Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 27 17:22:35 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dre_27676/04_2023/8dre_27676_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dre_27676/04_2023/8dre_27676.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dre_27676/04_2023/8dre_27676.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dre_27676/04_2023/8dre_27676.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dre_27676/04_2023/8dre_27676_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dre_27676/04_2023/8dre_27676_updated.pdb" } resolution = 3.18 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.019 sd= 0.067 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: 5 Type Number sf(0) Gaussians P 9 5.49 5 S 138 5.16 5 C 17031 2.51 5 N 4192 2.21 5 O 4570 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 292": "OD1" <-> "OD2" Residue "A GLU 354": "OE1" <-> "OE2" Residue "A GLU 358": "OE1" <-> "OE2" Residue "A TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 396": "OE1" <-> "OE2" Residue "A PHE 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 477": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 611": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 668": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 682": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 689": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 703": "OD1" <-> "OD2" Residue "B ASP 29": "OD1" <-> "OD2" Residue "B ASP 100": "OD1" <-> "OD2" Residue "B TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 154": "OE1" <-> "OE2" Residue "B TYR 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 354": "OE1" <-> "OE2" Residue "B GLU 396": "OE1" <-> "OE2" Residue "C PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 102": "OD1" <-> "OD2" Residue "C GLU 115": "OE1" <-> "OE2" Residue "C PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 154": "OE1" <-> "OE2" Residue "C GLU 255": "OE1" <-> "OE2" Residue "C TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 102": "OD1" <-> "OD2" Residue "D GLU 154": "OE1" <-> "OE2" Residue "D PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 255": "OE1" <-> "OE2" Residue "D GLU 256": "OE1" <-> "OE2" Residue "D TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 358": "OE1" <-> "OE2" Residue "D GLU 396": "OE1" <-> "OE2" Residue "E TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 102": "OD1" <-> "OD2" Residue "E TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 245": "OE1" <-> "OE2" Residue "E PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 256": "OE1" <-> "OE2" Residue "E TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 298": "OD1" <-> "OD2" Residue "E TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 380": "OD1" <-> "OD2" Residue "E TYR 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 399": "OE1" <-> "OE2" Residue "F ASP 50": "OD1" <-> "OD2" Residue "F GLU 117": "OE1" <-> "OE2" Residue "F TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 177": "OE1" <-> "OE2" Residue "F GLU 243": "OE1" <-> "OE2" Residue "F ASP 299": "OD1" <-> "OD2" Residue "F PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 357": "OE1" <-> "OE2" Residue "F ASP 361": "OD1" <-> "OD2" Residue "F ASP 365": "OD1" <-> "OD2" Residue "F TYR 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 500": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 520": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 595": "OE1" <-> "OE2" Residue "F GLU 628": "OE1" <-> "OE2" Residue "F PHE 667": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 764": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 795": "OD1" <-> "OD2" Residue "F GLU 798": "OE1" <-> "OE2" Residue "F ASP 803": "OD1" <-> "OD2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 25940 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 5915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 717, 5915 Classifications: {'peptide': 717} Link IDs: {'PTRANS': 27, 'TRANS': 689} Chain breaks: 2 Chain: "B" Number of atoms: 5911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 716, 5911 Classifications: {'peptide': 716} Link IDs: {'PTRANS': 27, 'TRANS': 688} Chain breaks: 2 Chain: "C" Number of atoms: 2519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2519 Classifications: {'peptide': 300} Link IDs: {'PTRANS': 9, 'TRANS': 290} Chain breaks: 2 Chain: "D" Number of atoms: 2653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2653 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 9, 'TRANS': 306} Chain breaks: 2 Chain: "E" Number of atoms: 2651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2651 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 9, 'TRANS': 306} Chain breaks: 2 Chain: "F" Number of atoms: 5751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 704, 5751 Classifications: {'peptide': 704} Link IDs: {'PTRANS': 24, 'TRANS': 679} Chain breaks: 2 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 70 Unusual residues: {'PEE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PEE:plan-2': 2} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 116 Unusual residues: {'PEE': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 88 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PEE:plan-2': 2} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 55 Unusual residues: {'PEE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PEE:plan-2': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 115 Unusual residues: {'PEE': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PEE:plan-2': 2} Unresolved non-hydrogen planarities: 8 Chain: "E" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 64 Unusual residues: {'PEE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PEE:plan-2': 2} Unresolved non-hydrogen planarities: 8 Chain: "F" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 114 Unusual residues: {'PEE': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 90 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PEE:plan-2': 2} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 13.01, per 1000 atoms: 0.50 Number of scatterers: 25940 At special positions: 0 Unit cell: (119.472, 124.712, 195.976, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 138 16.00 P 9 15.00 O 4570 8.00 N 4192 7.00 C 17031 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=17, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 310 " distance=2.03 Simple disulfide: pdb=" SG CYS A 57 " - pdb=" SG CYS A 65 " distance=2.03 Simple disulfide: pdb=" SG CYS A 113 " - pdb=" SG CYS A 295 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 310 " distance=2.03 Simple disulfide: