Starting phenix.real_space_refine on Sun Feb 18 09:41:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yfh_33790/02_2024/7yfh_33790_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yfh_33790/02_2024/7yfh_33790.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yfh_33790/02_2024/7yfh_33790_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yfh_33790/02_2024/7yfh_33790_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yfh_33790/02_2024/7yfh_33790_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yfh_33790/02_2024/7yfh_33790.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yfh_33790/02_2024/7yfh_33790.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yfh_33790/02_2024/7yfh_33790_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yfh_33790/02_2024/7yfh_33790_neut_updated.pdb" } resolution = 3.0 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= 0.003 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 98 5.16 5 C 13462 2.51 5 N 3658 2.21 5 O 4072 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 188": "OE1" <-> "OE2" Residue "A GLU 213": "OE1" <-> "OE2" Residue "A GLU 215": "OE1" <-> "OE2" Residue "A GLU 698": "OE1" <-> "OE2" Residue "B GLU 102": "OE1" <-> "OE2" Residue "B GLU 134": "OE1" <-> "OE2" Residue "B GLU 712": "OE1" <-> "OE2" Residue "C GLU 213": "OE1" <-> "OE2" Residue "C GLU 751": "OE1" <-> "OE2" Residue "D GLU 158": "OE1" <-> "OE2" Residue "D TYR 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 741": "OE1" <-> "OE2" Residue "B GLU 903": "OE1" <-> "OE2" Residue "D GLU 903": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 21290 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 5185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 653, 5185 Classifications: {'peptide': 653} Link IDs: {'PTRANS': 29, 'TRANS': 623} Chain breaks: 1 Chain: "B" Number of atoms: 5045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 652, 5045 Classifications: {'peptide': 652} Link IDs: {'PTRANS': 37, 'TRANS': 614} Chain breaks: 1 Chain: "C" Number of atoms: 5238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 659, 5238 Classifications: {'peptide': 659} Link IDs: {'PTRANS': 30, 'TRANS': 628} Chain breaks: 1 Chain: "D" Number of atoms: 5047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 652, 5047 Classifications: {'peptide': 652} Link IDs: {'PTRANS': 37, 'TRANS': 614} Chain breaks: 1 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "b" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "e" 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: "k" 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: "m" 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: "t" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "v" 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "3" 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: "5" 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'NAG': 4} Classifications: {'peptide': 1, 'undetermined': 4} Modifications used: {'COO': 1} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 70 Unusual residues: {'IWB': 1, 'NAG': 2} Inner-chain residues flagged as termini: ['pdbres="GLU B 903 "'] Classifications: {'peptide': 1, 'undetermined': 3} Modifications used: {'COO': 1} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'NAG': 5} Classifications: {'peptide': 1, 'undetermined': 5} Modifications used: {'COO': 1} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "D" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'NAG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 11.72, per 1000 atoms: 0.55 Number of scatterers: 21290 At special positions: 0 Unit cell: (125.307, 143.514, 137.088, 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 98 16.00 O 4072 8.00 N 3658 7.00 C 13462 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 79 " - pdb=" SG CYS A 308 " distance=2.02 Simple disulfide: pdb=" SG CYS A 420 " - pdb=" SG CYS A 454 " distance=2.03 Simple disulfide: pdb=" SG CYS B 82 " - pdb=" SG CYS B 317 " distance=2.03 Simple disulfide: pdb=" SG CYS B 426 " - pdb=" SG CYS B 453 " distance=2.03 Simple disulfide: pdb=" SG CYS B 433 " - pdb=" SG CYS B 454 " distance=2.03 Simple disulfide: pdb=" SG CYS C 79 " - pdb=" SG CYS C 308 " distance=2.03 Simple disulfide: pdb=" SG CYS C 420 " - pdb=" SG CYS C 454 " distance=2.04 Simple disulfide: pdb=" SG CYS C 436 " - pdb=" SG CYS C 455 " distance=2.03 Simple disulfide: pdb=" SG CYS D 82 " - pdb=" SG CYS D 317 " distance=2.03 Simple disulfide: pdb=" SG CYS D 426 " - pdb=" SG CYS D 453 " distance=2.03 Simple disulfide: pdb=" SG CYS D 433 " - pdb=" SG CYS D 454 " distance=2.03 Simple disulfide: pdb=" SG CYS D 743 " - pdb=" SG CYS D 798 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-4 " NAG E 2 " - " MAN E 3 " " NAG H 2 " - " MAN H 3 " " NAG K 2 " - " MAN K 3 " " NAG b 2 " - " MAN b 3 " " NAG y 2 " - " MAN y 3 " BETA1-4 " NAG 3 1 " - " NAG 3 2 " " NAG 5 1 " - " NAG 5 2 " " NAG E 1 " - " NAG E 2 " " NAG H 1 " - " NAG H 2 " " NAG K 1 " - " NAG K 2 " " NAG N 1 " - " NAG N 2 " " NAG P 1 " - " NAG P 2 " " NAG T 1 " - " NAG T 2 " " NAG W 1 " - " NAG W 2 " " NAG b 1 " - " NAG b 2 " " NAG e 1 " - " NAG e 2 " " NAG k 1 " - " NAG k 2 " " NAG m 1 " - " NAG m 2 " " NAG r 1 " - " NAG r 2 " " NAG t 1 " - " NAG t 2 " " NAG v 1 " - " NAG v 2 " " NAG y 1 " - " NAG y 2 " NAG-ASN " NAG 3 1 " - " ASN D 685 " " NAG 5 1 " - " ASN D 337 " " NAG A 901 " - " ASN A 239 " " NAG A 902 " - " ASN A 300 " " NAG A 903 " - " ASN A 491 " " NAG A 904 " - " ASN A 440 " " NAG B 901 " - " ASN B 438 " " NAG B 902 " - " ASN B 70 " " NAG C 901 " - " ASN C 491 " " NAG C 902 " - " ASN C 350 " " NAG C 903 " - " ASN C 300 " " NAG C 904 " - " ASN C 239 " " NAG C 905 " - " ASN C 440 " " NAG D 901 " - " ASN D 438 " " NAG D 902 " - " ASN D 70 " " NAG E 1 " - " ASN A 771 " " NAG H 1 " - " ASN A 276 " " NAG K 1 " - " ASN A 368 " " NAG N 1 " - " ASN A 61 " " NAG P 1 " - " ASN A 203 " " NAG T 1 " - " ASN A 350 " " NAG W 1 " - " ASN A 471 " " NAG b 1 " - " ASN B 685 " " NAG e 1 " - " ASN B 337 " " NAG k 1 " - " ASN C 471 " " NAG m 1 " - " ASN C 368 " " NAG r 1 " - " ASN C 203 " " NAG t 1 " - " ASN C 61 " " NAG v 1 " - " ASN C 771 " " NAG y 1 " - " ASN C 276 " Time building additional restraints: 8.65 Conformation dependent library (CDL) restraints added in 3.9 seconds 5200 Ramachandran restraints generated. 2600 Oldfield, 0 Emsley, 2600 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4848 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 86 helices and 30 sheets defined 33.3% alpha, 13.