Starting phenix.real_space_refine on Thu Feb 5 01:31:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9o2q_70018/02_2026/9o2q_70018.cif Found real_map, /net/cci-nas-00/data/ceres_data/9o2q_70018/02_2026/9o2q_70018.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9o2q_70018/02_2026/9o2q_70018.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9o2q_70018/02_2026/9o2q_70018.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9o2q_70018/02_2026/9o2q_70018.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9o2q_70018/02_2026/9o2q_70018.map" } resolution = 2.9 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= 0.035 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 108 5.16 5 C 8769 2.51 5 N 2376 2.21 5 O 2757 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14010 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 3418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3418 Classifications: {'peptide': 433} Link IDs: {'PTRANS': 20, 'TRANS': 412} Chain breaks: 5 Chain: "B" Number of atoms: 975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 975 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain breaks: 1 Chain: "C" Number of atoms: 3418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3418 Classifications: {'peptide': 433} Link IDs: {'PTRANS': 20, 'TRANS': 412} Chain breaks: 5 Chain: "D" Number of atoms: 975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 975 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain breaks: 1 Chain: "E" Number of atoms: 3418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3418 Classifications: {'peptide': 433} Link IDs: {'PTRANS': 20, 'TRANS': 412} Chain breaks: 5 Chain: "F" Number of atoms: 975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 975 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain breaks: 1 Chain: "G" 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: "H" 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: 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: "J" 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: "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: "L" 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 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: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 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: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 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: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "D" 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: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "F" 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 Time building chain proxies: 3.12, per 1000 atoms: 0.22 Number of scatterers: 14010 At special positions: 0 Unit cell: (127.296, 123.136, 120.64, 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 108 16.00 O 2757 8.00 N 2376 7.00 C 8769 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=31, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 201 " - pdb=" SG CYS A 433 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.05 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 201 " - pdb=" SG CYS C 433 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.05 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 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=2.07 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.04 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " 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 E 501 " - pdb=" SG CYS F 605 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " 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 BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " NAG-ASN " NAG A 601 " - " ASN A 88 " " NAG A 602 " - " ASN A 234 " " NAG A 603 " - " ASN A 295 " " NAG A 604 " - " ASN A 363 " " NAG A 605 " - " ASN A 386 " " NAG A 606 " - " ASN A 133 " " NAG B 701 " - " ASN B 611 " " NAG C 601 " - " ASN C 88 " " NAG C 602 " - " ASN C 234 " " NAG C 603 " - " ASN C 295 " " NAG C 604 " - " ASN C 363 " " NAG C 605 " - " ASN C 386 " " NAG C 606 " - " ASN C 133 " " NAG D 701 " - " ASN D 611 " " NAG E 601 " - " ASN E 88 " " NAG E 602 " - " ASN E 156 " " NAG E 603 " - " ASN E 234 " " NAG E 604 " - " ASN E 295 " " NAG E 605 " - " ASN E 386 " " NAG E 606 " - " ASN E 133 " " NAG F 701 " - " ASN F 611 " " NAG G 1 " - " ASN A 156 " " NAG H 1 " - " ASN A 160 " " NAG I 1 " - " ASN A 197 " " NAG J 1 " - " ASN A 262 " " NAG K 1 " - " ASN A 332 " " NAG L 1 " - " ASN A 448 " " NAG M 1 " - " ASN C 156 " " NAG N 1 " - " ASN C 160 " " NAG O 1 " - " ASN C 197 " " NAG P 1 " - " ASN C 262 " " NAG Q 1 " - " ASN C 332 " " NAG R 1 " - " ASN C 448 " " NAG S 1 " - " ASN E 160 " " NAG T 1 " - " ASN E 197 " " NAG U 1 " - " ASN E 262 " " NAG V 1 " - " ASN E 332 " " NAG W 1 " - " ASN E 363 " " NAG X 1 " - " ASN E 448 " Time building additional restraints: 1.29 Conformation dependent library (CDL) restraints added in 471.7 milliseconds 3234 Ramachandran restraints generated. 1617 Oldfield, 0 Emsley, 1617 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3120 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 25 sheets defined 24.9% alpha, 32.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 98 through 113 removed outlier: 3.898A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 335 through 350 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 475 through 481 removed outlier: 3.624A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 527 removed outlier: 4.381A pdb=" N GLY B 527 " --> pdb=" O GLY B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 543 removed outlier: 3.774A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 596 Processing helix chain 'B' and resid 619 through 624 Processing helix chain 'B' and resid 627 through 635 removed outlier: 3.550A pdb=" N GLU B 634 " --> pdb=" O GLN B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 661 Processing helix chain 'C' and resid 98 through 115 removed outlier: 3.888A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER C 115 " --> pdb=" O LEU C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 147 through 151 Processing helix chain 'C' and resid 195 through 197 No H-bonds generated for 'chain 'C' and resid 195 through 197' Processing helix chain 'C' and resid 335 through 350 Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 475 through 481 removed outlier: 3.705A pdb=" N TRP C 479 " --> pdb=" O MET C 475 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 527 removed outlier: 4.440A pdb=" N GLY D 527 " --> pdb=" O GLY D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 536 through 542 removed outlier: 3.846A pdb=" N GLN D 540 " --> pdb=" O THR D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 571 through 596 removed outlier: 3.511A pdb=" N ASP D 589 " --> pdb=" O ARG D 585 " (cutoff:3.500A) Processing helix chain 'D' and resid 619 through 624 removed outlier: 3.585A pdb=" N TRP D 623 " --> pdb=" O LEU D 619 