Starting phenix.real_space_refine on Sat Jan 20 00:40:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i6v_35208/01_2024/8i6v_35208_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i6v_35208/01_2024/8i6v_35208.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i6v_35208/01_2024/8i6v_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_35208/01_2024/8i6v_35208_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i6v_35208/01_2024/8i6v_35208_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i6v_35208/01_2024/8i6v_35208.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i6v_35208/01_2024/8i6v_35208.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i6v_35208/01_2024/8i6v_35208_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i6v_35208/01_2024/8i6v_35208_updated.pdb" } resolution = 3.06 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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: 7.35, per 1000 atoms: 0.56 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: 5.44 Conformation dependent library (CDL) restraints added in 2.2 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: 3.16 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: 4.29 Time building geometry restraints manager: 5.85 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: 7618 27.12 - 54.23: 421 54.23 - 81.35: 23 81.35 - 108.46: 13 108.46 - 135.58: 1 Dihedral angle restraints: 8076 sinusoidal: 3394 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 8073 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: 2.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 10.930 Check model and map are aligned: 0.200 Set scattering table: 0.120 Process input model: 37.930 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.010 ------------------------------------------------------------------------------- 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 : 15.335 135.580 5040 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 % Allowed : 0.76 % Favored : 98.96 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 267 HIS 0.004 0.001 HIS D 35 PHE 0.017 0.001 PHE C 39 TYR 0.027 0.001 TYR D 169 ARG 0.011 0.000 ARG E 196 *********************** 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 : 1.523 Fit side-chains revert: symmetry clash REVERT: B 64 LEU cc_start: 0.5598 (tp) cc_final: 0.5394 (tp) REVERT: D 141 VAL cc_start: 0.8887 (m) cc_final: 0.8594 (p) REVERT: D 343 PHE cc_start: 0.7503 (m-80) cc_final: 0.7303 (m-80) REVERT: E 323 LYS cc_start: 0.7648 (ttmm) cc_final: 0.7316 (ptmt) outliers start: 4 outliers final: 3 residues processed: 174 average time/residue: 0.2543 time to fit residues: 65.5126 Evaluate side-chains 140 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 137 time to evaluate : 1.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 35 HIS Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 86 LYS 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: 9.9990 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 84 ASN D 95 ASN E 435 GLN ** E 717 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.0662 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= 0.143 Angle : 0.450 6.219 18198 Z= 0.236 Chirality : 0.037 0.140 2005 Planarity : 0.004 0.052 2299 Dihedral : 6.239 83.805 1801 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.83 % Allowed : 6.04 % Favored : 93.13 % 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: 2.50 (0.22), residues: 1570 helix: 2.76 (0.17), residues: 921 sheet: 1.49 (0.40), residues: 176 loop : -0.58 (0.30), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 267 HIS 0.003 0.001 HIS D 35 PHE 0.022 0.001 PHE B 27 TYR 0.014 0.001 TYR D 169 ARG 0.010 0.000 ARG E 196 *********************** 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 165 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 153 time to evaluate : 1.403 Fit side-chains REVERT: D 141 VAL cc_start: 0.8892 (m) cc_final: 0.8600 (p) REVERT: D 173 PHE cc_start: 0.7570 (t80) cc_final: 0.7233 (t80) REVERT: D 343 PHE cc_start: 0.7539 (m-80) cc_final: 0.7332 (m-80) REVERT: E 323 LYS cc_start: 0.7661 (ttmm) cc_final: 0.7319 (ptmt) outliers start: 12 outliers final: 8 residues processed: 160 average time/residue: 0.2536 time to fit residues: 59.5436 Evaluate side-chains 147 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 139 time to evaluate : 1.