Starting phenix.real_space_refine on Wed Apr 10 14:37:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sb0_40286/04_2024/8sb0_40286.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sb0_40286/04_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_40286/04_2024/8sb0_40286.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sb0_40286/04_2024/8sb0_40286.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sb0_40286/04_2024/8sb0_40286.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sb0_40286/04_2024/8sb0_40286.pdb" } 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 Residue "A TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 657": "OE1" <-> "OE2" Residue "C GLU 10": "OE1" <-> "OE2" Residue "C GLU 82": "OE1" <-> "OE2" Residue "F GLU 370": "OE1" <-> "OE2" Residue "G GLU 647": "OE1" <-> "OE2" Residue "H GLU 10": "OE1" <-> "OE2" Residue "L GLU 647": "OE1" <-> "OE2" Residue "M GLU 10": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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: 11.25, per 1000 atoms: 0.57 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 - 3.50 Amino acid : False - 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: 8.54 Conformation dependent library (CDL) restraints added in 3.7 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: 2.52 Creating SS restraints... Processing helix chain 'A' and resid 68 through 74 removed outlier: 4.143A pdb=" N HIS A 72 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA A 73 " --> pdb=" O TRP A 69 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N CYS A 74 " --> pdb=" O ALA A 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 68 through 74' Processing helix chain 'A' and resid 98 through 117 removed outlier: 4.505A pdb=" N ASP A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLU A 106 " --> pdb=" O ASP A 102 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER A 115 " --> pdb=" O LEU A 111 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU A 116 " --> pdb=" O TRP A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 127 removed outlier: 3.550A pdb=" N CYS A 126 " --> pdb=" O THR A 123 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL A 127 " --> pdb=" O PRO A 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 123 through 127' Processing helix chain 'A' and resid 177 through 179 No H-bonds generated for 'chain 'A' and resid 177 through 179' Processing helix chain 'A' and resid 335 through 353 removed outlier: 4.013A pdb=" N HIS A 352 " --> pdb=" O GLU A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 481 Processing helix chain 'B' and resid 529 through 535 removed outlier: 4.226A pdb=" N MET B 535 " --> pdb=" O GLY B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 537 through 543 removed outlier: 4.176A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 576 removed outlier: 3.552A pdb=" N LEU B 576 " --> pdb=" O GLY B 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 576 through 596 removed outlier: 3.715A pdb=" N LEU B 581 " --> pdb=" O GLN B 577 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N ALA B 582 " --> pdb=" O ALA B 578 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N VAL B 583 " --> pdb=" O ARG B 579 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N TRP B 596 " --> pdb=" O LEU B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 611 through 615 Processing helix chain 'B' and resid 618 through 622 Processing helix chain 'B' and resid 627 through 636 removed outlier: 3.578A pdb=" N GLU B 634 " --> pdb=" O GLN B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 659 removed outlier: 4.170A pdb=" N GLY B 644 " --> pdb=" O GLN B 640 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LEU B 645 " --> pdb=" O ILE B 641 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASP B 659 " --> pdb=" O LYS B 655 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 65 removed outlier: 3.681A pdb=" N GLN C 65 " --> pdb=" O ARG C 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 62 through 65' Processing helix chain 'C' and resid 87 through 91 Processing helix chain 'D' and resid 311 through 315 Processing helix chain 'F' and resid 68 through 74 removed outlier: 4.128A pdb=" N HIS F 72 " --> pdb=" O VAL F 68 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA F 73 " --> pdb=" O TRP F 69 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N CYS F 74 " --> pdb=" O ALA F 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 68 through 74' Processing helix chain 'F' and resid 98 through 115 removed outlier: 4.472A pdb=" N ASP F 102 " --> pdb=" O ASN F 98 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N GLU F 106 " --> pdb=" O ASP F 102 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER F 115 " --> pdb=" O LEU F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 123 through 127 removed outlier: 3.611A pdb=" N VAL F 127 " --> pdb=" O PRO F 124 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 179 No H-bonds generated for 'chain 'F' and resid 177 through 179' Processing helix chain 'F' and resid 335 through 353 removed outlier: 4.005A pdb=" N HIS F 352 " --> pdb=" O GLU F 348 " (cutoff:3.500A) Processing helix chain 'F' and resid 476 through 481 Processing helix chain 'F' and resid 482 through 484 No H-bonds generated for 'chain 'F' and resid 482 through 484' Processing helix chain 'G' and resid 529 through 535 removed outlier: 4.164A pdb=" N MET G 535 " --> pdb=" O GLY G 531 " (cutoff:3.500A) Processing helix chain 'G' and resid 536 through 543 removed outlier: 4.324A pdb=" N GLN G 540 " --> pdb=" O THR G 536 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ASN G 543 " --> pdb=" O VAL G 539 " (cutoff:3.500A) Processing helix chain 'G' and resid 571 