Starting phenix.real_space_refine on Tue Jun 17 10:37:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sb0_40286/06_2025/8sb0_40286.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sb0_40286/06_2025/8sb0_40286.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8sb0_40286/06_2025/8sb0_40286.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sb0_40286/06_2025/8sb0_40286.map" model { file = "/net/cci-nas-00/data/ceres_data/8sb0_40286/06_2025/8sb0_40286.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sb0_40286/06_2025/8sb0_40286.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 19741 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 3596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3596 Classifications: {'peptide': 460} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 434} Chain: "B" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 942 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 1, 'TRANS': 116} Chain: "C" Number of atoms: 995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 995 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "D" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 805 Classifications: {'peptide': 110} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 103} Chain: "F" Number of atoms: 3614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3614 Classifications: {'peptide': 462} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 436} Chain: "G" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 942 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 1, 'TRANS': 116} Chain: "H" Number of atoms: 995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 995 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "I" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 805 Classifications: {'peptide': 110} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 103} Chain: "K" Number of atoms: 3606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 461, 3606 Classifications: {'peptide': 461} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 435} Chain breaks: 1 Chain: "L" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 942 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 1, 'TRANS': 116} Chain: "M" Number of atoms: 995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 995 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "N" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 805 Classifications: {'peptide': 110} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 103} Chain: "E" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "J" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "R" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "V" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 12.50, per 1000 atoms: 0.63 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: 5.31 Conformation dependent library (CDL) restraints added in 2.6 seconds 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: 2.65 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: 9.01 Time building geometry restraints manager: 6.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 6134 1.34 - 1.47: 5189 1.47 - 1.60: 8657 1.60 - 1.72: 0 1.72 - 1.85: 177 Bond restraints: 20157 Sorted by residual: bond pdb=" N VAL G 608 " pdb=" CA VAL G 608 " ideal model delta sigma weight residual 1.460 1.492 -0.032 9.30e-03 1.16e+04 1.20e+01 bond pdb=" C2 MAN J 4 " pdb=" O2 MAN J 4 " ideal model delta sigma weight residual 1.407 1.462 -0.055 2.00e-02 2.50e+03 7.70e+00 bond pdb=" C2 MAN J 8 " pdb=" O2 MAN J 8 " ideal model delta sigma weight residual 1.407 1.460 -0.053 2.00e-02 2.50e+03 6.95e+00 bond pdb=" C2 MAN V 8 " pdb=" O2 MAN V 8 " ideal model delta sigma weight residual 1.407 1.459 -0.052 2.00e-02 2.50e+03 6.88e+00 bond pdb=" C1 MAN J 8 " pdb=" C2 MAN J 8 " ideal model delta sigma weight residual 1.526 1.577 -0.051 2.00e-02 2.50e+03 6.61e+00 ... (remaining 20152 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.65: 26758 2.65 - 5.31: 562 5.31 - 7.96: 68 7.96 - 10.61: 15 10.61 - 13.26: 3 Bond angle restraints: 27406 Sorted by residual: angle pdb=" C ASN K 67 " pdb=" N VAL K 68 " pdb=" CA VAL K 68 " ideal model delta sigma weight residual 121.70 134.96 -13.26 1.80e+00 3.09e-01 5.43e+01 angle pdb=" C ASN F 67 " pdb=" N VAL F 68 " pdb=" CA VAL F 68 " ideal model delta sigma weight residual 121.70 134.90 -13.20 1.80e+00 3.09e-01 5.38e+01 angle pdb=" C ASN A 67 " pdb=" N VAL A 68 " pdb=" CA VAL A 68 " ideal model delta sigma weight residual 121.70 134.89 -13.19 1.80e+00 3.09e-01 5.37e+01 angle pdb=" N TRP F 35 " pdb=" CA TRP F 35 " pdb=" C TRP F 35 " ideal model delta sigma weight residual 109.41 101.38 8.03 1.52e+00 4.33e-01 2.79e+01 angle pdb=" C ASN F 403 " pdb=" N SER F 404 " pdb=" CA SER F 404 " ideal model delta sigma weight residual 121.70 130.85 -9.15 1.80e+00 3.09e-01 2.58e+01 ... (remaining 27401 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.27: 11984 22.27 - 44.55: 655 44.55 - 66.82: 71 66.82 - 89.09: 59 89.09 - 111.36: 26 Dihedral angle restraints: 12795 sinusoidal: 5746 harmonic: 7049 Sorted by residual: dihedral pdb=" CA LEU A 184 " pdb=" C LEU A 184 " pdb=" N SER A 185 " pdb=" CA SER A 185 " ideal model delta harmonic sigma weight residual -180.00 -138.30 -41.70 0 5.00e+00 4.00e-02 6.96e+01 dihedral pdb=" CA THR B 569 " pdb=" C THR B 569 " pdb=" N VAL B 