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.51 Creating SS restraints... Processing helix chain 'A' and resid 38 through 52 Processing helix chain 'A' and resid 71 through 81 Processing helix chain 'A' and resid 100 through 113 removed outlier: 3.932A pdb=" N THR A 103 " --> pdb=" O ASP A 100 " (cutoff:3.500A) Proline residue: A 104 - end of helix removed outlier: 3.796A pdb=" N VAL A 107 " --> pdb=" O PRO A 104 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ALA A 111 " --> pdb=" O SER A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 129 No H-bonds generated for 'chain 'A' and resid 127 through 129' Processing helix chain 'A' and resid 144 through 157 removed outlier: 3.798A pdb=" N VAL A 150 " --> pdb=" O GLN A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 187 removed outlier: 3.565A pdb=" N GLU A 186 " --> pdb=" O THR A 182 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG A 187 " --> pdb=" O LEU A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 213 Processing helix chain 'A' and resid 225 through 237 Processing helix chain 'A' and resid 251 through 254 Processing helix chain 'A' and resid 256 through 261 removed outlier: 3.580A pdb=" N ARG A 260 " --> pdb=" O ASN A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 298 Processing helix chain 'A' and resid 318 through 326 Processing helix chain 'A' and resid 458 through 470 Processing helix chain 'A' and resid 500 through 507 Processing helix chain 'A' and resid 521 through 524 No H-bonds generated for 'chain 'A' and resid 521 through 524' Processing helix chain 'A' and resid 666 through 668 No H-bonds generated for 'chain 'A' and resid 666 through 668' Processing helix chain 'A' and resid 670 through 673 No H-bonds generated for 'chain 'A' and resid 670 through 673' Processing helix chain 'A' and resid 688 through 694 Processing helix chain 'A' and resid 700 through 709 removed outlier: 3.692A pdb=" N HIS A 709 " --> pdb=" O HIS A 705 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 722 Processing helix chain 'A' and resid 733 through 743 Processing helix chain 'A' and resid 769 through 781 Processing helix chain 'A' and resid 784 through 791 Processing helix chain 'B' and resid 43 through 54 removed outlier: 4.067A pdb=" N SER B 52 " --> pdb=" O ARG B 49 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N GLN B 53 " --> pdb=" O LEU B 50 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ASN B 54 " --> pdb=" O THR B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 87 Processing helix chain 'B' and resid 104 through 115 Processing helix chain 'B' and resid 146 through 160 Processing helix chain 'B' and resid 175 through 187 Processing helix chain 'B' and resid 212 through 218 removed outlier: 3.725A pdb=" N GLN B 218 " --> pdb=" O ARG B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 242 Processing helix chain 'B' and resid 279 through 281 No H-bonds generated for 'chain 'B' and resid 279 through 281' Processing helix chain 'B' and resid 285 through 307 Processing helix chain 'B' and resid 326 through 336 Processing helix chain 'B' and resid 457 through 469 Processing helix chain 'B' and resid 493 through 499 Processing helix chain 'B' and resid 514 through 517 No H-bonds generated for 'chain 'B' and resid 514 through 517' Processing helix chain 'B' and resid 666 through 669 No H-bonds generated for 'chain 'B' and resid 666 through 669' Processing helix chain 'B' and resid 688 through 695 Processing helix chain 'B' and resid 697 through 706 removed outlier: 3.920A pdb=" N LYS B 705 " --> pdb=" O THR B 701 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N PHE B 706 " --> pdb=" O HIS B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 711 through 720 Processing helix chain 'B' and resid 730 through 738 removed outlier: 3.530A pdb=" N TYR B 735 " --> pdb=" O ALA B 731 " (cutoff:3.500A) Processing helix chain 'B' and resid 769 through 783 Processing helix chain 'B' and resid 785 through 793 Processing helix chain 'C' and resid 38 through 53 Processing helix chain 'C' and resid 71 through 81 Processing helix chain 'C' and resid 103 through 113 Proline residue: C 106 - end of helix removed outlier: 3.546A pdb=" N ALA C 111 " --> pdb=" O SER C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 127 through 129 No H-bonds generated for 'chain 'C' and resid 127 through 129' Processing helix chain 'C' and resid 144 through 158 removed outlier: 3.711A pdb=" N VAL C 150 " --> pdb=" O GLN C 147 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N TYR C 158 " --> pdb=" O MET C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 186 removed outlier: 3.645A pdb=" N GLU C 186 " --> pdb=" O THR C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 212 Processing helix chain 'C' and resid 225 through 237 Processing helix chain 'C' and resid 257 through 261 Processing helix chain 'C' and resid 277 through 296 Processing helix chain 'C' and resid 316 through 326 removed outlier: 4.725A pdb=" N LEU C 320 " --> pdb=" O LYS C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 470 Processing helix chain 'C' and resid 500 through 507 Processing helix chain 'C' and resid 521 through 524 No H-bonds generated for 'chain 'C' and resid 521 through 524' Processing helix chain 'C' and resid 670 through 673 No H-bonds generated for 'chain 'C' and resid 670 through 673' Processing helix chain 'C' and resid 688 through 695 Processing helix chain 'C' and resid 700 through 709 removed outlier: 3.655A pdb=" N HIS C 709 " --> pdb=" O HIS C 705 " (cutoff:3.500A) Processing helix chain 'C' and resid 714 through 722 Processing helix chain 'C' and resid 733 through 743 Processing helix chain 'C' and resid 769 through 782 Processing helix chain 'C' and resid 784 through 791 Processing helix chain 'D' and resid 42 through 48 Processing helix chain 'D' and resid 74 through 88 removed outlier: 3.681A pdb=" N ALA D 87 " --> pdb=" O GLY D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 115 Processing helix chain 'D' and resid 125 through 127 No H-bonds generated for 'chain 'D' and resid 125 through 127' Processing helix chain 'D' and resid 146 through 159 Processing helix chain 'D' and resid 175 through 187 Processing helix chain 'D' and resid 210 through 216 removed outlier: 3.584A pdb=" N LEU D 215 " --> pdb=" O ARG D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 242 Processing helix chain 'D' and resid 279 through 282 removed outlier: 4.369A pdb=" N ARG D 282 " --> pdb=" O GLU D 279 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 279 through 282' Processing helix chain 'D' and resid 285 through 307 Processing helix chain 'D' and resid 326 through 336 Processing helix chain 'D' and resid 457 through 469 Processing helix chain 'D' and resid 493 through 499 Processing helix chain 'D' and resid 514 through 519 removed outlier: 3.859A pdb=" N ILE D 519 " --> pdb=" O GLU D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 666 through 669 No H-bonds generated for 'chain 'D' and resid 666 through 669' Processing helix chain 'D' and resid 687 through 695 Processing helix chain 'D' and resid 697 through 703 Processing helix chain 'D' and resid 711 through 720 Processing helix chain 'D' and resid 730 through 738 removed outlier: 3.525A pdb=" N TYR D 735 " --> pdb=" O ALA D 731 " (cutoff:3.500A) Processing helix chain 'D' and resid 749 through 752 Processing helix chain 'D' and resid 770 through 783 Processing helix chain 'D' and resid 785 through 793 Processing sheet with id= A, first strand: chain 'A' and resid 60 through 66 removed outlier: 6.491A pdb=" N VAL A 27 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N THR A 63 " --> pdb=" O VAL A 27 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N ILE A 29 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N VAL A 65 " --> pdb=" O ILE A 29 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N ALA A 31 " --> pdb=" O VAL A 65 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 193 through 197 removed outlier: 4.039A pdb=" N LYS A 193 " --> pdb=" O ILE A 163 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N VAL A 218 " --> pdb=" O ILE A 164 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N LEU A 166 " --> pdb=" O VAL A 218 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ILE A 220 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N SER A 168 " --> pdb=" O ILE A 220 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N SER A 222 " --> pdb=" O SER A 168 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N VAL A 246 " --> pdb=" O ILE A 219 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N LEU A 221 " --> pdb=" O VAL A 246 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N LEU A 248 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 267 through 