Starting phenix.real_space_refine on Sat Sep 28 16:21:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x9s_22109/09_2024/6x9s_22109.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x9s_22109/09_2024/6x9s_22109.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x9s_22109/09_2024/6x9s_22109.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x9s_22109/09_2024/6x9s_22109.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x9s_22109/09_2024/6x9s_22109.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x9s_22109/09_2024/6x9s_22109.cif" } resolution = 3.1 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= 0.000 sd= 0.007 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 126 5.16 5 C 12258 2.51 5 N 3273 2.21 5 O 3933 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 19590 Number of models: 1 Model: "" Number of chains: 33 Chain: "A" Number of atoms: 3405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3405 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 22, 'TRANS': 409} Chain breaks: 4 Chain: "B" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 971 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Chain: "H" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 943 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "L" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 811 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "C" 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: "D" 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: "E" 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: "F" 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: "G" 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: "A" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} 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: "I" Number of atoms: 3405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3405 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 22, 'TRANS': 409} Chain breaks: 4 Chain: "J" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 971 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Chain: "K" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 943 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "M" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 811 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "N" 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: "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: 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: "Q" 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: "R" 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: "I" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "J" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} 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: "S" Number of atoms: 3405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3405 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 22, 'TRANS': 409} Chain breaks: 4 Chain: "T" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 971 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Chain: "U" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 943 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "V" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 811 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} 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 Chain: "Y" 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: "Z" 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: "0" 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: "S" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "T" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} 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 Time building chain proxies: 11.59, per 1000 atoms: 0.59 Number of scatterers: 19590 At special positions: 0 Unit cell: (122.57, 127.72, 150.38, 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 126 16.00 O 3933 8.00 N 3273 7.00 C 12258 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.06 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=2.02 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=2.14 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=2.02 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.02 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.11 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS I 119 " - pdb=" SG CYS I 205 " distance=2.06 Simple disulfide: pdb=" SG CYS I 126 " - pdb=" SG CYS I 196 " distance=2.03 Simple disulfide: pdb=" SG CYS I 131 " - pdb=" SG CYS I 157 " distance=2.02 Simple disulfide: pdb=" SG CYS I 218 " - pdb=" SG CYS I 247 " distance=2.03 Simple disulfide: pdb=" SG CYS I 228 " - pdb=" SG CYS I 239 " distance=2.14 Simple disulfide: pdb=" SG CYS I 296 " - pdb=" SG CYS I 331 " distance=2.03 Simple disulfide: pdb=" SG CYS I 378 " - pdb=" SG CYS I 445 " distance=2.02 Simple disulfide: pdb=" SG CYS I 385 " - pdb=" SG CYS I 418 " distance=2.02 Simple disulfide: pdb=" SG CYS I 501 " - pdb=" SG CYS J 605 " distance=2.11 Simple disulfide: pdb=" SG CYS J 598 " - pdb=" SG CYS J 604 " distance=2.02 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.04 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.03 Simple disulfide: pdb=" SG CYS S 119 " - pdb=" SG CYS S 205 " distance=2.06 Simple disulfide: pdb=" SG CYS S 126 " - pdb=" SG CYS S 196 " distance=2.03 Simple disulfide: pdb=" SG CYS S 131 " - pdb=" SG CYS S 157 " distance=2.02 Simple disulfide: pdb=" SG CYS S 218 " - pdb=" SG CYS S 247 " distance=2.03 Simple disulfide: pdb=" SG CYS S 228 " - pdb=" SG CYS S 239 " distance=2.14 Simple disulfide: pdb=" SG CYS S 296 " - pdb=" SG CYS S 331 " distance=2.03 Simple disulfide: pdb=" SG CYS S 378 " - pdb=" SG CYS S 445 " distance=2.02 Simple disulfide: pdb=" SG CYS S 385 " - pdb=" SG CYS S 418 " distance=2.02 Simple disulfide: pdb=" SG CYS S 501 " - pdb=" SG CYS T 605 " distance=2.11 Simple disulfide: pdb=" SG CYS T 598 " - pdb=" SG CYS T 604 " distance=2.02 Simple disulfide: pdb=" SG CYS U 22 " - pdb=" SG CYS U 92 " distance=2.04 Simple disulfide: pdb=" SG CYS V 23 " - pdb=" SG CYS V 88 " 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 ALPHA1-3 " BMA E 3 " - " MAN E 4 " " BMA P 3 " - " MAN P 4 " " BMA Y 3 " - " MAN Y 4 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " NAG-ASN " NAG 0 1 " - " ASN S 448 " " NAG A 601 " - " ASN A 88 " " NAG A 602 " - " ASN A 133 " " NAG A 603 " - " ASN A 137 " " NAG A 606 " - " ASN A 160 " " NAG A 609 " - " ASN A 234 " " NAG A 614 " - " ASN A 276 " " NAG A 615 " - " ASN A 295 " " NAG A 616 " - " ASN A 301 " " NAG A 617 " - " ASN A 332 " " NAG A 618 " - " ASN A 339 " " NAG A 619 " - " ASN A 355 " " NAG A 620 " - " ASN A 363 " " NAG A 623 " - " ASN A 392 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 618 " " NAG B 703 " - " ASN B 625 " " NAG B 704 " - " ASN B 637 " " NAG C 1 " - " ASN A 156 " " NAG D 1 " - " ASN A 197 " " NAG E 1 " - " ASN A 262 " " NAG F 1 " - " ASN A 386 " " NAG G 1 " - " ASN A 448 " " NAG I 601 " - " ASN I 88 " " NAG I 602 " - " ASN I 133 " " NAG I 603 " - " ASN I 137 " " NAG I 606 " - " ASN I 160 " " NAG I 609 " - " ASN I 234 " " NAG I 614 " - " ASN I 276 " " NAG I 615 " - " ASN I 295 " " NAG I 616 " - " ASN I 301 " " NAG I 617 " - " ASN I 332 " " NAG I 618 " - " ASN I 339 " " NAG I 619 " - " ASN I 355 " " NAG I 620 " - " ASN I 363 " " NAG I 623 " - " ASN I 392 " " NAG J 701 " - " ASN J 611 " " NAG J 702 " - " ASN J 618 " " NAG J 703 " - " ASN J 625 " " NAG J 704 " - " ASN J 637 " " NAG N 1 " - " ASN I 156 " " NAG O 1 " - " ASN I 197 " " NAG P 1 " - " ASN I 262 " " NAG Q 1 " - " ASN I 386 " " NAG R 1 " - " ASN I 448 " " NAG S 601 " - " ASN S 88 " " NAG S 602 " - " ASN S 133 " " NAG S 603 " - " ASN S 137 " " NAG S 606 " - " ASN S 160 " " NAG S 609 " - " ASN S 234 " " NAG S 614 " - " ASN S 276 " " NAG S 615 " - " ASN S 295 " " NAG S 616 " - " ASN S 301 " " NAG S 617 " - " ASN S 332 " " NAG S 618 " - " ASN S 339 " " NAG S 619 " - " ASN S 355 " " NAG S 620 " - " ASN S 363 " " NAG S 623 " - " ASN S 392 " " NAG T 701 " - " ASN T 611 " " NAG T 702 " - " ASN T 618 " " NAG T 703 " - " ASN T 625 " " NAG T 704 " - " ASN T 637 " " NAG W 1 " - " ASN S 156 " " NAG X 1 " - " ASN S 197 " " NAG Y 1 " - " ASN S 262 " " NAG Z 1 " - " ASN S 386 " Time building additional restraints: 5.25 Conformation dependent library (CDL) restraints added in 2.1 seconds 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4332 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 45 sheets defined 21.4% alpha, 37.