Starting phenix.real_space_refine on Sun Aug 24 12:21:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sb0_40286/08_2025/8sb0_40286.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sb0_40286/08_2025/8sb0_40286.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8sb0_40286/08_2025/8sb0_40286.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sb0_40286/08_2025/8sb0_40286.map" model { file = "/net/cci-nas-00/data/ceres_data/8sb0_40286/08_2025/8sb0_40286.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sb0_40286/08_2025/8sb0_40286.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.010 sd= 0.216 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 132 5.16 5 C 12330 2.51 5 N 3308 2.21 5 O 3971 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19741 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 3596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3596 Classifications: {'peptide': 460} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 434} Chain: "B" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 942 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 1, 'TRANS': 116} Chain: "C" Number of atoms: 995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 995 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "D" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 805 Classifications: {'peptide': 110} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 103} Chain: "F" Number of atoms: 3614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3614 Classifications: {'peptide': 462} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 436} Chain: "G" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 942 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 1, 'TRANS': 116} Chain: "H" Number of atoms: 995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 995 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "I" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 805 Classifications: {'peptide': 110} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 103} Chain: "K" Number of atoms: 3606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 461, 3606 Classifications: {'peptide': 461} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 435} Chain breaks: 1 Chain: "L" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 942 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 1, 'TRANS': 116} Chain: "M" Number of atoms: 995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 995 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "N" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 805 Classifications: {'peptide': 110} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 103} Chain: "E" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "J" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "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: 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: "R" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "V" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 5.15, per 1000 atoms: 0.26 Number of scatterers: 19741 At special positions: 0 Unit cell: (158.76, 159.84, 136.08, 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 132 16.00 O 3971 8.00 N 3308 7.00 C 12330 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.04 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 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 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 252 " - pdb=" SG CYS D 320 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 74 " distance=2.04 Simple disulfide: pdb=" SG CYS F 119 " - pdb=" SG CYS F 205 " distance=2.03 Simple disulfide: pdb=" SG CYS F 126 " - pdb=" SG CYS F 196 " distance=2.03 Simple disulfide: pdb=" SG CYS F 131 " - pdb=" SG CYS F 157 " distance=2.03 Simple disulfide: pdb=" SG CYS F 201 " - pdb=" SG CYS F 433 " distance=2.03 Simple disulfide: pdb=" SG CYS F 218 " - pdb=" SG CYS F 247 " distance=2.03 Simple disulfide: pdb=" SG CYS F 228 " - pdb=" SG CYS F 239 " distance=2.04 Simple disulfide: pdb=" SG CYS F 296 " - pdb=" SG CYS F 331 " distance=2.03 Simple disulfide: pdb=" SG CYS F 378 " - pdb=" SG CYS F 445 " distance=2.03 Simple disulfide: pdb=" SG CYS F 385 " - pdb=" SG CYS F 418 " distance=2.03 Simple disulfide: pdb=" SG CYS F 501 " - pdb=" SG CYS G 605 " distance=2.02 Simple disulfide: pdb=" SG CYS G 598 " - pdb=" SG CYS G 604 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 252 " - pdb=" SG CYS I 320 " distance=2.03 Simple disulfide: pdb=" SG CYS K 54 " - pdb=" SG CYS K 74 " distance=2.04 Simple disulfide: pdb=" SG CYS K 119 " - pdb=" SG CYS K 205 " distance=2.03 Simple disulfide: pdb=" SG CYS K 126 " - pdb=" SG CYS K 196 " distance=2.03 Simple disulfide: pdb=" SG CYS K 131 " - pdb=" SG CYS K 157 " distance=2.03 Simple disulfide: pdb=" SG CYS K 201 " - pdb=" SG CYS K 433 " distance=2.03 Simple disulfide: pdb=" SG CYS K 218 " - pdb=" SG CYS K 247 " distance=2.03 Simple disulfide: pdb=" SG CYS K 228 " - pdb=" SG CYS K 239 " distance=2.04 Simple disulfide: pdb=" SG CYS K 296 " - pdb=" SG CYS K 331 " distance=2.03 Simple disulfide: pdb=" SG CYS K 378 " - pdb=" SG CYS K 445 " distance=2.03 Simple disulfide: pdb=" SG CYS K 385 " - pdb=" SG CYS K 418 " distance=2.03 Simple disulfide: pdb=" SG CYS K 501 " - pdb=" SG CYS L 605 " distance=2.05 Simple disulfide: pdb=" SG CYS L 598 " - pdb=" SG CYS L 604 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 252 " - pdb=" SG CYS N 320 " 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 E 4 " - " MAN E 5 " " MAN J 4 " - " MAN J 5 " " MAN J 5 " - " MAN J 6 " " MAN J 8 " - " MAN J 9 " " MAN Q 4 " - " MAN Q 5 " " MAN R 4 " - " MAN R 5 " " MAN R 5 " - " MAN R 6 " " MAN R 8 " - " MAN R 9 " " MAN V 4 " - " MAN V 5 " " MAN V 5 " - " MAN V 6 " " MAN V 8 " - " MAN V 9 " ALPHA1-3 " BMA E 3 " - " MAN E 4 " " BMA J 3 " - " MAN J 4 " " MAN J 7 " - " MAN J 10 " " BMA Q 3 " - " MAN Q 4 " " BMA R 3 " - " MAN R 4 " " MAN R 7 " - " MAN R 10 " " BMA U 3 " - " MAN U 4 " " BMA V 3 " - " MAN V 4 " " MAN V 7 " - " MAN V 10 " ALPHA1-6 " BMA J 3 " - " MAN J 7 " " MAN J 7 " - " MAN J 8 " " BMA Q 3 " - " MAN Q 6 " " BMA R 3 " - " MAN R 7 " " MAN R 7 " - " MAN R 8 " " BMA V 3 " - " MAN V 7 " " MAN V 7 " - " MAN V 8 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " NAG-ASN " NAG E 1 " - " ASN A 301 " " NAG J 1 " - " ASN A 332 " " NAG O 1 " - " ASN A 156 " " NAG P 1 " - " ASN A 442 " " NAG Q 1 " - " ASN F 301 " " NAG R 1 " - " ASN F 332 " " NAG S 1 " - " ASN F 156 " " NAG T 1 " - " ASN F 442 " " NAG U 1 " - " ASN K 301 " " NAG V 1 " - " ASN K 332 " " NAG W 1 " - " ASN K 156 " " NAG X 1 " - " ASN K 442 " Time building additional restraints: 2.01 Conformation dependent library (CDL) restraints added in 812.1 milliseconds Enol-peptide restraints added in 1.4 microseconds 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4512 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 45 sheets defined 19.0% alpha, 31.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'A' and resid 68 through 74 removed outlier: 4.143A pdb=" N HIS A 72 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA A 73 " --> pdb=" O TRP A 69 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N CYS A 74 " --> pdb=" O ALA A 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 68 through 74' Processing helix chain 'A' and resid 98 through 117 removed outlier: 4.505A pdb=" N ASP A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLU A 106 " --> pdb=" O ASP A 102 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER A 115 " --> pdb=" O LEU A 111 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU A 116 " --> pdb=" O TRP A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 127 removed outlier: 3.550A pdb=" N CYS A 126 " --> pdb=" O THR A 123 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL A 127 " --> pdb=" O PRO A 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 123 through 127' Processing helix chain 'A' and resid 177 through 179 No H-bonds generated for 'chain 'A' and resid 177 through 179' Processing helix chain 'A' and resid 335 through 353 removed outlier: 4.013A pdb=" N HIS A 352 " --> pdb=" O GLU A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 481 Processing helix chain 'B' and resid 529 through 535 removed outlier: 4.226A pdb=" N MET B 535 " --> pdb=" O GLY B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 537 through 543 removed outlier: 4.176A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 