Starting phenix.real_space_refine on Tue Oct 15 05:54:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sb0_40286/10_2024/8sb0_40286.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sb0_40286/10_2024/8sb0_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sb0_40286/10_2024/8sb0_40286.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sb0_40286/10_2024/8sb0_40286.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sb0_40286/10_2024/8sb0_40286.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sb0_40286/10_2024/8sb0_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/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: 12.07, per 1000 atoms: 0.61 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: 5.93 Conformation dependent library (CDL) restraints added in 2.5 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: 2.75 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: 6.65 Time building geometry restraints manager: 6.47 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: 1.680 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: 0.730 Check model and map are aligned: 0.140 Set scattering table: 0.190 Process input model: 45.190 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.110 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:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.850 ------------------------------------------------------------------------------- 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 20157 Z= 0.366 Angle : 0.948 13.263 27406 Z= 0.497 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 *********************** 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 fitting. rotamer outliers: 1 poor density : 364 time to evaluate : 2.174 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: 0.3490 time to fit residues: 189.1137 Evaluate side-chains 215 residues out of total 2118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 215 time to evaluate : 2.470 ------------------------------------------------------------------------------- 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: 4.9990 chunk 62 optimal weight: 3.9990 chunk 122 optimal weight: 6.9990 chunk 97 optimal weight: 2.9990 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 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 20157 Z= 0.378 Angle : 0.795 9.898 27406 Z= 0.416 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 *********************** 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 fitting. rotamer outliers: 4 poor density : 295 time to evaluate : 2.161 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: 0.8600 (t) cc_final: 0.8333 (t) REVERT: C 48 MET cc_start: 0.7734 (tpp) cc_final: 0.7403 (mmt) REVERT: C 102 ILE cc_start: 0.9404 (tp) cc_final: 0.9075 (pt) REVERT: F 411 THR cc_start: 0.7612 (p) cc_final: 0.7160 (m) REVERT: G 609 PRO cc_start: 0.8363 (Cg_exo) cc_final: 0.8103 (Cg_endo) REVERT: G 626 MET cc_start: 0.7604 (tpp) cc_final: 0.7306 (tpt) REVERT: I 234 LEU cc_start: 0.6512 (mm) cc_final: 0.6143 (mm) REVERT: I 263 ASN cc_start: 0.8039 (t0) cc_final: 0.7802 (t0) REVERT: K 95 MET cc_start: 0.8043 (ttm) cc_final: 0.7756 (ttm) REVERT: K 154 MET cc_start: 0.8951 (mmm) cc_final: 0.8575 (mmt) REVERT: K 411 THR cc_start: 0.7913 (p) cc_final: 0.7330 (m) REVERT: L 609 PRO cc_start: 0.7945 (Cg_exo) cc_final: 0.7563 (Cg_endo) REVERT: M 29 PHE cc_start: 0.5957 (p90) cc_final: 0.5050 (p90) REVERT: M 76 ILE cc_start: 0.8321 (pt) cc_final: 0.8071 (tp) REVERT: M 102 ILE cc_start: 0.9373 (tp) cc_final: 0.9034 (pt) REVERT: N 263 ASN cc_start: 0.7629 (t0) cc_final: 0.7181 (t0) outliers start: 4 outliers final: 2 residues processed: 298 average time/residue: 0.3357 time to fit residues: 150.9415 Evaluate side-chains 219 residues out of total 2118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 217 time to evaluate : 2.