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.22 Creating SS restraints... Processing helix chain 'A' and resid 98 through 115 removed outlier: 4.195A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 139 through 151 Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 334 through 354 removed outlier: 4.015A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 476 through 484 removed outlier: 3.763A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 528 removed outlier: 4.437A pdb=" N GLY B 527 " --> pdb=" O GLY B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 542 removed outlier: 3.542A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 596 Processing helix chain 'B' and resid 618 through 625 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 660 removed outlier: 3.602A pdb=" N GLN B 658 " --> pdb=" O GLU B 654 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'I' and resid 98 through 115 removed outlier: 4.195A pdb=" N GLU I 102 " --> pdb=" O ASN I 98 " (cutoff:3.500A) Processing helix chain 'I' and resid 122 through 126 Processing helix chain 'I' and resid 139 through 151 Processing helix chain 'I' and resid 195 through 198 Processing helix chain 'I' and resid 334 through 354 removed outlier: 4.015A pdb=" N LYS I 351 " --> pdb=" O LYS I 347 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N HIS I 352 " --> pdb=" O GLN I 348 " (cutoff:3.500A) Processing helix chain 'I' and resid 368 through 373 Processing helix chain 'I' and resid 476 through 484 removed outlier: 3.763A pdb=" N SER I 481 " --> pdb=" O ASP I 477 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N GLU I 482 " --> pdb=" O ASN I 478 " (cutoff:3.500A) Processing helix chain 'J' and resid 523 through 528 removed outlier: 4.438A pdb=" N GLY J 527 " --> pdb=" O GLY J 524 " (cutoff:3.500A) Processing helix chain 'J' and resid 536 through 542 removed outlier: 3.542A pdb=" N GLN J 540 " --> pdb=" O THR J 536 " (cutoff:3.500A) Processing helix chain 'J' and resid 569 through 596 Processing helix chain 'J' and resid 618 through 625 Processing helix chain 'J' and resid 627 through 635 Processing helix chain 'J' and resid 638 through 660 removed outlier: 3.602A pdb=" N GLN J 658 " --> pdb=" O GLU J 654 " (cutoff:3.500A) Processing helix chain 'K' and resid 28 through 32 Processing helix chain 'K' and resid 61 through 64 Processing helix chain 'K' and resid 83 through 87 Processing helix chain 'M' and resid 79 through 83 Processing helix chain 'S' and resid 98 through 115 removed outlier: 4.195A pdb=" N GLU S 102 " --> pdb=" O ASN S 98 " (cutoff:3.500A) Processing helix chain 'S' and resid 122 through 126 Processing helix chain 'S' and resid 139 through 151 Processing helix chain 'S' and resid 195 through 198 Processing helix chain 'S' and resid 334 through 354 removed outlier: 4.015A pdb=" N LYS S 351 " --> pdb=" O LYS S 347 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N HIS S 352 " --> pdb=" O GLN S 348 " (cutoff:3.500A) Processing helix chain 'S' and resid 368 through 373 Processing helix chain 'S' and resid 476 through 484 removed outlier: 3.764A pdb=" N SER S 481 " --> pdb=" O ASP S 477 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N GLU S 482 " --> pdb=" O ASN S 478 " (cutoff:3.500A) Processing helix chain 'T' and resid 523 through 528 removed outlier: 4.437A pdb=" N GLY T 527 " --> pdb=" O GLY T 524 " (cutoff:3.500A) Processing helix chain 'T' and resid 536 through 542 removed outlier: 3.542A pdb=" N GLN T 540 " --> pdb=" O THR T 536 " (cutoff:3.500A) Processing helix chain 'T' and resid 569 through 596 Processing helix chain 'T' and resid 618 through 625 Processing helix chain 'T' and resid 627 through 635 Processing helix chain 'T' and resid 638 through 660 removed outlier: 3.603A pdb=" N GLN T 658 " --> pdb=" O GLU T 654 " (cutoff:3.500A) Processing helix chain 'U' and resid 28 through 32 Processing helix chain 'U' and resid 61 through 64 Processing helix chain 'U' and resid 83 through 87 Processing helix chain 'V' and resid 79 through 83 Processing sheet with id=1, first strand: chain 'A' and resid 494 through 498 Processing sheet with id=2, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.776A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'A' and resid 75 through 76 Processing sheet with id=4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=5, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=6, first strand: chain 'A' and resid 201 through 203 removed outlier: 6.540A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=7, first strand: chain 'A' and resid 259 through 261 removed outlier: 3.657A pdb=" N GLY A 451 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N GLY A 441 " --> pdb=" O ASN A 300 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N ASN A 300 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.539A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 11.870A pdb=" N ILE A 453 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 11.845A pdb=" N PHE A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 10.820A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 10.833A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 10.952A pdb=" N ASP A 457 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 12.179A pdb=" N ILE A 284 " --> pdb=" O ASP A 457 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=8, first strand: chain 'A' and resid 271 through 274 removed outlier: 12.179A pdb=" N ILE A 284 " --> pdb=" O ASP A 457 " (cutoff:3.500A) removed outlier: 10.952A pdb=" N ASP A 457 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 10.833A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 10.820A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 11.845A pdb=" N PHE A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 11.870A pdb=" N ILE A 453 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 10.539A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N ASN A 300 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N GLY A 441 " --> pdb=" O ASN A 300 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ILE A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N PHE A 468 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=9, first strand: chain 'A' and resid 304 through 312 removed outlier: 6.555A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=10, first strand: chain 'H' and resid 3 through 8 Processing sheet with id=11, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.031A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=12, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=13, first strand: chain 'L' and resid 11 through 13 removed outlier: 6.644A pdb=" N VAL L 11 " --> pdb=" O THR L 105 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N TRP L 35 " --> pdb=" O MET L 47 " (cutoff:3.500A) Processing sheet with id=14, first strand: chain 'L' and resid 11 through 13 removed outlier: 6.644A pdb=" N VAL L 11 " --> pdb=" O THR L 105 " (cutoff:3.500A) Processing sheet with id=15, first strand: chain 'L' and resid 19 through 24 Processing sheet with id=16, first strand: chain 'I' and resid 494 through 498 Processing sheet with id=17, first strand: chain 'I' and resid 45 through 47 removed outlier: 3.776A pdb=" N ILE I 225 " --> pdb=" O VAL I 245 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N VAL I 242 " --> pdb=" O LEU I 86 " (cutoff:3.500A) Processing sheet with id=18, first strand: chain 'I' and resid 75 through 76 Processing sheet with id=19, first strand: chain 'I' and resid 91 through 94 Processing sheet