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASP D 624 " --> pdb=" O SER D 620 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 619 through 624' Processing helix chain 'D' and resid 627 through 635 Processing helix chain 'D' and resid 638 through 661 Processing helix chain 'E' and resid 98 through 115 removed outlier: 3.987A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N SER E 115 " --> pdb=" O LEU E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 removed outlier: 3.588A pdb=" N CYS E 126 " --> pdb=" O THR E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 350 Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 387 through 390 Processing helix chain 'E' and resid 475 through 481 removed outlier: 3.667A pdb=" N TRP E 479 " --> pdb=" O MET E 475 " (cutoff:3.500A) Processing helix chain 'F' and resid 523 through 527 removed outlier: 4.535A pdb=" N GLY F 527 " --> pdb=" O GLY F 524 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 536 through 542 removed outlier: 3.710A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) Processing helix chain 'F' and resid 572 through 596 Processing helix chain 'F' and resid 619 through 624 Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 638 through 662 Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.111A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.662A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 91 through 94 removed outlier: 3.560A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 169 through 177 removed outlier: 3.772A pdb=" N LYS A 189 " --> pdb=" O CYS A 131 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 202 through 203 removed outlier: 6.505A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.060A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N GLY A 441 " --> pdb=" O ASN A 300 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N ASN A 300 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE A 443 " --> pdb=" O ARG A 298 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.600A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 12.009A pdb=" N ILE A 453 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 12.283A pdb=" N PHE A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 10.667A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 10.881A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 271 through 274 removed outlier: 10.881A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 10.667A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 12.283A pdb=" N PHE A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 12.009A pdb=" N ILE A 453 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 10.600A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE A 443 " --> pdb=" O ARG A 298 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N ASN A 300 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N GLY A 441 " --> pdb=" O ASN A 300 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 304 through 308 Processing sheet with id=AA9, first strand: chain 'C' and resid 494 through 499 removed outlier: 4.988A pdb=" N VAL D 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N VAL C 38 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N THR D 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N TYR C 40 " --> pdb=" O CYS D 604 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N CYS D 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.668A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 91 through 94 removed outlier: 3.563A pdb=" N GLU C 91 " --> pdb=" O CYS C 239 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 169 through 177 removed outlier: 3.785A pdb=" N LYS C 189 " --> pdb=" O CYS C 131 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 202 through 203 removed outlier: 6.459A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 259 through 261 removed outlier: 6.065A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N GLY C 441 " --> pdb=" O ASN C 300 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N ASN C 300 " --> pdb=" O GLY C 441 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE C 443 " --> pdb=" O ARG C 298 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N GLY C 451 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.646A pdb=" N THR C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 12.059A pdb=" N ILE C 453 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 12.330A pdb=" N PHE C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 10.696A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 10.892A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 271 through 274 removed outlier: 10.892A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 10.696A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 12.330A pdb=" N PHE C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 12.059A pdb=" N ILE C 453 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 10.646A pdb=" N THR C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N GLY C 451 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE C 443 " --> pdb=" O ARG C 298 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N ASN C 300 " --> pdb=" O GLY C 441 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N GLY C 441 " --> pdb=" O ASN C 300 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 304 through 308 Processing sheet with id=AB8, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.102A pdb=" N VAL F 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N VAL E 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N THR F 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N TYR E 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N CYS F 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 45 through 47 removed outlier: 4.203A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N VAL E 242 " --> pdb=" O LEU E 86 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 75 through 76 removed outlier: 3.556A pdb=" N VAL E 75 " --> pdb=" O CYS E 54 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 91 through 94 removed outlier: 3.537A pdb=" N GLU E 91 " --> pdb=" O CYS E 239 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 169 through 177 removed outlier: 3.620A pdb=" N LYS E 189 " --> pdb=" O CYS E 131 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 202 through 203 removed outlier: 6.854A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 259 through 261 removed outlier: 6.035A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N GLY E 441 " --> pdb=" O ASN E 300 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N ASN E 300 " --> pdb=" O GLY E 441 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE E 443 " --> pdb=" O ARG E 298 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N GLY E 451 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 10.460A pdb=" N THR E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 12.029A pdb=" N ILE E 453 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 