Starting phenix.real_space_refine on Sat Dec 9 12:51:49 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6of3_20041/12_2023/6of3_20041_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6of3_20041/12_2023/6of3_20041.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6of3_20041/12_2023/6of3_20041.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6of3_20041/12_2023/6of3_20041.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6of3_20041/12_2023/6of3_20041_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6of3_20041/12_2023/6of3_20041_updated.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.657 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 56 5.16 5 C 7070 2.51 5 N 1938 2.21 5 O 2024 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 289": "NH1" <-> "NH2" Residue "B PHE 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 626": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 289": "NH1" <-> "NH2" Residue "E PHE 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 626": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 11096 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1471 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 8, 'TRANS': 178} Chain breaks: 2 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 4045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4045 Classifications: {'peptide': 528} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 52, 'TRANS': 475} Unresolved chain links: 1 Chain breaks: 4 Unresolved chain link angles: 5 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "D" Number of atoms: 1471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1471 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 8, 'TRANS': 178} Chain breaks: 2 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "E" Number of atoms: 4045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4045 Classifications: {'peptide': 528} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 52, 'TRANS': 475} Unresolved chain links: 1 Chain breaks: 4 Unresolved chain link angles: 5 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.64, per 1000 atoms: 0.51 Number of scatterers: 11096 At special positions: 0 Unit cell: (150.12, 87.48, 88.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 56 16.00 P 6 15.00 Mg 2 11.99 O 2024 8.00 N 1938 7.00 C 7070 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 3.83 Conformation dependent library (CDL) restraints added in 1.9 seconds 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2668 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 44 helices and 14 sheets defined 35.5% alpha, 13.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 165.71 Creating SS restraints... Processing helix chain 'A' and resid 12 through 22 Processing helix chain 'A' and resid 24 through 27 No H-bonds generated for 'chain 'A' and resid 24 through 27' Processing helix chain 'A' and resid 41 through 63 Processing helix chain 'A' and resid 68 through 83 Processing helix chain 'A' and resid 94 through 114 Processing helix chain 'A' and resid 124 through 131 Processing helix chain 'A' and resid 135 through 145 Processing helix chain 'A' and resid 152 through 169 Processing helix chain 'A' and resid 171 through 174 Processing helix chain 'B' and resid 196 through 206 Processing helix chain 'B' and resid 208 through 210 No H-bonds generated for 'chain 'B' and resid 208 through 210' Processing helix chain 'B' and resid 243 through 258 removed outlier: 3.704A pdb=" N ARG B 258 " --> pdb=" O THR B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 287 Processing helix chain 'B' and resid 331 through 333 No H-bonds generated for 'chain 'B' and resid 331 through 333' Processing helix chain 'B' and resid 368 through 388 removed outlier: 4.415A pdb=" N GLN B 388 " --> pdb=" O ARG B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 416 removed outlier: 3.814A pdb=" N LEU B 416 " --> pdb=" O ILE B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 442 Processing helix chain 'B' and resid 471 through 483 removed outlier: 3.529A pdb=" N PHE B 483 " --> pdb=" O MET B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 543 removed outlier: 4.226A pdb=" N SER B 540 " --> pdb=" O PRO B 536 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ASP B 541 " --> pdb=" O GLU B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 626 No H-bonds generated for 