pdb=" SG CYS B 57 " - pdb=" SG CYS B 65 " distance=2.03 Simple disulfide: pdb=" SG CYS B 113 " - pdb=" SG CYS B 295 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 310 " distance=2.03 Simple disulfide: pdb=" SG CYS C 57 " - pdb=" SG CYS C 65 " distance=2.04 Simple disulfide: pdb=" SG CYS C 113 " - pdb=" SG CYS C 295 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 310 " distance=2.03 Simple disulfide: pdb=" SG CYS D 57 " - pdb=" SG CYS D 65 " distance=2.03 Simple disulfide: pdb=" SG CYS D 113 " - pdb=" SG CYS D 295 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 310 " distance=2.03 Simple disulfide: pdb=" SG CYS E 57 " - pdb=" SG CYS E 65 " distance=2.03 Simple disulfide: pdb=" SG CYS E 113 " - pdb=" SG CYS E 295 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 308 " distance=2.03 Simple disulfide: pdb=" SG CYS F 115 " - pdb=" SG CYS F 293 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.28 Conformation dependent library (CDL) restraints added in 3.4 seconds 6066 Ramachandran restraints generated. 3033 Oldfield, 0 Emsley, 3033 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5966 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 128 helices and 14 sheets defined 51.3% alpha, 6.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.94 Creating SS restraints... Processing helix chain 'A' and resid 17 through 20 Processing helix chain 'A' and resid 23 through 49 Processing helix chain 'A' and resid 103 through 116 Processing helix chain 'A' and resid 120 through 140 Proline residue: A 126 - end of helix Processing helix chain 'A' and resid 142 through 145 No H-bonds generated for 'chain 'A' and resid 142 through 145' Processing helix chain 'A' and resid 147 through 164 removed outlier: 4.203A pdb=" N LYS A 152 " --> pdb=" O ARG A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 174 Processing helix chain 'A' and resid 234 through 254 Processing helix chain 'A' and resid 259 through 288 removed outlier: 4.729A pdb=" N HIS A 287 " --> pdb=" O VAL A 283 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N ASN A 288 " --> pdb=" O TYR A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 345 removed outlier: 4.278A pdb=" N THR A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N LEU A 317 " --> pdb=" O LEU A 314 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE A 318 " --> pdb=" O ALA A 315 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ARG A 345 " --> pdb=" O TRP A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 359 Processing helix chain 'A' and resid 370 through 382 Processing helix chain 'A' and resid 384 through 393 removed outlier: 4.052A pdb=" N VAL A 392 " --> pdb=" O LYS A 388 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N PHE A 393 " --> pdb=" O ARG A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 410 Processing helix chain 'A' and resid 413 through 419 Processing helix chain 'A' and resid 440 through 443 No H-bonds generated for 'chain 'A' and resid 440 through 443' Processing helix chain 'A' and resid 463 through 466 Processing helix chain 'A' and resid 485 through 494 Processing helix chain 'A' and resid 537 through 541 removed outlier: 3.628A pdb=" N ARG A 541 " --> pdb=" O ASP A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 565 Processing helix chain 'A' and resid 586 through 589 removed outlier: 4.032A pdb=" N LYS A 589 " --> pdb=" O SER A 586 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 586 through 589' Processing helix chain 'A' and resid 609 through 612 No H-bonds generated for 'chain 'A' and resid 609 through 612' Processing helix chain 'A' and resid 630 through 637 removed outlier: 3.954A pdb=" N ILE A 633 " --> pdb=" O GLU A 630 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLN A 636 " --> pdb=" O ILE A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 660 Processing helix chain 'A' and resid 681 through 683 No H-bonds generated for 'chain 'A' and resid 681 through 683' Processing helix chain 'A' and resid 702 through 705 Processing helix chain 'A' and resid 725 through 729 Processing helix chain 'A' and resid 748 through 752 Processing helix chain 'A' and resid 771 through 775 Processing helix chain 'A' and resid 788 through 793 Processing helix chain 'A' and resid 796 through 807 Processing helix chain 'B' and resid 17 through 20 Processing helix chain 'B' and resid 23 through 48 Processing helix chain 'B' and resid 103 through 116 Processing helix chain 'B' and resid 120 through 145 Proline residue: B 126 - end of helix removed outlier: 4.559A pdb=" N TRP B 143 " --> pdb=" O CYS B 139 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N PHE B 144 " --> pdb=" O SER B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 164 removed outlier: 3.917A pdb=" N LYS B 152 " --> pdb=" O ARG B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 174 removed outlier: 3.647A pdb=" N ARG B 171 " --> pdb=" O PRO B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 254 Processing helix chain 'B' and resid 260 through 288 removed outlier: 4.778A pdb=" N HIS B 287 " --> pdb=" O VAL B 283 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N ASN B 288 " --> pdb=" O TYR B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 342 removed outlier: 4.095A pdb=" N PHE B 324 " --> pdb=" O ILE B 320 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N TYR B 325 " --> pdb=" O LEU B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 359 Processing helix chain 'B' and resid 370 through 382 Processing helix chain 'B' and resid 384 through 393 removed outlier: 4.267A pdb=" N VAL B 392 " --> pdb=" O LYS B 388 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N PHE B 393 " --> pdb=" O ARG B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 410 Processing helix chain 'B' and resid 413 through 419 Processing helix chain 'B' and resid 441 through 444 No H-bonds generated for 'chain 'B' and resid 441 through 444' Processing helix chain 'B' and resid 463 through 467 Processing helix chain 'B' and resid 485 through 494 removed outlier: 3.647A pdb=" N GLU B 493 " --> pdb=" O ALA B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 507 removed outlier: 3.878A pdb=" N GLU B 507 " --> pdb=" O ASP B 504 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 504 through 507' Processing helix chain 'B' and resid 560 through 568 removed outlier: 4.712A pdb=" N VAL B 567 " --> pdb=" O THR B 563 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N HIS B 568 " --> pdb=" O ASP B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 587 through 589 No H-bonds generated for 'chain 'B' and resid 587 through 589' Processing helix chain 'B' and resid 