Starting phenix.real_space_refine (version: 1.21rc1) on Tue Oct 10 19:25:36 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yfg_33789/10_2023/7yfg_33789_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yfg_33789/10_2023/7yfg_33789.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yfg_33789/10_2023/7yfg_33789.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yfg_33789/10_2023/7yfg_33789.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yfg_33789/10_2023/7yfg_33789_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yfg_33789/10_2023/7yfg_33789_neut.pdb" } resolution = 3.6 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 13413 2.51 5 N 3656 2.21 5 O 4048 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 329": "OE1" <-> "OE2" Residue "B GLU 514": "OE1" <-> "OE2" Residue "B PHE 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 689": "OE1" <-> "OE2" Residue "B GLU 741": "OE1" <-> "OE2" Residue "B GLU 790": "OE1" <-> "OE2" Residue "C GLU 192": "OE1" <-> "OE2" Residue "C GLU 251": "OE1" <-> "OE2" Residue "C GLU 737": "OE1" <-> "OE2" Residue "D GLU 102": "OE1" <-> "OE2" Residue "D PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 180": "OE1" <-> "OE2" Residue "D GLU 239": "OE1" <-> "OE2" Residue "D GLU 279": "OE1" <-> "OE2" Residue "D GLU 409": "OE1" <-> "OE2" Residue "D TYR 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 785": "OE1" <-> "OE2" Residue "D GLU 790": "OE1" <-> "OE2" Residue "B GLU 904": "OE1" <-> "OE2" Residue "D GLU 904": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 21215 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: 5048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 652, 5048 Classifications: {'peptide': 652} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 37, 'TRANS': 614} Chain breaks: 1 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 chiralities: 2 Chain: "J" 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 chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 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 chiralities: 3 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 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 chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "a" 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 chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 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 chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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 chiralities: 2 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 chiralities: 2 Chain: "q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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 chiralities: 2 Chain: "A" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 47 Unusual residues: {'NAG': 3} Classifications: {'peptide': 1, 'undetermined': 3} Modifications used: {'COO': 1} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 52 Unusual residues: {'NAG': 3} Classifications: {'peptide': 1, 'undetermined': 3} Modifications used: {'COO': 1} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "C" 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 chiralities: 4 Chain: "D" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 52 Unusual residues: {'NAG': 3} Classifications: {'peptide': 1, 'undetermined': 3} Modifications used: {'COO': 1} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 10.26, per 1000 atoms: 0.48 Number of scatterers: 21215 At special positions: 0 Unit cell: (122.094, 149.94, 133.875, 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 4048 8.00 N 3656 7.00 C 13413 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=2.03 Simple disulfide: pdb=" SG CYS A 420 " - pdb=" SG CYS A 454 " distance=2.03 Simple disulfide: pdb=" SG CYS A 436 " - pdb=" SG CYS A 455 " 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=2.03 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=2.04 Simple disulfide: pdb=" SG CYS D 433 " - pdb=" SG CYS D 454 " distance=2.04 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=1, symmetry=0 Links applied ALPHA1-4 " NAG H 2 " - " MAN H 3 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG O 1 " - " NAG O 2 " " NAG S 1 " - " NAG S 2 " " NAG X 1 " - " NAG X 2 " " NAG a 1 " - " NAG a 2 " " NAG c 1 " - " NAG c 2 " " NAG e 1 " - " NAG e 2 " " NAG g 1 " - " NAG g 2 " " NAG k 1 " - " NAG k 2 " " NAG n 1 " - " NAG n 2 " " NAG q 1 " - " NAG q 2 " " NAG v 1 " - " NAG v 2 " NAG-ASN " NAG A 901 " - " ASN A 300 " " NAG A 902 " - " ASN A 491 " " NAG A 903 " - " ASN A 440 " " NAG B 901 " - " ASN B 685 " " NAG B 902 " - " ASN B 70 " " NAG B 903 " - " ASN B 438 " " NAG C 901 " - " ASN C 300 " " NAG C 902 " - " ASN C 350 " " NAG C 903 " - " ASN C 491 " " NAG C 904 " - " ASN C 440 " " NAG D 901 " - " ASN D 685 " " NAG D 902 " - " ASN D 70 " " NAG D 903 " - " ASN D 438 " " NAG E 1 " - " ASN A 276 " " NAG G 1 " - " ASN A 771 " " NAG H 1 " - " ASN A 368 " " NAG J 1 " - " ASN A 350 " " NAG K 1 " - " ASN A 61 " " NAG M 1 " - " ASN A 203 " " NAG O 1 " - " ASN A 239 " " NAG S 1 " - " ASN A 471 " " NAG X 1 " - " ASN B 337 " " NAG a 1 " - " ASN C 61 " " NAG c 1 " - " ASN C 203 " " NAG e 1 " - " ASN C 239 " " NAG g 1 " - " ASN C 276 " " NAG k 1 " - " ASN C 771 " " NAG n 1 " - " ASN C 471 " " NAG q 1 " - " ASN C 368 " " NAG v 1 " - " ASN D 337 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 7.95 Conformation dependent library (CDL) restraints added in 2.6 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... Secondary structure from input PDB file: 86 helices and 32 sheets defined 37.8% alpha, 15.