570 " pdb=" CA VAL B 570 " ideal model delta harmonic sigma weight residual 180.00 -143.05 -36.95 0 5.00e+00 4.00e-02 5.46e+01 dihedral pdb=" CA LEU K 184 " pdb=" C LEU K 184 " pdb=" N SER K 185 " pdb=" CA SER K 185 " ideal model delta harmonic sigma weight residual -180.00 -143.55 -36.45 0 5.00e+00 4.00e-02 5.31e+01 ... (remaining 12792 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 2608 0.059 - 0.119: 494 0.119 - 0.178: 117 0.178 - 0.238: 14 0.238 - 0.297: 9 Chirality restraints: 3242 Sorted by residual: chirality pdb=" C5 BMA J 3 " pdb=" C4 BMA J 3 " pdb=" C6 BMA J 3 " pdb=" O5 BMA J 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.57 0.30 2.00e-01 2.50e+01 2.21e+00 chirality pdb=" C5 BMA U 3 " pdb=" C4 BMA U 3 " pdb=" C6 BMA U 3 " pdb=" O5 BMA U 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" C5 BMA Q 3 " pdb=" C4 BMA Q 3 " pdb=" C6 BMA Q 3 " pdb=" O5 BMA Q 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.29 2.00e-01 2.50e+01 2.09e+00 ... (remaining 3239 not shown) Planarity restraints: 3423 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN L 658 " 0.022 2.00e-02 2.50e+03 4.46e-02 1.99e+01 pdb=" CD GLN L 658 " -0.077 2.00e-02 2.50e+03 pdb=" OE1 GLN L 658 " 0.029 2.00e-02 2.50e+03 pdb=" NE2 GLN L 658 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG K 166 " 0.385 9.50e-02 1.11e+02 1.73e-01 1.88e+01 pdb=" NE ARG K 166 " -0.027 2.00e-02 2.50e+03 pdb=" CZ ARG K 166 " 0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG K 166 " -0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG K 166 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 35 " -0.019 2.00e-02 2.50e+03 2.02e-02 1.02e+01 pdb=" CG TRP A 35 " 0.055 2.00e-02 2.50e+03 pdb=" CD1 TRP A 35 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP A 35 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 35 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 35 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A 35 " -0.014 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 35 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 35 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP A 35 " 0.001 2.00e-02 2.50e+03 ... (remaining 3420 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 190 2.62 - 3.19: 17580 3.19 - 3.76: 27850 3.76 - 4.33: 38464 4.33 - 4.90: 63769 Nonbonded interactions: 147853 Sorted by model distance: nonbonded pdb=" OE2 GLU N 282 " pdb=" O4 MAN V 4 " model vdw 2.050 3.040 nonbonded pdb=" OG1 THR K 37 " pdb=" O ALA K 497 " model vdw 2.063 3.040 nonbonded pdb=" O VAL A 36 " pdb=" OG1 THR B 606 " model vdw 2.071 3.040 nonbonded pdb=" OG1 THR A 37 " pdb=" O ALA A 497 " model vdw 2.083 3.040 nonbonded pdb=" OE2 GLU I 282 " pdb=" O4 MAN R 4 " model vdw 2.086 3.040 ... (remaining 147848 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 32 or resid 34 through 503)) selection = (chain 'F' and (resid 32 or resid 34 through 503)) selection = (chain 'K' and resid 32 through 503) } ncs_group { reference = chain 'B' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'C' selection = chain 'H' selection = chain 'M' } ncs_group { reference = chain 'D' selection = chain 'I' selection = chain 'N' } ncs_group { reference = chain 'J' selection = chain 'R' selection = chain 'V' } ncs_group { reference = chain 'O' selection = chain 'P' selection = chain 'S' selection = chain 'T' selection = chain 'W' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.220 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: 0.020 Extract box with map and model: 0.740 Check model and map are aligned: 0.150 Set scattering table: 0.190 Process input model: 49.400 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.160 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: 0.010 Load rotamer database and sin/cos tables:3.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 20256 Z= 0.267 Angle : 0.991 13.263 27661 Z= 0.506 Chirality : 0.053 0.297 3242 Planarity : 0.006 0.173 3411 Dihedral : 15.003 111.365 8157 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 2.37 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.055 0.002 TRP A 35 HIS 0.008 0.002 HIS A 249 PHE 0.035 0.002 PHE M 29 TYR 0.018 0.002 TYR K 399 ARG 0.026 0.001 ARG F 166 Details of bonding type rmsd link_NAG-ASN : bond 0.00245 ( 12) link_NAG-ASN : angle 2.46677 ( 36) link_ALPHA1-6 : bond 0.00535 ( 7) link_ALPHA1-6 : angle 3.96902 ( 21) link_BETA1-4 : bond 0.00870 ( 18) link_BETA1-4 : angle 3.33917 ( 54) link_ALPHA1-2 : bond 0.01382 ( 11) link_ALPHA1-2 : angle 4.52955 ( 33) link_ALPHA1-3 : bond 0.01520 ( 9) link_ALPHA1-3 : angle 4.19129 ( 27) hydrogen bonds : bond 0.22357 ( 616) hydrogen bonds : angle 9.35467 ( 1629) SS BOND : bond 0.00462 ( 42) SS BOND : angle 1.75500 ( 84) covalent geometry : bond 0.00562 (20157) covalent geometry : angle 0.94766 (27406) *********************** 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 : 2.339 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: 0.6998 (t80) REVERT: G 609 PRO cc_start: 0.8143 (Cg_exo) cc_final: 0.7729 (Cg_endo) REVERT: I 263 ASN cc_start: 0.7963 (t0) cc_final: 0.7526 (t0) REVERT: N 263 ASN cc_start: 0.7596 (t0) cc_final: 0.7257 (t0) outliers start: 1 outliers final: 0 residues processed: 364 average time/residue: 0.3471 time to fit residues: 188.6970 Evaluate side-chains 215 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 215 time to evaluate : 2.