Starting phenix.real_space_refine on Thu Feb 5 10:30:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9o2r_70019/02_2026/9o2r_70019.cif Found real_map, /net/cci-nas-00/data/ceres_data/9o2r_70019/02_2026/9o2r_70019.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9o2r_70019/02_2026/9o2r_70019.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9o2r_70019/02_2026/9o2r_70019.map" model { file = "/net/cci-nas-00/data/ceres_data/9o2r_70019/02_2026/9o2r_70019.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9o2r_70019/02_2026/9o2r_70019.cif" } resolution = 3.0 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= 0.028 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 698 atoms to isotropic. 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 116 5.16 5 C 9962 2.51 5 N 2682 2.21 5 O 3142 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 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: 15902 Number of models: 1 Model: "" Number of chains: 32 Chain: "A" Number of atoms: 3403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3403 Classifications: {'peptide': 431} Link IDs: {'PTRANS': 20, 'TRANS': 410} Chain breaks: 6 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: "H" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 965 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 121} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'ARG:plan': 5, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "L" Number of atoms: 826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 826 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 100} Chain: "G" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 97 Unusual residues: {'BMA': 1, 'GAL': 1, 'MAN': 3, 'NAG': 3} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "I" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} 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: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 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: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 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: 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: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 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: "Z" 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: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 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: 3.85, per 1000 atoms: 0.24 Number of scatterers: 15902 At special positions: 0 Unit cell: (128.128, 123.136, 161.408, 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 116 16.00 O 3142 8.00 N 2682 7.00 C 9962 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=35, 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=2.03 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=2.04 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 445 " distance=2.04 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.02 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 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=2.02 Simple disulfide: pdb=" SG CYS C 201 " - pdb=" SG CYS C 433 " distance=2.02 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=2.02 Simple disulfide: pdb=" SG CYS E 201 " - pdb=" SG CYS E 433 " distance=2.04 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.05 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 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN G 7 " - " MAN G 8 " ALPHA1-3 " BMA G 3 " - " MAN G 7 " " BMA I 3 " - " MAN I 6 " " MAN I 4 " - " MAN I 5 " ALPHA1-6 " BMA G 3 " - " MAN G 4 " " BMA I 3 " - " MAN I 4 " BETA1-2 " MAN G 4 " - " NAG G 5 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG G 5 " - " GAL G 6 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " NAG-ASN " NAG A 601 " - " ASN A 88 " " NAG A 602 " - " ASN A 133 " " NAG A 603 " - " ASN A 234 " " NAG A 604 " - " ASN A 295 " " NAG A 605 " - " ASN A 332 " " NAG A 606 " - " ASN A 363 " " NAG A 607 " - " ASN A 448 " " 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 I 1 " - " ASN A 301 " " NAG J 1 " - " ASN A 160 " " NAG K 1 " - " ASN A 197 " " NAG M 1 " - " ASN A 262 " " NAG N 1 " - " ASN A 386 " " NAG O 1 " - " ASN C 156 " " NAG P 1 " - " ASN C 160 " " NAG Q 1 " - " ASN C 197 " " NAG R 1 " - " ASN C 262 " " NAG S 1 " - " ASN C 332 " " NAG T 1 " - " ASN C 448 " " NAG U 1 " - " ASN E 160 " " NAG V 1 " - " ASN E 197 " " NAG W 1 " - " ASN E 262 " " NAG X 1 " - " ASN E 332 " " NAG Y 1 " - " ASN E 363 " " NAG Z 1 " - " ASN E 448 " Time building additional restraints: 1.71 Conformation dependent library (CDL) restraints added in 448.0 milliseconds 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3538 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 25 sheets defined 22.2% alpha, 22.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'A' and resid 70 through 74 removed outlier: 3.759A pdb=" N ALA A 73 " --> pdb=" O ALA A 70 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N CYS A 74 " --> pdb=" O THR A 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 70 through 74' Processing helix chain 'A' and resid 98 through 115 removed outlier: 3.773A 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 149 through 152 removed outlier: 3.543A pdb=" N GLY A 152 " --> pdb=" O ASP A 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 149 through 152' 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 480 removed outlier: 3.742A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 527 removed outlier: 4.459A 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 542 removed outlier: 3.835A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (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 633 Processing helix chain 'B' and resid 638 through 661 removed outlier: 3.515A pdb=" N GLU B 647 " --> pdb=" O TYR B 643 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 116 removed outlier: 3.928A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU C 116 " --> pdb=" O TRP C 112 " (cutoff:3.500A) 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 351 through 353 No H-bonds generated for 'chain 'C' and resid 351 through 353' Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 475 through 481 removed outlier: 3.603A pdb=" N TRP C 479 " --> pdb=" O MET C 475 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER C 481 " --> pdb=" O ASP C 477 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 527 removed outlier: 4.385A 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: 4.002A pdb=" N GLN D 540 " --> pdb=" O THR D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 571 through 596 removed outlier: 3.576A pdb=" N ASP D 589 " --> pdb=" O ARG D 585 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 622 removed outlier: 3.569A pdb=" N ILE D 622 " --> pdb=" O LEU D 619 " (cutoff:3.500A) 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 114 removed outlier: 3.934A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 126 removed outlier: 3.601A pdb=" N CYS E 126 " --> pdb=" O THR E 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 123 through 126' 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: 3.665A pdb=" N TRP E 479 " --> pdb=" O MET E 475 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER E 481 " --> pdb=" O ASP E 477 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 536 through 542 removed outlier: 3.801A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) Processing helix chain 'F' and resid 572 through 596 removed outlier: 3.529A pdb=" N ARG F 579 " --> pdb=" O GLN F 575 " (cutoff:3.500A) 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 661 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 