Starting phenix.real_space_refine (version: 1.21rc1) on Sat Apr 22 02:12:09 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6of3_20041/04_2023/6of3_20041_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6of3_20041/04_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_20041/04_2023/6of3_20041.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6of3_20041/04_2023/6of3_20041.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6of3_20041/04_2023/6of3_20041_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6of3_20041/04_2023/6of3_20041_updated.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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: 6.35, per 1000 atoms: 0.57 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 1.7 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: 1.26 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: 3.34 Time building geometry restraints manager: 4.61 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: 6611 33.07 - 66.13: 169 66.13 - 99.20: 2 99.20 - 132.26: 0 132.26 - 165.33: 2 Dihedral angle restraints: 6784 sinusoidal: 2666 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 6781 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: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 3.590 Check model and map are aligned: 0.160 Set scattering table: 0.120 Process input model: 30.520 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.070 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:11.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.770 ------------------------------------------------------------------------------- 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 : 14.696 165.331 4116 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 % 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 *********************** 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 : 1.344 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: 0.9790 time to fit residues: 400.3552 Evaluate side-chains 225 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 221 time to evaluate : 1.384 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 3 residues processed: 1 average time/residue: 0.1619 time to fit residues: 2.2711 ------------------------------------------------------------------------------- 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: 0.6760 moved from start: 0.3458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 11398 Z= 0.251 Angle : 0.920 13.415 15570 Z= 0.446 Chirality : 0.047 0.179 1744 Planarity : 0.007 0.055 1990 Dihedral : 9.086 165.083 1556 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.79 % Allowed : 9.61 % Favored : 89.60 % Rotamer Outliers : 5.52 % 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: 1.58 (0.23), residues: 452 sheet: -0.80 (0.35), residues: 212 loop : -2.87 (0.22), residues: 730 *********************** 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 308 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 243 time to evaluate : 1.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 65 outliers final: 26 residues processed: 284 average time/residue: 0.8542 time to fit residues: 269.8555 Evaluate side-chains 234 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 208 time to evaluate : 1.202 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 19 residues processed: 7 average time/residue: 0.2904 time to fit residues: 4.4771 ------------------------------------------------------------------------------- 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: 2.9990 chunk 105 optimal weight: 3.9990 chunk 86 optimal weight: 0.5980 chunk 35 optimal weight: 0.7980 chunk 127 optimal weight: 0.4980 chunk 137 optimal weight: 0.9990 chunk 113 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 41 GLN E 357 HIS E 689 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.5972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.090 11398 Z= 0.295 Angle : 0.885 14.172 15570 Z= 0.434 Chirality : 0.048 0.213 1744 Planarity : 0.006 0.057 1990 Dihedral : 8.810 164.533 1556 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.36 % Allowed : 10.47 % Favored : 89.17 % Rotamer Outliers : 6.37 % 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: -0.93 (0.22), residues: 1394 helix: 2.07 (0.23), residues: 456 sheet: -0.56 (0.36), residues: 212 loop : -2.59 (0.21), residues: 726 *********************** 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 323 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 248 time to evaluate : 1.398 Fit side-chains revert: symmetry clash outliers start: 75 outliers final: 25 residues processed: 300 average time/residue: 0.8842 time to fit residues: 294.5906 Evaluate side-chains 218 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 193 time to evaluate : 1.432 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 19 residues processed: 7 average time/residue: 0.3396 time to fit residues: 4.9651 ------------------------------------------------------------------------------- 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: 0.8980 chunk 95 optimal weight: 4.9990 chunk 66 optimal weight: 0.3980 chunk 14 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 chunk 127 optimal weight: 0.5980 chunk 135 optimal weight: 6.9990 chunk 121 optimal weight: 4.9990 chunk 36 optimal weight: 10.0000 chunk 112 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 68 HIS ** E 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 HIS E 533 GLN E 644 ASN E 689 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.7233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.062 11398 Z= 0.264 Angle : 0.788 10.271 15570 Z= 0.376 Chirality : 0.046 0.245 1744 Planarity : 0.007 0.122 1990 Dihedral : 8.885 162.824 1556 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.03 % Favored : 91.82 % Rotamer Outliers : 5.77 % 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: -0.66 (0.23), residues: 1394 helix: 2.50 (0.24), residues: 448 sheet: -0.53 (0.39), residues: 174 loop : -2.39 (0.20), residues: 772 *********************** 