576 removed outlier: 3.552A pdb=" N LEU B 576 " --> pdb=" O GLY B 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 576 through 596 removed outlier: 3.715A pdb=" N LEU B 581 " --> pdb=" O GLN B 577 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N ALA B 582 " --> pdb=" O ALA B 578 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N VAL B 583 " --> pdb=" O ARG B 579 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N TRP B 596 " --> pdb=" O LEU B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 611 through 615 Processing helix chain 'B' and resid 618 through 622 Processing helix chain 'B' and resid 627 through 636 removed outlier: 3.578A pdb=" N GLU B 634 " --> pdb=" O GLN B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 659 removed outlier: 4.170A pdb=" N GLY B 644 " --> pdb=" O GLN B 640 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LEU B 645 " --> pdb=" O ILE B 641 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASP B 659 " --> pdb=" O LYS B 655 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 65 removed outlier: 3.681A pdb=" N GLN C 65 " --> pdb=" O ARG C 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 62 through 65' Processing helix chain 'C' and resid 87 through 91 Processing helix chain 'D' and resid 311 through 315 Processing helix chain 'F' and resid 68 through 74 removed outlier: 4.128A pdb=" N HIS F 72 " --> pdb=" O VAL F 68 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA F 73 " --> pdb=" O TRP F 69 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N CYS F 74 " --> pdb=" O ALA F 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 68 through 74' Processing helix chain 'F' and resid 98 through 115 removed outlier: 4.472A pdb=" N ASP F 102 " --> pdb=" O ASN F 98 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N GLU F 106 " --> pdb=" O ASP F 102 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER F 115 " --> pdb=" O LEU F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 123 through 127 removed outlier: 3.611A pdb=" N VAL F 127 " --> pdb=" O PRO F 124 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 179 No H-bonds generated for 'chain 'F' and resid 177 through 179' Processing helix chain 'F' and resid 335 through 353 removed outlier: 4.005A pdb=" N HIS F 352 " --> pdb=" O GLU F 348 " (cutoff:3.500A) Processing helix chain 'F' and resid 476 through 481 Processing helix chain 'F' and resid 482 through 484 No H-bonds generated for 'chain 'F' and resid 482 through 484' Processing helix chain 'G' and resid 529 through 535 removed outlier: 4.164A pdb=" N MET G 535 " --> pdb=" O GLY G 531 " (cutoff:3.500A) Processing helix chain 'G' and resid 536 through 543 removed outlier: 4.324A pdb=" N GLN G 540 " --> pdb=" O THR G 536 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ASN G 543 " --> pdb=" O VAL G 539 " (cutoff:3.500A) Processing helix chain 'G' and resid 571 through 576 Processing helix chain 'G' and resid 576 through 596 removed outlier: 3.669A pdb=" N LEU G 581 " --> pdb=" O GLN G 577 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ALA G 582 " --> pdb=" O ALA G 578 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N VAL G 583 " --> pdb=" O ARG G 579 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N TRP G 596 " --> pdb=" O LEU G 592 " (cutoff:3.500A) Processing helix chain 'G' and resid 611 through 615 Processing helix chain 'G' and resid 618 through 622 Processing helix chain 'G' and resid 627 through 636 removed outlier: 3.739A pdb=" N GLU G 634 " --> pdb=" O GLN G 630 " (cutoff:3.500A) Processing helix chain 'G' and resid 638 through 659 removed outlier: 4.020A pdb=" N GLY G 644 " --> pdb=" O GLN G 640 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LEU G 645 " --> pdb=" O ILE G 641 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ASP G 659 " --> pdb=" O LYS G 655 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 30 No H-bonds generated for 'chain 'H' and resid 28 through 30' Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.502A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'I' and resid 311 through 315 Processing helix chain 'K' and resid 68 through 74 removed outlier: 4.126A pdb=" N HIS K 72 " --> pdb=" O VAL K 68 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA K 73 " --> pdb=" O TRP K 69 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N CYS K 74 " --> pdb=" O ALA K 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 68 through 74' Processing helix chain 'K' and resid 99 through 115 removed outlier: 4.299A pdb=" N GLU K 106 " --> pdb=" O ASP K 102 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER K 115 " --> pdb=" O LEU K 111 " (cutoff:3.500A) Processing helix chain 'K' and resid 123 through 127 removed outlier: 3.633A pdb=" N VAL K 127 " --> pdb=" O PRO K 124 " (cutoff:3.500A) Processing helix chain 'K' and resid 177 through 179 No H-bonds generated for 'chain 'K' and resid 177 through 179' Processing helix chain 'K' and resid 335 through 353 removed outlier: 4.023A pdb=" N HIS K 352 " --> pdb=" O GLU K 348 " (cutoff:3.500A) Processing helix chain 'K' and resid 476 through 481 Processing helix chain 'L' and resid 529 through 535 removed outlier: 4.100A pdb=" N MET L 535 " --> pdb=" O GLY L 531 " (cutoff:3.500A) Processing helix chain 'L' and resid 537 through 543 removed outlier: 4.171A pdb=" N ASN L 543 " --> pdb=" O VAL L 539 " (cutoff:3.500A) Processing helix chain 'L' and resid 571 through 576 removed outlier: 3.505A pdb=" N LEU L 576 " --> pdb=" O GLY L 572 " (cutoff:3.500A) Processing helix chain 'L' and resid 576 through 596 removed outlier: 3.709A pdb=" N LEU L 581 " --> pdb=" O GLN L 577 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N ALA L 582 " --> pdb=" O ALA L 578 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N VAL L 583 " --> pdb=" O ARG L 579 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N TRP L 596 " --> pdb=" O LEU L 592 " (cutoff:3.500A) Processing helix chain 'L' and resid 611 through 615 Processing helix chain 'L' and resid 618 through 622 Processing helix chain 'L' and resid 627 through 636 removed outlier: 3.690A pdb=" N GLU L 634 " --> pdb=" O GLN L 630 " (cutoff:3.500A) Processing helix chain 'L' and resid 638 through 659 removed outlier: 4.013A pdb=" N GLY L 644 " --> pdb=" O GLN L 640 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LEU L 645 " --> pdb=" O ILE L 641 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASP L 659 " --> pdb=" O LYS L 655 " (cutoff:3.500A) Processing helix chain 'M' and resid 87 through 91 Processing helix chain 'N' and resid 311 through 315 Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 497 removed outlier: 5.253A pdb=" N VAL A 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR B 606 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.872A pdb=" N LYS A 46 " --> pdb=" O LYS A 490 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 55 through 56 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 172 through 174 removed outlier: 3.855A pdb=" N LEU A 129 " --> pdb=" O TYR A 191 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 215 through 218 removed outlier: 4.449A pdb=" N TYR A 217 " --> pdb=" O HIS A 249 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N HIS A 249 " --> pdb=" O TYR A 217 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 261 removed outlier: 4.093A pdb=" N GLY A 451 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 10.375A pdb=" N THR A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.606A pdb=" N ILE A 294 " --> pdb=" O THR A 444 " (cutoff:3.500A) removed outlier: 9.884A pdb=" N ARG A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 10.901A pdb=" N VAL A 292 " --> pdb=" O ARG A 446 " (cutoff:3.500A) removed outlier: 9.310A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.305A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N GLU A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N SER A 334 " --> pdb=" O GLU A 293 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 271 through 273 removed outlier: 6.666A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 10.305A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.310A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.901A pdb=" N VAL A 292 " --> pdb=" O ARG A 446 " (cutoff:3.500A) removed outlier: 9.884A pdb=" N ARG A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.606A pdb=" N ILE A 294 " --> pdb=" O