4.860A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.090A 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: 4.001A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 4.438A 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: 3.668A 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 Processing sheet with id=AA5, first strand: chain 'A' and resid 202 through 203 removed outlier: 6.834A 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 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 259 through 261 current: chain 'A' and resid 284 through 312 removed outlier: 6.139A pdb=" N GLY A 324 " --> pdb=" O PRO A 299 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ASN A 301 " --> pdb=" O ILE A 323 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N ILE A 323 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 315 through 325 current: chain 'A' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 381 through 385 current: chain 'A' and resid 465 through 470 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 465 through 470 current: chain 'H' and resid 100E through 100J Processing sheet with id=AA7, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.036A pdb=" N VAL D 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N VAL C 38 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N THR D 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N TYR C 40 " --> pdb=" O CYS D 604 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N CYS D 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.691A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 91 through 94 removed outlier: 3.603A pdb=" N GLU C 91 " --> pdb=" O CYS C 239 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 169 through 177 removed outlier: 3.752A pdb=" N LYS C 189 " --> pdb=" O CYS C 131 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 202 through 203 removed outlier: 6.579A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 259 through 261 current: chain 'C' and resid 284 through 302 removed outlier: 7.781A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 330 through 334 current: chain 'C' and resid 382 through 385 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 382 through 385 current: chain 'C' and resid 465 through 470 Processing sheet with id=AB4, first strand: chain 'C' and resid 304 through 308 Processing sheet with id=AB5, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.114A pdb=" N VAL F 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N VAL E 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N THR F 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N TYR E 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N CYS F 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 45 through 47 removed outlier: 4.119A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N VAL E 242 " --> pdb=" O LEU E 86 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 75 through 76 removed outlier: 3.684A pdb=" N VAL E 75 " --> pdb=" O CYS E 54 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AB9, first strand: chain 'E' and resid 121 through 122 removed outlier: 4.436A pdb=" N CYS E 201 " --> pdb=" O LEU E 122 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 169 through 177 removed outlier: 3.595A pdb=" N SER E 158 " --> pdb=" O GLN E 130 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS E 189 " --> pdb=" O CYS E 131 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 259 through 261 current: chain 'E' and resid 284 through 302 removed outlier: 7.748A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 330 through 334 current: chain 'E' and resid 382 through 385 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 382 through 385 current: chain 'E' and resid 465 through 470 Processing sheet with id=AC3, first strand: chain 'E' and resid 304 through 312 removed outlier: 6.629A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AC5, first strand: chain 'H' and resid 57 through 59 removed outlier: 5.712A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.719A pdb=" N SER L 72 " --> pdb=" O ALA L 65 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.587A pdb=" N VAL L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ARG L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N LEU L 46 " --> pdb=" O ARG L 37 " (cutoff:3.500A) 452 hydrogen bonds defined for protein. 1248 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: 2.61 Time building geometry restraints manager: 2.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 5006 1.34 - 1.47: 3977 1.47 - 1.59: 7064 1.59 - 1.72: 0 1.72 - 1.85: 156 Bond restraints: 16203 Sorted by residual: bond pdb=" CA SER H 32 " pdb=" CB SER H 32 " ideal model delta sigma weight residual 1.527 1.478 0.049 1.49e-02 4.50e+03 1.08e+01 bond pdb=" N ILE C 138 " pdb=" CA ILE C 138 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.12e-02 7.97e+03 8.45e+00 bond pdb=" N TYR L 94 " pdb=" CA TYR L 94 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.13e-02 7.83e+03 7.39e+00 bond pdb=" N ILE E 138 " pdb=" CA ILE E 138 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.21e-02 6.83e+03 6.94e+00 bond pdb=" N HIS H 59 " pdb=" CA HIS H 59 " ideal model delta sigma weight residual 1.454 1.488 -0.033 1.27e-02 6.20e+03 6.85e+00 ... (remaining 16198 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.48: 21551 2.48 - 4.96: 379 4.96 - 7.44: 30 7.44 - 9.93: 8 9.93 - 12.41: 4 Bond angle restraints: 21972 Sorted by residual: angle pdb=" CA CYS A 445 " pdb=" CB CYS A 445 " pdb=" SG CYS A 445 " ideal model delta sigma weight residual 114.40 126.81 -12.41 2.30e+00 1.89e-01 2.91e+01 angle pdb=" CA PHE H 100K" pdb=" CB PHE H 100K" pdb=" CG PHE H 100K" ideal model delta sigma weight residual 113.80 118.56 -4.76 1.00e+00 1.00e+00 2.26e+01 angle pdb=" N GLU E 153 " pdb=" CA GLU E 153 " pdb=" C GLU E 153 " ideal model delta sigma weight residual 114.04 108.15 5.89 1.24e+00 6.50e-01 2.26e+01 angle pdb=" CA CYS A 296 " pdb=" CB CYS A 296 " pdb=" SG CYS A 296 " ideal model delta sigma weight residual 114.40 124.40 -10.00 2.30e+00 1.89e-01 1.89e+01 angle pdb=" CA PHE H 100K" pdb=" C PHE H 100K" pdb=" O PHE H 100K" ideal model delta sigma weight residual 120.32 115.90 4.42 1.02e+00 9.61e-01 1.88e+01 ... (remaining 21967 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.64: 10017 22.64 - 45.28: 488 45.28 - 67.91: 85 67.91 - 90.55: 37 90.55 - 113.19: 20 Dihedral angle restraints: 10647 sinusoidal: 5188 harmonic: 5459 Sorted by residual: dihedral pdb=" CB CYS A 501 " pdb=" SG CYS A 501 " pdb=" SG CYS B 605 " pdb=" CB CYS B 605 " ideal model delta sinusoidal sigma weight residual -86.00 -4.13 -81.87 1 1.00e+01 1.00e-02 8.24e+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 93.00 11.52 81.48 1 1.00e+01 1.00e-02 8.18e+01 dihedral pdb=" CB CYS A 296 " pdb=" SG CYS A 296 " pdb=" SG CYS A 445 " pdb=" CB CYS A 445 " ideal model delta sinusoidal sigma weight residual -86.00 -5.66 -80.34 1 1.00e+01 1.00e-02 7.99e+01 ... (remaining 10644 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.165: 2645 0.165 - 0.330: 31 0.330 - 0.495: 4 0.495 - 0.659: 0 0.659 - 0.824: 2 Chirality restraints: 2682 Sorted by residual: chirality pdb=" C1 MAN G 4 " pdb=" O6 BMA G 3 " pdb=" C2 MAN G 4 " pdb=" O5 MAN G 4 " both_signs ideal model delta sigma weight residual False 2.40 1.72 0.68 2.00e-02 2.50e+03 1.16e+03 chirality pdb=" C1 BMA I 3 " pdb=" O4 NAG I 2 " pdb=" C2 BMA I 3 " pdb=" O5 BMA I 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.96 -0.44 2.00e-02 2.50e+03 4.73e+02 chirality pdb=" C1 MAN G 7 " pdb=" O3 BMA G 3 " pdb=" C2 MAN G 7 " pdb=" O5 MAN G 7 " both_signs ideal model delta sigma weight residual False 2.40 2.10 0.30 2.00e-02 