through 576 Processing helix chain 'G' and resid 576 through 596 removed outlier: 3.669A pdb=" N LEU G 581 " --> pdb=" O GLN G 577 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ALA G 582 " --> pdb=" O ALA G 578 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N VAL G 583 " --> pdb=" O ARG G 579 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N TRP G 596 " --> pdb=" O LEU G 592 " (cutoff:3.500A) Processing helix chain 'G' and resid 611 through 615 Processing helix chain 'G' and resid 618 through 622 Processing helix chain 'G' and resid 627 through 636 removed outlier: 3.739A pdb=" N GLU G 634 " --> pdb=" O GLN G 630 " (cutoff:3.500A) Processing helix chain 'G' and resid 638 through 659 removed outlier: 4.020A pdb=" N GLY G 644 " --> pdb=" O GLN G 640 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LEU G 645 " --> pdb=" O ILE G 641 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ASP G 659 " --> pdb=" O LYS G 655 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 30 No H-bonds generated for 'chain 'H' and resid 28 through 30' Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.502A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'I' and resid 311 through 315 Processing helix chain 'K' and resid 68 through 74 removed outlier: 4.126A pdb=" N HIS K 72 " --> pdb=" O VAL K 68 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA K 73 " --> pdb=" O TRP K 69 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N CYS K 74 " --> pdb=" O ALA K 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 68 through 74' Processing helix chain 'K' and resid 99 through 115 removed outlier: 4.299A pdb=" N GLU K 106 " --> pdb=" O ASP K 102 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER K 115 " --> pdb=" O LEU K 111 " (cutoff:3.500A) Processing helix chain 'K' and resid 123 through 127 removed outlier: 3.633A pdb=" N VAL K 127 " --> pdb=" O PRO K 124 " (cutoff:3.500A) Processing helix chain 'K' and resid 177 through 179 No H-bonds generated for 'chain 'K' and resid 177 through 179' Processing helix chain 'K' and resid 335 through 353 removed outlier: 4.023A pdb=" N HIS K 352 " --> pdb=" O GLU K 348 " (cutoff:3.500A) Processing helix chain 'K' and resid 476 through 481 Processing helix chain 'L' and resid 529 through 535 removed outlier: 4.100A pdb=" N MET L 535 " --> pdb=" O GLY L 531 " (cutoff:3.500A) Processing helix chain 'L' and resid 537 through 543 removed outlier: 4.171A pdb=" N ASN L 543 " --> pdb=" O VAL L 539 " (cutoff:3.500A) Processing helix chain 'L' and resid 571 through 576 removed outlier: 3.505A pdb=" N LEU L 576 " --> pdb=" O GLY L 572 " (cutoff:3.500A) Processing helix chain 'L' and resid 576 through 596 removed outlier: 3.709A pdb=" N LEU L 581 " --> pdb=" O GLN L 577 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N ALA L 582 " --> pdb=" O ALA L 578 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N VAL L 583 " --> pdb=" O ARG L 579 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N TRP L 596 " --> pdb=" O LEU L 592 " (cutoff:3.500A) Processing helix chain 'L' and resid 611 through 615 Processing helix chain 'L' and resid 618 through 622 Processing helix chain 'L' and resid 627 through 636 removed outlier: 3.690A pdb=" N GLU L 634 " --> pdb=" O GLN L 630 " (cutoff:3.500A) Processing helix chain 'L' and resid 638 through 659 removed outlier: 4.013A pdb=" N GLY L 644 " --> pdb=" O GLN L 640 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LEU L 645 " --> pdb=" O ILE L 641 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASP L 659 " --> pdb=" O LYS L 655 " (cutoff:3.500A) Processing helix chain 'M' and resid 87 through 91 Processing helix chain 'N' and resid 311 through 315 Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 497 removed outlier: 5.253A pdb=" N VAL A 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR B 606 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.872A pdb=" N LYS A 46 " --> pdb=" O LYS A 490 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 55 through 56 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 172 through 174 removed outlier: 3.855A pdb=" N LEU A 129 " --> pdb=" O TYR A 191 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 215 through 218 removed outlier: 4.449A pdb=" N TYR A 217 " --> pdb=" O HIS A 249 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N HIS A 249 " --> pdb=" O TYR A 217 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 261 removed outlier: 4.093A pdb=" N GLY A 451 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 10.375A pdb=" N THR A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.606A pdb=" N ILE A 294 " --> pdb=" O THR A 444 " (cutoff:3.500A) removed outlier: 9.884A pdb=" N ARG A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 10.901A pdb=" N VAL A 292 " --> pdb=" O ARG A 446 " (cutoff:3.500A) removed outlier: 9.310A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.305A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N GLU A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N SER A 334 " --> pdb=" O GLU A 293 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 271 through 273 removed outlier: 6.666A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 10.305A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.310A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.901A pdb=" N VAL A 292 " --> pdb=" O ARG A 446 " (cutoff:3.500A) removed outlier: 9.884A pdb=" N ARG A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.606A pdb=" N ILE A 294 " --> pdb=" O THR A 444 " (cutoff:3.500A) removed outlier: 10.375A pdb=" N THR A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N THR A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N PHE A 468 " --> pdb=" O THR A 358 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LYS A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 302 through 308 removed outlier: 5.861A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 423 through 424 Processing sheet with id=AB2, first strand: chain 'C' and resid 3 through 6 removed outlier: 3.590A pdb=" N THR C 71 " --> pdb=" O TYR C 80 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 9 through 12 removed outlier: 4.549A pdb=" N TYR C 33 " --> pdb=" O GLY C 99 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ILE C 34 " --> pdb=" O TRP C 50 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N TRP C 50 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N TRP C 36 " --> pdb=" O MET C 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 239 through 241 removed outlier: 7.084A pdb=" N TRP D 267 " --> pdb=" O MET D 279 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N MET D 279 " --> pdb=" O TRP D 267 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 239 through 241 Processing sheet with id=AB6, first strand: chain 'D' and resid 247 through 253 Processing sheet with id=AB7, first strand: chain 'F' and resid 494 through 497 removed outlier: 5.031A pdb=" N VAL G 608 " --> pdb=" O VAL F 36 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N VAL F 38 " --> pdb=" O THR G 606 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N THR G 606 " --> pdb=" O VAL F 38 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N TYR F 40 " --> pdb=" O CYS G 604 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N CYS G 604 " --> pdb=" O TYR F 40 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 55 through 56 Processing sheet with id=AB9, first strand: chain 'F' and resid 84 through 86 removed outlier: 4.843A pdb=" N VAL F 242 " --> pdb=" O LEU F 86 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 91 through 94 Processing sheet with id=AC2, first strand: chain 'F' and resid 169 through 174 Processing sheet with id=AC3, first strand: chain 'F' and resid 215 through 218 removed outlier: 4.491A pdb=" N TYR F 217 " --> pdb=" O HIS F 249 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N HIS F 249 " --> pdb=" O TYR F 217 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 259 through 261 removed outlier: 4.103A pdb=" N GLY F 451 " --> pdb=" O LEU F 260 " (cutoff:3.500A) removed outlier: 10.304A pdb=" N THR F 444 " --> pdb=" O ILE F 294 " (cutoff:3.500A) removed outlier: 11.514A pdb=" N ILE F 294 " --> pdb=" O THR F 444 " (cutoff:3.500A) removed outlier: 9.839A pdb=" N ARG F 446 " --> pdb=" O VAL F 292 " (cutoff:3.500A) removed outlier: 10.857A pdb=" N VAL F 292 " --> pdb=" O ARG F 446 " (cutoff:3.500A) removed outlier: 9.291A pdb=" N ASN F 448 " --> pdb=" O THR F 290 " (cutoff:3.500A) removed outlier: 10.286A pdb=" N THR F 290 " --> pdb=" O ASN F 448 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N THR F 450 " --> pdb=" O LEU F 288 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU F 454 " --> pdb=" O ILE F 284 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N GLU F 293 " --> pdb=" O SER F 334 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N SER F 334 " --> pdb=" O GLU F 293 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 271 through 273 removed outlier: 3.512A pdb=" N LEU F 454 " --> pdb=" O ILE F 284 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N THR F 450 " --> pdb=" O LEU F 288 " (cutoff:3.500A) removed outlier: 10.286A pdb=" N THR F 290 " --> pdb=" O ASN F 448 " (cutoff:3.500A) removed outlier: 9.291A pdb=" N ASN F 448 " --> pdb=" O THR F 290 " (cutoff:3.500A) removed outlier: 10.857A pdb=" N VAL F 292 " --> pdb=" O ARG F 446 " (cutoff:3.500A) removed outlier: 9.839A pdb=" N ARG F 446 " --> pdb=" O VAL F 292 " (cutoff:3.500A) removed outlier: 11.514A pdb=" N ILE F 294 " --> pdb=" O THR F 444 " (cutoff:3.500A) removed outlier: 10.304A pdb=" N THR F 444 " --> pdb=" O ILE F 294 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N THR F 358 " --> pdb=" O GLU F 466 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N PHE F 468 " --> pdb=" O THR F 358 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N LYS F 360 " --> pdb=" O PHE F 468 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 302 through 308 removed outlier: 5.843A pdb=" N THR F 303 " --> pdb=" O GLY F 321 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 423 through 424 Processing sheet with id=AC8, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AC9, first strand: chain 'H' and resid 9 through 12 removed outlier: 4.540A pdb=" N TYR H 33 " --> pdb=" O GLY H 99 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ILE H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N TRP H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 239 through 241 removed outlier: 7.127A pdb=" N TRP I 267 " --> pdb=" O MET I 279 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N MET I 279 " --> pdb=" O TRP I 267 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 239 through 241 Processing sheet with id=AD3, first strand: chain 'I' and resid 247 through 253 Processing sheet with id=AD4, first strand: chain 'K' and resid 494 through 497 removed outlier: 4.576A pdb=" N VAL K 36 " --> pdb=" O THR L 606 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 55 through 56 Processing sheet with id=AD6, first strand: chain 'K' and resid 84 through 86 removed outlier: 4.882A pdb=" N VAL K 242 " --> pdb=" O LEU K 86 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'K' and resid 91 through 94 Processing sheet with id=AD8, first strand: chain 'K' and resid 172 through 174 removed outlier: 3.985A pdb=" N LEU K 129 " --> pdb=" O TYR K 191 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'K' and