Starting phenix.real_space_refine on Sat Jul 4 09:04:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8sb0_40286/07_2026/8sb0_40286.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sb0_40286/07_2026/8sb0_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 { model { file = "/net/cci-nas-00/data/ceres_data/8sb0_40286/07_2026/8sb0_40286.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sb0_40286/07_2026/8sb0_40286.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8sb0_40286/07_2026/8sb0_40286.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8sb0_40286/07_2026/8sb0_40286.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8sb0_40286/07_2026/8sb0_40286.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sb0_40286/07_2026/8sb0_40286.map" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.010 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-dev-6108/lib/python3.11/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 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 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 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 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 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 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 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 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 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 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 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 chiralities: 2 Time building chain proxies: 4.16, per 1000 atoms: 0.21 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: 1.72 Conformation dependent library (CDL) restraints added in 765.9 milliseconds 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: 0.52 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: 3.16 Time building geometry restraints manager: 2.23 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 - 17.99: 10635 17.99 - 35.99: 837 35.99 - 53.98: 141 53.98 - 71.97: 28 71.97 - 89.96: 23 Dihedral angle restraints: 11664 sinusoidal: 4615 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 11661 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: 1.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 17.400 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.060 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:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 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 : 13.581 89.964 7026 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 are 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/Z covalent geometry : bond 0.00562 / 0.27 (20157) covalent geometry : angle 0.94766 / 0.50 (27406) SS BOND : bond 0.00462 / 0.23 ( 42) SS BOND : angle 1.75500 / 1.17 ( 84) hydrogen bonds : bond 0.22357 / 14.81 ( 616) hydrogen bonds : angle 9.35467 / 6.37 ( 1629) link_ALPHA1-2 : bond 0.01382 / 0.78 ( 11) link_ALPHA1-2 : angle 4.52955 / 2.84 ( 33) link_ALPHA1-3 : bond 0.01520 / 0.78 ( 9) link_ALPHA1-3 : angle 4.19129 / 2.82 ( 27) link_ALPHA1-6 : bond 0.00535 / 0.28 ( 7) link_ALPHA1-6 : angle 3.96902 / 2.79 ( 21) link_BETA1-4 : bond 0.00870 / 0.53 ( 18) link_BETA1-4 : angle 3.33917 / 2.30 ( 54) link_NAG-ASN : bond 0.00245 / 0.12 ( 12) link_NAG-ASN : angle 2.46677 / 1.51 ( 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 : 0.763 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: 0.7595 (t0) cc_final: 0.7260 (t0) outliers start: 1 outliers final: 0 residues processed: 364 average time/residue: 0.1505 time to fit residues: 82.5947 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 : 0.585 ------------------------------------------------------------------------------- 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... 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 = 0.3804 r_free = 0.3804 target = 0.133382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.120308 restraints weight = 40667.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.119423 restraints weight = 79484.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.119164 restraints weight = 83743.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.118060 restraints weight = 77320.