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 121 optimal weight: 9.9990 chunk 67 optimal weight: 0.0050 chunk 181 optimal weight: 0.0470 chunk 148 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 218 optimal weight: 7.9990 chunk 235 optimal weight: 8.9990 chunk 194 optimal weight: 0.6980 chunk 216 optimal weight: 4.9990 chunk 74 optimal weight: 6.9990 chunk 175 optimal weight: 3.9990 overall best weight: 1.7496 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 20157 Z= 0.256 Angle : 0.689 10.144 27406 Z= 0.361 Chirality : 0.047 0.207 3242 Planarity : 0.005 0.075 3411 Dihedral : 10.499 78.497 3766 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.03 % Favored : 93.72 % Rotamer: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % 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: -1.62 (0.16), residues: 2420 helix: -0.49 (0.27), residues: 360 sheet: -0.50 (0.20), residues: 684 loop : -1.56 (0.16), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP M 47 HIS 0.005 0.001 HIS H 35 PHE 0.015 0.002 PHE C 64 TYR 0.031 0.001 TYR F 217 ARG 0.009 0.001 ARG N 293 *********************** 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 303 residues out of total 2118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 303 time to evaluate : 2.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 411 THR cc_start: 0.7666 (p) cc_final: 0.7301 (m) REVERT: C 48 MET cc_start: 0.7606 (tpp) cc_final: 0.7076 (mmt) REVERT: F 184 LEU cc_start: 0.7466 (tp) cc_final: 0.7190 (tp) REVERT: F 411 THR cc_start: 0.7576 (p) cc_final: 0.7186 (m) REVERT: F 424 ILE cc_start: 0.9472 (mm) cc_final: 0.9271 (mm) REVERT: G 648 GLU cc_start: 0.6444 (pp20) cc_final: 0.6108 (pp20) REVERT: H 48 MET cc_start: 0.8027 (tpp) cc_final: 0.7573 (mmt) REVERT: H 102 ILE cc_start: 0.9253 (tp) cc_final: 0.8900 (pt) REVERT: I 263 ASN cc_start: 0.7866 (t0) cc_final: 0.7369 (t0) REVERT: K 154 MET cc_start: 0.8984 (mmm) cc_final: 0.8555 (mmt) REVERT: K 342 LEU cc_start: 0.8705 (tp) cc_final: 0.8483 (tp) REVERT: K 411 THR cc_start: 0.7732 (p) cc_final: 0.7199 (m) REVERT: L 609 PRO cc_start: 0.8100 (Cg_exo) cc_final: 0.7742 (Cg_endo) REVERT: M 76 ILE cc_start: 0.8218 (pt) cc_final: 0.7950 (tp) REVERT: N 234 LEU cc_start: 0.6274 (mm) cc_final: 0.5991 (mm) REVERT: N 263 ASN cc_start: 0.7633 (t0) cc_final: 0.7232 (t0) outliers start: 0 outliers final: 0 residues processed: 303 average time/residue: 0.3339 time to fit residues: 153.7894 Evaluate side-chains 219 residues out of total 2118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 219 time to evaluate : 2.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 215 optimal weight: 7.9990 chunk 164 optimal weight: 7.9990 chunk 113 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 104 optimal weight: 5.9990 chunk 146 optimal weight: 9.9990 chunk 219 optimal weight: 1.9990 chunk 231 optimal weight: 20.0000 chunk 114 optimal weight: 0.8980 chunk 207 optimal weight: 10.0000 chunk 62 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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 D 292 ASN 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 20157 Z= 0.278 Angle : 0.688 9.889 27406 Z= 0.357 Chirality : 0.047 0.178 3242 Planarity : 0.005 0.051 3411 Dihedral : 9.988 75.760 3766 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.61 % Favored : 93.14 % Rotamer: Outliers : 0.05 % Allowed : 3.49 % Favored : 96.46 % 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: -1.64 (0.16), residues: 2420 helix: -0.29 (0.28), residues: 360 sheet: -0.53 (0.20), residues: 677 loop : -1.63 (0.16), residues: 1383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 69 HIS 0.005 0.002 HIS A 216 PHE 0.013 0.002 PHE H 64 TYR 0.013 0.001 TYR A 39 ARG 0.010 0.001 ARG D 293 *********************** 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 281 residues out of total 2118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 280 time to evaluate : 2.