12.206A pdb=" N PHE E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 10.720A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 10.857A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 271 through 274 removed outlier: 10.857A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 10.720A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 12.206A pdb=" N PHE E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 12.029A pdb=" N ILE E 453 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 10.460A pdb=" N THR E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N GLY E 451 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE E 443 " --> pdb=" O ARG E 298 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N ASN E 300 " --> pdb=" O GLY E 441 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N GLY E 441 " --> pdb=" O ASN E 300 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N ILE E 358 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N PHE E 468 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ARG E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 304 through 312 removed outlier: 6.578A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) 515 hydrogen bonds defined for protein. 1443 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: 2.44 Time building geometry restraints manager: 1.72 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: 4443 1.34 - 1.47: 3498 1.47 - 1.59: 6183 1.59 - 1.72: 0 1.72 - 1.84: 144 Bond restraints: 14268 Sorted by residual: bond pdb=" C1 NAG W 2 " pdb=" O5 NAG W 2 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.37e+00 bond pdb=" C MET E 434 " pdb=" N TYR E 435 " ideal model delta sigma weight residual 1.331 1.302 0.029 1.43e-02 4.89e+03 3.98e+00 bond pdb=" N CYS E 433 " pdb=" CA CYS E 433 " ideal model delta sigma weight residual 1.454 1.477 -0.023 1.15e-02 7.56e+03 3.96e+00 bond pdb=" C1 NAG E 602 " pdb=" O5 NAG E 602 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.92e+00 bond pdb=" C1 NAG S 2 " pdb=" O5 NAG S 2 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.84e+00 ... (remaining 14263 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 18679 1.62 - 3.25: 580 3.25 - 4.87: 52 4.87 - 6.49: 23 6.49 - 8.11: 7 Bond angle restraints: 19341 Sorted by residual: angle pdb=" C GLY E 431 " pdb=" N GLN E 432 " pdb=" CA GLN E 432 " ideal model delta sigma weight residual 122.95 117.26 5.69 1.44e+00 4.82e-01 1.56e+01 angle pdb=" N CYS E 433 " pdb=" CA CYS E 433 " pdb=" CB CYS E 433 " ideal model delta sigma weight residual 110.56 116.39 -5.83 1.56e+00 4.11e-01 1.40e+01 angle pdb=" N PRO E 240 " pdb=" CD PRO E 240 " pdb=" CG PRO E 240 " ideal model delta sigma weight residual 103.20 97.87 5.33 1.50e+00 4.44e-01 1.26e+01 angle pdb=" CA CYS E 433 " pdb=" CB CYS E 433 " pdb=" SG CYS E 433 " ideal model delta sigma weight residual 114.40 122.51 -8.11 2.30e+00 1.89e-01 1.24e+01 angle pdb=" N CYS E 201 " pdb=" CA CYS E 201 " pdb=" C CYS E 201 " ideal model delta sigma weight residual 108.99 114.42 -5.43 1.57e+00 4.06e-01 1.20e+01 ... (remaining 19336 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.50: 8777 21.50 - 43.01: 484 43.01 - 64.51: 70 64.51 - 86.02: 40 86.02 - 107.52: 13 Dihedral angle restraints: 9384 sinusoidal: 4581 harmonic: 4803 Sorted by residual: dihedral pdb=" CB CYS E 501 " pdb=" SG CYS E 501 " pdb=" SG CYS F 605 " pdb=" CB CYS F 605 " ideal model delta sinusoidal sigma weight residual -86.00 1.58 -87.58 1 1.00e+01 1.00e-02 9.19e+01 dihedral pdb=" CB CYS C 54 " pdb=" SG CYS C 54 " pdb=" SG CYS C 74 " pdb=" CB CYS C 74 " ideal model delta sinusoidal sigma weight residual -86.00 -6.32 -79.68 1 1.00e+01 1.00e-02 7.88e+01 dihedral pdb=" CB CYS A 54 " pdb=" SG CYS A 54 " pdb=" SG CYS A 74 " pdb=" CB CYS A 74 " ideal model delta sinusoidal sigma weight residual -86.00 -6.32 -79.68 1 1.00e+01 1.00e-02 7.88e+01 ... (remaining 9381 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1891 0.054 - 0.108: 389 0.108 - 0.162: 69 0.162 - 0.216: 6 0.216 - 0.271: 3 Chirality restraints: 2358 Sorted by residual: chirality pdb=" C5 BMA U 3 " pdb=" C4 BMA U 3 " pdb=" C6 BMA U 3 " pdb=" O5 BMA U 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" C5 BMA P 3 " pdb=" C4 BMA P 3 " pdb=" C6 BMA P 3 " pdb=" O5 BMA P 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" C5 BMA J 3 " pdb=" C4 BMA J 3 " pdb=" C6 BMA J 3 " pdb=" O5 BMA J 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.78e+00 ... (remaining 2355 not shown) Planarity restraints: 2418 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS C 239 " -0.061 5.00e-02 4.00e+02 9.09e-02 1.32e+01 pdb=" N PRO C 240 " 0.157 5.00e-02 4.00e+02 pdb=" CA PRO C 240 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO C 240 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS E 239 " -0.051 5.00e-02 4.00e+02 7.54e-02 9.08e+00 pdb=" N PRO E 240 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO E 240 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO E 240 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET E 434 " -0.009 2.00e-02 2.50e+03 1.92e-02 3.70e+00 pdb=" C MET E 434 " 0.033 2.00e-02 2.50e+03 pdb=" O MET E 434 " -0.012 2.00e-02 2.50e+03 pdb=" N TYR E 435 " -0.012 2.00e-02 2.50e+03 ... (remaining 2415 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 274 2.69 - 3.24: 12775 3.24 - 3.79: 21791 3.79 - 4.35: 30989 4.35 - 4.90: 50355 Nonbonded interactions: 116184 Sorted by model distance: nonbonded pdb=" OG SER B 528 " pdb=" O7 NAG A 601 " model vdw 2.132 3.040 nonbonded pdb=" O LEU A 369 " pdb=" OG1 THR A 373 " model vdw 2.141 3.040 nonbonded pdb=" O LEU C 369 " pdb=" OG1 THR C 373 " model vdw 2.149 3.040 nonbonded pdb=" OG SER D 528 " pdb=" O7 NAG C 601 " model vdw 2.156 3.040 nonbonded pdb=" O VAL A 36 " pdb=" OG1 THR B 606 " model vdw 2.159 3.040 ... (remaining 116179 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'V' selection = chain 'W' selection = chain 'X' } ncs_group { reference = chain 'J' selection = chain 'P' selection = chain 'U' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.010 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: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 13.380 Find NCS groups from input model: 0.230 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:6.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 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 0.053 14359 Z= 0.210 Angle : 0.701 17.764 19583 Z= 0.338 Chirality : 0.047 0.271 2358 Planarity : 0.004 0.091 2379 Dihedral : 13.945 107.521 6171 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % 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: -1.56 (0.20), residues: 1617 helix: -1.47 (0.23), residues: 420 sheet: -1.05 (0.24), residues: 435 loop : -0.55 (0.21), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 542 TYR 0.022 0.001 TYR E 318 PHE 0.010 0.001 PHE C 93 TRP 0.016 0.001 TRP E 479 HIS 0.003 0.001 HIS C 216 Details of bonding type rmsd covalent geometry : bond 0.00446 (14268) covalent geometry : angle 0.65724 (19341) SS BOND : bond 0.00908 ( 31) SS BOND : angle 2.99959 ( 62) hydrogen bonds : bond 0.24138 ( 494) hydrogen bonds : angle 8.70765 ( 1443) link_BETA1-4 : bond 0.00753 ( 21) link_BETA1-4 : angle 1.76145 ( 63) link_NAG-ASN : bond 0.00301 ( 39) link_NAG-ASN : angle 2.08020 ( 117) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3234 Ramachandran restraints generated. 