Starting phenix.real_space_refine on Fri Mar 15 08:30:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6of3_20041/03_2024/6of3_20041_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6of3_20041/03_2024/6of3_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_20041/03_2024/6of3_20041.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6of3_20041/03_2024/6of3_20041.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6of3_20041/03_2024/6of3_20041_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6of3_20041/03_2024/6of3_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-dev-5265/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: 6.16, per 1000 atoms: 0.56 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: 4.24 Conformation dependent library (CDL) restraints added in 2.0 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: 2.08 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: 2.95 Time building geometry restraints manager: 4.63 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: 0.490 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: 0.000 Extract box with map and model: 3.040 Check model and map are aligned: 0.170 Set scattering table: 0.100 Process input model: 31.540 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.050 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:13.000 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.850 ------------------------------------------------------------------------------- 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 : 1.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 ILE cc_start: 0.7568 (mm) cc_final: 0.7278 (mm) REVERT: A 23 TYR cc_start: 0.7407 (m-80) cc_final: 0.7143 (m-80) REVERT: A 107 PHE cc_start: 0.6231 (t80) cc_final: 0.6028 (t80) REVERT: B 364 PRO cc_start: 0.5826 (Cg_exo) cc_final: 0.5620 (Cg_endo) REVERT: D 5 ILE cc_start: 0.7433 (mm) cc_final: 0.7118 (mm) REVERT: E 222 GLN cc_start: 0.7540 (OUTLIER) cc_final: 0.7209 (pp30) REVERT: E 349 GLU cc_start: 0.7657 (mt-10) cc_final: 0.7355 (mp0) REVERT: E 432 THR cc_start: 0.8161 (t) cc_final: 0.7928 (m) outliers start: 10 outliers final: 4 residues processed: 372 average time/residue: 0.8967 time to fit residues: 365.6776 Evaluate side-chains 227 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 222 time to evaluate : 1.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain E residue 222 GLN Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain E residue 668 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 118 optimal weight: 1.9990 chunk 106 optimal weight: 5.9990 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: 0.9990 chunk 42 optimal weight: 0.7980 chunk 66 optimal weight: 0.0470 chunk 81 optimal weight: 3.9990 chunk 127 optimal weight: 2.9990 overall best weight: 0.6480 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 644 ASN B 689 ASN D 26 HIS E 117 ASN E 174 HIS E 185 ASN E 222 GLN ** 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: 0.6819 moved from start: 0.3558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 11398 Z= 0.265 Angle : 0.927 13.499 15570 Z= 0.453 Chirality : 0.047 0.170 1744 Planarity : 0.007 0.059 1990 Dihedral : 10.037 164.668 1588 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.86 % Allowed : 9.97 % Favored : 89.17 % Rotamer: Outliers : 5.35 % Allowed : 17.74 % Favored : 76.91 % 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: -1.46 (0.22), residues: 1394 helix: 1.63 (0.23), residues: 450 sheet: -0.80 (0.35), residues: 212 loop : -2.90 (0.22), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 722 HIS 0.012 0.002 HIS B 150 PHE 0.042 0.003 PHE E 139 TYR 0.017 0.002 TYR E 225 ARG 0.006 0.001 ARG E 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: 63 poor density : 246 time to evaluate : 1.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 ILE cc_start: 0.8008 (mm) cc_final: 0.7749 (mm) REVERT: A 23 TYR cc_start: 0.7521 (m-80) cc_final: 0.6970 (m-80) REVERT: A 71 GLU cc_start: 0.6275 (tp30) cc_final: 0.6025 (tt0) REVERT: A 107 PHE cc_start: 0.6773 (t80) cc_final: 0.6303 (t80) REVERT: B 479 MET cc_start: 0.7831 (tpp) cc_final: 0.6887 (tpt) REVERT: D 5 ILE cc_start: 0.7882 (mm) cc_final: 0.7564 (mm) REVERT: D 23 TYR cc_start: 0.7443 (m-80) cc_final: 0.6956 (m-80) REVERT: D 172 LYS cc_start: 0.7019 (tppt) cc_final: 0.6653 (ttmt) REVERT: E 222 GLN cc_start: 0.7539 (pp30) cc_final: 0.7004 (pp30) REVERT: E 318 VAL cc_start: 0.7897 (m) cc_final: 0.7696 (m) REVERT: E 364 PRO cc_start: 0.5635 (Cg_exo) cc_final: 0.5384 (Cg_endo) REVERT: E 479 MET cc_start: 0.7907 (tpp) cc_final: 0.7517 (tpt) REVERT: E 537 GLU cc_start: 0.7483 (mp0) cc_final: 0.7273 (mp0) REVERT: E 546 MET cc_start: 0.6800 (mmm) cc_final: 0.6594 (mpp) REVERT: E 644 ASN cc_start: 0.6378 (OUTLIER) cc_final: 0.6119 (m-40) outliers start: 63 outliers final: 27 residues processed: 286 average time/residue: 0.8250 time to fit residues: 262.4223 Evaluate side-chains 238 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 