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.02 Creating SS restraints... Processing helix chain 'A' and resid 37 through 52 removed outlier: 3.503A pdb=" N MET A 41 " --> pdb=" O LYS A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 80 Processing helix chain 'A' and resid 104 through 114 removed outlier: 4.031A pdb=" N TYR A 114 " --> pdb=" O THR A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 130 Processing helix chain 'A' and resid 146 through 158 removed outlier: 3.942A pdb=" N VAL A 150 " --> pdb=" O HIS A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 187 Processing helix chain 'A' and resid 204 through 214 removed outlier: 3.767A pdb=" N GLU A 213 " --> pdb=" O MET A 209 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU A 214 " --> pdb=" O GLU A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 238 Processing helix chain 'A' and resid 250 through 254 Processing helix chain 'A' and resid 256 through 262 removed outlier: 3.985A pdb=" N ARG A 260 " --> pdb=" O GLY A 256 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N TYR A 261 " --> pdb=" O ASN A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 296 removed outlier: 3.547A pdb=" N VAL A 287 " --> pdb=" O ASP A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 299 No H-bonds generated for 'chain 'A' and resid 297 through 299' Processing helix chain 'A' and resid 317 through 327 removed outlier: 3.675A pdb=" N SER A 327 " --> pdb=" O ARG A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 471 Processing helix chain 'A' and resid 499 through 508 Processing helix chain 'A' and resid 520 through 525 Processing helix chain 'A' and resid 669 through 674 Processing helix chain 'A' and resid 687 through 695 Processing helix chain 'A' and resid 699 through 707 Processing helix chain 'A' and resid 713 through 723 Processing helix chain 'A' and resid 733 through 744 removed outlier: 3.754A pdb=" N PHE A 738 " --> pdb=" O ALA A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 782 removed outlier: 3.546A pdb=" N VAL A 772 " --> pdb=" O TRP A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 793 Processing helix chain 'B' and resid 43 through 51 removed outlier: 3.567A pdb=" N ARG B 47 " --> pdb=" O GLN B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 54 No H-bonds generated for 'chain 'B' and resid 52 through 54' Processing helix chain 'B' and resid 73 through 88 removed outlier: 3.610A pdb=" N ALA B 88 " --> pdb=" O LEU B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 116 Processing helix chain 'B' and resid 145 through 161 removed outlier: 3.611A pdb=" N GLN B 149 " --> pdb=" O SER B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 188 Processing helix chain 'B' and resid 212 through 218 removed outlier: 3.833A pdb=" N GLN B 218 " --> pdb=" O ARG B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 243 Processing helix chain 'B' and resid 280 through 283 Processing helix chain 'B' and resid 284 through 308 Processing helix chain 'B' and resid 325 through 337 removed outlier: 3.794A pdb=" N ASN B 337 " --> pdb=" O ARG B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 470 Processing helix chain 'B' and resid 492 through 500 Processing helix chain 'B' and resid 513 through 518 Processing helix chain 'B' and resid 665 through 670 Processing helix chain 'B' and resid 687 through 696 Processing helix chain 'B' and resid 696 through 707 removed outlier: 4.226A pdb=" N LYS B 705 " --> pdb=" O THR B 701 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N PHE B 706 " --> pdb=" O HIS B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 710 through 721 Processing helix chain 'B' and resid 730 through 740 Processing helix chain 'B' and resid 769 through 784 Processing helix chain 'B' and resid 784 through 794 Processing helix chain 'C' and resid 37 through 53 removed outlier: 3.539A pdb=" N MET C 41 " --> pdb=" O LYS C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 81 Processing helix chain 'C' and resid 103 through 114 removed outlier: 4.659A pdb=" N VAL C 107 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N TYR C 114 " --> pdb=" O THR C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 130 removed outlier: 3.834A pdb=" N TYR C 128 " --> pdb=" O MET C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 158 removed outlier: 3.941A pdb=" N VAL C 150 " --> pdb=" O HIS C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 186 removed outlier: 3.918A pdb=" N GLU C 186 " --> pdb=" O THR C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 213 removed outlier: 3.594A pdb=" N GLU C 210 " --> pdb=" O ALA C 206 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA C 211 " --> pdb=" O LEU C 207 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU C 213 " --> pdb=" O MET C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 237 Processing helix chain 'C' and resid 251 through 254 removed outlier: 3.521A pdb=" N ILE C 254 " --> pdb=" O GLU C 251 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 251 through 254' Processing helix chain 'C' and resid 255 through 262 Processing helix chain 'C' and resid 276 through 296 Processing helix chain 'C' and resid 317 through 327 Processing helix chain 'C' and resid 458 through 471 Processing helix chain 'C' and resid 499 through 507 Processing helix chain 'C' and resid 520 through 526 removed outlier: 4.126A pdb=" N TYR C 526 " --> pdb=" O GLU C 522 " (cutoff:3.500A) Processing helix chain 'C' and resid 687 through 696 Processing helix chain 'C' and resid 699 through 708 removed outlier: 3.777A pdb=" N LYS C 708 " --> pdb=" O ARG C 704 " (cutoff:3.500A) Processing helix chain 'C' and resid 713 through 724 Processing helix chain 'C' and resid 733 through 744 