1617 Oldfield, 0 Emsley, 1617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3234 Ramachandran restraints generated. 1617 Oldfield, 0 Emsley, 1617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 263 time to evaluate : 0.595 Fit side-chains revert: symmetry clash REVERT: A 208 VAL cc_start: 0.8190 (t) cc_final: 0.7972 (m) REVERT: E 475 MET cc_start: 0.8776 (tpp) cc_final: 0.8535 (tpp) outliers start: 0 outliers final: 1 residues processed: 263 average time/residue: 0.6627 time to fit residues: 188.3204 Evaluate side-chains 215 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 214 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 457 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.2980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 3.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 ASN A 82 GLN A 94 ASN A 137 ASN A 183 GLN A 246 GLN A 352 HIS A 355 ASN A 377 ASN B 543 ASN C 82 GLN C 137 ASN ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 640 GLN E 98 ASN E 136 ASN E 137 ASN E 188 ASN E 356 ASN F 543 ASN F 577 GLN F 616 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.134381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.105784 restraints weight = 16029.882| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 2.21 r_work: 0.3224 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.1485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 14359 Z= 0.211 Angle : 0.673 8.076 19583 Z= 0.340 Chirality : 0.047 0.217 2358 Planarity : 0.004 0.058 2379 Dihedral : 8.542 95.678 3017 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.97 % Allowed : 9.92 % Favored : 87.11 % 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: -0.88 (0.20), residues: 1617 helix: -0.19 (0.25), residues: 423 sheet: -0.94 (0.24), residues: 444 loop : -0.40 (0.22), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 585 TYR 0.019 0.002 TYR A 173 PHE 0.016 0.002 PHE E 383 TRP 0.012 0.001 TRP C 69 HIS 0.004 0.001 HIS C 352 Details of bonding type rmsd covalent geometry : bond 0.00500 (14268) covalent geometry : angle 0.64046 (19341) SS BOND : bond 0.00525 ( 31) SS BOND : angle 1.76355 ( 62) hydrogen bonds : bond 0.05421 ( 494) hydrogen bonds : angle 5.66813 ( 1443) link_BETA1-4 : bond 0.00514 ( 21) link_BETA1-4 : angle 1.81392 ( 63) link_NAG-ASN : bond 0.00386 ( 39) link_NAG-ASN : angle 2.14386 ( 117) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3234 Ramachandran restraints generated. 1617 Oldfield, 0 Emsley, 1617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3234 Ramachandran restraints generated. 1617 Oldfield, 0 Emsley, 1617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 203 time to evaluate : 0.516 Fit side-chains REVERT: A 164 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7082 (mm-30) REVERT: A 269 GLU cc_start: 0.8267 (pt0) cc_final: 0.7974 (mt-10) REVERT: A 327 ARG cc_start: 0.7751 (OUTLIER) cc_final: 0.7410 (mtp85) REVERT: A 335 LYS cc_start: 0.8344 (ttpp) cc_final: 0.8091 (ttpp) REVERT: A 358 ILE cc_start: 0.8137 (mt) cc_final: 0.7915 (mt) REVERT: B 543 ASN cc_start: 0.8685 (m-40) cc_final: 0.8455 (m110) REVERT: C 322 ASP cc_start: 0.8150 (OUTLIER) cc_final: 0.7913 (m-30) REVERT: D 634 GLU cc_start: 0.7804 (mt-10) cc_final: 0.7466 (mt-10) REVERT: E 46 LYS cc_start: 0.8520 (pttp) cc_final: 0.8075 (ptpp) REVERT: E 150 MET cc_start: 0.7840 (OUTLIER) cc_final: 0.7605 (tpp) REVERT: E 308 ARG cc_start: 0.8309 (mtt180) cc_final: 0.7845 (mtp180) REVERT: F 634 GLU cc_start: 0.7521 (mt-10) cc_final: 0.7280 (mt-10) outliers start: 44 outliers final: 17 residues processed: 227 average time/residue: 0.7217 time to fit residues: 177.0559 Evaluate side-chains 215 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 194 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain A residue 327 ARG Chi-restraints excluded: chain A residue 440 GLN Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 315 GLN Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain D residue 636 SER Chi-restraints excluded: chain D residue 653 GLN Chi-restraints excluded: chain E residue 150 MET Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 375 SER Chi-restraints excluded: chain E residue 425 ASN Chi-restraints excluded: chain F residue 636 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 95 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 68 optimal weight: 0.9990 chunk 163 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 156 optimal weight: 1.9990 chunk 2 optimal weight: 0.0010 chunk 74 optimal weight: 0.6980 chunk 114 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 overall best weight: 0.9190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN A 246 GLN A 293 GLN C 137 ASN C 183 GLN ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 GLN C 293 GLN C 348 GLN C 355 ASN C 377 ASN D 625 ASN E 137 ASN E 425 ASN F 543 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.150207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.123552 restraints weight = 15524.491| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 2.10 r_work: 0.3261 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14359 Z= 0.163 Angle : 0.601 7.972 19583 Z= 0.301 Chirality : 0.045 0.202 2358 Planarity : 0.004 0.045 2379 Dihedral : 6.784 51.982 3015 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.17 % Allowed : 12.21 % Favored : 84.62 % 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: -0.51 (0.20), residues: 1617 helix: 0.29 (0.26), residues: 423 sheet: -0.63 (0.25), residues: 414 loop : -0.37 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 585 TYR 0.018 0.001 TYR C 173 PHE 0.014 0.001 PHE A 383 TRP 0.013 0.001 TRP A 69 HIS 0.003 0.001 HIS C 352 Details of bonding type rmsd covalent geometry : bond 0.00381 (14268) covalent geometry : angle 0.56934 (19341) SS BOND : bond 0.00392 ( 31) SS BOND : angle 1.48377 ( 62) hydrogen bonds : bond 0.04685 ( 494) hydrogen bonds : angle 5.26564 ( 1443) link_BETA1-4 : bond 0.00513 ( 21) link_BETA1-4 : angle 1.69718 ( 63) link_NAG-ASN : bond 0.00322 ( 39) link_NAG-ASN : angle 2.02365 ( 117) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3234 Ramachandran restraints generated. 1617 Oldfield, 0 Emsley, 1617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3234 Ramachandran restraints generated. 