210 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 174 HIS Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 506 THR Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 61 MET Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 217 THR Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain E residue 249 ILE Chi-restraints excluded: chain E residue 302 VAL Chi-restraints excluded: chain E residue 353 THR Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain E residue 363 THR Chi-restraints excluded: chain E residue 473 THR Chi-restraints excluded: chain E residue 506 THR Chi-restraints excluded: chain E residue 639 SER Chi-restraints excluded: chain E residue 644 ASN Chi-restraints excluded: chain E residue 668 LEU 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: 0.7980 chunk 105 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 127 optimal weight: 0.6980 chunk 137 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 126 optimal weight: 0.7980 chunk 43 optimal weight: 0.7980 chunk 102 optimal weight: 2.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN A 115 HIS ** B 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 644 ASN B 689 ASN D 21 GLN E 120 ASN E 357 HIS E 644 ASN E 689 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.5927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.113 11398 Z= 0.336 Angle : 0.915 13.728 15570 Z= 0.448 Chirality : 0.047 0.185 1744 Planarity : 0.007 0.068 1990 Dihedral : 9.460 162.091 1583 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.36 % Allowed : 10.04 % Favored : 89.60 % Rotamer: Outliers : 6.11 % Allowed : 19.02 % Favored : 74.87 % Cbeta Deviations : 0.07 % 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: -1.05 (0.22), residues: 1394 helix: 1.94 (0.23), residues: 456 sheet: -0.65 (0.35), residues: 212 loop : -2.64 (0.21), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP E 500 HIS 0.010 0.001 HIS B 150 PHE 0.027 0.003 PHE B 265 TYR 0.020 0.002 TYR E 225 ARG 0.006 0.001 ARG B 514 *********************** 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 322 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 250 time to evaluate : 1.237 Fit side-chains revert: symmetry clash REVERT: A 21 GLN cc_start: 0.7395 (OUTLIER) cc_final: 0.7163 (tt0) REVERT: A 23 TYR cc_start: 0.8162 (m-80) cc_final: 0.7241 (m-80) REVERT: A 61 MET cc_start: 0.8269 (mmm) cc_final: 0.7862 (tpp) REVERT: A 62 GLN cc_start: 0.8924 (mm110) cc_final: 0.8690 (tp40) REVERT: B 333 CYS cc_start: 0.7572 (OUTLIER) cc_final: 0.7314 (m) REVERT: B 630 VAL cc_start: 0.7905 (OUTLIER) cc_final: 0.7555 (m) REVERT: D 21 GLN cc_start: 0.7137 (OUTLIER) cc_final: 0.6834 (tt0) REVERT: D 23 TYR cc_start: 0.7833 (m-80) cc_final: 0.7109 (m-80) REVERT: D 68 HIS cc_start: 0.8226 (t70) cc_final: 0.7997 (t-170) REVERT: D 153 THR cc_start: 0.8179 (m) cc_final: 0.7950 (p) REVERT: D 172 LYS cc_start: 0.7673 (OUTLIER) cc_final: 0.7395 (ttmt) REVERT: E 121 PHE cc_start: 0.6851 (OUTLIER) cc_final: 0.6556 (t80) REVERT: E 312 PHE cc_start: 0.8013 (m-80) cc_final: 0.7776 (m-80) REVERT: E 554 GLU cc_start: 0.7464 (tt0) cc_final: 0.7099 (mt-10) REVERT: E 672 LYS cc_start: 0.8860 (mmmm) cc_final: 0.8591 (mmmt) outliers start: 72 outliers final: 27 residues processed: 296 average time/residue: 0.8535 time to fit residues: 280.3327 Evaluate side-chains 234 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 201 time to evaluate : 1.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLN Chi-restraints excluded: chain A residue 115 HIS Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain B residue 121 PHE Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 333 CYS Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 556 LYS Chi-restraints excluded: chain B residue 623 SER Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain D residue 21 GLN Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 172 LYS Chi-restraints excluded: chain E residue 121 PHE Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain E residue 164 ILE Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 217 THR Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain E residue 249 ILE Chi-restraints excluded: chain E residue 363 THR Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 450 MET Chi-restraints excluded: chain E residue 473 THR Chi-restraints excluded: chain E residue 556 LYS Chi-restraints excluded: chain E residue 625 GLN Chi-restraints excluded: chain E residue 639 SER Chi-restraints excluded: chain E residue 650 LEU Chi-restraints excluded: chain E residue 720 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 125 optimal weight: 0.8980 chunk 95 optimal weight: 1.9990 chunk 66 optimal weight: 0.4980 chunk 14 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 85 optimal weight: 0.9980 chunk 127 optimal weight: 3.9990 chunk 135 optimal weight: 0.8980 chunk 121 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 chunk 112 