Starting phenix.real_space_refine on Tue Dec 12 14:12:38 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yfg_33789/12_2023/7yfg_33789_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yfg_33789/12_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_33789/12_2023/7yfg_33789.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yfg_33789/12_2023/7yfg_33789.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yfg_33789/12_2023/7yfg_33789_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yfg_33789/12_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: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 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 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: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "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: "q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "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 dihedrals: 9 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 dihedrals: 9 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 dihedrals: 12 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 10.38, per 1000 atoms: 0.49 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: 8.83 Conformation dependent library (CDL) restraints added in 3.6 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: 2.50 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: 6.88 Time building geometry restraints manager: 9.50 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 - 24.40: 12475 24.40 - 48.81: 935 48.81 - 73.21: 141 73.21 - 97.62: 54 97.62 - 122.02: 11 Dihedral angle restraints: 13616 sinusoidal: 6075 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 13613 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: 0.990 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: 6.180 Check model and map are aligned: 0.290 Set scattering table: 0.180 Process input model: 55.140 Find NCS groups from input model: 1.550 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: 0.000 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.510 ------------------------------------------------------------------------------- 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 : 17.464 122.025 8732 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 381 HIS 0.008 0.001 HIS C 371 PHE 0.012 0.001 PHE C 197 TYR 0.033 0.001 TYR D 675 ARG 0.022 0.001 ARG B 209 *********************** 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 : 2.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 197 average time/residue: 0.3510 time to fit residues: 107.8144 Evaluate side-chains 184 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 183 time to evaluate : 2.481 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1888 time to fit residues: 3.7262 ------------------------------------------------------------------------------- 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** D 439 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.0716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 21673 Z= 0.240 Angle : 0.612 13.370 29406 Z= 0.307 Chirality : 0.047 0.528 3429 Planarity : 0.005 0.092 3725 Dihedral : 9.725 110.583 3840 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.31 % Favored : 93.62 % 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: 1.34 (0.17), residues: 938 sheet: -1.34 (0.24), residues: 427 loop : -1.66 (0.17), residues: 1235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 56 HIS 0.005 0.001 HIS D 301 PHE 0.011 0.001 PHE C 197 TYR 0.024 0.001 TYR D 675 ARG 0.004 0.000 ARG B 209 *********************** 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 272 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 195 time to evaluate : 2.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 77 outliers final: 42 residues processed: 255 average time/residue: 0.3274 time to fit residues: 131.1610 Evaluate side-chains 221 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 179 time to evaluate : 2.234 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 0 residues processed: 42 average time/residue: 0.2226 time to fit residues: 19.4001 ------------------------------------------------------------------------------- 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: 1.9990 chunk 73 optimal weight: 5.9990 chunk 196 optimal weight: 6.9990 chunk 160 optimal weight: 3.9990 chunk 65 optimal weight: 10.0000 chunk 236 optimal weight: 2.9990 chunk 255 optimal weight: 4.9990 chunk 210 optimal weight: 0.7980 chunk 234 optimal weight: 0.9980 chunk 80 optimal weight: 0.6980 chunk 189 optimal weight: 3.