with id=20, first strand: chain 'I' and resid 169 through 177 Processing sheet with id=21, first strand: chain 'I' and resid 201 through 203 removed outlier: 6.540A pdb=" N THR I 202 " --> pdb=" O TYR I 435 " (cutoff:3.500A) Processing sheet with id=22, first strand: chain 'I' and resid 259 through 261 removed outlier: 3.657A pdb=" N GLY I 451 " --> pdb=" O LEU I 260 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N GLY I 441 " --> pdb=" O ASN I 300 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N ASN I 300 " --> pdb=" O GLY I 441 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLY I 451 " --> pdb=" O THR I 290 " (cutoff:3.500A) removed outlier: 10.538A pdb=" N THR I 290 " --> pdb=" O GLY I 451 " (cutoff:3.500A) removed outlier: 11.871A pdb=" N ILE I 453 " --> pdb=" O PHE I 288 " (cutoff:3.500A) removed outlier: 11.845A pdb=" N PHE I 288 " --> pdb=" O ILE I 453 " (cutoff:3.500A) removed outlier: 10.820A pdb=" N THR I 455 " --> pdb=" O VAL I 286 " (cutoff:3.500A) removed outlier: 10.833A pdb=" N VAL I 286 " --> pdb=" O THR I 455 " (cutoff:3.500A) removed outlier: 10.952A pdb=" N ASP I 457 " --> pdb=" O ILE I 284 " (cutoff:3.500A) removed outlier: 12.179A pdb=" N ILE I 284 " --> pdb=" O ASP I 457 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ALA I 329 " --> pdb=" O CYS I 418 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N PHE I 382 " --> pdb=" O LYS I 421 " (cutoff:3.500A) Processing sheet with id=23, first strand: chain 'I' and resid 271 through 274 removed outlier: 12.179A pdb=" N ILE I 284 " --> pdb=" O ASP I 457 " (cutoff:3.500A) removed outlier: 10.952A pdb=" N ASP I 457 " --> pdb=" O ILE I 284 " (cutoff:3.500A) removed outlier: 10.833A pdb=" N VAL I 286 " --> pdb=" O THR I 455 " (cutoff:3.500A) removed outlier: 10.820A pdb=" N THR I 455 " --> pdb=" O VAL I 286 " (cutoff:3.500A) removed outlier: 11.845A pdb=" N PHE I 288 " --> pdb=" O ILE I 453 " (cutoff:3.500A) removed outlier: 11.871A pdb=" N ILE I 453 " --> pdb=" O PHE I 288 " (cutoff:3.500A) removed outlier: 10.538A pdb=" N THR I 290 " --> pdb=" O GLY I 451 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLY I 451 " --> pdb=" O THR I 290 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N ASN I 300 " --> pdb=" O GLY I 441 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N GLY I 441 " --> pdb=" O ASN I 300 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ILE I 358 " --> pdb=" O GLU I 466 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N PHE I 468 " --> pdb=" O ILE I 358 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ARG I 360 " --> pdb=" O PHE I 468 " (cutoff:3.500A) Processing sheet with id=24, first strand: chain 'I' and resid 304 through 312 removed outlier: 6.555A pdb=" N GLN I 315 " --> pdb=" O ILE I 309 " (cutoff:3.500A) Processing sheet with id=25, first strand: chain 'K' and resid 3 through 8 Processing sheet with id=26, first strand: chain 'K' and resid 11 through 12 removed outlier: 6.032A pdb=" N ARG K 38 " --> pdb=" O TRP K 47 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N TRP K 47 " --> pdb=" O ARG K 38 " (cutoff:3.500A) Processing sheet with id=27, first strand: chain 'K' and resid 11 through 12 Processing sheet with id=28, first strand: chain 'M' and resid 11 through 13 removed outlier: 6.643A pdb=" N VAL M 11 " --> pdb=" O THR M 105 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N TRP M 35 " --> pdb=" O MET M 47 " (cutoff:3.500A) Processing sheet with id=29, first strand: chain 'M' and resid 11 through 13 removed outlier: 6.643A pdb=" N VAL M 11 " --> pdb=" O THR M 105 " (cutoff:3.500A) Processing sheet with id=30, first strand: chain 'M' and resid 19 through 24 Processing sheet with id=31, first strand: chain 'S' and resid 494 through 498 Processing sheet with id=32, first strand: chain 'S' and resid 45 through 47 removed outlier: 3.776A pdb=" N ILE S 225 " --> pdb=" O VAL S 245 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N VAL S 242 " --> pdb=" O LEU S 86 " (cutoff:3.500A) Processing sheet with id=33, first strand: chain 'S' and resid 75 through 76 Processing sheet with id=34, first strand: chain 'S' and resid 91 through 94 Processing sheet with id=35, first strand: chain 'S' and resid 169 through 177 Processing sheet with id=36, first strand: chain 'S' and resid 201 through 203 removed outlier: 6.540A pdb=" N THR S 202 " --> pdb=" O TYR S 435 " (cutoff:3.500A) Processing sheet with id=37, first strand: chain 'S' and resid 259 through 261 removed outlier: 3.658A pdb=" N GLY S 451 " --> pdb=" O LEU S 260 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N GLY S 441 " --> pdb=" O ASN S 300 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N ASN S 300 " --> pdb=" O GLY S 441 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLY S 451 " --> pdb=" O THR S 290 " (cutoff:3.500A) removed outlier: 10.539A pdb=" N THR S 290 " --> pdb=" O GLY S 451 " (cutoff:3.500A) removed outlier: 11.870A pdb=" N ILE S 453 " --> pdb=" O PHE S 288 " (cutoff:3.500A) removed outlier: 11.844A pdb=" N PHE S 288 " --> pdb=" O ILE S 453 " (cutoff:3.500A) removed outlier: 10.820A pdb=" N THR S 455 " --> pdb=" O VAL S 286 " (cutoff:3.500A) removed outlier: 10.832A pdb=" N VAL S 286 " --> pdb=" O THR S 455 " (cutoff:3.500A) removed outlier: 10.952A pdb=" N ASP S 457 " --> pdb=" O ILE S 284 " (cutoff:3.500A) removed outlier: 12.178A pdb=" N ILE S 284 " --> pdb=" O ASP S 457 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ALA S 329 " --> pdb=" O CYS S 418 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N PHE S 382 " --> pdb=" O LYS S 421 " (cutoff:3.500A) Processing sheet with id=38, first strand: chain 'S' and resid 271 through 274 removed outlier: 12.178A pdb=" N ILE S 284 " --> pdb=" O ASP S 457 " (cutoff:3.500A) removed outlier: 10.952A pdb=" N ASP S 457 " --> pdb=" O ILE S 284 " (cutoff:3.500A) removed outlier: 10.832A pdb=" N VAL S 286 " --> pdb=" O THR S 455 " (cutoff:3.500A) removed outlier: 10.820A pdb=" N THR S 455 " --> pdb=" O VAL S 286 " (cutoff:3.500A) removed outlier: 11.844A pdb=" N PHE S 288 " --> pdb=" O ILE S 453 " (cutoff:3.500A) removed outlier: 11.870A pdb=" N ILE S 453 " --> pdb=" O PHE S 288 " (cutoff:3.500A) removed outlier: 10.539A pdb=" N THR S 290 " --> pdb=" O GLY S 451 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLY S 451 " --> pdb=" O THR S 290 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N ASN S 300 " --> pdb=" O GLY S 441 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N GLY S 441 " --> pdb=" O ASN S 300 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ILE S 358 " --> pdb=" O GLU S 466 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N PHE S 468 " --> pdb=" O ILE S 358 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ARG S 360 " --> pdb=" O PHE S 468 " (cutoff:3.500A) Processing sheet with id=39, first strand: chain 'S' and resid 304 through 312 removed outlier: 6.555A pdb=" N GLN S 315 " --> pdb=" O ILE S 309 " (cutoff:3.500A) Processing sheet with id=40, first strand: chain 'U' and resid 3 through 8 Processing sheet with id=41, first strand: chain 'U' and resid 11 through 12 removed outlier: 6.031A pdb=" N ARG U 38 " --> pdb=" O TRP U 47 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N TRP U 47 " --> pdb=" O ARG U 38 " (cutoff:3.500A) Processing sheet with id=42, first strand: chain 'U' and resid 11 through 12 Processing sheet with id=43, first strand: chain 'V' and resid 11 through 13 removed outlier: 6.644A pdb=" N VAL V 11 " --> pdb=" O THR V 105 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N TRP V 35 " --> pdb=" O MET V 47 " (cutoff:3.500A) Processing sheet with id=44, first strand: chain 'V' and resid 11 through 13 removed outlier: 6.644A pdb=" N VAL V 11 " --> pdb=" O THR V 105 " (cutoff:3.500A) Processing sheet with id=45, first strand: chain 'V' and resid 19 through 24 789 hydrogen bonds defined for protein. 2025 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: 7.84 Time building geometry restraints manager: 6.