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN ** B 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 644 ASN D 21 GLN ** E 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 HIS E 533 GLN E 689 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.6736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 11398 Z= 0.230 Angle : 0.779 11.168 15570 Z= 0.369 Chirality : 0.044 0.165 1744 Planarity : 0.006 0.053 1990 Dihedral : 9.312 160.219 1579 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.39 % Favored : 91.46 % Rotamer: Outliers : 5.26 % Allowed : 24.02 % Favored : 70.71 % 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: -0.72 (0.22), residues: 1394 helix: 2.37 (0.24), residues: 458 sheet: -0.50 (0.39), residues: 174 loop : -2.46 (0.20), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP E 500 HIS 0.022 0.001 HIS A 115 PHE 0.031 0.002 PHE D 107 TYR 0.016 0.001 TYR D 23 ARG 0.008 0.000 ARG E 289 *********************** 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 276 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 214 time to evaluate : 0.976 Fit side-chains REVERT: A 23 TYR cc_start: 0.8303 (m-80) cc_final: 0.7653 (m-80) REVERT: A 61 MET cc_start: 0.8325 (mmm) cc_final: 0.7989 (tpp) REVERT: A 62 GLN cc_start: 0.8935 (mm110) cc_final: 0.8730 (tp40) REVERT: B 121 PHE cc_start: 0.7197 (OUTLIER) cc_final: 0.6886 (m-80) REVERT: B 188 VAL cc_start: 0.8447 (OUTLIER) cc_final: 0.8229 (t) REVERT: B 320 LEU cc_start: 0.7387 (pt) cc_final: 0.6983 (pp) REVERT: B 333 CYS cc_start: 0.7690 (m) cc_final: 0.7474 (m) REVERT: B 630 VAL cc_start: 0.7899 (OUTLIER) cc_final: 0.7674 (p) REVERT: B 672 LYS cc_start: 0.8709 (mmmm) cc_final: 0.8400 (mmmt) REVERT: D 21 GLN cc_start: 0.7253 (OUTLIER) cc_final: 0.6929 (tt0) REVERT: D 23 TYR cc_start: 0.8084 (m-80) cc_final: 0.7289 (m-80) REVERT: D 153 THR cc_start: 0.8222 (m) cc_final: 0.7963 (p) REVERT: D 172 LYS cc_start: 0.7788 (OUTLIER) cc_final: 0.7493 (ttmt) REVERT: E 121 PHE cc_start: 0.6986 (OUTLIER) cc_final: 0.6663 (m-80) REVERT: E 237 ARG cc_start: 0.7149 (OUTLIER) cc_final: 0.6907 (mtt180) REVERT: E 312 PHE cc_start: 0.8184 (m-80) cc_final: 0.7951 (m-80) REVERT: E 424 MET cc_start: 0.7740 (mmm) cc_final: 0.5945 (mtm) outliers start: 62 outliers final: 26 residues processed: 252 average time/residue: 0.8822 time to fit residues: 245.5978 Evaluate side-chains 225 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 192 time to evaluate : 1.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 121 PHE Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 174 HIS Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 396 ASN Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 556 LYS Chi-restraints excluded: chain B residue 623 SER Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 21 GLN Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain D residue 172 LYS Chi-restraints excluded: chain E residue 121 PHE Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain E residue 237 ARG Chi-restraints excluded: chain E residue 249 ILE Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 302 VAL Chi-restraints excluded: chain E residue 363 THR Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 425 SER Chi-restraints excluded: chain E residue 450 MET Chi-restraints excluded: chain E residue 543 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 76 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 100 optimal weight: 10.0000 chunk 55 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 chunk 69 optimal weight: 0.6980 chunk 121 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 45 optimal weight: 6.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 118 ASN ** B 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 309 GLN ** B 484 HIS ** 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 151 GLN E 357 HIS ** E 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 689 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.9156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.098 11398 Z= 0.428 Angle : 0.908 15.812 15570 Z= 0.444 Chirality : 0.049 0.191 1744 Planarity : 0.007 0.051 1990 Dihedral : 9.215 155.382 1579 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.29 % Allowed : 9.83 % Favored : 89.89 % Rotamer: Outliers : 7.72 % Allowed : 21.82 % Favored : 70.46 % 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: -0.99 (0.22), residues: 1394 helix: 1.76 (0.24), residues: 456 sheet: -0.35 (0.36), residues: 212 loop : -2.51 (0.20), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP D 347 HIS 0.009 0.002 HIS B 150 PHE 0.048 0.003 PHE D 107 TYR 0.024 0.002 TYR D 23 ARG 0.004 0.001 ARG E 417 *********************** 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 324 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 233 time to evaluate : 1.048 Fit side-chains TARDY: cannot create tardy model for: "THR B 568 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 23 TYR cc_start: 0.8599 (m-80) cc_final: 0.7622 (m-80) REVERT: A 94 TYR cc_start: 0.7956 (OUTLIER) cc_final: 0.7688 (m-80) REVERT: B 237 ARG cc_start: 0.7723 (mtt180) cc_final: 0.7324 (mtm-85) REVERT: B 333 CYS cc_start: 0.8331 (OUTLIER) cc_final: 0.8112 (m) REVERT: B 377 ASP cc_start: 0.8422 (t70) cc_final: 0.7985 (t0) REVERT: B 420 GLU cc_start: 0.7423 (mm-30) cc_final: 0.7164 (mm-30) REVERT: B 506 THR cc_start: 0.9186 (m) cc_final: 0.8861 (p) REVERT: B 525 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8338 (tp) REVERT: B 527 ILE cc_start: 0.8053 (OUTLIER) cc_final: 0.7715 (mp) REVERT: D 21 GLN cc_start: 0.7838 (OUTLIER) cc_final: 0.7509 (tt0) REVERT: D 23 TYR cc_start: 0.8374 (m-80) cc_final: 0.7619 (m-80) REVERT: D 61 MET cc_start: 0.8581 (tpp) cc_final: 0.8302 (tpp) REVERT: D 153 THR cc_start: 0.8458 (m) cc_final: 0.8174 (p) REVERT: D 172 LYS cc_start: 0.8738 (OUTLIER) cc_final: 0.8432 (ttmt) REVERT: E 202 GLU cc_start: 0.8550 (tp30) cc_final: 0.8340 (tt0) REVERT: E 212 ARG cc_start: 0.8253 (OUTLIER) cc_final: 0.7844 (pmm-80) REVERT: E 266 ILE cc_start: 0.8195 (pt) cc_final: 0.7949 (pp) REVERT: E 377 ASP cc_start: 0.8407 (t70) cc_final: 0.7978 (t0) REVERT: E 407 ASP cc_start: 0.8921 (t0) cc_final: 0.8592 (m-30) REVERT: E 420 GLU cc_start: 0.7388 (mm-30) cc_final: 0.7079 (mm-30) REVERT: E 527 ILE cc_start: 0.7962 (OUTLIER) cc_final: 0.7703 (mp) outliers start: 91 outliers final: 36 residues processed: 297 average time/residue: 0.8318 time to fit residues: 274.7661 Evaluate side-chains 231 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 187 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 TYR Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 174 HIS Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 333 CYS Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain B residue 543 ILE Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 623 SER Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 720 VAL Chi-restraints excluded: chain D residue 21 GLN Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 172 LYS Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 212 ARG Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain E residue 320 LEU Chi-restraints excluded: chain E residue 338 SER Chi-restraints excluded: chain E residue 363 THR Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 425 SER Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain E residue 473 THR Chi-restraints excluded: chain E residue 527 ILE Chi-restraints excluded: chain E residue 543 ILE Chi-restraints excluded: chain E residue 562 LEU Chi-restraints excluded: chain E residue 623 SER Chi-restraints excluded: chain E residue 625 GLN Chi-restraints excluded: chain E residue 651 THR Chi-restraints excluded: chain E residue 720 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 121 optimal weight: 3.9990 chunk 26 optimal weight: 20.0000 chunk 79 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 135 optimal weight: 0.9990 chunk 112 optimal weight: 0.5980 chunk 62 optimal weight: 0.9990 chunk 11 optimal weight: 10.0000 chunk 44 optimal weight: 0.9980 chunk 71 optimal weight: 0.8980 chunk 130 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 GLN ** B 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 644 ASN ** E 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 144 ASN E 533 GLN E 644 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.9528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11398 Z= 0.232 Angle : 0.774 16.063 15570 Z= 0.363 Chirality : 0.044 0.210 1744 Planarity : 0.006 0.076 1990 Dihedral : 9.027 154.022 1579 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.46 % Favored : 91.39 % Rotamer: Outliers : 5.26 % Allowed : 26.91 % Favored : 67.83 % 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: -0.52 (0.22), residues: 1394 helix: 2.29 (0.24), residues: 466 sheet: -0.30 (0.35), residues: 212 loop : -2.32 (0.21), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 347 HIS 0.004 0.001 HIS B 532 PHE 0.032 0.002 PHE A 107 TYR 0.012 0.001 TYR B 382 ARG 0.005 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 260 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 198 time to evaluate : 1.139 Fit side-chains TARDY: cannot create tardy model for: "THR B 568 " (corrupted residue). Skipping it. REVERT: A 23 TYR cc_start: 0.8612 (m-80) cc_final: 0.7615 (m-80) REVERT: B 135 ASP cc_start: 0.8309 (t70) cc_final: 0.8063 (t70) REVERT: B 209 LEU cc_start: 0.8592 (tp) cc_final: 0.8297 (tm) REVERT: B 237 ARG cc_start: 0.7690 (mtt180) cc_final: 0.7444 (mtm-85) REVERT: B 320 LEU cc_start: 0.7539 (OUTLIER) cc_final: 0.6950 (pp) REVERT: B 506 THR cc_start: 0.9109 (m) cc_final: 0.8795 (p) REVERT: B 525 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8440 (tp) REVERT: D 23 TYR cc_start: 0.8510 (m-80) cc_final: 0.7630 (m-80) REVERT: D 172 LYS cc_start: 0.8656 (tppt) cc_final: 0.8392 (ttmt) REVERT: E 135 ASP cc_start: 0.8441 (t70) cc_final: 0.8235 (t70) REVERT: E 202 GLU cc_start: 0.8492 (tp30) cc_final: 0.8241 (tt0) REVERT: E 237 ARG cc_start: 0.7825 (OUTLIER) cc_final: 0.7547 (mtm-85) REVERT: E 320 LEU cc_start: 0.7455 (OUTLIER) cc_final: 0.6826 (pp) REVERT: E 377 ASP cc_start: 0.8405 (t70) cc_final: 0.8001 (t0) REVERT: E 407 ASP cc_start: 0.8917 (t0) cc_final: 0.8630 (m-30) REVERT: E 420 GLU cc_start: 0.7388 (mm-30) cc_final: 0.7128 (mm-30) REVERT: E 424 MET cc_start: 0.8141 (mmm) cc_final: 0.6794 (mtm) REVERT: E 567 ASP cc_start: 0.5887 (OUTLIER) cc_final: 0.5564 (p0) outliers start: 62 outliers final: 25 residues processed: 239 average time/residue: 0.8491 time to fit residues: 225.8776 Evaluate side-chains 221 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 191 time to evaluate : 1.