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 411 THR cc_start: 0.7621 (p) cc_final: 0.7256 (m) REVERT: C 48 MET cc_start: 0.7804 (tpp) cc_final: 0.7127 (mmt) REVERT: F 426 MET cc_start: 0.6013 (mtm) cc_final: 0.5588 (mtt) REVERT: G 626 MET cc_start: 0.7255 (tpp) cc_final: 0.6782 (tpt) REVERT: I 263 ASN cc_start: 0.8028 (t0) cc_final: 0.7234 (t0) REVERT: K 154 MET cc_start: 0.8944 (mmm) cc_final: 0.8427 (mmt) REVERT: K 342 LEU cc_start: 0.8700 (tp) cc_final: 0.8443 (tp) REVERT: K 411 THR cc_start: 0.7680 (p) cc_final: 0.7223 (m) REVERT: L 609 PRO cc_start: 0.8213 (Cg_exo) cc_final: 0.7913 (Cg_endo) REVERT: M 86 LEU cc_start: 0.7933 (mp) cc_final: 0.7664 (mp) REVERT: N 263 ASN cc_start: 0.7829 (t0) cc_final: 0.7301 (t0) outliers start: 1 outliers final: 0 residues processed: 280 average time/residue: 0.3430 time to fit residues: 145.7988 Evaluate side-chains 203 residues out of total 2118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 203 time to evaluate : 2.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 193 optimal weight: 1.9990 chunk 131 optimal weight: 0.8980 chunk 3 optimal weight: 0.0870 chunk 172 optimal weight: 8.9990 chunk 95 optimal weight: 0.7980 chunk 197 optimal weight: 0.0970 chunk 160 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 118 optimal weight: 1.9990 chunk 208 optimal weight: 4.9990 chunk 58 optimal weight: 6.9990 overall best weight: 0.7758 ------------------------------------------------------------------------------- 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 C 43 GLN G 591 GLN G 651 ASN H 6 GLN L 651 ASN ** L 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20157 Z= 0.178 Angle : 0.633 10.293 27406 Z= 0.329 Chirality : 0.045 0.193 3242 Planarity : 0.004 0.049 3411 Dihedral : 9.557 72.668 3766 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.07 % Favored : 93.68 % Rotamer: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % 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: -1.56 (0.16), residues: 2420 helix: -0.27 (0.27), residues: 360 sheet: -0.54 (0.20), residues: 666 loop : -1.51 (0.16), residues: 1394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP F 69 HIS 0.004 0.001 HIS F 374 PHE 0.010 0.001 PHE K 376 TYR 0.029 0.001 TYR B 586 ARG 0.009 0.001 ARG I 293 *********************** 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 281 residues out of total 2118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 281 time to evaluate : 2.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 411 THR cc_start: 0.7564 (p) cc_final: 0.7227 (m) REVERT: C 48 MET cc_start: 0.7753 (tpp) cc_final: 0.7189 (mmt) REVERT: F 104 MET cc_start: 0.8932 (tpp) cc_final: 0.8558 (tpt) REVERT: F 369 MET cc_start: 0.8149 (ttp) cc_final: 0.7929 (ttp) REVERT: F 426 MET cc_start: 0.5744 (mtm) cc_final: 0.5238 (mtt) REVERT: G 626 MET cc_start: 0.6983 (tpp) cc_final: 0.6619 (tpt) REVERT: I 263 ASN cc_start: 0.8016 (t0) cc_final: 0.7306 (t0) REVERT: K 104 MET cc_start: 0.9101 (ttt) cc_final: 0.8718 (tpp) REVERT: K 154 MET cc_start: 0.8904 (mmm) cc_final: 0.8513 (mmt) REVERT: K 342 LEU cc_start: 0.8584 (tp) cc_final: 0.8363 (tp) REVERT: K 411 THR cc_start: 0.7566 (p) cc_final: 0.7194 (m) REVERT: L 609 PRO cc_start: 0.8201 (Cg_exo) cc_final: 0.7929 (Cg_endo) REVERT: N 263 ASN cc_start: 0.7750 (t0) cc_final: 0.7313 (t0) outliers start: 0 outliers final: 0 residues processed: 281 average time/residue: 0.3226 time to fit residues: 138.1007 Evaluate side-chains 203 residues out of total 2118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 203 time to evaluate : 2.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 78 optimal weight: 0.6980 chunk 208 optimal weight: 0.0670 chunk 45 optimal weight: 2.9990 chunk 136 optimal weight: 6.9990 chunk 57 optimal weight: 0.9990 chunk 232 optimal weight: 7.9990 chunk 192 optimal weight: 0.6980 chunk 107 optimal weight: 4.9990 chunk 19 optimal weight: 10.0000 chunk 76 optimal weight: 10.0000 chunk 121 optimal weight: 10.0000 overall best weight: 1.0922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN B 651 ASN C 43 GLN G 651 ASN L 651 ASN M 43 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.3235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 20157 Z= 0.190 Angle : 0.618 10.204 27406 Z= 0.320 Chirality : 0.045 0.271 3242 Planarity : 0.004 0.061 3411 Dihedral : 9.061 70.437 3766 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.28 % Favored : 93.47 % Rotamer: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.49 (0.17), residues: 2420 