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 303 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 235 time to evaluate : 1.204 Fit side-chains outliers start: 68 outliers final: 31 residues processed: 274 average time/residue: 0.9435 time to fit residues: 285.6365 Evaluate side-chains 226 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 195 time to evaluate : 1.253 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 23 residues processed: 8 average time/residue: 0.1411 time to fit residues: 3.6889 ------------------------------------------------------------------------------- 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: 0.9990 chunk 1 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 chunk 121 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- 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 ** B 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 HIS B 689 ASN D 21 GLN ** 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 533 GLN E 689 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.8591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.053 11398 Z= 0.339 Angle : 0.807 10.397 15570 Z= 0.394 Chirality : 0.046 0.161 1744 Planarity : 0.007 0.118 1990 Dihedral : 8.719 158.045 1556 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.75 % Favored : 91.10 % Rotamer Outliers : 6.54 % 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: -0.62 (0.23), residues: 1394 helix: 2.31 (0.24), residues: 454 sheet: -0.49 (0.36), residues: 212 loop : -2.34 (0.21), residues: 728 *********************** 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 297 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 220 time to evaluate : 1.265 Fit side-chains TARDY: cannot create tardy model for: "THR B 568 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 77 outliers final: 37 residues processed: 276 average time/residue: 0.8794 time to fit residues: 270.3362 Evaluate side-chains 219 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 182 time to evaluate : 1.265 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 29 residues processed: 9 average time/residue: 0.1647 time to fit residues: 3.9553 ------------------------------------------------------------------------------- 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: 0.9990 chunk 26 optimal weight: 7.9990 chunk 79 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 135 optimal weight: 0.9980 chunk 112 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 11 optimal weight: 6.9990 chunk 44 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 130 optimal weight: 0.1980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN A 115 HIS ** B 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 21 GLN E 144 ASN E 533 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.9021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 11398 Z= 0.213 Angle : 0.739 11.636 15570 Z= 0.351 Chirality : 0.043 0.218 1744 Planarity : 0.006 0.049 1990 Dihedral : 8.562 157.223 1556 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.11 % Favored : 91.75 % Rotamer Outliers : 6.28 % 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: -0.36 (0.23), residues: 1394 helix: 2.54 (0.24), residues: 460 sheet: -0.44 (0.35), residues: 212 loop : -2.19 (0.21), residues: 722 *********************** 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 279 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 205 time to evaluate : 1.359 Fit side-chains TARDY: cannot create tardy model for: "THR B 568 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 74 outliers final: 45 residues processed: 259 average time/residue: 0.9074 time to fit residues: 260.7091 Evaluate side-chains 230 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 185 time to evaluate : 1.209 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 34 residues processed: 11 average time/residue: 0.5834 time to fit residues: 9.1773 ------------------------------------------------------------------------------- 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: 0.4980 chunk 77 optimal weight: 10.0000 chunk 98 optimal weight: 3.9990 chunk 76 optimal weight: 0.9980 chunk 114 optimal weight: 0.7980 chunk 75 optimal weight: 0.5980 chunk 134 optimal weight: 3.9990 chunk 84 optimal weight: 0.6980 chunk 82 optimal weight: 0.0970 chunk 62 optimal weight: 0.9980 chunk 83 optimal weight: 0.8980 overall best weight: 0.5378 ------------------------------------------------------------------------------- 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 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 396 ASN D 21 GLN E 533 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.9306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 11398 Z= 0.196 Angle : 0.737 11.750 15570 Z= 0.347 Chirality : 0.043 0.221 1744 Planarity : 0.006 0.048 1990 Dihedral : 8.375 155.554 1556 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.25 % Favored : 91.61 % Rotamer Outliers : 5.43 % 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: -0.18 (0.23), residues: 1394 helix: 2.66 (0.24), residues: 460 sheet: -0.37 (0.35), residues: 212 loop : -2.05 (0.22), residues: 722 *********************** 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 261 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 197 time to evaluate : 1.318 Fit side-chains outliers start: 64 outliers final: 40 residues processed: 246 average time/residue: 0.8658 time to fit residues: 237.4657 Evaluate side-chains 210 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 170 time to evaluate : 1.326 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 32 residues processed: 8 average time/residue: 0.4881 time to fit residues: 6.5516 ------------------------------------------------------------------------------- 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: 2.9990 chunk 80 optimal weight: 4.9990 chunk 40 optimal weight: 0.1980 chunk 26 optimal weight: 6.9990 chunk 85 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 66 optimal weight: 0.0040 chunk 12 optimal