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 GLU Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 174 HIS Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 567 ASP Chi-restraints excluded: chain B residue 623 SER Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 644 ASN Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain D residue 25 GLU Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain E residue 237 ARG Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 320 LEU Chi-restraints excluded: chain E residue 321 THR Chi-restraints excluded: chain E residue 363 THR Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 425 SER Chi-restraints excluded: chain E residue 436 LEU Chi-restraints excluded: chain E residue 473 THR Chi-restraints excluded: chain E residue 567 ASP Chi-restraints excluded: chain E residue 623 SER Chi-restraints excluded: chain E residue 644 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 15 optimal weight: 0.7980 chunk 77 optimal weight: 7.9990 chunk 98 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 114 optimal weight: 0.5980 chunk 75 optimal weight: 0.3980 chunk 134 optimal weight: 0.6980 chunk 84 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 62 optimal weight: 0.0030 chunk 83 optimal weight: 0.7980 overall best weight: 0.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN ** B 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 HIS B 396 ASN D 21 GLN ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 142 HIS E 533 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.9694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11398 Z= 0.196 Angle : 0.750 15.713 15570 Z= 0.351 Chirality : 0.044 0.209 1744 Planarity : 0.006 0.068 1990 Dihedral : 8.842 151.977 1579 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.61 % Favored : 91.25 % Rotamer: Outliers : 5.35 % Allowed : 26.83 % Favored : 67.83 % 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: -0.32 (0.23), residues: 1394 helix: 2.44 (0.24), residues: 466 sheet: -0.24 (0.34), residues: 212 loop : -2.16 (0.21), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 347 HIS 0.003 0.001 HIS E 532 PHE 0.035 0.002 PHE A 107 TYR 0.024 0.001 TYR B 382 ARG 0.007 0.000 ARG B 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 253 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 190 time to evaluate : 1.225 Fit side-chains TARDY: cannot create tardy model for: "THR B 568 " (corrupted residue). Skipping it. REVERT: A 23 TYR cc_start: 0.8560 (m-80) cc_final: 0.7539 (m-80) REVERT: B 135 ASP cc_start: 0.8287 (t70) cc_final: 0.8041 (t70) REVERT: B 200 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8393 (mt) REVERT: B 237 ARG cc_start: 0.7716 (mtt180) cc_final: 0.7399 (mtm-85) REVERT: B 320 LEU cc_start: 0.7403 (OUTLIER) cc_final: 0.6854 (pp) REVERT: B 424 MET cc_start: 0.8097 (mmm) cc_final: 0.6891 (mtm) REVERT: B 506 THR cc_start: 0.9063 (m) cc_final: 0.8751 (p) REVERT: B 525 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8422 (tp) REVERT: B 527 ILE cc_start: 0.8142 (OUTLIER) cc_final: 0.7774 (mp) REVERT: D 23 TYR cc_start: 0.8489 (m-80) cc_final: 0.7508 (m-80) REVERT: D 172 LYS cc_start: 0.8613 (OUTLIER) cc_final: 0.8290 (ttmt) REVERT: D 362 ILE cc_start: 0.9219 (tt) cc_final: 0.8795 (pt) REVERT: E 109 MET cc_start: 0.3801 (pmm) cc_final: 0.3221 (pmm) REVERT: E 121 PHE cc_start: 0.6972 (m-80) cc_final: 0.6464 (t80) REVERT: E 131 LEU cc_start: 0.7234 (OUTLIER) cc_final: 0.6839 (pp) REVERT: E 202 GLU cc_start: 0.8483 (tp30) cc_final: 0.8262 (tt0) REVERT: E 212 ARG cc_start: 0.8300 (OUTLIER) cc_final: 0.7995 (pmt170) REVERT: E 237 ARG cc_start: 0.7815 (OUTLIER) cc_final: 0.7557 (mtm-85) REVERT: E 320 LEU cc_start: 0.7359 (OUTLIER) cc_final: 0.6807 (pp) REVERT: E 407 ASP cc_start: 0.8893 (t0) cc_final: 0.8630 (m-30) REVERT: E 420 GLU cc_start: 0.7413 (mm-30) cc_final: 0.7170 (mm-30) REVERT: E 424 MET cc_start: 0.8086 (mmm) cc_final: 0.6756 (mtm) REVERT: E 480 GLN cc_start: 0.8512 (OUTLIER) cc_final: 0.8163 (tt0) REVERT: E 527 ILE cc_start: 0.8054 (OUTLIER) cc_final: 0.7789 (mp) REVERT: E 567 ASP cc_start: 0.5945 (OUTLIER) cc_final: 0.5649 (p0) outliers start: 63 outliers final: 27 residues processed: 236 average time/residue: 0.8263 time to