Starting phenix.real_space_refine (version: 1.21rc1) on Sat Apr 22 19:09:45 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i6v_35208/04_2023/8i6v_35208_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i6v_35208/04_2023/8i6v_35208.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i6v_35208/04_2023/8i6v_35208_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i6v_35208/04_2023/8i6v_35208_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i6v_35208/04_2023/8i6v_35208_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i6v_35208/04_2023/8i6v_35208.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i6v_35208/04_2023/8i6v_35208.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i6v_35208/04_2023/8i6v_35208_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i6v_35208/04_2023/8i6v_35208_updated.pdb" } resolution = 3.06 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= 0.000 sd= 0.004 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 Mn 1 7.51 5 P 7 5.49 5 S 36 5.16 5 C 8515 2.51 5 N 2219 2.21 5 O 2394 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 49": "OE1" <-> "OE2" Residue "D GLU 54": "OE1" <-> "OE2" Residue "D PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 412": "OE1" <-> "OE2" Residue "D PHE 795": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 135": "OD1" <-> "OD2" Residue "E ASP 243": "OD1" <-> "OD2" Residue "E GLU 285": "OE1" <-> "OE2" Residue "E GLU 333": "OE1" <-> "OE2" Residue "E PHE 476": "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: 13172 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 811 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "B" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 804 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 3, 'TRANS': 97} Chain: "C" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 810 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "D" Number of atoms: 5640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 678, 5640 Classifications: {'peptide': 678} Link IDs: {'PTRANS': 31, 'TRANS': 646} Chain breaks: 4 Chain: "E" Number of atoms: 5022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 611, 5022 Classifications: {'peptide': 611} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 584} Chain breaks: 3 Chain: "C" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 10 Unusual residues: {'PO4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 19 Unusual residues: {' MN': 1, '3PO': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Time building chain proxies: 7.24, per 1000 atoms: 0.55 Number of scatterers: 13172 At special positions: 0 Unit cell: (149.776, 117.438, 154.031, 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) Mn 1 24.99 S 36 16.00 P 7 15.00 O 2394 8.00 N 2219 7.00 C 8515 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: 5.69 Conformation dependent library (CDL) restraints added in 1.6 seconds 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3036 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 54 helices and 4 sheets defined 56.8% alpha, 9.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.35 Creating SS restraints... Processing helix chain 'A' and resid 23 through 52 removed outlier: 4.135A pdb=" N PHE A 39 " --> pdb=" O SER A 35 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N THR A 40 " --> pdb=" O TRP A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 83 removed outlier: 4.048A pdb=" N GLY A 63 " --> pdb=" O ARG A 59 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU A 64 " --> pdb=" O VAL A 60 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 121 removed outlier: 3.910A pdb=" N PHE A 107 " --> pdb=" O LEU A 103 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LEU A 108 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N LEU A 109 " --> pdb=" O CYS A 105 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS A 121 " --> pdb=" O ILE A 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 53 removed outlier: 3.652A pdb=" N PHE B 53 " --> pdb=" O GLY B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 86 Processing helix chain 'B' and resid 100 through 121 Processing helix chain 'C' and resid 23 through 52 Processing helix chain 'C' and resid 56 through 88 Processing helix chain 'C' and resid 99 through 120 Processing helix chain 'D' and resid 3 through 9 Processing helix chain 'D' and resid 13 through 15 No