271 Processing sheet with id= D, first strand: chain 'A' and resid 398 through 402 Processing sheet with id= E, first strand: chain 'A' and resid 410 through 413 Processing sheet with id= F, first strand: chain 'A' and resid 527 through 529 Processing sheet with id= G, first strand: chain 'A' and resid 534 through 536 removed outlier: 3.851A pdb=" N LYS A 534 " --> pdb=" O PHE A 758 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 728 through 732 removed outlier: 3.851A pdb=" N ILE A 540 " --> pdb=" O THR A 749 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 63 through 67 removed outlier: 6.419A pdb=" N GLY B 92 " --> pdb=" O ALA B 33 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N VAL B 35 " --> pdb=" O GLY B 92 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N VAL B 94 " --> pdb=" O VAL B 35 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N PHE B 95 " --> pdb=" O PRO B 118 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N LEU B 120 " --> pdb=" O PHE B 95 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N ASP B 97 " --> pdb=" O LEU B 120 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N ILE B 122 " --> pdb=" O ASP B 97 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 198 through 200 removed outlier: 6.695A pdb=" N VAL B 167 " --> pdb=" O LEU B 199 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N VAL B 251 " --> pdb=" O LEU B 224 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N ALA B 226 " --> pdb=" O VAL B 251 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU B 253 " --> pdb=" O ALA B 226 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 274 through 278 removed outlier: 5.936A pdb=" N ALA B 362 " --> pdb=" O MET B 371 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N MET B 371 " --> pdb=" O ALA B 362 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASP B 376 " --> pdb=" O VAL B 379 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 402 through 407 removed outlier: 6.594A pdb=" N SER B 472 " --> pdb=" O LEU B 403 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N VAL B 405 " --> pdb=" O SER B 472 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N ASP B 474 " --> pdb=" O VAL B 405 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N THR B 407 " --> pdb=" O ASP B 474 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N TYR B 476 " --> pdb=" O THR B 407 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'B' and resid 415 through 417 removed outlier: 3.804A pdb=" N THR B 450 " --> pdb=" O ARG B 435 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 527 through 529 removed outlier: 3.984A pdb=" N VAL B 527 " --> pdb=" O TYR B 759 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 725 through 729 Processing sheet with id= P, first strand: chain 'C' and resid 59 through 66 removed outlier: 4.511A pdb=" N ALA C 89 " --> pdb=" O ASN C 28 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N VAL C 92 " --> pdb=" O PRO C 117 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N LEU C 119 " --> pdb=" O VAL C 92 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 193 through 197 removed outlier: 3.796A pdb=" N LYS C 193 " --> pdb=" O ILE C 163 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N VAL C 218 " --> pdb=" O ILE C 164 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N LEU C 166 " --> pdb=" O VAL C 218 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N ILE C 220 " --> pdb=" O LEU C 166 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N SER C 168 " --> pdb=" O ILE C 220 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N SER C 222 " --> pdb=" O SER C 168 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N VAL C 246 " --> pdb=" O ILE C 219 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N LEU C 221 " --> pdb=" O VAL C 246 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N LEU C 248 " --> pdb=" O LEU C 221 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 267 through 271 removed outlier: 3.940A pdb=" N GLY C 365 " --> pdb=" O ILE C 353 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N ASN C 355 " --> pdb=" O GLN C 363 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N GLN C 363 " --> pdb=" O ASN C 355 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 397 through 402 removed outlier: 6.951A pdb=" N THR C 473 " --> pdb=" O LEU C 398 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N ILE C 400 " --> pdb=" O THR C 473 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N GLU C 475 " --> pdb=" O ILE C 400 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N THR C 402 " --> pdb=" O GLU C 475 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N HIS C 477 " --> pdb=" O THR C 402 " (cutoff:3.500A) No H-bonds generated for sheet with id= S Processing sheet with id= T, first strand: chain 'C' and resid 410 through 412 Processing sheet with id= U, first strand: chain 'C' and resid 487 through 489 Processing sheet with id= V, first strand: chain 'C' and resid 534 through 536 removed outlier: 3.881A pdb=" N LYS C 534 " --> pdb=" O PHE C 758 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'C' and resid 728 through 732 removed outlier: 3.749A pdb=" N ILE C 540 " --> pdb=" O THR C 749 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'D' and resid 63 through 66 removed outlier: 6.512A pdb=" N GLY D 92 " --> pdb=" O ALA D 33 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N VAL D 35 " --> pdb=" O GLY D 92 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N VAL D 94 " --> pdb=" O VAL D 35 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N PHE D 95 " --> pdb=" O PRO D 118 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N LEU D 120 " --> pdb=" O PHE D 95 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'D' and resid 198 through 201 removed outlier: 9.320A pdb=" N LEU D 199 " --> pdb=" O PHE D 165 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N VAL D 167 " --> pdb=" O LEU D 199 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N LEU D 201 " --> pdb=" O VAL D 167 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N THR D 169 " --> pdb=" O LEU D 201 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N VAL D 223 " --> pdb=" O ALA D 166 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N ILE D 168 " --> pdb=" O VAL D 223 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N VAL D 225 " --> pdb=" O ILE D 168 " (cutoff:3.500A) removed outlier: 8.153A pdb=" N SER D 170 " --> pdb=" O VAL D 225 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N TYR D 227 " --> pdb=" O SER D 170 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N VAL D 251 " --> pdb=" O LEU D 224 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N ALA D 226 " --> pdb=" O VAL D 251 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LEU D 253 " --> pdb=" O ALA D 226 " (cutoff:3.500A) No H-bonds generated for sheet with id= Y Processing sheet with id= Z, first strand: chain 'D' and resid 274 through 278 removed outlier: 6.034A pdb=" N ALA D 362 " --> pdb=" O MET D 371 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N MET D 371 " --> pdb=" O ALA D 362 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'D' and resid 402 through 407 removed outlier: 6.616A pdb=" N SER D 472 " --> pdb=" O LEU D 403 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N VAL D 405 " --> pdb=" O SER D 472 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ASP D 474 " --> pdb=" O VAL D 405 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N THR D 407 " --> pdb=" O ASP D 474 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N TYR D 476 " --> pdb=" O THR D 407 " (cutoff:3.500A) No H-bonds generated for sheet with id= AA Processing sheet with id= AB, first strand: chain 'D' and resid 415 through 418 Processing sheet with id= AC, first strand: chain 'D' and resid 527 through 529 removed outlier: 4.163A pdb=" N VAL D 527 " --> pdb=" O TYR D 759 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'D' and resid 531 through 534 661 hydrogen bonds defined for protein. 