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.118195 restraints weight = 76629.797| |-----------------------------------------------------------------------------| r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 20256 Z= 0.132 Angle : 0.702 10.407 27661 Z= 0.363 Chirality : 0.046 0.201 3242 Planarity : 0.005 0.050 3411 Dihedral : 6.308 33.905 2635 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.00 % Favored : 94.75 % Rotamer: Outliers : 0.09 % Allowed : 3.40 % Favored : 96.51 % 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 are not related in a simple way. whole: -1.47 (0.16), residues: 2420 helix: -0.42 (0.26), residues: 336 sheet: -0.58 (0.19), residues: 702 loop : -1.33 (0.16), residues: 1382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 166 TYR 0.012 0.001 TYR C 33 PHE 0.019 0.001 PHE C 64 TRP 0.038 0.002 TRP H 47 HIS 0.006 0.001 HIS A 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.13 (20157) covalent geometry : angle 0.68232 / 0.36 (27406) SS BOND : bond 0.00240 / 0.16 ( 42) SS BOND : angle 0.88861 / 0.62 ( 84) hydrogen bonds : bond 0.05426 / 3.56 ( 616) hydrogen bonds : angle 6.63882 / 4.50 ( 1629) link_ALPHA1-2 : bond 0.01272 / 0.75 ( 11) link_ALPHA1-2 : angle 3.36288 / 2.07 ( 33) link_ALPHA1-3 : bond 0.00922 / 0.55 ( 9) link_ALPHA1-3 : angle 1.87557 / 1.30 ( 27) link_ALPHA1-6 : bond 0.00204 / 0.11 ( 7) link_ALPHA1-6 : angle 1.90675 / 1.17 ( 21) link_BETA1-4 : bond 0.00423 / 0.24 ( 18) link_BETA1-4 : angle 1.82493 / 1.32 ( 54) link_NAG-ASN : bond 0.00271 / 0.14 ( 12) link_NAG-ASN : angle 1.64769 / 1.02 ( 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 : 0.779 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: 0.8246 (t) cc_final: 0.7933 (t) REVERT: A 411 THR cc_start: 0.7777 (p) cc_final: 0.7412 (m) REVERT: C 48 MET cc_start: 0.7482 (tpp) cc_final: 0.7148 (mmt) REVERT: C 102 ILE cc_start: 0.9319 (tp) cc_final: 0.8876 (pt) REVERT: F 411 THR cc_start: 0.7626 (p) cc_final: 0.7220 (m) REVERT: F 424 ILE cc_start: 0.9472 (mm) cc_final: 0.9270 (mm) REVERT: G 609 PRO cc_start: 0.8171 (Cg_exo) cc_final: 0.7884 (Cg_endo) REVERT: H 102 ILE cc_start: 0.9172 (tp) cc_final: 0.8749 (pt) REVERT: I 234 LEU cc_start: 0.6517 (mm) cc_final: 0.6197 (mm) REVERT: I 263 ASN cc_start: 0.8035 (t0) cc_final: 0.7557 (t0) REVERT: K 127 VAL cc_start: 0.7664 (t) cc_final: 0.7450 (t) REVERT: M 29 PHE cc_start: 0.5861 (p90) cc_final: 0.5017 (p90) REVERT: M 76 ILE cc_start: 0.8312 (pt) cc_final: 0.8034 (tp) REVERT: N 263 ASN cc_start: 0.7645 (t0) cc_final: 0.7315 (t0) outliers start: 2 outliers final: 1 residues processed: 327 average time/residue: 0.1581 time to fit residues: 77.4213 Evaluate side-chains 221 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 220 time to evaluate : 0.702 ------------------------------------------------------------------------------- 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: 10.0000 chunk 183 optimal weight: 2.9990 chunk 74 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 94 optimal weight: 4.9990 chunk 77 optimal weight: 10.0000 chunk 152 optimal weight: 8.9990 chunk 162 optimal weight: 8.9990 chunk 154 optimal weight: 1.9990 chunk 201 optimal weight: 0.4980 chunk 116 optimal weight: 9.9990 overall best weight: 3.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 160 ASN B 651 ASN D 292 ASN F 328 GLN 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.124528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.111651 restraints weight = 41178.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.110333 restraints weight = 89406.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.109987 restraints weight = 97747.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.109297 restraints weight = 80981.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.109187 restraints weight = 84180.999| |-----------------------------------------------------------------------------| r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 20256 Z= 0.286 Angle : 0.821 9.819 27661 Z= 0.423 Chirality : 0.051 0.212 3242 Planarity : 0.006 0.078 3411 Dihedral : 6.573 33.564 2635 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.90 % Favored : 92.85 % Rotamer: Outliers : 0.24 % Allowed : 4.53 % Favored : 95.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.80 (0.16), residues: 2420 helix: -0.64 (0.27), residues: 360 sheet: -0.61 (0.20), residues: 685 loop : -1.69 (0.16), residues: 1375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG N 293 TYR 0.025 0.002 TYR M 33 PHE 0.019 0.003 PHE C 64 TRP 0.029 0.002 TRP F 35 HIS 0.011 0.003 HIS A 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00686 / 0.29 (20157) covalent geometry : angle 0.80332 / 0.42 (27406) SS BOND : bond 0.00840 / 0.57 ( 42) SS BOND : angle 1.00962 / 0.66 ( 84) hydrogen bonds : bond 0.05397 / 3.52 ( 616) hydrogen bonds : angle 6.42482 / 4.36 ( 1629) link_ALPHA1-2 : bond 0.01035 / 0.60 ( 11) link_ALPHA1-2 : angle 2.94661 / 1.78 ( 33) link_ALPHA1-3 : bond 0.01006 / 0.57 ( 9) link_ALPHA1-3 : angle 1.72010 / 1.20 ( 27) link_ALPHA1-6 : bond 0.00146 / 0.06 ( 7) link_ALPHA1-6 : angle 2.15311 / 1.31 ( 21) link_BETA1-4 : bond 0.00584 / 0.36 ( 18) link_BETA1-4 : angle 2.23919 / 1.66 ( 54) link_NAG-ASN : bond 0.00655 / 0.38 ( 12) link_NAG-ASN : angle 2.05592 / 1.26 ( 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 283 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 