H-bonds generated for 'chain 'D' and resid 13 through 15' Processing helix chain 'D' and resid 22 through 28 Processing helix chain 'D' and resid 31 through 35 Processing helix chain 'D' and resid 46 through 86 removed outlier: 3.511A pdb=" N ARG D 76 " --> pdb=" O ASN D 72 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU D 81 " --> pdb=" O LYS D 77 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASN D 84 " --> pdb=" O ASP D 80 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N THR D 85 " --> pdb=" O LEU D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 133 Processing helix chain 'D' and resid 142 through 150 Processing helix chain 'D' and resid 162 through 176 Processing helix chain 'D' and resid 188 through 194 removed outlier: 4.024A pdb=" N LYS D 193 " --> pdb=" O SER D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 214 through 225 removed outlier: 3.963A pdb=" N ILE D 217 " --> pdb=" O ASP D 214 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N MET D 218 " --> pdb=" O ASP D 215 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU D 219 " --> pdb=" O ASN D 216 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 313 Processing helix chain 'D' and resid 330 through 332 No H-bonds generated for 'chain 'D' and resid 330 through 332' Processing helix chain 'D' and resid 366 through 370 Processing helix chain 'D' and resid 376 through 388 Processing helix chain 'D' and resid 392 through 412 Processing helix chain 'D' and resid 475 through 478 Processing helix chain 'D' and resid 508 through 514 Processing helix chain 'D' and resid 527 through 536 Processing helix chain 'D' and resid 551 through 553 No H-bonds generated for 'chain 'D' and resid 551 through 553' Processing helix chain 'D' and resid 561 through 586 Processing helix chain 'D' and resid 697 through 730 removed outlier: 3.996A pdb=" N SER D 727 " --> pdb=" O SER D 723 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N VAL D 728 " --> pdb=" O ILE D 724 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N GLN D 729 " --> pdb=" O TYR D 725 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N LYS D 730 " --> pdb=" O ASN D 726 " (cutoff:3.500A) Processing helix chain 'D' and resid 734 through 766 removed outlier: 3.787A pdb=" N ASP D 738 " --> pdb=" O PRO D 734 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N LEU D 739 " --> pdb=" O GLN D 735 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU D 740 " --> pdb=" O LEU D 736 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA D 741 " --> pdb=" O ALA D 737 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N TYR D 742 " --> pdb=" O ASP D 738 " (cutoff:3.500A) Processing helix chain 'D' and resid 777 through 804 removed outlier: 3.715A pdb=" N ALA D 784 " --> pdb=" O PRO D 780 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ALA D 803 " --> pdb=" O PHE D 799 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ARG D 804 " --> pdb=" O LYS D 800 " (cutoff:3.500A) Processing helix chain 'D' and resid 823 through 833 removed outlier: 3.650A pdb=" N ASP D 827 " --> pdb=" O LYS D 823 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 8 Processing helix chain 'E' and resid 13 through 15 No H-bonds generated for 'chain 'E' and resid 13 through 15' Processing helix chain 'E' and resid 22 through 36 Processing helix chain 'E' and resid 42 through 86 Processing helix chain 'E' and resid 98 through 137 Processing helix chain 'E' and resid 143 through 152 removed outlier: 3.831A pdb=" N VAL E 148 " --> pdb=" O PRO E 144 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG E 149 " --> pdb=" O VAL E 145 " (cutoff:3.500A) Processing helix chain 'E' and resid 161 through 177 Processing helix chain 'E' and resid 205 through 217 removed outlier: 3.517A pdb=" N ILE E 208 " --> pdb=" O PRO E 205 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N THR E 209 " --> pdb=" O ASP E 206 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU E 210 " --> pdb=" O ASN E 207 " (cutoff:3.500A) Processing helix chain 'E' and resid 248 through 254 Processing helix chain 'E' and resid 304 through 309 Processing helix chain 'E' and resid 314 through 317 No H-bonds generated for 'chain 'E' and resid 314 through 317' Processing helix chain 'E' and resid 319 through 324 Processing helix chain 'E' and resid 329 through 349 Processing helix chain 'E' and resid 414 through 416 No H-bonds