1617 Oldfield, 0 Emsley, 1617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 199 time to evaluate : 0.563 Fit side-chains REVERT: A 153 GLU cc_start: 0.7159 (mm-30) cc_final: 0.6850 (tp30) REVERT: A 164 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7287 (mm-30) REVERT: A 208 VAL cc_start: 0.7838 (t) cc_final: 0.7546 (m) REVERT: A 269 GLU cc_start: 0.8265 (pt0) cc_final: 0.7944 (mt-10) REVERT: A 335 LYS cc_start: 0.8297 (ttpp) cc_final: 0.8043 (ttpp) REVERT: A 358 ILE cc_start: 0.8177 (mt) cc_final: 0.7960 (mt) REVERT: B 543 ASN cc_start: 0.8661 (m-40) cc_final: 0.8440 (m110) REVERT: C 308 ARG cc_start: 0.8188 (mtp180) cc_final: 0.7808 (mtp180) REVERT: C 322 ASP cc_start: 0.8160 (OUTLIER) cc_final: 0.7890 (m-30) REVERT: D 634 GLU cc_start: 0.7764 (mt-10) cc_final: 0.7383 (mt-10) REVERT: E 308 ARG cc_start: 0.8298 (mtt180) cc_final: 0.7811 (mtp180) outliers start: 47 outliers final: 18 residues processed: 228 average time/residue: 0.6076 time to fit residues: 151.1654 Evaluate side-chains 208 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 188 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 315 GLN Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain D residue 636 SER Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 322 ASP Chi-restraints excluded: chain E residue 425 ASN Chi-restraints excluded: chain E residue 501 CYS Chi-restraints excluded: chain F residue 636 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 46 optimal weight: 4.9990 chunk 119 optimal weight: 0.9980 chunk 127 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 54 optimal weight: 0.7980 chunk 147 optimal weight: 0.0770 chunk 163 optimal weight: 3.9990 chunk 1 optimal weight: 0.5980 chunk 53 optimal weight: 3.9990 chunk 123 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN C 98 ASN C 137 ASN C 183 GLN C 246 GLN C 355 ASN D 543 ASN E 195 ASN E 293 GLN E 425 ASN E 440 GLN F 543 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.153347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.129401 restraints weight = 15352.255| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 1.84 r_work: 0.3234 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14359 Z= 0.137 Angle : 0.566 7.250 19583 Z= 0.284 Chirality : 0.044 0.185 2358 Planarity : 0.003 0.039 2379 Dihedral : 5.862 51.511 3015 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.77 % Allowed : 14.17 % Favored : 83.06 % 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: -0.31 (0.21), residues: 1617 helix: 0.58 (0.27), residues: 423 sheet: -0.47 (0.25), residues: 408 loop : -0.38 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 585 TYR 0.021 0.001 TYR C 173 PHE 0.013 0.001 PHE E 383 TRP 0.011 0.001 TRP E 69 HIS 0.002 0.000 HIS C 352 Details of bonding type rmsd covalent geometry : bond 0.00315 (14268) covalent geometry : angle 0.53518 (19341) SS BOND : bond 0.00490 ( 31) SS BOND : angle 1.45288 ( 62) hydrogen bonds : bond 0.04077 ( 494) hydrogen bonds : angle 5.02680 ( 1443) link_BETA1-4 : bond 0.00493 ( 21) link_BETA1-4 : angle 1.61570 ( 63) link_NAG-ASN : bond 0.00279 ( 39) link_NAG-ASN : angle 1.92236 ( 117) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3234 Ramachandran restraints generated. 1617 Oldfield, 0 Emsley, 1617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3234 Ramachandran restraints generated. 1617 Oldfield, 0 Emsley, 1617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 199 time to evaluate : 0.407 Fit side-chains REVERT: A 153 GLU cc_start: 0.7318 (mm-30) cc_final: 0.7032 (tp30) REVERT: A 208 VAL cc_start: 0.7970 (t) cc_final: 0.7679 (m) REVERT: A 269 GLU cc_start: 0.8286 (pt0) cc_final: 0.7982 (mt-10) REVERT: A 348 GLN cc_start: 0.8145 (OUTLIER) cc_final: 0.6989 (mp10) REVERT: A 358 ILE cc_start: 0.8236 (mt) cc_final: 0.8033 (mt) REVERT: C 272 ILE cc_start: 0.9085 (OUTLIER) cc_final: 0.8800 (mp) REVERT: C 322 ASP cc_start: 0.8146 (OUTLIER) cc_final: 0.7894 (m-30) REVERT: D 634 GLU cc_start: 0.7899 (mt-10) cc_final: 0.7468 (mt-10) REVERT: E 166 ARG cc_start: 0.8257 (ttp-110) cc_final: 0.8040 (ttp80) REVERT: E 308 ARG cc_start: 0.8298 (mtt180) cc_final: 0.7852 (mtp180) REVERT: F 626 MET cc_start: 0.9114 (ttm) cc_final: 0.8765 (mtm) REVERT: F 634 GLU cc_start: 0.7835 (tt0) cc_final: 0.7442 (mt-10) REVERT: F 653 GLN cc_start: 0.7627 (mt0) cc_final: 0.7251 (tt0) outliers start: 41 outliers final: 19 residues processed: 224 average time/residue: 0.5914 time to fit residues: 144.4701 Evaluate side-chains 208 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 186 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain A residue 348 GLN Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 315 GLN Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain D residue 636 SER Chi-restraints excluded: chain D residue 661 LEU Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain E residue 322 ASP Chi-restraints excluded: chain E residue 425 ASN Chi-restraints excluded: chain E residue 501 CYS Chi-restraints excluded: chain F residue 636 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 112 optimal weight: 0.9990 chunk 52 optimal weight: 0.6980 chunk 69 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 159 optimal weight: 3.9990 chunk 137 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 148 optimal weight: 2.9990 chunk 157 optimal weight: 2.9990 chunk 125 optimal weight: 0.4980 chunk 23 optimal weight: 1.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN B 543 ASN C 137 ASN C 183 GLN C 195 ASN C 246 GLN C 355 ASN D 543 ASN F 543 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.151753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.127855 restraints weight = 15387.258| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 1.83 r_work: 0.3253 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14359 Z= 0.175 Angle : 0.595 7.750 19583 Z= 0.297 Chirality : 0.045 0.188 2358 Planarity : 0.003 0.034 2379 Dihedral : 5.608 51.779 3015 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.10 % Allowed : 15.11 % Favored : 81.78 % 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: -0.29 (0.21), residues: 1617 helix: 0.65 (0.27), residues: 423 sheet: -0.46 (0.25), residues: 408 loop : -0.39 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 476 TYR 0.019 0.002 TYR A 173 PHE 0.015 0.002 PHE E 383 TRP 0.011 0.001 TRP E 69 HIS 0.003 0.001 HIS C 352 Details of bonding type rmsd covalent geometry : bond 0.00412 (14268) covalent geometry : angle 0.56416 (19341) SS BOND : bond 0.00425 ( 31) SS BOND : angle 1.51083 ( 62) hydrogen bonds : bond 0.04191 ( 494) hydrogen bonds : angle 4.99476 ( 1443) link_BETA1-4 : bond 0.00486 ( 21) link_BETA1-4 : angle 1.62269 ( 63) link_NAG-ASN : bond 0.00354 ( 39) link_NAG-ASN : angle 2.00532 ( 117) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3234 Ramachandran restraints generated. 1617 Oldfield, 0 Emsley, 1617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3234 Ramachandran restraints generated. 