1788 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.49 Time building geometry restraints manager: 9.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.87 - 1.06: 1 1.06 - 1.25: 3032 1.25 - 1.44: 6301 1.44 - 1.63: 12257 1.63 - 1.82: 160 Bond restraints: 21751 Sorted by residual: bond pdb=" CB PRO D 323 " pdb=" CG PRO D 323 " ideal model delta sigma weight residual 1.492 0.865 0.627 5.00e-02 4.00e+02 1.57e+02 bond pdb=" C24 IWB B 904 " pdb=" N6 IWB B 904 " ideal model delta sigma weight residual 1.498 1.349 0.149 2.00e-02 2.50e+03 5.54e+01 bond pdb=" CG PRO D 323 " pdb=" CD PRO D 323 " ideal model delta sigma weight residual 1.503 1.290 0.213 3.40e-02 8.65e+02 3.94e+01 bond pdb=" C7 IWB B 904 " pdb=" N6 IWB B 904 " ideal model delta sigma weight residual 1.585 1.461 0.124 2.00e-02 2.50e+03 3.87e+01 bond pdb=" C22 IWB B 904 " pdb=" C24 IWB B 904 " ideal model delta sigma weight residual 1.396 1.484 -0.088 2.00e-02 2.50e+03 1.95e+01 ... (remaining 21746 not shown) Histogram of bond angle deviations from ideal: 75.43 - 96.21: 2 96.21 - 116.99: 15879 116.99 - 137.77: 13633 137.77 - 158.55: 0 158.55 - 179.32: 1 Bond angle restraints: 29515 Sorted by residual: angle pdb=" CB PRO D 323 " pdb=" CG PRO D 323 " pdb=" CD PRO D 323 " ideal model delta sigma weight residual 106.10 179.32 -73.22 3.20e+00 9.77e-02 5.24e+02 angle pdb=" N PRO D 323 " pdb=" CD PRO D 323 " pdb=" CG PRO D 323 " ideal model delta sigma weight residual 103.20 79.84 23.36 1.50e+00 4.44e-01 2.42e+02 angle pdb=" CA PRO D 323 " pdb=" CB PRO D 323 " pdb=" CG PRO D 323 " ideal model delta sigma weight residual 104.50 75.43 29.07 1.90e+00 2.77e-01 2.34e+02 angle pdb=" CA PRO D 323 " pdb=" N PRO D 323 " pdb=" CD PRO D 323 " ideal model delta sigma weight residual 112.00 101.99 10.01 1.40e+00 5.10e-01 5.11e+01 angle pdb=" C1 IWB B 904 " pdb=" C2 IWB B 904 " pdb=" C3 IWB B 904 " ideal model delta sigma weight residual 146.14 130.60 15.54 3.00e+00 1.11e-01 2.68e+01 ... (remaining 29510 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.92: 12310 20.92 - 41.84: 1081 41.84 - 62.76: 253 62.76 - 83.68: 56 83.68 - 104.60: 19 Dihedral angle restraints: 13719 sinusoidal: 6178 harmonic: 7541 Sorted by residual: dihedral pdb=" CB CYS D 743 " pdb=" SG CYS D 743 " pdb=" SG CYS D 798 " pdb=" CB CYS D 798 " ideal model delta sinusoidal sigma weight residual -86.00 -147.80 61.80 1 1.00e+01 1.00e-02 5.06e+01 dihedral pdb=" CA LYS D 133 " pdb=" C LYS D 133 " pdb=" N GLU D 134 " pdb=" CA GLU D 134 " ideal model delta harmonic sigma weight residual 180.00 153.49 26.51 0 5.00e+00 4.00e-02 2.81e+01 dihedral pdb=" N PRO D 323 " pdb=" CG PRO D 323 " pdb=" CD PRO D 323 " pdb=" CB PRO D 323 " ideal model delta sinusoidal sigma weight residual 30.00 96.86 -66.86 1 1.50e+01 4.44e-03 2.59e+01 ... (remaining 13716 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.139: 3421 0.139 - 0.277: 26 0.277 - 0.416: 2 0.416 - 0.554: 0 0.554 - 0.693: 1 Chirality restraints: 3450 Sorted by residual: chirality pdb=" C1 MAN K 3 " pdb=" O4 NAG K 2 " pdb=" C2 MAN K 3 " pdb=" O5 MAN K 3 " both_signs ideal model delta sigma weight residual False 2.40 2.10 0.30 2.00e-02 2.50e+03 2.25e+02 chirality pdb=" C1 NAG K 1 " pdb=" ND2 ASN A 368 " pdb=" C2 NAG K 1 " pdb=" O5 NAG K 1 " both_signs ideal model delta sigma weight residual False -2.40 -3.09 0.69 2.00e-01 2.50e+01 1.20e+01 chirality pdb=" C1 NAG N 2 " pdb=" O4 NAG N 1 " pdb=" C2 NAG N 2 " pdb=" O5 NAG N 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.33 -0.07 2.00e-02 2.50e+03 1.13e+01 ... (remaining 3447 not shown) Planarity restraints: 3759 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG K 1 " 0.322 2.00e-02 2.50e+03 2.74e-01 9.41e+02 pdb=" C7 NAG K 1 " -0.074 2.00e-02 2.50e+03 pdb=" C8 NAG K 1 " 0.008 2.00e-02 2.50e+03 pdb=" N2 NAG K 1 " -0.470 2.00e-02 2.50e+03 pdb=" O7 NAG K 1 " 0.215 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG H 2 " 0.080 2.00e-02 2.50e+03 6.59e-02 5.43e+01 pdb=" C7 NAG H 2 " -0.021 2.00e-02 2.50e+03 pdb=" C8 NAG H 2 " 0.061 2.00e-02 2.50e+03 pdb=" N2 NAG H 2 " -0.105 2.00e-02 2.50e+03 pdb=" O7 NAG H 2 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG K 2 " 0.070 2.00e-02 2.50e+03 5.84e-02 4.27e+01 pdb=" C7 NAG K 2 " -0.016 2.00e-02 2.50e+03 pdb=" C8 NAG K 2 " -0.020 2.00e-02 2.50e+03 pdb=" N2 NAG K 2 " -0.091 2.00e-02 2.50e+03 pdb=" O7 NAG K 2 " 0.057 2.00e-02 2.50e+03 ... (remaining 3756 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.40: 43 2.40 - 3.02: 12825 3.02 - 3.65: 30760 3.65 - 4.27: 47385 4.27 - 4.90: 80383 Nonbonded interactions: 171396 Sorted by model distance: nonbonded pdb=" O SER D 509 " pdb=" N GLU D 903 " model vdw 1.773 2.520 nonbonded pdb=" OD2 ASP D 729 " pdb=" OH TYR D 759 " model vdw 2.046 2.440 nonbonded pdb=" O SER B 509 " pdb=" N GLU B 903 " model vdw 2.071 2.520 nonbonded pdb=" ND2 ASN B 256 " pdb=" O VAL B 276 " model vdw 2.084 2.520 nonbonded pdb=" NH1 ARG D 516 " pdb=" OXT GLU D 903 " model vdw 2.092 2.520 ... (remaining 171391 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain '3' selection = chain '5' selection = chain 'N' selection = chain 'P' selection = chain 'T' selection = chain 'W' selection = chain 'e' selection = chain 'k' selection = chain 'm' selection = chain 'r' selection = chain 't' selection = chain 'v' } ncs_group { reference = chain 'A' selection = (chain 'C' and (resid 25 through 545 or resid 663 through 794 or resid 902 throu \ gh 906)) } ncs_group { reference = (chain 'B' and (resid 29 through 537 or resid 658 through 799 or resid 902)) selection = (chain 'D' and (resid 29 through 799 or resid 901)) } ncs_group { reference = chain 'E' selection = chain 'H' selection = chain 'K' selection = chain 'b' selection = chain 'y' } 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: 1.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 6.510 Check model and map are aligned: 0.350 Set scattering table: 0.210 Process input model: 56.290 Find NCS groups from input model: 1.490 Set up NCS constraints: 0.260 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:13.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 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 : 0.007 0.627 21751 Z= 0.541 Angle : 0.869 73.224 29515 Z= 0.407 Chirality : 0.050 0.693 3450 Planarity : 0.007 0.274 3729 Dihedral : 16.776 104.599 8835 Min Nonbonded Distance : 1.773 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.35 % Favored : 94.42 % Rotamer: Outliers : 0.13 % Allowed : 22.66 % Favored : 77.20 % 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: -0.63 (0.16), residues: 2600 helix: 1.31 (0.17), residues: 947 sheet: -1.00 (0.24), residues: 455 loop : -1.63 (0.17), residues: 1198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 768 HIS 0.008 0.001 HIS A 780 PHE 0.017 0.002 PHE C 533 TYR 0.017 0.001 TYR D 476 ARG 0.006 0.001 ARG B 318 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5200 Ramachandran restraints generated. 2600 Oldfield, 0 Emsley, 2600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5200 Ramachandran restraints generated. 2600 Oldfield, 0 Emsley, 2600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 97 time to evaluate : 2.524 Fit side-chains REVERT: C 101 HIS cc_start: 0.6562 (m90) cc_final: 0.6113 (t70) outliers start: 3 outliers final: 0 residues processed: 100 average time/residue: 1.3322 time to fit residues: 153.6599 Evaluate side-chains 92 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 2.