'chain 'B' and resid 624 through 626' Processing helix chain 'B' and resid 655 through 659 Processing helix chain 'B' and resid 677 through 690 removed outlier: 4.016A pdb=" N VAL B 681 " --> pdb=" O THR B 677 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N GLY B 683 " --> pdb=" O ALA B 679 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N LEU B 684 " --> pdb=" O TYR B 680 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 22 Processing helix chain 'D' and resid 24 through 27 No H-bonds generated for 'chain 'D' and resid 24 through 27' Processing helix chain 'D' and resid 41 through 63 Processing helix chain 'D' and resid 68 through 83 Processing helix chain 'D' and resid 94 through 114 Processing helix chain 'D' and resid 124 through 131 Processing helix chain 'D' and resid 135 through 145 Processing helix chain 'D' and resid 152 through 169 Processing helix chain 'D' and resid 171 through 174 Processing helix chain 'E' and resid 196 through 206 Processing helix chain 'E' and resid 208 through 210 No H-bonds generated for 'chain 'E' and resid 208 through 210' Processing helix chain 'E' and resid 243 through 258 removed outlier: 3.704A pdb=" N ARG E 258 " --> pdb=" O THR E 254 " (cutoff:3.500A) Processing helix chain 'E' and resid 274 through 287 Processing helix chain 'E' and resid 331 through 333 No H-bonds generated for 'chain 'E' and resid 331 through 333' Processing helix chain 'E' and resid 368 through 388 removed outlier: 4.415A pdb=" N GLN E 388 " --> pdb=" O ARG E 384 " (cutoff:3.500A) Processing helix chain 'E' and resid 403 through 416 removed outlier: 3.814A pdb=" N LEU E 416 " --> pdb=" O ILE E 413 " (cutoff:3.500A) Processing helix chain 'E' and resid 430 through 442 Processing helix chain 'E' and resid 471 through 483 removed outlier: 3.529A pdb=" N PHE E 483 " --> pdb=" O MET E 479 " (cutoff:3.500A) Processing helix chain 'E' and resid 536 through 543 removed outlier: 4.227A pdb=" N SER E 540 " --> pdb=" O PRO E 536 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ASP E 541 " --> pdb=" O GLU E 537 " (cutoff:3.500A) Processing helix chain 'E' and resid 624 through 626 No H-bonds generated for 'chain 'E' and resid 624 through 626' Processing helix chain 'E' and resid 655 through 659 Processing helix chain 'E' and resid 677 through 690 removed outlier: 4.017A pdb=" N VAL E 681 " --> pdb=" O THR E 677 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLY E 683 " --> pdb=" O ALA E 679 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N LEU E 684 " --> pdb=" O TYR E 680 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 122 through 125 removed outlier: 3.765A pdb=" N GLN B 151 " --> pdb=" O VAL B 188 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N GLU B 190 " --> pdb=" O VAL B 149 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N VAL B 149 " --> pdb=" O GLU B 190 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N LEU B 192 " --> pdb=" O VAL B 147 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N VAL B 147 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLY B 143 " --> pdb=" O ALA B 172 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 137 through 140 removed outlier: 3.920A pdb=" N GLU B 153 " --> pdb=" O ALA B 184 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 141 through 143 removed outlier: 3.572A pdb=" N LEU B 142 " --> pdb=" O GLN B 222 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 447 through 450 removed outlier: 6.925A pdb=" N LEU B 393 " --> pdb=" O LEU B 264 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N ILE B 266 " --> pdb=" O LEU B 393 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N VAL B 395 " --> pdb=" O ILE B 266 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N MET B 301 " --> pdb=" O VAL B 394 " (cutoff:3.500A) removed outlier: 8.363A pdb=" N ASN B 396 " --> pdb=" O MET B 301 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N LEU B 303 " --> pdb=" O ASN B 396 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ARG B 355 " --> pdb=" O LEU B 320 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N LYS B 322 " --> pdb=" O THR B 353 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N THR B 353 " --> pdb=" O LYS B 322 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 511 through 514 Processing sheet with id= F, first strand: chain 'B' and resid 527 through 529 removed outlier: 6.681A