fit residues: 217.6749 Evaluate side-chains 206 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 167 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 GLU Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 139 PHE Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 174 HIS Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain B residue 567 ASP Chi-restraints excluded: chain B residue 623 SER Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain D residue 25 GLU Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain D residue 172 LYS Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain E residue 212 ARG Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain E residue 237 ARG Chi-restraints excluded: chain E residue 320 LEU Chi-restraints excluded: chain E residue 363 THR Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 425 SER Chi-restraints excluded: chain E residue 436 LEU Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain E residue 473 THR Chi-restraints excluded: chain E residue 480 GLN Chi-restraints excluded: chain E residue 527 ILE Chi-restraints excluded: chain E residue 567 ASP Chi-restraints excluded: chain E residue 623 SER Chi-restraints excluded: chain E residue 640 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 53 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 40 optimal weight: 0.0030 chunk 26 optimal weight: 20.0000 chunk 85 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 106 optimal weight: 10.0000 chunk 122 optimal weight: 0.8980 chunk 129 optimal weight: 0.7980 overall best weight: 0.7392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN ** B 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 644 ASN D 21 GLN ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 309 GLN E 533 GLN E 644 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.9949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11398 Z= 0.210 Angle : 0.751 15.853 15570 Z= 0.351 Chirality : 0.044 0.234 1744 Planarity : 0.006 0.064 1990 Dihedral : 8.585 149.819 1579 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.82 % Favored : 91.03 % Rotamer: Outliers : 4.84 % Allowed : 28.27 % Favored : 66.89 % 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: -0.21 (0.23), residues: 1394 helix: 2.39 (0.24), residues: 470 sheet: -0.21 (0.34), residues: 212 loop : -2.00 (0.22), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 400 HIS 0.003 0.001 HIS A 115 PHE 0.032 0.002 PHE A 107 TYR 0.025 0.002 TYR E 382 ARG 0.007 0.001 ARG E 279 *********************** 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 243 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 186 time to evaluate : 1.139 Fit side-chains TARDY: cannot create tardy model for: "THR B 568 " (corrupted residue). Skipping it. REVERT: A 23 TYR cc_start: 0.8594 (m-80) cc_final: 0.7515 (m-80) REVERT: A 362 ILE cc_start: 0.9236 (tt) cc_final: 0.8824 (pt) REVERT: B 141 ILE cc_start: 0.9038 (mt) cc_final: 0.8789 (mp) REVERT: B 200 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8406 (mt) REVERT: B 237 ARG cc_start: 0.7774 (mtt180) cc_final: 0.7509 (mtm-85) REVERT: B 320 LEU cc_start: 0.7311 (OUTLIER) cc_final: 0.6689 (pp) REVERT: B 374 CYS cc_start: 0.8280 (m) cc_final: 0.7988 (m) REVERT: B 382 TYR cc_start: 0.7562 (t80) cc_final: 0.7358 (t80) REVERT: B 424 MET cc_start: 0.8094 (mmm) cc_final: 0.6904 (mtm) REVERT: B 525 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8436 (tp) REVERT: B 527 ILE cc_start: 0.8149 (OUTLIER) cc_final: 0.7906 (mp) REVERT: D 23 TYR cc_start: 0.8522 (m-80) cc_final: 0.7659 (m-80) REVERT: D 172 LYS cc_start: 0.8610 (tppt) cc_final: 0.8287 (tmmt) REVERT: D 362 ILE cc_start: 0.9198 (tt) cc_final: 0.8833 (pt) REVERT: E 109 MET cc_start: 0.3677 (pmm) cc_final: 0.3316 (pmm) REVERT: E 121 PHE cc_start: 0.6919 (OUTLIER) cc_final: 0.6705 (m-80) REVERT: E 237 ARG cc_start: 0.7827 (ptp-170) cc_final: 0.7508 (mtm-85) REVERT: E 320 LEU cc_start: 0.7404 (OUTLIER) cc_final: 0.6791 (pp) REVERT: E 377 ASP cc_start: 0.8382 (t70) cc_final: 0.7984 (t0) REVERT: E 407 ASP cc_start: 0.8931 (t0) cc_final: 0.8681 (m-30) REVERT: E 420 GLU cc_start: 0.7529 (mm-30) cc_final: 0.7249 (mm-30) REVERT: E 424 MET cc_start: 0.8124 (mmm) cc_final: 0.6845 (mtm) REVERT: E 527 ILE cc_start: 0.8131 (OUTLIER) cc_final: 0.7841 (mp) REVERT: E 567 ASP cc_start: 0.6146 (OUTLIER) cc_final: 0.5929 (p0) REVERT: E 664 ASP cc_start: 0.5639 (m-30) cc_final: 0.5413 (m-30) outliers start: 57 outliers final: 25 residues processed: 226 average time/residue: 0.8252 time to fit residues: 208.1894 Evaluate side-chains 208 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 175 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 GLU Chi-restraints excluded: chain B residue 109 MET Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 174 HIS Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain B residue 623 SER Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain E residue 121 