278 time to evaluate : 0.796 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 411 THR cc_start: 0.7757 (p) cc_final: 0.7414 (m) REVERT: C 48 MET cc_start: 0.7730 (tpp) cc_final: 0.7074 (mmt) REVERT: F 411 THR cc_start: 0.7606 (p) cc_final: 0.7271 (m) REVERT: G 626 MET cc_start: 0.7576 (tpp) cc_final: 0.7088 (tpt) REVERT: H 102 ILE cc_start: 0.9305 (tp) cc_final: 0.9072 (pt) REVERT: I 263 ASN cc_start: 0.7995 (t0) cc_final: 0.7118 (t0) REVERT: K 127 VAL cc_start: 0.8380 (t) cc_final: 0.8178 (t) REVERT: K 154 MET cc_start: 0.8889 (mmm) cc_final: 0.8447 (mmt) REVERT: K 411 THR cc_start: 0.7849 (p) cc_final: 0.7349 (m) REVERT: L 609 PRO cc_start: 0.8195 (Cg_exo) cc_final: 0.7847 (Cg_endo) REVERT: M 76 ILE cc_start: 0.8142 (pt) cc_final: 0.7822 (tp) REVERT: N 263 ASN cc_start: 0.7958 (t0) cc_final: 0.7444 (t0) outliers start: 5 outliers final: 2 residues processed: 282 average time/residue: 0.1470 time to fit residues: 63.2601 Evaluate side-chains 209 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 207 time to evaluate : 0.808 ------------------------------------------------------------------------------- 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: 3.9990 chunk 226 optimal weight: 9.9990 chunk 41 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 chunk 200 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 134 optimal weight: 6.9990 chunk 71 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 chunk 65 optimal weight: 10.0000 chunk 93 optimal weight: 0.7980 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 160 ASN B 651 ASN C 43 GLN G 651 ASN H 6 GLN H 113 ASN K 249 HIS L 651 ASN ** L 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 113 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.125845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.112057 restraints weight = 41427.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.110782 restraints weight = 87719.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.110489 restraints weight = 95777.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.109190 restraints weight = 85309.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.109425 restraints weight = 82085.181| |-----------------------------------------------------------------------------| r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 20256 Z= 0.211 Angle : 0.725 10.075 27661 Z= 0.372 Chirality : 0.047 0.204 3242 Planarity : 0.005 0.051 3411 Dihedral : 6.364 36.807 2635 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.45 % Favored : 93.31 % Rotamer: Outliers : 0.05 % Allowed : 4.39 % Favored : 95.56 % 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 are not related in a simple way. whole: -1.74 (0.16), residues: 2420 helix: -0.26 (0.28), residues: 342 sheet: -0.61 (0.20), residues: 675 loop : -1.70 (0.16), residues: 1403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG K 166 TYR 0.013 0.001 TYR K 191 PHE 0.013 0.002 PHE I 294 TRP 0.036 0.002 TRP M 47 HIS 0.008 0.002 HIS K 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00503 / 0.21 (20157) covalent geometry : angle 0.70750 / 0.37 (27406) SS BOND : bond 0.00457 / 0.30 ( 42) SS BOND : angle 1.00191 / 0.65 ( 84) hydrogen bonds : bond 0.04629 / 3.01 ( 616) hydrogen bonds : angle 6.03262 / 4.09 ( 1629) link_ALPHA1-2 : bond 0.01027 / 0.60 ( 11) link_ALPHA1-2 : angle 2.66976 / 1.59 ( 33) link_ALPHA1-3 : bond 0.00864 / 0.48 ( 9) link_ALPHA1-3 : angle 1.66981 / 1.12 ( 27) link_ALPHA1-6 : bond 0.00115 / 0.05 ( 7) link_ALPHA1-6 : angle 2.07223 / 1.28 ( 21) link_BETA1-4 : bond 0.00456 / 0.27 ( 18) link_BETA1-4 : angle 1.95160 / 1.44 ( 54) link_NAG-ASN : bond 0.00389 / 0.23 ( 12) link_NAG-ASN : angle 1.81231 / 1.11 ( 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 266 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 265 time to evaluate : 0.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 411 THR cc_start: 0.7713 (p) cc_final: 0.7401 (m) REVERT: B 575 GLN cc_start: 0.7939 (tm-30) cc_final: 0.7687 (tm-30) REVERT: C 48 MET cc_start: 0.7851 (tpp) cc_final: 0.7152 (mmt) REVERT: F 411 THR cc_start: 0.7768 (p) cc_final: 0.7427 (m) REVERT: G 609 PRO cc_start: 0.8603 (Cg_exo) cc_final: 0.8355 (Cg_endo) REVERT: G 626 MET cc_start: 0.7607 (tpp) cc_final: 0.7255 (tpt) REVERT: I 263 ASN cc_start: 0.7969 (t0) cc_final: 0.7183 (t0) REVERT: K 411 THR cc_start: 0.7735 (p) cc_final: 0.7340 (m) REVERT: L 609 PRO cc_start: 0.8277 (Cg_exo) cc_final: 0.7977 (Cg_endo) REVERT: M 76 ILE cc_start: 0.7989 (pt) cc_final: 0.7776 (tp) REVERT: N 263 ASN cc_start: 0.7789 (t0) cc_final: 0.7381 (t0) outliers start: 1 outliers final: 0 residues processed: 266 average time/residue: 0.1363 time to fit residues: 56.1923 Evaluate side-chains 199 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 199 time to evaluate : 0.688 ------------------------------------------------------------------------------- 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: 0.9990 chunk 129 optimal weight: 0.5980 chunk 79 optimal weight: 9.9990 chunk 55 optimal weight: 10.0000 chunk 68 optimal weight: 5.9990 chunk 136 optimal weight: 8.9990 chunk 197 optimal weight: 1.9990 chunk 127 optimal weight: 6.9990 chunk 76 optimal weight: 10.0000 chunk 7 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 160 ASN B 651 ASN C 43 GLN G 651 ASN K 249 HIS K 328 GLN L 651 ASN L 653 GLN M 6 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.125648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.112162 restraints weight = 40501.