pdb=" N LEU B 668 " --> pdb=" O VAL B 528 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 551 through 553 Processing sheet with id= H, first strand: chain 'E' and resid 122 through 125 removed outlier: 3.764A pdb=" N GLN E 151 " --> pdb=" O VAL E 188 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N GLU E 190 " --> pdb=" O VAL E 149 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N VAL E 149 " --> pdb=" O GLU E 190 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N LEU E 192 " --> pdb=" O VAL E 147 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N VAL E 147 " --> pdb=" O LEU E 192 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLY E 143 " --> pdb=" O ALA E 172 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 137 through 140 removed outlier: 3.920A pdb=" N GLU E 153 " --> pdb=" O ALA E 184 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 141 through 143 removed outlier: 3.573A pdb=" N LEU E 142 " --> pdb=" O GLN E 222 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 447 through 450 removed outlier: 6.924A pdb=" N LEU E 393 " --> pdb=" O LEU E 264 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N ILE E 266 " --> pdb=" O LEU E 393 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N VAL E 395 " --> pdb=" O ILE E 266 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N MET E 301 " --> pdb=" O VAL E 394 " (cutoff:3.500A) removed outlier: 8.364A pdb=" N ASN E 396 " --> pdb=" O MET E 301 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N LEU E 303 " --> pdb=" O ASN E 396 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ARG E 355 " --> pdb=" O LEU E 320 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N LYS E 322 " --> pdb=" O THR E 353 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N THR E 353 " --> pdb=" O LYS E 322 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 511 through 514 Processing sheet with id= M, first strand: chain 'E' and resid 527 through 529 removed outlier: 6.683A pdb=" N LEU E 668 " --> pdb=" O VAL E 528 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 551 through 553 438 hydrogen bonds defined for protein. 1146 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: 3.45 Time building geometry restraints manager: 4.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.37: 3761 1.37 - 1.51: 3752 1.51 - 1.65: 3795 1.65 - 1.80: 60 1.80 - 1.94: 30 Bond restraints: 11398 Sorted by residual: bond pdb=" C GLN E 115 " pdb=" N PRO E 116 " ideal model delta sigma weight residual 1.334 1.401 -0.067 2.34e-02 1.83e+03 8.14e+00 bond pdb=" C GLN B 115 " pdb=" N PRO B 116 " ideal model delta sigma weight residual 1.334 1.400 -0.066 2.34e-02 1.83e+03 8.06e+00 bond pdb=" O3G AGS E 801 " pdb=" PG AGS E 801 " ideal model delta sigma weight residual 1.558 1.503 0.055 2.00e-02 2.50e+03 7.55e+00 bond pdb=" O3G AGS B 801 " pdb=" PG AGS B 801 " ideal model delta sigma weight residual 1.558 1.504 0.054 2.00e-02 2.50e+03 7.37e+00 bond pdb=" O2G AGS B 801 " pdb=" PG AGS B 801 " ideal model delta sigma weight residual 1.557 1.503 0.054 2.00e-02 2.50e+03 7.31e+00 ... (remaining 11393 not shown) Histogram of bond angle deviations from ideal: 97.60 - 105.69: 547 105.69 - 113.78: 6146 113.78 - 121.87: 5912 121.87 - 129.97: 2813 129.97 - 138.06: 152 Bond angle restraints: 15570 Sorted by residual: angle pdb=" C THR B 641 " pdb=" N ALA B 642 " pdb=" CA ALA B 642 " ideal model delta sigma weight residual 121.54 138.06 -16.52 1.91e+00 2.74e-01 7.48e+01 angle pdb=" C THR E 641 " pdb=" N ALA E 642 " pdb=" CA ALA E 642 " ideal model delta sigma weight residual 121.54 138.00 -16.46 1.91e+00 2.74e-01 7.42e+01 angle pdb=" C ALA E 184 " pdb=" N ASN E 185 " pdb=" CA ASN E 185 " ideal model delta sigma weight residual 121.54 137.98 -16.44 1.91e+00 2.74e-01 7.41e+01 angle pdb=" C ALA B 184 " pdb=" N ASN B 185 " pdb=" CA ASN B 185 " ideal model delta sigma weight residual 121.54 137.97 -16.43 1.91e+00 2.74e-01 7.40e+01 angle pdb=" C LYS B 293 " pdb=" N SER B 294 " pdb=" CA SER B 294 " ideal model delta sigma weight residual 121.54 137.35 -15.81 1.91e+00 2.74e-01 6.86e+01 ... (remaining 15565 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.07: 6621 33.07 - 66.13: 181 66.13 - 99.20: 2 99.20 - 132.26: 0 132.26 - 165.33: 2 Dihedral angle restraints: 6806 sinusoidal: 2688 harmonic: 4118 Sorted by residual: dihedral pdb=" CA ALA E 184 " pdb=" C ALA E 184 " pdb=" N