PHE Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain E residue 320 LEU Chi-restraints excluded: chain E residue 363 THR Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 425 SER Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain E residue 473 THR Chi-restraints excluded: chain E residue 527 ILE Chi-restraints excluded: chain E residue 567 ASP Chi-restraints excluded: chain E residue 623 SER Chi-restraints excluded: chain E residue 640 LEU Chi-restraints excluded: chain E residue 651 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 117 optimal weight: 0.9990 chunk 125 optimal weight: 1.9990 chunk 129 optimal weight: 0.9980 chunk 75 optimal weight: 0.0980 chunk 54 optimal weight: 1.9990 chunk 98 optimal weight: 0.0050 chunk 38 optimal weight: 3.9990 chunk 113 optimal weight: 0.6980 chunk 118 optimal weight: 2.9990 chunk 82 optimal weight: 5.9990 chunk 132 optimal weight: 0.2980 overall best weight: 0.4194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN D 21 GLN ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 62 GLN E 533 GLN E 644 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 1.0132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 11398 Z= 0.182 Angle : 0.746 15.718 15570 Z= 0.345 Chirality : 0.043 0.279 1744 Planarity : 0.006 0.064 1990 Dihedral : 8.432 148.360 1579 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.75 % Favored : 91.10 % Rotamer: Outliers : 3.82 % Allowed : 29.63 % Favored : 66.55 % 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: -0.07 (0.23), residues: 1394 helix: 2.48 (0.24), residues: 470 sheet: -0.24 (0.34), residues: 210 loop : -1.85 (0.23), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 214 HIS 0.003 0.001 HIS B 532 PHE 0.027 0.002 PHE A 107 TYR 0.024 0.001 TYR E 382 ARG 0.006 0.000 ARG E 279 *********************** 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 236 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 191 time to evaluate : 1.121 Fit side-chains TARDY: cannot create tardy model for: "THR B 568 " (corrupted residue). Skipping it. REVERT: A 167 TRP cc_start: 0.8540 (t-100) cc_final: 0.8202 (t-100) REVERT: A 362 ILE cc_start: 0.9210 (tt) cc_final: 0.8808 (pt) REVERT: B 131 LEU cc_start: 0.7184 (OUTLIER) cc_final: 0.6859 (pp) REVERT: B 135 ASP cc_start: 0.8383 (t70) cc_final: 0.8159 (t70) REVERT: B 141 ILE cc_start: 0.8989 (mt) cc_final: 0.8763 (mp) REVERT: B 237 ARG cc_start: 0.7817 (mtt180) cc_final: 0.7512 (mtm-85) REVERT: B 374 CYS cc_start: 0.8159 (m) cc_final: 0.7947 (m) REVERT: B 424 MET cc_start: 0.8141 (mmm) cc_final: 0.6967 (mtm) REVERT: B 525 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8431 (tp) REVERT: D 23 TYR cc_start: 0.8521 (m-80) cc_final: 0.7666 (m-80) REVERT: D 172 LYS cc_start: 0.8525 (tppt) cc_final: 0.8246 (tmmt) REVERT: D 362 ILE cc_start: 0.9171 (tt) cc_final: 0.8834 (pt) REVERT: E 109 MET cc_start: 0.3507 (pmm) cc_final: 0.3119 (pmm) REVERT: E 121 PHE cc_start: 0.6746 (OUTLIER) cc_final: 0.6522 (m-80) REVERT: E 237 ARG cc_start: 0.7872 (OUTLIER) cc_final: 0.7619 (mtm-85) REVERT: E 309 GLN cc_start: 0.7917 (mt0) cc_final: 0.7656 (mp10) REVERT: E 374 CYS cc_start: 0.8154 (m) cc_final: 0.7931 (m) REVERT: E 377 ASP cc_start: 0.8363 (t70) cc_final: 0.7957 (t0) REVERT: E 407 ASP cc_start: 0.8909 (t0) cc_final: 0.8674 (m-30) REVERT: E 420 GLU cc_start: 0.7568 (mm-30) cc_final: 0.7276 (mm-30) REVERT: E 424 MET cc_start: 0.8102 (mmm) cc_final: 0.6852 (mtm) REVERT: E 527 ILE cc_start: 0.8160 (OUTLIER) cc_final: 0.7871 (mp) outliers start: 45 outliers final: 26 residues processed: 222 average time/residue: 0.8413 time to fit residues: 207.7271 Evaluate side-chains 206 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 175 time to evaluate : 1.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 GLU Chi-restraints excluded: chain B residue 109 MET Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 174 HIS Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 309 GLN Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 543 ILE Chi-restraints excluded: chain B residue 623 SER Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain E residue 121 PHE Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain E residue 237 ARG Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 338 SER Chi-restraints excluded: chain E residue 363 THR Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 425 SER Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain E residue 473 THR Chi-restraints excluded: chain E residue 521 GLU Chi-restraints excluded: chain E residue 527 ILE Chi-restraints excluded: chain E residue 640 LEU Chi-restraints excluded: chain E residue 651 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 81 optimal weight: 8.9990 chunk 63 optimal weight: 5.9990 chunk 92 optimal weight: 2.9990 chunk 139 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 chunk 111 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 88 optimal weight: 3.9990 chunk 118 optimal weight: 3.