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 219 optimal weight: 0.8980 chunk 197 optimal weight: 7.9990 chunk 109 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 132 optimal weight: 0.7980 chunk 105 optimal weight: 0.8980 chunk 203 optimal weight: 0.9980 chunk 78 optimal weight: 0.6980 chunk 123 optimal weight: 0.9990 chunk 151 optimal weight: 3.9990 chunk 236 optimal weight: 6.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.0447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 21751 Z= 0.185 Angle : 0.536 12.465 29515 Z= 0.264 Chirality : 0.043 0.242 3450 Planarity : 0.004 0.078 3729 Dihedral : 8.078 93.059 3943 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.19 % Favored : 94.62 % Rotamer: Outliers : 2.18 % Allowed : 20.70 % Favored : 77.11 % 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: -0.53 (0.17), residues: 2600 helix: 1.45 (0.17), residues: 948 sheet: -1.00 (0.24), residues: 457 loop : -1.60 (0.18), residues: 1195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 768 HIS 0.005 0.001 HIS A 449 PHE 0.014 0.001 PHE C 458 TYR 0.012 0.001 TYR D 476 ARG 0.003 0.000 ARG B 709 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5200 Ramachandran restraints generated. 2600 Oldfield, 0 Emsley, 2600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5200 Ramachandran restraints generated. 2600 Oldfield, 0 Emsley, 2600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 100 time to evaluate : 2.494 Fit side-chains REVERT: B 287 GLN cc_start: 0.8078 (OUTLIER) cc_final: 0.7539 (mt0) REVERT: B 390 TYR cc_start: 0.7518 (OUTLIER) cc_final: 0.7114 (p90) REVERT: B 505 MET cc_start: 0.9239 (ptp) cc_final: 0.8918 (ptt) REVERT: C 101 HIS cc_start: 0.6576 (m90) cc_final: 0.6106 (t70) REVERT: D 745 LEU cc_start: 0.7462 (OUTLIER) cc_final: 0.7244 (mp) REVERT: D 903 GLU cc_start: 0.6451 (mm-30) cc_final: 0.6231 (mm-30) outliers start: 49 outliers final: 15 residues processed: 138 average time/residue: 1.1905 time to fit residues: 192.0538 Evaluate side-chains 111 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 93 time to evaluate : 2.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 287 GLN Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 390 TYR Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain C residue 56 TRP Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 527 VAL Chi-restraints excluded: chain D residue 745 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 131 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 196 optimal weight: 6.9990 chunk 160 optimal weight: 8.9990 chunk 65 optimal weight: 5.9990 chunk 236 optimal weight: 0.9990 chunk 255 optimal weight: 0.0070 chunk 210 optimal weight: 4.9990 chunk 234 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 189 optimal weight: 2.9990 overall best weight: 2.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 742 GLN C 146 HIS C 509 GLN D 148 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.0751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 21751 Z= 0.342 Angle : 0.578 11.509 29515 Z= 0.287 Chirality : 0.046 0.249 3450 Planarity : 0.004 0.079 3729 Dihedral : 7.197 94.646 3943 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.85 % Favored : 93.96 % Rotamer: Outliers : 3.43 % Allowed : 20.57 % Favored : 76.00 % 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: -0.62 (0.17), residues: 2600 helix: 1.32 (0.17), residues: 948 sheet: -1.14 (0.23), residues: 476 loop : -1.55 (0.18), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 375 HIS 0.006 0.001 HIS A 780 PHE 0.018 0.002 PHE C 533 TYR 0.012 0.001 TYR C 410 ARG 0.005 0.000 ARG D 318 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5200 Ramachandran restraints generated. 2600 Oldfield, 0 Emsley, 2600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5200 Ramachandran restraints generated. 2600 Oldfield, 0 Emsley, 2600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 99 time to evaluate : 2.408 Fit side-chains revert: symmetry clash REVERT: A 118 VAL cc_start: 0.8461 (OUTLIER) cc_final: 0.8238 (m) REVERT: A 155 MET cc_start: 0.7919 (mtm) cc_final: 0.7698 (mtp) REVERT: A 786 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7730 (mp0) REVERT: B 287 GLN cc_start: 0.8128 (OUTLIER) cc_final: 0.7623 (mt0) REVERT: B 390 TYR cc_start: 0.7632 (OUTLIER) cc_final: 0.7261 (p90) REVERT: B 505 MET cc_start: 0.9243 (ptp) cc_final: 0.8908 (ptt) REVERT: B 720 MET cc_start: 0.8138 (OUTLIER) cc_final: 0.7625 (mpt) REVERT: C 101 HIS cc_start: 0.6798 (m90) cc_final: 0.6076 (t70) REVERT: C 240 MET cc_start: 0.9067 (mtp) cc_final: 0.8642 (ttm) REVERT: D 218 GLN cc_start: 0.8336 (OUTLIER) cc_final: 0.7553 (mt0) REVERT: D 745 LEU cc_start: 0.7676 (OUTLIER) cc_final: 0.7449 (mp) outliers start: 77 outliers final: 36 residues processed: 166 average time/residue: 1.1014 time to fit residues: 215.8220 Evaluate side-chains 133 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 90 time to evaluate : 2.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 786 GLU Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 287 GLN Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 390 TYR Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 720 MET Chi-restraints excluded: chain B residue 756 THR Chi-restraints excluded: chain C residue 56 TRP Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain C residue 427 ASN Chi-restraints excluded: chain C residue 702 MET Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 765 ASP Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 218 GLN Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 386 VAL Chi-restraints excluded: chain D residue 527 VAL Chi-restraints excluded: chain D residue 660 VAL Chi-restraints excluded: chain D residue 685 ASN Chi-restraints excluded: chain D residue 716 THR Chi-restraints excluded: chain D residue 724 ASP Chi-restraints excluded: chain D residue 745 LEU Chi-restraints excluded: chain D residue 747 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 233 optimal weight: 0.1980 chunk 177 optimal weight: 0.9980 chunk 122 optimal weight: 0.7980 chunk 26 optimal weight: 0.5980 chunk 112 optimal weight: 2.9990 chunk 158 optimal weight: 7.9990 chunk 237 optimal weight: 1.9990 chunk 251 optimal weight: 0.9980 chunk 124 optimal weight: 3.9990 chunk 224 optimal weight: 0.0980 chunk 67 optimal weight: 4.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 742 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.0910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 21751 Z= 0.147 Angle : 0.514 14.469 29515 Z= 0.252 Chirality : 0.043 0.248 3450 Planarity : 0.004 0.079 3729 Dihedral : 6.359 93.745 3943 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.27 % Favored : 94.54 % Rotamer: Outliers : 2.89 % Allowed : 21.24 % Favored : 75.87 % 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 (0.17), residues: 2600 helix: 1.52 (0.17), residues: 945 sheet: -0.94 (0.24), residues: 459 loop : -1.49 (0.18), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 381 HIS 0.004 0.001 HIS A 449 PHE 0.013 0.001 PHE C 458 TYR 0.012 0.001 TYR D 476 ARG 0.006 0.000 ARG D 318 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5200 Ramachandran restraints generated. 2600 Oldfield, 0 Emsley, 2600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5200 Ramachandran restraints generated. 