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 202 optimal weight: 6.9990 chunk 181 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 122 optimal weight: 6.9990 chunk 97 optimal weight: 5.9990 chunk 188 optimal weight: 4.9990 chunk 72 optimal weight: 0.9980 chunk 114 optimal weight: 2.9990 chunk 140 optimal weight: 6.9990 chunk 217 optimal weight: 6.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN A 203 GLN A 249 HIS B 651 ASN F 417 GLN G 591 GLN G 651 ASN H 6 GLN H 65 GLN ** 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 Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.126668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.115772 restraints weight = 40960.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.114489 restraints weight = 88812.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.113662 restraints weight = 106403.257| |-----------------------------------------------------------------------------| r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 20256 Z= 0.250 Angle : 0.819 9.898 27661 Z= 0.420 Chirality : 0.052 0.223 3242 Planarity : 0.006 0.069 3411 Dihedral : 10.903 79.387 3766 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.45 % Favored : 93.31 % Rotamer: Outliers : 0.19 % Allowed : 5.24 % Favored : 94.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.16), residues: 2420 helix: -0.46 (0.27), residues: 339 sheet: -0.73 (0.19), residues: 724 loop : -1.48 (0.16), residues: 1357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP H 47 HIS 0.009 0.002 HIS A 330 PHE 0.020 0.002 PHE C 64 TYR 0.023 0.002 TYR C 33 ARG 0.006 0.001 ARG A 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00429 ( 12) link_NAG-ASN : angle 2.01715 ( 36) link_ALPHA1-6 : bond 0.00343 ( 7) link_ALPHA1-6 : angle 2.03499 ( 21) link_BETA1-4 : bond 0.00464 ( 18) link_BETA1-4 : angle 2.51734 ( 54) link_ALPHA1-2 : bond 0.01018 ( 11) link_ALPHA1-2 : angle 3.35001 ( 33) link_ALPHA1-3 : bond 0.01109 ( 9) link_ALPHA1-3 : angle 2.50324 ( 27) hydrogen bonds : bond 0.05661 ( 616) hydrogen bonds : angle 6.78422 ( 1629) SS BOND : bond 0.00433 ( 42) SS BOND : angle 1.00627 ( 84) covalent geometry : bond 0.00589 (20157) covalent geometry : angle 0.79532 (27406) *********************** 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 299 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 295 time to evaluate : 2.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 VAL cc_start: 0.8577 (t) cc_final: 0.8310 (t) REVERT: C 48 MET cc_start: 0.7708 (tpp) cc_final: 0.7395 (mmt) REVERT: C 102 ILE cc_start: 0.9423 (tp) cc_final: 0.9090 (pt) REVERT: F 411 THR cc_start: 0.7593 (p) cc_final: 0.7134 (m) REVERT: G 609 PRO cc_start: 0.8295 (Cg_exo) cc_final: 0.8033 (Cg_endo) REVERT: G 626 MET cc_start: 0.7573 (tpp) cc_final: 0.7274 (tpt) REVERT: I 234 LEU cc_start: 0.6478 (mm) cc_final: 0.6121 (mm) REVERT: I 263 ASN cc_start: 0.8003 (t0) cc_final: 0.7763 (t0) REVERT: K 95 MET cc_start: 0.7997 (ttm) cc_final: 0.7718 (ttm) REVERT: K 154 MET cc_start: 0.8917 (mmm) cc_final: 0.8554 (mmt) REVERT: K 411 THR cc_start: 0.7889 (p) cc_final: 0.7311 (m) REVERT: L 609 PRO cc_start: 0.7880 (Cg_exo) cc_final: 0.7494 (Cg_endo) REVERT: M 29 PHE cc_start: 0.5898 (p90) cc_final: 0.4996 (p90) REVERT: M 76 ILE cc_start: 0.8272 (pt) cc_final: 0.8018 (tp) REVERT: M 102 ILE cc_start: 0.9388 (tp) cc_final: 0.9047 (pt) REVERT: N 263 ASN cc_start: 0.7612 (t0) cc_final: 0.7163 (t0) outliers start: 4 outliers final: 2 residues processed: 298 average time/residue: 0.3254 time to fit residues: 146.9159 Evaluate side-chains 219 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 217 time to evaluate : 2.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 7 optimal weight: 1.9990 chunk 108 optimal weight: 0.8980 chunk 224 optimal weight: 8.9990 chunk 25 optimal weight: 2.9990 chunk 206 optimal weight: 7.9990 chunk 120 optimal weight: 0.8980 chunk 122 optimal weight: 6.9990 chunk 44 optimal weight: 3.9990 chunk 203 optimal weight: 2.9990 chunk 185 optimal weight: 4.9990 chunk 198 optimal weight: 0.6980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN B 651 ASN G 651 ASN L 651 ASN ** L 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 43 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.128431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.114896 restraints weight = 40247.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.113552 restraints weight = 81165.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.113320 restraints weight = 84759.740| |-----------------------------------------------------------------------------| r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.2237 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= 0.160 Angle : 0.699 10.208 27661 Z= 0.359 Chirality : 0.047 0.207 3242 Planarity : 0.005 0.074 3411 Dihedral : 10.444 78.160 3766 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.87 % Favored : 93.88 % Rotamer: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.16), residues: 2420 helix: -0.48 (0.27), residues: 360 sheet: -0.49 (0.20), residues: 684 loop : -1.54 (0.16), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP M 47 HIS 0.004 0.001 HIS H 35 PHE 0.015 0.002 PHE C 64 TYR 0.030 0.001 TYR F 217 ARG 0.009 0.001 ARG N 293 Details of bonding type rmsd link_NAG-ASN : bond 0.00235 ( 12) link_NAG-ASN : angle 1.85291 ( 36) link_ALPHA1-6 : bond 0.00256 ( 7) link_ALPHA1-6 : angle 2.17290 ( 21) link_BETA1-4 : bond 0.00511 ( 18) link_BETA1-4 : angle 2.05404 ( 54) link_ALPHA1-2 : bond 0.01199 ( 11) link_ALPHA1-2 : angle 3.18910 ( 33) link_ALPHA1-3 : bond 0.01225 ( 9) link_ALPHA1-3 : angle 1.67944 ( 27) hydrogen bonds : bond 0.04818 ( 616) hydrogen bonds : angle 6.12683 ( 1629) SS BOND : bond 0.00567 ( 42) SS BOND : angle 0.78266 ( 84) covalent geometry : bond 0.00364 (20157) covalent geometry : angle 0.67811 (27406) *********************** 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 306 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 306 time to evaluate : 2.