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.111253 restraints weight = 86191.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.110884 restraints weight = 91146.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.110177 restraints weight = 75461.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.110116 restraints weight = 76617.309| |-----------------------------------------------------------------------------| r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.3040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 20256 Z= 0.203 Angle : 0.718 9.909 27661 Z= 0.368 Chirality : 0.047 0.205 3242 Planarity : 0.005 0.050 3411 Dihedral : 6.189 34.991 2635 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.53 % Favored : 93.22 % Rotamer: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.70 (0.16), residues: 2420 helix: -0.04 (0.28), residues: 342 sheet: -0.57 (0.20), residues: 667 loop : -1.74 (0.16), residues: 1411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG K 166 TYR 0.012 0.001 TYR K 217 PHE 0.013 0.002 PHE H 64 TRP 0.044 0.002 TRP K 69 HIS 0.007 0.002 HIS K 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00486 / 0.20 (20157) covalent geometry : angle 0.70076 / 0.36 (27406) SS BOND : bond 0.00334 / 0.21 ( 42) SS BOND : angle 1.16367 / 0.73 ( 84) hydrogen bonds : bond 0.04540 / 2.94 ( 616) hydrogen bonds : angle 5.87202 / 3.98 ( 1629) link_ALPHA1-2 : bond 0.00835 / 0.50 ( 11) link_ALPHA1-2 : angle 2.48401 / 1.47 ( 33) link_ALPHA1-3 : bond 0.00919 / 0.51 ( 9) link_ALPHA1-3 : angle 1.61108 / 1.09 ( 27) link_ALPHA1-6 : bond 0.00085 / 0.04 ( 7) link_ALPHA1-6 : angle 2.07137 / 1.28 ( 21) link_BETA1-4 : bond 0.00463 / 0.27 ( 18) link_BETA1-4 : angle 1.92147 / 1.41 ( 54) link_NAG-ASN : bond 0.00427 / 0.26 ( 12) link_NAG-ASN : angle 1.79641 / 1.10 ( 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 268 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 268 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 411 THR cc_start: 0.7680 (p) cc_final: 0.7405 (m) REVERT: B 575 GLN cc_start: 0.7924 (tm-30) cc_final: 0.7592 (tm-30) REVERT: C 48 MET cc_start: 0.8009 (tpp) cc_final: 0.7292 (mmt) REVERT: F 369 MET cc_start: 0.8182 (ttp) cc_final: 0.7943 (ttp) REVERT: G 609 PRO cc_start: 0.8752 (Cg_exo) cc_final: 0.8496 (Cg_endo) REVERT: G 626 MET cc_start: 0.7559 (tpp) cc_final: 0.7188 (tpt) REVERT: I 263 ASN cc_start: 0.7975 (t0) cc_final: 0.7157 (t0) REVERT: K 104 MET cc_start: 0.9215 (ttm) cc_final: 0.8819 (tpp) REVERT: K 154 MET cc_start: 0.8836 (mmm) cc_final: 0.8369 (mmt) REVERT: L 609 PRO cc_start: 0.8266 (Cg_exo) cc_final: 0.8021 (Cg_endo) REVERT: M 76 ILE cc_start: 0.8117 (pt) cc_final: 0.7842 (tp) REVERT: N 263 ASN cc_start: 0.8037 (t0) cc_final: 0.7430 (t0) outliers start: 0 outliers final: 0 residues processed: 268 average time/residue: 0.1351 time to fit residues: 56.0331 Evaluate side-chains 197 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 197 time to evaluate : 0.511 ------------------------------------------------------------------------------- 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: 0.5980 chunk 228 optimal weight: 0.9980 chunk 230 optimal weight: 30.0000 chunk 28 optimal weight: 4.9990 chunk 120 optimal weight: 2.9990 chunk 70 optimal weight: 10.0000 chunk 103 optimal weight: 8.9990 chunk 180 optimal weight: 3.9990 chunk 61 optimal weight: 6.9990 chunk 137 optimal weight: 6.9990 chunk 63 optimal weight: 7.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 160 ASN B 651 ASN C 43 GLN D 270 GLN G 651 ASN I 270 GLN K 249 HIS L 651 ASN M 43 GLN N 270 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.124669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.114063 restraints weight = 40920.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.111329 restraints weight = 89615.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.109984 restraints weight = 95734.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.109132 restraints weight = 97578.