Processing helix chain 'C' and resid 768 through 782 Processing helix chain 'C' and resid 783 through 792 Processing helix chain 'D' and resid 41 through 47 Processing helix chain 'D' and resid 73 through 89 Processing helix chain 'D' and resid 103 through 116 removed outlier: 3.647A pdb=" N LEU D 107 " --> pdb=" O ALA D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 128 removed outlier: 4.225A pdb=" N SER D 126 " --> pdb=" O SER D 123 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL D 128 " --> pdb=" O GLY D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 160 removed outlier: 3.529A pdb=" N GLN D 149 " --> pdb=" O SER D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 188 Processing helix chain 'D' and resid 208 through 217 removed outlier: 4.311A pdb=" N THR D 212 " --> pdb=" O PRO D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 243 Processing helix chain 'D' and resid 255 through 259 Processing helix chain 'D' and resid 284 through 308 Processing helix chain 'D' and resid 325 through 337 removed outlier: 4.082A pdb=" N ASN D 337 " --> pdb=" O ARG D 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 456 through 470 Processing helix chain 'D' and resid 492 through 500 Processing helix chain 'D' and resid 513 through 520 removed outlier: 3.871A pdb=" N ILE D 519 " --> pdb=" O GLU D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 665 through 670 Processing helix chain 'D' and resid 686 through 696 Processing helix chain 'D' and resid 696 through 704 Processing helix chain 'D' and resid 710 through 721 Processing helix chain 'D' and resid 730 through 739 removed outlier: 3.558A pdb=" N TYR D 735 " --> pdb=" O ALA D 731 " (cutoff:3.500A) Processing helix chain 'D' and resid 768 through 783 removed outlier: 4.637A pdb=" N ALA D 772 " --> pdb=" O HIS D 768 " (cutoff:3.500A) Processing helix chain 'D' and resid 784 through 794 Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 66 removed outlier: 7.858A pdb=" N ASN A 28 " --> pdb=" O TYR A 88 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ILE A 90 " --> pdb=" O ASN A 28 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N GLY A 30 " --> pdb=" O ILE A 90 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N VAL A 92 " --> pdb=" O GLY A 30 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N VAL A 32 " --> pdb=" O VAL A 92 " (cutoff:3.500A) removed outlier: 8.676A pdb=" N LEU A 119 " --> pdb=" O TYR A 88 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ILE A 90 " --> pdb=" O LEU A 119 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N VAL A 118 " --> pdb=" O LEU A 138 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 193 through 197 removed outlier: 6.919A pdb=" N ILE A 163 " --> pdb=" O LYS A 193 " (cutoff:3.500A) removed outlier: 8.554A pdb=" N LEU A 195 " --> pdb=" O ILE A 163 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU A 165 " --> pdb=" O LEU A 195 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N PHE A 197 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N VAL A 167 " --> pdb=" O PHE A 197 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 267 through 271 removed outlier: 6.383A pdb=" N TYR A 351 " --> pdb=" O ILE A 366 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ILE A 366 " --> pdb=" O TYR A 351 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ILE A 353 " --> pdb=" O VAL A 364 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 409 through 413 removed outlier: 3.556A pdb=" N VAL A 451 " --> pdb=" O GLY A 438 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ILE A 435 " --> pdb=" O VAL A 476 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N LEU A 478 " --> pdb=" O ILE A 435 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N THR A 437 " --> pdb=" O LEU A 478 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 488 through 489 Processing sheet with id=AA6, first strand: chain 'A' and resid 527 through 529 Processing sheet with id=AA7, first strand: chain 'A' and resid 534 through 536 removed outlier: 3.895A pdb=" N LYS A 534 " --> pdb=" O PHE A 758 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 681 through 682 removed outlier: 6.765A pdb=" N ALA A 682 " --> pdb=" O ILE A 730 " (cutoff:3.500A) removed outlier: 9.204A pdb=" N ASP A 732 " --> pdb=" O ALA A 682 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ILE A 540 " --> pdb=" O THR A 749 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 62 through 67 removed outlier: 6.319A pdb=" N VAL B 30 " --> pdb=" O GLN B 63 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N LEU B 65 " --> pdb=" O VAL B 30 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N VAL B 32 " --> pdb=" O LEU B 65 " (cutoff:3.500A) removed outlier: 8.291A pdb=" N VAL B 67 " --> pdb=" O VAL B 32 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N VAL B 34 " --> pdb=" O VAL B 67 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ILE B 93 " --> pdb=" O LEU B 120 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N ILE B 122 " --> pdb=" O ILE B 93 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N PHE B 95 " --> pdb=" O ILE B 122 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 194 through 200 removed outlier: 7.923A pdb=" N PHE B 165 " --> pdb=" O LEU B 196 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N VAL B 198 " --> pdb=" O PHE B 165 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N VAL B 167 " --> pdb=" O VAL B 198 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N THR B 200 " --> pdb=" O VAL B 167 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N THR B 169 " --> pdb=" O THR B 200 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N