resid 215 through 218 removed outlier: 4.386A pdb=" N TYR K 217 " --> pdb=" O HIS K 249 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N HIS K 249 " --> pdb=" O TYR K 217 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'K' and resid 259 through 261 removed outlier: 4.104A pdb=" N GLY K 451 " --> pdb=" O LEU K 260 " (cutoff:3.500A) removed outlier: 10.366A pdb=" N THR K 444 " --> pdb=" O ILE K 294 " (cutoff:3.500A) removed outlier: 11.584A pdb=" N ILE K 294 " --> pdb=" O THR K 444 " (cutoff:3.500A) removed outlier: 9.899A pdb=" N ARG K 446 " --> pdb=" O VAL K 292 " (cutoff:3.500A) removed outlier: 10.905A pdb=" N VAL K 292 " --> pdb=" O ARG K 446 " (cutoff:3.500A) removed outlier: 9.297A pdb=" N ASN K 448 " --> pdb=" O THR K 290 " (cutoff:3.500A) removed outlier: 10.302A pdb=" N THR K 290 " --> pdb=" O ASN K 448 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N THR K 450 " --> pdb=" O LEU K 288 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU K 454 " --> pdb=" O ILE K 284 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N GLU K 293 " --> pdb=" O SER K 334 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N SER K 334 " --> pdb=" O GLU K 293 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ALA K 329 " --> pdb=" O CYS K 418 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'K' and resid 271 through 273 removed outlier: 3.500A pdb=" N LEU K 454 " --> pdb=" O ILE K 284 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N THR K 450 " --> pdb=" O LEU K 288 " (cutoff:3.500A) removed outlier: 10.302A pdb=" N THR K 290 " --> pdb=" O ASN K 448 " (cutoff:3.500A) removed outlier: 9.297A pdb=" N ASN K 448 " --> pdb=" O THR K 290 " (cutoff:3.500A) removed outlier: 10.905A pdb=" N VAL K 292 " --> pdb=" O ARG K 446 " (cutoff:3.500A) removed outlier: 9.899A pdb=" N ARG K 446 " --> pdb=" O VAL K 292 " (cutoff:3.500A) removed outlier: 11.584A pdb=" N ILE K 294 " --> pdb=" O THR K 444 " (cutoff:3.500A) removed outlier: 10.366A pdb=" N THR K 444 " --> pdb=" O ILE K 294 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N THR K 358 " --> pdb=" O GLU K 466 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N PHE K 468 " --> pdb=" O THR K 358 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N LYS K 360 " --> pdb=" O PHE K 468 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'K' and resid 302 through 308 removed outlier: 5.792A pdb=" N THR K 303 " --> pdb=" O GLY K 321 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'K' and resid 423 through 424 Processing sheet with id=AE5, first strand: chain 'M' and resid 3 through 6 Processing sheet with id=AE6, first strand: chain 'M' and resid 9 through 12 removed outlier: 4.581A pdb=" N TYR M 33 " --> pdb=" O GLY M 99 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ILE M 34 " --> pdb=" O TRP M 50 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N TRP M 50 " --> pdb=" O ILE M 34 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N TRP M 36 " --> pdb=" O MET M 48 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'N' and resid 239 through 241 removed outlier: 7.106A pdb=" N TRP N 267 " --> pdb=" O MET N 279 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N MET N 279 " --> pdb=" O TRP N 267 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'N' and resid 239 through 241 Processing sheet with id=AE9, first strand: chain 'N' and resid 247 through 253 641 hydrogen bonds defined for protein. 1629 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.60 Time building geometry restraints manager: 9.36 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: 98.30 - 105.64: 402 105.64 - 112.97: 11093 112.97 - 120.30: 7416 120.30 - 127.63: 8211 127.63 - 134.96: 284 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 2.440 nonbonded pdb=" OG1 THR K 37 " pdb=" O ALA K 497 " model vdw 2.063 2.440 nonbonded pdb=" O VAL A 36 " pdb=" OG1 THR B 606 " model vdw 2.071 2.440 nonbonded pdb=" OG1 THR A 37 " pdb=" O ALA A 497 " model vdw 2.083 2.440 nonbonded pdb=" OE2 GLU I 282 " pdb=" O4 MAN R 4 " model vdw 2.086 2.440 ... (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 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: 1.180 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: 6.720 Check model and map are aligned: 0.280 Set scattering table: 0.170 Process input model: 54.120 Find NCS groups from input model: 1.340 Set up NCS constraints: 0.180 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:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.990 ------------------------------------------------------------------------------- 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 : 2.296 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: 0.3486 time to fit residues: 188.8749 Evaluate side-chains 215 residues out of total 2118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 215 time to evaluate : 2.131 ------------------------------------------------------------------------------- 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: 4.9990 chunk 100 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 122 optimal weight: 6.9990 chunk 97 optimal weight: 5.9990 chunk 188 optimal weight: 4.9990 chunk 72 optimal weight: 0.9980 chunk 114 optimal weight: 2.9990 chunk 140 optimal weight: 7.9990 chunk 217 optimal weight: 3.