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3525 1.31 - 1.44: 5410 1.44 - 1.57: 10801 1.57 - 1.69: 64 1.69 - 1.82: 174 Bond restraints: 19974 Sorted by residual: bond pdb=" C1 NAG B 703 " pdb=" O5 NAG B 703 " ideal model delta sigma weight residual 1.406 1.547 -0.141 2.00e-02 2.50e+03 4.94e+01 bond pdb=" C1 NAG T 703 " pdb=" O5 NAG T 703 " ideal model delta sigma weight residual 1.406 1.546 -0.140 2.00e-02 2.50e+03 4.93e+01 bond pdb=" C1 NAG J 703 " pdb=" O5 NAG J 703 " ideal model delta sigma weight residual 1.406 1.546 -0.140 2.00e-02 2.50e+03 4.93e+01 bond pdb=" C1 NAG R 2 " pdb=" O5 NAG R 2 " ideal model delta sigma weight residual 1.406 1.546 -0.140 2.00e-02 2.50e+03 4.89e+01 bond pdb=" C1 NAG G 2 " pdb=" O5 NAG G 2 " ideal model delta sigma weight residual 1.406 1.546 -0.140 2.00e-02 2.50e+03 4.88e+01 ... (remaining 19969 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.34: 23225 2.34 - 4.67: 3343 4.67 - 7.01: 456 7.01 - 9.35: 57 9.35 - 11.68: 12 Bond angle restraints: 27093 Sorted by residual: angle pdb=" N PRO M 7 " pdb=" CA PRO M 7 " pdb=" C PRO M 7 " ideal model delta sigma weight residual 110.70 122.38 -11.68 1.22e+00 6.72e-01 9.17e+01 angle pdb=" N PRO L 7 " pdb=" CA PRO L 7 " pdb=" C PRO L 7 " ideal model delta sigma weight residual 110.70 122.38 -11.68 1.22e+00 6.72e-01 9.16e+01 angle pdb=" N PRO V 7 " pdb=" CA PRO V 7 " pdb=" C PRO V 7 " ideal model delta sigma weight residual 110.70 122.38 -11.68 1.22e+00 6.72e-01 9.16e+01 angle pdb=" C GLU S 492 " pdb=" N PRO S 493 " pdb=" CA PRO S 493 " ideal model delta sigma weight residual 119.56 127.33 -7.77 1.01e+00 9.80e-01 5.92e+01 angle pdb=" C GLU A 492 " pdb=" N PRO A 493 " pdb=" CA PRO A 493 " ideal model delta sigma weight residual 119.56 127.30 -7.74 1.01e+00 9.80e-01 5.87e+01 ... (remaining 27088 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.89: 12609 21.89 - 43.79: 276 43.79 - 65.68: 108 65.68 - 87.57: 33 87.57 - 109.46: 12 Dihedral angle restraints: 13038 sinusoidal: 6291 harmonic: 6747 Sorted by residual: dihedral pdb=" CB CYS A 228 " pdb=" SG CYS A 228 " pdb=" SG CYS A 239 " pdb=" CB CYS A 239 " ideal model delta sinusoidal sigma weight residual 93.00 163.30 -70.30 1 1.00e+01 1.00e-02 6.36e+01 dihedral pdb=" CB CYS S 228 " pdb=" SG CYS S 228 " pdb=" SG CYS S 239 " pdb=" CB CYS S 239 " ideal model delta sinusoidal sigma weight residual 93.00 163.30 -70.30 1 1.00e+01 1.00e-02 6.36e+01 dihedral pdb=" CB CYS I 228 " pdb=" SG CYS I 228 " pdb=" SG CYS I 239 " pdb=" CB CYS I 239 " ideal model delta sinusoidal sigma weight residual 93.00 163.27 -70.27 1 1.00e+01 1.00e-02 6.36e+01 ... (remaining 13035 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 2249 0.093 - 0.185: 796 0.185 - 0.278: 204 0.278 - 0.370: 27 0.370 - 0.463: 3 Chirality restraints: 3279 Sorted by residual: chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.65 0.25 2.00e-02 2.50e+03 1.52e+02 chirality pdb=" C1 NAG Q 2 " pdb=" O4 NAG Q 1 " pdb=" C2 NAG Q 2 " pdb=" O5 NAG Q 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.65 0.25 2.00e-02 2.50e+03 1.52e+02 chirality pdb=" C1 NAG Z 2 " pdb=" O4 NAG Z 1 " pdb=" C2 NAG Z 2 " pdb=" O5 NAG Z 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-02 2.50e+03 1.50e+02 ... (remaining 3276 not shown) Planarity restraints: 3405 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 702 " 0.057 2.00e-02 2.50e+03 4.71e-02 2.77e+01 pdb=" C7 NAG B 702 " -0.011 2.00e-02 2.50e+03 pdb=" C8 NAG B 702 " 0.042 2.00e-02 2.50e+03 pdb=" N2 NAG B 702 " -0.076 2.00e-02 2.50e+03 pdb=" O7 NAG B 702 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG T 702 " 0.057 2.00e-02 2.50e+03 4.70e-02 2.76e+01 pdb=" C7 NAG T 702 " -0.011 2.00e-02 2.50e+03 pdb=" C8 NAG T 702 " 0.042 2.00e-02 2.50e+03 pdb=" N2 NAG T 702 " -0.076 2.00e-02 2.50e+03 pdb=" O7 NAG T 702 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG J 702 " -0.057 2.00e-02 2.50e+03 4.70e-02 2.76e+01 pdb=" C7 NAG J 702 " 0.011 2.00e-02 2.50e+03 pdb=" C8 NAG J 702 " -0.042 2.00e-02 2.50e+03 pdb=" N2 NAG J 702 " 0.076 2.00e-02 2.50e+03 pdb=" O7 NAG J 702 " 0.012 2.00e-02 2.50e+03 ... (remaining 3402 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 6654 2.84 - 3.36: 16547 3.36 - 3.87: 32269 3.87 - 4.39: 37908 4.39 - 4.90: 63051 Nonbonded interactions: 156429 Sorted by model distance: nonbonded pdb=" N ASN I 355 " pdb=" OD1 ASN I 355 " model vdw 2.329 3.120 nonbonded pdb=" N ASN A 355 " pdb=" OD1 ASN A 355 " model vdw 2.329 3.120 nonbonded pdb=" N ASN S 355 " pdb=" OD1 ASN S 355 " model vdw 2.330 3.120 nonbonded pdb=" N LEU K 100A" pdb=" N GLN K 100B" model vdw 2.331 2.560 nonbonded pdb=" N LEU H 100A" pdb=" N GLN H 100B" model vdw 2.332 2.560 ... (remaining 156424 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 '0' selection = chain 'C' selection = chain 'D' selection = chain 'F' selection = chain 'G' selection = chain 'N' selection = chain 'O' selection = chain 'Q' selection = chain 'R' selection = chain 'W' selection = chain 'X' selection = chain 'Z' } ncs_group { reference = chain 'A' selection = chain 'I' selection = chain 'S' } ncs_group { reference = chain 'B' selection = chain 'J' selection = chain 'T' } ncs_group { reference = chain 'E' selection = chain 'P' selection = chain 'Y' } ncs_group { reference = chain 'H' selection = chain 'K' selection = chain 'U' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'V' } 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 individual isotropic 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: 1.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.740 Check model and map are aligned: 0.160 Set scattering table: 0.170 Process input model: 46.540 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.140 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:3.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 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 : 0.025 0.145 19974 Z= 1.588 Angle : 1.695 11.683 27093 Z= 1.111 Chirality : 0.099 0.463 3279 Planarity : 0.009 0.061 3339 Dihedral : 11.649 109.464 8598 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 1.04 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.65 % Favored : 96.09 % Rotamer: Outliers : 0.44 % Allowed : 0.15 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.54 (0.17), residues: 2304 helix: -0.30 (0.25), residues: 387 sheet: 0.81 (0.20), residues: 666 loop : 0.48 (0.18), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.011 TRP S 479 HIS 0.006 0.002 HIS H 82A PHE 0.036 0.006 PHE I 383 TYR 0.054 0.008 TYR L 36 ARG 0.005 0.001 ARG K 53 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 444 time to evaluate : 2.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 MET cc_start: 0.7835 (mtp) cc_final: 0.7634 (mtp) REVERT: H 82 MET cc_start: 0.8617 (mtt) cc_final: 0.8401 (mtt) REVERT: L 94 ARG cc_start: 0.5628 (mmt180) cc_final: 0.4648 (mtm-85) REVERT: I 277 ILE cc_start: 0.8783 (tp) cc_final: 0.8521 (tp) REVERT: M 94 ARG cc_start: 0.5849 (mmt180) cc_final: 0.4832 (mtm-85) REVERT: V 94 ARG cc_start: 0.5814 (mmt180) cc_final: 0.4800 (mtm-85) outliers start: 9 outliers final: 4 residues processed: 447 average time/residue: 0.3752 time to fit residues: 239.5214 Evaluate side-chains 265 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 261 time to evaluate : 2.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain I residue 355 ASN Chi-restraints excluded: chain J residue 618 ASN Chi-restraints excluded: chain T residue 618 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 195 optimal weight: 1.9990 chunk 175 optimal weight: 0.8980 chunk 97 optimal weight: 0.6980 chunk 59 optimal weight: 3.9990 chunk 118 optimal weight: 0.8980 chunk 93 optimal weight: 7.9990 chunk 181 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 110 optimal weight: 0.9980 chunk 134 optimal weight: 2.9990 chunk 209 optimal weight: 5.