VAL B 223 " --> pdb=" O ALA B 164 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N VAL B 276 " --> pdb=" O VAL B 254 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N ALA B 362 " --> pdb=" O MET B 371 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N MET B 371 " --> pdb=" O ALA B 362 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 472 through 477 removed outlier: 6.928A pdb=" N LEU B 403 " --> pdb=" O ASP B 474 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N TYR B 476 " --> pdb=" O LEU B 403 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N VAL B 405 " --> pdb=" O TYR B 476 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N MET B 505 " --> pdb=" O THR B 404 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 415 through 417 removed outlier: 3.948A pdb=" N THR B 450 " --> pdb=" O ARG B 435 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 680 through 681 removed outlier: 6.056A pdb=" N GLY B 681 " --> pdb=" O ILE B 727 " (cutoff:3.500A) removed outlier: 8.245A pdb=" N ASP B 729 " --> pdb=" O GLY B 681 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 680 through 681 removed outlier: 6.056A pdb=" N GLY B 681 " --> pdb=" O ILE B 727 " (cutoff:3.500A) removed outlier: 8.245A pdb=" N ASP B 729 " --> pdb=" O GLY B 681 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N VAL B 527 " --> pdb=" O GLY B 758 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N GLY B 758 " --> pdb=" O VAL B 527 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N THR B 529 " --> pdb=" O THR B 756 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N THR B 756 " --> pdb=" O THR B 529 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 59 through 66 removed outlier: 7.956A pdb=" N TYR C 88 " --> pdb=" O ILE C 26 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N ASN C 28 " --> pdb=" O TYR C 88 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ILE C 90 " --> pdb=" O ASN C 28 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N GLY C 30 " --> pdb=" O ILE C 90 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N VAL C 92 " --> pdb=" O GLY C 30 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL C 32 " --> pdb=" O VAL C 92 " (cutoff:3.500A) removed outlier: 8.596A pdb=" N LEU C 119 " --> pdb=" O TYR C 88 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ILE C 90 " --> pdb=" O LEU C 119 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 193 through 197 removed outlier: 6.604A pdb=" N LEU C 165 " --> pdb=" O LEU C 195 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N PHE C 197 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N VAL C 167 " --> pdb=" O PHE C 197 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ILE C 219 " --> pdb=" O LEU C 248 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 267 through 271 removed outlier: 6.549A pdb=" N TYR C 351 " --> pdb=" O ILE C 366 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N ILE C 366 " --> pdb=" O TYR C 351 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ILE C 353 " --> pdb=" O VAL C 364 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 339 through 340 removed outlier: 4.626A pdb=" N GLU C 339 " --> pdb=" O LYS C 347 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 409 through 413 removed outlier: 6.184A pdb=" N ILE C 435 " --> pdb=" O VAL C 476 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N LEU C 478 " --> pdb=" O ILE C 435 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N THR C 437 " --> pdb=" O LEU C 478 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 487 through 489 Processing sheet with id=AC3, first strand: chain 'C' and resid 534 through 536 removed outlier: 4.010A pdb=" N LYS C 534 " --> pdb=" O PHE C 758 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 681 through 682 removed outlier: 3.555A pdb=" N ILE C 730 " --> pdb=" O ALA C 682 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE C 540 " --> pdb=" O THR C 749 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 64 through 66 removed outlier: 6.803A pdb=" N ILE D 93 " --> pdb=" O LEU D 120 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N ILE D 122 " --> pdb=" O ILE D 93 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N PHE D 95 " --> pdb=" O ILE D 122 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 198 through 200 removed outlier: 8.981A pdb=" N LEU D 199 " --> pdb=" O PHE D 165 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N VAL D 167 " --> pdb=" O LEU D 199 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 274 through 278 removed outlier: 6.562A pdb=" N MET D 358 " --> pdb=" O ARG D 374 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ARG D 374 " --> pdb=" O MET D 358 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N VAL D 360 " --> pdb=" O VAL D 372 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 339 through 340 Processing sheet with id=AC9, first strand: chain 'D' and resid 389 through 390 removed outlier: 4.272A pdb=" N ARG D 389 " --> pdb=" O VAL D 397 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 472 through 477 removed outlier: 3.843A pdb=" N VAL D 405 " --> pdb=" O ASP D 474 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 415 through 417 Processing sheet with id=AD3, first strand: chain 'D' and resid 486 through 487 Processing sheet with id=AD4, first strand: chain 'D' and resid 680 through 681 removed outlier: 6.666A pdb=" N GLY D 681 " --> pdb=" O ILE D 727 " (cutoff:3.500A) removed outlier: 9.063A pdb=" N ASP D 729 " --> pdb=" O GLY D 681 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 680 through 681 removed outlier: 6.666A pdb=" N GLY D 681 " --> pdb=" O ILE D 727 " (cutoff:3.500A) removed outlier: 9.063A pdb=" N ASP D 729 " --> pdb=" O GLY D 681 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL D 527 " --> pdb=" O GLY D 758 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N GLY D 758 " --> pdb=" O VAL D 527 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N THR D 529 " --> pdb=" O THR D 756 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N THR D 756 " --> pdb=" O THR D 529 " (cutoff:3.500A) 830 hydrogen bonds defined for protein. 