610 through 612 No H-bonds generated for 'chain 'B' and resid 610 through 612' Processing helix chain 'B' and resid 634 through 637 removed outlier: 3.756A pdb=" N HIS B 637 " --> pdb=" O SER B 634 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 634 through 637' Processing helix chain 'B' and resid 656 through 660 Processing helix chain 'B' and resid 680 through 683 Processing helix chain 'B' and resid 702 through 704 No H-bonds generated for 'chain 'B' and resid 702 through 704' Processing helix chain 'B' and resid 725 through 729 Processing helix chain 'B' and resid 748 through 751 Processing helix chain 'B' and resid 771 through 775 Processing helix chain 'B' and resid 788 through 793 removed outlier: 4.063A pdb=" N THR B 793 " --> pdb=" O ASP B 789 " (cutoff:3.500A) Processing helix chain 'B' and resid 796 through 807 Processing helix chain 'C' and resid 23 through 48 Processing helix chain 'C' and resid 103 through 116 Processing helix chain 'C' and resid 120 through 145 Proline residue: C 126 - end of helix removed outlier: 4.420A pdb=" N TRP C 143 " --> pdb=" O CYS C 139 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N PHE C 144 " --> pdb=" O SER C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 164 Processing helix chain 'C' and resid 168 through 174 Processing helix chain 'C' and resid 241 through 254 Processing helix chain 'C' and resid 259 through 288 removed outlier: 3.577A pdb=" N PHE C 275 " --> pdb=" O LYS C 271 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N HIS C 287 " --> pdb=" O VAL C 283 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N ASN C 288 " --> pdb=" O TYR C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 343 removed outlier: 3.500A pdb=" N ALA C 322 " --> pdb=" O PHE C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 354 through 359 Processing helix chain 'C' and resid 370 through 382 Processing helix chain 'C' and resid 384 through 391 Processing helix chain 'C' and resid 396 through 400 Processing helix chain 'D' and resid 16 through 20 removed outlier: 3.959A pdb=" N ILE D 19 " --> pdb=" O ALA D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 48 Processing helix chain 'D' and resid 103 through 116 Processing helix chain 'D' and resid 120 through 145 Proline residue: D 126 - end of helix removed outlier: 4.706A pdb=" N TRP D 143 " --> pdb=" O CYS D 139 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N PHE D 144 " --> pdb=" O SER D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 165 Processing helix chain 'D' and resid 167 through 174 Processing helix chain 'D' and resid 234 through 256 removed outlier: 3.644A pdb=" N GLU D 255 " --> pdb=" O ARG D 251 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N GLU D 256 " --> pdb=" O THR D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 288 removed outlier: 4.923A pdb=" N HIS D 287 " --> pdb=" O VAL D 283 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N ASN D 288 " --> pdb=" O TYR D 284 " (cutoff:3.500A) Processing helix chain 'D' and resid 315 through 345 Processing helix chain 'D' and resid 354 through 359 Processing helix chain 'D' and resid 370 through 382 Processing helix chain 'D' and resid 384 through 393 removed outlier: 4.682A pdb=" N VAL D 392 " --> pdb=" O LYS D 388 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N PHE D 393 " --> pdb=" O ARG D 389 " (cutoff:3.500A) Processing helix chain 'D' and resid 396 through 409 Processing helix chain 'E' and resid 16 through 18 No H-bonds generated for 'chain 'E' and resid 16 through 18' Processing helix chain 'E' and resid 23 through 49 Processing helix chain 'E' and resid 103 through 116 Processing helix chain 'E' and resid 120 through 145 Proline residue: E 126 - end of helix removed outlier: 4.499A pdb=" N TRP E 143 " --> pdb=" O CYS E 139 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N PHE E 144 " --> pdb=" O SER E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 164 Processing helix chain 'E' and resid 167 through 174 removed outlier: 3.858A pdb=" N ARG E 171 " --> pdb=" O PRO E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 234 through 254 Processing helix chain 'E' and resid 260 through 288 removed outlier: 4.720A pdb=" N HIS E 287 " --> pdb=" O VAL E 283 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N ASN E 288 " --> pdb=" O TYR E 284 " (cutoff:3.500A) Processing helix chain 'E' and resid 315 through 344 removed outlier: 3.542A pdb=" N ALA E 322 " --> pdb=" O PHE E 318 " (cutoff:3.500A) Processing helix chain 'E' and resid 353 through 357 removed outlier: 4.239A pdb=" N ARG E 357 " --> pdb=" O GLU E 354 " (cutoff:3.500A) Processing helix chain 'E' and resid 370 through 382 Processing helix chain 'E' and resid 384 through 393 removed outlier: 4.164A pdb=" N VAL E 392 " --> pdb=" O LYS E 388 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N PHE E 393 " --> pdb=" O ARG E 389 " (cutoff:3.500A) Processing helix chain 'E' and resid 396 through 408 Processing helix chain 'F' and resid 23 through 46 Processing helix chain 'F' and resid 105 through 118 Processing helix chain 'F' and resid 122 through 142 Proline residue: F 128 - end of helix Processing helix chain 'F' and resid 149 through 166 Processing helix chain 'F' and resid 169 through 178 Processing helix chain 'F' and resid 233 through 252 Processing helix chain 'F' and resid 257 through 286 removed outlier: 4.843A pdb=" N SER F 285 " --> pdb=" O SER F 281 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N LYS F 286 " --> pdb=" O ALA F 282 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 343 Processing helix chain 'F' and resid 352 through 357 removed outlier: 4.191A pdb=" N GLU F 357 " --> pdb=" O TYR F 353 " (cutoff:3.500A) Processing helix chain 'F' and resid 368 through 380 Processing helix chain 'F' and resid 382 through 391 removed outlier: 4.651A pdb=" N VAL F 390 " --> pdb=" O LYS F 386 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N PHE F 391 " --> pdb=" O ARG F 387 " (cutoff:3.500A) Processing helix chain 'F' and resid 395 through 408 Processing helix chain 'F' and resid 411 through 417 Processing helix chain 'F' and resid 461 through 465 Processing helix chain 'F' and resid 483 through 492 Processing helix chain 'F' and resid 503 through 505 No H-bonds generated for 'chain 'F' and resid 503 through 505' Processing helix chain 'F' and resid 509 through 512 Processing helix chain 'F' and resid 535 through 539 removed outlier: 4.042A pdb=" N ARG F 539 " --> pdb=" O GLU F 536 " (cutoff:3.500A) Processing helix chain 'F' and resid 558 through 563 Processing helix chain 'F' and resid 582 through 587 Processing helix chain 'F' and