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 39 HIS I 103 GLN I 246 GLN I 302 ASN ** K 82AHIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 39 HIS ** S 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 114 GLN ** S 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 19974 Z= 0.238 Angle : 0.669 7.905 27093 Z= 0.357 Chirality : 0.047 0.217 3279 Planarity : 0.005 0.046 3339 Dihedral : 8.135 67.759 4343 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.17 % Favored : 96.57 % Rotamer: Outliers : 1.86 % Allowed : 4.69 % Favored : 93.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.55 (0.17), residues: 2304 helix: 1.16 (0.27), residues: 402 sheet: 0.42 (0.19), residues: 687 loop : 0.18 (0.18), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP S 479 HIS 0.006 0.001 HIS K 82A PHE 0.021 0.002 PHE S 383 TYR 0.014 0.001 TYR M 96 ARG 0.006 0.001 ARG A 444 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 308 time to evaluate : 2.338 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 444 ARG cc_start: 0.8233 (ttt90) cc_final: 0.8027 (ttt-90) REVERT: L 49 TYR cc_start: 0.9196 (p90) cc_final: 0.8715 (p90) REVERT: L 54 ARG cc_start: 0.8479 (mtm-85) cc_final: 0.8200 (mtp-110) REVERT: L 94 ARG cc_start: 0.5230 (mmt180) cc_final: 0.4393 (mtm-85) REVERT: I 434 MET cc_start: 0.9042 (OUTLIER) cc_final: 0.8774 (ttp) REVERT: K 46 GLU cc_start: 0.8300 (tt0) cc_final: 0.8093 (tt0) REVERT: M 94 ARG cc_start: 0.5223 (mmt180) cc_final: 0.4391 (mtm-85) REVERT: S 107 ASP cc_start: 0.8416 (m-30) cc_final: 0.8182 (m-30) REVERT: S 434 MET cc_start: 0.9097 (OUTLIER) cc_final: 0.8875 (ttp) REVERT: V 94 ARG cc_start: 0.5551 (mmt180) cc_final: 0.4670 (mtm-85) outliers start: 38 outliers final: 26 residues processed: 331 average time/residue: 0.3415 time to fit residues: 166.5259 Evaluate side-chains 270 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 242 time to evaluate : 2.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain I residue 167 ASP Chi-restraints excluded: chain I residue 434 MET Chi-restraints excluded: chain J residue 613 SER Chi-restraints excluded: chain J residue 618 ASN Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain K residue 68 THR Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain M residue 67 SER Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain S residue 355 ASN Chi-restraints excluded: chain S residue 434 MET Chi-restraints excluded: chain S residue 485 LYS Chi-restraints excluded: chain T residue 613 SER Chi-restraints excluded: chain T residue 618 ASN Chi-restraints excluded: chain U residue 30 SER Chi-restraints excluded: chain U residue 68 THR Chi-restraints excluded: chain V residue 24 THR Chi-restraints excluded: chain V residue 67 SER Chi-restraints excluded: chain V residue 74 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 116 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 174 optimal weight: 0.1980 chunk 142 optimal weight: 0.2980 chunk 57 optimal weight: 7.9990 chunk 210 optimal weight: 10.0000 chunk 227 optimal weight: 20.0000 chunk 187 optimal weight: 4.9990 chunk 208 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 168 optimal weight: 0.9980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 82AHIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 82AHIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 19974 Z= 0.196 Angle : 0.572 8.652 27093 Z= 0.301 Chirality : 0.045 0.240 3279 Planarity : 0.004 0.053 3339 Dihedral : 6.424 52.357 4341 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.65 % Favored : 96.09 % Rotamer: Outliers : 1.81 % Allowed : 6.74 % Favored : 91.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.60 (0.18), residues: 2304 helix: 1.54 (0.27), residues: 396 sheet: 0.36 (0.19), residues: 705 loop : 0.14 (0.18), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 571 HIS 0.005 0.001 HIS H 82A PHE 0.018 0.002 PHE I 383 TYR 0.017 0.001 TYR V 49 ARG 0.006 0.001 ARG I 444 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 273 time to evaluate : 2.255 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 46 LYS cc_start: 0.8586 (mmtt) cc_final: 0.8210 (mttm) REVERT: A 444 ARG cc_start: 0.8188 (ttt90) cc_final: 0.7947 (ttt-90) REVERT: B 634 GLU cc_start: 0.7780 (tt0) cc_final: 0.7465 (tt0) REVERT: L 49 TYR cc_start: 0.9166 (p90) cc_final: 0.8696 (p90) REVERT: L 94 ARG cc_start: 0.5083 (mmt180) cc_final: 0.4224 (mtm-85) REVERT: M 59 SER cc_start: 0.6994 (p) cc_final: 0.6774 (m) REVERT: M 94 ARG cc_start: 0.5143 (mmt180) cc_final: 0.4276 (mtm-85) REVERT: S 434 MET cc_start: 0.9122 (OUTLIER) cc_final: 0.8921 (ttp) REVERT: V 47 MET cc_start: 0.8776 (mmm) cc_final: 0.8548 (mmm) REVERT: V 94 ARG cc_start: 0.5292 (mmt180) cc_final: 0.4269 (mtm-85) outliers start: 37 outliers final: 26 residues processed: 294 average time/residue: 0.3499 time to fit residues: 150.6812 Evaluate side-chains 268 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 241 time to evaluate : 2.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 99 SER Chi-restraints excluded: chain L residue 52 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain I residue 92 GLU Chi-restraints excluded: chain I residue 355 ASN Chi-restraints excluded: chain J residue 613 SER Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain K residue 98 SER Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain M residue 56 SER Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 85 ASP Chi-restraints excluded: chain S residue 434 MET Chi-restraints excluded: chain S residue 485 LYS Chi-restraints excluded: chain T residue 599 SER Chi-restraints excluded: chain T residue 613 SER Chi-restraints excluded: chain T residue 618 ASN Chi-restraints excluded: chain U residue 98 SER Chi-restraints excluded: chain V residue 74 THR Chi-restraints excluded: chain V residue 85 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 207 optimal weight: 2.9990 chunk 158 optimal weight: 0.7980 chunk 109 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 100 optimal weight: 6.9990 chunk 141 optimal weight: 10.0000 chunk 210 optimal weight: 10.0000 chunk 223 optimal weight: 10.0000 chunk 110 optimal weight: 1.9990 chunk 199 optimal weight: 6.9990 chunk 60 optimal weight: 0.8980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 82AHIS I 67 ASN M 53 GLN ** S 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 377 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 19974 Z= 0.279 Angle : 0.593 9.126 27093 Z= 0.308 Chirality : 0.046 0.252 3279 Planarity : 0.004 0.056 3339 Dihedral : 5.932 59.535 4337 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.17 % Favored : 95.70 % Rotamer: Outliers : 2.39 % Allowed : 7.67 % Favored : 89.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.41 (0.18), residues: 2304 helix: 1.43 (0.27), residues: 399 sheet: 0.35 (0.19), residues: 711 loop : -0.09 (0.18), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 479 HIS 0.004 0.001 HIS I 105 PHE 0.018 0.002 PHE I 383 TYR 0.016 0.001 TYR V 49 ARG 0.007 0.001 ARG I 444 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 254 time to evaluate : 2.070 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 46 LYS cc_start: 0.8530 (mmtt) cc_final: 0.8258 (mttm) REVERT: A 213 ILE cc_start: 0.8513 (OUTLIER) cc_final: 0.8165 (mm) REVERT: L 49 TYR cc_start: 0.9231 (p90) cc_final: 0.8749 (p90) REVERT: L 94 ARG cc_start: 0.5270 (mmt180) cc_final: 0.4283 (mtm-85) REVERT: M 59 SER cc_start: 0.7436 (p) cc_final: 0.7204 (m) REVERT: M 94 ARG cc_start: 0.5182 (mmt180) cc_final: 0.4338 (mtm-85) REVERT: S 434 MET cc_start: 0.9173 (OUTLIER) cc_final: 0.8971 (ttp) REVERT: V 47 MET cc_start: 0.8776 (mmm) cc_final: 0.8523 (mmm) REVERT: V 94 ARG cc_start: 0.5480 (mmt180) cc_final: 0.4639 (mtm-85) outliers start: 49 outliers final: 31 residues processed: 285 average time/residue: 0.3497 time to fit residues: 146.9789 Evaluate side-chains 279 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 246 time to evaluate : 2.