2376 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.62 Time building geometry restraints manager: 8.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.91 - 1.21: 8 1.21 - 1.51: 13639 1.51 - 1.82: 8024 1.82 - 2.12: 1 2.12 - 2.42: 1 Bond restraints: 21673 Sorted by residual: bond pdb=" N PRO C 670 " pdb=" CD PRO C 670 " ideal model delta sigma weight residual 1.473 0.942 0.531 1.40e-02 5.10e+03 1.44e+03 bond pdb=" CB PRO D 676 " pdb=" CG PRO D 676 " ideal model delta sigma weight residual 1.492 2.421 -0.929 5.00e-02 4.00e+02 3.45e+02 bond pdb=" CG PRO D 676 " pdb=" CD PRO D 676 " ideal model delta sigma weight residual 1.503 0.907 0.596 3.40e-02 8.65e+02 3.07e+02 bond pdb=" CB PRO B 59 " pdb=" CG PRO B 59 " ideal model delta sigma weight residual 1.492 0.965 0.527 5.00e-02 4.00e+02 1.11e+02 bond pdb=" CG PRO A 304 " pdb=" CD PRO A 304 " ideal model delta sigma weight residual 1.503 1.145 0.358 3.40e-02 8.65e+02 1.11e+02 ... (remaining 21668 not shown) Histogram of bond angle deviations from ideal: 0.01 - 30.60: 1 30.60 - 61.19: 0 61.19 - 91.78: 9 91.78 - 122.37: 26169 122.37 - 152.96: 3227 Bond angle restraints: 29406 Sorted by residual: angle pdb=" CB PRO D 676 " pdb=" CG PRO D 676 " pdb=" CD PRO D 676 " ideal model delta sigma weight residual 106.10 0.01 106.09 3.20e+00 9.77e-02 1.10e+03 angle pdb=" N PRO B 59 " pdb=" CD PRO B 59 " pdb=" CG PRO B 59 " ideal model delta sigma weight residual 103.20 73.25 29.95 1.50e+00 4.44e-01 3.99e+02 angle pdb=" CA PRO B 59 " pdb=" CB PRO B 59 " pdb=" CG PRO B 59 " ideal model delta sigma weight residual 104.50 68.69 35.81 1.90e+00 2.77e-01 3.55e+02 angle pdb=" N PRO A 304 " pdb=" CD PRO A 304 " pdb=" CG PRO A 304 " ideal model delta sigma weight residual 103.20 76.00 27.20 1.50e+00 4.44e-01 3.29e+02 angle pdb=" CA PRO D 676 " pdb=" N PRO D 676 " pdb=" CD PRO D 676 " ideal model delta sigma weight residual 112.00 87.87 24.13 1.40e+00 5.10e-01 2.97e+02 ... (remaining 29401 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.02: 10975 18.02 - 36.04: 1262 36.04 - 54.06: 271 54.06 - 72.08: 73 72.08 - 90.10: 48 Dihedral angle restraints: 12629 sinusoidal: 5088 harmonic: 7541 Sorted by residual: dihedral pdb=" CA GLU C 299 " pdb=" C GLU C 299 " pdb=" N ASN C 300 " pdb=" CA ASN C 300 " ideal model delta harmonic sigma weight residual 180.00 -142.51 -37.49 0 5.00e+00 4.00e-02 5.62e+01 dihedral pdb=" CB CYS D 82 " pdb=" SG CYS D 82 " pdb=" SG CYS D 317 " pdb=" CB CYS D 317 " ideal model delta sinusoidal sigma weight residual 93.00 150.30 -57.30 1 1.00e+01 1.00e-02 4.41e+01 dihedral pdb=" N PRO B 59 " pdb=" CG PRO B 59 " pdb=" CD PRO B 59 " pdb=" CB PRO B 59 " ideal model delta sinusoidal sigma weight residual 30.00 108.98 -78.98 1 1.50e+01 4.44e-03 3.45e+01 ... (remaining 12626 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.120: 3354 0.120 - 0.239: 66 0.239 - 0.359: 4 0.359 - 0.479: 1 0.479 - 0.599: 4 Chirality restraints: 3429 Sorted by residual: chirality pdb=" C1 NAG e 2 " pdb=" O4 NAG e 1 " pdb=" C2 NAG e 2 " pdb=" O5 NAG e 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.31 -0.09 2.00e-02 2.50e+03 1.88e+01 chirality pdb=" C1 NAG O 2 " pdb=" O4 NAG O 1 " pdb=" C2 NAG O 2 " pdb=" O5 NAG O 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.33 -0.07 2.00e-02 2.50e+03 1.15e+01 chirality pdb=" C1 NAG O 1 " pdb=" ND2 ASN A 239 " pdb=" C2 NAG O 1 " pdb=" O5 NAG O 1 " both_signs ideal model delta sigma weight residual False -2.40 -3.00 0.60 2.00e-01 2.50e+01 8.96e+00 ... (remaining 3426 not shown) Planarity restraints: 3755 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 239 " -0.344 2.00e-02 2.50e+03 3.23e-01 1.30e+03 pdb=" CG ASN A 239 " 0.139 2.00e-02 2.50e+03 pdb=" OD1 ASN A 239 " 0.096 2.00e-02 2.50e+03 pdb=" ND2 ASN A 239 " 0.484 2.00e-02 2.50e+03 pdb=" C1 NAG O 1 " -0.375 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 904 " -0.318 2.00e-02 2.50e+03 2.67e-01 8.91e+02 pdb=" C7 NAG C 904 " 0.080 2.00e-02 2.50e+03 pdb=" C8 NAG C 904 " -0.190 2.00e-02 2.50e+03 pdb=" N2 NAG C 904 " 0.460 2.00e-02 2.50e+03 pdb=" O7 NAG C 904 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG O 1 " 0.313 2.00e-02 2.50e+03 2.66e-01 8.86e+02 pdb=" C7 NAG O 1 " -0.080 2.00e-02 2.50e+03 pdb=" C8 NAG O 1 " 0.182 2.00e-02 2.50e+03 pdb=" N2 NAG O 1 " -0.463 2.00e-02 2.50e+03 pdb=" O7 NAG O 1 " 0.047 2.00e-02 2.50e+03 ... (remaining 3752 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 216 2.61 - 3.18: 18438 3.18 - 3.75: 31888 3.75 - 4.33: 43390 4.33 - 4.90: 73031 Nonbonded interactions: 166963 Sorted by model distance: nonbonded pdb=" O ARG A 36 " pdb=" NH1 ARG A 36 " model vdw 2.035 2.520 nonbonded pdb=" OD1 ASN C 300 " pdb=" C1 NAG C 901 " model vdw 2.045 2.776 nonbonded pdb=" OE1 GLU B 410 " pdb=" OG SER B 509 " model vdw 2.054 2.440 nonbonded pdb=" O THR D 791 " pdb=" OG SER D 795 " model vdw 2.125 2.440 nonbonded pdb=" OD2 ASP C 732 " pdb=" N GLY C 905 " model vdw 2.155 2.520 ... (remaining 166958 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'C' and (resid 25 through 545 or resid 663 through 794 or resid 902 throu \ gh 905)) } ncs_group { reference = (chain 'B' and (resid 29 through 537 or resid 658 through 