weight: 5.9990 chunk 106 optimal weight: 7.9990 chunk 122 optimal weight: 1.9990 chunk 129 optimal weight: 0.6980 overall best weight: 0.9796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN A 115 HIS B 144 ASN B 168 GLN D 21 GLN ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 142 HIS E 533 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.9747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 11398 Z= 0.237 Angle : 0.764 11.841 15570 Z= 0.359 Chirality : 0.044 0.218 1744 Planarity : 0.006 0.050 1990 Dihedral : 8.296 154.859 1556 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.75 % Favored : 91.10 % Rotamer Outliers : 5.26 % 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: -0.18 (0.23), residues: 1394 helix: 2.60 (0.24), residues: 460 sheet: -0.29 (0.35), residues: 208 loop : -2.02 (0.22), residues: 726 *********************** 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: 62 poor density : 186 time to evaluate : 1.431 Fit side-chains TARDY: cannot create tardy model for: "THR B 568 " (corrupted residue). Skipping it. outliers start: 62 outliers final: 41 residues processed: 236 average time/residue: 0.8716 time to fit residues: 229.0570 Evaluate side-chains 217 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 176 time to evaluate : 1.316 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 35 residues processed: 6 average time/residue: 0.9226 time to fit residues: 7.9335 ------------------------------------------------------------------------------- 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: 0.7980 chunk 125 optimal weight: 0.7980 chunk 129 optimal weight: 0.7980 chunk 75 optimal weight: 0.9980 chunk 54 optimal weight: 0.5980 chunk 98 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 113 optimal weight: 2.9990 chunk 118 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 132 optimal weight: 9.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 533 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 1.0015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 11398 Z= 0.219 Angle : 0.747 11.963 15570 Z= 0.351 Chirality : 0.044 0.256 1744 Planarity : 0.006 0.048 1990 Dihedral : 8.198 153.894 1556 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.54 % Favored : 91.32 % Rotamer Outliers : 4.41 % 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: -0.12 (0.23), residues: 1394 helix: 2.64 (0.24), residues: 460 sheet: -0.38 (0.35), residues: 208 loop : -1.94 (0.23), residues: 726 *********************** 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 233 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 181 time to evaluate : 1.289 Fit side-chains TARDY: cannot create tardy model for: "THR B 568 " (corrupted residue). Skipping it. outliers start: 52 outliers final: 39 residues processed: 222 average time/residue: 0.8498 time to fit residues: 210.6462 Evaluate side-chains 217 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 178 time to evaluate : 1.231 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 35 residues processed: 5 average time/residue: 0.7710 time to fit residues: 6.0565 ------------------------------------------------------------------------------- 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: 0.9990 chunk 63 optimal weight: 3.9990 chunk 92 optimal weight: 0.0970 chunk 139 optimal weight: 0.9990 chunk 128 optimal weight: 0.8980 chunk 111 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 88 optimal weight: 4.9990 chunk 118 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN A 115 HIS D 21 GLN ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 1.0273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 11398 Z= 0.213 Angle : 0.763 12.463 15570 Z= 0.355 Chirality : 0.044 0.275 1744 Planarity : 0.006 0.048 1990 Dihedral : 8.090 152.004 1556 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.46 % Favored : 91.39 % Rotamer Outliers : 4.07 % 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: -0.09 (0.23), residues: 1394 helix: 2.62 (0.24), residues: 462 sheet: -0.40 (0.37), residues: 186 loop : -1.85 (0.22), residues: 746 ********************** 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: 48 poor density : 184 time to evaluate : 1.348 Fit side-chains outliers start: 48 outliers final: 41 residues processed: 224 average time/residue: 0.8245 time to fit residues: 207.5956 Evaluate side-chains 215 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 174 time to evaluate : 1.354 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 36 residues processed: 5 average time/residue: 0.5364 time to fit residues: 5.0274 ------------------------------------------------------------------------------- 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: 3.9990 chunk 102 optimal weight: 0.0980 chunk 16 optimal weight: 0.4980 chunk 30 optimal weight: 8.9990 chunk 111 optimal weight: 0.0010 chunk 46 optimal weight: 0.9980 chunk 114 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 97 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 overall best weight: 0.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN A 115 HIS ** B 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.114621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.092527 restraints weight = 18352.772| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 3.44 r_work: 0.3145 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 1.0472 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= 0.231 Angle : 0.764 11.692 15570 Z= 0.357 Chirality : 0.044 0.284 1744 Planarity : 0.006 0.047 1990 Dihedral : 8.042 151.519 1556 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.46 % Favored : 91.39 % Rotamer Outliers : 3.65 % 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: -0.13 (0.23), residues: 1394 helix: 2.55 (0.24), residues: 462 sheet: -0.51 (0.36), residues: 186 loop : -1.81 (0.22), residues: 746 =============================================================================== Job complete usr+sys time: 4365.81 seconds wall clock time: 77 minutes 54.86 seconds (4674.86 seconds total)