THR A 444 " (cutoff:3.500A) removed outlier: 10.375A pdb=" N THR A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N THR A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N PHE A 468 " --> pdb=" O THR A 358 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LYS A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 302 through 308 removed outlier: 5.861A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 423 through 424 Processing sheet with id=AB2, first strand: chain 'C' and resid 3 through 6 removed outlier: 3.590A pdb=" N THR C 71 " --> pdb=" O TYR C 80 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 9 through 12 removed outlier: 4.549A pdb=" N TYR C 33 " --> pdb=" O GLY C 99 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ILE C 34 " --> pdb=" O TRP C 50 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N TRP C 50 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N TRP C 36 " --> pdb=" O MET C 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 239 through 241 removed outlier: 7.084A pdb=" N TRP D 267 " --> pdb=" O MET D 279 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N MET D 279 " --> pdb=" O TRP D 267 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 239 through 241 Processing sheet with id=AB6, first strand: chain 'D' and resid 247 through 253 Processing sheet with id=AB7, first strand: chain 'F' and resid 494 through 497 removed outlier: 5.031A pdb=" N VAL G 608 " --> pdb=" O VAL F 36 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N VAL F 38 " --> pdb=" O THR G 606 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N THR G 606 " --> pdb=" O VAL F 38 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N TYR F 40 " --> pdb=" O CYS G 604 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N CYS G 604 " --> pdb=" O TYR F 40 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 55 through 56 Processing sheet with id=AB9, first strand: chain 'F' and resid 84 through 86 removed outlier: 4.843A pdb=" N VAL F 242 " --> pdb=" O LEU F 86 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 91 through 94 Processing sheet with id=AC2, first strand: chain 'F' and resid 169 through 174 Processing sheet with id=AC3, first strand: chain 'F' and resid 215 through 218 removed outlier: 4.491A pdb=" N TYR F 217 " --> pdb=" O HIS F 249 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N HIS F 249 " --> pdb=" O TYR F 217 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 259 through 261 removed outlier: 4.103A pdb=" N GLY F 451 " --> pdb=" O LEU F 260 " (cutoff:3.500A) removed outlier: 10.304A pdb=" N THR F 444 " --> pdb=" O ILE F 294 " (cutoff:3.500A) removed outlier: 11.514A pdb=" N ILE F 294 " --> pdb=" O THR F 444 " (cutoff:3.500A) removed outlier: 9.839A pdb=" N ARG F 446 " --> pdb=" O VAL F 292 " (cutoff:3.500A) removed outlier: 10.857A pdb=" N VAL F 292 " --> pdb=" O ARG F 446 " (cutoff:3.500A) removed outlier: 9.291A pdb=" N ASN F 448 " --> pdb=" O THR F 290 " (cutoff:3.500A) removed outlier: 10.286A pdb=" N THR F 290 " --> pdb=" O ASN F 448 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N THR F 450 " --> pdb=" O LEU F 288 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU F 454 " --> pdb=" O ILE F 284 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N GLU F 293 " --> pdb=" O SER F 334 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N SER F 334 " --> pdb=" O GLU F 293 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 271 through 273 removed outlier: 3.512A pdb=" N LEU F 454 " --> pdb=" O ILE F 284 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N THR F 450 " --> pdb=" O LEU F 288 " (cutoff:3.500A) removed outlier: 10.286A pdb=" N THR F 290 " --> pdb=" O ASN F 448 " (cutoff:3.500A) removed outlier: 9.291A pdb=" N ASN F 448 " --> pdb=" O THR F 290 " (cutoff:3.500A) removed outlier: 10.857A pdb=" N VAL F 292 " --> pdb=" O ARG F 446 " (cutoff:3.500A) removed outlier: 9.839A pdb=" N ARG F 446 " --> pdb=" O VAL F 292 " (cutoff:3.500A) removed outlier: 11.514A pdb=" N ILE F 294 " --> pdb=" O THR F 444 " (cutoff:3.500A) removed outlier: 10.304A pdb=" N THR F 444 " --> pdb=" O ILE F 294 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N THR F 358 " --> pdb=" O GLU F 466 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N PHE F 468 " --> pdb=" O THR F 358 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N LYS F 360 " --> pdb=" O PHE F 468 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 302 through 308 removed outlier: 5.843A pdb=" N THR F 303 " --> pdb=" O GLY F 321 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 423 through 424 Processing sheet with id=AC8, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AC9, first strand: chain 'H' and resid 9 through 12 removed outlier: 4.540A pdb=" N TYR H 33 " --> pdb=" O GLY H 99 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ILE H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N TRP H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 239 through 241 removed outlier: 7.127A pdb=" N TRP I 267 " --> pdb=" O MET I 279 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N MET I 279 " --> pdb=" O TRP I 267 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 239 through 241 Processing sheet with id=AD3, first strand: chain 'I' and resid 247 through 253 Processing sheet with id=AD4, first strand: chain 'K' and resid 494 through 497 removed outlier: 4.576A pdb=" N VAL K 36 " --> pdb=" O THR L 606 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 55 through 56 Processing sheet with id=AD6, first strand: chain 'K' and resid 84 through 86 removed outlier: 4.882A pdb=" N VAL K 242 " --> pdb=" O LEU K 86 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'K' and resid 91 through 94 Processing sheet with id=AD8, first strand: chain 'K' and resid 172 through 174 removed outlier: 3.985A pdb=" N LEU K 129 " --> pdb=" O TYR K 191 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'K' and resid 215 through 218 removed outlier: 4.386A pdb=" N TYR K 217 " --> pdb=" O HIS K 249 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N HIS K 249 " --> pdb=" O TYR K 217 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'K' and resid 259 through 261 removed outlier: 4.104A pdb=" N GLY K 451 " --> pdb=" O LEU K 260 " (cutoff:3.500A) removed outlier: 10.366A pdb=" N THR K 444 " --> pdb=" O ILE K 294 " (cutoff:3.500A) removed outlier: 11.584A pdb=" N ILE K 294 " --> pdb=" O THR K 444 " (cutoff:3.500A) removed outlier: 9.899A pdb=" N ARG K 446 " --> pdb=" O VAL K 292 " (cutoff:3.500A) removed outlier: 10.905A pdb=" N VAL K 292 " --> pdb=" O ARG K 446 " (cutoff:3.500A) removed outlier: 9.297A pdb=" N ASN K 448 " --> pdb=" O THR K 290 " (cutoff:3.500A) removed outlier: 10.302A pdb=" N THR K 290 " --> pdb=" O ASN K 448 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N THR K 450 " --> pdb=" O LEU K 288 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU K 454 " --> pdb=" O ILE K 284 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N GLU K 293 " --> pdb=" O SER K 334 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N SER K 334 " --> pdb=" O GLU K 293 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ALA K 329 " --> pdb=" O CYS K 418 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'K' and resid 271 through 273 removed outlier: 3.500A pdb=" N LEU K 454 " --> pdb=" O ILE K 284 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N THR K 450 " --> pdb=" O LEU K 288 " (cutoff:3.500A) removed outlier: 10.302A pdb=" N THR K 290 " --> pdb=" O ASN K 448 " (cutoff:3.500A) removed outlier: 9.297A pdb=" N ASN K 448 " --> pdb=" O THR K 290 " (cutoff:3.500A) removed outlier: 10.905A pdb=" N VAL K 292 " --> pdb=" O ARG K 446 " (cutoff:3.500A) removed outlier: 9.899A pdb=" N ARG K 446 " --> pdb=" O VAL K 292 " (cutoff:3.500A) removed outlier: 11.584A pdb=" N ILE K 294 " --> pdb=" O THR K 444 " (cutoff:3.500A) removed outlier: 10.366A pdb=" N THR K 444 " --> pdb=" O ILE K 294 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N THR K 358 " --> pdb=" O GLU K 466 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N PHE K 468 " --> pdb=" O THR K 358 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N LYS K 360 " --> pdb=" O PHE K 468 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'K' and resid 302 through 308 removed outlier: 5.792A pdb=" N THR K 303 " --> pdb=" O GLY K 321 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'K' and resid 423 through 424 Processing sheet with id=AE5, first strand: chain 'M' and resid 3 through 6 Processing sheet with id=AE6, first strand: chain 'M' and resid 9 through 12 removed outlier: 4.581A pdb=" N TYR M 33 " --> pdb=" O GLY M 99 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ILE M 34 " --> pdb=" O TRP M 50 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N TRP M 50 " --> pdb=" O ILE M 34 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N TRP M 36 " --> pdb=" O MET M 48 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'N' and resid 239 through 241 removed outlier: 7.106A pdb=" N TRP N 267 " --> pdb=" O MET N 279 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N MET N 279 " --> pdb=" O TRP N 267 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'N' and resid 239 through 241 Processing sheet with id=AE9, first strand: chain 'N' and resid 247 through 253 641 hydrogen bonds defined for protein. 