1617 Oldfield, 0 Emsley, 1617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 194 time to evaluate : 0.396 Fit side-chains REVERT: A 164 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7418 (mm-30) REVERT: A 208 VAL cc_start: 0.8005 (t) cc_final: 0.7713 (m) REVERT: A 358 ILE cc_start: 0.8290 (mt) cc_final: 0.8081 (mt) REVERT: C 272 ILE cc_start: 0.9095 (OUTLIER) cc_final: 0.8798 (mp) REVERT: C 308 ARG cc_start: 0.8259 (mtp180) cc_final: 0.8048 (mtp180) REVERT: C 322 ASP cc_start: 0.8189 (OUTLIER) cc_final: 0.7958 (m-30) REVERT: D 634 GLU cc_start: 0.7939 (mt-10) cc_final: 0.7472 (mt-10) REVERT: E 269 GLU cc_start: 0.8443 (mt-10) cc_final: 0.7375 (mm-30) REVERT: E 308 ARG cc_start: 0.8287 (mtt180) cc_final: 0.7841 (mtp180) REVERT: F 626 MET cc_start: 0.9085 (ttm) cc_final: 0.8838 (mtm) REVERT: F 634 GLU cc_start: 0.7928 (tt0) cc_final: 0.7522 (mt-10) REVERT: F 653 GLN cc_start: 0.7642 (mt0) cc_final: 0.7271 (tt0) outliers start: 46 outliers final: 23 residues processed: 226 average time/residue: 0.6176 time to fit residues: 151.9948 Evaluate side-chains 216 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 190 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 315 GLN Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain D residue 636 SER Chi-restraints excluded: chain D residue 661 LEU Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 322 ASP Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain E residue 375 SER Chi-restraints excluded: chain E residue 425 ASN Chi-restraints excluded: chain E residue 501 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 103 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 164 optimal weight: 1.9990 chunk 140 optimal weight: 6.9990 chunk 40 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 112 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN A 348 GLN C 137 ASN C 183 GLN C 246 GLN C 348 GLN C 355 ASN D 543 ASN F 543 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.148710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.123996 restraints weight = 15316.634| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 1.89 r_work: 0.3217 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 14359 Z= 0.296 Angle : 0.731 9.234 19583 Z= 0.360 Chirality : 0.050 0.195 2358 Planarity : 0.004 0.037 2379 Dihedral : 6.254 57.605 3015 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.37 % Allowed : 15.65 % Favored : 80.97 % 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: -0.79 (0.20), residues: 1617 helix: 0.02 (0.25), residues: 459 sheet: -0.80 (0.24), residues: 423 loop : -0.53 (0.21), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 308 TYR 0.018 0.002 TYR A 173 PHE 0.017 0.002 PHE A 383 TRP 0.013 0.002 TRP D 623 HIS 0.004 0.001 HIS C 352 Details of bonding type rmsd covalent geometry : bond 0.00713 (14268) covalent geometry : angle 0.69409 (19341) SS BOND : bond 0.00624 ( 31) SS BOND : angle 2.02790 ( 62) hydrogen bonds : bond 0.04896 ( 494) hydrogen bonds : angle 5.28792 ( 1443) link_BETA1-4 : bond 0.00502 ( 21) link_BETA1-4 : angle 1.79800 ( 63) link_NAG-ASN : bond 0.00626 ( 39) link_NAG-ASN : angle 2.42022 ( 117) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3234 Ramachandran restraints generated. 1617 Oldfield, 0 Emsley, 1617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3234 Ramachandran restraints generated. 1617 Oldfield, 0 Emsley, 1617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 190 time to evaluate : 0.418 Fit side-chains REVERT: A 164 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.7527 (mm-30) REVERT: A 208 VAL cc_start: 0.7939 (t) cc_final: 0.7637 (m) REVERT: A 358 ILE cc_start: 0.8210 (mt) cc_final: 0.8008 (mt) REVERT: C 272 ILE cc_start: 0.9127 (OUTLIER) cc_final: 0.8822 (mp) REVERT: C 308 ARG cc_start: 0.8249 (mtp180) cc_final: 0.7992 (mtp180) REVERT: C 322 ASP cc_start: 0.8175 (OUTLIER) cc_final: 0.7937 (m-30) REVERT: D 530 MET cc_start: 0.9042 (mtp) cc_final: 0.8799 (mtm) REVERT: D 605 CYS cc_start: 0.9019 (OUTLIER) cc_final: 0.8697 (m) REVERT: D 634 GLU cc_start: 0.7898 (mt-10) cc_final: 0.7407 (mt-10) REVERT: E 91 GLU cc_start: 0.8639 (OUTLIER) cc_final: 0.7407 (tm-30) REVERT: E 114 GLN cc_start: 0.7542 (pt0) cc_final: 0.7065 (mp10) REVERT: E 269 GLU cc_start: 0.8457 (mt-10) cc_final: 0.7200 (mm-30) REVERT: E 308 ARG cc_start: 0.8308 (mtt180) cc_final: 0.7768 (mtp180) REVERT: E 444 ARG cc_start: 0.9025 (OUTLIER) cc_final: 0.8375 (mmm-85) REVERT: F 543 ASN cc_start: 0.8622 (m-40) cc_final: 0.8413 (m110) REVERT: F 626 MET cc_start: 0.9114 (ttm) cc_final: 0.8860 (mtm) REVERT: F 634 GLU cc_start: 0.7917 (tt0) cc_final: 0.7355 (mt-10) outliers start: 50 outliers final: 24 residues processed: 228 average time/residue: 0.5328 time to fit residues: 131.9256 Evaluate side-chains 205 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 175 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 315 GLN Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain D residue 605 CYS Chi-restraints excluded: chain D residue 636 SER Chi-restraints excluded: chain D residue 661 LEU Chi-restraints excluded: chain E residue 91 GLU Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 322 ASP Chi-restraints excluded: chain E residue 375 SER Chi-restraints excluded: chain E residue 425 ASN Chi-restraints excluded: chain E residue 444 ARG Chi-restraints excluded: chain E residue 501 CYS Chi-restraints excluded: chain F residue 636 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 123 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 83 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 126 optimal weight: 0.8980 chunk 44 optimal weight: 0.5980 chunk 70 optimal weight: 0.3980 chunk 82 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 183 GLN A 246 GLN C 137 ASN C 183 GLN C 246 GLN D 543 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.152656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.129221 restraints weight = 15314.376| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 1.80 r_work: 0.3147 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14359 Z= 0.140 Angle : 0.579 7.734 19583 Z= 0.289 Chirality : 0.044 0.160 2358 Planarity : 0.003 0.031 2379 Dihedral : 5.666 59.582 3015 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.36 % Allowed : 17.81 % Favored : 79.82 % 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: -0.48 (0.21), residues: 1617 helix: 0.50 (0.27), residues: 441 sheet: -0.69 (0.24), residues: 432 loop : -0.44 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 166 TYR 0.024 0.001 TYR A 173 PHE 0.014 0.001 PHE E 383 TRP 0.015 0.001 TRP E 69 HIS 0.002 0.001 HIS C 352 Details of bonding type rmsd covalent geometry : bond 0.00323 (14268) covalent geometry : angle 0.54637 (19341) SS BOND : bond 0.00470 ( 31) SS BOND : angle 1.54060 ( 62) hydrogen bonds : bond 0.03865 ( 494) hydrogen bonds : angle 4.97519 ( 1443) link_BETA1-4 : bond 0.00497 ( 21) link_BETA1-4 : angle 1.53694 ( 63) link_NAG-ASN : bond 0.00291 ( 39) link_NAG-ASN : angle 2.04158 ( 117) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3234 Ramachandran restraints generated. 1617 Oldfield, 0 Emsley, 1617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3234 Ramachandran restraints generated. 