368 through 373 Processing helix chain 'G' and resid 425 through 429 removed outlier: 3.636A pdb=" N ARG G 429 " --> pdb=" O MET G 426 " (cutoff:3.500A) Processing helix chain 'G' and resid 474 through 483 removed outlier: 3.842A pdb=" N ASN G 478 " --> pdb=" O ASP G 474 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 64 Processing sheet with id=AA1, first strand: chain 'A' and resid 604 through 609 removed outlier: 3.680A pdb=" N CYS A 604 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL E 38 " --> pdb=" O CYS A 604 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THR A 606 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N VAL E 36 " --> pdb=" O THR A 606 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 604 through 609 removed outlier: 3.682A pdb=" N CYS B 604 " --> pdb=" O VAL F 38 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL F 38 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N THR B 606 " --> pdb=" O VAL F 36 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N VAL F 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 604 through 609 removed outlier: 3.683A pdb=" N CYS C 604 " --> pdb=" O VAL G 38 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL G 38 " --> pdb=" O CYS C 604 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR C 606 " --> pdb=" O VAL G 36 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N VAL G 36 " --> pdb=" O THR C 606 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.570A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AA6, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AA7, first strand: chain 'E' and resid 129 through 130 Processing sheet with id=AA8, first strand: chain 'E' and resid 157 through 162 Processing sheet with id=AA9, first strand: chain 'E' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 259 through 261 current: chain 'E' and resid 284 through 298 removed outlier: 7.149A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 330 through 334 current: chain 'E' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 381 through 385 current: chain 'E' and resid 465 through 470 Processing sheet with id=AB1, first strand: chain 'E' and resid 301 through 307 removed outlier: 7.303A pdb=" N ASN E 301 " --> pdb=" O ILE E 322 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N ILE E 322 " --> pdb=" O ASN E 301 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N THR E 303 " --> pdb=" O GLY E 321 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 423 through 424 Processing sheet with id=AB3, first strand: chain 'F' and resid 45 through 47 removed outlier: 3.570A pdb=" N ILE F 225 " --> pdb=" O VAL F 245 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 53 through 55 Processing sheet with id=AB5, first strand: chain 'F' and resid 91 through 94 Processing sheet with id=AB6, first strand: chain 'F' and resid 129 through 130 Processing sheet with id=AB7, first strand: chain 'F' and resid 157 through 162 Processing sheet with id=AB8, first strand: chain 'F' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 259 through 261 current: chain 'F' and resid 284 through 298 removed outlier: 7.150A pdb=" N GLN F 293 " --> pdb=" O SER F 334 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N SER F 334 " --> pdb=" O GLN F 293 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 330 through 334 current: chain 'F' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 381 through 385 current: chain 'F' and resid 465 through 470 Processing sheet with id=AB9, first strand: chain 'F' and resid 301 through 307 removed outlier: 7.304A pdb=" N ASN F 301 " --> pdb=" O ILE F 322 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N ILE F 322 " --> pdb=" O ASN F 301 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N THR F 303 " --> pdb=" O GLY F 321 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 423 through 424 Processing sheet with id=AC2, first strand: chain 'G' and resid 45 through 47 removed outlier: 3.569A pdb=" N ILE G 225 " --> pdb=" O VAL G 245 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 53 through 55 Processing sheet with id=AC4, first strand: chain 'G' and resid 91 through 94 Processing sheet with id=AC5, first strand: chain 'G' and resid 129 through 130 Processing sheet with id=AC6, first strand: chain 'G' and resid 157 through 162 Processing sheet with id=AC7, first strand: chain 'G' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 259 through 261 current: chain 'G' and resid 284 through 298 removed outlier: 7.149A pdb=" N GLN G 293 " --> pdb=" O SER G 334 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N SER G 334 " --> pdb=" O GLN G 293 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 330 through 334 current: chain 'G' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 381 through 385 current: chain 'G' and resid 465 through 470 Processing sheet with id=AC8, first strand: chain 'G' and resid 301 through 307 removed outlier: 7.304A pdb=" N ASN G 301 " --> pdb=" O ILE G 322 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N ILE G 322 " --> pdb=" O ASN G 301 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N THR G 303 " --> pdb=" O GLY G 321 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 423 through 424 Processing sheet with id=AD1, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.582A pdb=" N GLY H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 18 through 23 Processing sheet with id=AD3, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.555A pdb=" N LEU L 11 " --> pdb=" O LYS L 103 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ASP L 105 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR L 102 " --> pdb=" O TYR L 86 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL L 85 " --> pdb=" O GLN L 38 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N LEU L 37 " --> pdb=" O ARG L 46 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N ARG L 46 " --> pdb=" O LEU L 37 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'L' and resid 19 through 23 448 hydrogen bonds defined for protein. 1224 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: 2.03 Time building geometry restraints manager: 1.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5034 1.34 - 1.46: 3760 1.46 - 1.58: 7336 1.58 - 1.70: 0 1.70 - 1.82: 148 Bond restraints: 16278 Sorted by residual: bond pdb=" N TYR H 100J" pdb=" CA TYR H 100J" ideal model delta sigma weight residual 1.457 1.497 -0.040 1.29e-02 6.01e+03 9.45e+00 bond pdb=" N TYR H 33 " pdb=" CA TYR H 33 " ideal model delta sigma weight residual 1.460 1.496 -0.035 1.51e-02 4.39e+03 5.48e+00 bond pdb=" N TYR H 53 " pdb=" CA TYR H 53 " ideal model delta sigma weight residual 1.463 1.491 -0.027 1.29e-02 6.01e+03 4.54e+00 bond pdb=" C TYR H 100J" pdb=" O TYR H 100J" ideal model delta sigma weight residual 1.235 1.261 -0.026 1.26e-02 6.30e+03 4.23e+00 bond pdb=" C1 MAN V 5 " pdb=" O5 MAN V 5 " ideal model delta sigma weight residual 1.399 1.432 -0.033 2.00e-02 2.50e+03 2.69e+00 ... (remaining 16273 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 21550 1.84 - 3.67: 503 3.67 - 5.51: 38 5.51 - 7.34: 6 7.34 - 9.18: 8 Bond angle restraints: 22105 Sorted by residual: angle pdb=" CA TYR H 100J" pdb=" C TYR H 100J" pdb=" O TYR H 100J" ideal model delta sigma weight residual 120.51 114.51 6.00 1.43e+00 4.89e-01 1.76e+01 angle pdb=" C TYR H 53 " pdb=" CA TYR H 53 " pdb=" CB TYR H 53 " ideal model delta sigma weight residual 112.00 117.18 -5.18 1.61e+00 3.86e-01 1.03e+01 angle pdb=" CA TYR H 33 " pdb=" C TYR H 33 " pdb=" O TYR H 33 " ideal model delta sigma weight residual 121.84 118.35 3.49 1.16e+00 7.43e-01 9.07e+00 angle pdb=" C1 BMA V 3 " pdb=" O5 BMA V 3 " pdb=" C5 BMA V 3 " ideal model