2600 Oldfield, 0 Emsley, 2600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 101 time to evaluate : 2.578 Fit side-chains REVERT: A 786 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7637 (mp0) REVERT: B 390 TYR cc_start: 0.7480 (OUTLIER) cc_final: 0.7002 (p90) REVERT: B 744 LYS cc_start: 0.7997 (mtmm) cc_final: 0.7759 (mtmt) REVERT: C 101 HIS cc_start: 0.6656 (m90) cc_final: 0.6038 (t70) REVERT: C 240 MET cc_start: 0.9036 (mtp) cc_final: 0.8632 (ttm) REVERT: C 246 VAL cc_start: 0.9031 (OUTLIER) cc_final: 0.8698 (m) REVERT: D 89 ARG cc_start: 0.7656 (ptm160) cc_final: 0.7172 (ttt90) REVERT: D 98 ASN cc_start: 0.7885 (OUTLIER) cc_final: 0.7332 (p0) REVERT: D 745 LEU cc_start: 0.7559 (OUTLIER) cc_final: 0.7334 (mp) outliers start: 65 outliers final: 25 residues processed: 157 average time/residue: 1.1228 time to fit residues: 208.3095 Evaluate side-chains 124 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 94 time to evaluate : 2.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 786 GLU Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 390 TYR Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain C residue 56 TRP Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 98 ASN Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 417 GLU Chi-restraints excluded: chain D residue 423 THR Chi-restraints excluded: chain D residue 450 THR Chi-restraints excluded: chain D residue 527 VAL Chi-restraints excluded: chain D residue 660 VAL Chi-restraints excluded: chain D residue 724 ASP Chi-restraints excluded: chain D residue 745 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 209 optimal weight: 5.9990 chunk 142 optimal weight: 0.7980 chunk 3 optimal weight: 3.9990 chunk 187 optimal weight: 0.8980 chunk 103 optimal weight: 2.9990 chunk 214 optimal weight: 4.9990 chunk 173 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 128 optimal weight: 0.5980 chunk 225 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 742 GLN D 429 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.1011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21751 Z= 0.214 Angle : 0.526 10.457 29515 Z= 0.259 Chirality : 0.044 0.253 3450 Planarity : 0.004 0.078 3729 Dihedral : 6.052 92.582 3943 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.54 % Favored : 94.27 % Rotamer: Outliers : 2.72 % Allowed : 21.86 % Favored : 75.42 % 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: -0.43 (0.17), residues: 2600 helix: 1.51 (0.17), residues: 945 sheet: -1.00 (0.24), residues: 469 loop : -1.47 (0.18), residues: 1186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 375 HIS 0.004 0.001 HIS A 449 PHE 0.015 0.001 PHE C 458 TYR 0.011 0.001 TYR D 476 ARG 0.004 0.000 ARG D 488 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5200 Ramachandran restraints generated. 2600 Oldfield, 0 Emsley, 2600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5200 Ramachandran restraints generated. 2600 Oldfield, 0 Emsley, 2600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 97 time to evaluate : 2.567 Fit side-chains REVERT: A 118 VAL cc_start: 0.8386 (OUTLIER) cc_final: 0.8163 (m) REVERT: A 786 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7651 (mp0) REVERT: B 287 GLN cc_start: 0.8075 (OUTLIER) cc_final: 0.7521 (mt0) REVERT: B 390 TYR cc_start: 0.7483 (OUTLIER) cc_final: 0.7050 (p90) REVERT: B 505 MET cc_start: 0.9215 (ptp) cc_final: 0.8904 (ptt) REVERT: B 678 PHE cc_start: 0.6732 (OUTLIER) cc_final: 0.6522 (t80) REVERT: C 101 HIS cc_start: 0.6725 (m90) cc_final: 0.6010 (t70) REVERT: C 240 MET cc_start: 0.9065 (mtp) cc_final: 0.8669 (ttm) REVERT: C 246 VAL cc_start: 0.9043 (OUTLIER) cc_final: 0.8725 (m) REVERT: C 680 ILE cc_start: 0.8100 (mm) cc_final: 0.7899 (tt) REVERT: D 98 ASN cc_start: 0.7890 (OUTLIER) cc_final: 0.7339 (p0) REVERT: D 318 ARG cc_start: 0.8493 (ptt-90) cc_final: 0.8287 (ppt90) REVERT: D 371 MET cc_start: 0.8704 (OUTLIER) cc_final: 0.7892 (tmm) REVERT: D 745 LEU cc_start: 0.7592 (OUTLIER) cc_final: 0.7353 (mp) outliers start: 61 outliers final: 31 residues processed: 150 average time/residue: 1.1638 time to fit residues: 204.8450 Evaluate side-chains 129 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 89 time to evaluate : 2.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 GLN Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 786 GLU Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 287 GLN Chi-restraints excluded: chain B residue 390 TYR Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 678 PHE Chi-restraints excluded: chain C residue 56 TRP Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 765 ASP Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 98 ASN Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 371 MET Chi-restraints excluded: chain D residue 417 GLU Chi-restraints excluded: chain D residue 423 THR Chi-restraints excluded: chain D residue 429 ASN Chi-restraints excluded: chain D residue 450 THR Chi-restraints excluded: chain D residue 527 VAL Chi-restraints excluded: chain D residue 660 VAL Chi-restraints excluded: chain D residue 724 ASP Chi-restraints excluded: chain D residue 745 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 84 optimal weight: 0.9980 chunk 226 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 chunk 147 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 251 optimal weight: 0.3980 chunk 208 optimal weight: 4.9990 chunk 116 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 83 optimal weight: 0.9990 chunk 132 optimal weight: 0.2980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 742 GLN B 768 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.1108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21751 Z= 0.169 Angle : 0.507 10.233 29515 Z= 0.250 Chirality : 0.043 0.251 3450 Planarity : 0.004 0.078 3729 Dihedral : 5.840 91.693 3943 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.42 % Favored : 94.38 % Rotamer: Outliers : 2.72 % Allowed : 22.48 % Favored : 74.80 % 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 (0.17), residues: 2600 helix: 1.49 (0.17), residues: 954 sheet: -0.96 (0.24), residues: 468 loop : -1.49 (0.18), residues: 1178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 381 HIS 0.004 0.001 HIS A 449 PHE 0.013 0.001 PHE C 458 TYR 0.011 0.001 TYR D 476 ARG 0.004 0.000 ARG D 488 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5200 Ramachandran restraints generated. 2600 Oldfield, 0 Emsley, 2600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5200 Ramachandran restraints generated. 2600 Oldfield, 0 Emsley, 2600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 99 time to evaluate : 2.370 Fit side-chains REVERT: A 118 VAL cc_start: 0.8376 (OUTLIER) cc_final: 0.8169 (m) REVERT: A 786 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7667 (mp0) REVERT: B 287 GLN cc_start: 0.8059 (OUTLIER) cc_final: 0.7496 (mt0) REVERT: B 390 TYR cc_start: 0.7494 (OUTLIER) cc_final: 0.7063 (p90) REVERT: C 101 HIS cc_start: 0.6725 (m90) cc_final: 0.6017 (t70) REVERT: C 115 ARG cc_start: 0.9140 (OUTLIER) cc_final: 0.8619 (mpt180) REVERT: C 240 MET cc_start: 0.9048 (mtp) cc_final: 0.8667 (ttm) REVERT: C 246 VAL cc_start: 0.9039 (OUTLIER) cc_final: 0.8715 (m) REVERT: D 89 ARG cc_start: 0.7473 (ptm160) cc_final: 0.6995 (ttt90) REVERT: D 98 ASN cc_start: 0.7865 (OUTLIER) cc_final: 0.7337 (p0) REVERT: D 371 MET cc_start: 0.8689 (OUTLIER) cc_final: 0.7919 (tmm) REVERT: D 745 LEU cc_start: 0.7538 (OUTLIER) cc_final: 0.7297 (mp) outliers start: 61 outliers final: 33 residues processed: 153 average time/residue: 1.1775 time to fit residues: 210.4780 Evaluate side-chains 132 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 90 time to evaluate : 2.