generated for 'chain 'E' and resid 414 through 416' Processing helix chain 'E' and resid 439 through 445 Processing helix chain 'E' and resid 458 through 466 Processing helix chain 'E' and resid 479 through 482 removed outlier: 4.585A pdb=" N ASP E 482 " --> pdb=" O PRO E 479 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 479 through 482' Processing helix chain 'E' and resid 511 through 523 Processing helix chain 'E' and resid 624 through 648 removed outlier: 4.079A pdb=" N GLU E 628 " --> pdb=" O TYR E 624 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ILE E 637 " --> pdb=" O SER E 633 " (cutoff:3.500A) Processing helix chain 'E' and resid 654 through 686 removed outlier: 3.938A pdb=" N MET E 657 " --> pdb=" O PRO E 654 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N ILE E 658 " --> pdb=" O THR E 655 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLY E 659 " --> pdb=" O ALA E 656 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARG E 686 " --> pdb=" O VAL E 683 " (cutoff:3.500A) Processing helix chain 'E' and resid 698 through 717 Processing sheet with id= A, first strand: chain 'D' and resid 519 through 521 Processing sheet with id= B, first strand: chain 'D' and resid 353 through 361 removed outlier: 4.383A pdb=" N ILE D 336 " --> pdb=" O MET D 361 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N LEU D 322 " --> pdb=" O PHE D 301 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU D 418 " --> pdb=" O TYR D 300 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N ASP D 302 " --> pdb=" O PRO D 416 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'E' and resid 450 through 452 removed outlier: 6.962A pdb=" N TYR E 241 " --> pdb=" O VAL E 354 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ARG E 356 " --> pdb=" O SER E 239 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N SER E 239 " --> pdb=" O ARG E 356 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N PHE E 358 " --> pdb=" O ILE E 237 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N ILE E 237 " --> pdb=" O PHE E 358 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N HIS E 263 " --> pdb=" O PHE E 242 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ALA E 260 " --> pdb=" O HIS E 283 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N TYR E 268 " --> pdb=" O THR E 275 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N THR E 275 " --> pdb=" O TYR E 268 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'E' and resid 355 through 358 763 hydrogen bonds defined for protein. 2136 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: 4.09 Time building geometry restraints manager: 5.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2184 1.32 - 1.45: 3611 1.45 - 1.57: 7598 1.57 - 1.69: 5 1.69 - 1.82: 64 Bond restraints: 13462 Sorted by residual: bond pdb=" O12 POV C 201 " pdb=" P POV C 201 " ideal model delta sigma weight residual 1.657 1.739 -0.082 2.00e-02 2.50e+03 1.68e+01 bond pdb=" N VAL D 74 " pdb=" CA VAL D 74 " ideal model delta sigma weight residual 1.460 1.502 -0.042 1.19e-02 7.06e+03 1.22e+01 bond pdb=" C PRO D 456 " pdb=" O PRO D 456 " ideal model delta sigma weight residual 1.233 1.197 0.036 1.16e-02 7.43e+03 9.43e+00 bond pdb=" N SER D 43 " pdb=" CA SER D 43 " ideal model delta sigma weight residual 1.456 1.491 -0.035 1.14e-02 7.69e+03 9.35e+00 bond pdb=" O3 PO4 D 901 " pdb=" P PO4 D 901 " ideal model delta sigma weight residual 1.569 1.509 0.060 2.00e-02 2.50e+03 9.07e+00 ... (remaining 13457 not shown) Histogram of bond angle deviations from ideal: 94.30 - 102.24: 33 102.24 - 110.18: 2194 110.18 - 118.12: 7911 118.12 - 126.06: 7868 126.06 - 134.01: 192 Bond angle restraints: 18198 Sorted by residual: angle pdb=" C ARG C 90 " pdb=" CA ARG C 90 " pdb=" CB ARG C 90 " ideal model delta sigma weight residual 116.54 110.06 6.48 1.15e+00 7.56e-01 3.18e+01 angle pdb=" C ASN D 454 " pdb=" N ARG D 455 " pdb=" CA ARG D 455 " ideal model delta sigma weight residual 123.15 117.28 5.87 1.21e+00 6.83e-01 2.35e+01 angle pdb=" N LEU D 81 " pdb=" CA LEU D 81 " pdb=" C LEU D 81 " ideal model delta sigma weight residual 112.34 106.65 5.69 1.30e+00 5.92e-01 1.92e+01 angle pdb=" CA PRO D 456 " pdb=" C PRO D 456 " pdb=" O PRO D 456 " ideal model delta sigma weight residual 121.34 116.82 4.52 1.14e+00 7.69e-01 1.57e+01 angle pdb=" N ILE D 457 " pdb=" CA ILE D 457 " pdb=" C ILE D 457 " ideal model