delta sigma weight residual 118.82 109.84 8.98 3.00e+00 1.11e-01 8.96e+00 angle pdb=" N TYR H 33 " pdb=" CA TYR H 33 " pdb=" CB TYR H 33 " ideal model delta sigma weight residual 111.70 107.60 4.10 1.48e+00 4.57e-01 7.67e+00 ... (remaining 22100 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.57: 10367 34.57 - 69.13: 279 69.13 - 103.70: 52 103.70 - 138.26: 21 138.26 - 172.83: 2 Dihedral angle restraints: 10721 sinusoidal: 5238 harmonic: 5483 Sorted by residual: dihedral pdb=" CB CYS G 54 " pdb=" SG CYS G 54 " pdb=" SG CYS G 74 " pdb=" CB CYS G 74 " ideal model delta sinusoidal sigma weight residual -86.00 -17.36 -68.64 1 1.00e+01 1.00e-02 6.10e+01 dihedral pdb=" CB CYS F 54 " pdb=" SG CYS F 54 " pdb=" SG CYS F 74 " pdb=" CB CYS F 74 " ideal model delta sinusoidal sigma weight residual -86.00 -17.38 -68.62 1 1.00e+01 1.00e-02 6.10e+01 dihedral pdb=" CB CYS E 54 " pdb=" SG CYS E 54 " pdb=" SG CYS E 74 " pdb=" CB CYS E 74 " ideal model delta sinusoidal sigma weight residual -86.00 -17.38 -68.62 1 1.00e+01 1.00e-02 6.10e+01 ... (remaining 10718 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.009: 2685 1.009 - 2.019: 0 2.019 - 3.028: 0 3.028 - 4.037: 0 4.037 - 5.046: 4 Chirality restraints: 2689 Sorted by residual: chirality pdb=" C2 MAN V 8 " pdb=" C1 MAN V 8 " pdb=" C3 MAN V 8 " pdb=" O2 MAN V 8 " both_signs ideal model delta sigma weight residual False 2.52 -2.53 5.05 2.00e-01 2.50e+01 6.37e+02 chirality pdb=" C3 MAN V 5 " pdb=" C2 MAN V 5 " pdb=" C4 MAN V 5 " pdb=" O3 MAN V 5 " both_signs ideal model delta sigma weight residual False 2.47 -2.50 4.97 2.00e-01 2.50e+01 6.17e+02 chirality pdb=" C3 MAN V 7 " pdb=" C2 MAN V 7 " pdb=" C4 MAN V 7 " pdb=" O3 MAN V 7 " both_signs ideal model delta sigma weight residual False 2.47 -2.48 4.95 2.00e-01 2.50e+01 6.13e+02 ... (remaining 2686 not shown) Planarity restraints: 2775 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR H 53 " -0.018 2.00e-02 2.50e+03 1.93e-02 7.42e+00 pdb=" CG TYR H 53 " 0.002 2.00e-02 2.50e+03 pdb=" CD1 TYR H 53 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR H 53 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR H 53 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR H 53 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR H 53 " 0.038 2.00e-02 2.50e+03 pdb=" OH TYR H 53 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER L 7 " -0.034 5.00e-02 4.00e+02 5.20e-02 4.32e+00 pdb=" N PRO L 8 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO L 8 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO L 8 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY H 32 " 0.008 2.00e-02 2.50e+03 1.68e-02 2.82e+00 pdb=" C GLY H 32 " -0.029 2.00e-02 2.50e+03 pdb=" O GLY H 32 " 0.011 2.00e-02 2.50e+03 pdb=" N TYR H 33 " 0.010 2.00e-02 2.50e+03 ... (remaining 2772 not shown) Histogram of nonbonded interaction distances: 2.48 - 2.96: 7436 2.96 - 3.45: 15119 3.45 - 3.93: 25595 3.93 - 4.42: 27616 4.42 - 4.90: 46158 Nonbonded interactions: 121924 Sorted by model distance: nonbonded pdb=" C4 BMA V 3 " pdb=" O6 BMA V 3 " model vdw 2.475 2.776 nonbonded pdb=" O LEU A 629 " pdb=" OD1 ASP A 632 " model vdw 2.577 3.040 nonbonded pdb=" O LEU C 629 " pdb=" OD1 ASP C 632 " model vdw 2.577 3.040 nonbonded pdb=" O LEU B 629 " pdb=" OD1 ASP B 632 " model vdw 2.578 3.040 nonbonded pdb=" O5 MAN V 5 " pdb=" O6 MAN V 5 " model vdw 2.621 2.432 ... (remaining 121919 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' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'U' selection = chain 'W' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' } ncs_group { reference = chain 'I' selection = chain 'O' selection = chain 'T' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.020 Process input model: 11.490 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 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 : 0.004 0.040 16386 Z= 0.219 Angle : 0.627 9.178 22393 Z= 0.274 Chirality : 0.196 5.046 2689 Planarity : 0.003 0.052 2727 Dihedral : 16.787 172.826 7073 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.59 % Allowed : 6.94 % Favored : 92.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.20), residues: 1853 helix: 1.93 (0.28), residues: 396 sheet: 0.26 (0.24), residues: 428 loop : -0.97 (0.19), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 46 TYR 0.038 0.001 TYR H 53 PHE 0.006 0.001 PHE E 383 TRP 0.007 0.001 TRP E 112 HIS 0.002 0.000 HIS G 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.22 (16278) covalent geometry : angle 0.61146 / 0.27 (22105) SS BOND : bond 0.00218 / 0.12 ( 36) SS BOND : angle 0.53848 / 0.39 ( 72) hydrogen bonds : bond 0.10894 / 7.25 ( 448) hydrogen bonds : angle 5.62937 / 4.11 ( 1224) link_ALPHA1-2 : bond 0.00238 / 0.13 ( 1) link_ALPHA1-2 : angle 0.63943 / 0.33 ( 3) link_ALPHA1-3 : bond 0.00512 / 0.26 ( 2) link_ALPHA1-3 : angle 1.47297 / 0.63 ( 6) link_ALPHA1-6 : bond 0.00499 / 0.26 ( 2) link_ALPHA1-6 : angle 1.96130 / 1.02 ( 6) link_BETA1-4 : bond 0.00538 / 0.34 ( 19) link_BETA1-4 : angle 1.36417 / 0.87 ( 57) link_NAG-ASN : bond 0.00272 / 0.18 ( 48) link_NAG-ASN : angle 1.60259 / 1.06 ( 144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3706 Ramachandran restraints generated. 1853 Oldfield, 0 Emsley, 1853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3706 Ramachandran restraints generated. 1853 Oldfield, 0 Emsley, 1853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 468 time to evaluate : 0.366 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 619 LEU cc_start: 0.8940 (mm) cc_final: 0.8144 (tt) REVERT: A 626 MET cc_start: 0.7255 (ttm) cc_final: 0.6451 (ttm) REVERT: A 630 GLN cc_start: 0.8858 (mp10) cc_final: 0.8277 (mp10) REVERT: A 634 GLU cc_start: 0.7772 (mt-10) cc_final: 0.7175 (mt-10) REVERT: A 638 TYR cc_start: 0.7024 (m-80) cc_final: 0.6313 (m-80) REVERT: B 530 MET cc_start: 0.6325 (tpp) cc_final: 0.6040 (tpp) REVERT: B 534 SER cc_start: 0.8972 (m) cc_final: 0.8751 (t) REVERT: B 574 LYS cc_start: 0.8473 (ttmm) cc_final: 0.7734 (pttt) REVERT: B 627 THR cc_start: 0.8042 (p) cc_final: 0.7839 (t) REVERT: B 633 LYS cc_start: 0.9188 (mttm) cc_final: 0.8543 (ttmm) REVERT: C 530 MET cc_start: 0.7176 (tpp) cc_final: 0.6870 (mmt) REVERT: C 546 SER cc_start: 0.6836 (p) cc_final: 0.6485 (t) REVERT: C 592 LEU cc_start: 0.9546 (tp) cc_final: 0.9185 (mt) REVERT: C 638 TYR cc_start: 0.7291 (m-80) cc_final: 0.6898 (m-80) REVERT: C 647 GLU cc_start: 0.7973 (tm-30) cc_final: 0.7681 (tm-30) REVERT: C 658 GLN cc_start: 0.8526 (tm-30) cc_final: 0.8308 (tm-30) REVERT: E 46 LYS cc_start: 0.8588 (pttp) cc_final: 0.8213 (pttm) REVERT: E 102 GLU cc_start: 0.8417 (mp0) cc_final: 0.7993 (mp0) REVERT: E 208 VAL cc_start: 0.9195 (t) cc_final: 0.8906 (m) REVERT: E 257 THR cc_start: 0.9615 (m) cc_final: 0.9272 (p) REVERT: E 297 THR cc_start: 0.8439 (m) cc_final: 0.7999 (p) REVERT: E 432 GLN cc_start: 0.7090 (tm-30) cc_final: 0.6735 (tm-30) REVERT: F 99 ASN cc_start: 0.8278 (t0) cc_final: 0.7912 (t0) REVERT: F 107 ASP cc_start: 0.7558 (t0) cc_final: 0.7354 (t0) REVERT: F 114 GLN cc_start: 0.8609 (tt0) cc_final: 0.8182 (tm-30) REVERT: F 125 LEU cc_start: 0.9399 (tp) cc_final: 0.9078 (tp) REVERT: F 161 MET cc_start: 0.8106 (tpt) cc_final: 0.7616 (tpt) REVERT: F 180 ASP cc_start: 0.9140 (m-30) cc_final: 0.8729 (m-30) REVERT: F 217 TYR cc_start: 0.8064 (m-10) cc_final: 0.6302 (m-10) REVERT: F 300 ASN cc_start: 0.8826 (p0) cc_final: 0.8553 (p0) REVERT: F 428 GLN cc_start: 0.8758 (mp-120) cc_final: 0.8304 (mp10) REVERT: F 484 TYR cc_start: 0.8869 (p90) cc_final: 0.8615 (p90) REVERT: G 104 MET cc_start: 0.9233 (ttt) cc_final: 0.9014 (ttt) REVERT: G 125 LEU cc_start: 0.9491 (tp) cc_final: 0.9173 (tp) REVERT: G 217 TYR cc_start: 0.8586 (m-10) cc_final: 0.8143 (m-80) REVERT: G 289 ASN cc_start: 0.9214 (p0) cc_final: 0.8808 (p0) REVERT: G 412 ASP cc_start: 0.8264 (p0) cc_final: 0.7683 (m-30) REVERT: L 30 ASN cc_start: 0.6501 (p0) cc_final: 0.6151 (t0) REVERT: L 49 TYR cc_start: 0.8473 (p90) cc_final: 0.7651 (p90) REVERT: L 53 ASN cc_start: 0.8292 (t0) cc_final: 0.7545 (t0) outliers start: 10 outliers final: 9 residues processed: 477 average time/residue: 0.1083 time to fit residues: 76.5187 Evaluate side-chains 287 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 278 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.0670 chunk 77 optimal weight: 0.4980 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 3.9990 overall best weight: 0.8920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 591 GLN ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 585 HIS B 590 GLN ** C 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 246 GLN E 344 ASN E 425 ASN E 440 GLN F 103 GLN F 241 ASN F 246 GLN F 302 ASN F 330 HIS F 344 ASN F 425 ASN G 105 HIS G 246 GLN G 302 ASN G 330 HIS G 344 ASN G 425 ASN G 440 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.113512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.091340 restraints weight = 32586.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.093678 restraints weight = 20476.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.095346 restraints weight = 14884.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.096476 restraints weight = 11796.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.097205 restraints weight = 9966.484| |-----------------------------------------------------------------------------| r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16386 Z= 0.127 Angle : 0.649 15.366 22393 Z= 0.300 Chirality : 0.049 0.602 2689 Planarity : 0.003 0.050 2727 Dihedral : 8.696 103.843 3519 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 0.30 % Allowed : 3.50 % Favored : 96.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.20), residues: 1853 helix: 1.96 (0.28), residues: 399 sheet: 0.37 (0.24), residues: 440 loop : -0.93 (0.19), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 444 TYR 0.019 0.001 TYR C 586 PHE 0.021 0.001 PHE E 382 TRP 0.019 0.001 TRP F 35 HIS 0.009 0.001 HIS C 585 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (16278) covalent geometry : angle 0.59996 / 0.29 (22105) SS BOND : bond 0.00232 / 0.16 ( 36) SS BOND : angle 1.78668 / 1.40 ( 72) hydrogen bonds : bond 0.03470 / 2.29 ( 448) hydrogen bonds : angle 4.64715 / 3.31 ( 1224) link_ALPHA1-2 : bond 0.00206 / 0.11 ( 1) link_ALPHA1-2 : angle 2.60958 / 1.36 ( 3) link_ALPHA1-3 : bond 0.00721 / 0.38 ( 2) link_ALPHA1-3 : angle 7.78018 / 4.17 ( 6) link_ALPHA1-6 : bond 0.00024 / 0.01 ( 2) link_ALPHA1-6 : angle 2.11758 / 1.23 ( 6) link_BETA1-4 : bond 0.00520 / 0.33 ( 19) link_BETA1-4 : angle 1.75228 / 1.16 ( 57) link_NAG-ASN : bond 0.00308 / 0.18 ( 48) link_NAG-ASN : angle 2.15338 / 1.45 ( 144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3706 Ramachandran restraints generated. 1853 Oldfield, 0 Emsley, 1853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3706 Ramachandran restraints generated. 1853 Oldfield, 0 Emsley, 1853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 347 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 619 LEU cc_start: 0.8980 (mm) cc_final: 0.8192 (tt) REVERT: A 630 GLN cc_start: 0.8854 (mp10) cc_final: 0.8652 (mp10) REVERT: A 634 GLU cc_start: 0.7523 (mt-10) cc_final: 0.7005 (mt-10) REVERT: B 530 MET cc_start: 0.6537 (tpp) cc_final: 0.6119 (tpp) REVERT: B 534 SER cc_start: 0.8909 (m) cc_final: 0.8691 (t) REVERT: B 574 LYS cc_start: 0.8668 (ttmm) cc_final: 0.7649 (pttt) REVERT: B 633 LYS cc_start: 0.9015 (mttm) cc_final: 0.8630 (ttmm) REVERT: C 592 LEU cc_start: 0.9614 (tp) cc_final: 0.9399 (tp) REVERT: C 638 TYR cc_start: 0.7081 (m-80) cc_final: 0.6636 (m-80) REVERT: C 658 GLN cc_start: 0.8749 (tm-30) cc_final: 0.8480 (tm-30) REVERT: E 161 MET cc_start: 0.8729 (tpp) cc_final: 0.8070 (tpt) REVERT: E 208 VAL cc_start: 0.9188 (t) cc_final: 0.8874 (m) REVERT: E 257 THR cc_start: 0.9606 (m) cc_final: 0.9264 (p) REVERT: E 297 THR cc_start: 0.8605 (m) cc_final: 0.8116 (p) REVERT: E 320 THR cc_start: 0.9617 (m) cc_final: 0.9288 (p) REVERT: E 432 GLN cc_start: 0.6952 (tm-30) cc_final: 0.6676 (tm-30) REVERT: F 114 GLN cc_start: 0.8595 (tt0) cc_final: 0.8351 (tm-30) REVERT: F 161 MET cc_start: 0.7996 (tpt) cc_final: 0.7536 (tpt) REVERT: F 180 ASP cc_start: 0.9122 (m-30) cc_final: 0.8643 (m-30) REVERT: F 213 ILE cc_start: 0.8738 (pt) cc_final: 0.8508 (pt) REVERT: F 300 ASN cc_start: 0.8802 (p0) cc_final: 0.8521 (p0) REVERT: F 428 GLN cc_start: 0.8832 (mp-120) cc_final: 0.8309 (mp10) REVERT: F 484 TYR cc_start: 0.8860 (p90) cc_final: 0.8635 (p90) REVERT: G 104 MET cc_start: 0.9354 (ttt) cc_final: 0.9105 (ttt) REVERT: G 125 LEU cc_start: 0.9565 (tp) cc_final: 0.9245 (tp) REVERT: G 213 ILE cc_start: 0.7853 (pt) cc_final: 0.7628 (pt) REVERT: G 217 TYR cc_start: 0.8390 (m-10) cc_final: 0.8040 (m-80) REVERT: G 289 ASN cc_start: 0.9114 (p0) cc_final: 0.8704 (p0) REVERT: L 38 GLN cc_start: 0.8460 (tt0) cc_final: 0.8247 (tt0) outliers start: 5 outliers final: 2 residues processed: 352 average time/residue: 0.1039 time to fit residues: 55.6458 Evaluate side-chains 257 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 255 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 168 optimal weight: 8.9990 chunk 77 optimal weight: 0.7980 chunk 113 optimal weight: 8.9990 chunk 146 optimal weight: 7.9990 chunk 164 optimal weight: 6.9990 chunk 178 optimal weight: 9.9990 chunk 82 optimal weight: 20.0000 chunk 136 optimal weight: 0.8980 chunk 135 optimal weight: 2.9990 chunk 26 optimal weight: 7.9990 chunk 23 optimal weight: 2.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 618 ASN ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 590 GLN ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 72 HIS E 103 GLN E 302 ASN F 241 ASN G 99 ASN G 280 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.105484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.082891 restraints weight = 34062.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.085086 restraints weight = 22093.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.086585 restraints weight = 16443.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.087586 restraints weight = 13355.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.088335 restraints weight = 11524.687| |-----------------------------------------------------------------------------| r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.2810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 16386 Z= 0.255 Angle : 0.717 12.069 22393 Z= 0.345 Chirality : 0.048 0.417 2689 Planarity : 0.004 0.050 2727 Dihedral : 6.893 76.237 3519 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.99 % Favored : 93.96 % Rotamer: Outliers : 0.18 % Allowed : 5.75 % Favored : 94.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.19), residues: 1853 helix: 1.40 (0.27), residues: 402 sheet: 0.27 (0.24), residues: 416 loop : -1.01 (0.19), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG G 166 TYR 0.025 0.002 TYR L 32 PHE 0.020 0.002 PHE L 62 TRP 0.019 0.002 TRP E 112 HIS 0.005 0.001 HIS G 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00591 / 0.26 (16278) covalent geometry : angle 0.68525 / 0.34 (22105) SS BOND : bond 0.00367 / 0.23 ( 36) SS BOND : angle 1.47848 / 1.03 ( 72) hydrogen bonds : bond 0.04093 / 2.68 ( 448) hydrogen bonds : angle 4.70626 / 3.34 ( 1224) link_ALPHA1-2 : bond 0.00634 / 0.33 ( 1) link_ALPHA1-2 : angle 1.11584 / 0.59 ( 3) link_ALPHA1-3 : bond 0.00259 / 0.13 ( 2) link_ALPHA1-3 : angle 5.72354 / 3.03 ( 6) link_ALPHA1-6 : bond 0.00364 / 0.19 ( 2) link_ALPHA1-6 : angle 3.03887 / 1.72 ( 6) link_BETA1-4 : bond 0.00403 / 0.25 ( 19) link_BETA1-4 : angle 1.64099 / 1.09 ( 57) link_NAG-ASN : bond 0.00423 / 0.27 ( 48) link_NAG-ASN : angle 1.98731 / 1.38 ( 144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3706 Ramachandran restraints generated. 