799 or resid 901 throu \ gh 904)) selection = (chain 'D' and (resid 29 through 799 or resid 901 through 904)) } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'S' selection = chain 'X' selection = chain 'a' selection = chain 'c' selection = chain 'e' selection = chain 'g' selection = chain 'k' selection = chain 'n' selection = chain 'q' selection = chain 'v' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 6.080 Check model and map are aligned: 0.280 Set scattering table: 0.170 Process input model: 52.750 Find NCS groups from input model: 1.780 Set up NCS constraints: 0.250 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 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 : 0.011 0.929 21673 Z= 0.656 Angle : 1.142 106.094 29406 Z= 0.556 Chirality : 0.052 0.599 3429 Planarity : 0.010 0.267 3725 Dihedral : 16.984 90.101 7745 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.88 % Favored : 93.92 % Rotamer: Outliers : 0.22 % Allowed : 21.19 % Favored : 78.58 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.16), residues: 2600 helix: 1.11 (0.17), residues: 924 sheet: -1.26 (0.24), residues: 444 loop : -1.78 (0.17), residues: 1232 *********************** 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 197 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 192 time to evaluate : 2.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 197 average time/residue: 0.3428 time to fit residues: 105.0573 Evaluate side-chains 184 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 183 time to evaluate : 2.421 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1889 time to fit residues: 3.6347 ------------------------------------------------------------------------------- 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: 1.9990 chunk 197 optimal weight: 5.9990 chunk 109 optimal weight: 1.9990 chunk 67 optimal weight: 6.9990 chunk 132 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 203 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 123 optimal weight: 0.6980 chunk 151 optimal weight: 0.2980 chunk 236 optimal weight: 7.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 67 HIS A 293 HIS ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 256 ASN C 371 HIS D 43 GLN ** D 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.0698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.103 21673 Z= 0.240 Angle : 0.608 13.611 29406 Z= 0.306 Chirality : 0.047 0.555 3429 Planarity : 0.005 0.093 3725 Dihedral : 4.640 76.830 2853 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.35 % Favored : 93.58 % Rotamer: Outliers : 3.43 % Allowed : 20.21 % Favored : 76.36 % 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: -0.74 (0.16), residues: 2600 helix: 1.35 (0.17), residues: 938 sheet: -1.34 (0.24), residues: 427 loop : -1.66 (0.17), residues: 1235 *********************** 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 270 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 193 time to evaluate : 2.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 77 outliers final: 42 residues processed: 253 average time/residue: 0.3212 time to fit residues: 128.6491 Evaluate side-chains 218 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 176 time to evaluate : 2.322 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 0 residues processed: 42 average time/residue: 0.2345 time to fit residues: 20.2893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 131 optimal weight: 0.0010 chunk 73 optimal weight: 5.9990 chunk 196 optimal weight: 7.9990 chunk 160 optimal weight: 4.9990 chunk 65 optimal weight: 9.9990 chunk 236 optimal weight: 4.9990 chunk 255 optimal weight: 4.9990 chunk 210 optimal weight: 0.9990 chunk 234 optimal weight: 0.0770 chunk 80 optimal weight: 0.5980 chunk 189 optimal weight: 3.9990 overall best weight: 1.1348 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 86 GLN ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.0967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21673 Z= 0.220 Angle : 0.563 7.291 29406 Z= 0.285 Chirality : 0.045 0.432 3429 Planarity : 0.004 0.083 3725 Dihedral : 4.599 75.752 2853 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.54 % Favored : 93.38 % Rotamer: Outliers : 1.74 % Allowed : 21.15 % 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: -0.67 (0.16), residues: 2600 helix: 1.36 (0.17), residues: 942 sheet: -1.33 (0.24), residues: 427 loop : -1.58 (0.17), residues: 1231 *********************** 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 230 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 191 time to evaluate : 2.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 14 residues processed: 224 average time/residue: 0.3337 time to fit residues: 117.5664 Evaluate side-chains 197 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 183 time to evaluate : 2.432 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1896 time to fit residues: 8.3163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 233 optimal weight: 0.8980 chunk 177 optimal weight: 0.9990 chunk 122 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 112 optimal weight: 4.9990 chunk 158 optimal weight: 0.0050 chunk 237 optimal weight: 1.9990 chunk 251 optimal weight: 0.8980 chunk 124 optimal weight: 3.9990 chunk 224 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 overall best weight: 0.9598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 702 HIS ** C 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 429 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.1169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21673 Z= 0.196 Angle : 0.542 7.033 29406 Z= 0.275 Chirality : 0.044 0.426 3429 Planarity : 0.004 0.084 3725 Dihedral : 4.535 76.473 2853 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.04 % Favored : 93.88 % Rotamer: Outliers : 2.09 % Allowed : 21.82 % Favored : 76.09 % 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: -0.58 (0.17), residues: 2600 helix: 1.41 (0.17), residues: 943 sheet: -1.28 (0.24), residues: 427 loop : -1.51 (0.17), residues: 1230 *********************** 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 244 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 197 time to evaluate : 2.