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 VAL cc_start: 0.8023 (t) cc_final: 0.7821 (t) REVERT: A 359 ILE cc_start: 0.8064 (mt) cc_final: 0.7817 (mm) REVERT: A 411 THR cc_start: 0.7760 (p) cc_final: 0.7421 (m) REVERT: C 48 MET cc_start: 0.7602 (tpp) cc_final: 0.7269 (mmt) REVERT: F 411 THR cc_start: 0.7639 (p) cc_final: 0.7258 (m) REVERT: F 424 ILE cc_start: 0.9422 (mm) cc_final: 0.9203 (mm) REVERT: G 648 GLU cc_start: 0.6561 (pp20) cc_final: 0.6219 (pp20) REVERT: H 102 ILE cc_start: 0.9241 (tp) cc_final: 0.8887 (pt) REVERT: I 263 ASN cc_start: 0.7868 (t0) cc_final: 0.7349 (t0) REVERT: K 154 MET cc_start: 0.8951 (mmm) cc_final: 0.8521 (mmt) REVERT: K 342 LEU cc_start: 0.8690 (tp) cc_final: 0.8458 (tp) REVERT: K 411 THR cc_start: 0.7785 (p) cc_final: 0.7279 (m) REVERT: L 609 PRO cc_start: 0.8021 (Cg_exo) cc_final: 0.7661 (Cg_endo) REVERT: M 76 ILE cc_start: 0.8177 (pt) cc_final: 0.7905 (tp) REVERT: N 234 LEU cc_start: 0.6315 (mm) cc_final: 0.6035 (mm) REVERT: N 263 ASN cc_start: 0.7651 (t0) cc_final: 0.7233 (t0) outliers start: 0 outliers final: 0 residues processed: 306 average time/residue: 0.3168 time to fit residues: 148.2560 Evaluate side-chains 215 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 215 time to evaluate : 2.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 224 optimal weight: 8.9990 chunk 124 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 chunk 111 optimal weight: 5.9990 chunk 203 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 66 optimal weight: 7.9990 chunk 83 optimal weight: 3.9990 chunk 211 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN B 651 ASN F 328 GLN G 651 ASN H 6 GLN ** K 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 651 ASN ** L 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.126615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.113513 restraints weight = 40968.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.112634 restraints weight = 88426.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.112411 restraints weight = 89291.239| |-----------------------------------------------------------------------------| r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.2689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 20256 Z= 0.206 Angle : 0.730 10.461 27661 Z= 0.372 Chirality : 0.048 0.177 3242 Planarity : 0.005 0.053 3411 Dihedral : 10.100 76.488 3766 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.02 % Favored : 92.73 % Rotamer: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.16), residues: 2420 helix: -0.35 (0.28), residues: 360 sheet: -0.56 (0.20), residues: 675 loop : -1.67 (0.16), residues: 1385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP N 267 HIS 0.006 0.002 HIS A 216 PHE 0.013 0.002 PHE K 376 TYR 0.015 0.002 TYR M 33 ARG 0.008 0.001 ARG D 293 Details of bonding type rmsd link_NAG-ASN : bond 0.00435 ( 12) link_NAG-ASN : angle 1.96612 ( 36) link_ALPHA1-6 : bond 0.00265 ( 7) link_ALPHA1-6 : angle 2.13317 ( 21) link_BETA1-4 : bond 0.00591 ( 18) link_BETA1-4 : angle 2.31360 ( 54) link_ALPHA1-2 : bond 0.01000 ( 11) link_ALPHA1-2 : angle 2.86621 ( 33) link_ALPHA1-3 : bond 0.01166 ( 9) link_ALPHA1-3 : angle 1.75448 ( 27) hydrogen bonds : bond 0.04621 ( 616) hydrogen bonds : angle 5.97065 ( 1629) SS BOND : bond 0.00358 ( 42) SS BOND : angle 1.07604 ( 84) covalent geometry : bond 0.00491 (20157) covalent geometry : angle 0.70886 (27406) *********************** 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 278 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 278 time to evaluate : 2.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 VAL cc_start: 0.8171 (t) cc_final: 0.7900 (t) REVERT: A 411 THR cc_start: 0.7653 (p) cc_final: 0.7298 (m) REVERT: C 48 MET cc_start: 0.7839 (tpp) cc_final: 0.7123 (mmt) REVERT: F 426 MET cc_start: 0.6136 (mtm) cc_final: 0.5683 (mtt) REVERT: G 626 MET cc_start: 0.7258 (tpp) cc_final: 0.6774 (tpt) REVERT: H 102 ILE cc_start: 0.9255 (tp) cc_final: 0.9049 (pt) REVERT: I 263 ASN cc_start: 0.7997 (t0) cc_final: 0.7749 (t0) REVERT: K 154 MET cc_start: 0.8922 (mmm) cc_final: 0.8426 (mmt) REVERT: K 342 LEU cc_start: 0.8745 (tp) cc_final: 0.8481 (tp) REVERT: K 411 THR cc_start: 0.7722 (p) cc_final: 0.7290 (m) REVERT: L 609 PRO cc_start: 0.8225 (Cg_exo) cc_final: 0.7930 (Cg_endo) REVERT: M 86 LEU cc_start: 0.8100 (mp) cc_final: 0.7851 (mp) REVERT: N 263 ASN cc_start: 0.7851 (t0) cc_final: 0.7318 (t0) outliers start: 0 outliers final: 0 residues processed: 278 average time/residue: 0.3241 time to fit residues: 136.7412 Evaluate side-chains 203 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 203 time to evaluate : 2.