helix: -0.08 (0.28), residues: 356 sheet: -0.57 (0.20), residues: 663 loop : -1.46 (0.16), residues: 1401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP F 69 HIS 0.004 0.001 HIS F 249 PHE 0.013 0.001 PHE H 64 TYR 0.013 0.001 TYR A 39 ARG 0.020 0.001 ARG K 166 *********************** 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 261 residues out of total 2118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 261 time to evaluate : 2.204 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: 0.7684 (p) cc_final: 0.7339 (m) REVERT: A 475 MET cc_start: 0.7357 (tpp) cc_final: 0.7032 (mmt) REVERT: C 48 MET cc_start: 0.7836 (tpp) cc_final: 0.7204 (mmt) REVERT: F 369 MET cc_start: 0.8297 (ttp) cc_final: 0.8034 (ttp) REVERT: F 411 THR cc_start: 0.7590 (p) cc_final: 0.7262 (m) REVERT: F 426 MET cc_start: 0.5892 (mtm) cc_final: 0.5403 (mtt) REVERT: G 626 MET cc_start: 0.6982 (tpp) cc_final: 0.6586 (tpt) REVERT: I 263 ASN cc_start: 0.8050 (t0) cc_final: 0.7537 (t0) REVERT: K 104 MET cc_start: 0.8950 (ttt) cc_final: 0.8602 (tpp) REVERT: K 154 MET cc_start: 0.8843 (mmm) cc_final: 0.8327 (mmt) REVERT: K 342 LEU cc_start: 0.8555 (tp) cc_final: 0.8258 (tp) REVERT: L 609 PRO cc_start: 0.8295 (Cg_exo) cc_final: 0.8070 (Cg_endo) REVERT: N 263 ASN cc_start: 0.7872 (t0) cc_final: 0.7464 (t0) outliers start: 0 outliers final: 0 residues processed: 261 average time/residue: 0.3352 time to fit residues: 135.0487 Evaluate side-chains 193 residues out of total 2118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 193 time to evaluate : 2.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 223 optimal weight: 6.9990 chunk 26 optimal weight: 4.9990 chunk 132 optimal weight: 10.0000 chunk 169 optimal weight: 0.9990 chunk 131 optimal weight: 1.9990 chunk 195 optimal weight: 10.0000 chunk 129 optimal weight: 2.9990 chunk 231 optimal weight: 20.0000 chunk 144 optimal weight: 4.9990 chunk 141 optimal weight: 5.9990 chunk 106 optimal weight: 0.9980 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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 G 651 ASN ** K 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 651 ASN M 113 ASN N 270 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.3408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 20157 Z= 0.307 Angle : 0.674 9.854 27406 Z= 0.349 Chirality : 0.047 0.201 3242 Planarity : 0.005 0.049 3411 Dihedral : 9.121 71.223 3766 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.98 % Favored : 92.77 % Rotamer: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % 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: -1.55 (0.17), residues: 2420 helix: -0.13 (0.29), residues: 354 sheet: -0.53 (0.20), residues: 650 loop : -1.54 (0.16), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP N 267 HIS 0.005 0.002 HIS H 35 PHE 0.013 0.002 PHE K 376 TYR 0.046 0.002 TYR F 217 ARG 0.013 0.001 ARG F 166 *********************** 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 246 residues out of total 2118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 246 time to evaluate : 2.381 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 96 TRP cc_start: 0.8317 (m100) cc_final: 0.7746 (m100) REVERT: A 154 MET cc_start: 0.9058 (mmm) cc_final: 0.8731 (mmt) REVERT: A 411 THR cc_start: 0.7703 (p) cc_final: 0.7418 (m) REVERT: C 48 MET cc_start: 0.8026 (tpp) cc_final: 0.7302 (mmt) REVERT: F 426 MET cc_start: 0.6032 (mtm) cc_final: 0.5584 (mtt) REVERT: G 626 MET cc_start: 0.7034 (tpp) cc_final: 0.6526 (tpt) REVERT: K 154 MET cc_start: 0.8715 (mmm) cc_final: 0.8268 (mmt) REVERT: K 342 LEU cc_start: 0.8726 (tp) cc_final: 0.8409 (tp) REVERT: L 609 PRO cc_start: 0.8396 (Cg_exo) cc_final: 0.8169 (Cg_endo) REVERT: M 86 LEU cc_start: 0.7805 (mp) cc_final: 0.7593 (mp) REVERT: M 115 ASP cc_start: 0.8599 (p0) cc_final: 0.8303 (p0) outliers start: 0 outliers final: 0 residues processed: 246 average time/residue: 0.3208 time to fit residues: 122.5491 Evaluate side-chains 191 residues out of total 2118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 191 time to evaluate : 2.