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 47 outliers final: 22 residues processed: 236 average time/residue: 0.3273 time to fit residues: 122.2061 Evaluate side-chains 207 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 185 time to evaluate : 2.402 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.1998 time to fit residues: 11.6544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 209 optimal weight: 0.9980 chunk 142 optimal weight: 0.9990 chunk 3 optimal weight: 10.0000 chunk 187 optimal weight: 8.9990 chunk 103 optimal weight: 0.7980 chunk 214 optimal weight: 0.8980 chunk 173 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 128 optimal weight: 0.9990 chunk 225 optimal weight: 0.9990 chunk 63 optimal weight: 0.7980 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 101 HIS ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 256 ASN ** C 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.1325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21673 Z= 0.178 Angle : 0.535 8.019 29406 Z= 0.270 Chirality : 0.044 0.417 3429 Planarity : 0.004 0.083 3725 Dihedral : 4.466 76.413 2853 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.27 % Favored : 93.65 % Rotamer: Outliers : 1.83 % Allowed : 22.89 % Favored : 75.29 % 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: -0.49 (0.17), residues: 2600 helix: 1.48 (0.17), residues: 943 sheet: -1.22 (0.24), residues: 425 loop : -1.44 (0.17), residues: 1232 *********************** 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 245 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 204 time to evaluate : 2.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 16 residues processed: 236 average time/residue: 0.3255 time to fit residues: 120.5516 Evaluate side-chains 202 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 186 time to evaluate : 2.317 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1911 time to fit residues: 9.0824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 84 optimal weight: 7.9990 chunk 226 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 147 optimal weight: 3.9990 chunk 62 optimal weight: 0.0000 chunk 251 optimal weight: 0.7980 chunk 208 optimal weight: 0.9990 chunk 116 optimal weight: 9.9990 chunk 20 optimal weight: 0.7980 chunk 83 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 overall best weight: 1.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 63 GLN ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 218 GLN ** D 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 439 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21673 Z= 0.215 Angle : 0.550 6.555 29406 Z= 0.278 Chirality : 0.045 0.415 3429 Planarity : 0.004 0.082 3725 Dihedral : 4.523 75.965 2853 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.58 % Favored : 93.35 % Rotamer: Outliers : 1.69 % Allowed : 22.48 % Favored : 75.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.17), residues: 2600 helix: 1.48 (0.17), residues: 942 sheet: -1.22 (0.25), residues: 424 loop : -1.43 (0.17), residues: 1234 *********************** 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 237 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 199 time to evaluate : 2.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 17 residues processed: 229 average time/residue: 0.3125 time to fit residues: 113.9186 Evaluate side-chains 205 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 188 time to evaluate : 2.152 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.2028 time to fit residues: 9.7139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 242 optimal weight: 0.9990 chunk 28 optimal weight: 6.9990 chunk 143 optimal weight: 0.9980 chunk 183 optimal weight: 1.9990 chunk 142 optimal weight: 0.9990 chunk 211 optimal weight: 8.9990 chunk 140 optimal weight: 0.3980 chunk 250 optimal weight: 7.9990 chunk 156 optimal weight: 1.9990 chunk 152 optimal weight: 0.9980 chunk 115 optimal weight: 5.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 371 HIS ** D 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21673 Z= 0.186 Angle : 0.539 10.857 29406 Z= 0.272 Chirality : 0.044 0.408 3429 Planarity : 0.004 0.083 3725 Dihedral : 4.500 77.124 2853 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.12 % Favored : 93.81 % Rotamer: Outliers : 1.29 % Allowed : 22.62 % Favored : 76.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.17), residues: 2600 helix: 1.52 (0.17), residues: 941 sheet: -1.15 (0.25), residues: 423 loop : -1.40 (0.17), residues: 1236 *********************** 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 227 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 198 time to evaluate : 2.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 10 residues processed: 219 average time/residue: 0.3212 time to fit residues: 112.6137 Evaluate side-chains 195 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 185 time to evaluate : 2.498 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1956 time to fit residues: 7.0206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 149 optimal weight: 0.5980 chunk 75 optimal weight: 0.9980 chunk 49 optimal weight: 0.0570 chunk 48 optimal weight: 1.9990 chunk 159 optimal weight: 0.6980 chunk 170 optimal weight: 0.6980 chunk 123 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 196 optimal weight: 0.