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 155 optimal weight: 30.0000 chunk 74 optimal weight: 2.9990 chunk 166 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 98 optimal weight: 10.0000 chunk 115 optimal weight: 0.9990 chunk 163 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 222 optimal weight: 7.9990 chunk 54 optimal weight: 9.9990 chunk 108 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN A 258 GLN B 651 ASN G 651 ASN ** K 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 651 ASN ** L 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.126560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.113046 restraints weight = 40972.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.111827 restraints weight = 87184.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.111631 restraints weight = 98252.206| |-----------------------------------------------------------------------------| r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 20256 Z= 0.194 Angle : 0.712 10.144 27661 Z= 0.363 Chirality : 0.047 0.200 3242 Planarity : 0.005 0.056 3411 Dihedral : 9.966 75.476 3766 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.90 % Favored : 92.85 % Rotamer: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.16), residues: 2420 helix: -0.12 (0.28), residues: 342 sheet: -0.59 (0.20), residues: 672 loop : -1.67 (0.16), residues: 1406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP K 69 HIS 0.007 0.002 HIS F 216 PHE 0.013 0.002 PHE K 376 TYR 0.012 0.001 TYR K 39 ARG 0.010 0.001 ARG I 293 Details of bonding type rmsd link_NAG-ASN : bond 0.00387 ( 12) link_NAG-ASN : angle 1.91534 ( 36) link_ALPHA1-6 : bond 0.00267 ( 7) link_ALPHA1-6 : angle 2.11884 ( 21) link_BETA1-4 : bond 0.00591 ( 18) link_BETA1-4 : angle 2.29444 ( 54) link_ALPHA1-2 : bond 0.00913 ( 11) link_ALPHA1-2 : angle 2.75072 ( 33) link_ALPHA1-3 : bond 0.01219 ( 9) link_ALPHA1-3 : angle 1.61111 ( 27) hydrogen bonds : bond 0.04436 ( 616) hydrogen bonds : angle 5.81119 ( 1629) SS BOND : bond 0.00361 ( 42) SS BOND : angle 1.01397 ( 84) covalent geometry : bond 0.00461 (20157) covalent geometry : angle 0.69116 (27406) *********************** 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 269 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 269 time to evaluate : 2.046 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: 0.7642 (p) cc_final: 0.7344 (m) REVERT: C 48 MET cc_start: 0.7947 (tpp) cc_final: 0.7263 (mmt) REVERT: F 369 MET cc_start: 0.8218 (ttp) cc_final: 0.8015 (ttp) REVERT: F 426 MET cc_start: 0.6225 (mtm) cc_final: 0.5718 (mtt) REVERT: G 609 PRO cc_start: 0.8747 (Cg_exo) cc_final: 0.8444 (Cg_endo) REVERT: G 626 MET cc_start: 0.7101 (tpp) cc_final: 0.6685 (tpt) REVERT: I 263 ASN cc_start: 0.8031 (t0) cc_final: 0.7821 (t0) REVERT: K 104 MET cc_start: 0.9058 (ttt) cc_final: 0.8601 (tpp) REVERT: K 154 MET cc_start: 0.8870 (mmm) cc_final: 0.8488 (mmt) REVERT: K 342 LEU cc_start: 0.8728 (tp) cc_final: 0.8447 (tp) REVERT: K 369 MET cc_start: 0.8522 (ttp) cc_final: 0.8208 (ttp) REVERT: K 411 THR cc_start: 0.7635 (p) cc_final: 0.7280 (m) REVERT: L 609 PRO cc_start: 0.8258 (Cg_exo) cc_final: 0.7993 (Cg_endo) REVERT: N 263 ASN cc_start: 0.7777 (t0) cc_final: 0.7320 (t0) outliers start: 0 outliers final: 0 residues processed: 269 average time/residue: 0.3111 time to fit residues: 128.2630 Evaluate side-chains 198 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 198 time to evaluate : 2.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 137 optimal weight: 6.9990 chunk 157 optimal weight: 10.0000 chunk 109 optimal weight: 0.7980 chunk 159 optimal weight: 0.9980 chunk 134 optimal weight: 8.9990 chunk 142 optimal weight: 5.9990 chunk 44 optimal weight: 0.9990 chunk 40 optimal weight: 0.4980 chunk 14 optimal weight: 0.9990 chunk 223 optimal weight: 9.9990 chunk 11 optimal weight: 0.4980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN B 651 ASN F 249 HIS G 651 ASN ** G 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 6 GLN L 651 ASN M 43 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.129530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.115780 restraints weight = 40813.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.114743 restraints weight = 85088.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.114970 restraints weight = 90962.838| |-----------------------------------------------------------------------------| r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.3182 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= 0.122 Angle : 0.643 10.240 27661 Z= 0.329 Chirality : 0.045 0.279 3242 Planarity : 0.004 0.050 3411 Dihedral : 9.327 72.069 3766 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.07 % Favored : 93.68 % Rotamer: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.16), residues: 2420 helix: -0.26 (0.28), residues: 360 sheet: -0.51 (0.20), residues: 666 loop : -1.52 (0.16), residues: 1394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP F 69 HIS 0.012 0.001 HIS F 249 PHE 0.010 0.001 PHE A 53 TYR 0.013 0.001 TYR A 39 ARG 0.011 0.001 ARG K 166 Details of bonding type rmsd link_NAG-ASN : bond 0.00270 ( 12) link_NAG-ASN : angle 1.60494 ( 36) link_ALPHA1-6 : bond 0.00239 ( 7) link_ALPHA1-6 : angle 2.11315 ( 21) link_BETA1-4 : bond 0.00508 ( 18) link_BETA1-4 : angle 1.98981 ( 54) link_ALPHA1-2 : bond 0.00918 ( 11) link_ALPHA1-2 : angle 2.71495 ( 33) link_ALPHA1-3 : bond 0.01168 ( 9) link_ALPHA1-3 : angle 1.63154 ( 27) hydrogen bonds : bond 0.03948 ( 616) hydrogen bonds : angle 5.48402 ( 1629) SS BOND : bond 0.00241 ( 42) SS BOND : angle 0.88147 ( 84) covalent geometry : bond 0.00273 (20157) covalent geometry : angle 0.62358 (27406) *********************** 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 262 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 262 time to evaluate : 2.