1853 Oldfield, 0 Emsley, 1853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3706 Ramachandran restraints generated. 1853 Oldfield, 0 Emsley, 1853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 302 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 630 GLN cc_start: 0.8944 (mp10) cc_final: 0.8172 (mp10) REVERT: A 634 GLU cc_start: 0.7995 (mt-10) cc_final: 0.7624 (mt-10) REVERT: B 534 SER cc_start: 0.8904 (m) cc_final: 0.8570 (t) REVERT: B 574 LYS cc_start: 0.8865 (ttmm) cc_final: 0.7835 (pttt) REVERT: B 627 THR cc_start: 0.7938 (m) cc_final: 0.7469 (m) REVERT: B 647 GLU cc_start: 0.8275 (pt0) cc_final: 0.8002 (pt0) REVERT: C 543 ASN cc_start: 0.8762 (t0) cc_final: 0.8556 (t0) REVERT: C 658 GLN cc_start: 0.8917 (tm-30) cc_final: 0.8520 (tm-30) REVERT: E 161 MET cc_start: 0.8952 (tpp) cc_final: 0.8280 (tpt) REVERT: E 180 ASP cc_start: 0.9311 (m-30) cc_final: 0.9098 (m-30) REVERT: E 297 THR cc_start: 0.9011 (m) cc_final: 0.8535 (p) REVERT: E 432 GLN cc_start: 0.7180 (tm-30) cc_final: 0.6924 (tm-30) REVERT: F 67 ASN cc_start: 0.8968 (t0) cc_final: 0.8667 (t0) REVERT: F 114 GLN cc_start: 0.8711 (tt0) cc_final: 0.8467 (tm-30) REVERT: F 161 MET cc_start: 0.8278 (tpt) cc_final: 0.7842 (tpt) REVERT: F 300 ASN cc_start: 0.8865 (p0) cc_final: 0.8647 (p0) REVERT: F 381 GLU cc_start: 0.8617 (tp30) cc_final: 0.8376 (tp30) REVERT: F 428 GLN cc_start: 0.8881 (mp-120) cc_final: 0.8495 (mp10) REVERT: G 125 LEU cc_start: 0.9534 (tp) cc_final: 0.9075 (tp) REVERT: G 129 LEU cc_start: 0.9382 (mt) cc_final: 0.9156 (mp) REVERT: G 161 MET cc_start: 0.8532 (tpt) cc_final: 0.8321 (tpt) REVERT: H 47 TRP cc_start: 0.8900 (t60) cc_final: 0.8665 (t60) REVERT: H 96 TYR cc_start: 0.6820 (m-10) cc_final: 0.5540 (m-80) REVERT: L 17 GLN cc_start: 0.7975 (mp10) cc_final: 0.7688 (mp10) REVERT: L 38 GLN cc_start: 0.8477 (tt0) cc_final: 0.8251 (tt0) outliers start: 3 outliers final: 3 residues processed: 305 average time/residue: 0.1039 time to fit residues: 47.9726 Evaluate side-chains 229 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 226 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 48 optimal weight: 0.6980 chunk 47 optimal weight: 5.9990 chunk 65 optimal weight: 0.7980 chunk 6 optimal weight: 7.9990 chunk 63 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 165 optimal weight: 9.9990 chunk 153 optimal weight: 0.4980 chunk 37 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 chunk 38 optimal weight: 5.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 650 GLN F 241 ASN ** F 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.108774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.086373 restraints weight = 33147.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.088644 restraints weight = 21153.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.090176 restraints weight = 15537.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.091278 restraints weight = 12517.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.091870 restraints weight = 10700.497| |-----------------------------------------------------------------------------| r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.2906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 16386 Z= 0.115 Angle : 0.611 11.730 22393 Z= 0.292 Chirality : 0.047 0.465 2689 Planarity : 0.003 0.052 2727 Dihedral : 6.033 71.076 3519 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.19), residues: 1853 helix: 1.36 (0.27), residues: 417 sheet: 0.30 (0.23), residues: 440 loop : -0.94 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 100H TYR 0.023 0.001 TYR H 53 PHE 0.014 0.001 PHE L 62 TRP 0.015 0.001 TRP E 112 HIS 0.009 0.001 HIS G 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.11 (16278) covalent geometry : angle 0.57045 / 0.28 (22105) SS BOND : bond 0.00502 / 0.35 ( 36) SS BOND : angle 1.86328 / 1.48 ( 72) hydrogen bonds : bond 0.03308 / 2.16 ( 448) hydrogen bonds : angle 4.48032 / 3.18 ( 1224) link_ALPHA1-2 : bond 0.00567 / 0.30 ( 1) link_ALPHA1-2 : angle 1.40470 / 0.74 ( 3) link_ALPHA1-3 : bond 0.00362 / 0.17 ( 2) link_ALPHA1-3 : angle 5.25351 / 2.78 ( 6) link_ALPHA1-6 : bond 0.00168 / 0.08 ( 2) link_ALPHA1-6 : angle 2.58352 / 1.43 ( 6) link_BETA1-4 : bond 0.00357 / 0.22 ( 19) link_BETA1-4 : angle 1.42294 / 0.94 ( 57) link_NAG-ASN : bond 0.00286 / 0.19 ( 48) link_NAG-ASN : angle 2.03715 / 1.38 ( 144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3706 Ramachandran restraints generated. 1853 Oldfield, 0 Emsley, 1853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3706 Ramachandran restraints generated. 1853 Oldfield, 0 Emsley, 1853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 308 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 626 MET cc_start: 0.6982 (ttm) cc_final: 0.6779 (ttm) REVERT: A 630 GLN cc_start: 0.8890 (mp10) cc_final: 0.8058 (mp10) REVERT: A 634 GLU cc_start: 0.7832 (mt-10) cc_final: 0.7394 (mt-10) REVERT: B 534 SER cc_start: 0.9088 (m) cc_final: 0.8837 (t) REVERT: B 536 THR cc_start: 0.8330 (t) cc_final: 0.7980 (t) REVERT: B 574 LYS cc_start: 0.8731 (ttmm) cc_final: 0.7775 (pttt) REVERT: B 627 THR cc_start: 0.7799 (m) cc_final: 0.7573 (m) REVERT: B 647 GLU cc_start: 0.8182 (pt0) cc_final: 0.7912 (pt0) REVERT: C 543 ASN cc_start: 0.8671 (t0) cc_final: 0.8429 (t0) REVERT: C 640 GLN cc_start: 0.8455 (tp40) cc_final: 0.7940 (tm-30) REVERT: C 652 GLN cc_start: 0.8170 (tp40) cc_final: 0.7926 (tp40) REVERT: C 658 GLN cc_start: 0.8891 (tm-30) cc_final: 0.8492 (tm-30) REVERT: E 161 MET cc_start: 0.8843 (tpp) cc_final: 0.8299 (tpt) REVERT: E 180 ASP cc_start: 0.9327 (m-30) cc_final: 0.9111 (m-30) REVERT: E 297 THR cc_start: 0.8998 (m) cc_final: 0.8533 (p) REVERT: E 320 THR cc_start: 0.9625 (m) cc_final: 0.9273 (p) REVERT: E 432 GLN cc_start: 0.7218 (tm-30) cc_final: 0.6930 (tm-30) REVERT: F 161 MET cc_start: 0.8215 (tpt) cc_final: 0.7825 (tpt) REVERT: F 180 ASP cc_start: 0.9097 (m-30) cc_final: 0.8608 (m-30) REVERT: F 300 ASN cc_start: 0.8800 (p0) cc_final: 0.8498 (p0) REVERT: F 381 GLU cc_start: 0.8673 (tp30) cc_final: 0.8455 (tp30) REVERT: F 428 GLN cc_start: 0.8703 (mp-120) cc_final: 0.8351 (mp10) REVERT: F 482 GLU cc_start: 0.8710 (tp30) cc_final: 0.8475 (tp30) REVERT: G 104 MET cc_start: 0.9327 (ttt) cc_final: 0.8769 (tpp) REVERT: G 125 LEU cc_start: 0.9536 (tp) cc_final: 0.9077 (tp) REVERT: G 129 LEU cc_start: 0.9303 (mt) cc_final: 0.9055 (mp) REVERT: G 207 LYS cc_start: 0.7908 (tmtt) cc_final: 0.7678 (tptt) REVERT: G 297 THR cc_start: 0.9072 (m) cc_final: 0.8871 (t) REVERT: G 370 GLU cc_start: 0.7696 (mp0) cc_final: 0.7389 (mp0) REVERT: G 432 GLN cc_start: 0.8560 (mt0) cc_final: 0.8263 (mt0) REVERT: H 47 TRP cc_start: 0.8945 (t60) cc_final: 0.8701 (t60) REVERT: H 96 TYR cc_start: 0.6838 (m-10) cc_final: 0.5594 (m-80) REVERT: L 17 GLN cc_start: 0.8057 (mp10) cc_final: 0.7854 (mp10) outliers start: 0 outliers final: 0 residues processed: 308 average time/residue: 0.1033 time to fit residues: 48.6898 Evaluate side-chains 242 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 242 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 3 optimal weight: 2.9990 chunk 112 optimal weight: 4.9990 chunk 130 optimal weight: 0.1980 chunk 152 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 chunk 174 optimal weight: 7.9990 chunk 155 optimal weight: 3.9990 chunk 58 optimal weight: 10.0000 chunk 187 optimal weight: 9.9990 chunk 5 optimal weight: 0.8980 chunk 131 optimal weight: 3.