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.109218 restraints weight = 87222.119| |-----------------------------------------------------------------------------| r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.3310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 20256 Z= 0.227 Angle : 0.739 9.772 27661 Z= 0.380 Chirality : 0.048 0.298 3242 Planarity : 0.005 0.067 3411 Dihedral : 6.224 35.596 2635 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.19 % Favored : 92.56 % Rotamer: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % 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 are not related in a simple way. whole: -1.76 (0.16), residues: 2420 helix: -0.08 (0.29), residues: 342 sheet: -0.58 (0.20), residues: 659 loop : -1.80 (0.15), residues: 1419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 166 TYR 0.035 0.002 TYR F 217 PHE 0.015 0.002 PHE M 64 TRP 0.049 0.002 TRP H 47 HIS 0.006 0.002 HIS K 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00543 / 0.23 (20157) covalent geometry : angle 0.72224 / 0.38 (27406) SS BOND : bond 0.00508 / 0.33 ( 42) SS BOND : angle 1.21180 / 0.79 ( 84) hydrogen bonds : bond 0.04559 / 2.96 ( 616) hydrogen bonds : angle 5.88345 / 3.99 ( 1629) link_ALPHA1-2 : bond 0.00795 / 0.48 ( 11) link_ALPHA1-2 : angle 2.36272 / 1.38 ( 33) link_ALPHA1-3 : bond 0.00903 / 0.49 ( 9) link_ALPHA1-3 : angle 1.58811 / 1.06 ( 27) link_ALPHA1-6 : bond 0.00107 / 0.05 ( 7) link_ALPHA1-6 : angle 2.03338 / 1.26 ( 21) link_BETA1-4 : bond 0.00500 / 0.30 ( 18) link_BETA1-4 : angle 1.97807 / 1.46 ( 54) link_NAG-ASN : bond 0.00511 / 0.30 ( 12) link_NAG-ASN : angle 1.88563 / 1.16 ( 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 244 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 244 time to evaluate : 0.608 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: C 48 MET cc_start: 0.8011 (tpp) cc_final: 0.7301 (mmt) REVERT: G 609 PRO cc_start: 0.8698 (Cg_exo) cc_final: 0.8471 (Cg_endo) REVERT: G 626 MET cc_start: 0.7609 (tpp) cc_final: 0.7235 (tpt) REVERT: I 263 ASN cc_start: 0.7990 (t0) cc_final: 0.7387 (t0) REVERT: K 154 MET cc_start: 0.8813 (mmm) cc_final: 0.8259 (mmt) REVERT: K 439 ILE cc_start: 0.9434 (mt) cc_final: 0.9092 (mm) REVERT: L 609 PRO cc_start: 0.8398 (Cg_exo) cc_final: 0.8153 (Cg_endo) REVERT: M 76 ILE cc_start: 0.8122 (pt) cc_final: 0.7814 (tp) REVERT: M 115 ASP cc_start: 0.8559 (p0) cc_final: 0.8264 (p0) REVERT: N 263 ASN cc_start: 0.7844 (t0) cc_final: 0.7470 (t0) outliers start: 0 outliers final: 0 residues processed: 244 average time/residue: 0.1372 time to fit residues: 51.5866 Evaluate side-chains 187 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 0.757 ------------------------------------------------------------------------------- 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: 0.8980 chunk 65 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 chunk 140 optimal weight: 6.9990 chunk 205 optimal weight: 6.9990 chunk 110 optimal weight: 1.9990 chunk 199 optimal weight: 0.0170 chunk 53 optimal weight: 7.9990 chunk 169 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 overall best weight: 1.1222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 160 ASN B 651 ASN F 249 HIS G 651 ASN ** G 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 249 HIS L 651 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.127795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.113697 restraints weight = 40668.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.112244 restraints weight = 86971.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.112214 restraints weight = 93174.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.111265 restraints weight = 75701.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.111448 restraints weight = 82183.112| |-----------------------------------------------------------------------------| r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.3454 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= 0.131 Angle : 0.647 9.978 27661 Z= 0.331 Chirality : 0.044 0.237 3242 Planarity : 0.005 0.061 3411 Dihedral : 5.812 34.152 2635 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.07 % Favored : 93.68 % Rotamer: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % 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 are not related in a simple way. whole: -1.60 (0.17), residues: 2420 helix: 0.11 (0.29), residues: 342 sheet: -0.55 (0.20), residues: 656 loop : -1.66 (0.16), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG K 166 TYR 0.012 0.001 TYR A 39 PHE 0.017 0.001 PHE M 64 TRP 0.031 0.002 TRP H 47 HIS 0.012 0.001 HIS F 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (20157) covalent geometry : angle 0.63181 / 0.33 (27406) SS BOND : bond 0.00257 / 0.16 ( 42) SS BOND : angle 0.88717 / 0.59 ( 84) hydrogen bonds : bond 0.04002 / 2.60 ( 616) hydrogen bonds : angle 5.54338 / 3.77 ( 1629) link_ALPHA1-2 : bond 0.00794 / 0.47 ( 11) link_ALPHA1-2 : angle 2.32636 / 1.36 ( 33) link_ALPHA1-3 : bond 0.00850 / 0.47 ( 9) link_ALPHA1-3 : angle 1.58943 / 1.08 ( 27) link_ALPHA1-6 : bond 0.00099 / 0.05 ( 7) link_ALPHA1-6 : angle 1.99837 / 1.26 ( 21) link_BETA1-4 : bond 0.00384 / 0.22 ( 18) link_BETA1-4 : angle 1.64120 / 1.19 ( 54) link_NAG-ASN : bond 0.00271 / 0.15 ( 12) link_NAG-ASN : angle 1.50964 / 0.94 ( 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 256 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 256 time to evaluate : 0.745 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: C 48 MET cc_start: 0.7959 (tpp) cc_final: 0.7264 (mmt) REVERT: F 107 ASP cc_start: 0.8089 (m-30) cc_final: 0.7768 (t0) REVERT: I 263 ASN cc_start: 0.7966 (t0) cc_final: 0.7366 (t0) REVERT: K 104 MET cc_start: 0.9137 (ttm) cc_final: 0.8777 (tpp) REVERT: K 154 MET cc_start: 0.8695 (mmm) cc_final: 0.8273 (mmt) REVERT: L 609 PRO cc_start: 0.8415 (Cg_exo) cc_final: 0.8186 (Cg_endo) REVERT: M 76 ILE cc_start: 0.8069 (pt) cc_final: 0.7765 (tp) REVERT: M 115 ASP cc_start: 0.8592 (p0) cc_final: 0.8253 (p0) outliers start: 0 outliers final: 0 residues processed: 256 average time/residue: 0.1247 time to fit residues: 50.7611 Evaluate side-chains 189 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 0.759 ------------------------------------------------------------------------------- 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: 8.9990 chunk 88 optimal weight: 1.9990 chunk 184 optimal weight: 7.9990 chunk 135 optimal weight: 4.9990 chunk 195 optimal weight: 9.9990 chunk 234 optimal weight: 3.9990 chunk 18 optimal weight: 0.0010 chunk 114 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 217 optimal weight: 8.9990 chunk 171 optimal weight: 4.9990 overall best weight: 2.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 160 ASN B 651 ASN C 43 GLN G 651 ASN ** G 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 6 GLN L 575 GLN L 651 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.124847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.111197 restraints weight = 41047.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.110043 restraints weight = 89058.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.109911 restraints weight = 85385.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.108986 restraints weight = 75813.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.108827 restraints weight = 75896.864| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.3603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 20256 Z= 0.230 Angle : 0.725 9.919 27661 Z= 0.373 Chirality : 0.048 0.251 3242 Planarity : 0.005 0.073 3411 Dihedral : 6.031 33.832 2635 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.64 % Favored : 92.11 % Rotamer: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % 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 are not related in a simple way. whole: -1.77 (0.16), residues: 2420 helix: -0.05 (0.29), residues: 342 sheet: -0.59 (0.20), residues: 646 loop : -1.80 (0.15), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 166 TYR 0.016 0.002 TYR C 95 PHE 0.022 0.002 PHE M 64 TRP 0.046 0.002 TRP M 47 HIS 0.007 0.002 HIS K 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00550 / 0.23 (20157) covalent geometry : angle 0.70986 / 0.37 (27406) SS BOND : bond 0.00398 / 0.27 ( 42) SS BOND : angle 1.13117 / 0.71 ( 84) hydrogen bonds : bond 0.04442 / 2.88 ( 616) hydrogen bonds : angle 5.85525 / 3.97 ( 1629) link_ALPHA1-2 : bond 0.00709 / 0.41 ( 11) link_ALPHA1-2 : angle 2.13981 / 1.25 ( 33) link_ALPHA1-3 : bond 0.00920 / 0.50 ( 9) link_ALPHA1-3 : angle 1.55312 / 1.05 ( 27) link_ALPHA1-6 : bond 0.00195 / 0.09 ( 7) link_ALPHA1-6 : angle 1.96384 / 1.23 ( 21) link_BETA1-4 : bond 0.00524 / 0.31 ( 18) link_BETA1-4 : angle 1.95840 / 1.44 ( 54) link_NAG-ASN : bond 0.00557 / 0.33 ( 12) link_NAG-ASN : angle 1.86071 / 1.14 ( 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 236 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 236 time to evaluate : 0.785 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: 0.9096 (mmm) cc_final: 0.8820 (mmt) REVERT: C 48 MET cc_start: 0.7958 (tpp) cc_final: 0.7423 (mmt) REVERT: I 263 ASN cc_start: 0.7998 (t0) cc_final: 0.7344 (t0) REVERT: K 154 MET cc_start: 0.8669 (mmm) cc_final: 0.8174 (mmt) REVERT: K 213 ILE cc_start: 0.9028 (mm) cc_final: 0.8581 (mt) REVERT: M 76 ILE cc_start: 0.8002 (pt) cc_final: 0.7747 (tp) REVERT: M 115 ASP cc_start: 0.8631 (p0) cc_final: 0.8268 (p0) outliers start: 0 outliers final: 0 residues processed: 236 average time/residue: 0.1280 time to fit residues: 47.7705 Evaluate side-chains 184 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 0.561 ------------------------------------------------------------------------------- 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: 10.0000 chunk 207 optimal weight: 3.9990 chunk 90 optimal weight: 0.0020 chunk 84 optimal weight: 7.9990 chunk 16 optimal weight: 0.1980 chunk 69 optimal weight: 20.0000 chunk 164 optimal weight: 4.9990 chunk 38 optimal weight: 0.6980 chunk 180 optimal weight: 5.9990 chunk 197 optimal weight: 0.9990 overall best weight: 1.1792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 160 ASN B 651 ASN G 651 ASN ** G 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 651 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.128374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.115184 restraints weight = 40989.