ASN E 185 " pdb=" CA ASN E 185 " ideal model delta harmonic sigma weight residual -180.00 -136.55 -43.45 0 5.00e+00 4.00e-02 7.55e+01 dihedral pdb=" CA ALA B 184 " pdb=" C ALA B 184 " pdb=" N ASN B 185 " pdb=" CA ASN B 185 " ideal model delta harmonic sigma weight residual -180.00 -136.58 -43.42 0 5.00e+00 4.00e-02 7.54e+01 dihedral pdb=" CA TYR E 225 " pdb=" C TYR E 225 " pdb=" N THR E 226 " pdb=" CA THR E 226 " ideal model delta harmonic sigma weight residual -180.00 -145.87 -34.13 0 5.00e+00 4.00e-02 4.66e+01 ... (remaining 6803 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1201 0.066 - 0.132: 370 0.132 - 0.198: 133 0.198 - 0.264: 35 0.264 - 0.330: 5 Chirality restraints: 1744 Sorted by residual: chirality pdb=" CB ILE B 391 " pdb=" CA ILE B 391 " pdb=" CG1 ILE B 391 " pdb=" CG2 ILE B 391 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.33 2.00e-01 2.50e+01 2.73e+00 chirality pdb=" CB ILE E 391 " pdb=" CA ILE E 391 " pdb=" CG1 ILE E 391 " pdb=" CG2 ILE E 391 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.33 2.00e-01 2.50e+01 2.71e+00 chirality pdb=" CB VAL B 667 " pdb=" CA VAL B 667 " pdb=" CG1 VAL B 667 " pdb=" CG2 VAL B 667 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.14e+00 ... (remaining 1741 not shown) Planarity restraints: 1990 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN E 644 " 0.018 2.00e-02 2.50e+03 3.46e-02 1.20e+01 pdb=" C ASN E 644 " -0.060 2.00e-02 2.50e+03 pdb=" O ASN E 644 " 0.022 2.00e-02 2.50e+03 pdb=" N PRO E 645 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 644 " -0.017 2.00e-02 2.50e+03 3.41e-02 1.16e+01 pdb=" C ASN B 644 " 0.059 2.00e-02 2.50e+03 pdb=" O ASN B 644 " -0.021 2.00e-02 2.50e+03 pdb=" N PRO B 645 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS E 259 " -0.053 5.00e-02 4.00e+02 7.98e-02 1.02e+01 pdb=" N PRO E 260 " 0.138 5.00e-02 4.00e+02 pdb=" CA PRO E 260 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO E 260 " -0.045 5.00e-02 4.00e+02 ... (remaining 1987 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 106 2.63 - 3.20: 9320 3.20 - 3.76: 15751 3.76 - 4.33: 19854 4.33 - 4.90: 35057 Nonbonded interactions: 80088 Sorted by model distance: nonbonded pdb=" O2B AGS B 801 " pdb="MG MG B 802 " model vdw 2.058 2.170 nonbonded pdb=" O2B AGS E 801 " pdb="MG MG E 802 " model vdw 2.059 2.170 nonbonded pdb=" O3G AGS E 801 " pdb="MG MG E 802 " model vdw 2.131 2.170 nonbonded pdb=" O3G AGS B 801 " pdb="MG MG B 802 " model vdw 2.131 2.170 nonbonded pdb=" OG SER B 275 " pdb="MG MG B 802 " model vdw 2.188 2.170 ... (remaining 80083 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 'D' } ncs_group { reference = chain 'B' selection = chain 'E' } 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: 2.180 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: 0.000 Extract box with map and model: 3.630 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 29.280 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.080 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:11.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6305 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 : 0.008 0.069 11398 Z= 0.531 Angle : 1.590 16.517 15570 Z= 0.886 Chirality : 0.076 0.330 1744 Planarity : 0.011 0.080 1990 Dihedral : 14.843 165.331 4138 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 2.01 % Allowed : 16.07 % Favored : 81.92 % Rotamer: Outliers : 0.85 % Allowed : 4.67 % Favored : 94.48 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % 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: -4.36 (0.18), residues: 1394 helix: -2.16 (0.17), residues: 446 sheet: -1.48 (0.32), residues: 234 loop : -4.03 (0.19), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP B 297 HIS 0.007 0.002 HIS B 334 PHE 0.029 0.004 PHE D 104 TYR 0.036 0.004 TYR E 685 ARG 0.009 0.001 ARG B 355 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 366 time to evaluate : 1.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 4 residues processed: 372 average time/residue: 0.9382 time to fit residues: 383.4568 Evaluate side-chains 225 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 221 time to evaluate : 1.156 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 3 residues processed: 1 average time/residue: 0.1403 time to fit residues: 1.9486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 118 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 chunk 58 optimal weight: 0.5980 chunk 36 optimal weight: 6.9990 chunk 71 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 109 optimal weight: 0.5980 chunk 42 optimal weight: 0.7980 chunk 66 optimal weight: 0.0570 chunk 81 optimal weight: 3.9990 chunk 127 optimal weight: 4.