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 650 GLN ** C 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 103 GLN F 241 ASN ** F 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 99 ASN ** G 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.107019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.084712 restraints weight = 33673.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.086912 restraints weight = 21908.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.088355 restraints weight = 16274.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.089315 restraints weight = 13322.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.090149 restraints weight = 11533.940| |-----------------------------------------------------------------------------| r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.3127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16386 Z= 0.168 Angle : 0.633 11.746 22393 Z= 0.302 Chirality : 0.047 0.465 2689 Planarity : 0.004 0.053 2727 Dihedral : 5.833 63.491 3519 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.19), residues: 1853 helix: 1.20 (0.27), residues: 420 sheet: 0.31 (0.24), residues: 429 loop : -0.97 (0.19), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 100H TYR 0.023 0.001 TYR H 53 PHE 0.021 0.001 PHE L 98 TRP 0.017 0.001 TRP L 35 HIS 0.009 0.001 HIS G 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.17 (16278) covalent geometry : angle 0.59476 / 0.29 (22105) SS BOND : bond 0.00391 / 0.25 ( 36) SS BOND : angle 1.53758 / 1.22 ( 72) hydrogen bonds : bond 0.03550 / 2.28 ( 448) hydrogen bonds : angle 4.51989 / 3.23 ( 1224) link_ALPHA1-2 : bond 0.00324 / 0.17 ( 1) link_ALPHA1-2 : angle 1.26127 / 0.67 ( 3) link_ALPHA1-3 : bond 0.00253 / 0.12 ( 2) link_ALPHA1-3 : angle 5.37034 / 2.81 ( 6) link_ALPHA1-6 : bond 0.00323 / 0.16 ( 2) link_ALPHA1-6 : angle 2.49511 / 1.40 ( 6) link_BETA1-4 : bond 0.00317 / 0.20 ( 19) link_BETA1-4 : angle 1.37095 / 0.95 ( 57) link_NAG-ASN : bond 0.00221 / 0.14 ( 48) link_NAG-ASN : angle 2.12966 / 1.45 ( 144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3706 Ramachandran restraints generated. 1853 Oldfield, 0 Emsley, 1853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3706 Ramachandran restraints generated. 1853 Oldfield, 0 Emsley, 1853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 297 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 626 MET cc_start: 0.7045 (ttm) cc_final: 0.6828 (ttm) REVERT: A 630 GLN cc_start: 0.8890 (mp10) cc_final: 0.8016 (mp10) REVERT: A 634 GLU cc_start: 0.7877 (mt-10) cc_final: 0.7582 (mt-10) REVERT: B 534 SER cc_start: 0.9040 (m) cc_final: 0.8712 (t) REVERT: B 574 LYS cc_start: 0.8790 (ttmm) cc_final: 0.7758 (pttt) REVERT: B 647 GLU cc_start: 0.8133 (pt0) cc_final: 0.7918 (pt0) REVERT: C 542 ARG cc_start: 0.8011 (tmt-80) cc_final: 0.7634 (tpt170) REVERT: C 543 ASN cc_start: 0.8726 (t0) cc_final: 0.8372 (t0) REVERT: C 640 GLN cc_start: 0.8489 (tp40) cc_final: 0.7962 (tm-30) REVERT: C 652 GLN cc_start: 0.8235 (tp40) cc_final: 0.8025 (tp40) REVERT: C 658 GLN cc_start: 0.8912 (tm-30) cc_final: 0.8469 (tm-30) REVERT: E 120 VAL cc_start: 0.9328 (t) cc_final: 0.8950 (t) REVERT: E 161 MET cc_start: 0.8915 (tpp) cc_final: 0.8310 (tpt) REVERT: E 180 ASP cc_start: 0.9318 (m-30) cc_final: 0.9096 (m-30) REVERT: E 297 THR cc_start: 0.9078 (m) cc_final: 0.8635 (p) REVERT: E 432 GLN cc_start: 0.7266 (tm-30) cc_final: 0.7012 (tm-30) REVERT: F 161 MET cc_start: 0.8304 (tpt) cc_final: 0.7828 (tpt) REVERT: F 180 ASP cc_start: 0.9074 (m-30) cc_final: 0.8582 (m-30) REVERT: F 300 ASN cc_start: 0.8833 (p0) cc_final: 0.8520 (p0) REVERT: F 428 GLN cc_start: 0.8739 (mp-120) cc_final: 0.8415 (mp10) REVERT: G 104 MET cc_start: 0.9336 (ttt) cc_final: 0.9100 (tpp) REVERT: G 207 LYS cc_start: 0.7950 (tmtt) cc_final: 0.7738 (tptt) REVERT: G 217 TYR cc_start: 0.8967 (m-10) cc_final: 0.8311 (m-10) REVERT: G 432 GLN cc_start: 0.8519 (mt0) cc_final: 0.8247 (mt0) REVERT: H 47 TRP cc_start: 0.8883 (t60) cc_final: 0.8649 (t60) REVERT: H 96 TYR cc_start: 0.6956 (m-10) cc_final: 0.5714 (m-80) REVERT: L 17 GLN cc_start: 0.8120 (mp10) cc_final: 0.7900 (mp10) outliers start: 0 outliers final: 0 residues processed: 297 average time/residue: 0.1002 time to fit residues: 45.4799 Evaluate side-chains 232 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 232 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 64 optimal weight: 0.6980 chunk 123 optimal weight: 5.9990 chunk 149 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 8 optimal weight: 0.0670 chunk 31 optimal weight: 0.8980 chunk 12 optimal weight: 8.9990 chunk 158 optimal weight: 0.6980 chunk 79 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 39 optimal weight: 8.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 105 HIS F 241 ASN ** F 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 99 ASN ** G 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.108482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.086150 restraints weight = 33048.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.088358 restraints weight = 21244.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.089867 restraints weight = 15730.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.090948 restraints weight = 12770.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.091643 restraints weight = 10904.679| |-----------------------------------------------------------------------------| r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.3219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16386 Z= 0.108 Angle : 0.598 11.302 22393 Z= 0.288 Chirality : 0.046 0.462 2689 Planarity : 0.003 0.050 2727 Dihedral : 5.467 57.990 3519 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.19), residues: 1853 helix: 1.20 (0.27), residues: 420 sheet: 0.47 (0.24), residues: 438 loop : -0.98 (0.19), residues: 995 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 100H TYR 0.025 0.001 TYR H 53 PHE 0.017 0.001 PHE L 98 TRP 0.013 0.001 TRP L 35 HIS 0.011 0.001 HIS G 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (16278) covalent geometry : angle 0.56505 / 0.28 (22105) SS BOND : bond 0.00326 / 0.25 ( 36) SS BOND : angle 1.16453 / 0.90 ( 72) hydrogen bonds : bond 0.03225 / 2.11 ( 448) hydrogen bonds : angle 4.47674 / 3.18 ( 1224) link_ALPHA1-2 : bond 0.00525 / 0.28 ( 1) link_ALPHA1-2 : angle 1.48891 / 0.78 ( 3) link_ALPHA1-3 : bond 0.00524 / 0.25 ( 2) link_ALPHA1-3 : angle 5.02242 / 2.63 ( 6) link_ALPHA1-6 : bond 0.00174 / 0.09 ( 2) link_ALPHA1-6 : angle 2.38510 / 1.33 ( 6) link_BETA1-4 : bond 0.00355 / 0.22 ( 19) link_BETA1-4 : angle 1.30072 / 0.89 ( 57) link_NAG-ASN : bond 0.00284 / 0.19 ( 48) link_NAG-ASN : angle 1.96996 / 1.32 ( 144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3706 Ramachandran restraints generated. 1853 Oldfield, 0 Emsley, 1853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3706 Ramachandran restraints generated. 