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- 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 328 GLN F 417 GLN G 591 GLN G 651 ASN H 6 GLN H 65 GLN H 113 ASN ** K 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 249 HIS L 651 ASN ** L 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 658 GLN M 113 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 20157 Z= 0.424 Angle : 0.818 9.876 27406 Z= 0.428 Chirality : 0.053 0.210 3242 Planarity : 0.006 0.061 3411 Dihedral : 10.897 79.521 3766 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.82 % Favored : 92.93 % Rotamer: Outliers : 0.19 % Allowed : 5.90 % Favored : 93.91 % 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: -1.75 (0.16), residues: 2420 helix: -0.54 (0.27), residues: 342 sheet: -0.74 (0.19), residues: 724 loop : -1.58 (0.16), residues: 1354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP H 47 HIS 0.010 0.003 HIS A 330 PHE 0.019 0.002 PHE C 64 TYR 0.025 0.002 TYR M 33 ARG 0.006 0.001 ARG B 617 *********************** 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 297 residues out of total 2118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 293 time to evaluate : 2.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 VAL cc_start: 0.8683 (t) cc_final: 0.8357 (t) REVERT: C 48 MET cc_start: 0.7739 (tpp) cc_final: 0.7426 (mmt) REVERT: C 102 ILE cc_start: 0.9411 (tp) cc_final: 0.9081 (pt) REVERT: F 411 THR cc_start: 0.7636 (p) cc_final: 0.7185 (m) REVERT: G 609 PRO cc_start: 0.8403 (Cg_exo) cc_final: 0.8137 (Cg_endo) REVERT: G 626 MET cc_start: 0.7690 (tpp) cc_final: 0.7311 (tpt) REVERT: H 102 ILE cc_start: 0.9322 (tp) cc_final: 0.8894 (pt) REVERT: K 95 MET cc_start: 0.8004 (ttm) cc_final: 0.7679 (ttm) REVERT: K 154 MET cc_start: 0.8957 (mmm) cc_final: 0.8600 (mmt) REVERT: K 411 THR cc_start: 0.7910 (p) cc_final: 0.7311 (m) REVERT: L 609 PRO cc_start: 0.8007 (Cg_exo) cc_final: 0.7636 (Cg_endo) REVERT: M 102 ILE cc_start: 0.9366 (tp) cc_final: 0.9026 (pt) REVERT: N 263 ASN cc_start: 0.7640 (t0) cc_final: 0.7180 (t0) outliers start: 4 outliers final: 3 residues processed: 296 average time/residue: 0.3444 time to fit residues: 153.6449 Evaluate side-chains 214 residues out of total 2118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 211 time to evaluate : 2.316 ------------------------------------------------------------------------------- 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: 7.9990 chunk 67 optimal weight: 5.9990 chunk 181 optimal weight: 0.6980 chunk 148 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 218 optimal weight: 10.0000 chunk 235 optimal weight: 7.9990 chunk 194 optimal weight: 0.9980 chunk 216 optimal weight: 0.9990 chunk 74 optimal weight: 10.0000 chunk 175 optimal weight: 0.3980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN A 249 HIS G 651 ASN K 249 HIS L 651 ASN ** L 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 292 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20157 Z= 0.191 Angle : 0.646 10.526 27406 Z= 0.338 Chirality : 0.045 0.197 3242 Planarity : 0.005 0.052 3411 Dihedral : 10.245 76.642 3766 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.95 % Favored : 93.80 % Rotamer: Outliers : 0.05 % Allowed : 2.97 % Favored : 96.98 % 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: -1.56 (0.16), residues: 2420 helix: -0.33 (0.28), residues: 342 sheet: -0.58 (0.20), residues: 696 loop : -1.48 (0.16), residues: 1382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP M 47 HIS 0.008 0.001 HIS A 249 PHE 0.015 0.001 PHE C 64 TYR 0.010 0.001 TYR M 95 ARG 0.009 0.001 ARG K 166 *********************** 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 312 residues out of total 2118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 311 time to evaluate : 2.462 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 359 ILE cc_start: 0.8130 (mt) cc_final: 0.7604 (mm) REVERT: A 411 THR cc_start: 0.7720 (p) cc_final: 0.7356 (m) REVERT: C 48 MET cc_start: 0.7553 (tpp) cc_final: 0.6969 (mmt) REVERT: F 411 THR cc_start: 0.7548 (p) cc_final: 0.7121 (m) REVERT: F 424 ILE cc_start: 0.9452 (mm) cc_final: 0.9234 (mm) REVERT: H 102 ILE cc_start: 0.9216 (tp) cc_final: 0.8974 (pt) REVERT: I 234 LEU cc_start: 0.6369 (mm) cc_final: 0.6136 (mm) REVERT: K 154 MET cc_start: 0.8909 (mmm) cc_final: 0.8595 (mmt) REVERT: K 411 THR cc_start: 0.7720 (p) cc_final: 0.7187 (m) REVERT: L 609 PRO cc_start: 0.7950 (Cg_exo) cc_final: 0.7578 (Cg_endo) REVERT: N 263 ASN cc_start: 0.7667 (t0) cc_final: 0.7227 (t0) outliers start: 1 outliers final: 0 residues processed: 311 average time/residue: 0.3437 time to fit residues: 161.4627 Evaluate side-chains 217 residues out of total 2118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 217 time to evaluate : 2.178 ------------------------------------------------------------------------------- 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: 0.0980 chunk 164 optimal weight: 6.9990 chunk 113 optimal weight: 0.9980 chunk 24 optimal weight: 5.9990 chunk 104 optimal weight: 6.9990 chunk 146 optimal weight: 5.9990 chunk 219 optimal weight: 6.9990 chunk 231 optimal weight: 20.0000 chunk 114 optimal weight: 0.7980 chunk 207 optimal weight: 9.9990 chunk 62 optimal weight: 1.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 651 ASN G 651 ASN K 160 ASN K 249 HIS 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: 0.7656 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 20157 Z= 0.281 Angle : 0.674 10.037 27406 Z= 0.349 Chirality : 0.047 0.177 3242 Planarity : 0.005 0.060 3411 Dihedral : 9.904 75.637 3766 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.02 % Favored : 92.73 % Rotamer: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % 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: -0.34 (0.28), residues: 360 sheet: -0.57 (0.20), residues: 689 loop : -1.57 (0.16), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP N 267 HIS 0.012 0.002 HIS K 249 PHE 0.013 0.002 PHE C 64 TYR 0.013 0.002 TYR M 33 ARG 0.009 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 280 residues out of total 2118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 280 time to evaluate : 2.