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 311 ASN ** 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.1069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 21673 Z= 0.266 Angle : 0.590 7.479 29406 Z= 0.298 Chirality : 0.046 0.439 3429 Planarity : 0.005 0.083 3725 Dihedral : 8.814 108.819 3840 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.69 % Favored : 93.23 % Rotamer: Outliers : 2.27 % Allowed : 20.93 % Favored : 76.80 % 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: -0.74 (0.16), residues: 2600 helix: 1.30 (0.17), residues: 941 sheet: -1.40 (0.24), residues: 436 loop : -1.60 (0.17), residues: 1223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 56 HIS 0.005 0.001 HIS B 700 PHE 0.014 0.001 PHE A 458 TYR 0.025 0.001 TYR D 675 ARG 0.004 0.000 ARG B 209 *********************** 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 244 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 193 time to evaluate : 2.318 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 51 outliers final: 25 residues processed: 235 average time/residue: 0.3175 time to fit residues: 119.2442 Evaluate side-chains 207 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 182 time to evaluate : 2.601 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.1939 time to fit residues: 12.8306 ------------------------------------------------------------------------------- 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: 0.6980 chunk 177 optimal weight: 3.9990 chunk 122 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 112 optimal weight: 4.9990 chunk 158 optimal weight: 4.9990 chunk 237 optimal weight: 0.9990 chunk 251 optimal weight: 7.9990 chunk 124 optimal weight: 5.9990 chunk 224 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 101 HIS A 177 GLN B 91 HIS B 114 GLN B 702 HIS ** C 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 371 HIS C 709 HIS ** 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: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 21673 Z= 0.414 Angle : 0.683 7.958 29406 Z= 0.346 Chirality : 0.050 0.472 3429 Planarity : 0.005 0.083 3725 Dihedral : 8.559 107.449 3840 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.50 % Favored : 92.42 % Rotamer: Outliers : 3.78 % Allowed : 21.55 % Favored : 74.67 % 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: -0.98 (0.16), residues: 2600 helix: 1.04 (0.17), residues: 930 sheet: -1.65 (0.23), residues: 460 loop : -1.59 (0.17), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 375 HIS 0.009 0.002 HIS D 768 PHE 0.020 0.002 PHE C 197 TYR 0.021 0.002 TYR D 476 ARG 0.004 0.001 ARG B 389 *********************** 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 270 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 185 time to evaluate : 2.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 85 outliers final: 44 residues processed: 255 average time/residue: 0.3266 time to fit residues: 131.5026 Evaluate side-chains 215 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 171 time to evaluate : 2.441 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 44 outliers final: 1 residues processed: 44 average time/residue: 0.1916 time to fit residues: 19.3721 ------------------------------------------------------------------------------- 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: 1.9990 chunk 142 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 187 optimal weight: 8.9990 chunk 103 optimal weight: 0.6980 chunk 214 optimal weight: 2.9990 chunk 173 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 128 optimal weight: 0.9990 chunk 225 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 HIS ** 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: 0.7776 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21673 Z= 0.185 Angle : 0.571 8.594 29406 Z= 0.288 Chirality : 0.045 0.448 3429 Planarity : 0.004 0.084 3725 Dihedral : 7.864 103.319 3840 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.46 % Favored : 93.46 % Rotamer: Outliers : 1.60 % Allowed : 22.80 % Favored : 75.60 % 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: -0.76 (0.16), residues: 2600 helix: 1.24 (0.17), residues: 943 sheet: -1.39 (0.25), residues: 424 loop : -1.57 (0.17), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 792 HIS 0.005 0.001 HIS C 371 PHE 0.013 0.001 PHE A 458 TYR 0.011 0.001 TYR B 476 ARG 0.004 0.000 ARG D 194 *********************** 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 239 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 203 time to evaluate : 2.493 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 13 residues processed: 230 average time/residue: 0.3223 time to fit residues: 118.0532 Evaluate side-chains 199 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 186 time to evaluate : 2.421 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1980 time to fit residues: 8.0022 ------------------------------------------------------------------------------- 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: 2.9990 chunk 226 optimal weight: 4.9990 chunk 49 optimal weight: 0.4980 chunk 147 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 251 optimal weight: 1.9990 chunk 208 optimal weight: 5.9990 chunk 116 optimal weight: 9.9990 chunk 20 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 132 optimal weight: 3.