1853 Oldfield, 0 Emsley, 1853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 303 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 603 ILE cc_start: 0.9297 (mm) cc_final: 0.8947 (mm) REVERT: A 630 GLN cc_start: 0.8835 (mp10) cc_final: 0.7979 (mp10) REVERT: A 634 GLU cc_start: 0.7842 (mt-10) cc_final: 0.7496 (mt-10) REVERT: B 574 LYS cc_start: 0.8757 (ttmm) cc_final: 0.7745 (pttt) REVERT: B 647 GLU cc_start: 0.8110 (pt0) cc_final: 0.7897 (pt0) REVERT: C 530 MET cc_start: 0.7814 (tpp) cc_final: 0.7538 (tpp) REVERT: C 543 ASN cc_start: 0.8660 (t0) cc_final: 0.8260 (t0) REVERT: C 640 GLN cc_start: 0.8527 (tp40) cc_final: 0.7980 (tm-30) REVERT: C 652 GLN cc_start: 0.8291 (tp40) cc_final: 0.8079 (tp40) REVERT: C 658 GLN cc_start: 0.8874 (tm-30) cc_final: 0.8465 (tm-30) REVERT: E 161 MET cc_start: 0.8842 (tpp) cc_final: 0.8359 (tpt) REVERT: E 180 ASP cc_start: 0.9330 (m-30) cc_final: 0.9111 (m-30) REVERT: E 297 THR cc_start: 0.9036 (m) cc_final: 0.8627 (p) REVERT: E 320 THR cc_start: 0.9645 (m) cc_final: 0.9303 (p) REVERT: E 432 GLN cc_start: 0.7319 (tm-30) cc_final: 0.7040 (tm-30) REVERT: F 161 MET cc_start: 0.8320 (tpt) cc_final: 0.7836 (tpt) REVERT: F 180 ASP cc_start: 0.9056 (m-30) cc_final: 0.8656 (m-30) REVERT: F 300 ASN cc_start: 0.8788 (p0) cc_final: 0.8493 (p0) REVERT: F 381 GLU cc_start: 0.8537 (tp30) cc_final: 0.8206 (tp30) REVERT: F 427 TRP cc_start: 0.8680 (m-90) cc_final: 0.8477 (m-90) REVERT: F 428 GLN cc_start: 0.8725 (mp-120) cc_final: 0.8367 (mp10) REVERT: F 477 ASP cc_start: 0.8864 (m-30) cc_final: 0.8656 (m-30) REVERT: G 104 MET cc_start: 0.9310 (ttt) cc_final: 0.9061 (tpp) REVERT: G 207 LYS cc_start: 0.7914 (tmtt) cc_final: 0.7695 (tptt) REVERT: G 217 TYR cc_start: 0.8945 (m-10) cc_final: 0.8251 (m-10) REVERT: G 368 ASP cc_start: 0.8013 (p0) cc_final: 0.7785 (p0) REVERT: G 432 GLN cc_start: 0.8505 (mt0) cc_final: 0.8221 (mt0) REVERT: H 47 TRP cc_start: 0.8890 (t60) cc_final: 0.8679 (t60) REVERT: H 96 TYR cc_start: 0.6941 (m-10) cc_final: 0.5551 (m-80) REVERT: L 17 GLN cc_start: 0.8120 (mp10) cc_final: 0.7902 (mp10) outliers start: 0 outliers final: 0 residues processed: 303 average time/residue: 0.0935 time to fit residues: 43.8268 Evaluate side-chains 244 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 244 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 24 optimal weight: 9.9990 chunk 83 optimal weight: 4.9990 chunk 118 optimal weight: 7.9990 chunk 12 optimal weight: 0.7980 chunk 174 optimal weight: 5.9990 chunk 126 optimal weight: 10.0000 chunk 18 optimal weight: 0.2980 chunk 31 optimal weight: 0.4980 chunk 115 optimal weight: 0.0980 chunk 11 optimal weight: 3.9990 chunk 117 optimal weight: 0.9980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 241 ASN ** F 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 99 ASN ** G 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.109545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.087554 restraints weight = 32747.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.089821 restraints weight = 20904.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.091390 restraints weight = 15383.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.092454 restraints weight = 12362.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.093065 restraints weight = 10569.190| |-----------------------------------------------------------------------------| r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.3282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16386 Z= 0.110 Angle : 0.614 10.948 22393 Z= 0.292 Chirality : 0.046 0.461 2689 Planarity : 0.003 0.047 2727 Dihedral : 5.318 53.992 3519 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.19), residues: 1853 helix: 1.24 (0.27), residues: 420 sheet: 0.61 (0.24), residues: 426 loop : -0.99 (0.19), residues: 1007 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 100H TYR 0.025 0.001 TYR H 53 PHE 0.016 0.001 PHE H 100K TRP 0.012 0.001 TRP A 596 HIS 0.009 0.001 HIS G 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (16278) covalent geometry : angle 0.57970 / 0.28 (22105) SS BOND : bond 0.00267 / 0.21 ( 36) SS BOND : angle 1.17930 / 0.93 ( 72) hydrogen bonds : bond 0.03219 / 2.09 ( 448) hydrogen bonds : angle 4.50786 / 3.21 ( 1224) link_ALPHA1-2 : bond 0.00413 / 0.22 ( 1) link_ALPHA1-2 : angle 1.49753 / 0.79 ( 3) link_ALPHA1-3 : bond 0.00588 / 0.29 ( 2) link_ALPHA1-3 : angle 4.84032 / 2.53 ( 6) link_ALPHA1-6 : bond 0.00260 / 0.12 ( 2) link_ALPHA1-6 : angle 2.30140 / 1.27 ( 6) link_BETA1-4 : bond 0.00681 / 0.43 ( 19) link_BETA1-4 : angle 1.48790 / 1.10 ( 57) link_NAG-ASN : bond 0.00637 / 0.25 ( 48) link_NAG-ASN : angle 2.04597 / 1.33 ( 144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3706 Ramachandran restraints generated. 1853 Oldfield, 0 Emsley, 1853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3706 Ramachandran restraints generated. 1853 Oldfield, 0 Emsley, 1853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 304 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 626 MET cc_start: 0.7032 (ttm) cc_final: 0.6830 (ttm) REVERT: A 630 GLN cc_start: 0.8838 (mp10) cc_final: 0.7942 (mp10) REVERT: A 634 GLU cc_start: 0.7873 (mt-10) cc_final: 0.7500 (mt-10) REVERT: B 574 LYS cc_start: 0.8776 (ttmm) cc_final: 0.7767 (pttt) REVERT: B 647 GLU cc_start: 0.8139 (pt0) cc_final: 0.7899 (pt0) REVERT: C 543 ASN cc_start: 0.8687 (t0) cc_final: 0.8304 (t0) REVERT: C 640 GLN cc_start: 0.8544 (tp40) cc_final: 0.8036 (tm-30) REVERT: C 652 GLN cc_start: 0.8255 (tp40) cc_final: 0.8011 (tp40) REVERT: C 658 GLN cc_start: 0.8867 (tm-30) cc_final: 0.8458 (tm-30) REVERT: E 161 MET cc_start: 0.8839 (tpp) cc_final: 0.8341 (tpt) REVERT: E 180 ASP cc_start: 0.9301 (m-30) cc_final: 0.9076 (m-30) REVERT: E 257 THR cc_start: 0.9516 (m) cc_final: 0.9311 (p) REVERT: E 297 THR cc_start: 0.9041 (m) cc_final: 0.8642 (p) REVERT: E 320 THR cc_start: 0.9657 (m) cc_final: 0.9324 (p) REVERT: E 368 ASP cc_start: 0.7277 (p0) cc_final: 0.7065 (p0) REVERT: E 432 GLN cc_start: 0.7362 (tm-30) cc_final: 0.7023 (tm-30) REVERT: F 161 MET cc_start: 0.8345 (tpt) cc_final: 0.7841 (tpt) REVERT: F 180 ASP cc_start: 0.9027 (m-30) cc_final: 0.8604 (m-30) REVERT: F 325 ASP cc_start: 0.7418 (m-30) cc_final: 0.7073 (p0) REVERT: F 428 GLN cc_start: 0.8729 (mp-120) cc_final: 0.8350 (mp10) REVERT: G 95 MET cc_start: 0.9143 (ppp) cc_final: 0.8268 (ppp) REVERT: G 104 MET cc_start: 0.9320 (ttt) cc_final: 0.9043 (tpp) REVERT: G 161 MET cc_start: 0.8237 (mmm) cc_final: 0.7948 (tpt) REVERT: G 207 LYS cc_start: 0.7895 (tmtt) cc_final: 0.7653 (tptt) REVERT: G 217 TYR cc_start: 0.8946 (m-10) cc_final: 0.8270 (m-10) REVERT: G 368 ASP cc_start: 0.7928 (p0) cc_final: 0.7698 (p0) REVERT: G 432 GLN cc_start: 0.8427 (mt0) cc_final: 0.8168 (mt0) REVERT: H 47 TRP cc_start: 0.8854 (t60) cc_final: 0.8308 (t60) REVERT: H 96 TYR cc_start: 0.6921 (m-10) cc_final: 0.5541 (m-80) REVERT: L 17 GLN cc_start: 0.8188 (mp10) cc_final: 0.7960 (mp10) outliers start: 0 outliers final: 0 residues processed: 304 average time/residue: 0.0952 time to fit residues: 45.0136 Evaluate side-chains 237 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 237 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 59 optimal weight: 4.9990 chunk 75 optimal weight: 0.4980 chunk 164 optimal weight: 2.9990 chunk 163 optimal weight: 3.9990 chunk 46 optimal weight: 6.9990 chunk 51 optimal weight: 0.4980 chunk 83 optimal weight: 2.9990 chunk 67 optimal weight: 0.0770 chunk 124 optimal weight: 0.0970 chunk 155 optimal weight: 4.9990 chunk 103 optimal weight: 0.9980 overall best weight: 0.4336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 590 GLN ** C 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 241 ASN F 279 ASN ** F 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 99 ASN ** G 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 93 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.110817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.088779 restraints weight = 33204.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.091039 restraints weight = 21371.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.092622 restraints weight = 15797.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.093696 restraints weight = 12705.