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 359 ILE cc_start: 0.8190 (mt) cc_final: 0.7581 (mm) REVERT: A 411 THR cc_start: 0.7581 (p) cc_final: 0.7254 (m) REVERT: C 48 MET cc_start: 0.7735 (tpp) cc_final: 0.7138 (mmt) REVERT: F 359 ILE cc_start: 0.8382 (mt) cc_final: 0.7922 (mm) REVERT: G 626 MET cc_start: 0.7506 (tpp) cc_final: 0.7030 (tpt) REVERT: I 263 ASN cc_start: 0.7786 (t0) cc_final: 0.7143 (t0) REVERT: K 154 MET cc_start: 0.8906 (mmm) cc_final: 0.8431 (mmt) REVERT: K 411 THR cc_start: 0.7692 (p) cc_final: 0.7225 (m) REVERT: L 609 PRO cc_start: 0.8214 (Cg_exo) cc_final: 0.7900 (Cg_endo) REVERT: N 263 ASN cc_start: 0.7794 (t0) cc_final: 0.7283 (t0) outliers start: 0 outliers final: 0 residues processed: 280 average time/residue: 0.3420 time to fit residues: 145.5220 Evaluate side-chains 215 residues out of total 2118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 215 time to evaluate : 2.561 ------------------------------------------------------------------------------- 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: 0.7980 chunk 3 optimal weight: 0.0010 chunk 172 optimal weight: 9.9990 chunk 95 optimal weight: 0.9980 chunk 197 optimal weight: 1.9990 chunk 160 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 118 optimal weight: 0.9990 chunk 208 optimal weight: 0.5980 chunk 58 optimal weight: 9.9990 overall best weight: 0.6788 ------------------------------------------------------------------------------- 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 246 GLN F 302 ASN G 651 ASN L 651 ASN ** L 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 292 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.2936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20157 Z= 0.166 Angle : 0.607 10.168 27406 Z= 0.315 Chirality : 0.044 0.201 3242 Planarity : 0.004 0.047 3411 Dihedral : 9.270 70.878 3766 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.12 % Favored : 93.64 % Rotamer: Outliers : 0.05 % Allowed : 1.98 % Favored : 97.97 % 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: -1.42 (0.17), residues: 2420 helix: -0.17 (0.28), residues: 360 sheet: -0.46 (0.19), residues: 690 loop : -1.43 (0.16), residues: 1370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 267 HIS 0.004 0.001 HIS F 374 PHE 0.010 0.001 PHE I 294 TYR 0.023 0.001 TYR B 586 ARG 0.007 0.001 ARG B 617 *********************** 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 288 residues out of total 2118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 287 time to evaluate : 2.402 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: 0.7517 (p) cc_final: 0.7187 (m) REVERT: A 475 MET cc_start: 0.7322 (tpp) cc_final: 0.7055 (mmt) REVERT: F 154 MET cc_start: 0.8702 (mmt) cc_final: 0.8106 (mmt) REVERT: G 609 PRO cc_start: 0.8647 (Cg_exo) cc_final: 0.8375 (Cg_endo) REVERT: K 154 MET cc_start: 0.8833 (mmm) cc_final: 0.8459 (mmt) REVERT: K 411 THR cc_start: 0.7593 (p) cc_final: 0.7176 (m) REVERT: L 609 PRO cc_start: 0.8224 (Cg_exo) cc_final: 0.7906 (Cg_endo) REVERT: N 263 ASN cc_start: 0.7860 (t0) cc_final: 0.7041 (t0) outliers start: 1 outliers final: 0 residues processed: 287 average time/residue: 0.3273 time to fit residues: 144.0716 Evaluate side-chains 212 residues out of total 2118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 212 time to evaluate : 2.361 ------------------------------------------------------------------------------- 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: 9.9990 chunk 208 optimal weight: 0.8980 chunk 45 optimal weight: 0.7980 chunk 136 optimal weight: 10.0000 chunk 57 optimal weight: 4.9990 chunk 232 optimal weight: 5.9990 chunk 192 optimal weight: 6.9990 chunk 107 optimal weight: 0.0870 chunk 19 optimal weight: 6.9990 chunk 76 optimal weight: 7.9990 chunk 121 optimal weight: 10.0000 overall best weight: 2.5562 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 651 ASN D 246 GLN F 105 HIS G 651 ASN H 6 GLN ** K 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 328 GLN L 651 ASN M 6 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.3122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 20157 Z= 0.333 Angle : 0.688 9.960 27406 Z= 0.358 Chirality : 0.047 0.198 3242 Planarity : 0.005 0.077 3411 Dihedral : 9.424 72.738 3766 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.40 % Favored : 92.36 % Rotamer: Outliers : 0.05 % Allowed : 2.27 % Favored : 97.69 % 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: -1.60 (0.17), residues: 2420 helix: -0.23 (0.28), residues: 361 sheet: -0.67 (0.19), residues: 693 loop : -1.51 (0.16), residues: 1366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP M 47 HIS 0.007 0.002 HIS F 216 PHE 0.014 0.002 PHE K 376 TYR 0.016 0.002 TYR M 33 ARG 0.013 0.001 ARG F 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 252 residues out of total 2118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 251 time to evaluate : 2.056 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 MET cc_start: 0.9161 (mmm) cc_final: 0.8759 (mmt) REVERT: C 48 MET cc_start: 0.7888 (mmt) cc_final: 0.7496 (mmt) REVERT: G 609 PRO cc_start: 0.8661 (Cg_exo) cc_final: 0.8433 (Cg_endo) REVERT: H 47 TRP cc_start: 0.8560 (t60) cc_final: 0.8285 (t60) REVERT: I 263 ASN cc_start: 0.7905 (t0) cc_final: 0.7442 (t0) REVERT: K 154 MET cc_start: 0.8836 (mmm) cc_final: 0.8360 (mmt) REVERT: L 609 PRO cc_start: 0.8265 (Cg_exo) cc_final: 0.7990 (Cg_endo) REVERT: N 263 ASN cc_start: 0.8012 (t0) cc_final: 0.7605 (t0) outliers start: 1 outliers final: 0 residues processed: 251 average time/residue: 0.3134 time to fit residues: 121.8217 Evaluate side-chains 198 residues out of