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 144 ASN B 171 HIS B 357 HIS B 644 ASN B 689 ASN D 26 HIS E 117 ASN E 174 HIS E 185 ASN ** E 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 644 ASN E 689 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6756 moved from start: 0.3463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11398 Z= 0.236 Angle : 0.917 13.358 15570 Z= 0.443 Chirality : 0.046 0.178 1744 Planarity : 0.007 0.055 1990 Dihedral : 9.698 164.416 1578 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.86 % Allowed : 9.76 % Favored : 89.38 % Rotamer: Outliers : 5.52 % Allowed : 17.32 % Favored : 77.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % 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: -1.41 (0.22), residues: 1394 helix: 1.63 (0.23), residues: 452 sheet: -0.70 (0.35), residues: 208 loop : -2.86 (0.22), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 722 HIS 0.013 0.002 HIS B 150 PHE 0.029 0.002 PHE E 139 TYR 0.019 0.002 TYR E 225 ARG 0.007 0.001 ARG B 662 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 244 time to evaluate : 1.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 65 outliers final: 24 residues processed: 285 average time/residue: 0.8605 time to fit residues: 272.7129 Evaluate side-chains 232 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 208 time to evaluate : 1.237 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 18 residues processed: 6 average time/residue: 0.3219 time to fit residues: 4.2187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 70 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 86 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 127 optimal weight: 0.0570 chunk 137 optimal weight: 0.8980 chunk 113 optimal weight: 2.9990 chunk 126 optimal weight: 0.9990 chunk 43 optimal weight: 4.9990 chunk 102 optimal weight: 1.9990 overall best weight: 0.9502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 HIS A 115 HIS B 174 HIS B 689 ASN D 21 GLN E 357 HIS E 689 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.5391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 11398 Z= 0.293 Angle : 0.853 13.337 15570 Z= 0.414 Chirality : 0.046 0.167 1744 Planarity : 0.006 0.060 1990 Dihedral : 9.331 163.045 1578 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.29 % Allowed : 9.68 % Favored : 90.03 % Rotamer: Outliers : 5.69 % Allowed : 18.85 % Favored : 75.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % 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: -0.78 (0.23), residues: 1394 helix: 2.27 (0.23), residues: 456 sheet: -0.55 (0.35), residues: 212 loop : -2.52 (0.22), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP E 500 HIS 0.008 0.001 HIS B 150 PHE 0.023 0.003 PHE E 332 TYR 0.023 0.002 TYR E 225 ARG 0.006 0.001 ARG B 417 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 236 time to evaluate : 1.222 Fit side-chains outliers start: 67 outliers final: 24 residues processed: 281 average time/residue: 0.8439 time to fit residues: 263.8688 Evaluate side-chains 219 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 195 time to evaluate : 1.188 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 18 residues processed: 7 average time/residue: 0.3183 time to fit residues: 4.5772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 125 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 66 optimal weight: 10.0000 chunk 14 optimal weight: 0.7980 chunk 60 optimal weight: 3.9990 chunk 85 optimal weight: 0.2980 chunk 127 optimal weight: 2.9990 chunk 135 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 112 optimal weight: 4.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN ** B 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 68 HIS E 171 HIS E 174 HIS E 283 ASN ** E 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 689 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.8380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.089 11398 Z= 0.416 Angle : 0.901 16.630 15570 Z= 0.438 Chirality : 0.049 0.172 1744 Planarity : 0.007 0.058 1990 Dihedral : 9.457 156.031 1578 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.22 % Allowed : 9.25 % Favored : 90.53 % Rotamer: Outliers : 6.54 % Allowed : 23.01 % Favored : 70.