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 399 LYS Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 436 CYS Chi-restraints excluded: chain A residue 786 GLU Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 287 GLN Chi-restraints excluded: chain B residue 390 TYR Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain C residue 56 TRP Chi-restraints excluded: chain C residue 115 ARG Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 765 ASP Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 98 ASN Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 371 MET Chi-restraints excluded: chain D residue 380 LEU Chi-restraints excluded: chain D residue 417 GLU Chi-restraints excluded: chain D residue 423 THR Chi-restraints excluded: chain D residue 450 THR Chi-restraints excluded: chain D residue 527 VAL Chi-restraints excluded: chain D residue 660 VAL Chi-restraints excluded: chain D residue 716 THR Chi-restraints excluded: chain D residue 724 ASP Chi-restraints excluded: chain D residue 745 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 242 optimal weight: 0.2980 chunk 28 optimal weight: 0.9980 chunk 143 optimal weight: 4.9990 chunk 183 optimal weight: 0.0470 chunk 142 optimal weight: 0.9980 chunk 211 optimal weight: 10.0000 chunk 140 optimal weight: 2.9990 chunk 250 optimal weight: 0.9980 chunk 156 optimal weight: 4.9990 chunk 152 optimal weight: 0.7980 chunk 115 optimal weight: 5.9990 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 742 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.1224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 21751 Z= 0.156 Angle : 0.496 10.093 29515 Z= 0.244 Chirality : 0.042 0.249 3450 Planarity : 0.004 0.078 3729 Dihedral : 5.562 89.385 3943 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.50 % Favored : 94.31 % Rotamer: Outliers : 2.58 % Allowed : 22.84 % Favored : 74.58 % 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: -0.37 (0.17), residues: 2600 helix: 1.53 (0.17), residues: 955 sheet: -0.94 (0.24), residues: 466 loop : -1.46 (0.18), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 381 HIS 0.008 0.001 HIS C 709 PHE 0.013 0.001 PHE C 458 TYR 0.011 0.001 TYR D 476 ARG 0.006 0.000 ARG C 36 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5200 Ramachandran restraints generated. 2600 Oldfield, 0 Emsley, 2600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5200 Ramachandran restraints generated. 2600 Oldfield, 0 Emsley, 2600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 96 time to evaluate : 2.561 Fit side-chains REVERT: A 118 VAL cc_start: 0.8383 (OUTLIER) cc_final: 0.8161 (m) REVERT: A 786 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7689 (mp0) REVERT: B 203 LEU cc_start: 0.7970 (OUTLIER) cc_final: 0.7678 (mt) REVERT: B 287 GLN cc_start: 0.8040 (OUTLIER) cc_final: 0.7469 (mt0) REVERT: B 390 TYR cc_start: 0.7478 (OUTLIER) cc_final: 0.7049 (p90) REVERT: C 101 HIS cc_start: 0.6747 (m90) cc_final: 0.6014 (t70) REVERT: C 115 ARG cc_start: 0.9129 (OUTLIER) cc_final: 0.8600 (mpt180) REVERT: C 196 GLN cc_start: 0.8922 (OUTLIER) cc_final: 0.8492 (mt0) REVERT: C 240 MET cc_start: 0.9028 (mtp) cc_final: 0.8653 (ttm) REVERT: C 246 VAL cc_start: 0.9026 (OUTLIER) cc_final: 0.8723 (m) REVERT: C 437 THR cc_start: 0.8575 (OUTLIER) cc_final: 0.8016 (p) REVERT: D 89 ARG cc_start: 0.7379 (ptm160) cc_final: 0.6776 (ttt180) REVERT: D 745 LEU cc_start: 0.7488 (OUTLIER) cc_final: 0.7233 (mp) outliers start: 58 outliers final: 34 residues processed: 147 average time/residue: 1.2310 time to fit residues: 211.1239 Evaluate side-chains 134 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 90 time to evaluate : 2.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 436 CYS Chi-restraints excluded: chain A residue 786 GLU Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 287 GLN Chi-restraints excluded: chain B residue 390 TYR Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain C residue 56 TRP Chi-restraints excluded: chain C residue 115 ARG Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 196 GLN Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 380 LEU Chi-restraints excluded: chain D residue 386 VAL Chi-restraints excluded: chain D residue 417 GLU Chi-restraints excluded: chain D residue 423 THR Chi-restraints excluded: chain D residue 429 ASN Chi-restraints excluded: chain D residue 450 THR Chi-restraints excluded: chain D residue 527 VAL Chi-restraints excluded: chain D residue 660 VAL Chi-restraints excluded: chain D residue 699 MET Chi-restraints excluded: chain D residue 745 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 155 optimal weight: 0.9980 chunk 100 optimal weight: 0.0070 chunk 149 optimal weight: 0.5980 chunk 75 optimal weight: 0.7980 chunk 49 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 chunk 159 optimal weight: 0.0770 chunk 170 optimal weight: 0.0010 chunk 123 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 196 optimal weight: 0.0270 overall best weight: 0.1420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN A 742 GLN C 509 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.1386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 21751 Z= 0.131 Angle : 0.491 11.220 29515 Z= 0.240 Chirality : 0.042 0.245 3450 Planarity : 0.004 0.077 3729 Dihedral : 5.239 86.331 3943 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.65 % Favored : 94.19 % Rotamer: Outliers : 2.00 % Allowed : 23.24 % Favored : 74.76 % 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: -0.26 (0.17), residues: 2600 helix: 1.65 (0.17), residues: 954 sheet: -0.88 (0.24), residues: 480 loop : -1.42 (0.18), residues: 1166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 381 HIS 0.003 0.000 HIS A 449 PHE 0.011 0.001 PHE C 458 TYR 0.011 0.001 TYR D 476 ARG 0.004 0.000 ARG C 36 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5200 Ramachandran restraints generated. 2600 Oldfield, 0 Emsley, 2600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5200 Ramachandran restraints generated. 2600 Oldfield, 0 Emsley, 2600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 105 time to evaluate : 2.582 Fit side-chains REVERT: A 118 VAL cc_start: 0.8384 (OUTLIER) cc_final: 0.8167 (m) REVERT: A 786 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7688 (mp0) REVERT: B 390 TYR cc_start: 0.7383 (OUTLIER) cc_final: 0.6873 (p90) REVERT: C 40 GLN cc_start: 0.8242 (tm-30) cc_final: 0.8029 (tm-30) REVERT: C 101 HIS cc_start: 0.6709 (m90) cc_final: 0.6006 (t70) REVERT: C 115 ARG cc_start: 0.9102 (OUTLIER) cc_final: 0.8625 (mpt180) REVERT: C 240 MET cc_start: 0.9012 (mtp) cc_final: 0.8587 (ttm) REVERT: C 246 VAL cc_start: 0.8961 (OUTLIER) cc_final: 0.8720 (m) REVERT: C 437 THR cc_start: 0.8513 (OUTLIER) cc_final: 0.8007 (p) outliers start: 45 outliers final: 23 residues processed: 144 average time/residue: 1.2350 time to fit residues: 206.8944 Evaluate side-chains 121 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 92 time to evaluate : 2.