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN A 26 HIS B 327 ASN ** B 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 21 GLN ** E 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 648 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 1.0491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.095 11398 Z= 0.398 Angle : 0.820 14.140 15570 Z= 0.389 Chirality : 0.047 0.273 1744 Planarity : 0.006 0.062 1990 Dihedral : 8.336 146.729 1579 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.54 % Favored : 90.32 % Rotamer: Outliers : 3.82 % Allowed : 30.65 % Favored : 65.53 % 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: -0.45 (0.23), residues: 1394 helix: 2.05 (0.24), residues: 482 sheet: -0.59 (0.31), residues: 252 loop : -2.09 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 169 HIS 0.005 0.001 HIS B 110 PHE 0.026 0.002 PHE D 107 TYR 0.033 0.002 TYR B 382 ARG 0.016 0.001 ARG E 522 ********************** 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 228 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 183 time to evaluate : 1.222 Fit side-chains TARDY: cannot create tardy model for: "THR B 568 " (corrupted residue). Skipping it. REVERT: A 94 TYR cc_start: 0.7958 (OUTLIER) cc_final: 0.7504 (m-80) REVERT: A 362 ILE cc_start: 0.9204 (tt) cc_final: 0.8847 (pt) REVERT: B 200 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8448 (mt) REVERT: B 237 ARG cc_start: 0.8034 (mtt180) cc_final: 0.7695 (mtm-85) REVERT: B 477 MET cc_start: 0.8210 (mtp) cc_final: 0.7991 (mtm) REVERT: B 506 THR cc_start: 0.9041 (m) cc_final: 0.8741 (p) REVERT: B 525 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8510 (tp) REVERT: B 527 ILE cc_start: 0.8253 (OUTLIER) cc_final: 0.7995 (mp) REVERT: D 23 TYR cc_start: 0.8735 (m-80) cc_final: 0.7599 (m-80) REVERT: D 94 TYR cc_start: 0.7759 (OUTLIER) cc_final: 0.7484 (m-80) REVERT: D 172 LYS cc_start: 0.8768 (tppt) cc_final: 0.8446 (ttmt) REVERT: D 362 ILE cc_start: 0.9187 (tt) cc_final: 0.8882 (pt) REVERT: E 237 ARG cc_start: 0.8073 (OUTLIER) cc_final: 0.7751 (mtm-85) REVERT: E 407 ASP cc_start: 0.8937 (t0) cc_final: 0.8726 (m-30) REVERT: E 420 GLU cc_start: 0.7531 (mm-30) cc_final: 0.7210 (mm-30) outliers start: 45 outliers final: 30 residues processed: 217 average time/residue: 0.8948 time to fit residues: 215.3846 Evaluate side-chains 213 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 177 time to evaluate : 1.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 GLU Chi-restraints excluded: chain A residue 94 TYR Chi-restraints excluded: chain B residue 109 MET Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 139 PHE Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 174 HIS Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 309 GLN Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain B residue 623 SER Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain D residue 94 TYR Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain E residue 202 GLU Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain E residue 237 ARG Chi-restraints excluded: chain E residue 338 SER Chi-restraints excluded: chain E residue 363 THR Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 425 SER Chi-restraints excluded: chain E residue 436 LEU Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain E residue 473 THR Chi-restraints excluded: chain E residue 521 GLU Chi-restraints excluded: chain E residue 533 GLN Chi-restraints excluded: chain E residue 640 LEU Chi-restraints excluded: chain E residue 651 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 34 optimal weight: 0.7980 chunk 102 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 30 optimal weight: 0.2980 chunk 111 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 114 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN D 21 GLN ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 533 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.114398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.092572 restraints weight = 18339.515| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 3.43 r_work: 0.3120 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 1.0615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 11398 Z= 0.215 Angle : 0.769 14.238 15570 Z= 0.359 Chirality : 0.044 0.279 1744 Planarity : 0.006 0.061 1990 Dihedral : 8.310 147.219 1579 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.11 % Favored : 90.75 % Rotamer: Outliers : 3.31 % Allowed : 31.83 % Favored : 64.86 % 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: -0.26 (0.23), residues: 1394 helix: 2.22 (0.24), residues: 480 sheet: -0.51 (0.32), residues: 234 loop : -1.92 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 214 HIS 0.004 0.001 HIS B 532 PHE 0.026 0.002 PHE A 107 TYR 0.039 0.002 TYR E 382 ARG 0.005 0.000 ARG E 279 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4303.73 seconds wall clock time: 76 minutes 28.85 seconds (4588.85 seconds total)