resid 606 through 610 Processing helix chain 'F' and resid 630 through 635 removed outlier: 4.564A pdb=" N GLN F 634 " --> pdb=" O VAL F 631 " (cutoff:3.500A) Processing helix chain 'F' and resid 654 through 658 Processing helix chain 'F' and resid 677 through 681 Processing helix chain 'F' and resid 700 through 704 removed outlier: 4.000A pdb=" N GLY F 703 " --> pdb=" O PRO F 700 " (cutoff:3.500A) Processing helix chain 'F' and resid 724 through 727 No H-bonds generated for 'chain 'F' and resid 724 through 727' Processing helix chain 'F' and resid 769 through 773 Processing helix chain 'F' and resid 786 through 790 Processing helix chain 'F' and resid 794 through 801 removed outlier: 3.839A pdb=" N MET F 800 " --> pdb=" O VAL F 796 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 53 through 56 Processing sheet with id= B, first strand: chain 'A' and resid 429 through 433 removed outlier: 6.809A pdb=" N VAL A 450 " --> pdb=" O LEU A 430 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N LEU A 432 " --> pdb=" O VAL A 450 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N LYS A 452 " --> pdb=" O LEU A 432 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N GLU A 473 " --> pdb=" O LEU A 451 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N LEU A 453 " --> pdb=" O GLU A 473 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N TRP A 475 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ALA A 497 " --> pdb=" O LEU A 474 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N LEU A 476 " --> pdb=" O ALA A 497 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N HIS A 499 " --> pdb=" O LEU A 476 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N GLU A 520 " --> pdb=" O LEU A 498 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N ILE A 500 " --> pdb=" O GLU A 520 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N HIS A 522 " --> pdb=" O ILE A 500 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N VAL A 548 " --> pdb=" O LEU A 521 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N LEU A 523 " --> pdb=" O VAL A 548 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ARG A 550 " --> pdb=" O LEU A 523 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N LYS A 571 " --> pdb=" O LEU A 549 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N LEU A 551 " --> pdb=" O LYS A 571 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N SER A 573 " --> pdb=" O LEU A 551 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N GLU A 595 " --> pdb=" O LEU A 572 " (cutoff:3.500A) removed outlier: 8.363A pdb=" N ILE A 574 " --> pdb=" O GLU A 595 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N GLU A 597 " --> pdb=" O ILE A 574 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N GLU A 618 " --> pdb=" O LEU A 596 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N LEU A 598 " --> pdb=" O GLU A 618 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ASP A 620 " --> pdb=" O LEU A 598 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N CYS A 643 " --> pdb=" O ILE A 619 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 459 through 461 Processing sheet with id= D, first strand: chain 'A' and resid 666 through 668 removed outlier: 6.568A pdb=" N TYR A 689 " --> pdb=" O LEU A 667 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'B' and resid 53 through 56 Processing sheet with id= F, first strand: chain 'B' and resid 420 through 422 removed outlier: 7.556A pdb=" N VAL B 450 " --> pdb=" O LEU B 430 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N LEU B 432 " --> pdb=" O VAL B 450 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LYS B 452 " --> pdb=" O LEU B 432 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N GLU B 473 " --> pdb=" O LEU B 451 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N LEU B 453 " --> pdb=" O GLU B 473 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N TRP B 475 " --> pdb=" O LEU B 453 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N ALA B 497 " --> pdb=" O LEU B 474 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N LEU B 476 " --> pdb=" O ALA B 497 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N HIS B 499 " --> pdb=" O LEU B 476 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N GLU B 520 " --> pdb=" O LEU B 498 " (cutoff:3.500A) removed outlier: 8.563A pdb=" N ILE B 500 " --> pdb=" O GLU B 520 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N HIS B 522 " --> pdb=" O ILE B 500 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N VAL B 548 " --> pdb=" O LEU B 521 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N LEU B 523 " --> pdb=" O VAL B 548 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ARG B 550 " --> pdb=" O LEU B 523 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N LYS B 571 " --> pdb=" O LEU B 549 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N LEU B 551 " --> pdb=" O LYS B 571 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N SER B 573 " --> pdb=" O LEU B 551 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N GLU B 595 " --> pdb=" O LEU B 572 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N ILE B 574 " --> pdb=" O GLU B 595 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N GLU B 597 " --> pdb=" O ILE B 574 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N GLU B 618 " --> pdb=" O LEU B 596 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N LEU B 598 " --> pdb=" O GLU B 618 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N ASP B 620 " --> pdb=" O LEU B 598 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N CYS B 643 " --> pdb=" O ILE B 619 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ARG B 666 " --> pdb=" O LEU B 644 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N TYR B 689 " --> pdb=" O LEU B 667 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 459 through 461 Processing sheet with id= H, first strand: chain 'B' and resid 712 through 714 removed outlier: 6.748A pdb=" N ALA B 735 " --> pdb=" O LEU B 713 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N GLN B 758 " --> pdb=" O LEU B 736 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'C' and resid 53 through 56 Processing sheet with id= J, first strand: chain 'D' and resid 52 through 56 Processing sheet with id= K, first strand: chain 'E' and resid 53 through 56 Processing sheet with id= L, first strand: chain 'F' and resid 52 through 56 Processing sheet with id= M, first strand: chain 'F' and resid 427 through 431 removed outlier: 7.314A pdb=" N SER F 448 " --> pdb=" O LEU F 428 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N LEU F 430 " --> pdb=" O SER F 448 