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 786 GLU Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 390 TYR Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain C residue 56 TRP Chi-restraints excluded: chain C residue 115 ARG Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 380 LEU Chi-restraints excluded: chain D residue 386 VAL Chi-restraints excluded: chain D residue 417 GLU Chi-restraints excluded: chain D residue 423 THR Chi-restraints excluded: chain D residue 429 ASN Chi-restraints excluded: chain D residue 660 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 227 optimal weight: 0.3980 chunk 240 optimal weight: 2.9990 chunk 219 optimal weight: 2.9990 chunk 233 optimal weight: 0.1980 chunk 140 optimal weight: 0.7980 chunk 101 optimal weight: 0.0870 chunk 183 optimal weight: 0.0980 chunk 71 optimal weight: 2.9990 chunk 211 optimal weight: 5.9990 chunk 220 optimal weight: 10.0000 chunk 232 optimal weight: 0.6980 overall best weight: 0.2958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 686 GLN A 742 GLN ** C 709 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.1466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 21751 Z= 0.130 Angle : 0.498 16.035 29515 Z= 0.241 Chirality : 0.042 0.246 3450 Planarity : 0.004 0.076 3729 Dihedral : 5.083 83.042 3943 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.27 % Favored : 94.58 % Rotamer: Outliers : 1.65 % Allowed : 23.86 % Favored : 74.49 % 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 (0.17), residues: 2600 helix: 1.68 (0.17), residues: 956 sheet: -0.77 (0.24), residues: 471 loop : -1.41 (0.18), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 768 HIS 0.003 0.000 HIS A 449 PHE 0.011 0.001 PHE C 458 TYR 0.011 0.001 TYR D 476 ARG 0.008 0.000 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5200 Ramachandran restraints generated. 2600 Oldfield, 0 Emsley, 2600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5200 Ramachandran restraints generated. 2600 Oldfield, 0 Emsley, 2600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 98 time to evaluate : 2.368 Fit side-chains REVERT: A 118 VAL cc_start: 0.8400 (OUTLIER) cc_final: 0.8132 (m) REVERT: A 489 ARG cc_start: 0.5390 (OUTLIER) cc_final: 0.5165 (ttt90) REVERT: A 786 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7662 (mp0) REVERT: B 390 TYR cc_start: 0.7415 (OUTLIER) cc_final: 0.6954 (p90) REVERT: C 40 GLN cc_start: 0.8209 (tm-30) cc_final: 0.7989 (tm-30) REVERT: C 101 HIS cc_start: 0.6739 (m90) cc_final: 0.6008 (t70) REVERT: C 240 MET cc_start: 0.8955 (mtp) cc_final: 0.8565 (ttm) REVERT: C 246 VAL cc_start: 0.8934 (OUTLIER) cc_final: 0.8696 (m) REVERT: C 437 THR cc_start: 0.8556 (OUTLIER) cc_final: 0.8083 (p) REVERT: D 89 ARG cc_start: 0.7368 (ptm160) cc_final: 0.6756 (ttt180) REVERT: D 395 GLN cc_start: 0.6872 (mm-40) cc_final: 0.6597 (mm-40) outliers start: 37 outliers final: 27 residues processed: 132 average time/residue: 1.2861 time to fit residues: 195.9677 Evaluate side-chains 124 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 91 time to evaluate : 2.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 489 ARG Chi-restraints excluded: chain A residue 786 GLU Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 390 TYR Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain C residue 56 TRP Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 380 LEU Chi-restraints excluded: chain D residue 386 VAL Chi-restraints excluded: chain D residue 417 GLU Chi-restraints excluded: chain D residue 423 THR Chi-restraints excluded: chain D residue 429 ASN Chi-restraints excluded: chain D residue 527 VAL Chi-restraints excluded: chain D residue 660 VAL Chi-restraints excluded: chain D residue 724 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 153 optimal weight: 1.9990 chunk 246 optimal weight: 0.9990 chunk 150 optimal weight: 0.7980 chunk 117 optimal weight: 0.6980 chunk 171 optimal weight: 6.9990 chunk 259 optimal weight: 2.9990 chunk 238 optimal weight: 1.9990 chunk 206 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 chunk 159 optimal weight: 0.9990 chunk 126 optimal weight: 2.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 HIS A 742 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 21751 Z= 0.185 Angle : 0.519 16.464 29515 Z= 0.251 Chirality : 0.043 0.251 3450 Planarity : 0.004 0.076 3729 Dihedral : 5.052 77.784 3943 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.42 % Favored : 94.42 % Rotamer: Outliers : 1.74 % Allowed : 23.95 % Favored : 74.31 % 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: -0.21 (0.17), residues: 2600 helix: 1.65 (0.17), residues: 954 sheet: -0.77 (0.24), residues: 471 loop : -1.40 (0.18), residues: 1175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 381 HIS 0.004 0.001 HIS A 449 PHE 0.013 0.001 PHE C 458 TYR 0.011 0.001 TYR D 476 ARG 0.006 0.000 ARG B 49 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5200 Ramachandran restraints generated. 2600 Oldfield, 0 Emsley, 2600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5200 Ramachandran restraints generated. 2600 Oldfield, 0 Emsley, 2600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 92 time to evaluate : 2.802 Fit side-chains REVERT: A 118 VAL cc_start: 0.8418 (OUTLIER) cc_final: 0.8148 (m) REVERT: A 489 ARG cc_start: 0.5449 (OUTLIER) cc_final: 0.5244 (ttt90) REVERT: A 786 GLU cc_start: 0.7888 (OUTLIER) cc_final: 0.7672 (mp0) REVERT: B 390 TYR cc_start: 0.7430 (OUTLIER) cc_final: 0.6963 (p90) REVERT: B 743 CYS cc_start: 0.7359 (p) cc_final: 0.6724 (m) REVERT: C 40 GLN cc_start: 0.8254 (tm-30) cc_final: 0.8017 (tm-30) REVERT: C 101 HIS cc_start: 0.6682 (m90) cc_final: 0.5920 (t70) REVERT: C 240 MET cc_start: 0.9005 (mtp) cc_final: 0.8622 (ttm) REVERT: C 246 VAL cc_start: 0.9007 (OUTLIER) cc_final: 0.8718 (m) REVERT: C 437 THR cc_start: 0.8633 (OUTLIER) cc_final: 0.8207 (p) REVERT: D 89 ARG cc_start: 0.7421 (ptm160) cc_final: 0.6837 (ttt180) outliers start: 39 outliers final: 29 residues processed: 128 average time/residue: 1.2931 time to fit residues: 192.4540 Evaluate side-chains 125 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 90 time to evaluate : 2.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 489 ARG Chi-restraints excluded: chain A residue 776 ILE Chi-restraints excluded: chain A residue 786 GLU Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 390 TYR Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain C residue 56 TRP Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 380 LEU Chi-restraints excluded: chain D residue 386 VAL Chi-restraints excluded: chain D residue 417 GLU Chi-restraints excluded: chain D residue 423 THR Chi-restraints excluded: chain D residue 429 ASN Chi-restraints excluded: chain D residue 527 VAL Chi-restraints excluded: chain D residue 660 VAL Chi-restraints excluded: chain D residue 724 ASP Chi-restraints excluded: chain D residue 745 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 163 optimal weight: 4.9990 chunk 219 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 190 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 206 optimal weight: 0.9990 chunk 86 optimal weight: 0.0470 chunk 212 optimal weight: 5.9990 chunk 26 optimal weight: 0.6980 chunk 38 optimal weight: 0.5980 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 742 GLN D 395 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.114462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.082143 restraints weight = 34574.793| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 2.98 r_work: 0.2921 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 21751 Z= 0.157 Angle : 0.510 15.826 29515 Z= 0.247 Chirality : 0.042 0.249 3450 Planarity : 0.004 0.076 3729 Dihedral : 4.885 70.332 3943 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.27 % Favored : 94.58 % Rotamer: Outliers : 1.65 % Allowed : 24.04 % Favored : 74.31 % 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: -0.18 (0.17), residues: 2600 helix: 1.68 (0.17), residues: 953 sheet: -0.74 (0.24), residues: 471 loop : -1.39 (0.18), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 768 HIS 0.004 0.001 HIS A 449 PHE 0.012 0.001 PHE C 458 TYR 0.011 0.001 TYR D 476 ARG 0.006 0.000 ARG B 49 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4976.58 seconds wall clock time: 90 minutes 58.84 seconds (5458.84 seconds total)