2.50e+03 2.21e+02 ... (remaining 2679 not shown) Planarity restraints: 2735 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 602 " 0.234 2.00e-02 2.50e+03 1.96e-01 4.81e+02 pdb=" C7 NAG E 602 " -0.063 2.00e-02 2.50e+03 pdb=" C8 NAG E 602 " 0.163 2.00e-02 2.50e+03 pdb=" N2 NAG E 602 " -0.327 2.00e-02 2.50e+03 pdb=" O7 NAG E 602 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG I 1 " 0.138 2.00e-02 2.50e+03 1.14e-01 1.63e+02 pdb=" C7 NAG I 1 " -0.040 2.00e-02 2.50e+03 pdb=" C8 NAG I 1 " 0.103 2.00e-02 2.50e+03 pdb=" N2 NAG I 1 " -0.183 2.00e-02 2.50e+03 pdb=" O7 NAG I 1 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG G 2 " -0.106 2.00e-02 2.50e+03 8.76e-02 9.60e+01 pdb=" C7 NAG G 2 " 0.030 2.00e-02 2.50e+03 pdb=" C8 NAG G 2 " -0.080 2.00e-02 2.50e+03 pdb=" N2 NAG G 2 " 0.140 2.00e-02 2.50e+03 pdb=" O7 NAG G 2 " 0.015 2.00e-02 2.50e+03 ... (remaining 2732 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 235 2.65 - 3.21: 13980 3.21 - 3.78: 24056 3.78 - 4.34: 35597 4.34 - 4.90: 58016 Nonbonded interactions: 131884 Sorted by model distance: nonbonded pdb=" OG SER D 528 " pdb=" O7 NAG C 601 " model vdw 2.091 3.040 nonbonded pdb=" O LEU C 369 " pdb=" OG1 THR C 373 " model vdw 2.114 3.040 nonbonded pdb=" OG SER B 528 " pdb=" O7 NAG A 601 " model vdw 2.149 3.040 nonbonded pdb=" OG SER F 528 " pdb=" O7 NAG E 601 " model vdw 2.197 3.040 nonbonded pdb=" O VAL E 36 " pdb=" OG1 THR F 606 " model vdw 2.220 3.040 ... (remaining 131879 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 34 through 606) selection = (chain 'C' and (resid 34 through 137 or resid 148 through 606)) selection = (chain 'E' and (resid 34 through 137 or resid 148 through 606)) } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' } ncs_group { reference = chain 'R' selection = chain 'W' } 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: 3.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 15.230 Find NCS groups from input model: 0.370 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:6.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 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 : 0.006 0.049 16308 Z= 0.289 Angle : 0.827 13.833 22252 Z= 0.404 Chirality : 0.060 0.824 2682 Planarity : 0.006 0.196 2695 Dihedral : 14.303 113.191 7004 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 0.30 % Allowed : 0.60 % Favored : 99.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % 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: -1.55 (0.19), residues: 1843 helix: -1.36 (0.24), residues: 410 sheet: -0.66 (0.23), residues: 523 loop : -0.97 (0.20), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 444 TYR 0.023 0.001 TYR L 49 PHE 0.026 0.002 PHE H 100K TRP 0.015 0.001 TRP H 34 HIS 0.004 0.001 HIS A 330 Details of bonding type rmsd covalent geometry : bond 0.00600 (16203) covalent geometry : angle 0.75646 (21972) SS BOND : bond 0.00633 ( 35) SS BOND : angle 2.66115 ( 70) hydrogen bonds : bond 0.24022 ( 452) hydrogen bonds : angle 8.62646 ( 1248) link_ALPHA1-2 : bond 0.00643 ( 1) link_ALPHA1-2 : angle 3.40088 ( 3) link_ALPHA1-3 : bond 0.02101 ( 3) link_ALPHA1-3 : angle 6.53734 ( 9) link_ALPHA1-6 : bond 0.00379 ( 2) link_ALPHA1-6 : angle 3.58702 ( 6) link_BETA1-2 : bond 0.00202 ( 1) link_BETA1-2 : angle 3.52266 ( 3) link_BETA1-4 : bond 0.01250 ( 23) link_BETA1-4 : angle 3.27258 ( 69) link_NAG-ASN : bond 0.00710 ( 40) link_NAG-ASN : angle 2.68243 ( 120) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 287 time to evaluate : 0.623 Fit side-chains revert: symmetry clash REVERT: A 54 CYS cc_start: 0.6841 (t) cc_final: 0.6607 (t) REVERT: A 318 TYR cc_start: 0.8548 (m-80) cc_final: 0.8275 (m-80) REVERT: A 475 MET cc_start: 0.8265 (tpp) cc_final: 0.8046 (tpp) REVERT: B 621 GLU cc_start: 0.7781 (pt0) cc_final: 0.6891 (tm-30) REVERT: B 624 ASP cc_start: 0.7918 (m-30) cc_final: 0.7626 (m-30) REVERT: C 129 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8163 (mt) REVERT: C 211 GLU cc_start: 0.7615 (tt0) cc_final: 0.7358 (tt0) REVERT: D 584 GLU cc_start: 0.8225 (pt0) cc_final: 0.7885 (pt0) REVERT: E 308 ARG cc_start: 0.7756 (mtt-85) cc_final: 0.7167 (mtp-110) REVERT: E 347 LYS cc_start: 0.7764 (ttpt) cc_final: 0.7559 (ttmt) REVERT: F 632 ASP cc_start: 0.8493 (t0) cc_final: 0.8248 (t0) REVERT: H 5 GLN cc_start: 0.7015 (mt0) cc_final: 0.6610 (mt0) REVERT: H 69 MET cc_start: 0.6866 (mtm) cc_final: 0.6615 (mtm) outliers start: 5 outliers final: 1 residues processed: 289 average time/residue: 0.7080 time to fit residues: 223.3763 Evaluate side-chains 210 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 208 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain H residue 54 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 98 optimal weight: 0.3980 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.2980 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 3.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN A 103 GLN A 195 ASN A 328 GLN A 356 ASN A 411 ASN B 607 ASN C 94 ASN C 195 ASN D 625 ASN D 653 GLN E 103 GLN E 137 ASN E 356 ASN F 616 ASN H 57 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.149796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.116725 restraints weight = 18230.480| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 2.64 r_work: 0.3220 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.1329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16308 Z= 0.143 Angle : 0.656 15.605 22252 Z= 0.319 Chirality : 0.046 0.339 2682 Planarity : 0.004 0.053 2695 Dihedral : 9.261 81.515 3462 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.40 % Allowed : 9.05 % Favored : 88.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % 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: -0.97 (0.19), residues: 1843 helix: -0.12 (0.26), residues: 414 sheet: -0.67 (0.22), residues: 552 loop : -0.75 (0.21), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 585 TYR 0.014 0.001 TYR L 49 PHE 0.013 0.001 PHE A 233 TRP 0.018 0.001 TRP H 34 HIS 0.003 0.001 HIS E 216 Details of bonding type rmsd covalent geometry : bond 0.00326 (16203) covalent geometry : angle 0.60763 (21972) SS BOND : bond 0.00539 ( 35) SS BOND : angle 2.56350 ( 70) hydrogen bonds : bond 0.05095 ( 452) hydrogen bonds : angle 5.54347 ( 1248) link_ALPHA1-2 : bond 0.00018 ( 1) link_ALPHA1-2 : angle 1.71326 ( 3) link_ALPHA1-3 : bond 0.01090 ( 3) link_ALPHA1-3 : angle 4.59301 ( 9) link_ALPHA1-6 : bond 0.01077 ( 2) link_ALPHA1-6 : angle 1.79271 ( 6) link_BETA1-2 : bond 0.00332 ( 1) link_BETA1-2 : angle 2.08615 ( 3) link_BETA1-4 : bond 0.00632 ( 23) link_BETA1-4 : angle 2.14332 ( 69) link_NAG-ASN : bond 0.00304 ( 40) link_NAG-ASN : angle 1.92841 ( 120) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 214 time to evaluate : 0.602 Fit side-chains revert: symmetry clash REVERT: A 54 CYS cc_start: 0.7833 (t) cc_final: 0.7544 (t) REVERT: A 112 TRP cc_start: 0.8183 (t-100) cc_final: 0.7818 (t60) REVERT: A 150 MET cc_start: 0.7783 (tpt) cc_final: 0.7555 (ttp) REVERT: A 188 ASN cc_start: 0.6957 (p0) cc_final: 0.6662 (p0) REVERT: A 191 TYR cc_start: 0.9359 (m-80) cc_final: 0.9142 (m-80) REVERT: A 327 ARG cc_start: 0.8504 (mtm110) cc_final: 0.8227 (mtp85) REVERT: A 475 MET cc_start: 0.8360 (tpp) cc_final: 0.8094 (tpp) REVERT: B 621 GLU cc_start: 0.8211 (pt0) cc_final: 0.6943 (tm-30) REVERT: C 103 GLN cc_start: 0.7986 (OUTLIER) cc_final: 0.7366 (tt0) REVERT: C 136 ASN cc_start: 0.6829 (m110) cc_final: 0.5644 (p0) REVERT: C 211 GLU cc_start: 0.7931 (tt0) cc_final: 0.7663 (tt0) REVERT: C 315 GLN cc_start: 0.8185 (OUTLIER) cc_final: 0.7445 (mm110) REVERT: C 347 LYS cc_start: 0.7736 (tttm) cc_final: 0.7358 (ttpt) REVERT: D 651 ASN cc_start: 0.7693 (p0) cc_final: 0.7441 (p0) REVERT: D 655 LYS cc_start: 0.7136 (ttmm) cc_final: 0.6795 (ttpp) REVERT: E 57 ASP cc_start: 0.6906 (OUTLIER) cc_final: 0.6561 (m-30) REVERT: E 155 LYS cc_start: 0.8521 (OUTLIER) cc_final: 0.8271 (mtpt) REVERT: E 308 ARG cc_start: 0.8403 (mtt-85) cc_final: 0.7564 (mtp-110) REVERT: F 632 ASP cc_start: 0.8603 (t0) cc_final: 0.8397 (t0) REVERT: H 5 GLN cc_start: 0.6955 (mt0) cc_final: 0.6586 (mt0) REVERT: H 69 MET cc_start: 0.6958 (mtm) cc_final: 0.6635 (mtm) REVERT: H 100 GLU cc_start: 0.7212 (tt0) cc_final: 0.6805 (mm-30) outliers start: 40 outliers final: 10 residues processed: 236 average time/residue: 0.6940 time to fit residues: 178.7943 Evaluate side-chains 199 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 185 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain B residue 653 GLN Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 246 GLN Chi-restraints excluded: chain C residue 315 GLN Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 155 LYS Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain H residue 108 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 183 optimal weight: 20.0000 chunk 17 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 112 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 133 optimal weight: 3.9990 chunk 164 optimal weight: 7.9990 chunk 141 optimal weight: 0.4980 chunk 179 optimal weight: 7.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN A 411 ASN C 183 GLN D 652 GLN E 85 HIS ** E 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 543 ASN ** F 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.146199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.113064 restraints weight = 18438.015| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.64 r_work: 0.3146 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 16308 Z= 0.214 Angle : 0.675 10.444 22252 Z= 0.325 Chirality : 0.047 0.293 2682 Planarity : 0.004 0.050 2695 Dihedral : 8.408 91.110 3460 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.00 % Allowed : 12.16 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % 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: -0.94 (0.20), residues: 1843 helix: 0.03 (0.26), residues: 420 sheet: -0.73 (0.22), residues: 540 loop : -0.75 (0.21), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 542 TYR 0.017 0.002 TYR A 318 PHE 0.012 0.002 PHE C 383 TRP 0.016 0.001 TRP H 34 HIS 0.003 0.001 HIS H 53 Details of bonding type rmsd covalent geometry : bond 0.00517 (16203) covalent geometry : angle 0.63304 (21972) SS BOND : bond 0.00491 ( 35) SS BOND : angle 2.17832 ( 70) hydrogen bonds : bond 0.04578 ( 452) hydrogen bonds : angle 5.18512 ( 1248) link_ALPHA1-2 : bond 0.00100 ( 1) link_ALPHA1-2 : angle 1.96910 ( 3) link_ALPHA1-3 : bond 0.00988 ( 3) link_ALPHA1-3 : angle 4.29041 ( 9) link_ALPHA1-6 : bond 0.00777 ( 2) link_ALPHA1-6 : angle 1.44230 ( 6) link_BETA1-2 : bond 0.00051 ( 1) link_BETA1-2 : angle 2.14446 ( 3) link_BETA1-4 : bond 0.00560 ( 23) link_BETA1-4 : angle 2.05277 ( 69) link_NAG-ASN : bond 0.00422 ( 40) link_NAG-ASN : angle 2.08492 ( 120) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 193 time to evaluate : 0.594 Fit side-chains REVERT: A 91 GLU cc_start: 0.7874 (tp30) cc_final: 0.7583 (tp30) REVERT: A 112 TRP cc_start: 0.8423 (t-100) cc_final: 0.7910 (t60) REVERT: A 166 ARG cc_start: 0.8458 (OUTLIER) cc_final: 0.8181 (ttp-110) REVERT: A 327 ARG cc_start: 0.8539 (mtm110) cc_final: 0.8249 (mtp85) REVERT: A 475 MET cc_start: 0.8368 (tpp) cc_final: 0.8151 (tpp) REVERT: B 542 ARG cc_start: 0.7965 (OUTLIER) cc_final: 0.7347 (ptt-90) REVERT: C 103 GLN cc_start: 0.8035 (OUTLIER) cc_final: 0.7366 (tt0) REVERT: C 136 ASN cc_start: 0.7022 (m110) cc_final: 0.5948 (p0) REVERT: C 211 GLU cc_start: 0.8003 (tt0) cc_final: 0.7776 (tt0) REVERT: C 315 GLN cc_start: 0.8220 (OUTLIER) cc_final: 0.7414 (mm110) REVERT: D 655 LYS cc_start: 0.7182 (ttmm) cc_final: 0.6763 (ttpp) REVERT: D 661 LEU cc_start: 0.7916 (OUTLIER) cc_final: 0.7264 (mp) REVERT: E 308 ARG cc_start: 0.8423 (mtt-85) cc_final: 0.7618 (mtp-110) REVERT: F 632 ASP cc_start: 0.8717 (t0) cc_final: 0.8503 (t0) REVERT: H 5 GLN cc_start: 0.7004 (mt0) cc_final: 0.6536 (mt0) REVERT: H 69 MET cc_start: 0.6995 (mtm) cc_final: 0.6650 (mtm) REVERT: H 100 GLU cc_start: 0.7414 (tt0) cc_final: 0.6955 (mm-30) outliers start: 50 outliers final: 19 residues processed: 224 average time/residue: 0.6664 time to fit residues: 163.7949 Evaluate side-chains 202 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 178 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 166 ARG Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 432 GLN Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 464 THR Chi-restraints excluded: chain B residue 542 ARG Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 246 GLN Chi-restraints excluded: chain C residue 315 GLN Chi-restraints excluded: chain C residue 412 ASP Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain D residue 661 LEU Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 100 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 9 optimal weight: 0.8980 chunk 66 optimal weight: 0.0970 chunk 141 optimal weight: 0.5980 chunk 113 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 164 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 411 ASN C 67 ASN D 652 GLN ** E 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 377 ASN F 543 ASN F 630 GLN F 653 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.148727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.115692 restraints weight = 18234.525| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 2.63 r_work: 0.3206 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16308 Z= 0.134 Angle : 0.598 8.702 22252 Z= 0.287 Chirality : 0.045 0.263 2682 Planarity : 0.003 0.052 2695 Dihedral : 7.497 95.922 3460 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 3.36 % Allowed : 12.94 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % 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: -0.77 (0.20), residues: 1843 helix: 0.42 (0.27), residues: 417 sheet: -0.64 (0.22), residues: 548 loop : -0.78 (0.21), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 542 TYR 0.016 0.001 TYR A 191 PHE 0.010 0.001 PHE C 53 TRP 0.013 0.001 TRP E 69 HIS 0.003 0.001 HIS A 216 Details of bonding type rmsd covalent geometry : bond 0.00314 (16203) covalent geometry : angle 0.55922 (21972) SS BOND : bond 0.00439 ( 35) SS BOND : angle 1.69021 ( 70) hydrogen bonds : bond 0.03825 ( 452) hydrogen bonds : angle 4.90573 ( 1248) link_ALPHA1-2 : bond 0.00023 ( 1) link_ALPHA1-2 : angle 1.77183 ( 3) link_ALPHA1-3 : bond 0.01072 ( 3) link_ALPHA1-3 : angle 4.35766 ( 9) link_ALPHA1-6 : bond 0.00928 ( 2) link_ALPHA1-6 : angle 1.32361 ( 6) link_BETA1-2 : bond 0.00234 ( 1) link_BETA1-2 : angle 2.04299 ( 3) link_BETA1-4 : bond 0.00554 ( 23) link_BETA1-4 : angle 1.92946 ( 69) link_NAG-ASN : bond 0.00236 ( 40) link_NAG-ASN : angle 1.85662 ( 120) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 200 time to evaluate : 0.655 Fit side-chains REVERT: A 91 GLU cc_start: 0.7906 (tp30) cc_final: 0.7602 (tp30) REVERT: A 112 TRP cc_start: 0.8398 (t-100) cc_final: 0.7908 (t60) REVERT: A 327 ARG cc_start: 0.8503 (mtm110) cc_final: 0.8279 (mtp85) REVERT: B 542 ARG cc_start: 0.7883 (OUTLIER) cc_final: 0.7286 (ptt180) REVERT: B 655 LYS cc_start: 0.7684 (OUTLIER) cc_final: 0.7187 (ptpp) REVERT: C 136 ASN cc_start: 0.7174 (m110) cc_final: 0.6082 (p0) REVERT: C 211 GLU cc_start: 0.7989 (tt0) cc_final: 0.7745 (tt0) REVERT: C 246 GLN cc_start: 0.7699 (OUTLIER) cc_final: 0.7418 (mt0) REVERT: C 315 GLN cc_start: 0.8121 (OUTLIER) cc_final: 0.7439 (mm110) REVERT: C 347 LYS cc_start: 0.7727 (tttm) cc_final: 