delta sigma weight residual 110.72 106.80 3.92 1.01e+00 9.80e-01 1.51e+01 ... (remaining 18193 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.12: 7617 27.12 - 54.23: 418 54.23 - 81.35: 21 81.35 - 108.46: 13 108.46 - 135.58: 1 Dihedral angle restraints: 8070 sinusoidal: 3388 harmonic: 4682 Sorted by residual: dihedral pdb=" CA TYR D 507 " pdb=" C TYR D 507 " pdb=" N GLU D 508 " pdb=" CA GLU D 508 " ideal model delta harmonic sigma weight residual 180.00 -155.57 -24.43 0 5.00e+00 4.00e-02 2.39e+01 dihedral pdb=" C37 POV C 201 " pdb=" C38 POV C 201 " pdb=" C39 POV C 201 " pdb="C310 POV C 201 " ideal model delta sinusoidal sigma weight residual -179.61 -44.03 -135.58 1 3.00e+01 1.11e-03 1.83e+01 dihedral pdb=" C27 POV C 201 " pdb=" C28 POV C 201 " pdb=" C29 POV C 201 " pdb="C210 POV C 201 " ideal model delta sinusoidal sigma weight residual 127.48 -131.63 -100.89 1 3.00e+01 1.11e-03 1.27e+01 ... (remaining 8067 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1460 0.039 - 0.079: 417 0.079 - 0.118: 101 0.118 - 0.158: 22 0.158 - 0.197: 5 Chirality restraints: 2005 Sorted by residual: chirality pdb=" CA LYS D 86 " pdb=" N LYS D 86 " pdb=" C LYS D 86 " pdb=" CB LYS D 86 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.72e-01 chirality pdb=" CA LEU D 75 " pdb=" N LEU D 75 " pdb=" C LEU D 75 " pdb=" CB LEU D 75 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.09e-01 chirality pdb=" CA THR D 85 " pdb=" N THR D 85 " pdb=" C THR D 85 " pdb=" CB THR D 85 " both_signs ideal model delta sigma weight residual False 2.53 2.71 -0.18 2.00e-01 2.50e+01 8.37e-01 ... (remaining 2002 not shown) Planarity restraints: 2299 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 100 " -0.056 5.00e-02 4.00e+02 8.53e-02 1.16e+01 pdb=" N PRO A 101 " 0.148 5.00e-02 4.00e+02 pdb=" CA PRO A 101 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 101 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE D 34 " -0.012 2.00e-02 2.50e+03 2.52e-02 6.34e+00 pdb=" C ILE D 34 " 0.044 2.00e-02 2.50e+03 pdb=" O ILE D 34 " -0.017 2.00e-02 2.50e+03 pdb=" N HIS D 35 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY D 779 " 0.033 5.00e-02 4.00e+02 4.97e-02 3.96e+00 pdb=" N PRO D 780 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO D 780 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO D 780 " 0.028 5.00e-02 4.00e+02 ... (remaining 2296 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 136 2.67 - 3.23: 12085 3.23 - 3.79: 19564 3.79 - 4.34: 25843 4.34 - 4.90: 43851 Nonbonded interactions: 101479 Sorted by model distance: nonbonded pdb=" O3A 3PO E 801 " pdb="MN MN E 802 " model vdw 2.114 2.320 nonbonded pdb=" O ALA D 189 " pdb=" OG SER D 192 " model vdw 2.242 2.440 nonbonded pdb=" O1G 3PO E 801 " pdb=" O HOH E 901 " model vdw 2.259 2.440 nonbonded pdb=" O PRO D 780 " pdb=" OH TYR E 631 " model vdw 2.274 2.440 nonbonded pdb=" O4 PO4 D 901 " pdb=" O HOH D1001 " model vdw 2.302 2.440 ... (remaining 101474 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 22 through 121) selection = (chain 'B' and resid 22 through 121) selection = (chain 'C' and resid 22 through 121) } 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: 1.970 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: 0.010 Extract box with map and model: 11.140 Check model and map are aligned: 0.190 Set scattering table: 0.120 Process input model: 35.470 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 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 : 0.004 0.082 13462 Z= 0.240 Angle : 0.572 8.769 18198 Z= 0.322 Chirality : 0.041 0.197 2005 Planarity : 0.004 0.085 2299 Dihedral : 15.262 135.580 5034 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.25 % Favored : 96.56 % Rotamer Outliers : 0.