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.39 % 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: -1.08 (0.22), residues: 1394 helix: 1.86 (0.24), residues: 456 sheet: -0.63 (0.39), residues: 164 loop : -2.51 (0.20), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP E 500 HIS 0.019 0.002 HIS D 68 PHE 0.035 0.003 PHE D 107 TYR 0.021 0.002 TYR B 382 ARG 0.005 0.001 ARG B 417 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 249 time to evaluate : 1.162 Fit side-chains outliers start: 77 outliers final: 32 residues processed: 302 average time/residue: 0.8860 time to fit residues: 297.0825 Evaluate side-chains 216 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 184 time to evaluate : 1.288 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 26 residues processed: 7 average time/residue: 0.1607 time to fit residues: 3.5913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 76 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 chunk 100 optimal weight: 10.0000 chunk 55 optimal weight: 1.9990 chunk 115 optimal weight: 0.8980 chunk 93 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 121 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN ** B 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 HIS D 21 GLN ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 644 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.8933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 11398 Z= 0.236 Angle : 0.765 16.420 15570 Z= 0.365 Chirality : 0.044 0.197 1744 Planarity : 0.006 0.072 1990 Dihedral : 9.144 155.207 1578 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.46 % Favored : 91.39 % Rotamer: Outliers : 6.28 % Allowed : 25.38 % Favored : 68.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.22), residues: 1394 helix: 2.25 (0.24), residues: 464 sheet: -0.57 (0.35), residues: 212 loop : -2.39 (0.21), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 347 HIS 0.005 0.001 HIS A 68 PHE 0.036 0.002 PHE D 107 TYR 0.013 0.001 TYR D 23 ARG 0.007 0.001 ARG E 289 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 200 time to evaluate : 1.282 Fit side-chains outliers start: 74 outliers final: 37 residues processed: 256 average time/residue: 0.8317 time to fit residues: 239.2470 Evaluate side-chains 225 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 188 time to evaluate : 1.259 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 30 residues processed: 7 average time/residue: 0.1837 time to fit residues: 3.6672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 121 optimal weight: 1.9990 chunk 26 optimal weight: 20.0000 chunk 79 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 135 optimal weight: 0.7980 chunk 112 optimal weight: 5.9990 chunk 62 optimal weight: 0.0570 chunk 11 optimal weight: 6.9990 chunk 44 optimal weight: 0.0030 chunk 71 optimal weight: 3.9990 chunk 130 optimal weight: 0.0040 overall best weight: 0.3320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN ** B 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 ASN B 309 GLN B 396 ASN D 21 GLN ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 644 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.9157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 11398 Z= 0.188 Angle : 0.735 16.540 15570 Z= 0.346 Chirality : 0.043 0.210 1744 Planarity : 0.006 0.050 1990 Dihedral : 8.828 150.442 1578 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.46 % Favored : 91.39 % Rotamer: Outliers : 5.60 % Allowed : 27.59 % Favored : 66.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: -0.40 (0.23), residues: 1394 helix: 2.53 (0.24), residues: 460 sheet: -0.47 (0.35), residues: 212 loop : -2.23 (0.21), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 500 HIS 0.004 0.001 HIS D 68 PHE 0.036 0.002 PHE D 107 TYR 0.014 0.001 TYR B 382 ARG 0.003 0.000 ARG E 128 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 196 time to evaluate : 1.236 Fit side-chains outliers start: 66 outliers final: 42 residues processed: 246 average time/residue: 0.9333 time to fit residues: 253.6967 Evaluate side-chains 216 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 174 time to evaluate : 1.191 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 31 