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 143 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 chunk 138 optimal weight: 7.9990 chunk 69 optimal weight: 20.0000 chunk 45 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 147 optimal weight: 4.9990 chunk 157 optimal weight: 9.9990 chunk 114 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 181 optimal weight: 0.8980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN B 651 ASN G 651 ASN L 651 ASN M 43 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.3508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 20157 Z= 0.230 Angle : 0.639 10.055 27406 Z= 0.331 Chirality : 0.046 0.199 3242 Planarity : 0.005 0.108 3411 Dihedral : 9.010 69.635 3766 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.94 % Favored : 92.81 % Rotamer: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % 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: -1.56 (0.17), residues: 2420 helix: -0.13 (0.29), residues: 354 sheet: -0.56 (0.20), residues: 650 loop : -1.54 (0.16), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP H 47 HIS 0.004 0.001 HIS F 216 PHE 0.010 0.001 PHE K 376 TYR 0.018 0.001 TYR B 586 ARG 0.011 0.001 ARG K 166 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 245 time to evaluate : 2.701 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: 0.9057 (mmm) cc_final: 0.8758 (mmt) REVERT: C 48 MET cc_start: 0.7915 (tpp) cc_final: 0.7283 (mmt) REVERT: F 426 MET cc_start: 0.5831 (mtm) cc_final: 0.5412 (mtt) REVERT: K 154 MET cc_start: 0.8741 (mmm) cc_final: 0.8298 (mmt) REVERT: K 342 LEU cc_start: 0.8625 (tp) cc_final: 0.8362 (tp) REVERT: L 609 PRO cc_start: 0.8453 (Cg_exo) cc_final: 0.8233 (Cg_endo) REVERT: M 115 ASP cc_start: 0.8586 (p0) cc_final: 0.8285 (p0) outliers start: 0 outliers final: 0 residues processed: 245 average time/residue: 0.3238 time to fit residues: 123.8883 Evaluate side-chains 191 residues out of total 2118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 191 time to evaluate : 2.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 210 optimal weight: 3.9990 chunk 221 optimal weight: 4.9990 chunk 202 optimal weight: 0.9980 chunk 215 optimal weight: 9.9990 chunk 129 optimal weight: 0.9980 chunk 93 optimal weight: 0.7980 chunk 169 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 194 optimal weight: 0.5980 chunk 203 optimal weight: 0.7980 chunk 214 optimal weight: 10.0000 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN B 651 ASN G 651 ASN L 651 ASN M 113 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.3657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20157 Z= 0.175 Angle : 0.611 10.083 27406 Z= 0.316 Chirality : 0.045 0.212 3242 Planarity : 0.004 0.046 3411 Dihedral : 8.528 65.837 3766 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.61 % Favored : 93.14 % Rotamer: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.50 (0.17), residues: 2420 helix: -0.22 (0.28), residues: 364 sheet: -0.53 (0.20), residues: 648 loop : -1.46 (0.16), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP F 35 HIS 0.005 0.001 HIS K 216 PHE 0.009 0.001 PHE K 376 TYR 0.021 0.001 TYR K 217 ARG 0.012 0.001 ARG F 166 *********************** 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 244 residues out of total 2118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 244 time to evaluate : 2.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 MET cc_start: 0.9037 (mmm) cc_final: 0.8767 (mmt) REVERT: C 48 MET cc_start: 0.7957 (tpp) cc_final: 0.7300 (mmt) REVERT: F 426 MET cc_start: 0.5703 (mtm) cc_final: 0.5259 (mtt) REVERT: K 154 MET cc_start: 0.8713 (mmm) cc_final: 0.8275 (mmt) REVERT: K 342 LEU cc_start: 0.8522 (tp) cc_final: 0.8251 (tp) REVERT: L 609 PRO cc_start: 0.8445 (Cg_exo) cc_final: 0.8236 (Cg_endo) REVERT: M 115 ASP cc_start: 0.8585 (p0) cc_final: 0.8249 (p0) outliers start: 0 outliers final: 0 residues processed: 244 average time/residue: 0.3220 time to fit residues: 122.5143 Evaluate side-chains 189 residues out of total 2118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 189 time to evaluate : 2.