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 148 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 21673 Z= 0.292 Angle : 0.606 8.508 29406 Z= 0.305 Chirality : 0.047 0.433 3429 Planarity : 0.005 0.083 3725 Dihedral : 7.597 99.467 3840 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.50 % Favored : 92.42 % Rotamer: Outliers : 2.32 % Allowed : 22.97 % Favored : 74.71 % 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: -0.81 (0.16), residues: 2600 helix: 1.20 (0.17), residues: 942 sheet: -1.48 (0.24), residues: 438 loop : -1.57 (0.17), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 375 HIS 0.005 0.001 HIS A 477 PHE 0.014 0.002 PHE C 197 TYR 0.015 0.001 TYR D 476 ARG 0.004 0.000 ARG D 194 *********************** 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 246 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 194 time to evaluate : 2.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 52 outliers final: 29 residues processed: 235 average time/residue: 0.3050 time to fit residues: 115.1701 Evaluate side-chains 213 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 184 time to evaluate : 2.280 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.2437 time to fit residues: 16.7047 ------------------------------------------------------------------------------- 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: 2.9990 chunk 28 optimal weight: 3.9990 chunk 143 optimal weight: 0.6980 chunk 183 optimal weight: 0.8980 chunk 142 optimal weight: 0.9990 chunk 211 optimal weight: 0.6980 chunk 140 optimal weight: 0.9980 chunk 250 optimal weight: 8.9990 chunk 156 optimal weight: 1.9990 chunk 152 optimal weight: 0.5980 chunk 115 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.1884 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= 0.181 Angle : 0.575 9.135 29406 Z= 0.287 Chirality : 0.045 0.416 3429 Planarity : 0.004 0.083 3725 Dihedral : 7.074 94.746 3840 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.50 % Favored : 93.42 % Rotamer: Outliers : 0.76 % Allowed : 23.86 % Favored : 75.38 % 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: -0.65 (0.17), residues: 2600 helix: 1.34 (0.17), residues: 943 sheet: -1.29 (0.25), residues: 422 loop : -1.55 (0.17), residues: 1235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 792 HIS 0.006 0.001 HIS A 709 PHE 0.012 0.001 PHE C 458 TYR 0.011 0.001 TYR B 476 ARG 0.005 0.000 ARG D 194 *********************** 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 212 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 195 time to evaluate : 2.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 8 residues processed: 209 average time/residue: 0.3247 time to fit residues: 108.1443 Evaluate side-chains 188 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 180 time to evaluate : 2.657 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.2637 time to fit residues: 7.0881 ------------------------------------------------------------------------------- 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: 1.9990 chunk 100 optimal weight: 1.9990 chunk 149 optimal weight: 0.8980 chunk 75 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 159 optimal weight: 0.9980 chunk 170 optimal weight: 0.0770 chunk 123 optimal weight: 1.9990 chunk 23 optimal weight: 7.9990 chunk 196 optimal weight: 1.9990 overall best weight: 0.7940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.1935 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= 0.183 Angle : 0.567 12.212 29406 Z= 0.282 Chirality : 0.045 0.398 3429 Planarity : 0.004 0.083 3725 Dihedral : 6.629 89.311 3840 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.73 % Favored : 93.19 % Rotamer: Outliers : 0.93 % Allowed : 24.22 % Favored : 74.84 % 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: -0.56 (0.17), residues: 2600 helix: 1.44 (0.17), residues: 941 sheet: -1.22 (0.25), residues: 422 loop : -1.52 (0.17), residues: 1237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 381 HIS 0.006 0.001 HIS A 293 PHE 0.011 0.001 PHE A 533 TYR 0.011 0.001 TYR B 476 ARG 0.009 0.000 ARG D 194 *********************** 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 213 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 192 time to evaluate : 2.588 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 6 residues processed: 210 average time/residue: 0.3128 time to fit residues: 107.2218 Evaluate side-chains 179 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 173 time to evaluate : 2.200 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1915 time to fit residues: 5.5639 ------------------------------------------------------------------------------- 