0.7344 (ttpt) REVERT: D 626 MET cc_start: 0.8909 (ttp) cc_final: 0.8654 (ttm) REVERT: D 655 LYS cc_start: 0.7165 (ttmm) cc_final: 0.6730 (ttpp) REVERT: E 153 GLU cc_start: 0.7530 (tp30) cc_final: 0.7329 (tp30) REVERT: E 155 LYS cc_start: 0.8735 (OUTLIER) cc_final: 0.7953 (mmpt) REVERT: E 308 ARG cc_start: 0.8350 (mtt-85) cc_final: 0.7578 (mtp-110) REVERT: F 632 ASP cc_start: 0.8630 (t0) cc_final: 0.8419 (t0) REVERT: H 5 GLN cc_start: 0.6960 (mt0) cc_final: 0.6587 (mt0) REVERT: H 69 MET cc_start: 0.6975 (mtm) cc_final: 0.6629 (mtm) REVERT: H 100 GLU cc_start: 0.7307 (tt0) cc_final: 0.6935 (mm-30) outliers start: 56 outliers final: 16 residues processed: 235 average time/residue: 0.6367 time to fit residues: 165.0449 Evaluate side-chains 205 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 184 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain B residue 542 ARG Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 653 GLN Chi-restraints excluded: chain B residue 655 LYS Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 246 GLN Chi-restraints excluded: chain C residue 315 GLN Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 155 LYS Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 433 CYS Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain H residue 78 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 121 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 55 optimal weight: 0.1980 chunk 80 optimal weight: 2.9990 chunk 148 optimal weight: 0.7980 chunk 166 optimal weight: 3.9990 chunk 174 optimal weight: 3.9990 chunk 162 optimal weight: 0.8980 chunk 52 optimal weight: 4.9990 chunk 168 optimal weight: 0.9990 chunk 144 optimal weight: 2.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 411 ASN C 67 ASN ** E 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 195 ASN F 543 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.149571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.116037 restraints weight = 18274.198| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 2.69 r_work: 0.3165 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 16308 Z= 0.158 Angle : 0.608 7.964 22252 Z= 0.292 Chirality : 0.045 0.248 2682 Planarity : 0.003 0.050 2695 Dihedral : 6.814 70.279 3458 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.71 % Allowed : 13.72 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % 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: -0.73 (0.20), residues: 1843 helix: 0.51 (0.27), residues: 415 sheet: -0.67 (0.22), residues: 552 loop : -0.75 (0.21), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 542 TYR 0.012 0.001 TYR L 49 PHE 0.011 0.001 PHE H 100 TRP 0.013 0.001 TRP H 34 HIS 0.003 0.001 HIS A 216 Details of bonding type rmsd covalent geometry : bond 0.00378 (16203) covalent geometry : angle 0.56981 (21972) SS BOND : bond 0.00381 ( 35) SS BOND : angle 1.75613 ( 70) hydrogen bonds : bond 0.03759 ( 452) hydrogen bonds : angle 4.78562 ( 1248) link_ALPHA1-2 : bond 0.00074 ( 1) link_ALPHA1-2 : angle 1.82031 ( 3) link_ALPHA1-3 : bond 0.01063 ( 3) link_ALPHA1-3 : angle 4.25951 ( 9) link_ALPHA1-6 : bond 0.00875 ( 2) link_ALPHA1-6 : angle 1.24722 ( 6) link_BETA1-2 : bond 0.00161 ( 1) link_BETA1-2 : angle 2.04985 ( 3) link_BETA1-4 : bond 0.00539 ( 23) link_BETA1-4 : angle 1.90426 ( 69) link_NAG-ASN : bond 0.00299 ( 40) link_NAG-ASN : angle 1.91823 ( 120) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 186 time to evaluate : 0.477 Fit side-chains REVERT: A 91 GLU cc_start: 0.7898 (tp30) cc_final: 0.7563 (tp30) REVERT: A 112 TRP cc_start: 0.8400 (t-100) cc_final: 0.7868 (t60) REVERT: A 166 ARG cc_start: 0.8341 (ttp80) cc_final: 0.8102 (ttp-110) REVERT: A 304 ARG cc_start: 0.8565 (ttm170) cc_final: 0.8364 (ttm170) REVERT: A 327 ARG cc_start: 0.8511 (mtm110) cc_final: 0.8307 (mtp85) REVERT: A 355 ASN cc_start: 0.7235 (m-40) cc_final: 0.7035 (m110) REVERT: B 542 ARG cc_start: 0.7848 (OUTLIER) cc_final: 0.7256 (ptt-90) REVERT: B 655 LYS cc_start: 0.7639 (OUTLIER) cc_final: 0.7127 (ptpp) REVERT: C 136 ASN cc_start: 0.7174 (m110) cc_final: 0.6137 (p0) REVERT: C 211 GLU cc_start: 0.8089 (tt0) cc_final: 0.7856 (tt0) REVERT: C 315 GLN cc_start: 0.8090 (OUTLIER) cc_final: 0.7440 (mm110) REVERT: C 347 LYS cc_start: 0.7719 (tttm) cc_final: 0.7311 (ttpt) REVERT: D 655 LYS cc_start: 0.7118 (OUTLIER) cc_final: 0.6684 (ttpp) REVERT: E 87 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.7732 (mp0) REVERT: E 155 LYS cc_start: 0.8714 (OUTLIER) cc_final: 0.7966 (mmpt) REVERT: E 164 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.7486 (pt0) REVERT: E 232 LYS cc_start: 0.8416 (ptpt) cc_final: 0.7471 (tptt) REVERT: H 5 GLN cc_start: 0.6937 (mt0) cc_final: 0.6570 (mt0) REVERT: H 48 ILE cc_start: 0.8405 (OUTLIER) cc_final: 0.7942 (mp) REVERT: H 69 MET cc_start: 0.6988 (mtm) cc_final: 0.6661 (mtm) REVERT: H 100 GLU cc_start: 0.7328 (tt0) cc_final: 0.6961 (mm-30) outliers start: 62 outliers final: 24 residues processed: 225 average time/residue: 0.6444 time to fit residues: 159.4844 Evaluate side-chains 208 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 176 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 464 THR Chi-restraints excluded: chain B residue 542 ARG Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 655 LYS Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 207 LYS Chi-restraints excluded: chain C residue 315 GLN Chi-restraints excluded: chain C residue 412 ASP Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain D residue 655 LYS Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 87 GLU Chi-restraints excluded: chain E residue 155 LYS Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 433 CYS Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 108 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 6 optimal weight: 3.9990 chunk 185 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 160 optimal weight: 7.9990 chunk 108 optimal weight: 0.5980 chunk 130 optimal weight: 0.6980 chunk 19 optimal weight: 0.0570 chunk 37 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 156 optimal weight: 1.9990 overall best weight: 1.0702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 411 ASN C 246 GLN C 377 ASN ** E 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 543 ASN H 57 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.149182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.115863 restraints weight = 18189.868| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 2.68 r_work: 0.3161 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16308 Z= 0.168 Angle : 0.622 7.809 22252 Z= 0.299 Chirality : 0.045 0.243 2682 Planarity : 0.003 0.051 2695 Dihedral : 6.629 68.873 3458 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 3.83 % Allowed : 13.90 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % 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: -0.74 (0.20), residues: 1843 helix: 0.24 (0.26), residues: 439 sheet: -0.54 (0.23), residues: 529 loop : -0.72 (0.21), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 542 TYR 0.012 0.001 TYR L 49 PHE 0.012 0.001 PHE C 53 TRP 0.013 0.001 TRP H 34 HIS 0.003 0.001 HIS A 216 Details of bonding type rmsd covalent geometry : bond 0.00404 (16203) covalent geometry : angle 0.58345 (21972) SS BOND : bond 0.00469 ( 35) SS BOND : angle 1.93742 ( 70) hydrogen bonds : bond 0.03695 ( 452) hydrogen bonds : angle 4.72069 ( 1248) link_ALPHA1-2 : bond 0.00106 ( 1) link_ALPHA1-2 : angle 1.82066 ( 3) link_ALPHA1-3 : bond 0.01127 ( 3) link_ALPHA1-3 : angle 4.05370 ( 9) link_ALPHA1-6 : bond 0.00857 ( 2) link_ALPHA1-6 : angle 1.19100 ( 6) link_BETA1-2 : bond 0.00164 ( 1) link_BETA1-2 : angle 2.01792 ( 3) link_BETA1-4 : bond 