residues processed: 11 average time/residue: 0.4337 time to fit residues: 7.3826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 15 optimal weight: 0.6980 chunk 77 optimal weight: 10.0000 chunk 98 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 114 optimal weight: 2.9990 chunk 75 optimal weight: 0.0010 chunk 134 optimal weight: 0.8980 chunk 84 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 62 optimal weight: 0.3980 chunk 83 optimal weight: 5.9990 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN ** B 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 ASN B 309 GLN D 21 GLN ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 142 HIS E 144 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.9405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 11398 Z= 0.198 Angle : 0.731 16.206 15570 Z= 0.344 Chirality : 0.043 0.227 1744 Planarity : 0.006 0.048 1990 Dihedral : 8.644 149.180 1578 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.89 % Favored : 91.97 % Rotamer: Outliers : 5.35 % Allowed : 28.27 % Favored : 66.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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 (0.23), residues: 1394 helix: 2.52 (0.24), residues: 466 sheet: -0.35 (0.35), residues: 208 loop : -2.09 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 214 HIS 0.003 0.001 HIS B 648 PHE 0.034 0.002 PHE D 107 TYR 0.014 0.001 TYR B 382 ARG 0.008 0.000 ARG E 279 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 196 time to evaluate : 1.290 Fit side-chains outliers start: 63 outliers final: 39 residues processed: 243 average time/residue: 0.8384 time to fit residues: 227.5527 Evaluate side-chains 221 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 182 time to evaluate : 1.268 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 31 residues processed: 8 average time/residue: 0.4859 time to fit residues: 6.2650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 53 optimal weight: 0.8980 chunk 80 optimal weight: 5.9990 chunk 40 optimal weight: 0.2980 chunk 26 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 106 optimal weight: 7.9990 chunk 122 optimal weight: 0.8980 chunk 129 optimal weight: 0.7980 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 21 GLN ** B 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 21 GLN ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 HIS E 309 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.9705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11398 Z= 0.207 Angle : 0.736 14.888 15570 Z= 0.344 Chirality : 0.043 0.275 1744 Planarity : 0.006 0.047 1990 Dihedral : 8.406 146.856 1578 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.46 % Favored : 91.39 % Rotamer: Outliers : 4.92 % Allowed : 28.69 % Favored : 66.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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 (0.23), residues: 1394 helix: 2.53 (0.24), residues: 466 sheet: -0.51 (0.34), residues: 224 loop : -2.06 (0.23), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 168 HIS 0.006 0.001 HIS D 68 PHE 0.035 0.002 PHE D 107 TYR 0.019 0.002 TYR E 626 ARG 0.006 0.000 ARG B 237 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 190 time to evaluate : 1.287 Fit side-chains outliers start: 58 outliers final: 36 residues processed: 238 average time/residue: 0.8403 time to fit residues: 223.4222 Evaluate side-chains 211 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 175 time to evaluate : 1.168 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 33 residues processed: 3 average time/residue: 0.7209 time to fit residues: 4.1832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 117 optimal weight: 0.8980 chunk 125 optimal weight: 2.9990 chunk 129 optimal weight: 3.9990 chunk 75 optimal weight: 0.5980 chunk 54 optimal weight: 0.6980 chunk 98 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 chunk 113 optimal weight: 0.8980 chunk 118 optimal weight: 0.8980 chunk 82 optimal weight: 0.9990 chunk 132 optimal weight: 1.9990 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 21 GLN ** B 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 21 GLN ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 309 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.9924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 11398 Z= 0.220 Angle : 0.761 15.136 15570 Z= 0.353 Chirality : 0.043 0.272 1744 Planarity : 0.006 0.045 1990 Dihedral : 8.312 146.303 1578 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.18 % Favored : 91.61 % Rotamer: Outliers : 5.01 % Allowed : 29.20 % Favored : 65.