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 411 THR cc_start: 0.7718 (p) cc_final: 0.7377 (m) REVERT: A 475 MET cc_start: 0.7868 (tpp) cc_final: 0.7593 (tpp) REVERT: C 48 MET cc_start: 0.7915 (tpp) cc_final: 0.7314 (mmt) REVERT: F 369 MET cc_start: 0.8351 (ttp) cc_final: 0.8100 (ttp) REVERT: G 609 PRO cc_start: 0.8650 (Cg_exo) cc_final: 0.8398 (Cg_endo) REVERT: G 626 MET cc_start: 0.6952 (tpp) cc_final: 0.6451 (tpt) REVERT: I 263 ASN cc_start: 0.8016 (t0) cc_final: 0.7481 (t0) REVERT: K 154 MET cc_start: 0.8840 (mmm) cc_final: 0.8346 (mmt) REVERT: L 609 PRO cc_start: 0.8203 (Cg_exo) cc_final: 0.7968 (Cg_endo) REVERT: N 263 ASN cc_start: 0.7843 (t0) cc_final: 0.7300 (t0) outliers start: 0 outliers final: 0 residues processed: 262 average time/residue: 0.3262 time to fit residues: 130.8123 Evaluate side-chains 194 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 2.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 133 optimal weight: 10.0000 chunk 113 optimal weight: 3.9990 chunk 1 optimal weight: 8.9990 chunk 191 optimal weight: 2.9990 chunk 194 optimal weight: 0.0980 chunk 185 optimal weight: 0.9980 chunk 79 optimal weight: 5.9990 chunk 104 optimal weight: 2.9990 chunk 139 optimal weight: 10.0000 chunk 230 optimal weight: 6.9990 chunk 237 optimal weight: 9.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN B 651 ASN C 113 ASN D 270 GLN F 249 HIS G 651 ASN H 43 GLN H 113 ASN K 258 GLN L 575 GLN L 651 ASN M 43 GLN M 113 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.126891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.110788 restraints weight = 41182.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.107152 restraints weight = 47317.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.107028 restraints weight = 60130.077| |-----------------------------------------------------------------------------| r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.3372 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= 0.195 Angle : 0.702 10.014 27661 Z= 0.356 Chirality : 0.047 0.235 3242 Planarity : 0.005 0.093 3411 Dihedral : 9.374 72.489 3766 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.94 % Favored : 92.81 % Rotamer: Outliers : 0.05 % Allowed : 1.70 % Favored : 98.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.17), residues: 2420 helix: 0.08 (0.29), residues: 336 sheet: -0.52 (0.20), residues: 656 loop : -1.61 (0.16), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP K 69 HIS 0.012 0.002 HIS F 249 PHE 0.013 0.002 PHE K 376 TYR 0.013 0.001 TYR K 191 ARG 0.011 0.001 ARG F 166 Details of bonding type rmsd link_NAG-ASN : bond 0.00424 ( 12) link_NAG-ASN : angle 1.85714 ( 36) link_ALPHA1-6 : bond 0.00278 ( 7) link_ALPHA1-6 : angle 2.04096 ( 21) link_BETA1-4 : bond 0.00598 ( 18) link_BETA1-4 : angle 2.27694 ( 54) link_ALPHA1-2 : bond 0.00760 ( 11) link_ALPHA1-2 : angle 2.53854 ( 33) link_ALPHA1-3 : bond 0.01143 ( 9) link_ALPHA1-3 : angle 1.57123 ( 27) hydrogen bonds : bond 0.04177 ( 616) hydrogen bonds : angle 5.59050 ( 1629) SS BOND : bond 0.00368 ( 42) SS BOND : angle 1.06146 ( 84) covalent geometry : bond 0.00468 (20157) covalent geometry : angle 0.68229 (27406) *********************** 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 247 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 246 time to evaluate : 2.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 48 MET cc_start: 0.8076 (tpp) cc_final: 0.7266 (mmt) REVERT: G 609 PRO cc_start: 0.8916 (Cg_exo) cc_final: 0.8658 (Cg_endo) REVERT: G 626 MET cc_start: 0.7236 (tpp) cc_final: 0.6866 (tpt) REVERT: K 154 MET cc_start: 0.8684 (mmm) cc_final: 0.8243 (mmt) REVERT: K 369 MET cc_start: 0.8383 (ttp) cc_final: 0.8151 (ttp) REVERT: L 609 PRO cc_start: 0.8488 (Cg_exo) cc_final: 0.8274 (Cg_endo) REVERT: M 115 ASP cc_start: 0.8584 (p0) cc_final: 0.8301 (p0) REVERT: N 263 ASN cc_start: 0.8040 (t0) cc_final: 0.7590 (t0) outliers start: 1 outliers final: 1 residues processed: 246 average time/residue: 0.3266 time to fit residues: 123.7012 Evaluate side-chains 197 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 196 time to evaluate : 2.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 44 optimal weight: 0.9990 chunk 10 optimal weight: 0.3980 chunk 55 optimal weight: 9.9990 chunk 155 optimal weight: 10.0000 chunk 72 optimal weight: 8.9990 chunk 122 optimal weight: 8.9990 chunk 160 optimal weight: 10.0000 chunk 111 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 203 optimal weight: 4.9990 chunk 188 optimal weight: 6.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN B 651 ASN G 651 ASN L 651 ASN N 270 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.127067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.113547 restraints weight = 41576.