total 2118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 198 time to evaluate : 2.248 ------------------------------------------------------------------------------- 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: 0.0040 chunk 26 optimal weight: 0.9990 chunk 132 optimal weight: 1.9990 chunk 169 optimal weight: 0.0060 chunk 131 optimal weight: 1.9990 chunk 195 optimal weight: 9.9990 chunk 129 optimal weight: 0.8980 chunk 231 optimal weight: 3.9990 chunk 144 optimal weight: 9.9990 chunk 141 optimal weight: 4.9990 chunk 106 optimal weight: 0.9980 overall best weight: 0.5810 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN A 249 HIS B 651 ASN D 246 GLN G 651 ASN I 270 GLN L 651 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.3349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 20157 Z= 0.157 Angle : 0.596 10.217 27406 Z= 0.309 Chirality : 0.044 0.193 3242 Planarity : 0.004 0.065 3411 Dihedral : 8.847 66.827 3766 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.20 % Favored : 93.55 % Rotamer: Outliers : 0.09 % Allowed : 1.56 % Favored : 98.35 % 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: -1.45 (0.17), residues: 2420 helix: -0.38 (0.27), residues: 379 sheet: -0.65 (0.19), residues: 697 loop : -1.29 (0.17), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP M 47 HIS 0.005 0.001 HIS A 249 PHE 0.009 0.001 PHE I 294 TYR 0.012 0.001 TYR A 39 ARG 0.022 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 276 residues out of total 2118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 274 time to evaluate : 2.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 MET cc_start: 0.9056 (mmm) cc_final: 0.8828 (mmt) REVERT: F 104 MET cc_start: 0.9029 (ttt) cc_final: 0.8714 (tpp) REVERT: F 107 ASP cc_start: 0.8025 (m-30) cc_final: 0.7598 (t0) REVERT: G 609 PRO cc_start: 0.8667 (Cg_exo) cc_final: 0.8426 (Cg_endo) REVERT: I 263 ASN cc_start: 0.7912 (t0) cc_final: 0.7612 (t0) REVERT: K 154 MET cc_start: 0.8754 (mmm) cc_final: 0.8342 (mmt) REVERT: L 609 PRO cc_start: 0.8293 (Cg_exo) cc_final: 0.8042 (Cg_endo) REVERT: M 47 TRP cc_start: 0.6621 (t60) cc_final: 0.6356 (t60) REVERT: N 263 ASN cc_start: 0.7990 (t0) cc_final: 0.7425 (t0) outliers start: 2 outliers final: 0 residues processed: 275 average time/residue: 0.3246 time to fit residues: 138.3138 Evaluate side-chains 203 residues out of total 2118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 203 time to evaluate : 2.070 ------------------------------------------------------------------------------- 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: 6.9990 chunk 92 optimal weight: 3.9990 chunk 138 optimal weight: 6.9990 chunk 69 optimal weight: 0.0570 chunk 45 optimal weight: 0.8980 chunk 44 optimal weight: 4.9990 chunk 147 optimal weight: 3.9990 chunk 157 optimal weight: 9.9990 chunk 114 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 181 optimal weight: 4.9990 overall best weight: 1.7302 ------------------------------------------------------------------------------- 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: 0.7632 moved from start: 0.3476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 20157 Z= 0.248 Angle : 0.637 10.096 27406 Z= 0.328 Chirality : 0.046 0.304 3242 Planarity : 0.005 0.080 3411 Dihedral : 8.678 66.728 3766 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.78 % Favored : 92.98 % Rotamer: Outliers : 0.05 % Allowed : 1.04 % Favored : 98.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.17), residues: 2420 helix: -0.44 (0.27), residues: 379 sheet: -0.68 (0.19), residues: 698 loop : -1.39 (0.17), residues: 1343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP K 69 HIS 0.004 0.001 HIS A 216 PHE 0.012 0.002 PHE K 376 TYR 0.017 0.001 TYR M 95 ARG 0.011 0.001 ARG F 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 246 residues out of total 2118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 245 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 154 MET cc_start: 0.9053 (mmm) cc_final: 0.8814 (mmt) REVERT: A 475 MET cc_start: 0.7818 (tpp) cc_final: 0.7486 (tpp) REVERT: B 535 MET cc_start: 0.6542 (mmp) cc_final: 0.5972 (mtp) REVERT: F 104 MET cc_start: 0.9106 (ttt) cc_final: 0.8703 (tpp) REVERT: G 609 PRO cc_start: 0.8685 (Cg_exo) cc_final: 0.8479 (Cg_endo) REVERT: G 626 MET cc_start: 0.7460 (tpp) cc_final: 0.7151 (tpt) REVERT: H 47 TRP cc_start: 0.8411 (t60) cc_final: 0.7965 (t60) REVERT: K 104 MET cc_start: 0.9165 (ttm) cc_final: 0.8843 (tpp) REVERT: K 154 MET cc_start: 0.8734 (mmm) cc_final: 0.8328 (mmt) REVERT: L 609 PRO cc_start: 0.8370 (Cg_exo) cc_final: 0.8143 (Cg_endo) REVERT: M 115 ASP cc_start: 0.8613 (p0) cc_final: 0.8353 (p0) REVERT: N 263 ASN cc_start: 0.8001 (t0) cc_final: 0.7222 (t0) outliers start: 1 outliers final: 0 residues processed: 245 average time/residue: 0.3162 time to fit residues: 120.4660 Evaluate side-chains 190 residues out of total 2118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 190 time to evaluate : 2.088 ------------------------------------------------------------------------------- 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: 0.9990 chunk 202 optimal weight: 7.9990 chunk 215 optimal weight: 9.9990 chunk 129 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 chunk 169 optimal weight: 1.9990 chunk 66 optimal weight: 8.9990 chunk 194 optimal weight: 0.7980 chunk 203 optimal weight: 0.9980 chunk 214 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 H 113 ASN K 249 HIS L 651 ASN M 113 ASN N 246 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.3618 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= 0.193 Angle : 0.606 10.049 27406 Z= 0.313 Chirality : 0.045 0.315 3242 Planarity : 0.004 0.071 3411 Dihedral : 8.350 63.758 3766 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.57 % Favored : 93.18 % Rotamer: Outliers : 0.05 % Allowed : 0.71 % Favored : 99.24 % 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: -1.47 (0.17), residues: 2420 helix: -0.37 (0.28), residues: 376 sheet: -0.66 (0.19), residues: 698 loop : -1.31 (0.17), residues: 1346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP M 47 HIS 0.005 0.001 HIS F 249 PHE 0.034 0.001 PHE N 294 TYR 0.014 0.001 TYR M 95 ARG 0.014 0.001 ARG A 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 254 residues out of total 2118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 253 time to evaluate : 2.