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: 2.38 (0.22), residues: 1570 helix: 2.69 (0.17), residues: 924 sheet: 1.38 (0.39), residues: 176 loop : -0.71 (0.30), residues: 470 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 170 time to evaluate : 1.538 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 174 average time/residue: 0.2471 time to fit residues: 63.6480 Evaluate side-chains 137 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 134 time to evaluate : 1.418 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2218 time to fit residues: 3.0661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 133 optimal weight: 3.9990 chunk 119 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 40 optimal weight: 0.9980 chunk 80 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 123 optimal weight: 0.9980 chunk 47 optimal weight: 8.9990 chunk 75 optimal weight: 0.3980 chunk 92 optimal weight: 0.9990 chunk 143 optimal weight: 0.0020 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 95 ASN E 435 GLN ** E 717 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.0693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 13462 Z= 0.144 Angle : 0.449 6.120 18198 Z= 0.236 Chirality : 0.038 0.149 2005 Planarity : 0.004 0.055 2299 Dihedral : 5.782 83.647 1788 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer Outliers : 0.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: 2.51 (0.22), residues: 1570 helix: 2.76 (0.17), residues: 921 sheet: 1.50 (0.40), residues: 176 loop : -0.58 (0.30), residues: 473 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 151 time to evaluate : 1.530 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 8 residues processed: 157 average time/residue: 0.2689 time to fit residues: 61.6631 Evaluate side-chains 145 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 137 time to evaluate : 1.571 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1235 time to fit residues: 4.0648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 79 optimal weight: 0.1980 chunk 44 optimal weight: 6.9990 chunk 119 optimal weight: 4.9990 chunk 97 optimal weight: 7.9990 chunk 39 optimal weight: 10.0000 chunk 143 optimal weight: 0.7980 chunk 155 optimal weight: 5.9990 chunk 128 optimal weight: 4.9990 chunk 142 optimal weight: 0.0020 chunk 49 optimal weight: 1.9990 chunk 115 optimal weight: 3.9990 overall best weight: 1.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 111 GLN ** E 717 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.0875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 13462 Z= 0.202 Angle : 0.475 6.683 18198 Z= 0.247 Chirality : 0.039 0.139 2005 Planarity : 0.005 0.053 2299 Dihedral : 5.479 74.321 1788 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer Outliers : 0.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: 2.42 (0.22), residues: 1570 helix: 2.69 (0.17), residues: 924 sheet: 1.42 (0.39), residues: 176 loop : -0.63 (0.30), residues: 470 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 141 time to evaluate : 1.542 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 141 average time/residue: 0.2560 time to fit residues: 53.8094 Evaluate side-chains 132 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 131 time to evaluate : 1.547 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1134 time to fit residues: 2.2931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 142 optimal weight: 2.9990 chunk 108 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 15 optimal weight: 10.0000 chunk 68 optimal weight: 0.5980 chunk 96 optimal weight: 2.9990 chunk 144 optimal weight: 0.0020 chunk 152 optimal weight: 0.6980 chunk 75 optimal weight: 0.3980 chunk 136 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 101 ASN ** E 717 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.1002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.036 13462 Z= 0.128 Angle : 0.434 8.928 18198 Z= 0.223 Chirality : 0.037 0.139 2005 Planarity : 0.004 0.050 2299 Dihedral : 5.215 71.143 1788 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer Outliers : 0.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: 2.58 (0.22), residues: 1570 helix: 2.81 (0.17), residues: 921 sheet: 1.56 (0.40), residues: 176 loop : -0.53 (0.30), residues: 473 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 139 time to evaluate : 1.657 Fit side-chains outliers start: 9 outliers final: 6 residues processed: 144 average time/residue: 0.2599 time to fit residues: 55.4221 Evaluate side-chains 139 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 133 time to evaluate : 1.534 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1183 time to fit residues: 3.5155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 127 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 chunk 113 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 105 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 77 optimal weight: 3.9990 chunk 137 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 351 ASN D 794 ASN ** E 717 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.1249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.047 13462 Z= 0.299 Angle : 0.528 8.565 18198 Z= 0.272 Chirality : 0.040 0.163 2005 Planarity : 0.005 0.054 2299 Dihedral : 5.449 62.528 1788 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer Outliers : 0.