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.112945 restraints weight = 90278.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.112780 restraints weight = 89105.657| |-----------------------------------------------------------------------------| r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.3490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 20256 Z= 0.178 Angle : 0.689 10.065 27661 Z= 0.351 Chirality : 0.047 0.213 3242 Planarity : 0.005 0.095 3411 Dihedral : 9.243 71.586 3766 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.07 % Favored : 92.69 % Rotamer: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.16), residues: 2420 helix: -0.00 (0.29), residues: 336 sheet: -0.58 (0.20), residues: 657 loop : -1.65 (0.16), residues: 1427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP H 47 HIS 0.005 0.001 HIS F 216 PHE 0.011 0.002 PHE K 376 TYR 0.021 0.001 TYR F 217 ARG 0.013 0.001 ARG K 166 Details of bonding type rmsd link_NAG-ASN : bond 0.00372 ( 12) link_NAG-ASN : angle 1.82177 ( 36) link_ALPHA1-6 : bond 0.00290 ( 7) link_ALPHA1-6 : angle 2.01970 ( 21) link_BETA1-4 : bond 0.00558 ( 18) link_BETA1-4 : angle 2.23595 ( 54) link_ALPHA1-2 : bond 0.00753 ( 11) link_ALPHA1-2 : angle 2.49620 ( 33) link_ALPHA1-3 : bond 0.01163 ( 9) link_ALPHA1-3 : angle 1.49893 ( 27) hydrogen bonds : bond 0.04123 ( 616) hydrogen bonds : angle 5.58722 ( 1629) SS BOND : bond 0.00314 ( 42) SS BOND : angle 1.05535 ( 84) covalent geometry : bond 0.00421 (20157) covalent geometry : angle 0.67012 (27406) *********************** 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 242 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 242 time to evaluate : 2.321 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 154 MET cc_start: 0.9049 (mmm) cc_final: 0.8799 (mmt) REVERT: A 475 MET cc_start: 0.7758 (tpp) cc_final: 0.7327 (tpp) REVERT: C 48 MET cc_start: 0.8045 (tpp) cc_final: 0.7329 (mmt) REVERT: K 104 MET cc_start: 0.8964 (tpp) cc_final: 0.8759 (tpt) REVERT: K 154 MET cc_start: 0.8654 (mmm) cc_final: 0.8226 (mmt) REVERT: L 609 PRO cc_start: 0.8361 (Cg_exo) cc_final: 0.8131 (Cg_endo) REVERT: M 115 ASP cc_start: 0.8597 (p0) cc_final: 0.8280 (p0) outliers start: 0 outliers final: 0 residues processed: 242 average time/residue: 0.3207 time to fit residues: 120.7111 Evaluate side-chains 198 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 198 time to evaluate : 2.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 176 optimal weight: 0.5980 chunk 105 optimal weight: 1.9990 chunk 211 optimal weight: 0.5980 chunk 69 optimal weight: 30.0000 chunk 202 optimal weight: 7.9990 chunk 187 optimal weight: 2.9990 chunk 213 optimal weight: 8.9990 chunk 173 optimal weight: 0.8980 chunk 183 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN B 651 ASN G 651 ASN L 651 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.128672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.115037 restraints weight = 40740.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.114304 restraints weight = 85644.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.114212 restraints weight = 86789.546| |-----------------------------------------------------------------------------| r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.3643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20256 Z= 0.135 Angle : 0.646 10.639 27661 Z= 0.328 Chirality : 0.045 0.204 3242 Planarity : 0.005 0.070 3411 Dihedral : 8.832 68.675 3766 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.86 % Favored : 92.89 % Rotamer: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.17), residues: 2420 helix: -0.36 (0.28), residues: 363 sheet: -0.53 (0.20), residues: 648 loop : -1.60 (0.16), residues: 1409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP I 267 HIS 0.004 0.001 HIS F 374 PHE 0.009 0.001 PHE K 376 TYR 0.022 0.001 TYR F 217 ARG 0.013 0.001 ARG F 166 Details of bonding type rmsd link_NAG-ASN : bond 0.00287 ( 12) link_NAG-ASN : angle 1.60361 ( 36) link_ALPHA1-6 : bond 0.00296 ( 7) link_ALPHA1-6 : angle 1.94652 ( 21) link_BETA1-4 : bond 0.00498 ( 18) link_BETA1-4 : angle 2.08706 ( 54) link_ALPHA1-2 : bond 0.00718 ( 11) link_ALPHA1-2 : angle 2.43271 ( 33) link_ALPHA1-3 : bond 0.01150 ( 9) link_ALPHA1-3 : angle 1.46024 ( 27) hydrogen bonds : bond 0.03831 ( 616) hydrogen bonds : angle 5.42069 ( 1629) SS BOND : bond 0.00245 ( 42) SS BOND : angle 0.91681 ( 84) covalent geometry : bond 0.00313 (20157) covalent geometry : angle 0.62783 (27406) *********************** 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 253 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 253 time to evaluate : 2.205 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 154 MET cc_start: 0.9054 (mmm) cc_final: 0.8773 (mmt) REVERT: A 475 MET cc_start: 0.7557 (tpp) cc_final: 0.7245 (tpp) REVERT: C 48 MET cc_start: 0.7908 (tpp) cc_final: 0.7214 (mmt) REVERT: F 426 MET cc_start: 0.5742 (mtm) cc_final: 0.5374 (mtt) REVERT: K 154 MET cc_start: 0.8642 (mmm) cc_final: 0.8196 (mmt) REVERT: M 115 ASP cc_start: 0.8593 (p0) cc_final: 0.8268 (p0) outliers start: 0 outliers final: 0 residues processed: 253 average time/residue: 0.3221 time to fit residues: 126.0312 Evaluate side-chains 194 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 2.