0.00542 ( 23) link_BETA1-4 : angle 1.87057 ( 69) link_NAG-ASN : bond 0.00314 ( 40) link_NAG-ASN : angle 1.94759 ( 120) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 180 time to evaluate : 0.450 Fit side-chains REVERT: A 91 GLU cc_start: 0.7911 (tp30) cc_final: 0.7619 (tp30) REVERT: A 112 TRP cc_start: 0.8382 (t-100) cc_final: 0.7892 (t60) REVERT: A 166 ARG cc_start: 0.8385 (ttp80) cc_final: 0.8140 (ttp-110) REVERT: B 542 ARG cc_start: 0.7866 (OUTLIER) cc_final: 0.7263 (ptt-90) REVERT: B 655 LYS cc_start: 0.7639 (OUTLIER) cc_final: 0.7105 (ptpp) REVERT: C 136 ASN cc_start: 0.7253 (m110) cc_final: 0.6161 (p0) REVERT: C 211 GLU cc_start: 0.8093 (tt0) cc_final: 0.7836 (tt0) REVERT: C 315 GLN cc_start: 0.8140 (OUTLIER) cc_final: 0.7549 (mm110) REVERT: C 347 LYS cc_start: 0.7717 (tttm) cc_final: 0.7298 (ttpt) REVERT: D 542 ARG cc_start: 0.7894 (ptt-90) cc_final: 0.7281 (mtp180) REVERT: D 655 LYS cc_start: 0.7113 (OUTLIER) cc_final: 0.6705 (ttpp) REVERT: E 69 TRP cc_start: 0.8065 (OUTLIER) cc_final: 0.6226 (m100) REVERT: E 87 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7719 (mp0) REVERT: E 155 LYS cc_start: 0.8718 (OUTLIER) cc_final: 0.7971 (mmpt) REVERT: E 164 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7492 (pt0) REVERT: E 232 LYS cc_start: 0.8377 (ptpt) cc_final: 0.7438 (tptt) REVERT: E 444 ARG cc_start: 0.8592 (OUTLIER) cc_final: 0.7873 (tmm-80) REVERT: F 575 GLN cc_start: 0.7776 (OUTLIER) cc_final: 0.7343 (tp40) REVERT: H 5 GLN cc_start: 0.6908 (mt0) cc_final: 0.6517 (mt0) REVERT: H 48 ILE cc_start: 0.8409 (OUTLIER) cc_final: 0.7918 (mp) REVERT: H 69 MET cc_start: 0.6940 (mtm) cc_final: 0.6652 (mtm) REVERT: H 100 GLU cc_start: 0.7309 (tt0) cc_final: 0.6926 (mm-30) outliers start: 64 outliers final: 25 residues processed: 225 average time/residue: 0.5682 time to fit residues: 141.0981 Evaluate side-chains 209 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 173 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 464 THR Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain B residue 542 ARG Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 653 GLN Chi-restraints excluded: chain B residue 655 LYS Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 315 GLN Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain D residue 655 LYS Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 87 GLU Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 155 LYS Chi-restraints excluded: chain E residue 161 MET Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain E residue 433 CYS Chi-restraints excluded: chain E residue 444 ARG Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain F residue 575 GLN Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 108 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 101 optimal weight: 3.9990 chunk 56 optimal weight: 0.7980 chunk 100 optimal weight: 0.7980 chunk 147 optimal weight: 0.9980 chunk 121 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 chunk 177 optimal weight: 0.2980 chunk 94 optimal weight: 3.9990 chunk 44 optimal weight: 0.6980 chunk 112 optimal weight: 0.8980 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 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 355 ASN A 411 ASN C 195 ASN ** E 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 543 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.147433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.114175 restraints weight = 18025.548| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 2.74 r_work: 0.3102 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16308 Z= 0.133 Angle : 0.594 9.347 22252 Z= 0.286 Chirality : 0.044 0.236 2682 Planarity : 0.003 0.050 2695 Dihedral : 6.353 65.679 3458 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 3.00 % Allowed : 15.22 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % 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: -0.65 (0.20), residues: 1843 helix: 0.33 (0.26), residues: 439 sheet: -0.46 (0.23), residues: 533 loop : -0.69 (0.21), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 542 TYR 0.012 0.001 TYR L 49 PHE 0.010 0.001 PHE H 100 TRP 0.012 0.001 TRP E 69 HIS 0.003 0.000 HIS A 216 Details of bonding type rmsd covalent geometry : bond 0.00315 (16203) covalent geometry : angle 0.55634 (21972) SS BOND : bond 0.00619 ( 35) SS BOND : angle 1.92551 ( 70) hydrogen bonds : bond 0.03462 ( 452) hydrogen bonds : angle 4.59964 ( 1248) link_ALPHA1-2 : bond 0.00036 ( 1) link_ALPHA1-2 : angle 1.78060 ( 3) link_ALPHA1-3 : bond 0.01228 ( 3) link_ALPHA1-3 : angle 3.78809 ( 9) link_ALPHA1-6 : bond 0.00890 ( 2) link_ALPHA1-6 : angle 1.12663 ( 6) link_BETA1-2 : bond 0.00217 ( 1) link_BETA1-2 : angle 2.00006 ( 3) link_BETA1-4 : bond 0.00540 ( 23) link_BETA1-4 : angle 1.80234 ( 69) link_NAG-ASN : bond 0.00228 ( 40) link_NAG-ASN : angle 1.87318 ( 120) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 185 time to evaluate : 0.622 Fit side-chains REVERT: A 91 GLU cc_start: 0.7772 (tp30) cc_final: 0.7429 (tp30) REVERT: A 112 TRP cc_start: 0.8317 (t-100) cc_final: 0.7814 (t60) REVERT: A 166 ARG cc_start: 0.8320 (OUTLIER) cc_final: 0.8059 (ttp-110) REVERT: B 655 LYS cc_start: 0.7483 (OUTLIER) cc_final: 0.6946 (ptpp) REVERT: C 136 ASN cc_start: 0.7248 (m110) cc_final: 0.6166 (p0) REVERT: C 211 GLU cc_start: 0.8055 (tt0) cc_final: 0.7820 (tt0) REVERT: C 315 GLN cc_start: 0.7934 (OUTLIER) cc_final: 0.7407 (mm110) REVERT: C 347 LYS cc_start: 0.7629 (tttm) cc_final: 0.7231 (ttpt) REVERT: C 499 THR cc_start: 0.8133 (m) cc_final: 0.7632 (p) REVERT: D 655 LYS cc_start: 0.6972 (OUTLIER) cc_final: 0.6588 (ttpp) REVERT: E 69 TRP cc_start: 0.8010 (OUTLIER) cc_final: 0.6048 (m100) REVERT: E 87 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7635 (mp0) REVERT: E 155 LYS cc_start: 0.8641 (OUTLIER) cc_final: 0.7873 (mmpt) REVERT: E 164 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7438 (pt0) REVERT: E 232 LYS cc_start: 0.8282 (ptpt) cc_final: 0.7326 (tptt) REVERT: E 444 ARG cc_start: 0.8549 (OUTLIER) cc_final: 0.7639 (tmm-80) REVERT: F 575 GLN cc_start: 0.7669 (OUTLIER) cc_final: 0.7212 (tp40) REVERT: F 658 GLN cc_start: 0.8057 (OUTLIER) cc_final: 0.7086 (tt0) REVERT: H 5 GLN cc_start: 0.6845 (mt0) cc_final: 0.6511 (mt0) REVERT: H 48 ILE cc_start: 0.8303 (OUTLIER) cc_final: 0.7823 (mp) REVERT: H 69 MET cc_start: 0.6906 (mtm) cc_final: 0.6627 (mtm) outliers start: 50 outliers final: 23 residues processed: 218 average time/residue: 0.6205 time to fit residues: 149.4018 Evaluate side-chains 213 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 178 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 166 ARG Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 464 THR Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 655 LYS Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 315 GLN Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain D residue 655 LYS Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 87 GLU Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 155 LYS Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain E residue 433 CYS Chi-restraints excluded: chain E residue 444 ARG Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain F residue 575 GLN Chi-restraints excluded: chain F residue 658 GLN Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain H residue 102 MET Chi-restraints excluded: chain H residue 108 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 88 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 151 optimal weight: 0.7980 chunk 81 optimal weight: 5.9990 chunk 72 optimal weight: 0.9980 chunk 153 optimal weight: 0.5980 chunk 135 optimal weight: 1.9990 chunk 96 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 300 