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.094368 restraints weight = 10884.369| |-----------------------------------------------------------------------------| r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.3358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 16386 Z= 0.109 Angle : 0.628 12.649 22393 Z= 0.304 Chirality : 0.047 0.466 2689 Planarity : 0.003 0.046 2727 Dihedral : 5.110 53.187 3519 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.19), residues: 1853 helix: 1.33 (0.27), residues: 414 sheet: 0.56 (0.24), residues: 449 loop : -0.95 (0.19), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 456 TYR 0.026 0.001 TYR H 53 PHE 0.020 0.001 PHE H 100K TRP 0.013 0.001 TRP L 35 HIS 0.006 0.001 HIS G 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (16278) covalent geometry : angle 0.58983 / 0.29 (22105) SS BOND : bond 0.00458 / 0.36 ( 36) SS BOND : angle 1.98595 / 1.12 ( 72) hydrogen bonds : bond 0.03168 / 2.10 ( 448) hydrogen bonds : angle 4.49562 / 3.22 ( 1224) link_ALPHA1-2 : bond 0.00422 / 0.22 ( 1) link_ALPHA1-2 : angle 1.47557 / 0.78 ( 3) link_ALPHA1-3 : bond 0.00602 / 0.29 ( 2) link_ALPHA1-3 : angle 4.70466 / 2.46 ( 6) link_ALPHA1-6 : bond 0.00160 / 0.08 ( 2) link_ALPHA1-6 : angle 2.23702 / 1.24 ( 6) link_BETA1-4 : bond 0.00438 / 0.27 ( 19) link_BETA1-4 : angle 1.32417 / 0.93 ( 57) link_NAG-ASN : bond 0.00499 / 0.22 ( 48) link_NAG-ASN : angle 2.03180 / 1.33 ( 144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3706 Ramachandran restraints generated. 1853 Oldfield, 0 Emsley, 1853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3706 Ramachandran restraints generated. 1853 Oldfield, 0 Emsley, 1853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 301 time to evaluate : 0.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 626 MET cc_start: 0.7079 (ttm) cc_final: 0.6734 (ttm) REVERT: A 630 GLN cc_start: 0.8830 (mp10) cc_final: 0.8026 (mp10) REVERT: A 634 GLU cc_start: 0.7778 (mt-10) cc_final: 0.7279 (mt-10) REVERT: A 639 THR cc_start: 0.8813 (p) cc_final: 0.8370 (t) REVERT: B 574 LYS cc_start: 0.8820 (ttmm) cc_final: 0.7886 (pttt) REVERT: B 647 GLU cc_start: 0.8091 (pt0) cc_final: 0.7891 (pt0) REVERT: C 543 ASN cc_start: 0.8620 (t0) cc_final: 0.8205 (t0) REVERT: C 640 GLN cc_start: 0.8515 (tp40) cc_final: 0.7962 (tm-30) REVERT: C 658 GLN cc_start: 0.8836 (tm-30) cc_final: 0.8428 (tm-30) REVERT: E 161 MET cc_start: 0.8775 (tpp) cc_final: 0.8054 (tpt) REVERT: E 180 ASP cc_start: 0.9306 (m-30) cc_final: 0.9060 (m-30) REVERT: E 257 THR cc_start: 0.9568 (m) cc_final: 0.9336 (p) REVERT: E 297 THR cc_start: 0.9025 (m) cc_final: 0.8616 (p) REVERT: E 320 THR cc_start: 0.9657 (m) cc_final: 0.9323 (p) REVERT: E 368 ASP cc_start: 0.7247 (p0) cc_final: 0.7020 (p0) REVERT: E 432 GLN cc_start: 0.7326 (tm-30) cc_final: 0.6981 (tm-30) REVERT: F 114 GLN cc_start: 0.8614 (tt0) cc_final: 0.8231 (tm-30) REVERT: F 161 MET cc_start: 0.8328 (tpt) cc_final: 0.7842 (tpt) REVERT: F 180 ASP cc_start: 0.8995 (m-30) cc_final: 0.8581 (m-30) REVERT: F 325 ASP cc_start: 0.7410 (m-30) cc_final: 0.7021 (p0) REVERT: F 428 GLN cc_start: 0.8713 (mp-120) cc_final: 0.8342 (mp10) REVERT: G 95 MET cc_start: 0.9158 (ppp) cc_final: 0.8208 (ppp) REVERT: G 104 MET cc_start: 0.9328 (ttt) cc_final: 0.9031 (tpp) REVERT: G 207 LYS cc_start: 0.7887 (tmtt) cc_final: 0.7637 (tptt) REVERT: G 217 TYR cc_start: 0.8869 (m-10) cc_final: 0.8196 (m-10) REVERT: G 432 GLN cc_start: 0.8299 (mt0) cc_final: 0.8053 (mt0) REVERT: H 47 TRP cc_start: 0.8838 (t60) cc_final: 0.8308 (t60) REVERT: H 96 TYR cc_start: 0.6910 (m-10) cc_final: 0.5538 (m-80) REVERT: L 17 GLN cc_start: 0.8191 (mp10) cc_final: 0.7967 (mp10) outliers start: 0 outliers final: 0 residues processed: 301 average time/residue: 0.1031 time to fit residues: 48.0324 Evaluate side-chains 245 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 245 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 133 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 51 optimal weight: 7.9990 chunk 127 optimal weight: 6.9990 chunk 144 optimal weight: 3.9990 chunk 154 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 40 optimal weight: 10.0000 chunk 39 optimal weight: 5.9990 chunk 130 optimal weight: 9.9990 chunk 152 optimal weight: 0.9980 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 590 GLN ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 590 GLN E 103 GLN F 241 ASN ** F 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 99 ASN ** G 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.105318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.082980 restraints weight = 33917.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.085089 restraints weight = 22264.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.086557 restraints weight = 16758.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.087490 restraints weight = 13701.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.088062 restraints weight = 11930.899| |-----------------------------------------------------------------------------| r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.3667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.107 16386 Z= 0.227 Angle : 0.748 18.630 22393 Z= 0.361 Chirality : 0.050 0.496 2689 Planarity : 0.004 0.049 2727 Dihedral : 5.667 52.354 3519 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.58 % Favored : 93.36 % Rotamer: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.19), residues: 1853 helix: 0.97 (0.27), residues: 420 sheet: 0.44 (0.25), residues: 417 loop : -1.09 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 500 TYR 0.025 0.002 TYR H 53 PHE 0.019 0.002 PHE H 100K TRP 0.028 0.002 TRP E 45 HIS 0.008 0.001 HIS E 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00533 / 0.23 (16278) covalent geometry : angle 0.70705 / 0.35 (22105) SS BOND : bond 0.00643 / 0.33 ( 36) SS BOND : angle 2.53453 / 1.74 ( 72) hydrogen bonds : bond 0.03949 / 2.64 ( 448) hydrogen bonds : angle 4.64189 / 3.31 ( 1224) link_ALPHA1-2 : bond 0.00331 / 0.17 ( 1) link_ALPHA1-2 : angle 1.46498 / 0.77 ( 3) link_ALPHA1-3 : bond 0.00333 / 0.16 ( 2) link_ALPHA1-3 : angle 5.21879 / 2.69 ( 6) link_ALPHA1-6 : bond 0.00715 / 0.36 ( 2) link_ALPHA1-6 : angle 2.22301 / 1.24 ( 6) link_BETA1-4 : bond 0.00500 / 0.31 ( 19) link_BETA1-4 : angle 1.46465 / 1.05 ( 57) link_NAG-ASN : bond 0.00523 / 0.29 ( 48) link_NAG-ASN : angle 2.21338 / 1.51 ( 144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3706 Ramachandran restraints generated. 1853 Oldfield, 0 Emsley, 1853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3706 Ramachandran restraints generated. 1853 Oldfield, 0 Emsley, 1853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 285 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 603 ILE cc_start: 0.9397 (mm) cc_final: 0.9077 (mm) REVERT: A 626 MET cc_start: 0.7115 (ttm) cc_final: 0.6748 (ttm) REVERT: A 630 GLN cc_start: 0.8886 (mp10) cc_final: 0.8139 (mp10) REVERT: A 634 GLU cc_start: 0.8043 (mt-10) cc_final: 0.7558 (mt-10) REVERT: A 639 THR cc_start: 0.8940 (p) cc_final: 0.8580 (t) REVERT: B 574 LYS cc_start: 0.8870 (ttmm) cc_final: 0.7919 (pttt) REVERT: C 543 ASN cc_start: 0.8757 (t0) cc_final: 0.8260 (t0) REVERT: C 640 GLN cc_start: 0.8546 (tp40) cc_final: 0.7942 (tm-30) REVERT: C 652 GLN cc_start: 0.8482 (tp40) cc_final: 0.8061 (tp40) REVERT: C 658 GLN cc_start: 0.8898 (tm-30) cc_final: 0.8428 (tm-30) REVERT: E 161 MET cc_start: 0.8933 (tpp) cc_final: 0.8318 (tpt) REVERT: E 180 ASP cc_start: 0.9303 (m-30) cc_final: 0.9076 (m-30) REVERT: E 297 THR cc_start: 0.9211 (m) cc_final: 0.8963 (p) REVERT: E 432 GLN cc_start: 0.7399 (tm-30) cc_final: 0.7012 (tm-30) REVERT: F 161 MET cc_start: 0.8394 (tpt) cc_final: 0.7895 (tpt) REVERT: F 325 ASP cc_start: 0.7353 (m-30) cc_final: 0.7008 (p0) REVERT: F 428 GLN cc_start: 0.8776 (mp-120) cc_final: 0.8431 (mp10) REVERT: G 104 MET cc_start: 0.9326 (ttt) cc_final: 0.8995 (tpp) REVERT: G 161 MET cc_start: 0.8214 (mmm) cc_final: 0.7993 (tpt) REVERT: G 207 LYS cc_start: 0.8064 (tmtt) cc_final: 0.7824 (tptt) REVERT: G 217 TYR cc_start: 0.9069 (m-10) cc_final: 0.8375 (m-10) REVERT: G 368 ASP cc_start: 0.8007 (p0) cc_final: 0.7760 (p0) REVERT: G 370 GLU cc_start: 0.7815 (mp0) cc_final: 0.7540 (mp0) REVERT: H 47 TRP cc_start: 0.8858 (t60) cc_final: 0.8288 (t60) REVERT: H 96 TYR cc_start: 0.6965 (m-10) cc_final: 0.5960 (m-80) outliers start: 0 outliers final: 0 residues processed: 285 average time/residue: 0.0981 time to fit residues: 43.4076 Evaluate side-chains 228 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 228 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 115 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 8 optimal weight: 0.8980 chunk 87 optimal weight: 4.9990 chunk 38 optimal weight: 7.9990 chunk 148 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 142 optimal weight: 0.8980 chunk 110 optimal weight: 1.9990 chunk 112 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 241 ASN ** F 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 99 ASN ** G 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 93 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.107567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.085093 restraints weight = 33783.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.087295 restraints weight = 21782.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.088822 restraints weight = 16172.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.089895 restraints weight = 13133.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.090478 restraints weight = 11295.948| |-----------------------------------------------------------------------------| r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.3696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.097 16386 Z= 0.136 Angle : 0.677 15.685 22393 Z= 0.329 Chirality : 0.048 0.473 2689 Planarity : 0.003 0.053 2727 Dihedral : 5.433 51.883 3519 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.83 % Favored : 94.12 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.19), residues: 1853 helix: 1.16 (0.27), residues: 417 sheet: 0.39 (0.25), residues: 419 loop : -1.07 (0.19), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 54 TYR 0.026 0.001 TYR H 53 PHE 0.018 0.001 PHE H 100K TRP 0.018 0.001 TRP L 35 HIS 0.003 0.001 HIS G 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (16278) covalent geometry : angle 0.63544 / 0.32 (22105) SS BOND : bond 0.00427 / 0.22 ( 36) SS BOND : angle 2.48400 / 1.66 ( 72) hydrogen bonds : bond 0.03431 / 2.27 ( 448) hydrogen bonds : angle 4.58063 / 3.27 ( 1224) link_ALPHA1-2 : bond 0.00367 / 0.19 ( 1) link_ALPHA1-2 : angle 1.48188 / 0.78 ( 3) link_ALPHA1-3 : bond 0.00533 / 0.26 ( 2) link_ALPHA1-3 : angle 4.61693 / 2.39 ( 6) link_ALPHA1-6 : bond 0.00331 / 0.16 ( 2) link_ALPHA1-6 : angle 2.15765 / 1.20 ( 6) link_BETA1-4 : bond 0.00387 / 0.24 ( 19) link_BETA1-4 : angle 1.35267 / 0.97 ( 57) link_NAG-ASN : bond 0.00411 / 0.20 ( 48) link_NAG-ASN : angle 2.08420 / 1.40 ( 144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3706 Ramachandran restraints generated. 1853 Oldfield, 0 Emsley, 1853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3706 Ramachandran restraints generated. 1853 Oldfield, 0 Emsley, 1853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 282 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 603 ILE cc_start: 0.9332 (mm) cc_final: 0.9016 (mm) REVERT: A 626 MET cc_start: 0.7107 (ttm) cc_final: 0.6752 (ttm) REVERT: A 630 GLN cc_start: 0.8866 (mp10) cc_final: 0.8149 (mp10) REVERT: A 634 GLU cc_start: 0.7975 (mt-10) cc_final: 0.7509 (mt-10) REVERT: C 530 MET cc_start: 0.7976 (tpp) cc_final: 0.7701 (tpp) REVERT: C 543 ASN cc_start: 0.8731 (t0) cc_final: 0.8312 (t0) REVERT: C 640 GLN cc_start: 0.8587 (tp40) cc_final: 0.7971 (tm-30) REVERT: C 652 GLN cc_start: 0.8314 (tp40) cc_final: 0.8107 (tp40) REVERT: C 658 GLN cc_start: 0.8876 (tm-30) cc_final: 0.8415 (tm-30) REVERT: E 161 MET cc_start: 0.8858 (tpp) cc_final: 0.8100 (tpt) REVERT: E 180 ASP cc_start: 0.9325 (m-30) cc_final: 0.9082 (m-30) REVERT: E 257 THR cc_start: 0.9613 (m) cc_final: 0.9268 (p) REVERT: E 297 THR cc_start: 0.9182 (m) cc_final: 0.8952 (p) REVERT: E 432 GLN cc_start: 0.7433 (tm-30) cc_final: 0.7119 (tm-30) REVERT: F 161 MET cc_start: 0.8390 (tpt) cc_final: 0.7869 (tpt) REVERT: F 428 GLN cc_start: 0.8760 (mp-120) cc_final: 0.8408 (mp10) REVERT: G 104 MET cc_start: 0.9366 (ttt) cc_final: 0.9013 (tpp) REVERT: G 207 LYS cc_start: 0.7948 (tmtt) cc_final: 0.7735 (tptt) REVERT: G 217 TYR cc_start: 0.8983 (m-10) cc_final: 0.8346 (m-10) REVERT: G 368 ASP cc_start: 0.8002 (p0) cc_final: 0.7761 (p0) REVERT: G 370 GLU cc_start: 0.7818 (mp0) cc_final: 0.7565 (mp0) REVERT: H 47 TRP cc_start: 0.8841 (t60) cc_final: 0.8199 (t60) REVERT: H 96 TYR cc_start: 0.6948 (m-10) cc_final: 0.5784 (m-80) outliers start: 0 outliers final: 0 residues processed: 282 average time/residue: 0.1018 time to fit residues: 45.5210 Evaluate side-chains 231 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 231 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 158 optimal weight: 7.9990 chunk 127 optimal weight: 2.9990 chunk 116 optimal weight: 7.9990 chunk 107 optimal weight: 0.6980 chunk 91 optimal weight: 0.0670 chunk 161 optimal weight: 5.9990 chunk 105 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 128 optimal weight: 0.7980 overall best weight: 0.9122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 650 GLN F 241 ASN ** F 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 99 ASN ** G 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 93 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.108046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.085698 restraints weight = 33272.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.087900 restraints weight = 21537.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.089399 restraints weight = 16000.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.090432 restraints weight = 13006.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.091146 restraints weight = 11217.380| |-----------------------------------------------------------------------------| r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.3790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 16386 Z= 0.131 Angle : 0.674 15.407 22393 Z= 0.326 Chirality : 0.048 0.462 2689 Planarity : 0.004 0.053 2727 Dihedral : 5.358 52.884 3519 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.40 % Favored : 94.55 % Rotamer: Outliers : 0.00 % Allowed : 0.06 % Favored : 99.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.19), residues: 1853 helix: 1.19 (0.27), residues: 417 sheet: 0.49 (0.25), residues: 413 loop : -1.09 (0.19), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 617 TYR 0.027 0.001 TYR H 53 PHE 0.018 0.001 PHE F 361 TRP 0.019 0.001 TRP F 35 HIS 0.004 0.001 HIS G 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 (16278) covalent geometry : angle 0.63336 / 0.32 (22105) SS BOND : bond 0.00405 / 0.20 ( 36) SS BOND : angle 2.26107 / 1.43 ( 72) hydrogen bonds : bond 0.03400 / 2.28 ( 448) hydrogen bonds : angle 4.66412 / 3.34 ( 1224) link_ALPHA1-2 : bond 0.00364 / 0.19 ( 1) link_ALPHA1-2 : angle 1.44486 / 0.76 ( 3) link_ALPHA1-3 : bond 0.00557 / 0.27 ( 2) link_ALPHA1-3 : angle 4.43454 / 2.29 ( 6) link_ALPHA1-6 : bond 0.00254 / 0.12 ( 2) link_ALPHA1-6 : angle 2.10722 / 1.17 ( 6) link_BETA1-4 : bond 0.00535 / 0.35 ( 19) link_BETA1-4 : angle 1.42827 / 1.09 ( 57) link_NAG-ASN : bond 0.00531 / 0.22 ( 48) link_NAG-ASN : angle 2.14874 / 1.42 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2154.09 seconds wall clock time: 38 minutes 6.04 seconds (2286.04 seconds total)