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 MET cc_start: 0.9056 (mmm) cc_final: 0.8790 (mmt) REVERT: A 475 MET cc_start: 0.7697 (tpp) cc_final: 0.7382 (tpp) REVERT: B 535 MET cc_start: 0.6519 (mmp) cc_final: 0.5926 (mtp) REVERT: G 626 MET cc_start: 0.7383 (tpp) cc_final: 0.7076 (tpt) REVERT: H 47 TRP cc_start: 0.8266 (t60) cc_final: 0.7987 (t60) REVERT: K 154 MET cc_start: 0.8707 (mmm) cc_final: 0.8312 (mmt) REVERT: L 609 PRO cc_start: 0.8419 (Cg_exo) cc_final: 0.8200 (Cg_endo) REVERT: M 115 ASP cc_start: 0.8605 (p0) cc_final: 0.8338 (p0) outliers start: 1 outliers final: 0 residues processed: 253 average time/residue: 0.3211 time to fit residues: 125.4841 Evaluate side-chains 197 residues out of total 2118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 197 time to evaluate : 2.144 ------------------------------------------------------------------------------- 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: 0.7980 chunk 227 optimal weight: 1.9990 chunk 139 optimal weight: 9.9990 chunk 108 optimal weight: 2.9990 chunk 158 optimal weight: 2.9990 chunk 239 optimal weight: 9.9990 chunk 220 optimal weight: 1.9990 chunk 190 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 147 optimal weight: 0.7980 chunk 116 optimal weight: 0.8980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN B 651 ASN G 651 ASN K 105 HIS L 651 ASN M 113 ASN N 270 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.3731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 20157 Z= 0.209 Angle : 0.627 10.185 27406 Z= 0.321 Chirality : 0.046 0.455 3242 Planarity : 0.005 0.073 3411 Dihedral : 8.190 61.842 3766 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.78 % Favored : 93.02 % Rotamer: Outliers : 0.05 % Allowed : 0.61 % Favored : 99.34 % 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: -1.50 (0.17), residues: 2420 helix: -0.36 (0.28), residues: 375 sheet: -0.62 (0.20), residues: 678 loop : -1.37 (0.16), residues: 1367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP I 267 HIS 0.005 0.001 HIS F 249 PHE 0.038 0.001 PHE N 294 TYR 0.016 0.001 TYR A 361 ARG 0.016 0.001 ARG D 293 ********************** 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 245 residues out of total 2118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 244 time to evaluate : 2.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 MET cc_start: 0.9043 (mmm) cc_final: 0.8790 (mmt) REVERT: A 356 ASN cc_start: 0.6384 (p0) cc_final: 0.5938 (t0) REVERT: A 475 MET cc_start: 0.7709 (tpp) cc_final: 0.7389 (tpp) REVERT: B 535 MET cc_start: 0.6556 (mmp) cc_final: 0.6015 (mtp) REVERT: G 626 MET cc_start: 0.7280 (tpp) cc_final: 0.6986 (tpt) REVERT: H 47 TRP cc_start: 0.8255 (t60) cc_final: 0.7942 (t60) REVERT: K 154 MET cc_start: 0.8700 (mmm) cc_final: 0.8318 (mmt) REVERT: K 475 MET cc_start: 0.7767 (tpp) cc_final: 0.7290 (tpp) REVERT: M 115 ASP cc_start: 0.8659 (p0) cc_final: 0.8375 (p0) outliers start: 1 outliers final: 1 residues processed: 244 average time/residue: 0.3202 time to fit residues: 121.8332 Evaluate side-chains 194 residues out of total 2118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 193 time to evaluate : 2.207 ------------------------------------------------------------------------------- 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: 6.9990 chunk 202 optimal weight: 6.9990 chunk 58 optimal weight: 1.9990 chunk 175 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 52 optimal weight: 6.9990 chunk 190 optimal weight: 0.8980 chunk 79 optimal weight: 7.9990 chunk 195 optimal weight: 10.0000 chunk 24 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- 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 270 GLN F 302 ASN G 651 ASN ** K 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 651 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.125803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 111)---------------| | r_work = 0.3404 r_free = 0.3404 target = 0.107896 restraints weight = 40876.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.103597 restraints weight = 50755.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.103632 restraints weight = 62147.836| |-----------------------------------------------------------------------------| r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.3825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 20157 Z= 0.351 Angle : 0.720 10.027 27406 Z= 0.372 Chirality : 0.049 0.339 3242 Planarity : 0.005 0.087 3411 Dihedral : 8.662 64.873 3766 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.64 % Favored : 92.11 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.72 (0.17), residues: 2420 helix: -0.57 (0.27), residues: 382 sheet: -0.64 (0.20), residues: 667 loop : -1.58 (0.16), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.003 TRP M 47 HIS 0.006 0.002 HIS H 35 PHE 0.033 0.002 PHE N 294 TYR 0.026 0.002 TYR F 217 ARG 0.017 0.001 ARG A 166 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3758.25 seconds wall clock time: 75 minutes 23.94 seconds (4523.94 seconds total)