ASN A 411 ASN C 195 ASN C 246 GLN ** E 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 543 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.147092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.113669 restraints weight = 18125.207| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 2.75 r_work: 0.3095 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16308 Z= 0.146 Angle : 0.602 7.771 22252 Z= 0.290 Chirality : 0.044 0.233 2682 Planarity : 0.003 0.051 2695 Dihedral : 6.235 63.900 3458 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.36 % Allowed : 15.46 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % 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: -0.61 (0.20), residues: 1843 helix: 0.64 (0.27), residues: 415 sheet: -0.58 (0.22), residues: 548 loop : -0.69 (0.21), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 542 TYR 0.012 0.001 TYR L 49 PHE 0.010 0.001 PHE C 53 TRP 0.012 0.001 TRP H 34 HIS 0.003 0.000 HIS A 216 Details of bonding type rmsd covalent geometry : bond 0.00349 (16203) covalent geometry : angle 0.56416 (21972) SS BOND : bond 0.00403 ( 35) SS BOND : angle 1.78882 ( 70) hydrogen bonds : bond 0.03456 ( 452) hydrogen bonds : angle 4.57658 ( 1248) link_ALPHA1-2 : bond 0.00058 ( 1) link_ALPHA1-2 : angle 1.82227 ( 3) link_ALPHA1-3 : bond 0.01219 ( 3) link_ALPHA1-3 : angle 3.53883 ( 9) link_ALPHA1-6 : bond 0.00871 ( 2) link_ALPHA1-6 : angle 1.17323 ( 6) link_BETA1-2 : bond 0.00191 ( 1) link_BETA1-2 : angle 1.98919 ( 3) link_BETA1-4 : bond 0.00532 ( 23) link_BETA1-4 : angle 1.78509 ( 69) link_NAG-ASN : bond 0.00276 ( 40) link_NAG-ASN : angle 2.03675 ( 120) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 190 time to evaluate : 0.575 Fit side-chains REVERT: A 91 GLU cc_start: 0.7776 (tp30) cc_final: 0.7503 (tp30) REVERT: A 112 TRP cc_start: 0.8333 (t-100) cc_final: 0.7791 (t60) REVERT: A 114 GLN cc_start: 0.7422 (tt0) cc_final: 0.7144 (tt0) REVERT: A 166 ARG cc_start: 0.8331 (OUTLIER) cc_final: 0.8065 (ttp-110) REVERT: B 542 ARG cc_start: 0.7732 (OUTLIER) cc_final: 0.7128 (ptt-90) REVERT: C 136 ASN cc_start: 0.7269 (m110) cc_final: 0.6186 (p0) REVERT: C 211 GLU cc_start: 0.8057 (tt0) cc_final: 0.7822 (tt0) REVERT: C 347 LYS cc_start: 0.7631 (tttm) cc_final: 0.7238 (ttpt) REVERT: D 530 MET cc_start: 0.8487 (mtt) cc_final: 0.7892 (mtt) REVERT: D 655 LYS cc_start: 0.6958 (OUTLIER) cc_final: 0.6514 (ttpp) REVERT: E 155 LYS cc_start: 0.8617 (OUTLIER) cc_final: 0.7858 (mmpt) REVERT: E 164 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.7579 (pt0) REVERT: E 232 LYS cc_start: 0.8268 (ptpt) cc_final: 0.7316 (tptt) REVERT: E 308 ARG cc_start: 0.8284 (mtt-85) cc_final: 0.7455 (mtp-110) REVERT: E 444 ARG cc_start: 0.8558 (OUTLIER) cc_final: 0.7637 (tmm-80) REVERT: F 575 GLN cc_start: 0.7709 (OUTLIER) cc_final: 0.7265 (tp40) REVERT: F 658 GLN cc_start: 0.8061 (OUTLIER) cc_final: 0.7099 (tt0) REVERT: H 5 GLN cc_start: 0.6940 (mt0) cc_final: 0.6642 (mt0) REVERT: H 48 ILE cc_start: 0.8359 (OUTLIER) cc_final: 0.7854 (mp) REVERT: H 69 MET cc_start: 0.6900 (mtm) cc_final: 0.6610 (mtm) outliers start: 56 outliers final: 24 residues processed: 227 average time/residue: 0.6330 time to fit residues: 158.2348 Evaluate side-chains 218 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 185 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 166 ARG Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 464 THR Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain B residue 542 ARG Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain D residue 655 LYS Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 155 LYS Chi-restraints excluded: chain E residue 161 MET Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 433 CYS Chi-restraints excluded: chain E residue 444 ARG Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain F residue 575 GLN Chi-restraints excluded: chain F residue 658 GLN Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain H residue 108 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 21 optimal weight: 0.9990 chunk 176 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 chunk 82 optimal weight: 0.9980 chunk 131 optimal weight: 0.0000 chunk 89 optimal weight: 0.6980 chunk 144 optimal weight: 0.8980 chunk 136 optimal weight: 0.6980 chunk 124 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 overall best weight: 0.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 411 ASN ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 GLN ** E 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 543 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.148082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.114659 restraints weight = 17954.509| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 2.75 r_work: 0.3104 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16308 Z= 0.129 Angle : 0.594 8.975 22252 Z= 0.287 Chirality : 0.044 0.229 2682 Planarity : 0.003 0.057 2695 Dihedral : 6.108 61.345 3458 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.64 % Allowed : 16.30 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % 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: -0.53 (0.20), residues: 1843 helix: 0.67 (0.27), residues: 415 sheet: -0.40 (0.23), residues: 533 loop : -0.73 (0.21), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D 542 TYR 0.012 0.001 TYR L 49 PHE 0.011 0.001 PHE E 210 TRP 0.012 0.001 TRP H 34 HIS 0.003 0.000 HIS A 216 Details of bonding type rmsd covalent geometry : bond 0.00304 (16203) covalent geometry : angle 0.55832 (21972) SS BOND : bond 0.00358 ( 35) SS BOND : angle 1.71962 ( 70) hydrogen bonds : bond 0.03359 ( 452) hydrogen bonds : angle 4.53019 ( 1248) link_ALPHA1-2 : bond 0.00023 ( 1) link_ALPHA1-2 : angle 1.77378 ( 3) link_ALPHA1-3 : bond 0.01255 ( 3) link_ALPHA1-3 : angle 3.38686 ( 9) link_ALPHA1-6 : bond 0.00879 ( 2) link_ALPHA1-6 : angle 1.11651 ( 6) link_BETA1-2 : bond 0.00219 ( 1) link_BETA1-2 : angle 1.98835 ( 3) link_BETA1-4 : bond 0.00536 ( 23) link_BETA1-4 : angle 1.76122 ( 69) link_NAG-ASN : bond 0.00246 ( 40) link_NAG-ASN : angle 1.94128 ( 120) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 194 time to evaluate : 0.645 Fit side-chains REVERT: A 91 GLU cc_start: 0.7618 (tp30) cc_final: 0.7344 (tp30) REVERT: A 112 TRP cc_start: 0.8242 (t-100) cc_final: 0.7729 (t60) REVERT: A 114 GLN cc_start: 0.7320 (tt0) cc_final: 0.7064 (tt0) REVERT: A 166 ARG cc_start: 0.8228 (OUTLIER) cc_final: 0.7974 (ttp-110) REVERT: B 542 ARG cc_start: 0.7671 (OUTLIER) cc_final: 0.7032 (ptt-90) REVERT: C 136 ASN cc_start: 0.7323 (m110) cc_final: 0.6297 (p0) REVERT: C 211 GLU cc_start: 0.7984 (tt0) cc_final: 0.7750 (tt0) REVERT: C 347 LYS cc_start: 0.7583 (tttm) cc_final: 0.7198 (ttpt) REVERT: D 617 ARG cc_start: 0.8053 (mtp85) cc_final: 0.7773 (ptm160) REVERT: D 655 LYS cc_start: 0.7016 (OUTLIER) cc_final: 0.6599 (ttpp) REVERT: E 87 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7268 (mp0) REVERT: E 117 LYS cc_start: 0.7940 (mmtp) cc_final: 0.7576 (mmmt) REVERT: E 155 LYS cc_start: 0.8473 (OUTLIER) cc_final: 0.7670 (mmpt) REVERT: E 164 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.7393 (pt0) REVERT: E 232 LYS cc_start: 0.8280 (ptpt) cc_final: 0.7376 (tptt) REVERT: E 308 ARG cc_start: 0.8085 (mtt-85) cc_final: 0.7274 (mtp-110) REVERT: E 444 ARG cc_start: 0.8424 (OUTLIER) cc_final: 0.7455 (tmm-80) REVERT: F 575 GLN cc_start: 0.7633 (OUTLIER) cc_final: 0.7201 (tp40) REVERT: F 658 GLN cc_start: 0.8126 (OUTLIER) cc_final: 0.7145 (tt0) REVERT: H 5 GLN cc_start: 0.6925 (mt0) cc_final: 0.6594 (mt0) REVERT: H 12 LEU cc_start: 0.8023 (OUTLIER) cc_final: 0.7813 (mt) REVERT: H 48 ILE cc_start: 0.8185 (OUTLIER) cc_final: 0.7681 (mp) REVERT: H 69 MET