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 98 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain I residue 92 GLU Chi-restraints excluded: chain I residue 355 ASN Chi-restraints excluded: chain J residue 613 SER Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain K residue 98 SER Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 85 ASP Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain S residue 92 GLU Chi-restraints excluded: chain S residue 434 MET Chi-restraints excluded: chain S residue 485 LYS Chi-restraints excluded: chain T residue 599 SER Chi-restraints excluded: chain T residue 613 SER Chi-restraints excluded: chain U residue 20 LEU Chi-restraints excluded: chain U residue 30 SER Chi-restraints excluded: chain U residue 68 THR Chi-restraints excluded: chain U residue 98 SER Chi-restraints excluded: chain V residue 19 VAL Chi-restraints excluded: chain V residue 26 THR Chi-restraints excluded: chain V residue 52 THR Chi-restraints excluded: chain V residue 74 THR Chi-restraints excluded: chain V residue 102 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 185 optimal weight: 9.9990 chunk 126 optimal weight: 3.9990 chunk 3 optimal weight: 6.9990 chunk 166 optimal weight: 2.9990 chunk 92 optimal weight: 8.9990 chunk 190 optimal weight: 0.8980 chunk 154 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 114 optimal weight: 0.0040 chunk 200 optimal weight: 5.9990 chunk 56 optimal weight: 9.9990 overall best weight: 1.7796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 31 ASN I 67 ASN ** S 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.3069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 19974 Z= 0.250 Angle : 0.567 7.420 27093 Z= 0.296 Chirality : 0.045 0.227 3279 Planarity : 0.004 0.057 3339 Dihedral : 5.547 55.845 4335 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.21 % Favored : 95.66 % Rotamer: Outliers : 2.79 % Allowed : 7.67 % Favored : 89.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.38 (0.17), residues: 2304 helix: 1.50 (0.27), residues: 399 sheet: 0.40 (0.19), residues: 687 loop : -0.18 (0.18), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 479 HIS 0.004 0.001 HIS I 105 PHE 0.016 0.002 PHE I 383 TYR 0.016 0.001 TYR V 49 ARG 0.006 0.001 ARG I 444 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 251 time to evaluate : 2.141 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 46 LYS cc_start: 0.8534 (mmtt) cc_final: 0.8216 (mttm) REVERT: A 444 ARG cc_start: 0.8239 (ttt90) cc_final: 0.8010 (ttt-90) REVERT: L 49 TYR cc_start: 0.9220 (p90) cc_final: 0.8751 (p90) REVERT: L 94 ARG cc_start: 0.5279 (mmt180) cc_final: 0.4250 (mtm-85) REVERT: M 94 ARG cc_start: 0.5253 (mmt180) cc_final: 0.4383 (mtm-85) REVERT: S 381 GLU cc_start: 0.7939 (mt-10) cc_final: 0.7727 (tp30) REVERT: S 434 MET cc_start: 0.9171 (OUTLIER) cc_final: 0.8951 (ttp) REVERT: V 47 MET cc_start: 0.8772 (mmm) cc_final: 0.8538 (mmm) REVERT: V 94 ARG cc_start: 0.5518 (mmt180) cc_final: 0.4643 (mtm-85) outliers start: 57 outliers final: 41 residues processed: 290 average time/residue: 0.3379 time to fit residues: 143.5761 Evaluate side-chains 284 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 242 time to evaluate : 2.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 98 SER Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 52 THR Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain I residue 92 GLU Chi-restraints excluded: chain I residue 167 ASP Chi-restraints excluded: chain I residue 355 ASN Chi-restraints excluded: chain J residue 613 SER Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain K residue 98 SER Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain M residue 67 SER Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 85 ASP Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain S residue 92 GLU Chi-restraints excluded: chain S residue 167 ASP Chi-restraints excluded: chain S residue 426 MET Chi-restraints excluded: chain S residue 434 MET Chi-restraints excluded: chain S residue 485 LYS Chi-restraints excluded: chain T residue 599 SER Chi-restraints excluded: chain T residue 613 SER Chi-restraints excluded: chain U residue 20 LEU Chi-restraints excluded: chain U residue 30 SER Chi-restraints excluded: chain U residue 68 THR Chi-restraints excluded: chain U residue 98 SER Chi-restraints excluded: chain V residue 19 VAL Chi-restraints excluded: chain V residue 26 THR Chi-restraints excluded: chain V residue 52 THR Chi-restraints excluded: chain V residue 67 SER Chi-restraints excluded: chain V residue 74 THR Chi-restraints excluded: chain V residue 102 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 75 optimal weight: 10.0000 chunk 201 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 chunk 131 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 223 optimal weight: 10.0000 chunk 185 optimal weight: 6.9990 chunk 103 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 73 optimal weight: 10.0000 chunk 117 optimal weight: 6.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 HIS L 37 GLN I 103 GLN I 374 HIS M 37 GLN S 374 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.3214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.053 19974 Z= 0.491 Angle : 0.701 10.017 27093 Z= 0.359 Chirality : 0.049 0.230 3279 Planarity : 0.005 0.058 3339 Dihedral : 5.949 45.340 4335 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.77 % Favored : 95.10 % Rotamer: Outliers : 2.98 % Allowed : 8.11 % Favored : 88.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.06 (0.17), residues: 2304 helix: 0.95 (0.26), residues: 402 sheet: 0.26 (0.20), residues: 630 loop : -0.47 (0.17), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP I 427 HIS 0.006 0.002 HIS K 82A PHE 0.021 0.003 PHE S 383 TYR 0.016 0.002 TYR V 49 ARG 0.006 0.001 ARG A 444 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 240 time to evaluate : 2.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8531 (mmtt) cc_final: 0.8259 (mttm) REVERT: L 94 ARG cc_start: 0.5518 (mmt180) cc_final: 0.4504 (mtm-85) REVERT: M 42 LYS cc_start: 0.8120 (mmmm) cc_final: 0.7322 (mtmm) REVERT: M 94 ARG cc_start: 0.5365 (mmt180) cc_final: 0.4292 (mtm-85) REVERT: S 434 MET cc_start: 0.9179 (OUTLIER) cc_final: 0.8945 (ttp) REVERT: V 47 MET cc_start: 0.8732 (mmm) cc_final: 0.8488 (mmm) REVERT: V 94 ARG cc_start: 0.5644 (mmt180) cc_final: 0.4608 (mtm-85) outliers start: 61 outliers final: 55 residues processed: 280 average time/residue: 0.3538 time to fit residues: 145.2632 Evaluate side-chains 288 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 232 time to evaluate : 2.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 485 LYS Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 607 ASN Chi-restraints excluded: chain B residue 634 GLU Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 98 SER Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 52 THR Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain I residue 92 GLU Chi-restraints excluded: chain I residue 167 ASP Chi-restraints excluded: chain I residue 355 ASN Chi-restraints excluded: chain J residue 534 SER Chi-restraints excluded: chain J residue 613 SER Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain K residue 49 SER Chi-restraints excluded: chain K residue 68 THR Chi-restraints excluded: chain K residue 98 SER Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 26 THR Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain M residue 59 SER Chi-restraints excluded: chain M residue 67 SER Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 85 ASP Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain S residue 92 GLU Chi-restraints excluded: chain S residue 167 ASP Chi-restraints excluded: chain S residue 426 MET Chi-restraints excluded: chain S residue 434 MET Chi-restraints excluded: chain S residue 485 LYS Chi-restraints excluded: chain T residue 534 SER Chi-restraints excluded: chain T residue 613 SER Chi-restraints excluded: chain U residue 20 LEU Chi-restraints excluded: chain U residue 30 SER Chi-restraints excluded: chain U residue 68 THR Chi-restraints excluded: chain U residue 98 SER Chi-restraints excluded: chain V residue 24 THR Chi-restraints excluded: chain V residue 26 THR Chi-restraints excluded: chain V residue 52 THR Chi-restraints excluded: chain V residue 67 SER Chi-restraints excluded: chain V residue 74 THR Chi-restraints excluded: chain V residue 102 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 215 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 127 optimal weight: 0.8980 chunk 163 optimal weight: 5.9990 chunk 126 optimal weight: 0.7980 chunk 188 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 222 optimal weight: 20.0000 chunk 139 optimal weight: 4.9990 chunk 135 optimal weight: 0.9980 chunk 102 optimal weight: 2.