1629 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: 3.91 Time building geometry restraints manager: 2.52 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: 6134 1.34 - 1.47: 5189 1.47 - 1.60: 8657 1.60 - 1.72: 0 1.72 - 1.85: 177 Bond restraints: 20157 Sorted by residual: bond pdb=" N VAL G 608 " pdb=" CA VAL G 608 " ideal model delta sigma weight residual 1.460 1.492 -0.032 9.30e-03 1.16e+04 1.20e+01 bond pdb=" C2 MAN J 4 " pdb=" O2 MAN J 4 " ideal model delta sigma weight residual 1.407 1.462 -0.055 2.00e-02 2.50e+03 7.70e+00 bond pdb=" C2 MAN J 8 " pdb=" O2 MAN J 8 " ideal model delta sigma weight residual 1.407 1.460 -0.053 2.00e-02 2.50e+03 6.95e+00 bond pdb=" C2 MAN V 8 " pdb=" O2 MAN V 8 " ideal model delta sigma weight residual 1.407 1.459 -0.052 2.00e-02 2.50e+03 6.88e+00 bond pdb=" C1 MAN J 8 " pdb=" C2 MAN J 8 " ideal model delta sigma weight residual 1.526 1.577 -0.051 2.00e-02 2.50e+03 6.61e+00 ... (remaining 20152 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.65: 26758 2.65 - 5.31: 562 5.31 - 7.96: 68 7.96 - 10.61: 15 10.61 - 13.26: 3 Bond angle restraints: 27406 Sorted by residual: angle pdb=" C ASN K 67 " pdb=" N VAL K 68 " pdb=" CA VAL K 68 " ideal model delta sigma weight residual 121.70 134.96 -13.26 1.80e+00 3.09e-01 5.43e+01 angle pdb=" C ASN F 67 " pdb=" N VAL F 68 " pdb=" CA VAL F 68 " ideal model delta sigma weight residual 121.70 134.90 -13.20 1.80e+00 3.09e-01 5.38e+01 angle pdb=" C ASN A 67 " pdb=" N VAL A 68 " pdb=" CA VAL A 68 " ideal model delta sigma weight residual 121.70 134.89 -13.19 1.80e+00 3.09e-01 5.37e+01 angle pdb=" N TRP F 35 " pdb=" CA TRP F 35 " pdb=" C TRP F 35 " ideal model delta sigma weight residual 109.41 101.38 8.03 1.52e+00 4.33e-01 2.79e+01 angle pdb=" C ASN F 403 " pdb=" N SER F 404 " pdb=" CA SER F 404 " ideal model delta sigma weight residual 121.70 130.85 -9.15 1.80e+00 3.09e-01 2.58e+01 ... (remaining 27401 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.27: 11984 22.27 - 44.55: 655 44.55 - 66.82: 71 66.82 - 89.09: 59 89.09 - 111.36: 26 Dihedral angle restraints: 12795 sinusoidal: 5746 harmonic: 7049 Sorted by residual: dihedral pdb=" CA LEU A 184 " pdb=" C LEU A 184 " pdb=" N SER A 185 " pdb=" CA SER A 185 " ideal model delta harmonic sigma weight residual -180.00 -138.30 -41.70 0 5.00e+00 4.00e-02 6.96e+01 dihedral pdb=" CA THR B 569 " pdb=" C THR B 569 " pdb=" N VAL B 570 " pdb=" CA VAL B 570 " ideal model delta harmonic sigma weight residual 180.00 -143.05 -36.95 0 5.00e+00 4.00e-02 5.46e+01 dihedral pdb=" CA LEU K 184 " pdb=" C LEU K 184 " pdb=" N SER K 185 " pdb=" CA SER K 185 " ideal model delta harmonic sigma weight residual -180.00 -143.55 -36.45 0 5.00e+00 4.00e-02 5.31e+01 ... (remaining 12792 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 2608 0.059 - 0.119: 494 0.119 - 0.178: 117 0.178 - 0.238: 14 0.238 - 0.297: 9 Chirality restraints: 3242 Sorted by residual: chirality pdb=" C5 BMA J 3 " pdb=" C4 BMA J 3 " pdb=" C6 BMA J 3 " pdb=" O5 BMA J 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.57 0.30 2.00e-01 2.50e+01 2.21e+00 chirality pdb=" C5 BMA U 3 " pdb=" C4 BMA U 3 " pdb=" C6 BMA U 3 " pdb=" O5 BMA U 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" C5 BMA Q 3 " pdb=" C4 BMA Q 3 " pdb=" C6 BMA Q 3 " pdb=" O5 BMA Q 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.29 2.00e-01 2.50e+01 2.09e+00 ... (remaining 3239 not shown) Planarity restraints: 3423 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN L 658 " 0.022 2.00e-02 2.50e+03 4.46e-02 1.99e+01 pdb=" CD GLN L 658 " -0.077 2.00e-02 2.50e+03 pdb=" OE1 GLN L 658 " 0.029 2.00e-02 2.50e+03 pdb=" NE2 GLN L 658 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG K 166 " 0.385 9.50e-02 1.11e+02 1.73e-01 1.88e+01 pdb=" NE ARG K 166 " -0.027 2.00e-02 2.50e+03 pdb=" CZ ARG K 166 " 0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG K 166 " -0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG K 166 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 35 " -0.019 2.00e-02 2.50e+03 2.02e-02 1.02e+01 pdb=" CG TRP A 35 " 0.055 2.00e-02 2.50e+03 pdb=" CD1 TRP A 35 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP A 35 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 35 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 35 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A 35 " -0.014 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 35 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 35 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP A 35 " 0.001 2.00e-02 2.50e+03 ... (remaining 3420 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 190 2.62 - 3.19: 17580 3.19 - 3.76: 27850 3.76 - 4.33: 38464 4.33 - 4.90: 63769 Nonbonded interactions: 147853 Sorted by model distance: nonbonded pdb=" OE2 GLU N 282 " pdb=" O4 MAN V 4 " model vdw 2.050 3.040 nonbonded pdb=" OG1 THR K 37 " pdb=" O ALA K 497 " model vdw 2.063 3.040 nonbonded pdb=" O VAL A 36 " pdb=" OG1 THR B 606 " model vdw 2.071 3.040 nonbonded pdb=" OG1 THR A 37 " pdb=" O ALA A 497 " model vdw 2.083 3.040 nonbonded pdb=" OE2 GLU I 282 " pdb=" O4 MAN R 4 " model vdw 2.086 3.040 ... (remaining 147848 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 32 or resid 34 through 503)) selection = (chain 'F' and (resid 32 or resid 34 through 503)) selection = (chain 'K' and resid 32 through 503) } ncs_group { reference = chain 'B' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'C' selection = chain 'H' selection = chain 'M' } ncs_group { reference = chain 'D' selection = chain 'I' selection = chain 'N' } ncs_group { reference = chain 'J' selection = chain 'R' selection = chain 'V' } ncs_group { reference = chain 'O' selection = chain 'P' selection = chain 'S' selection = chain 'T' selection = chain 'W' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.340 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 19.610 Find NCS groups from input model: 0.260 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:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 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 0.071 20256 Z= 0.267 Angle : 0.991 13.263 27661 Z= 0.506 Chirality : 0.053 0.297 3242 Planarity : 0.006 0.173 3411 Dihedral : 15.003 111.365 8157 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.45 % Favored : 93.31 % Rotamer: Outliers : 0.05 % Allowed : 0.28 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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 aren not related in a simple way. whole: -1.76 (0.17), residues: 2420 helix: -1.14 (0.25), residues: 356 sheet: -0.74 (0.20), residues: 702 loop : -1.40 (0.16), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.001 ARG F 166 TYR 0.018 0.002 TYR K 399 PHE 0.035 0.002 PHE M 29 TRP 0.055 0.002 TRP A 35 HIS 0.008 0.002 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00562 (20157) covalent geometry : angle 0.94766 (27406) SS BOND : bond 0.00462 ( 42) SS BOND : angle 1.75500 ( 84) hydrogen bonds : bond 0.22357 ( 616) hydrogen bonds : angle 9.35467 ( 1629) link_ALPHA1-2 : bond 0.01382 ( 11) link_ALPHA1-2 : angle 4.52955 ( 33) link_ALPHA1-3 : bond 0.01520 ( 9) link_ALPHA1-3 : angle 4.19129 ( 27) link_ALPHA1-6 : bond 0.00535 ( 7) link_ALPHA1-6 : angle 3.96902 ( 21) link_BETA1-4 : bond 0.00870 ( 18) link_BETA1-4 : angle 3.33917 ( 54) link_NAG-ASN : bond 0.00245 ( 12) link_NAG-ASN : angle 2.46677 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 364 time to evaluate : 0.