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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 (0.23), residues: 1394 helix: 2.51 (0.24), residues: 466 sheet: -0.38 (0.33), residues: 238 loop : -2.06 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 168 HIS 0.003 0.001 HIS E 334 PHE 0.033 0.002 PHE D 107 TYR 0.033 0.002 TYR B 382 ARG 0.006 0.000 ARG E 237 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 183 time to evaluate : 1.295 Fit side-chains revert: symmetry clash outliers start: 59 outliers final: 42 residues processed: 227 average time/residue: 0.7980 time to fit residues: 203.1996 Evaluate side-chains 210 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 168 time to evaluate : 1.258 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 37 residues processed: 6 average time/residue: 0.5752 time to fit residues: 5.7386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 81 optimal weight: 7.9990 chunk 63 optimal weight: 3.9990 chunk 92 optimal weight: 0.0970 chunk 139 optimal weight: 3.9990 chunk 128 optimal weight: 0.9980 chunk 111 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 88 optimal weight: 10.0000 chunk 118 optimal weight: 0.8980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN B 327 ASN ** B 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 21 GLN ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 HIS E 357 HIS ** E 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 1.0326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 11398 Z= 0.269 Angle : 0.787 14.755 15570 Z= 0.368 Chirality : 0.044 0.283 1744 Planarity : 0.006 0.047 1990 Dihedral : 8.209 145.552 1578 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.40 % Favored : 90.46 % Rotamer: Outliers : 4.24 % Allowed : 30.98 % Favored : 64.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -0.28 (0.23), residues: 1394 helix: 2.34 (0.24), residues: 472 sheet: -0.46 (0.33), residues: 238 loop : -2.03 (0.24), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.004 0.001 HIS B 171 PHE 0.033 0.002 PHE D 107 TYR 0.034 0.002 TYR E 382 ARG 0.007 0.001 ARG B 279 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 182 time to evaluate : 1.146 Fit side-chains outliers start: 50 outliers final: 42 residues processed: 224 average time/residue: 0.8864 time to fit residues: 220.7930 Evaluate side-chains 213 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 171 time to evaluate : 1.153 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 36 residues processed: 6 average time/residue: 0.5598 time to fit residues: 5.4974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 34 optimal weight: 2.9990 chunk 102 optimal weight: 0.4980 chunk 16 optimal weight: 0.9990 chunk 30 optimal weight: 0.0050 chunk 111 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 chunk 114 optimal weight: 1.9990 chunk 14 optimal weight: 0.4980 chunk 20 optimal weight: 6.9990 chunk 97 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN ** A 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 480 GLN D 21 GLN ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.114264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.092563 restraints weight = 18532.346| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 3.43 r_work: 0.3150 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 1.0440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 11398 Z= 0.209 Angle : 0.773 14.675 15570 Z= 0.359 Chirality : 0.043 0.283 1744 Planarity : 0.006 0.044 1990 Dihedral : 8.156 145.344 1578 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.39 % Favored : 91.46 % Rotamer: Outliers : 3.90 % Allowed : 31.92 % Favored : 64.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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 (0.23), residues: 1394 helix: 2.42 (0.24), residues: 470 sheet: -0.45 (0.33), residues: 238 loop : -1.95 (0.24), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 214 HIS 0.013 0.001 HIS A 68 PHE 0.032 0.002 PHE D 107 TYR 0.025 0.002 TYR E 382 ARG 0.005 0.000 ARG B 279 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4313.07 seconds wall clock time: 79 minutes 47.01 seconds (4787.01 seconds total)