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N LYS F 450 " --> pdb=" O LEU F 430 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N GLU F 471 " --> pdb=" O LEU F 449 " (cutoff:3.500A) removed outlier: 8.307A pdb=" N LEU F 451 " --> pdb=" O GLU F 471 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N CYS F 473 " --> pdb=" O LEU F 451 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL F 495 " --> pdb=" O LEU F 472 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N LEU F 474 " --> pdb=" O VAL F 495 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N SER F 497 " --> pdb=" O LEU F 474 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N GLU F 518 " --> pdb=" O LEU F 496 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N VAL F 498 " --> pdb=" O GLU F 518 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N TYR F 520 " --> pdb=" O VAL F 498 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N ILE F 546 " --> pdb=" O LEU F 519 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LYS F 569 " --> pdb=" O LEU F 547 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N ILE F 549 " --> pdb=" O LYS F 569 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N CYS F 571 " --> pdb=" O ILE F 549 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N GLU F 593 " --> pdb=" O MET F 570 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N VAL F 572 " --> pdb=" O GLU F 593 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N GLU F 595 " --> pdb=" O VAL F 572 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N GLU F 616 " --> pdb=" O LEU F 594 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N LEU F 596 " --> pdb=" O GLU F 616 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N ASP F 618 " --> pdb=" O LEU F 596 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N VAL F 641 " --> pdb=" O LEU F 617 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N ARG F 664 " --> pdb=" O LEU F 642 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N TYR F 687 " --> pdb=" O LEU F 665 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N TYR F 710 " --> pdb=" O LEU F 688 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N THR F 733 " --> pdb=" O PHE F 711 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N TYR F 756 " --> pdb=" O LEU F 734 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'F' and resid 457 through 459 1073 hydrogen bonds defined for protein. 3015 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: 8.86 Time building geometry restraints manager: 10.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 4501 1.33 - 1.45: 6761 1.45 - 1.57: 15055 1.57 - 1.70: 10 1.70 - 1.82: 204 Bond restraints: 26531 Sorted by residual: bond pdb=" C LYS F 399 " pdb=" N LEU F 400 " ideal model delta sigma weight residual 1.335 1.445 -0.110 1.31e-02 5.83e+03 7.02e+01 bond pdb=" C10 PEE F 902 " pdb=" O4 PEE F 902 " ideal model delta sigma weight residual 1.206 1.358 -0.152 2.00e-02 2.50e+03 5.79e+01 bond pdb=" C10 PEE E 902 " pdb=" O4 PEE E 902 " ideal model delta sigma weight residual 1.206 1.358 -0.152 2.00e-02 2.50e+03 5.74e+01 bond pdb=" C10 PEE F 903 " pdb=" O4 PEE F 903 " ideal model delta sigma weight residual 1.206 1.357 -0.151 2.00e-02 2.50e+03 5.72e+01 bond pdb=" C10 PEE C 902 " pdb=" O4 PEE C 902 " ideal model delta sigma weight residual 1.206 1.357 -0.151 2.00e-02 2.50e+03 5.68e+01 ... (remaining 26526 not shown) Histogram of bond angle deviations from ideal: 90.62 - 99.40: 12 99.40 - 108.19: 1089 108.19 - 116.97: 17418 116.97 - 125.76: 16817 125.76 - 134.55: 454 Bond angle restraints: 35790 Sorted by residual: angle pdb=" C LYS F 399 " pdb=" N LEU F 400 " pdb=" CA LEU F 400 " ideal model delta sigma weight residual 120.28 110.14 10.14 1.34e+00 5.57e-01 5.73e+01 angle pdb=" CA LYS F 399 " pdb=" C LYS F 399 " pdb=" N LEU F 400 " ideal model delta sigma weight residual 117.17 109.59 7.58 1.18e+00 7.18e-01 4.12e+01 angle pdb=" O LYS F 399 " pdb=" C LYS F 399 " pdb=" N LEU F 400 " ideal model delta sigma weight residual 122.09 128.79 -6.70 1.08e+00 8.57e-01 3.85e+01 angle pdb=" C ASN F 368 " pdb=" CA ASN F 368 " pdb=" CB ASN F 368 " ideal model delta sigma weight residual 116.63 109.95 6.68 1.16e+00 7.43e-01 3.32e+01 angle pdb=" C ASN E 370 " pdb=" CA ASN E 370 " pdb=" CB ASN E 370 " ideal model delta sigma weight residual 116.63 110.17 6.46 1.16e+00 7.43e-01 3.10e+01 ... (remaining 35785 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.76: 15420 35.76 - 71.51: 533 71.51 - 107.27: 21 107.27 - 143.02: 9 143.02 - 178.78: 14 Dihedral angle restraints: 15997 sinusoidal: 6826 harmonic: 9171 Sorted by residual: dihedral pdb=" CB CYS C 57 " pdb=" SG CYS C 57 " pdb=" SG CYS C 65 " pdb=" CB CYS C 65 " ideal model delta sinusoidal sigma weight residual -86.00 -6.58 -79.42 1 1.00e+01 1.00e-02 7.84e+01 dihedral pdb=" CB CYS E 113 " pdb=" SG CYS E 113 " pdb=" SG CYS E 295 " pdb=" CB CYS E 295 " ideal model delta sinusoidal sigma weight residual 93.00 48.87 44.13 1 1.00e+01 1.00e-02 2.71e+01 dihedral pdb=" CB CYS D 113 " pdb=" SG CYS D 113 " pdb=" SG CYS D 295 " pdb=" CB CYS D 295 " ideal model delta sinusoidal sigma weight residual 93.00 51.95 41.05 1 1.00e+01 1.00e-02 2.36e+01 ... (remaining 15994 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 3762 0.084 - 0.168: 227 0.168 - 0.252: 9 0.252 - 0.336: 2 0.336 - 0.420: 7 Chirality restraints: 4007 Sorted by residual: chirality pdb=" C2 PEE D 901 " pdb=" C1 PEE D 901 " pdb=" C3 PEE D 901 " pdb=" O2 PEE D 901 " both_signs ideal model delta sigma weight residual False -2.33 -2.75 0.42 2.00e-01 2.50e+01 4.42e+00 chirality pdb=" C2 PEE D 904 " pdb=" C1 PEE D 904 " pdb=" C3 PEE D 904 " pdb=" O2 PEE D 904 " both_signs ideal model delta sigma weight residual False -2.33 -2.74 0.42 2.00e-01 2.50e+01 4.33e+00 chirality pdb=" C2 PEE C 901 " pdb=" C1 PEE C 901 " pdb=" C3 PEE C 901 " pdb=" O2 PEE C 901 " both_signs ideal model delta sigma weight residual False -2.33 -2.74 0.41 2.00e-01 2.50e+01 4.18e+00 ... (remaining 4004 not shown) Planarity restraints: 4356 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 23 " -0.023 2.00e-02 2.50e+03 2.21e-02 1.23e+01 pdb=" CG TRP C 23 " 0.060 2.00e-02 2.50e+03 pdb=" CD1 TRP C 23 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP C 23 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP C 23 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP C 23 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C 23 " -0.010 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 23 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 23 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP C 23 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS F 399 " 0.016 2.00e-02 2.50e+03 3.43e-02 1.18e+01 pdb=" C LYS F 399 " -0.059 2.00e-02 2.50e+03 pdb=" O LYS F 399 " 0.024 2.00e-02 2.50e+03 pdb=" N LEU F 400 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 795 " 0.047 5.00e-02 4.00e+02 7.16e-02 8.20e+00 pdb=" N PRO A 796 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO A 796 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 796 " 0.039 5.00e-02 4.00e+02 ... (remaining 4353 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 3030 2.75 - 3.29: 25509 3.29 - 3.83: 45438 3.83 - 4.36: 53961 4.36 - 4.90: 90741 Nonbonded interactions: 218679 Sorted by model distance: nonbonded pdb=" O SER F 168 " pdb=" OG1 THR F 171 " model vdw 2.216 2.440 nonbonded pdb=" O ILE B 356 " pdb=" OG SER B 360 " model vdw 2.240 2.440 nonbonded pdb=" O ILE F 556 " pdb=" ND2 ASN F 584 " model vdw 2.257 2.520 nonbonded pdb=" O THR A 44 " pdb=" OG1 THR A 48 " model vdw 2.260 2.440 nonbonded pdb=" O TRP A 411 " pdb=" OG1 THR A 441 " model vdw 2.272 2.440 ... (remaining 218674 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 15 through 175 or resid 231 through 808 or resid 901 or (r \ esid 902 and (name C10 or name C11 or name C12 or name C13 or name C14 or name C \ 15 or name C16 or name C17 or name C18 or name O2 or name O4 )) or (resid 903 an \ d (name C10 or name C11 or name C12 or name C13 or name C14 or name C15 or name \ C16 or name C17 or name O2 or name O4 )))) selection = (chain 'B' and (resid 15 through 808 or resid 901 through 903)) } ncs_group { reference = (chain 'C' and (resid 15 through 402 or (resid 901 through 902 and (name C10 or \ name C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C17 \ or name O2 or name O4 )))) selection = (chain 'D' and (resid 15 through 175 or resid 240 through 402 or (resid 903 thro \ ugh 904 and (name C10 or name C11 or name C12 or name C13 or name C14 or name C1 \ 5 or name C16 or name C17 or name O2 or name O4 )))) selection = (chain 'E' and (resid 15 through 175 or resid 240 through 402 or resid 902 throu \ gh 903)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.490 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: 17.260 Check model and map are aligned: 0.370 Set scattering table: 0.220 Process input model: 61.210 Find NCS groups from input model: 1.740 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.152 26531 Z= 0.360 Angle : 0.803 13.914 35790 Z= 0.404 Chirality : 0.047 0.420 4007 Planarity : 0.005 0.072 4356 Dihedral : 18.170 178.780 9980 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer Outliers : 0.25 % 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: -0.71 (0.15), residues: 3033 helix: 0.17 (0.12), residues: 1638 sheet: -1.32 (0.32), residues: 286 loop : -1.05 (0.18), residues: 1109 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6066 Ramachandran restraints generated. 3033 Oldfield, 0 Emsley, 3033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6066 Ramachandran restraints generated. 3033 Oldfield, 0 Emsley, 3033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 256 time to evaluate : 3.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 259 average time/residue: 0.3920 time to fit residues: 164.0254 Evaluate side-chains 212 residues out of total 2856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 209 time to evaluate : 3.339 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2684 time to fit residues: 6.0348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 256 optimal weight: 0.5980 chunk 230 optimal weight: 0.9990 chunk 127 optimal weight: 0.0040 chunk 78 optimal weight: 0.7980 chunk 155 optimal weight: 7.9990 chunk 123 optimal weight: 10.0000 chunk 238 optimal weight: 0.9980 chunk 92 optimal weight: 0.9980 chunk 144 optimal weight: 0.8980 chunk 177 optimal weight: 0.8980 chunk 276 optimal weight: 1.9990 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 711 GLN B 499 HIS ** B 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 66 ASN D 253 HIS ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 402 GLN ** F 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 635 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.0801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 26531 Z= 0.165 Angle : 0.480 8.251 35790 Z= 0.253 Chirality : 0.039 0.174 4007 Planarity : 0.004 0.055 4356 Dihedral : 14.287 179.281 3705 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer Outliers : 1.86 % 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: -0.11 (0.15), residues: 3033 helix: 0.79 (0.13), residues: 1632 sheet: -1.42 (0.32), residues: 284 loop : -0.87 (0.18), residues: 1117 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6066 Ramachandran restraints generated. 3033 Oldfield, 0 Emsley, 3033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6066 Ramachandran restraints generated. 3033 Oldfield, 0 Emsley, 3033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 217 time to evaluate : 2.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 53 outliers final: 24 residues processed: 257 average time/residue: 0.3694 time to fit residues: 157.4166 Evaluate side-chains 231 residues out of total 2856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 207 time to evaluate : 3.040 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.2518 time to fit residues: 15.5249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 153 optimal weight: 0.9980 chunk 85 optimal weight: 10.0000 chunk 229 optimal weight: 0.8980 chunk 187 optimal weight: 0.7980 chunk 76 optimal weight: 10.0000 chunk 276 optimal weight: 1.9990 chunk 298 optimal weight: 6.9990 chunk 246 optimal weight: 4.9990 chunk 274 optimal weight: 5.9990 chunk 94 optimal weight: 0.9980 chunk 221 optimal weight: 1.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 404 GLN D 408 ASN E 155 HIS ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 60 GLN F 107 GLN ** F 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.1223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 26531 Z= 0.236 Angle : 0.495 8.388 35790 Z= 0.259 Chirality : 0.040 0.175 4007 Planarity : 0.003 0.044 4356 Dihedral : 13.317 174.072 3705 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer Outliers : 1.96 % 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: -0.05 (0.15), residues: 3033 helix: 0.84 (0.13), residues: 1641 sheet: -1.39 (0.32), residues: 292 loop : -0.85 (0.19), residues: 1100 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6066 Ramachandran restraints generated. 3033 Oldfield, 0 Emsley, 3033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6066 Ramachandran restraints generated. 