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 399 TYR cc_start: 0.7219 (t80) cc_final: 0.6991 (t80) REVERT: G 609 PRO cc_start: 0.8143 (Cg_exo) cc_final: 0.7728 (Cg_endo) REVERT: I 263 ASN cc_start: 0.7963 (t0) cc_final: 0.7526 (t0) REVERT: N 263 ASN cc_start: 0.7596 (t0) cc_final: 0.7260 (t0) outliers start: 1 outliers final: 0 residues processed: 364 average time/residue: 0.1558 time to fit residues: 84.4434 Evaluate side-chains 216 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 216 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 216 optimal weight: 8.9990 chunk 98 optimal weight: 0.0170 chunk 194 optimal weight: 0.7980 chunk 227 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.4980 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.3980 chunk 103 optimal weight: 0.0970 chunk 235 optimal weight: 30.0000 overall best weight: 0.3616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN A 203 GLN A 249 HIS B 651 ASN F 417 GLN G 651 ASN H 6 GLN H 65 GLN K 249 HIS L 651 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.133470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.120617 restraints weight = 40557.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.119650 restraints weight = 76007.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.119447 restraints weight = 81211.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.118751 restraints weight = 67320.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.118720 restraints weight = 68939.044| |-----------------------------------------------------------------------------| r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20256 Z= 0.132 Angle : 0.710 10.320 27661 Z= 0.364 Chirality : 0.047 0.211 3242 Planarity : 0.005 0.049 3411 Dihedral : 10.416 77.270 3766 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.00 % Favored : 94.75 % Rotamer: Outliers : 0.09 % Allowed : 3.49 % Favored : 96.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 aren not related in a simple way. whole: -1.46 (0.16), residues: 2420 helix: -0.40 (0.26), residues: 336 sheet: -0.58 (0.19), residues: 702 loop : -1.32 (0.16), residues: 1382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 166 TYR 0.012 0.001 TYR C 33 PHE 0.017 0.001 PHE C 64 TRP 0.034 0.002 TRP H 47 HIS 0.006 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00271 (20157) covalent geometry : angle 0.68687 (27406) SS BOND : bond 0.00368 ( 42) SS BOND : angle 0.87121 ( 84) hydrogen bonds : bond 0.05191 ( 616) hydrogen bonds : angle 6.56792 ( 1629) link_ALPHA1-2 : bond 0.01190 ( 11) link_ALPHA1-2 : angle 3.42922 ( 33) link_ALPHA1-3 : bond 0.01203 ( 9) link_ALPHA1-3 : angle 2.21876 ( 27) link_ALPHA1-6 : bond 0.00285 ( 7) link_ALPHA1-6 : angle 2.08939 ( 21) link_BETA1-4 : bond 0.00460 ( 18) link_BETA1-4 : angle 2.04481 ( 54) link_NAG-ASN : bond 0.00286 ( 12) link_NAG-ASN : angle 1.71252 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 326 time to evaluate : 0.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 411 THR cc_start: 0.7777 (p) cc_final: 0.7393 (m) REVERT: C 48 MET cc_start: 0.7484 (tpp) cc_final: 0.7178 (mmt) REVERT: C 102 ILE cc_start: 0.9309 (tp) cc_final: 0.8889 (pt) REVERT: F 411 THR cc_start: 0.7560 (p) cc_final: 0.7149 (m) REVERT: F 424 ILE cc_start: 0.9468 (mm) cc_final: 0.9257 (mm) REVERT: G 609 PRO cc_start: 0.8172 (Cg_exo) cc_final: 0.7890 (Cg_endo) REVERT: H 102 ILE cc_start: 0.9155 (tp) cc_final: 0.8758 (pt) REVERT: I 234 LEU cc_start: 0.6492 (mm) cc_final: 0.6174 (mm) REVERT: I 263 ASN cc_start: 0.8059 (t0) cc_final: 0.7588 (t0) REVERT: K 127 VAL cc_start: 0.7629 (t) cc_final: 0.7425 (t) REVERT: M 29 PHE cc_start: 0.5879 (p90) cc_final: 0.5062 (p90) REVERT: M 76 ILE cc_start: 0.8322 (pt) cc_final: 0.8029 (tp) REVERT: N 263 ASN cc_start: 0.7601 (t0) cc_final: 0.7263 (t0) outliers start: 2 outliers final: 1 residues processed: 327 average time/residue: 0.1488 time to fit residues: 72.3719 Evaluate side-chains 220 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 219 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 160 optimal weight: 9.9990 chunk 183 optimal weight: 3.9990 chunk 74 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 94 optimal weight: 2.9990 chunk 77 optimal weight: 9.9990 chunk 152 optimal weight: 9.9990 chunk 162 optimal weight: 8.9990 chunk 154 optimal weight: 3.9990 chunk 201 optimal weight: 0.5980 chunk 116 optimal weight: 0.6980 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN B 651 ASN G 591 GLN G 651 ASN ** K 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 249 HIS L 651 ASN ** L 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 658 GLN M 43 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.127262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.116618 restraints weight = 41097.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.115788 restraints weight = 90443.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.113950 restraints weight = 92267.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.112650 restraints weight = 99800.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.112742 restraints weight = 80152.371| |-----------------------------------------------------------------------------| r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 20256 Z= 0.220 Angle : 0.749 10.072 27661 Z= 0.385 Chirality : 0.049 0.216 3242 Planarity : 0.005 0.051 3411 Dihedral : 10.376 79.325 3766 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.32 % Favored : 93.43 % Rotamer: Outliers : 0.14 % Allowed : 4.25 % Favored : 95.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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 aren not related in a simple way. whole: -1.65 (0.16), residues: 2420 helix: -0.53 (0.27), residues: 360 sheet: -0.56 (0.20), residues: 685 loop : -1.55 (0.16), residues: 1375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG N 293 TYR 0.020 0.002 TYR H 33 PHE 0.017 0.002 PHE C 64 TRP 0.037 0.002 TRP M 47 HIS 0.011 0.002 HIS K 249 Details of bonding type rmsd covalent geometry : bond 0.00520 (20157) covalent geometry : angle 0.72899 (27406) SS BOND : bond 0.00420 ( 42) SS BOND : angle 0.88470 ( 84) hydrogen bonds : bond 0.05055 ( 616) hydrogen bonds : angle 6.19244 ( 1629) link_ALPHA1-2 : bond 0.01097 ( 11) link_ALPHA1-2 : angle 3.10043 ( 33) link_ALPHA1-3 : bond 0.01260 ( 9) link_ALPHA1-3 : angle 1.64800 ( 27) link_ALPHA1-6 : bond 0.00282 ( 7) link_ALPHA1-6 : angle 2.13490 ( 21) link_BETA1-4 : bond 0.00590 ( 18) link_BETA1-4 : angle 2.19832 ( 54) link_NAG-ASN : bond 0.00450 ( 12) link_NAG-ASN : angle 2.10739 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 289 time to evaluate : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 VAL cc_start: 0.8320 (t) cc_final: 0.8024 (t) REVERT: A 411 THR cc_start: 0.7749 (p) cc_final: 0.7398 (m) REVERT: F 411 THR cc_start: 0.7506 (p) cc_final: 0.7153 (m) REVERT: G 626 MET cc_start: 0.7476 (tpp) cc_final: 0.7086 (tpt) REVERT: I 263 ASN cc_start: 0.7991 (t0) cc_final: 0.7249 (t0) REVERT: K 154 MET cc_start: 0.8880 (mmm) cc_final: 0.8410 (mmt) REVERT: K 166 ARG cc_start: 0.7766 (mmt90) cc_final: 0.7470 (mtp180) REVERT: K 411 THR cc_start: 0.7796 (p) cc_final: 0.7330 (m) REVERT: L 609 PRO cc_start: 0.8045 (Cg_exo) cc_final: 0.7668 (Cg_endo) REVERT: M 76 ILE cc_start: 0.8205 (pt) cc_final: 0.7864 (tp) REVERT: N 234 LEU cc_start: 0.6418 (mm) cc_final: 0.5990 (mm) REVERT: N 263 ASN cc_start: 0.7995 (t0) cc_final: 0.7493 (t0) outliers start: 3 outliers final: 1 residues processed: 291 average time/residue: 0.1424 time to fit residues: 62.8812 Evaluate side-chains 216 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 215 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 188 optimal weight: 5.9990 chunk 226 optimal weight: 5.9990 chunk 41 optimal weight: 10.0000 chunk 37 optimal weight: 0.9990 chunk 200 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 134 optimal weight: 9.9990 chunk 71 optimal weight: 8.9990 chunk 38 optimal weight: 0.6980 chunk 65 optimal weight: 9.9990 chunk 93 optimal weight: 0.9980 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN A 249 HIS B 651 ASN G 651 ASN H 6 GLN H 113 ASN K 249 HIS L 651 ASN ** L 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.125941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.112704 restraints weight = 40964.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.112196 restraints weight = 87609.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.111630 restraints weight = 88535.