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.3397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 19974 Z= 0.165 Angle : 0.544 9.229 27093 Z= 0.281 Chirality : 0.043 0.220 3279 Planarity : 0.004 0.057 3339 Dihedral : 5.336 40.787 4335 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.91 % Favored : 96.01 % Rotamer: Outliers : 2.20 % Allowed : 9.34 % Favored : 88.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.24 (0.18), residues: 2304 helix: 1.82 (0.28), residues: 381 sheet: 0.27 (0.19), residues: 690 loop : -0.38 (0.18), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 479 HIS 0.003 0.001 HIS K 82A PHE 0.013 0.001 PHE S 383 TYR 0.018 0.001 TYR M 49 ARG 0.006 0.001 ARG I 178 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 259 time to evaluate : 1.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8514 (mmtt) cc_final: 0.8259 (mttm) REVERT: A 213 ILE cc_start: 0.8608 (OUTLIER) cc_final: 0.8313 (mm) REVERT: A 444 ARG cc_start: 0.8230 (ttt90) cc_final: 0.7992 (ttt-90) REVERT: H 100 LEU cc_start: 0.9288 (OUTLIER) cc_final: 0.8881 (mp) REVERT: L 49 TYR cc_start: 0.9215 (p90) cc_final: 0.8916 (p90) REVERT: L 94 ARG cc_start: 0.5248 (mmt180) cc_final: 0.4348 (mtm-85) REVERT: K 100 LEU cc_start: 0.9400 (OUTLIER) cc_final: 0.9023 (mp) REVERT: M 42 LYS cc_start: 0.8112 (mmmm) cc_final: 0.7269 (mtmm) REVERT: M 94 ARG cc_start: 0.5217 (mmt180) cc_final: 0.4312 (mtm-85) REVERT: S 434 MET cc_start: 0.9146 (ptt) cc_final: 0.8934 (ttp) REVERT: V 47 MET cc_start: 0.8757 (mmm) cc_final: 0.8552 (mmm) REVERT: V 94 ARG cc_start: 0.5547 (mmt180) cc_final: 0.4610 (mtm-85) outliers start: 45 outliers final: 32 residues processed: 290 average time/residue: 0.3438 time to fit residues: 146.3397 Evaluate side-chains 278 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 243 time to evaluate : 2.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 98 SER Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain I residue 167 ASP Chi-restraints excluded: chain I residue 355 ASN Chi-restraints excluded: chain J residue 613 SER Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain K residue 98 SER Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain M residue 59 SER Chi-restraints excluded: chain M residue 67 SER Chi-restraints excluded: chain M residue 85 ASP Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain S residue 426 MET Chi-restraints excluded: chain S residue 485 LYS Chi-restraints excluded: chain T residue 534 SER Chi-restraints excluded: chain T residue 613 SER Chi-restraints excluded: chain U residue 18 LEU Chi-restraints excluded: chain U residue 20 LEU Chi-restraints excluded: chain U residue 30 SER Chi-restraints excluded: chain U residue 98 SER Chi-restraints excluded: chain V residue 52 THR Chi-restraints excluded: chain V residue 67 SER Chi-restraints excluded: chain V residue 102 THR Chi-restraints excluded: chain V residue 105 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 137 optimal weight: 4.9990 chunk 88 optimal weight: 6.9990 chunk 132 optimal weight: 6.9990 chunk 67 optimal weight: 9.9990 chunk 43 optimal weight: 0.9980 chunk 141 optimal weight: 6.9990 chunk 151 optimal weight: 8.9990 chunk 110 optimal weight: 4.9990 chunk 20 optimal weight: 0.9980 chunk 175 optimal weight: 6.9990 chunk 202 optimal weight: 0.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 114 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.3416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 19974 Z= 0.347 Angle : 0.619 8.645 27093 Z= 0.316 Chirality : 0.046 0.264 3279 Planarity : 0.005 0.056 3339 Dihedral : 5.484 40.243 4335 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.77 % Favored : 95.14 % Rotamer: Outliers : 2.64 % Allowed : 9.14 % Favored : 88.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.04 (0.17), residues: 2304 helix: 1.36 (0.27), residues: 399 sheet: 0.11 (0.19), residues: 666 loop : -0.40 (0.18), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 427 HIS 0.004 0.001 HIS K 82A PHE 0.018 0.002 PHE I 383 TYR 0.017 0.001 TYR V 49 ARG 0.005 0.001 ARG I 178 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 243 time to evaluate : 2.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8503 (mmtt) cc_final: 0.8235 (mttm) REVERT: A 213 ILE cc_start: 0.8697 (OUTLIER) cc_final: 0.8407 (mm) REVERT: H 100 LEU cc_start: 0.9340 (OUTLIER) cc_final: 0.8888 (mp) REVERT: L 94 ARG cc_start: 0.5340 (mmt180) cc_final: 0.4437 (mtm-85) REVERT: M 94 ARG cc_start: 0.5299 (mmt180) cc_final: 0.4350 (mtm-85) REVERT: S 434 MET cc_start: 0.9181 (OUTLIER) cc_final: 0.8956 (ttp) REVERT: U 100 LEU cc_start: 0.9413 (OUTLIER) cc_final: 0.9126 (mp) REVERT: V 47 MET cc_start: 0.8741 (mmm) cc_final: 0.8518 (mmm) REVERT: V 94 ARG cc_start: 0.5638 (mmt180) cc_final: 0.4559 (mtm-85) outliers start: 54 outliers final: 42 residues processed: 277 average time/residue: 0.3627 time to fit residues: 147.4242 Evaluate side-chains 283 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 237 time to evaluate : 2.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 485 LYS Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 98 SER Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain I residue 92 GLU Chi-restraints excluded: chain I residue 167 ASP Chi-restraints excluded: chain I residue 355 ASN Chi-restraints excluded: chain I residue 371 VAL Chi-restraints excluded: chain J residue 613 SER Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain K residue 49 SER Chi-restraints excluded: chain K residue 68 THR Chi-restraints excluded: chain K residue 98 SER Chi-restraints excluded: chain M residue 67 SER Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 85 ASP Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain S residue 167 ASP Chi-restraints excluded: chain S residue 213 ILE Chi-restraints excluded: chain S residue 426 MET Chi-restraints excluded: chain S residue 434 MET Chi-restraints excluded: chain S residue 485 LYS Chi-restraints excluded: chain T residue 534 SER Chi-restraints excluded: chain T residue 613 SER Chi-restraints excluded: chain U residue 30 SER Chi-restraints excluded: chain U residue 98 SER Chi-restraints excluded: chain U residue 100 LEU Chi-restraints excluded: chain V residue 26 THR Chi-restraints excluded: chain V residue 27 ASP Chi-restraints excluded: chain V residue 52 THR Chi-restraints excluded: chain V residue 67 SER Chi-restraints excluded: chain V residue 74 THR Chi-restraints excluded: chain V residue 102 THR Chi-restraints excluded: chain V residue 105 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 213 optimal weight: 1.9990 chunk 194 optimal weight: 4.9990 chunk 207 optimal weight: 0.9990 chunk 124 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 162 optimal weight: 0.6980 chunk 63 optimal weight: 8.9990 chunk 187 optimal weight: 2.9990 chunk 196 optimal weight: 0.9990 chunk 206 optimal weight: 1.9990 chunk 136 optimal weight: 1.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.3526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 19974 Z= 0.202 Angle : 0.556 8.890 27093 Z= 0.287 Chirality : 0.044 0.401 3279 Planarity : 0.004 0.056 3339 Dihedral : 5.279 37.076 4335 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.30 % Favored : 95.62 % Rotamer: Outliers : 2.35 % Allowed : 9.73 % Favored : 87.