1617 Oldfield, 0 Emsley, 1617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 189 time to evaluate : 0.575 Fit side-chains REVERT: A 164 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7219 (mm-30) REVERT: A 208 VAL cc_start: 0.7963 (t) cc_final: 0.7679 (m) REVERT: C 272 ILE cc_start: 0.9083 (OUTLIER) cc_final: 0.8744 (mp) REVERT: C 322 ASP cc_start: 0.8111 (OUTLIER) cc_final: 0.7844 (m-30) REVERT: C 500 ARG cc_start: 0.8169 (mmm160) cc_final: 0.7906 (mmm-85) REVERT: D 530 MET cc_start: 0.9043 (mtp) cc_final: 0.8830 (mtm) REVERT: D 634 GLU cc_start: 0.7837 (mt-10) cc_final: 0.7608 (mt-10) REVERT: E 35 TRP cc_start: 0.8715 (m100) cc_final: 0.8513 (m100) REVERT: E 114 GLN cc_start: 0.7559 (pt0) cc_final: 0.7046 (mp10) REVERT: E 269 GLU cc_start: 0.8407 (mt-10) cc_final: 0.7304 (mm-30) REVERT: E 308 ARG cc_start: 0.8336 (mtt180) cc_final: 0.7886 (mtp180) REVERT: E 444 ARG cc_start: 0.8977 (OUTLIER) cc_final: 0.8295 (mmm-85) REVERT: F 575 GLN cc_start: 0.7167 (OUTLIER) cc_final: 0.6373 (mm-40) REVERT: F 590 GLN cc_start: 0.8900 (OUTLIER) cc_final: 0.7909 (mp10) REVERT: F 626 MET cc_start: 0.9138 (ttm) cc_final: 0.8858 (mtm) REVERT: F 634 GLU cc_start: 0.7928 (tt0) cc_final: 0.7428 (mt-10) outliers start: 35 outliers final: 20 residues processed: 216 average time/residue: 0.6225 time to fit residues: 146.2306 Evaluate side-chains 204 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 178 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain C residue 67 ASN Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 315 GLN Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 636 SER Chi-restraints excluded: chain D residue 661 LEU Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain E residue 375 SER Chi-restraints excluded: chain E residue 425 ASN Chi-restraints excluded: chain E residue 444 ARG Chi-restraints excluded: chain E residue 501 CYS Chi-restraints excluded: chain F residue 575 GLN Chi-restraints excluded: chain F residue 590 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 127 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 45 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN C 137 ASN C 183 GLN C 246 GLN D 543 ASN D 625 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.152351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.129053 restraints weight = 15244.159| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 1.79 r_work: 0.3122 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14359 Z= 0.155 Angle : 0.590 7.956 19583 Z= 0.294 Chirality : 0.045 0.158 2358 Planarity : 0.003 0.030 2379 Dihedral : 5.576 59.660 3015 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.56 % Allowed : 17.95 % Favored : 79.49 % 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: -0.44 (0.21), residues: 1617 helix: 0.58 (0.27), residues: 441 sheet: -0.74 (0.23), residues: 447 loop : -0.38 (0.22), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 327 TYR 0.022 0.002 TYR A 173 PHE 0.014 0.001 PHE E 383 TRP 0.013 0.001 TRP C 69 HIS 0.002 0.000 HIS C 352 Details of bonding type rmsd covalent geometry : bond 0.00364 (14268) covalent geometry : angle 0.55818 (19341) SS BOND : bond 0.00465 ( 31) SS BOND : angle 1.55368 ( 62) hydrogen bonds : bond 0.03908 ( 494) hydrogen bonds : angle 4.90874 ( 1443) link_BETA1-4 : bond 0.00475 ( 21) link_BETA1-4 : angle 1.56407 ( 63) link_NAG-ASN : bond 0.00337 ( 39) link_NAG-ASN : angle 2.03174 ( 117) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3234 Ramachandran restraints generated. 1617 Oldfield, 0 Emsley, 1617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3234 Ramachandran restraints generated. 1617 Oldfield, 0 Emsley, 1617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 187 time to evaluate : 0.383 Fit side-chains REVERT: A 208 VAL cc_start: 0.7940 (t) cc_final: 0.7680 (m) REVERT: C 272 ILE cc_start: 0.9069 (OUTLIER) cc_final: 0.8734 (mp) REVERT: C 322 ASP cc_start: 0.8104 (OUTLIER) cc_final: 0.7844 (m-30) REVERT: C 500 ARG cc_start: 0.8184 (mmm160) cc_final: 0.7934 (mmm-85) REVERT: D 530 MET cc_start: 0.9053 (mtp) cc_final: 0.8812 (mtm) REVERT: D 634 GLU cc_start: 0.7883 (mt-10) cc_final: 0.7452 (mt-10) REVERT: E 114 GLN cc_start: 0.7528 (pt0) cc_final: 0.7026 (mp10) REVERT: E 166 ARG cc_start: 0.8326 (OUTLIER) cc_final: 0.8122 (ttm110) REVERT: E 269 GLU cc_start: 0.8405 (mt-10) cc_final: 0.7329 (mm-30) REVERT: E 308 ARG cc_start: 0.8302 (mtt180) cc_final: 0.7849 (mtp180) REVERT: E 444 ARG cc_start: 0.9000 (OUTLIER) cc_final: 0.8314 (mmm-85) REVERT: F 575 GLN cc_start: 0.7145 (OUTLIER) cc_final: 0.6370 (mm-40) REVERT: F 626 MET cc_start: 0.9142 (ttm) cc_final: 0.8867 (mtm) REVERT: F 634 GLU cc_start: 0.7954 (tt0) cc_final: 0.7439 (mt-10) REVERT: F 651 ASN cc_start: 0.7379 (m110) cc_final: 0.7165 (m110) outliers start: 38 outliers final: 23 residues processed: 212 average time/residue: 0.5819 time to fit residues: 134.4177 Evaluate side-chains 207 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 179 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain C residue 67 ASN Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 315 GLN Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 636 SER Chi-restraints excluded: chain D residue 661 LEU Chi-restraints excluded: chain E residue 166 ARG Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain E residue 375 SER Chi-restraints excluded: chain E residue 425 ASN Chi-restraints excluded: chain E residue 444 ARG Chi-restraints excluded: chain E residue 501 CYS Chi-restraints excluded: chain F residue 575 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 51 optimal weight: 3.9990 chunk 128 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 162 optimal weight: 4.9990 chunk 141 optimal weight: 0.0870 chunk 73 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 42 optimal weight: 0.5980 chunk 67 optimal weight: 1.9990 chunk 13 optimal weight: 0.3980 chunk 15 optimal weight: 0.0670 overall best weight: 0.4296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN A 246 GLN C 183 GLN C 246 GLN D 543 ASN E 137 ASN E 425 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.155179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.132033 restraints weight = 15313.122| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 1.79 r_work: 0.3186 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14359 Z= 0.111 Angle : 0.539 7.244 19583 Z= 0.271 Chirality : 0.043 0.155 2358 Planarity : 0.003 0.030 2379 Dihedral : 5.273 59.148 3015 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.96 % Allowed : 18.69 % Favored : 79.35 % 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: -0.26 (0.21), residues: 1617 helix: 0.74 (0.27), residues: 441 sheet: -0.40 (0.25), residues: 402 loop : -0.47 (0.21), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 542 TYR 0.024 0.001 TYR A 173 PHE 0.013 0.001 PHE E 383 TRP 0.013 0.001 TRP E 69 HIS 0.002 0.000 HIS A 216 Details of bonding type rmsd covalent geometry : bond 0.00251 (14268) covalent geometry : angle 0.51118 (19341) SS BOND : bond 0.00406 ( 31) SS BOND : angle 1.35546 ( 62) hydrogen bonds : bond 0.03494 ( 494) hydrogen bonds : angle 4.72298 ( 1443) link_BETA1-4 : bond 0.00473 ( 21) link_BETA1-4 : angle 1.45841 ( 63) link_NAG-ASN : bond 0.00214 ( 39) link_NAG-ASN : angle 1.83226 ( 117) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3234 Ramachandran restraints generated. 