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 141 optimal weight: 0.2980 chunk 227 optimal weight: 0.9980 chunk 139 optimal weight: 10.0000 chunk 108 optimal weight: 0.0370 chunk 158 optimal weight: 2.9990 chunk 239 optimal weight: 1.9990 chunk 220 optimal weight: 2.9990 chunk 190 optimal weight: 2.9990 chunk 19 optimal weight: 10.0000 chunk 147 optimal weight: 1.9990 chunk 116 optimal weight: 6.9990 overall best weight: 1.0662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 HIS A 160 ASN A 258 GLN B 651 ASN G 651 ASN H 6 GLN L 651 ASN M 113 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.3778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 20157 Z= 0.186 Angle : 0.619 10.132 27406 Z= 0.319 Chirality : 0.045 0.215 3242 Planarity : 0.005 0.076 3411 Dihedral : 8.200 63.433 3766 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.28 % Favored : 93.47 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.49 (0.17), residues: 2420 helix: -0.23 (0.28), residues: 367 sheet: -0.52 (0.20), residues: 649 loop : -1.45 (0.16), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP G 623 HIS 0.004 0.001 HIS K 374 PHE 0.010 0.001 PHE K 376 TYR 0.032 0.001 TYR F 217 ARG 0.016 0.001 ARG K 166 ********************** 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 246 residues out of total 2118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 246 time to evaluate : 2.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 MET cc_start: 0.9017 (mmm) cc_final: 0.8726 (mmt) REVERT: C 48 MET cc_start: 0.7974 (tpp) cc_final: 0.7270 (mmt) REVERT: D 279 MET cc_start: 0.7155 (pmm) cc_final: 0.6922 (pmm) REVERT: F 426 MET cc_start: 0.5778 (mtm) cc_final: 0.5340 (mtt) REVERT: I 279 MET cc_start: 0.7339 (pmm) cc_final: 0.7135 (pmm) REVERT: K 154 MET cc_start: 0.8713 (mmm) cc_final: 0.8276 (mmt) REVERT: K 342 LEU cc_start: 0.8537 (tp) cc_final: 0.8257 (tp) REVERT: K 475 MET cc_start: 0.7694 (tpp) cc_final: 0.7244 (tpp) REVERT: M 115 ASP cc_start: 0.8681 (p0) cc_final: 0.8368 (p0) outliers start: 0 outliers final: 0 residues processed: 246 average time/residue: 0.3343 time to fit residues: 126.0265 Evaluate side-chains 190 residues out of total 2118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 190 time to evaluate : 2.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 151 optimal weight: 8.9990 chunk 202 optimal weight: 0.0000 chunk 58 optimal weight: 10.0000 chunk 175 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 52 optimal weight: 6.9990 chunk 190 optimal weight: 0.9990 chunk 79 optimal weight: 6.9990 chunk 195 optimal weight: 9.9990 chunk 24 optimal weight: 3.9990 chunk 35 optimal weight: 6.9990 overall best weight: 2.7992 ------------------------------------------------------------------------------- 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 F 328 GLN G 651 ASN H 113 ASN K 105 HIS ** K 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 651 ASN M 43 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.125835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.112215 restraints weight = 41044.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.111641 restraints weight = 87736.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.111290 restraints weight = 90784.442| |-----------------------------------------------------------------------------| r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.3868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 20157 Z= 0.354 Angle : 0.730 10.047 27406 Z= 0.377 Chirality : 0.049 0.241 3242 Planarity : 0.005 0.047 3411 Dihedral : 8.733 66.685 3766 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.52 % Favored : 92.23 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.67 (0.17), residues: 2420 helix: -0.28 (0.29), residues: 361 sheet: -0.53 (0.20), residues: 643 loop : -1.65 (0.16), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP L 631 HIS 0.006 0.002 HIS F 216 PHE 0.028 0.002 PHE D 294 TYR 0.021 0.002 TYR B 586 ARG 0.018 0.001 ARG K 166 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3597.25 seconds wall clock time: 67 minutes 22.30 seconds (4042.30 seconds total)