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.114278 restraints weight = 83006.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.113521 restraints weight = 89977.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.112277 restraints weight = 89880.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.112475 restraints weight = 85708.553| |-----------------------------------------------------------------------------| r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.3729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 20256 Z= 0.136 Angle : 0.647 10.003 27661 Z= 0.332 Chirality : 0.045 0.255 3242 Planarity : 0.005 0.076 3411 Dihedral : 5.734 33.447 2635 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.24 % Favored : 93.51 % 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 are not related in a simple way. whole: -1.73 (0.16), residues: 2420 helix: -0.27 (0.28), residues: 354 sheet: -0.57 (0.20), residues: 652 loop : -1.71 (0.16), residues: 1414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 293 TYR 0.040 0.001 TYR F 217 PHE 0.021 0.001 PHE M 64 TRP 0.055 0.002 TRP M 47 HIS 0.010 0.001 HIS K 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (20157) covalent geometry : angle 0.63292 / 0.33 (27406) SS BOND : bond 0.00336 / 0.19 ( 42) SS BOND : angle 0.93203 / 0.59 ( 84) hydrogen bonds : bond 0.03945 / 2.56 ( 616) hydrogen bonds : angle 5.55483 / 3.77 ( 1629) link_ALPHA1-2 : bond 0.00765 / 0.46 ( 11) link_ALPHA1-2 : angle 2.18869 / 1.27 ( 33) link_ALPHA1-3 : bond 0.00849 / 0.47 ( 9) link_ALPHA1-3 : angle 1.56298 / 1.05 ( 27) link_ALPHA1-6 : bond 0.00108 / 0.06 ( 7) link_ALPHA1-6 : angle 1.92586 / 1.22 ( 21) link_BETA1-4 : bond 0.00370 / 0.21 ( 18) link_BETA1-4 : angle 1.62844 / 1.19 ( 54) link_NAG-ASN : bond 0.00267 / 0.15 ( 12) link_NAG-ASN : angle 1.44703 / 0.89 ( 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 243 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 243 time to evaluate : 0.695 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 104 MET cc_start: 0.9065 (ttt) cc_final: 0.8801 (ttt) REVERT: A 154 MET cc_start: 0.9055 (mmm) cc_final: 0.8805 (mmt) REVERT: A 475 MET cc_start: 0.7693 (tpp) cc_final: 0.7185 (tpp) REVERT: C 48 MET cc_start: 0.7895 (tpp) cc_final: 0.7344 (mmt) REVERT: I 263 ASN cc_start: 0.7887 (t0) cc_final: 0.7129 (t0) REVERT: K 127 VAL cc_start: 0.8665 (t) cc_final: 0.8451 (t) REVERT: K 154 MET cc_start: 0.8594 (mmm) cc_final: 0.8148 (mmt) REVERT: M 76 ILE cc_start: 0.8019 (pt) cc_final: 0.7748 (tp) REVERT: M 115 ASP cc_start: 0.8599 (p0) cc_final: 0.8293 (p0) outliers start: 0 outliers final: 0 residues processed: 243 average time/residue: 0.1352 time to fit residues: 51.7312 Evaluate side-chains 190 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 0.693 ------------------------------------------------------------------------------- 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: 5.9990 chunk 15 optimal weight: 4.9990 chunk 207 optimal weight: 10.0000 chunk 50 optimal weight: 0.7980 chunk 32 optimal weight: 4.9990 chunk 209 optimal weight: 0.8980 chunk 58 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 219 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 160 ASN B 651 ASN C 113 ASN G 651 ASN ** G 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 651 ASN M 43 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.125018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.112156 restraints weight = 41175.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.111753 restraints weight = 87626.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.111261 restraints weight = 86824.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.110674 restraints weight = 76005.