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: 2.20 (0.22), residues: 1570 helix: 2.56 (0.17), residues: 918 sheet: 1.19 (0.40), residues: 178 loop : -0.71 (0.29), residues: 474 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 139 time to evaluate : 1.520 Fit side-chains outliers start: 10 outliers final: 8 residues processed: 144 average time/residue: 0.2618 time to fit residues: 55.6115 Evaluate side-chains 142 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 134 time to evaluate : 1.659 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1174 time to fit residues: 3.8934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 51 optimal weight: 0.9990 chunk 137 optimal weight: 0.7980 chunk 30 optimal weight: 7.9990 chunk 89 optimal weight: 4.9990 chunk 37 optimal weight: 10.0000 chunk 152 optimal weight: 3.9990 chunk 126 optimal weight: 0.5980 chunk 70 optimal weight: 5.9990 chunk 12 optimal weight: 6.9990 chunk 50 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 826 GLN ** E 717 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.1354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 13462 Z= 0.245 Angle : 0.503 9.647 18198 Z= 0.259 Chirality : 0.039 0.147 2005 Planarity : 0.005 0.054 2299 Dihedral : 5.415 65.492 1788 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer Outliers : 0.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: 2.13 (0.22), residues: 1570 helix: 2.51 (0.17), residues: 919 sheet: 1.16 (0.39), residues: 177 loop : -0.76 (0.29), residues: 474 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 140 time to evaluate : 1.582 Fit side-chains outliers start: 11 outliers final: 6 residues processed: 146 average time/residue: 0.2663 time to fit residues: 57.1824 Evaluate side-chains 137 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 131 time to evaluate : 1.586 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1273 time to fit residues: 3.5452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 147 optimal weight: 7.9990 chunk 17 optimal weight: 6.9990 chunk 87 optimal weight: 1.9990 chunk 111 optimal weight: 8.9990 chunk 86 optimal weight: 0.9990 chunk 128 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 152 optimal weight: 0.9990 chunk 95 optimal weight: 20.0000 chunk 92 optimal weight: 0.4980 chunk 70 optimal weight: 5.9990 overall best weight: 1.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 717 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.1399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 13462 Z= 0.210 Angle : 0.494 10.518 18198 Z= 0.253 Chirality : 0.038 0.136 2005 Planarity : 0.005 0.054 2299 Dihedral : 5.341 63.950 1788 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer Outliers : 0.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: 2.15 (0.22), residues: 1570 helix: 2.52 (0.17), residues: 924 sheet: 1.12 (0.39), residues: 177 loop : -0.74 (0.30), residues: 469 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 137 time to evaluate : 1.563 Fit side-chains outliers start: 7 outliers final: 7 residues processed: 140 average time/residue: 0.2745 time to fit residues: 56.1502 Evaluate side-chains 138 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 131 time to evaluate : 1.512 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1211 time to fit residues: 3.8309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 94 optimal weight: 2.9990 chunk 60 optimal weight: 0.3980 chunk 90 optimal weight: 6.9990 chunk 45 optimal weight: 0.2980 chunk 29 optimal weight: 9.9990 chunk 96 optimal weight: 0.6980 chunk 103 optimal weight: 4.9990 chunk 75 optimal weight: 7.9990 chunk 14 optimal weight: 0.6980 chunk 119 optimal weight: 4.9990 chunk 138 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 717 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 13462 Z= 0.150 Angle : 0.471 10.853 18198 Z= 0.238 Chirality : 0.037 0.139 2005 Planarity : 0.004 0.052 2299 Dihedral : 5.090 61.509 1788 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer Outliers : 0.