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.110718 restraints weight = 86198.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.110869 restraints weight = 81429.752| |-----------------------------------------------------------------------------| r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 20256 Z= 0.213 Angle : 0.729 9.971 27661 Z= 0.372 Chirality : 0.048 0.191 3242 Planarity : 0.005 0.052 3411 Dihedral : 10.023 75.803 3766 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.49 % Favored : 93.26 % Rotamer: Outliers : 0.09 % Allowed : 3.92 % Favored : 95.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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 aren not related in a simple way. whole: -1.71 (0.16), residues: 2420 helix: -0.44 (0.27), residues: 360 sheet: -0.56 (0.20), residues: 667 loop : -1.65 (0.16), residues: 1393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 166 TYR 0.030 0.002 TYR F 217 PHE 0.012 0.002 PHE F 233 TRP 0.018 0.002 TRP A 69 HIS 0.007 0.002 HIS K 249 Details of bonding type rmsd covalent geometry : bond 0.00506 (20157) covalent geometry : angle 0.70840 (27406) SS BOND : bond 0.00333 ( 42) SS BOND : angle 0.83217 ( 84) hydrogen bonds : bond 0.04554 ( 616) hydrogen bonds : angle 5.98290 ( 1629) link_ALPHA1-2 : bond 0.00961 ( 11) link_ALPHA1-2 : angle 2.84947 ( 33) link_ALPHA1-3 : bond 0.01169 ( 9) link_ALPHA1-3 : angle 1.78568 ( 27) link_ALPHA1-6 : bond 0.00304 ( 7) link_ALPHA1-6 : angle 2.10188 ( 21) link_BETA1-4 : bond 0.00577 ( 18) link_BETA1-4 : angle 2.27593 ( 54) link_NAG-ASN : bond 0.00397 ( 12) link_NAG-ASN : angle 1.99424 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 268 time to evaluate : 0.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 VAL cc_start: 0.8512 (t) cc_final: 0.8296 (t) REVERT: A 411 THR cc_start: 0.7628 (p) cc_final: 0.7297 (m) REVERT: B 632 ASP cc_start: 0.6974 (t70) cc_final: 0.6744 (t0) REVERT: C 48 MET cc_start: 0.7789 (mmt) cc_final: 0.7402 (mmt) REVERT: F 369 MET cc_start: 0.8376 (ttp) cc_final: 0.8136 (ttp) REVERT: F 411 THR cc_start: 0.7594 (p) cc_final: 0.7273 (m) REVERT: I 263 ASN cc_start: 0.8071 (t0) cc_final: 0.7352 (t0) REVERT: K 104 MET cc_start: 0.9155 (ttm) cc_final: 0.7936 (ttm) REVERT: K 154 MET cc_start: 0.8860 (mmm) cc_final: 0.8391 (mmt) REVERT: K 411 THR cc_start: 0.7745 (p) cc_final: 0.7320 (m) REVERT: L 609 PRO cc_start: 0.8185 (Cg_exo) cc_final: 0.7863 (Cg_endo) REVERT: N 263 ASN cc_start: 0.7773 (t0) cc_final: 0.7298 (t0) outliers start: 2 outliers final: 0 residues processed: 270 average time/residue: 0.1380 time to fit residues: 57.3786 Evaluate side-chains 205 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 205 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 182 optimal weight: 0.4980 chunk 129 optimal weight: 1.9990 chunk 79 optimal weight: 9.9990 chunk 55 optimal weight: 0.7980 chunk 68 optimal weight: 0.9990 chunk 136 optimal weight: 1.9990 chunk 197 optimal weight: 1.9990 chunk 127 optimal weight: 7.9990 chunk 76 optimal weight: 6.9990 chunk 7 optimal weight: 3.9990 chunk 94 optimal weight: 0.5980 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 160 ASN B 651 ASN F 249 HIS G 651 ASN L 651 ASN ** L 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 292 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.129780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.118812 restraints weight = 40590.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.118059 restraints weight = 82068.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.117265 restraints weight = 89938.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.116451 restraints weight = 86340.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.116157 restraints weight = 96956.720| |-----------------------------------------------------------------------------| r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20256 Z= 0.131 Angle : 0.651 10.139 27661 Z= 0.332 Chirality : 0.045 0.211 3242 Planarity : 0.004 0.048 3411 Dihedral : 9.536 72.713 3766 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.12 % Favored : 93.64 % Rotamer: Outliers : 0.09 % Allowed : 2.22 % Favored : 97.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 aren not related in a simple way. whole: -1.56 (0.16), residues: 2420 helix: -0.25 (0.27), residues: 361 sheet: -0.56 (0.20), residues: 665 loop : -1.52 (0.16), residues: 1394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG N 293 TYR 0.011 0.001 TYR C 95 PHE 0.009 0.001 PHE D 294 TRP 0.017 0.001 TRP N 267 HIS 0.011 0.001 HIS F 249 Details of bonding type rmsd covalent geometry : bond 0.00296 (20157) covalent geometry : angle 0.63039 (27406) SS BOND : bond 0.00342 ( 42) SS BOND : angle 0.97355 ( 84) hydrogen bonds : bond 0.04013 ( 616) hydrogen bonds : angle 5.61322 ( 1629) link_ALPHA1-2 : bond 0.01002 ( 11) link_ALPHA1-2 : angle 2.76774 ( 33) link_ALPHA1-3 : bond 0.01213 ( 9) link_ALPHA1-3 : angle 1.63191 ( 27) link_ALPHA1-6 : bond 0.00240 ( 7) link_ALPHA1-6 : angle 2.11333 ( 21) link_BETA1-4 : bond 0.00520 ( 18) link_BETA1-4 : angle 2.03754 ( 54) link_NAG-ASN : bond 0.00258 ( 12) link_NAG-ASN : angle 1.68810 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 285 time to evaluate : 0.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 VAL cc_start: 0.9335 (p) cc_final: 0.9122 (p) REVERT: A 127 VAL cc_start: 0.8387 (t) cc_final: 0.8186 (t) REVERT: A 411 THR cc_start: 0.7545 (p) cc_final: 0.7245 (m) REVERT: B 623 TRP cc_start: 0.6609 (m-10) cc_final: 0.6383 (m-10) REVERT: C 48 MET cc_start: 0.7740 (mmt) cc_final: 0.7393 (mmt) REVERT: F 369 MET cc_start: 0.8502 (ttp) cc_final: 0.8223 (ttp) REVERT: F 411 THR cc_start: 0.7624 (p) cc_final: 0.7312 (m) REVERT: F 426 MET cc_start: 0.5823 (mtm) cc_final: 0.5364 (mtt) REVERT: I 263 ASN cc_start: 0.7955 (t0) cc_final: 0.7241 (t0) REVERT: K 154 MET cc_start: 0.8779 (mmm) cc_final: 0.8439 (mmt) REVERT: K 369 MET cc_start: 0.8350 (ttp) cc_final: 0.8098 (ttp) REVERT: K 411 THR cc_start: 0.7557 (p) cc_final: 0.7202 (m) REVERT: L 609 PRO cc_start: 0.8130 (Cg_exo) cc_final: 0.7864 (Cg_endo) REVERT: N 263 ASN cc_start: 0.7839 (t0) cc_final: 0.7346 (t0) outliers start: 2 outliers final: 1 residues processed: 285 average time/residue: 0.1459 time to fit residues: 64.1449 Evaluate side-chains 208 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 207 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 15 optimal weight: 3.9990 chunk 228 optimal weight: 7.9990 chunk 230 optimal weight: 30.0000 chunk 28 optimal weight: 0.9990 chunk 120 optimal weight: 0.1980 chunk 70 optimal weight: 9.9990 chunk 103 optimal weight: 10.0000 chunk 180 optimal weight: 1.9990 chunk 61 optimal weight: 9.9990 chunk 137 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 overall best weight: 2.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN B 651 ASN C 6 GLN G 651 ASN ** K 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 651 ASN M 6 GLN M 43 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.127005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.116057 restraints weight = 40985.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.114898 restraints weight = 87807.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.113944 restraints weight = 99642.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.112876 restraints weight = 97316.