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.20 (0.18), residues: 2304 helix: 1.90 (0.27), residues: 381 sheet: 0.23 (0.19), residues: 696 loop : -0.45 (0.18), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 479 HIS 0.003 0.001 HIS A 105 PHE 0.014 0.001 PHE S 383 TYR 0.017 0.001 TYR V 49 ARG 0.005 0.001 ARG I 178 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 249 time to evaluate : 2.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8505 (mmtt) cc_final: 0.8234 (mttm) REVERT: A 213 ILE cc_start: 0.8618 (OUTLIER) cc_final: 0.8323 (mm) REVERT: A 444 ARG cc_start: 0.8220 (ttt90) cc_final: 0.7980 (ttt-90) REVERT: B 635 ILE cc_start: 0.8534 (OUTLIER) cc_final: 0.8246 (tt) REVERT: H 100 LEU cc_start: 0.9279 (OUTLIER) cc_final: 0.8910 (mp) REVERT: L 49 TYR cc_start: 0.9227 (p90) cc_final: 0.8949 (p90) REVERT: L 94 ARG cc_start: 0.5181 (mmt180) cc_final: 0.4296 (mtm-85) REVERT: K 100 LEU cc_start: 0.9393 (OUTLIER) cc_final: 0.9041 (mp) REVERT: M 94 ARG cc_start: 0.5116 (mmt180) cc_final: 0.4236 (mtm-85) REVERT: S 434 MET cc_start: 0.9154 (OUTLIER) cc_final: 0.8941 (ttp) REVERT: U 100 LEU cc_start: 0.9396 (OUTLIER) cc_final: 0.9163 (mt) REVERT: V 47 MET cc_start: 0.8745 (mmm) cc_final: 0.8539 (mmm) REVERT: V 94 ARG cc_start: 0.5563 (mmt180) cc_final: 0.4545 (mtm-85) outliers start: 48 outliers final: 36 residues processed: 282 average time/residue: 0.3693 time to fit residues: 152.3192 Evaluate side-chains 283 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 241 time to evaluate : 2.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 98 SER Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 52 THR Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 85 ASP Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain I residue 92 GLU Chi-restraints excluded: chain I residue 167 ASP Chi-restraints excluded: chain I residue 355 ASN Chi-restraints excluded: chain I residue 371 VAL Chi-restraints excluded: chain J residue 613 SER Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain K residue 98 SER Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain M residue 67 SER Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 85 ASP Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain S residue 92 GLU Chi-restraints excluded: chain S residue 167 ASP Chi-restraints excluded: chain S residue 426 MET Chi-restraints excluded: chain S residue 434 MET Chi-restraints excluded: chain S residue 485 LYS Chi-restraints excluded: chain T residue 534 SER Chi-restraints excluded: chain T residue 613 SER Chi-restraints excluded: chain U residue 20 LEU Chi-restraints excluded: chain U residue 30 SER Chi-restraints excluded: chain U residue 98 SER Chi-restraints excluded: chain U residue 100 LEU Chi-restraints excluded: chain V residue 27 ASP Chi-restraints excluded: chain V residue 52 THR Chi-restraints excluded: chain V residue 67 SER Chi-restraints excluded: chain V residue 102 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 219 optimal weight: 4.9990 chunk 133 optimal weight: 5.9990 chunk 104 optimal weight: 0.8980 chunk 152 optimal weight: 8.9990 chunk 230 optimal weight: 3.9990 chunk 211 optimal weight: 0.9980 chunk 183 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 141 optimal weight: 9.9990 chunk 112 optimal weight: 0.6980 chunk 145 optimal weight: 9.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.3559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 19974 Z= 0.244 Angle : 0.569 9.047 27093 Z= 0.292 Chirality : 0.045 0.365 3279 Planarity : 0.004 0.055 3339 Dihedral : 5.261 35.262 4335 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.51 % Favored : 95.40 % Rotamer: Outliers : 2.20 % Allowed : 9.92 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.20 (0.18), residues: 2304 helix: 1.87 (0.27), residues: 381 sheet: 0.25 (0.19), residues: 696 loop : -0.46 (0.18), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 479 HIS 0.003 0.001 HIS I 105 PHE 0.015 0.002 PHE I 383 TYR 0.017 0.001 TYR V 49 ARG 0.008 0.001 ARG S 178 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 242 time to evaluate : 2.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8502 (mmtt) cc_final: 0.8240 (mttm) REVERT: A 213 ILE cc_start: 0.8681 (OUTLIER) cc_final: 0.8383 (mm) REVERT: A 444 ARG cc_start: 0.8231 (ttt90) cc_final: 0.7988 (ttt-90) REVERT: H 100 LEU cc_start: 0.9276 (OUTLIER) cc_final: 0.8921 (mp) REVERT: L 49 TYR cc_start: 0.9246 (p90) cc_final: 0.8969 (p90) REVERT: L 94 ARG cc_start: 0.5294 (mmt180) cc_final: 0.4446 (mtm-85) REVERT: K 100 LEU cc_start: 0.9367 (OUTLIER) cc_final: 0.8991 (mp) REVERT: M 94 ARG cc_start: 0.5130 (mmt180) cc_final: 0.4256 (mtm-85) REVERT: S 434 MET cc_start: 0.9158 (OUTLIER) cc_final: 0.8939 (ttp) REVERT: U 100 LEU cc_start: 0.9401 (OUTLIER) cc_final: 0.9154 (mt) REVERT: V 47 MET cc_start: 0.8740 (mmm) cc_final: 0.8531 (mmm) REVERT: V 94 ARG cc_start: 0.5612 (mmt180) cc_final: 0.4590 (mtm-85) outliers start: 45 outliers final: 37 residues processed: 272 average time/residue: 0.3567 time to fit residues: 141.4198 Evaluate side-chains 281 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 239 time to evaluate : 2.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 98 SER Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 52 THR Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 85 ASP Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain I residue 92 GLU Chi-restraints excluded: chain I residue 167 ASP Chi-restraints excluded: chain I residue 355 ASN Chi-restraints excluded: chain I residue 371 VAL Chi-restraints excluded: chain J residue 613 SER Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain K residue 49 SER Chi-restraints excluded: chain K residue 98 SER Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain M residue 67 SER Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 85 ASP Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain S residue 92 GLU Chi-restraints excluded: chain S residue 167 ASP Chi-restraints excluded: chain S residue 426 MET Chi-restraints excluded: chain S residue 434 MET Chi-restraints excluded: chain S residue 485 LYS Chi-restraints excluded: chain T residue 534 SER Chi-restraints excluded: chain T residue 613 SER Chi-restraints excluded: chain U residue 20 LEU Chi-restraints excluded: chain U residue 30 SER Chi-restraints excluded: chain U residue 98 SER Chi-restraints excluded: chain U residue 100 LEU Chi-restraints excluded: chain V residue 27 ASP Chi-restraints excluded: chain V residue 52 THR Chi-restraints excluded: chain V residue 67 SER Chi-restraints excluded: chain V residue 74 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 195 optimal weight: 2.9990 chunk 56 optimal weight: 8.9990 chunk 168 optimal weight: 6.9990 chunk 27 optimal weight: 0.8980 chunk 50 optimal weight: 0.9980 chunk 183 optimal weight: 3.9990 chunk 76 optimal weight: 0.9980 chunk 188 optimal weight: 4.9990 chunk 23 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 161 optimal weight: 0.0970 overall best weight: 0.9980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.134924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.101202 restraints weight = 25002.785| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 2.58 r_work: 0.2841 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2691 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.3660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 19974 Z= 0.167 Angle : 0.525 9.015 27093 Z= 0.272 Chirality : 0.043 0.291 3279 Planarity : 0.004 0.055 3339 Dihedral : 5.028 39.614 4335 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.95 % Favored : 95.96 % Rotamer: Outliers : 2.10 % Allowed : 10.22 % Favored : 87.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.42 (0.18), residues: 2304 helix: 2.13 (0.27), residues: 381 sheet: 0.38 (0.19), residues: 720 loop : -0.34 (0.18), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 479 HIS 0.003 0.001 HIS I 105 PHE 0.014 0.001 PHE A 53 TYR 0.018 0.001 TYR V 49 ARG 0.008 0.001 ARG I 444 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4254.40 seconds wall clock time: 76 minutes 42.87 seconds (4602.87 seconds total)