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: 2.41 (0.22), residues: 1570 helix: 2.72 (0.17), residues: 915 sheet: 1.26 (0.39), residues: 176 loop : -0.57 (0.29), residues: 479 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 142 time to evaluate : 1.446 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 145 average time/residue: 0.2735 time to fit residues: 58.3159 Evaluate side-chains 137 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 135 time to evaluate : 1.701 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1211 time to fit residues: 2.7723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 145 optimal weight: 7.9990 chunk 133 optimal weight: 1.9990 chunk 141 optimal weight: 0.5980 chunk 85 optimal weight: 4.9990 chunk 61 optimal weight: 0.3980 chunk 111 optimal weight: 5.9990 chunk 43 optimal weight: 0.3980 chunk 128 optimal weight: 0.0970 chunk 134 optimal weight: 0.7980 chunk 93 optimal weight: 0.9980 chunk 150 optimal weight: 3.9990 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 717 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.036 13462 Z= 0.126 Angle : 0.462 12.063 18198 Z= 0.230 Chirality : 0.037 0.142 2005 Planarity : 0.004 0.052 2299 Dihedral : 4.845 59.776 1788 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer Outliers : 0.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: 2.57 (0.22), residues: 1570 helix: 2.83 (0.17), residues: 914 sheet: 1.39 (0.39), residues: 176 loop : -0.50 (0.30), residues: 480 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 135 time to evaluate : 1.568 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 138 average time/residue: 0.2595 time to fit residues: 53.4050 Evaluate side-chains 136 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 134 time to evaluate : 1.451 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1183 time to fit residues: 2.6436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 91 optimal weight: 6.9990 chunk 71 optimal weight: 4.9990 chunk 104 optimal weight: 1.9990 chunk 157 optimal weight: 5.9990 chunk 144 optimal weight: 3.9990 chunk 125 optimal weight: 3.9990 chunk 13 optimal weight: 7.9990 chunk 96 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 133 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 111 GLN ** E 717 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.054 13462 Z= 0.370 Angle : 0.593 12.325 18198 Z= 0.300 Chirality : 0.042 0.179 2005 Planarity : 0.005 0.053 2299 Dihedral : 5.389 54.427 1788 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer Outliers : 0.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: 2.01 (0.22), residues: 1570 helix: 2.43 (0.17), residues: 919 sheet: 0.94 (0.39), residues: 178 loop : -0.77 (0.29), residues: 473 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 139 time to evaluate : 1.634 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 140 average time/residue: 0.2756 time to fit residues: 56.7540 Evaluate side-chains 140 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 135 time to evaluate : 1.541 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1224 time to fit residues: 3.3535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 38 optimal weight: 6.9990 chunk 115 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 125 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 128 optimal weight: 0.4980 chunk 15 optimal weight: 7.9990 chunk 23 optimal weight: 9.9990 chunk 110 optimal weight: 0.6980 chunk 7 optimal weight: 10.0000 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 717 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.186020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.141352 restraints weight = 15672.239| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 2.12 r_work: 0.3175 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 13462 Z= 0.185 Angle : 0.506 11.769 18198 Z= 0.252 Chirality : 0.038 0.138 2005 Planarity : 0.004 0.052 2299 Dihedral : 5.191 53.943 1788 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer Outliers : 0.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: 2.27 (0.22), residues: 1570 helix: 2.60 (0.17), residues: 921 sheet: 1.09 (0.38), residues: 175 loop : -0.60 (0.30), residues: 474 =============================================================================== Job complete usr+sys time: 2635.06 seconds wall clock time: 48 minutes 33.15 seconds (2913.15 seconds total)