3033 Oldfield, 0 Emsley, 3033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 223 time to evaluate : 2.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 56 outliers final: 26 residues processed: 271 average time/residue: 0.3645 time to fit residues: 162.1520 Evaluate side-chains 234 residues out of total 2856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 208 time to evaluate : 3.216 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.2379 time to fit residues: 15.8718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 273 optimal weight: 10.0000 chunk 207 optimal weight: 0.5980 chunk 143 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 131 optimal weight: 5.9990 chunk 185 optimal weight: 0.9990 chunk 277 optimal weight: 20.0000 chunk 293 optimal weight: 1.9990 chunk 145 optimal weight: 3.9990 chunk 263 optimal weight: 6.9990 chunk 79 optimal weight: 0.8980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 404 GLN E 155 HIS E 312 HIS ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 416 GLN ** F 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.1462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 26531 Z= 0.229 Angle : 0.491 10.743 35790 Z= 0.255 Chirality : 0.039 0.161 4007 Planarity : 0.003 0.041 4356 Dihedral : 12.750 175.484 3705 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer Outliers : 1.37 % 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: 0.02 (0.15), residues: 3033 helix: 0.91 (0.13), residues: 1630 sheet: -1.40 (0.32), residues: 285 loop : -0.83 (0.19), residues: 1118 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6066 Ramachandran restraints generated. 3033 Oldfield, 0 Emsley, 3033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6066 Ramachandran restraints generated. 3033 Oldfield, 0 Emsley, 3033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 214 time to evaluate : 3.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 12 residues processed: 242 average time/residue: 0.3524 time to fit residues: 144.7031 Evaluate side-chains 214 residues out of total 2856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 202 time to evaluate : 3.277 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.2502 time to fit residues: 9.8730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 244 optimal weight: 5.9990 chunk 166 optimal weight: 6.9990 chunk 4 optimal weight: 0.9980 chunk 218 optimal weight: 2.9990 chunk 121 optimal weight: 10.0000 chunk 250 optimal weight: 1.9990 chunk 203 optimal weight: 6.9990 chunk 0 optimal weight: 2.9990 chunk 150 optimal weight: 0.9980 chunk 263 optimal weight: 0.7980 chunk 74 optimal weight: 0.6980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 288 ASN ** F 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 26531 Z= 0.233 Angle : 0.489 9.458 35790 Z= 0.254 Chirality : 0.040 0.178 4007 Planarity : 0.003 0.040 4356 Dihedral : 12.138 179.402 3705 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer Outliers : 1.72 % 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: 0.05 (0.15), residues: 3033 helix: 0.92 (0.13), residues: 1631 sheet: -1.19 (0.33), residues: 272 loop : -0.87 (0.19), residues: 1130 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6066 Ramachandran restraints generated. 3033 Oldfield, 0 Emsley, 3033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6066 Ramachandran restraints generated. 3033 Oldfield, 0 Emsley, 3033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 209 time to evaluate : 3.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 49 outliers final: 25 residues processed: 245 average time/residue: 0.3518 time to fit residues: 144.1582 Evaluate side-chains 229 residues out of total 2856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 204 time to evaluate : 2.962 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.2885 time to fit residues: 17.0041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 98 optimal weight: 4.9990 chunk 264 optimal weight: 8.9990 chunk 58 optimal weight: 0.0040 chunk 172 optimal weight: 2.9990 chunk 72 optimal weight: 0.7980 chunk 294 optimal weight: 0.0060 chunk 244 optimal weight: 0.8980 chunk 136 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 154 optimal weight: 8.9990 overall best weight: 0.5410 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 155 HIS ** F 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.040 26531 Z= 0.158 Angle : 0.477 11.285 35790 Z= 0.244 Chirality : 0.039 0.455 4007 Planarity : 0.003 0.036 4356 Dihedral : 11.425 179.275 3705 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer Outliers : 0.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.16), residues: 3033 helix: 1.05 (0.13), residues: 1627 sheet: -1.20 (0.33), residues: 271 loop : -0.81 (0.19), residues: 1135 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6066 Ramachandran restraints generated. 3033 Oldfield, 0 Emsley, 3033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6066 Ramachandran restraints generated. 3033 Oldfield, 0 Emsley, 3033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 211 time to evaluate : 2.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 7 residues processed: 231 average time/residue: 0.3634 time to fit residues: 139.3852 Evaluate side-chains 210 residues out of total 2856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 203 time to evaluate : 3.030 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.3801 time to fit residues: 8.4131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 283 optimal weight: 20.0000 chunk 33 optimal weight: 0.4980 chunk 167 optimal weight: 7.9990 chunk 214 optimal weight: 0.9990 chunk 166 optimal weight: 0.7980 chunk 247 optimal weight: 2.9990 chunk 164 optimal weight: 3.9990 chunk 293 optimal weight: 0.9990 chunk 183 optimal weight: 3.9990 chunk 178 optimal weight: 0.7980 chunk 135 optimal weight: 10.0000 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 155 HIS ** F 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 26531 Z= 0.191 Angle : 0.489 13.449 35790 Z= 0.249 Chirality : 0.039 0.402 4007 Planarity : 0.003 0.034 4356 Dihedral : 10.942 175.278 3705 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer Outliers : 0.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.16), residues: 3033 helix: 1.04 (0.13), residues: 1632 sheet: -1.16 (0.33), residues: 271 loop : -0.77 (0.19), residues: 1130 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6066 Ramachandran restraints generated. 3033 Oldfield, 0 Emsley, 3033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6066 Ramachandran restraints generated. 3033 Oldfield, 0 Emsley, 3033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 210 time to evaluate : 3.