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.112951 restraints weight = 89157.764| |-----------------------------------------------------------------------------| r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.3240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 20256 Z= 0.196 Angle : 0.703 10.042 27661 Z= 0.359 Chirality : 0.047 0.204 3242 Planarity : 0.005 0.051 3411 Dihedral : 9.397 72.439 3766 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.24 % Favored : 93.51 % Rotamer: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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 aren not related in a simple way. whole: -1.59 (0.16), residues: 2420 helix: -0.08 (0.28), residues: 342 sheet: -0.53 (0.20), residues: 667 loop : -1.61 (0.16), residues: 1411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 166 TYR 0.032 0.002 TYR B 586 PHE 0.012 0.002 PHE K 376 TRP 0.047 0.002 TRP F 69 HIS 0.005 0.002 HIS K 216 Details of bonding type rmsd covalent geometry : bond 0.00467 (20157) covalent geometry : angle 0.68324 (27406) SS BOND : bond 0.00351 ( 42) SS BOND : angle 1.13959 ( 84) hydrogen bonds : bond 0.04301 ( 616) hydrogen bonds : angle 5.73370 ( 1629) link_ALPHA1-2 : bond 0.00828 ( 11) link_ALPHA1-2 : angle 2.60517 ( 33) link_ALPHA1-3 : bond 0.01168 ( 9) link_ALPHA1-3 : angle 1.64663 ( 27) link_ALPHA1-6 : bond 0.00291 ( 7) link_ALPHA1-6 : angle 2.04454 ( 21) link_BETA1-4 : bond 0.00570 ( 18) link_BETA1-4 : angle 2.22474 ( 54) link_NAG-ASN : bond 0.00419 ( 12) link_NAG-ASN : angle 1.90193 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 257 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 VAL cc_start: 0.8608 (t) cc_final: 0.8405 (t) REVERT: C 48 MET cc_start: 0.7897 (mmt) cc_final: 0.7403 (mmt) REVERT: F 426 MET cc_start: 0.5942 (mtm) cc_final: 0.5423 (mtt) REVERT: G 609 PRO cc_start: 0.8655 (Cg_exo) cc_final: 0.8424 (Cg_endo) REVERT: G 626 MET cc_start: 0.7104 (tpp) cc_final: 0.6716 (tpt) REVERT: I 263 ASN cc_start: 0.8065 (t0) cc_final: 0.7557 (t0) REVERT: K 154 MET cc_start: 0.8748 (mmm) cc_final: 0.8291 (mmt) REVERT: L 609 PRO cc_start: 0.8276 (Cg_exo) cc_final: 0.8036 (Cg_endo) REVERT: N 263 ASN cc_start: 0.7920 (t0) cc_final: 0.7554 (t0) outliers start: 0 outliers final: 0 residues processed: 257 average time/residue: 0.1393 time to fit residues: 54.6071 Evaluate side-chains 202 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 202 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 2 optimal weight: 0.9980 chunk 65 optimal weight: 10.0000 chunk 101 optimal weight: 1.9990 chunk 140 optimal weight: 0.8980 chunk 205 optimal weight: 6.9990 chunk 110 optimal weight: 0.9990 chunk 199 optimal weight: 0.0980 chunk 53 optimal weight: 10.0000 chunk 169 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN B 651 ASN C 43 GLN D 270 GLN F 249 HIS G 651 ASN L 651 ASN ** L 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 270 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.130055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.112777 restraints weight = 40611.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.108924 restraints weight = 50728.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.108900 restraints weight = 60109.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.109112 restraints weight = 57133.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.109017 restraints weight = 54296.621| |-----------------------------------------------------------------------------| r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.3443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20256 Z= 0.120 Angle : 0.634 10.165 27661 Z= 0.322 Chirality : 0.045 0.287 3242 Planarity : 0.004 0.061 3411 Dihedral : 8.933 68.656 3766 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.62 % Favored : 94.13 % Rotamer: Outliers : 0.05 % Allowed : 1.23 % Favored : 98.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 aren not related in a simple way. whole: -1.47 (0.17), residues: 2420 helix: -0.23 (0.28), residues: 361 sheet: -0.46 (0.20), residues: 677 loop : -1.46 (0.16), residues: 1382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG N 293 TYR 0.020 0.001 TYR A 217 PHE 0.010 0.001 PHE H 64 TRP 0.037 0.002 TRP K 69 HIS 0.012 0.001 HIS F 249 Details of bonding type rmsd covalent geometry : bond 0.00268 (20157) covalent geometry : angle 0.61572 (27406) SS BOND : bond 0.00261 ( 42) SS BOND : angle 0.77603 ( 84) hydrogen bonds : bond 0.03783 ( 616) hydrogen bonds : angle 5.40719 ( 1629) link_ALPHA1-2 : bond 0.00826 ( 11) link_ALPHA1-2 : angle 2.59267 ( 33) link_ALPHA1-3 : bond 0.01149 ( 9) link_ALPHA1-3 : angle 1.50819 ( 27) link_ALPHA1-6 : bond 0.00298 ( 7) link_ALPHA1-6 : angle 2.01022 ( 21) link_BETA1-4 : bond 0.00495 ( 18) link_BETA1-4 : angle 1.96604 ( 54) link_NAG-ASN : bond 0.00279 ( 12) link_NAG-ASN : angle 1.59120 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 260 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 VAL cc_start: 0.8489 (t) cc_final: 0.8167 (t) REVERT: B 535 MET cc_start: 0.7177 (mmp) cc_final: 0.6314 (mtp) REVERT: F 107 ASP cc_start: 0.8105 (m-30) cc_final: 0.7786 (t0) REVERT: F 424 ILE cc_start: 0.9496 (mm) cc_final: 0.9280 (mm) REVERT: F 426 MET cc_start: 0.5782 (mtm) cc_final: 0.5329 (mtt) REVERT: G 626 MET cc_start: 0.7214 (tpp) cc_final: 0.6821 (tpt) REVERT: I 263 ASN cc_start: 0.8263 (t0) cc_final: 0.7737 (t0) REVERT: K 154 MET cc_start: 0.8706 (mmm) cc_final: 0.8263 (mmt) REVERT: L 609 PRO cc_start: 0.8572 (Cg_exo) cc_final: 0.8329 (Cg_endo) REVERT: M 115 ASP cc_start: 0.8559 (p0) cc_final: 0.8355 (p0) outliers start: 1 outliers final: 1 residues processed: 260 average time/residue: 0.1388 time to fit residues: 55.3772 Evaluate side-chains 202 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 201 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 55 optimal weight: 10.0000 chunk 88 optimal weight: 1.9990 chunk 184 optimal weight: 5.9990 chunk 135 optimal weight: 9.9990 chunk 195 optimal weight: 3.9990 chunk 234 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 114 optimal weight: 0.9980 chunk 68 optimal weight: 0.5980 chunk 217 optimal weight: 3.9990 chunk 171 optimal weight: 6.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN B 651 ASN F 328 GLN G 651 ASN H 6 GLN I 270 GLN ** K 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 651 ASN M 113 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.126724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 94)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.110689 restraints weight = 40849.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.106868 restraints weight = 46655.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.106698 restraints weight = 60832.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.106714 restraints weight = 61698.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.106712 restraints weight = 52819.025| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.3557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 20256 Z= 0.202 Angle : 0.706 9.971 27661 Z= 0.359 Chirality : 0.047 0.260 3242 Planarity : 0.005 0.090 3411 Dihedral : 8.961 69.660 3766 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.57 % Favored : 93.18 % Rotamer: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 aren not related in a simple way. whole: -1.61 (0.17), residues: 2420 helix: -0.27 (0.28), residues: 361 sheet: -0.52 (0.20), residues: 661 loop : -1.59 (0.16), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 166 TYR 0.040 0.002 TYR F 217 PHE 0.015 0.002 PHE M 64 TRP 0.046 0.002 TRP M 47 HIS 0.005 0.002 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00483 (20157) covalent geometry : angle 0.68741 (27406) SS BOND : bond 0.00536 ( 42) SS BOND : angle 1.03481 ( 84) hydrogen bonds : bond 0.04246 ( 616) hydrogen bonds : angle 5.62867 ( 1629) link_ALPHA1-2 : bond 0.00702 ( 11) link_ALPHA1-2 : angle 2.41070 ( 33) link_ALPHA1-3 : bond 0.01198 ( 9) link_ALPHA1-3 : angle 1.51230 ( 27) link_ALPHA1-6 : bond 0.00347 ( 7) link_ALPHA1-6 : angle 1.96753 ( 21) link_BETA1-4 : bond 0.00568 ( 18) link_BETA1-4 : angle 2.25140 ( 54) link_NAG-ASN : bond 0.00454 ( 12) link_NAG-ASN : angle 1.88764 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 245 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 VAL cc_start: 0.8603 (t) cc_final: 0.8393 (t) REVERT: A 154 MET cc_start: 0.9062 (mmm) cc_final: 0.8785 (mmt) REVERT: B 535 MET cc_start: 0.7440 (mmp) cc_final: 0.6288 (mtp) REVERT: F 426 MET cc_start: 0.6045 (mtm) cc_final: 0.5595 (mtt) REVERT: G 626 MET cc_start: 0.7449 (tpp) cc_final: 0.7247 (tpt) REVERT: K 154 MET cc_start: 0.8656 (mmm) cc_final: 0.8246 (mmt) REVERT: K 213 ILE cc_start: 0.9017 (mm) cc_final: 0.8499 (mt) REVERT: K 369 MET cc_start: 0.8314 (ttp) cc_final: 0.8091 (ttp) REVERT: L 609 PRO cc_start: 0.8598 (Cg_exo) cc_final: 0.8381 (Cg_endo) REVERT: M 115 ASP cc_start: 0.8609 (p0) cc_final: 0.8287 (p0) outliers start: 0 outliers final: 0 residues processed: 245 average time/residue: 0.1399 time to fit residues: 52.6834 Evaluate side-chains 191 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 191 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 56 optimal weight: 8.9990 chunk 237 optimal weight: 9.9990 chunk 207 optimal weight: 0.2980 chunk 90 optimal weight: 0.8980 chunk 84 optimal weight: 7.9990 chunk 16 optimal weight: 4.9990 chunk 69 optimal weight: 30.0000 chunk 164 optimal weight: 3.9990 chunk 38 optimal weight: 0.0870 chunk 180 optimal weight: 10.0000 chunk 197 optimal weight: 0.9980 overall best weight: 1.2560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN B 651 ASN G 651 ASN L 651 ASN M 43 GLN M 113 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.128485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.113968 restraints weight = 40822.