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain D residue 764 THR Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 612 THR Chi-restraints excluded: chain E residue 617 VAL Chi-restraints excluded: chain E residue 647 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 79 optimal weight: 0.0270 chunk 44 optimal weight: 0.8980 chunk 119 optimal weight: 4.9990 chunk 97 optimal weight: 0.0470 chunk 39 optimal weight: 9.9990 chunk 143 optimal weight: 0.6980 chunk 155 optimal weight: 2.9990 chunk 128 optimal weight: 3.9990 chunk 142 optimal weight: 1.9990 chunk 49 optimal weight: 9.9990 chunk 115 optimal weight: 4.9990 overall best weight: 0.7338 ------------------------------------------------------------------------------- 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: 0.7822 moved from start: 0.0837 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= 0.143 Angle : 0.442 7.632 18198 Z= 0.229 Chirality : 0.037 0.161 2005 Planarity : 0.004 0.050 2299 Dihedral : 5.780 78.882 1794 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 0.76 % Allowed : 8.05 % Favored : 91.19 % 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: 2.54 (0.22), residues: 1570 helix: 2.79 (0.17), residues: 920 sheet: 1.44 (0.40), residues: 178 loop : -0.55 (0.30), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 267 HIS 0.002 0.000 HIS D 131 PHE 0.012 0.001 PHE E 664 TYR 0.014 0.001 TYR D 169 ARG 0.003 0.000 ARG E 689 *********************** 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 153 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 142 time to evaluate : 1.614 Fit side-chains REVERT: A 70 MET cc_start: 0.6345 (tpp) cc_final: 0.6068 (tpp) REVERT: D 36 ASP cc_start: 0.3178 (OUTLIER) cc_final: 0.2507 (t70) REVERT: D 54 GLU cc_start: 0.7332 (tt0) cc_final: 0.6960 (tt0) REVERT: D 141 VAL cc_start: 0.8887 (m) cc_final: 0.8593 (p) REVERT: D 173 PHE cc_start: 0.7581 (t80) cc_final: 0.7301 (t80) REVERT: D 343 PHE cc_start: 0.7543 (m-80) cc_final: 0.7334 (m-80) REVERT: E 323 LYS cc_start: 0.7661 (ttmm) cc_final: 0.7319 (ptmt) outliers start: 11 outliers final: 10 residues processed: 147 average time/residue: 0.2584 time to fit residues: 56.1138 Evaluate side-chains 148 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 137 time to evaluate : 1.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 36 ASP Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 764 THR Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 612 THR Chi-restraints excluded: chain E residue 617 VAL Chi-restraints excluded: chain E residue 647 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 142 optimal weight: 1.9990 chunk 108 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 15 optimal weight: 10.0000 chunk 68 optimal weight: 2.9990 chunk 96 optimal weight: 30.0000 chunk 144 optimal weight: 3.9990 chunk 152 optimal weight: 0.8980 chunk 75 optimal weight: 0.0670 chunk 136 optimal weight: 0.0070 chunk 41 optimal weight: 4.9990 overall best weight: 0.9940 ------------------------------------------------------------------------------- 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: 0.7838 moved from start: 0.0939 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= 0.159 Angle : 0.448 7.994 18198 Z= 0.231 Chirality : 0.037 0.136 2005 Planarity : 0.004 0.052 2299 Dihedral : 5.651 72.680 1794 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.18 % Allowed : 8.74 % Favored : 90.08 % 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: 2.55 (0.22), residues: 1570 helix: 2.78 (0.17), residues: 923 sheet: 1.52 (0.40), residues: 176 loop : -0.55 (0.30), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 267 HIS 0.002 0.001 HIS D 35 PHE 0.020 0.001 PHE D 205 TYR 0.014 0.001 TYR D 169 ARG 0.004 0.000 ARG E 689 *********************** 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 158 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 141 time to evaluate : 1.504 Fit side-chains REVERT: A 70 MET cc_start: 0.6685 (tpp) cc_final: 0.6447 (mmt) REVERT: D 36 ASP cc_start: 0.3186 (OUTLIER) cc_final: 0.2387 (t70) REVERT: D 141 VAL cc_start: 0.8894 (m) cc_final: 0.8594 (p) REVERT: D 173 PHE cc_start: 0.7641 (t80) cc_final: 0.7392 (t80) REVERT: D 343 PHE cc_start: 0.7566 (m-80) cc_final: 0.7336 (m-80) REVERT: E 323 LYS cc_start: 0.7665 (ttmm) cc_final: 0.7326 (ptmt) outliers start: 17 outliers final: 14 residues processed: 149 average time/residue: 0.2492 time to fit residues: 54.9890 Evaluate side-chains 151 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 136 time to evaluate : 1.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 36 ASP Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 764 THR Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 612 THR Chi-restraints excluded: chain E residue 615 VAL Chi-restraints excluded: chain E residue 617 VAL Chi-restraints excluded: chain E residue 638 SER Chi-restraints excluded: chain E residue 647 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 127 optimal weight: 3.9990 chunk 86 optimal weight: 0.6980 chunk 2 optimal weight: 6.9990 chunk 113 optimal weight: 4.9990 chunk 63 optimal weight: 0.9990 chunk 130 optimal weight: 3.9990 chunk 105 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 77 optimal weight: 3.9990 chunk 137 optimal weight: 4.9990 chunk 38 optimal weight: 9.