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 429 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 21673 Z= 0.162 Angle : 0.544 9.609 29406 Z= 0.272 Chirality : 0.044 0.440 3429 Planarity : 0.004 0.083 3725 Dihedral : 4.458 77.470 2853 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.12 % Favored : 93.81 % Rotamer: Outliers : 0.49 % Allowed : 23.60 % Favored : 75.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.17), residues: 2600 helix: 1.57 (0.17), residues: 941 sheet: -1.08 (0.25), residues: 422 loop : -1.39 (0.17), residues: 1237 *********************** 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 206 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 195 time to evaluate : 2.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 3 residues processed: 204 average time/residue: 0.3285 time to fit residues: 107.1623 Evaluate side-chains 187 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 184 time to evaluate : 2.379 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1882 time to fit residues: 4.3425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 227 optimal weight: 0.0970 chunk 240 optimal weight: 3.9990 chunk 219 optimal weight: 0.6980 chunk 233 optimal weight: 0.9990 chunk 140 optimal weight: 0.7980 chunk 101 optimal weight: 0.0670 chunk 183 optimal weight: 3.9990 chunk 71 optimal weight: 0.6980 chunk 211 optimal weight: 1.9990 chunk 220 optimal weight: 0.6980 chunk 232 optimal weight: 0.6980 overall best weight: 0.4516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 91 HIS ** D 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 21673 Z= 0.149 Angle : 0.538 11.380 29406 Z= 0.270 Chirality : 0.044 0.385 3429 Planarity : 0.004 0.082 3725 Dihedral : 4.363 76.929 2853 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.81 % Favored : 94.12 % Rotamer: Outliers : 0.49 % Allowed : 23.82 % Favored : 75.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.17), residues: 2600 helix: 1.59 (0.17), residues: 943 sheet: -1.04 (0.25), residues: 422 loop : -1.35 (0.17), residues: 1235 *********************** 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 200 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 189 time to evaluate : 2.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 6 residues processed: 197 average time/residue: 0.3866 time to fit residues: 126.7258 Evaluate side-chains 185 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 179 time to evaluate : 2.434 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1824 time to fit residues: 5.0278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 153 optimal weight: 3.9990 chunk 246 optimal weight: 8.9990 chunk 150 optimal weight: 1.9990 chunk 117 optimal weight: 6.9990 chunk 171 optimal weight: 0.9990 chunk 259 optimal weight: 0.9990 chunk 238 optimal weight: 1.9990 chunk 206 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 159 optimal weight: 0.7980 chunk 126 optimal weight: 2.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 449 HIS ** D 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 21673 Z= 0.247 Angle : 0.589 11.743 29406 Z= 0.294 Chirality : 0.046 0.400 3429 Planarity : 0.004 0.081 3725 Dihedral : 4.567 79.013 2853 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.12 % Favored : 92.81 % Rotamer: Outliers : 0.09 % Allowed : 24.04 % Favored : 75.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.17), residues: 2600 helix: 1.50 (0.17), residues: 942 sheet: -1.18 (0.25), residues: 436 loop : -1.36 (0.18), residues: 1222 ********************** 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 191 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 189 time to evaluate : 2.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 191 average time/residue: 0.3109 time to fit residues: 96.4328 Evaluate side-chains 185 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 184 time to evaluate : 2.364 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1950 time to fit residues: 3.7951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 163 optimal weight: 2.9990 chunk 219 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 190 optimal weight: 0.8980 chunk 30 optimal weight: 0.2980 chunk 57 optimal weight: 0.8980 chunk 206 optimal weight: 0.8980 chunk 86 optimal weight: 3.9990 chunk 212 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.143000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.113798 restraints weight = 31036.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.115187 restraints weight = 28846.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.116042 restraints weight = 22787.216| |-----------------------------------------------------------------------------| r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21673 Z= 0.168 Angle : 0.546 10.357 29406 Z= 0.274 Chirality : 0.044 0.388 3429 Planarity : 0.004 0.081 3725 Dihedral : 4.443 79.690 2853 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.04 % Favored : 93.88 % Rotamer: Outliers : 0.27 % Allowed : 23.95 % Favored : 75.78 % 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: -0.35 (0.17), residues: 2600 helix: 1.57 (0.17), residues: 942 sheet: -1.06 (0.25), residues: 420 loop : -1.38 (0.17), residues: 1238 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3446.46 seconds wall clock time: 64 minutes 29.29 seconds (3869.29 seconds total)