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: 0.0770 chunk 240 optimal weight: 1.9990 chunk 219 optimal weight: 0.8980 chunk 233 optimal weight: 0.7980 chunk 140 optimal weight: 0.9990 chunk 101 optimal weight: 0.8980 chunk 183 optimal weight: 0.0270 chunk 71 optimal weight: 8.9990 chunk 211 optimal weight: 8.9990 chunk 220 optimal weight: 1.9990 chunk 232 optimal weight: 0.9980 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 21673 Z= 0.156 Angle : 0.566 11.681 29406 Z= 0.280 Chirality : 0.046 0.568 3429 Planarity : 0.004 0.083 3725 Dihedral : 6.171 81.410 3840 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.81 % Favored : 94.12 % Rotamer: Outliers : 0.67 % Allowed : 24.27 % Favored : 75.07 % 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: 1.50 (0.17), residues: 942 sheet: -1.22 (0.25), residues: 416 loop : -1.46 (0.17), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 769 HIS 0.004 0.001 HIS A 709 PHE 0.011 0.001 PHE C 458 TYR 0.020 0.001 TYR D 352 ARG 0.007 0.000 ARG D 194 *********************** 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 203 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 188 time to evaluate : 2.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 8 residues processed: 197 average time/residue: 0.3323 time to fit residues: 105.5312 Evaluate side-chains 188 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 180 time to evaluate : 2.361 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.2061 time to fit residues: 6.2017 ------------------------------------------------------------------------------- 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: 0.8980 chunk 246 optimal weight: 1.9990 chunk 150 optimal weight: 2.9990 chunk 117 optimal weight: 4.9990 chunk 171 optimal weight: 0.9980 chunk 259 optimal weight: 3.9990 chunk 238 optimal weight: 0.9990 chunk 206 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 159 optimal weight: 0.0970 chunk 126 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21673 Z= 0.178 Angle : 0.569 12.526 29406 Z= 0.282 Chirality : 0.045 0.411 3429 Planarity : 0.004 0.082 3725 Dihedral : 5.950 81.354 3840 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.73 % Favored : 93.19 % Rotamer: Outliers : 0.22 % Allowed : 24.49 % Favored : 75.29 % 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: -0.44 (0.17), residues: 2600 helix: 1.53 (0.17), residues: 942 sheet: -1.18 (0.25), residues: 430 loop : -1.43 (0.17), residues: 1228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 768 HIS 0.004 0.001 HIS A 780 PHE 0.012 0.001 PHE A 533 TYR 0.014 0.001 TYR D 352 ARG 0.007 0.000 ARG D 194 ********************** 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 186 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 181 time to evaluate : 2.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 5 residues processed: 183 average time/residue: 0.3277 time to fit residues: 96.8092 Evaluate side-chains 183 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 178 time to evaluate : 2.407 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.3227 time to fit residues: 5.7927 ------------------------------------------------------------------------------- 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: 0.0970 chunk 219 optimal weight: 0.8980 chunk 63 optimal weight: 0.7980 chunk 190 optimal weight: 0.7980 chunk 30 optimal weight: 10.0000 chunk 57 optimal weight: 0.7980 chunk 206 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 212 optimal weight: 0.0870 chunk 26 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 overall best weight: 0.5156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3698 r_free = 0.3698 target = 0.143634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.114011 restraints weight = 30966.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.115812 restraints weight = 29374.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.116803 restraints weight = 22339.049| |-----------------------------------------------------------------------------| r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 21673 Z= 0.153 Angle : 0.552 10.125 29406 Z= 0.274 Chirality : 0.044 0.370 3429 Planarity : 0.004 0.082 3725 Dihedral : 5.604 81.639 3840 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.69 % Favored : 94.19 % Rotamer: Outliers : 0.18 % Allowed : 24.44 % Favored : 75.38 % 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: 1.57 (0.17), residues: 942 sheet: -1.06 (0.25), residues: 420 loop : -1.40 (0.17), residues: 1238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 381 HIS 0.003 0.001 HIS A 780 PHE 0.010 0.001 PHE C 458 TYR 0.014 0.001 TYR D 352 ARG 0.006 0.000 ARG D 194 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3542.48 seconds wall clock time: 66 minutes 9.65 seconds (3969.65 seconds total)