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- 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 D 826 GLN ** E 717 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.1374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 13462 Z= 0.333 Angle : 0.563 7.924 18198 Z= 0.291 Chirality : 0.042 0.171 2005 Planarity : 0.005 0.055 2299 Dihedral : 5.963 61.309 1794 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.32 % Allowed : 10.48 % Favored : 88.20 % 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: 2.02 (0.22), residues: 1570 helix: 2.39 (0.17), residues: 922 sheet: 1.13 (0.39), residues: 178 loop : -0.75 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 440 HIS 0.003 0.001 HIS D 35 PHE 0.022 0.002 PHE E 459 TYR 0.019 0.002 TYR D 169 ARG 0.004 0.001 ARG E 689 *********************** 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 156 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 137 time to evaluate : 1.604 Fit side-chains REVERT: D 141 VAL cc_start: 0.8915 (m) cc_final: 0.8620 (p) REVERT: D 173 PHE cc_start: 0.7586 (t80) cc_final: 0.7316 (t80) REVERT: D 343 PHE cc_start: 0.7597 (m-80) cc_final: 0.7308 (m-80) REVERT: D 730 LYS cc_start: 0.5778 (mmtm) cc_final: 0.5154 (mmtm) REVERT: E 323 LYS cc_start: 0.7652 (ttmm) cc_final: 0.7359 (ptmt) outliers start: 19 outliers final: 15 residues processed: 146 average time/residue: 0.2618 time to fit residues: 55.8233 Evaluate side-chains 144 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 129 time to evaluate : 1.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain D residue 764 THR Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 612 THR Chi-restraints excluded: chain E residue 615 VAL Chi-restraints excluded: chain E residue 617 VAL Chi-restraints excluded: chain E residue 638 SER Chi-restraints excluded: chain E residue 647 THR Chi-restraints excluded: chain E residue 666 THR Chi-restraints excluded: chain E residue 683 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 51 optimal weight: 0.5980 chunk 137 optimal weight: 0.4980 chunk 30 optimal weight: 6.9990 chunk 89 optimal weight: 0.9980 chunk 37 optimal weight: 9.9990 chunk 152 optimal weight: 0.9980 chunk 126 optimal weight: 1.9990 chunk 70 optimal weight: 5.9990 chunk 12 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0.7858 moved from start: 0.1270 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= 0.151 Angle : 0.456 9.358 18198 Z= 0.236 Chirality : 0.037 0.140 2005 Planarity : 0.004 0.052 2299 Dihedral : 5.677 61.788 1794 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.25 % Allowed : 11.10 % Favored : 87.65 % 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: 2.35 (0.22), residues: 1570 helix: 2.64 (0.17), residues: 922 sheet: 1.30 (0.39), residues: 176 loop : -0.60 (0.30), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 267 HIS 0.002 0.000 HIS E 218 PHE 0.016 0.001 PHE B 53 TYR 0.013 0.001 TYR D 169 ARG 0.004 0.000 ARG E 689 *********************** 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 156 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 138 time to evaluate : 1.502 Fit side-chains REVERT: D 141 VAL cc_start: 0.8887 (m) cc_final: 0.8582 (p) REVERT: D 173 PHE cc_start: 0.7614 (t80) cc_final: 0.7371 (t80) REVERT: D 343 PHE cc_start: 0.7635 (m-80) cc_final: 0.7335 (m-80) REVERT: D 760 LEU cc_start: 0.8097 (mt) cc_final: 0.7879 (mt) REVERT: E 323 LYS cc_start: 0.7665 (ttmm) cc_final: 0.7367 (ptmt) outliers start: 18 outliers final: 13 residues processed: 148 average time/residue: 0.2636 time to fit residues: 57.5091 Evaluate side-chains 144 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 131 time to evaluate : 1.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 764 THR Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 221 VAL Chi-restraints excluded: chain E residue 402 ASP Chi-restraints excluded: chain E residue 615 VAL Chi-restraints excluded: chain E residue 617 VAL Chi-restraints excluded: chain E residue 638 SER Chi-restraints excluded: chain E residue 647 THR Chi-restraints excluded: chain E residue 683 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 147 optimal weight: 0.0970 chunk 17 optimal weight: 20.0000 chunk 87 optimal weight: 0.9990 chunk 111 optimal weight: 9.9990 chunk 86 optimal weight: 0.9980 chunk 128 optimal weight: 0.0570 chunk 85 optimal weight: 3.9990 chunk 152 optimal weight: 0.8980 chunk 95 optimal weight: 0.6980 chunk 92 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 overall best weight: 0.5496 ------------------------------------------------------------------------------- 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: 0.7831 moved from start: 0.1311 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= 0.131 Angle : 0.455 10.839 18198 Z= 0.229 Chirality : 0.037 0.141 2005 Planarity : 0.004 0.051 2299 Dihedral : 5.413 60.763 1794 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.83 % Allowed : 12.21 % Favored : 86.95 % 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: 2.53 (0.22), residues: 1570 helix: 2.77 (0.17), residues: 923 sheet: 1.39 (0.39), residues: 176 loop : -0.51 (0.30), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 267 HIS 0.004 0.000 HIS D 35 PHE 0.015 0.001 PHE B 53 TYR 0.013 0.001 TYR D 169 ARG 0.003 0.000 ARG E 302 *********************** 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 149 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 137 time to evaluate : 1.429 Fit side-chains REVERT: D 54 GLU cc_start: 0.7307 (tt0) cc_final: 0.6940 (tt0) REVERT: D 173 PHE cc_start: 0.7651 (t80) cc_final: 0.7415 (t80) REVERT: D 343 PHE cc_start: 0.7622 (m-80) cc_final: 0.7332 (m-80) REVERT: E 323 LYS cc_start: 0.7665 (ttmm) cc_final: 0.7363 (ptmt) outliers start: 12 outliers final: 10 residues processed: 144 average time/residue: 0.2579 time to fit residues: 54.4123 Evaluate side-chains 140 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 130 time to evaluate : 1.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain D residue 242 ASP Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 221 VAL Chi-restraints excluded: chain E residue 612 THR Chi-restraints excluded: chain E residue 615 VAL Chi-restraints excluded: chain E residue 617 VAL Chi-restraints excluded: chain E residue 647 THR Chi-restraints excluded: chain E residue 683 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 94 optimal weight: 6.9990 chunk 60 optimal weight: 4.9990 chunk 90 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 29 optimal weight: 9.9990 chunk 96 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 chunk 75 optimal weight: 0.5980 chunk 14 optimal weight: 20.0000 chunk 119 optimal weight: 4.9990 chunk 138 optimal weight: 0.5980 overall best weight: 1.6384 ------------------------------------------------------------------------------- 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: 0.7879 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13462 Z= 0.222 Angle : 0.503 11.479 18198 Z= 0.254 Chirality : 0.039 0.141 2005 Planarity : 0.004 0.051 2299 Dihedral : 5.582 59.869 1794 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.11 % Allowed : 12.56 % Favored : 86.33 % 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: 2.35 (0.22), residues: 1570 helix: 2.69 (0.17), residues: 917 sheet: 1.20 (0.39), residues: 177 loop : -0.64 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 440 HIS 0.006 0.001 HIS D 131 PHE 0.016 0.001 PHE E 459 TYR 0.016 0.001 TYR D 169 ARG 0.006 0.000 ARG E 689 *********************** 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: 16 poor density : 130 time to evaluate : 1.487 Fit side-chains REVERT: D 343 PHE cc_start: 0.7620 (m-80) cc_final: 0.7326 (m-80) REVERT: E 323 LYS cc_start: 0.7674 (ttmm) cc_final: 0.7369 (ptmt) outliers start: 16 outliers final: 15 residues processed: 142 average time/residue: 0.2503 time to fit residues: 53.0692 Evaluate side-chains 141 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 126 time to evaluate : 1.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain D residue 242 ASP Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 764 THR Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 221 VAL Chi-restraints excluded: chain E residue 402 ASP Chi-restraints excluded: chain E residue 435 GLN Chi-restraints excluded: chain E residue 612 THR Chi-restraints excluded: chain E residue 615 VAL Chi-restraints excluded: chain E residue 617 VAL Chi-restraints excluded: chain E residue 647 THR Chi-restraints excluded: chain E residue 683 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 145 optimal weight: 10.0000 chunk 133 optimal weight: 3.9990 chunk 141 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 111 optimal weight: 4.9990 chunk 43 optimal weight: 6.9990 chunk 128 optimal weight: 0.0870 chunk 134 optimal weight: 2.9990 chunk 93 optimal weight: 5.9990 chunk 150 optimal weight: 3.9990 overall best weight: 2.8166 ------------------------------------------------------------------------------- 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: 0.7925 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 13462 Z= 0.348 Angle : 0.583 10.597 18198 Z= 0.298 Chirality : 0.042 0.172 2005 Planarity : 0.005 0.052 2299 Dihedral : 6.052 66.381 1794 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.11 % Allowed : 12.63 % Favored : 86.26 % 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: 1.78 (0.21), residues: 1570 helix: 2.29 (0.17), residues: 925 sheet: 0.83 (0.39), residues: 179 loop : -1.03 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 440 HIS 0.005 0.001 HIS D 131 PHE 0.023 0.002 PHE E 459 TYR 0.018 0.002 TYR D 169 ARG 0.011 0.001 ARG E 689 *********************** 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 145 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 129 time to evaluate : 1.492 Fit side-chains REVERT: D 343 PHE cc_start: 0.7641 (m-80) cc_final: 0.7325 (m-80) REVERT: E 323 LYS cc_start: 0.7659 (ttmm) cc_final: 0.7371 (ptmt) outliers start: 16 outliers final: 16 residues processed: 139 average time/residue: 0.2716 time to fit residues: 55.4195 Evaluate side-chains 141 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 125 time to evaluate : 1.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain D residue 242 ASP Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 764 THR Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 221 VAL Chi-restraints excluded: chain E residue 402 ASP Chi-restraints excluded: chain E residue 435 GLN Chi-restraints excluded: chain E residue 612 THR Chi-restraints excluded: chain E residue 615 VAL Chi-restraints excluded: chain E residue 617 VAL Chi-restraints excluded: chain E residue 647 THR Chi-restraints excluded: chain E residue 683 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 91 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 157 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 chunk 13 optimal weight: 6.9990 chunk 96 optimal weight: 0.0970 chunk 76 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 133 optimal weight: 0.9990 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13462 Z= 0.188 Angle : 0.496 10.662 18198 Z= 0.253 Chirality : 0.038 0.138 2005 Planarity : 0.004 0.052 2299 Dihedral : 5.830 65.196 1794 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.04 % Allowed : 12.77 % Favored : 86.19 % 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: 2.14 (0.22), residues: 1570 helix: 2.53 (0.17), residues: 918 sheet: 1.03 (0.39), residues: 175 loop : -0.72 (0.29), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 700 HIS 0.005 0.001 HIS D 131 PHE 0.017 0.001 PHE D 722 TYR 0.014 0.001 TYR D 169 ARG 0.007 0.000 ARG E 689 ********************** 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 146 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 131 time to evaluate : 1.591 Fit side-chains REVERT: D 343 PHE cc_start: 0.7642 (m-80) cc_final: 0.7322 (m-80) REVERT: E 323 LYS cc_start: 0.7669 (ttmm) cc_final: 0.7374 (ptmt) outliers start: 15 outliers final: 14 residues processed: 139 average time/residue: 0.2543 time to fit residues: 52.4308 Evaluate side-chains 142 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 128 time to evaluate : 1.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 242 ASP Chi-restraints excluded: chain D residue 764 THR Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 221 VAL Chi-restraints excluded: chain E residue 402 ASP Chi-restraints excluded: chain E residue 612 THR Chi-restraints excluded: chain E residue 615 VAL Chi-restraints excluded: chain E residue 617 VAL Chi-restraints excluded: chain E residue 647 THR Chi-restraints excluded: chain E residue 683 VAL 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: 2.9990 chunk 18 optimal weight: 4.9990 chunk 34 optimal weight: 20.0000 chunk 125 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 128 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 23 optimal weight: 7.9990 chunk 110 optimal weight: 2.9990 chunk 7 optimal weight: 9.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4103 r_free = 0.4103 target = 0.182715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.144932 restraints weight = 15726.812| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 1.76 r_work: 0.3144 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 13462 Z= 0.372 Angle : 0.590 10.406 18198 Z= 0.301 Chirality : 0.042 0.178 2005 Planarity : 0.005 0.054 2299 Dihedral : 6.088 69.613 1794 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.32 % Allowed : 13.05 % Favored : 85.63 % 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: 1.61 (0.21), residues: 1570 helix: 2.18 (0.17), residues: 926 sheet: 0.65 (0.39), residues: 179 loop : -1.11 (0.27), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 509 HIS 0.005 0.001 HIS D 131 PHE 0.024 0.002 PHE E 459 TYR 0.018 0.002 TYR D 169 ARG 0.006 0.001 ARG E 689 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3045.86 seconds wall clock time: 55 minutes 42.90 seconds (3342.90 seconds total)