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 16 residues processed: 226 average time/residue: 0.3851 time to fit residues: 143.0849 Evaluate side-chains 221 residues out of total 2856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 205 time to evaluate : 3.106 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.2606 time to fit residues: 12.1119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 181 optimal weight: 0.7980 chunk 117 optimal weight: 2.9990 chunk 174 optimal weight: 0.7980 chunk 88 optimal weight: 0.5980 chunk 57 optimal weight: 6.9990 chunk 56 optimal weight: 0.0040 chunk 186 optimal weight: 9.9990 chunk 199 optimal weight: 0.8980 chunk 144 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 230 optimal weight: 5.9990 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 46 GLN ** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 26531 Z= 0.166 Angle : 0.488 12.245 35790 Z= 0.248 Chirality : 0.039 0.393 4007 Planarity : 0.003 0.034 4356 Dihedral : 10.428 171.086 3705 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer Outliers : 0.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.16), residues: 3033 helix: 1.06 (0.13), residues: 1631 sheet: -1.34 (0.31), residues: 297 loop : -0.67 (0.19), residues: 1105 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6066 Ramachandran restraints generated. 3033 Oldfield, 0 Emsley, 3033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6066 Ramachandran restraints generated. 3033 Oldfield, 0 Emsley, 3033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 212 time to evaluate : 2.914 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 3 residues processed: 220 average time/residue: 0.3746 time to fit residues: 135.0266 Evaluate side-chains 202 residues out of total 2856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 199 time to evaluate : 3.126 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2668 time to fit residues: 5.7995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 266 optimal weight: 0.0970 chunk 280 optimal weight: 0.0470 chunk 256 optimal weight: 2.9990 chunk 273 optimal weight: 7.9990 chunk 164 optimal weight: 0.9990 chunk 118 optimal weight: 9.9990 chunk 214 optimal weight: 3.9990 chunk 83 optimal weight: 0.9990 chunk 246 optimal weight: 1.9990 chunk 258 optimal weight: 3.9990 chunk 272 optimal weight: 6.9990 overall best weight: 0.8282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 155 HIS E 404 GLN E 408 ASN ** F 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 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 : 0.003 0.042 26531 Z= 0.195 Angle : 0.508 13.006 35790 Z= 0.256 Chirality : 0.040 0.372 4007 Planarity : 0.003 0.037 4356 Dihedral : 9.994 165.725 3705 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer Outliers : 0.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.16), residues: 3033 helix: 1.03 (0.13), residues: 1637 sheet: -1.29 (0.31), residues: 308 loop : -0.66 (0.19), residues: 1088 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6066 Ramachandran restraints generated. 3033 Oldfield, 0 Emsley, 3033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6066 Ramachandran restraints generated. 3033 Oldfield, 0 Emsley, 3033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 207 time to evaluate : 3.223 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 212 average time/residue: 0.3896 time to fit residues: 136.0908 Evaluate side-chains 209 residues out of total 2856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 204 time to evaluate : 3.152 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.3189 time to fit residues: 7.3317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 179 optimal weight: 0.9990 chunk 288 optimal weight: 1.9990 chunk 176 optimal weight: 0.8980 chunk 136 optimal weight: 0.7980 chunk 200 optimal weight: 0.6980 chunk 302 optimal weight: 1.9990 chunk 278 optimal weight: 6.9990 chunk 241 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 186 optimal weight: 2.9990 chunk 147 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 650 HIS ** B 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 155 HIS ** F 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 26531 Z= 0.202 Angle : 0.507 11.506 35790 Z= 0.257 Chirality : 0.040 0.379 4007 Planarity : 0.003 0.043 4356 Dihedral : 9.229 155.672 3705 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer Outliers : 0.21 % 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: 0.22 (0.16), residues: 3033 helix: 1.00 (0.13), residues: 1637 sheet: -1.24 (0.31), residues: 303 loop : -0.62 (0.19), residues: 1093 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6066 Ramachandran restraints generated. 3033 Oldfield, 0 Emsley, 3033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6066 Ramachandran restraints generated. 3033 Oldfield, 0 Emsley, 3033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 211 time to evaluate : 3.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 216 average time/residue: 0.3908 time to fit residues: 139.7012 Evaluate side-chains 207 residues out of total 2856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 206 time to evaluate : 3.348 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2242 time to fit residues: 4.2994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 191 optimal weight: 0.8980 chunk 256 optimal weight: 0.7980 chunk 73 optimal weight: 2.9990 chunk 222 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 67 optimal weight: 0.0070 chunk 241 optimal weight: 0.6980 chunk 101 optimal weight: 0.9990 chunk 248 optimal weight: 4.9990 chunk 30 optimal weight: 0.6980 chunk 44 optimal weight: 7.9990 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 155 HIS ** F 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.130209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.093189 restraints weight = 61016.704| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 2.91 r_work: 0.3404 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 26531 Z= 0.170 Angle : 0.501 11.453 35790 Z= 0.254 Chirality : 0.039 0.364 4007 Planarity : 0.004 0.156 4356 Dihedral : 8.582 146.943 3705 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer Outliers : 0.21 % 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: 0.25 (0.16), residues: 3033 helix: 1.02 (0.13), residues: 1642 sheet: -1.19 (0.31), residues: 301 loop : -0.63 (0.19), residues: 1090 =============================================================================== Job complete usr+sys time: 4975.02 seconds wall clock time: 92 minutes 10.70 seconds (5530.70 seconds total)