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 150 optimal weight: 0.7980 chunk 184 optimal weight: 0.9990 chunk 203 optimal weight: 0.8980 chunk 107 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 194 optimal weight: 0.9990 chunk 163 optimal weight: 0.0770 chunk 177 optimal weight: 4.9990 chunk 136 optimal weight: 10.0000 chunk 66 optimal weight: 10.0000 chunk 166 optimal weight: 0.7980 overall best weight: 0.7140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN B 651 ASN C 6 GLN G 616 ASN G 651 ASN H 43 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 = 0.3759 r_free = 0.3759 target = 0.130286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.115319 restraints weight = 40719.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.114033 restraints weight = 81733.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.114398 restraints weight = 84572.973| |-----------------------------------------------------------------------------| r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.3822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20256 Z= 0.115 Angle : 0.636 10.157 27661 Z= 0.321 Chirality : 0.045 0.212 3242 Planarity : 0.005 0.073 3411 Dihedral : 8.302 64.921 3766 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.74 % Favored : 94.01 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.17), residues: 2420 helix: -0.25 (0.28), residues: 364 sheet: -0.52 (0.20), residues: 653 loop : -1.51 (0.16), residues: 1403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP L 631 HIS 0.005 0.001 HIS F 374 PHE 0.010 0.001 PHE I 294 TYR 0.019 0.001 TYR A 39 ARG 0.018 0.001 ARG F 166 Details of bonding type rmsd link_NAG-ASN : bond 0.00261 ( 12) link_NAG-ASN : angle 1.49837 ( 36) link_ALPHA1-6 : bond 0.00344 ( 7) link_ALPHA1-6 : angle 1.85245 ( 21) link_BETA1-4 : bond 0.00468 ( 18) link_BETA1-4 : angle 1.92791 ( 54) link_ALPHA1-2 : bond 0.00696 ( 11) link_ALPHA1-2 : angle 2.35315 ( 33) link_ALPHA1-3 : bond 0.01157 ( 9) link_ALPHA1-3 : angle 1.40751 ( 27) hydrogen bonds : bond 0.03631 ( 616) hydrogen bonds : angle 5.29477 ( 1629) SS BOND : bond 0.00230 ( 42) SS BOND : angle 0.95508 ( 84) covalent geometry : bond 0.00257 (20157) covalent geometry : angle 0.61938 (27406) ********************** 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 259 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 259 time to evaluate : 2.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 MET cc_start: 0.9041 (mmm) cc_final: 0.8770 (mmt) REVERT: A 475 MET cc_start: 0.7513 (tpp) cc_final: 0.7204 (tpp) REVERT: C 48 MET cc_start: 0.7971 (tpp) cc_final: 0.7307 (mmt) REVERT: F 426 MET cc_start: 0.5636 (mtm) cc_final: 0.5227 (mtt) REVERT: I 279 MET cc_start: 0.7368 (pmm) cc_final: 0.7092 (pmm) REVERT: K 154 MET cc_start: 0.8660 (mmm) cc_final: 0.8228 (mmt) REVERT: M 115 ASP cc_start: 0.8661 (p0) cc_final: 0.8390 (p0) outliers start: 0 outliers final: 0 residues processed: 259 average time/residue: 0.3099 time to fit residues: 124.0532 Evaluate side-chains 193 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 2.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 228 optimal weight: 4.9990 chunk 196 optimal weight: 0.0040 chunk 61 optimal weight: 5.9990 chunk 54 optimal weight: 6.9990 chunk 72 optimal weight: 6.9990 chunk 217 optimal weight: 9.9990 chunk 98 optimal weight: 0.1980 chunk 74 optimal weight: 0.9990 chunk 109 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 229 optimal weight: 20.0000 overall best weight: 1.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN A 258 GLN B 651 ASN G 651 ASN L 651 ASN M 6 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.128875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.115192 restraints weight = 41092.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.113858 restraints weight = 83974.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.113440 restraints weight = 91897.848| |-----------------------------------------------------------------------------| r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.3905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20256 Z= 0.142 Angle : 0.655 12.290 27661 Z= 0.332 Chirality : 0.046 0.260 3242 Planarity : 0.005 0.130 3411 Dihedral : 8.172 63.510 3766 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.53 % Favored : 93.22 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.17), residues: 2420 helix: -0.24 (0.28), residues: 364 sheet: -0.50 (0.20), residues: 661 loop : -1.53 (0.16), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP L 631 HIS 0.004 0.001 HIS F 249 PHE 0.011 0.001 PHE K 376 TYR 0.016 0.001 TYR A 361 ARG 0.024 0.001 ARG F 166 Details of bonding type rmsd link_NAG-ASN : bond 0.00301 ( 12) link_NAG-ASN : angle 1.62208 ( 36) link_ALPHA1-6 : bond 0.00404 ( 7) link_ALPHA1-6 : angle 1.78823 ( 21) link_BETA1-4 : bond 0.00519 ( 18) link_BETA1-4 : angle 2.01333 ( 54) link_ALPHA1-2 : bond 0.00647 ( 11) link_ALPHA1-2 : angle 2.25331 ( 33) link_ALPHA1-3 : bond 0.01092 ( 9) link_ALPHA1-3 : angle 1.39973 ( 27) hydrogen bonds : bond 0.03747 ( 616) hydrogen bonds : angle 5.33387 ( 1629) SS BOND : bond 0.00252 ( 42) SS BOND : angle 0.91864 ( 84) covalent geometry : bond 0.00333 (20157) covalent geometry : angle 0.63916 (27406) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5450.57 seconds wall clock time: 96 minutes 3.00 seconds (5763.00 seconds total)