1617 Oldfield, 0 Emsley, 1617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3234 Ramachandran restraints generated. 1617 Oldfield, 0 Emsley, 1617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 191 time to evaluate : 0.593 Fit side-chains REVERT: A 208 VAL cc_start: 0.7943 (t) cc_final: 0.7692 (m) REVERT: C 272 ILE cc_start: 0.9047 (OUTLIER) cc_final: 0.8709 (mp) REVERT: C 322 ASP cc_start: 0.8095 (OUTLIER) cc_final: 0.7826 (m-30) REVERT: C 500 ARG cc_start: 0.8176 (mmm160) cc_final: 0.7929 (mmm-85) REVERT: D 634 GLU cc_start: 0.7895 (mt-10) cc_final: 0.7486 (mt-10) REVERT: E 114 GLN cc_start: 0.7466 (pt0) cc_final: 0.6966 (mp10) REVERT: E 269 GLU cc_start: 0.8357 (mt-10) cc_final: 0.7319 (mm-30) REVERT: E 308 ARG cc_start: 0.8309 (mtt180) cc_final: 0.7855 (mtp180) REVERT: F 626 MET cc_start: 0.9142 (ttm) cc_final: 0.8853 (mtm) REVERT: F 634 GLU cc_start: 0.7901 (tt0) cc_final: 0.7396 (mt-10) REVERT: F 651 ASN cc_start: 0.7372 (m110) cc_final: 0.7135 (m110) REVERT: F 653 GLN cc_start: 0.7590 (mt0) cc_final: 0.7330 (tt0) outliers start: 29 outliers final: 17 residues processed: 209 average time/residue: 0.6234 time to fit residues: 141.4268 Evaluate side-chains 202 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 183 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain C residue 67 ASN Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 315 GLN Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 636 SER Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain E residue 375 SER Chi-restraints excluded: chain E residue 425 ASN Chi-restraints excluded: chain E residue 501 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 151 optimal weight: 0.9990 chunk 109 optimal weight: 0.9990 chunk 136 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 138 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 chunk 128 optimal weight: 1.9990 chunk 125 optimal weight: 0.6980 chunk 79 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN C 183 GLN C 246 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.151413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.128007 restraints weight = 15338.860| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 1.78 r_work: 0.3257 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 14359 Z= 0.209 Angle : 0.631 8.123 19583 Z= 0.314 Chirality : 0.046 0.166 2358 Planarity : 0.003 0.028 2379 Dihedral : 5.536 58.061 3015 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.89 % Allowed : 19.03 % Favored : 79.08 % 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: -0.40 (0.21), residues: 1617 helix: 0.56 (0.27), residues: 441 sheet: -0.61 (0.24), residues: 432 loop : -0.41 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 542 TYR 0.027 0.002 TYR C 191 PHE 0.016 0.002 PHE A 383 TRP 0.017 0.002 TRP A 35 HIS 0.002 0.001 HIS C 352 Details of bonding type rmsd covalent geometry : bond 0.00497 (14268) covalent geometry : angle 0.59952 (19341) SS BOND : bond 0.00538 ( 31) SS BOND : angle 1.72618 ( 62) hydrogen bonds : bond 0.04149 ( 494) hydrogen bonds : angle 4.89927 ( 1443) link_BETA1-4 : bond 0.00472 ( 21) link_BETA1-4 : angle 1.57534 ( 63) link_NAG-ASN : bond 0.00433 ( 39) link_NAG-ASN : angle 2.08543 ( 117) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3234 Ramachandran restraints generated. 1617 Oldfield, 0 Emsley, 1617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3234 Ramachandran restraints generated. 1617 Oldfield, 0 Emsley, 1617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 182 time to evaluate : 0.462 Fit side-chains REVERT: A 164 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.7463 (mm-30) REVERT: A 208 VAL cc_start: 0.8002 (t) cc_final: 0.7745 (m) REVERT: C 272 ILE cc_start: 0.9086 (OUTLIER) cc_final: 0.8745 (mp) REVERT: C 322 ASP cc_start: 0.8100 (OUTLIER) cc_final: 0.7861 (m-30) REVERT: C 500 ARG cc_start: 0.8250 (mmm160) cc_final: 0.7949 (mmm-85) REVERT: D 634 GLU cc_start: 0.7950 (mt-10) cc_final: 0.7556 (mt-10) REVERT: E 114 GLN cc_start: 0.7474 (pt0) cc_final: 0.7020 (mp10) REVERT: E 308 ARG cc_start: 0.8303 (mtt180) cc_final: 0.7833 (mtp180) REVERT: F 626 MET cc_start: 0.9112 (ttm) cc_final: 0.8859 (mtm) REVERT: F 634 GLU cc_start: 0.7987 (tt0) cc_final: 0.7437 (mt-10) outliers start: 28 outliers final: 20 residues processed: 200 average time/residue: 0.6233 time to fit residues: 135.2067 Evaluate side-chains 201 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 178 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain C residue 67 ASN Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 315 GLN Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 636 SER Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain E residue 375 SER Chi-restraints excluded: chain E residue 425 ASN Chi-restraints excluded: chain E residue 501 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 72 optimal weight: 1.9990 chunk 46 optimal weight: 0.3980 chunk 11 optimal weight: 0.4980 chunk 82 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 chunk 125 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 59 optimal weight: 0.9990 chunk 132 optimal weight: 1.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN C 137 ASN C 183 GLN C 195 ASN C 246 GLN E 425 ASN F 651 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.153563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.130322 restraints weight = 15352.677| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 1.80 r_work: 0.3285 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14359 Z= 0.138 Angle : 0.568 7.501 19583 Z= 0.284 Chirality : 0.044 0.153 2358 Planarity : 0.003 0.030 2379 Dihedral : 5.253 51.872 3015 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.96 % Allowed : 18.89 % Favored : 79.15 % 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: -0.30 (0.21), residues: 1617 helix: 0.68 (0.27), residues: 441 sheet: -0.40 (0.25), residues: 402 loop : -0.49 (0.21), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 542 TYR 0.024 0.001 TYR A 173 PHE 0.014 0.001 PHE E 383 TRP 0.016 0.001 TRP A 35 HIS 0.001 0.000 HIS A 216 Details of bonding type rmsd covalent geometry : bond 0.00321 (14268) covalent geometry : angle 0.53859 (19341) SS BOND : bond 0.00456 ( 31) SS BOND : angle 1.45744 ( 62) hydrogen bonds : bond 0.03715 ( 494) hydrogen bonds : angle 4.79772 ( 1443) link_BETA1-4 : bond 0.00472 ( 21) link_BETA1-4 : angle 1.47145 ( 63) link_NAG-ASN : bond 0.00282 ( 39) link_NAG-ASN : angle 1.94637 ( 117) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4598.59 seconds wall clock time: 79 minutes 11.55 seconds (4751.55 seconds total)