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.113521 restraints weight = 87201.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.113326 restraints weight = 87098.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.113137 restraints weight = 70491.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.113149 restraints weight = 74893.052| |-----------------------------------------------------------------------------| r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.3691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20256 Z= 0.138 Angle : 0.648 10.009 27661 Z= 0.331 Chirality : 0.045 0.235 3242 Planarity : 0.005 0.070 3411 Dihedral : 8.612 66.829 3766 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.99 % Favored : 93.76 % Rotamer: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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 aren not related in a simple way. whole: -1.56 (0.17), residues: 2420 helix: -0.31 (0.28), residues: 364 sheet: -0.51 (0.20), residues: 671 loop : -1.52 (0.16), residues: 1385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG F 166 TYR 0.031 0.001 TYR B 586 PHE 0.010 0.001 PHE H 64 TRP 0.052 0.002 TRP M 47 HIS 0.004 0.001 HIS F 216 Details of bonding type rmsd covalent geometry : bond 0.00321 (20157) covalent geometry : angle 0.62984 (27406) SS BOND : bond 0.00322 ( 42) SS BOND : angle 1.01838 ( 84) hydrogen bonds : bond 0.03911 ( 616) hydrogen bonds : angle 5.47148 ( 1629) link_ALPHA1-2 : bond 0.00725 ( 11) link_ALPHA1-2 : angle 2.43085 ( 33) link_ALPHA1-3 : bond 0.01121 ( 9) link_ALPHA1-3 : angle 1.44666 ( 27) link_ALPHA1-6 : bond 0.00344 ( 7) link_ALPHA1-6 : angle 1.90465 ( 21) link_BETA1-4 : bond 0.00476 ( 18) link_BETA1-4 : angle 2.00543 ( 54) link_NAG-ASN : bond 0.00278 ( 12) link_NAG-ASN : angle 1.65235 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 242 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 MET cc_start: 0.9044 (mmm) cc_final: 0.8757 (mmt) REVERT: A 475 MET cc_start: 0.7675 (tpp) cc_final: 0.7124 (tpp) REVERT: B 535 MET cc_start: 0.7257 (mmp) cc_final: 0.6328 (mtp) REVERT: F 426 MET cc_start: 0.5820 (mtm) cc_final: 0.5407 (mtt) REVERT: K 154 MET cc_start: 0.8680 (mmm) cc_final: 0.8232 (mmt) REVERT: L 609 PRO cc_start: 0.8440 (Cg_exo) cc_final: 0.8234 (Cg_endo) REVERT: M 115 ASP cc_start: 0.8569 (p0) cc_final: 0.8243 (p0) outliers start: 0 outliers final: 0 residues processed: 242 average time/residue: 0.1418 time to fit residues: 52.7144 Evaluate side-chains 194 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 112 optimal weight: 0.2980 chunk 15 optimal weight: 0.9990 chunk 207 optimal weight: 0.0980 chunk 50 optimal weight: 1.9990 chunk 32 optimal weight: 7.9990 chunk 209 optimal weight: 0.6980 chunk 58 optimal weight: 7.9990 chunk 49 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 219 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 HIS A 160 ASN B 651 ASN G 651 ASN I 246 GLN L 651 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.133106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.117036 restraints weight = 40971.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.116336 restraints weight = 79141.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.116460 restraints weight = 73520.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.115802 restraints weight = 66423.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.115835 restraints weight = 72269.214| |-----------------------------------------------------------------------------| r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.3860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20256 Z= 0.113 Angle : 0.630 10.116 27661 Z= 0.320 Chirality : 0.045 0.225 3242 Planarity : 0.005 0.108 3411 Dihedral : 8.065 61.541 3766 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.62 % Favored : 94.13 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 aren not related in a simple way. whole: -1.46 (0.17), residues: 2420 helix: -0.24 (0.28), residues: 367 sheet: -0.50 (0.20), residues: 674 loop : -1.42 (0.16), residues: 1379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 293 TYR 0.029 0.001 TYR B 586 PHE 0.010 0.001 PHE N 294 TRP 0.052 0.002 TRP M 47 HIS 0.004 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00249 (20157) covalent geometry : angle 0.61374 (27406) SS BOND : bond 0.00284 ( 42) SS BOND : angle 0.99591 ( 84) hydrogen bonds : bond 0.03668 ( 616) hydrogen bonds : angle 5.29937 ( 1629) link_ALPHA1-2 : bond 0.00715 ( 11) link_ALPHA1-2 : angle 2.36640 ( 33) link_ALPHA1-3 : bond 0.01119 ( 9) link_ALPHA1-3 : angle 1.42480 ( 27) link_ALPHA1-6 : bond 0.00407 ( 7) link_ALPHA1-6 : angle 1.81817 ( 21) link_BETA1-4 : bond 0.00517 ( 18) link_BETA1-4 : angle 1.83860 ( 54) link_NAG-ASN : bond 0.00260 ( 12) link_NAG-ASN : angle 1.48689 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 257 time to evaluate : 0.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 MET cc_start: 0.8993 (mmm) cc_final: 0.8713 (mmt) REVERT: A 475 MET cc_start: 0.7746 (tpp) cc_final: 0.7337 (tpp) REVERT: B 535 MET cc_start: 0.7295 (mmp) cc_final: 0.6264 (mtp) REVERT: F 107 ASP cc_start: 0.8127 (m-30) cc_final: 0.7880 (t0) REVERT: F 426 MET cc_start: 0.5719 (mtm) cc_final: 0.5241 (mtt) REVERT: K 154 MET cc_start: 0.8627 (mmm) cc_final: 0.8235 (mmt) REVERT: M 115 ASP cc_start: 0.8629 (p0) cc_final: 0.8330 (p0) outliers start: 0 outliers final: 0 residues processed: 257 average time/residue: 0.1359 time to fit residues: 53.8126 Evaluate side-chains 201 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 201 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 57 optimal weight: 6.9990 chunk 115 optimal weight: 6.9990 chunk 36 optimal weight: 40.0000 chunk 82 optimal weight: 6.9990 chunk 26 optimal weight: 3.9990 chunk 193 optimal weight: 1.9990 chunk 161 optimal weight: 7.9990 chunk 76 optimal weight: 9.9990 chunk 182 optimal weight: 4.9990 chunk 216 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN B 651 ASN G 651 ASN ** K 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 328 GLN L 651 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.123192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.110586 restraints weight = 41415.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.109208 restraints weight = 83579.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.107612 restraints weight = 81449.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.107050 restraints weight = 87481.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.106938 restraints weight = 77053.664| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.3925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.072 20256 Z= 0.328 Angle : 0.845 9.621 27661 Z= 0.433 Chirality : 0.052 0.249 3242 Planarity : 0.007 0.130 3411 Dihedral : 9.082 68.345 3766 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.89 % Favored : 91.86 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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 aren not related in a simple way. whole: -1.86 (0.16), residues: 2420 helix: -0.46 (0.28), residues: 361 sheet: -0.62 (0.20), residues: 658 loop : -1.80 (0.16), residues: 1401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG N 293 TYR 0.021 0.002 TYR M 33 PHE 0.017 0.003 PHE F 382 TRP 0.059 0.004 TRP M 47 HIS 0.009 0.003 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00793 (20157) covalent geometry : angle 0.82447 (27406) SS BOND : bond 0.00543 ( 42) SS BOND : angle 1.65595 ( 84) hydrogen bonds : bond 0.04835 ( 616) hydrogen bonds : angle 6.02987 ( 1629) link_ALPHA1-2 : bond 0.00576 ( 11) link_ALPHA1-2 : angle 2.30586 ( 33) link_ALPHA1-3 : bond 0.01319 ( 9) link_ALPHA1-3 : angle 1.53734 ( 27) link_ALPHA1-6 : bond 0.00521 ( 7) link_ALPHA1-6 : angle 1.90282 ( 21) link_BETA1-4 : bond 0.00761 ( 18) link_BETA1-4 : angle 2.62728 ( 54) link_NAG-ASN : bond 0.00836 ( 12) link_NAG-ASN : angle 2.29432 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2563.65 seconds wall clock time: 45 minutes 38.29 seconds (2738.29 seconds total)