cc_start: 0.6839 (mtm) cc_final: 0.6571 (mtm) REVERT: H 100 GLU cc_start: 0.6906 (tt0) cc_final: 0.6689 (mm-30) outliers start: 44 outliers final: 21 residues processed: 225 average time/residue: 0.6062 time to fit residues: 150.3543 Evaluate side-chains 220 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 188 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 166 ARG Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 464 THR Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain B residue 542 ARG Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain D residue 655 LYS Chi-restraints excluded: chain E residue 87 GLU Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 155 LYS Chi-restraints excluded: chain E residue 161 MET Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 433 CYS Chi-restraints excluded: chain E residue 444 ARG Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain F residue 575 GLN Chi-restraints excluded: chain F residue 658 GLN Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain L residue 39 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 173 optimal weight: 8.9990 chunk 113 optimal weight: 0.9990 chunk 29 optimal weight: 0.0870 chunk 162 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 178 optimal weight: 0.0030 chunk 41 optimal weight: 1.9990 chunk 96 optimal weight: 0.5980 chunk 52 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 overall best weight: 0.5372 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN A 300 ASN A 411 ASN ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 GLN ** E 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 543 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.148908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.115712 restraints weight = 18054.171| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 2.75 r_work: 0.3124 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16308 Z= 0.118 Angle : 0.589 8.803 22252 Z= 0.284 Chirality : 0.044 0.223 2682 Planarity : 0.003 0.055 2695 Dihedral : 5.932 56.957 3458 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.04 % Allowed : 17.02 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % 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: 1843 helix: 0.88 (0.28), residues: 403 sheet: -0.49 (0.22), residues: 561 loop : -0.71 (0.21), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG D 542 TYR 0.012 0.001 TYR L 49 PHE 0.012 0.001 PHE C 53 TRP 0.013 0.001 TRP E 96 HIS 0.003 0.000 HIS A 216 Details of bonding type rmsd covalent geometry : bond 0.00276 (16203) covalent geometry : angle 0.55213 (21972) SS BOND : bond 0.00400 ( 35) SS BOND : angle 1.99678 ( 70) hydrogen bonds : bond 0.03243 ( 452) hydrogen bonds : angle 4.46533 ( 1248) link_ALPHA1-2 : bond 0.00012 ( 1) link_ALPHA1-2 : angle 1.73569 ( 3) link_ALPHA1-3 : bond 0.01280 ( 3) link_ALPHA1-3 : angle 3.18038 ( 9) link_ALPHA1-6 : bond 0.00817 ( 2) link_ALPHA1-6 : angle 1.12286 ( 6) link_BETA1-2 : bond 0.00242 ( 1) link_BETA1-2 : angle 1.95125 ( 3) link_BETA1-4 : bond 0.00538 ( 23) link_BETA1-4 : angle 1.69141 ( 69) link_NAG-ASN : bond 0.00197 ( 40) link_NAG-ASN : angle 1.86750 ( 120) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 197 time to evaluate : 0.616 Fit side-chains revert: symmetry clash REVERT: A 91 GLU cc_start: 0.7610 (tp30) cc_final: 0.7352 (tp30) REVERT: A 112 TRP cc_start: 0.8223 (t-100) cc_final: 0.7738 (t60) REVERT: A 114 GLN cc_start: 0.7317 (tt0) cc_final: 0.7054 (tt0) REVERT: A 166 ARG cc_start: 0.8220 (OUTLIER) cc_final: 0.7966 (ttp-110) REVERT: B 542 ARG cc_start: 0.7634 (OUTLIER) cc_final: 0.7016 (ptt-90) REVERT: C 136 ASN cc_start: 0.7341 (m110) cc_final: 0.6330 (p0) REVERT: C 211 GLU cc_start: 0.7976 (tt0) cc_final: 0.7740 (tt0) REVERT: C 347 LYS cc_start: 0.7610 (tttm) cc_final: 0.7204 (ttpt) REVERT: D 655 LYS cc_start: 0.7039 (OUTLIER) cc_final: 0.6654 (ttpp) REVERT: E 87 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7241 (mp0) REVERT: E 117 LYS cc_start: 0.7912 (mmtp) cc_final: 0.7547 (mmmt) REVERT: E 132 THR cc_start: 0.8416 (OUTLIER) cc_final: 0.8078 (t) REVERT: E 155 LYS cc_start: 0.8445 (OUTLIER) cc_final: 0.7640 (mmpt) REVERT: E 164 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.7377 (pt0) REVERT: E 232 LYS cc_start: 0.8280 (ptpt) cc_final: 0.7373 (tptt) REVERT: E 308 ARG cc_start: 0.8093 (mtt-85) cc_final: 0.7276 (mtp-110) REVERT: E 485 LYS cc_start: 0.8307 (ptpt) cc_final: 0.7804 (pttt) REVERT: F 575 GLN cc_start: 0.7614 (OUTLIER) cc_final: 0.7185 (tp40) REVERT: F 658 GLN cc_start: 0.8206 (OUTLIER) cc_final: 0.7177 (tt0) REVERT: H 5 GLN cc_start: 0.6959 (mt0) cc_final: 0.6629 (mt0) REVERT: H 12 LEU cc_start: 0.8060 (OUTLIER) cc_final: 0.7855 (mt) REVERT: H 69 MET cc_start: 0.6864 (mtm) cc_final: 0.6607 (mtm) outliers start: 34 outliers final: 19 residues processed: 219 average time/residue: 0.6433 time to fit residues: 155.1845 Evaluate side-chains 213 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 184 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 166 ARG Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain B residue 542 ARG Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain D residue 655 LYS Chi-restraints excluded: chain E residue 87 GLU Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 155 LYS Chi-restraints excluded: chain E residue 161 MET Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 433 CYS Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain F residue 575 GLN Chi-restraints excluded: chain F residue 658 GLN Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain L residue 39 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 144 optimal weight: 0.0370 chunk 65 optimal weight: 1.9990 chunk 71 optimal weight: 0.5980 chunk 100 optimal weight: 2.9990 chunk 145 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 129 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 184 optimal weight: 10.0000 chunk 117 optimal weight: 0.6980 overall best weight: 0.8660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN A 103 GLN A 300 ASN A 411 ASN C 246 GLN ** E 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.148804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.115544 restraints weight = 17934.223| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 2.74 r_work: 0.3119 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.604 16308 Z= 0.320 Angle : 0.894 59.136 22252 Z= 0.484 Chirality : 0.047 0.704 2682 Planarity : 0.003 0.053 2695 Dihedral : 5.950 56.960 3458 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.10 % Allowed : 17.38 % Favored : 80.53 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.20), residues: 1843 helix: 0.87 (0.28), residues: 403 sheet: -0.49 (0.22), residues: 561 loop : -0.72 (0.21), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 542 TYR 0.012 0.001 TYR L 49 PHE 0.011 0.001 PHE C 53 TRP 0.012 0.001 TRP E 96 HIS 0.003 0.000 HIS A 216 Details of bonding type rmsd covalent geometry : bond 0.00752 (16203) covalent geometry : angle 0.77740 (21972) SS BOND : bond 0.07111 ( 35) SS BOND : angle 7.35546 ( 70) hydrogen bonds : bond 0.03255 ( 452) hydrogen bonds : angle 4.46625 ( 1248) link_ALPHA1-2 : bond 0.00131 ( 1) link_ALPHA1-2 : angle 1.69041 ( 3) link_ALPHA1-3 : bond 0.01257 ( 3) link_ALPHA1-3 : angle 3.18408 ( 9) link_ALPHA1-6 : bond 0.00796 ( 2) link_ALPHA1-6 : angle 1.11409 ( 6) link_BETA1-2 : bond 0.00248 ( 1) link_BETA1-2 : angle 1.93786 ( 3) link_BETA1-4 : bond 0.00547 ( 23) link_BETA1-4 : angle 1.70170 ( 69) link_NAG-ASN : bond 0.00197 ( 40) link_NAG-ASN : angle 1.85667 ( 120) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5330.31 seconds wall clock time: 91 minutes 47.73 seconds (5507.73 seconds total)