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.110037 restraints weight = 74118.545| |-----------------------------------------------------------------------------| r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.3797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 20256 Z= 0.226 Angle : 0.727 9.865 27661 Z= 0.374 Chirality : 0.048 0.389 3242 Planarity : 0.005 0.062 3411 Dihedral : 5.930 33.125 2635 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.48 % Favored : 92.27 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % 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 are not related in a simple way. whole: -1.85 (0.16), residues: 2420 helix: -0.40 (0.28), residues: 360 sheet: -0.58 (0.20), residues: 647 loop : -1.82 (0.15), residues: 1413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG D 293 TYR 0.020 0.002 TYR A 217 PHE 0.021 0.002 PHE M 64 TRP 0.051 0.002 TRP M 47 HIS 0.006 0.002 HIS F 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00543 / 0.23 (20157) covalent geometry : angle 0.71195 / 0.37 (27406) SS BOND : bond 0.00370 / 0.24 ( 42) SS BOND : angle 1.33656 / 0.90 ( 84) hydrogen bonds : bond 0.04305 / 2.79 ( 616) hydrogen bonds : angle 5.75032 / 3.90 ( 1629) link_ALPHA1-2 : bond 0.00645 / 0.39 ( 11) link_ALPHA1-2 : angle 2.02312 / 1.18 ( 33) link_ALPHA1-3 : bond 0.00908 / 0.50 ( 9) link_ALPHA1-3 : angle 1.54065 / 1.04 ( 27) link_ALPHA1-6 : bond 0.00134 / 0.06 ( 7) link_ALPHA1-6 : angle 1.90470 / 1.20 ( 21) link_BETA1-4 : bond 0.00489 / 0.29 ( 18) link_BETA1-4 : angle 1.90404 / 1.40 ( 54) link_NAG-ASN : bond 0.00537 / 0.32 ( 12) link_NAG-ASN : angle 1.79150 / 1.10 ( 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 231 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 231 time to evaluate : 0.715 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: 0.9092 (mmm) cc_final: 0.8792 (mmt) REVERT: C 48 MET cc_start: 0.8004 (tpp) cc_final: 0.7498 (mmt) REVERT: F 42 VAL cc_start: 0.9322 (p) cc_final: 0.9099 (p) REVERT: I 263 ASN cc_start: 0.7935 (t0) cc_final: 0.7258 (t0) REVERT: I 279 MET cc_start: 0.7758 (pmm) cc_final: 0.7324 (pmm) REVERT: K 104 MET cc_start: 0.9145 (ttm) cc_final: 0.8763 (tpp) REVERT: K 154 MET cc_start: 0.8624 (mmm) cc_final: 0.8174 (mmt) REVERT: M 76 ILE cc_start: 0.7983 (pt) cc_final: 0.7704 (tp) REVERT: M 115 ASP cc_start: 0.8721 (p0) cc_final: 0.8420 (p0) outliers start: 0 outliers final: 0 residues processed: 231 average time/residue: 0.1332 time to fit residues: 48.3447 Evaluate side-chains 182 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 0.712 ------------------------------------------------------------------------------- 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: 7.9990 chunk 115 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 193 optimal weight: 0.9980 chunk 161 optimal weight: 4.9990 chunk 76 optimal weight: 20.0000 chunk 182 optimal weight: 3.9990 chunk 216 optimal weight: 9.9990 chunk 43 optimal weight: 2.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 160 ASN B 651 ASN G 651 ASN ** G 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 651 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.126054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.111811 restraints weight = 41095.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.110212 restraints weight = 90239.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.110540 restraints weight = 88561.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.110341 restraints weight = 63713.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.110392 restraints weight = 66929.615| |-----------------------------------------------------------------------------| r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.3884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 20256 Z= 0.176 Angle : 0.688 9.917 27661 Z= 0.353 Chirality : 0.046 0.381 3242 Planarity : 0.005 0.043 3411 Dihedral : 5.854 33.285 2635 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.11 % Favored : 92.64 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % 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 are not related in a simple way. whole: -1.83 (0.16), residues: 2420 helix: -0.40 (0.28), residues: 360 sheet: -0.56 (0.20), residues: 647 loop : -1.80 (0.15), residues: 1413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG M 62 TYR 0.017 0.001 TYR A 217 PHE 0.027 0.002 PHE M 64 TRP 0.047 0.002 TRP M 47 HIS 0.005 0.002 HIS K 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.18 (20157) covalent geometry : angle 0.67330 / 0.35 (27406) SS BOND : bond 0.00315 / 0.20 ( 42) SS BOND : angle 1.22464 / 0.81 ( 84) hydrogen bonds : bond 0.04152 / 2.68 ( 616) hydrogen bonds : angle 5.64276 / 3.83 ( 1629) link_ALPHA1-2 : bond 0.00649 / 0.40 ( 11) link_ALPHA1-2 : angle 2.02414 / 1.17 ( 33) link_ALPHA1-3 : bond 0.00892 / 0.49 ( 9) link_ALPHA1-3 : angle 1.54211 / 1.04 ( 27) link_ALPHA1-6 : bond 0.00100 / 0.05 ( 7) link_ALPHA1-6 : angle 1.84633 / 1.16 ( 21) link_BETA1-4 : bond 0.00415 / 0.24 ( 18) link_BETA1-4 : angle 1.78458 / 1.31 ( 54) link_NAG-ASN : bond 0.00381 / 0.22 ( 12) link_NAG-ASN : angle 1.67791 / 1.03 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2546.40 seconds wall clock time: 45 minutes 20.15 seconds (2720.15 seconds total)