Starting phenix.real_space_refine on Fri Feb 14 10:21:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6pr5_20457/02_2025/6pr5_20457.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pr5_20457/02_2025/6pr5_20457.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6pr5_20457/02_2025/6pr5_20457.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pr5_20457/02_2025/6pr5_20457.map" model { file = "/net/cci-nas-00/data/ceres_data/6pr5_20457/02_2025/6pr5_20457.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pr5_20457/02_2025/6pr5_20457.cif" } resolution = 3.3 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 124 5.49 5 Mg 4 5.21 5 S 36 5.16 5 C 6073 2.51 5 N 1773 2.21 5 O 2182 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 45 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 10194 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 3823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3823 Classifications: {'peptide': 480} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 17, 'TRANS': 462} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "E" Number of atoms: 3823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3823 Classifications: {'peptide': 480} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 17, 'TRANS': 462} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 324 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "C" Number of atoms: 333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 333 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "D" Number of atoms: 616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 616 Classifications: {'DNA': 30} Link IDs: {'rna3p': 29} Chain: "F" Number of atoms: 181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 181 Classifications: {'DNA': 9} Link IDs: {'rna3p': 8} Chain: "G" Number of atoms: 333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 333 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "H" Number of atoms: 755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 755 Classifications: {'DNA': 37} Link IDs: {'rna3p': 36} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1720 SG CYS A 240 28.075 20.995 56.182 1.00 66.94 S ATOM 1746 SG CYS A 243 26.675 18.929 53.984 1.00 66.43 S ATOM 5543 SG CYS E 240 66.736 74.745 53.312 1.00 75.78 S ATOM 5569 SG CYS E 243 68.439 75.903 50.736 1.00 75.72 S Time building chain proxies: 6.33, per 1000 atoms: 0.62 Number of scatterers: 10194 At special positions: 0 Unit cell: (97.65, 101.85, 120.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 36 16.00 P 124 15.00 Mg 4 11.99 O 2182 8.00 N 1773 7.00 C 6073 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 - 3.00 Amino acid : True - 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: 2.61 Conformation dependent library (CDL) restraints added in 951.4 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 603 " pdb="ZN ZN A 603 " - pdb=" NE2 HIS A 408 " pdb="ZN ZN A 603 " - pdb=" NE2 HIS A 413 " pdb="ZN ZN A 603 " - pdb=" SG CYS A 243 " pdb="ZN ZN A 603 " - pdb=" SG CYS A 240 " pdb=" ZN E 603 " pdb="ZN ZN E 603 " - pdb=" NE2 HIS E 408 " pdb="ZN ZN E 603 " - pdb=" NE2 HIS E 413 " pdb="ZN ZN E 603 " - pdb=" SG CYS E 243 " pdb="ZN ZN E 603 " - pdb=" SG CYS E 240 " Number of angles added : 4 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1836 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 7 sheets defined 53.3% alpha, 15.0% beta 60 base pairs and 96 stacking pairs defined. Time for finding SS restraints: 3.90 Creating SS restraints... Processing helix chain 'A' and resid 25 through 36 Processing helix chain 'A' and resid 39 through 53 removed outlier: 3.535A pdb=" N GLU A 53 " --> pdb=" O THR A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 69 Processing helix chain 'A' and resid 70 through 73 Processing helix chain 'A' and resid 89 through 102 Processing helix chain 'A' and resid 186 through 203 Processing helix chain 'A' and resid 224 through 232 Processing helix chain 'A' and resid 252 through 258 removed outlier: 3.802A pdb=" N ILE A 256 " --> pdb=" O LYS A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 268 Processing helix chain 'A' and resid 271 through 289 removed outlier: 3.737A pdb=" N ARG A 276 " --> pdb=" O THR A 272 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE A 277 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ARG A 289 " --> pdb=" O HIS A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 322 Processing helix chain 'A' and resid 337 through 345 Processing helix chain 'A' and resid 347 through 356 removed outlier: 3.536A pdb=" N THR A 351 " --> pdb=" O PHE A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 374 removed outlier: 3.572A pdb=" N ILE A 362 " --> pdb=" O ASP A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 398 Processing helix chain 'A' and resid 404 through 412 Processing helix chain 'A' and resid 413 through 421 removed outlier: 3.764A pdb=" N ASN A 421 " --> pdb=" O ILE A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 446 removed outlier: 3.583A pdb=" N ASN A 438 " --> pdb=" O SER A 434 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LYS A 439 " --> pdb=" O GLU A 435 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG A 443 " --> pdb=" O LYS A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 469 Processing helix chain 'A' and resid 470 through 476 removed outlier: 3.749A pdb=" N THR A 476 " --> pdb=" O LEU A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 495 Processing helix chain 'E' and resid 25 through 36 Processing helix chain 'E' and resid 39 through 52 Processing helix chain 'E' and resid 61 through 69 Processing helix chain 'E' and resid 89 through 102 Processing helix chain 'E' and resid 186 through 203 Processing helix chain 'E' and resid 224 through 232 Processing helix chain 'E' and resid 246 through 251 removed outlier: 3.796A pdb=" N SER E 251 " --> pdb=" O THR E 248 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 258 Processing helix chain 'E' and resid 264 through 268 Processing helix chain 'E' and resid 271 through 289 removed outlier: 3.675A pdb=" N ARG E 276 " --> pdb=" O THR E 272 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE E 277 " --> pdb=" O LEU E 273 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ARG E 289 " --> pdb=" O HIS E 285 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 322 Processing helix chain 'E' and resid 337 through 347 removed outlier: 4.653A pdb=" N PHE E 347 " --> pdb=" O ARG E 343 " (cutoff:3.500A) Processing helix chain 'E' and resid 347 through 356 Processing helix chain 'E' and resid 358 through 374 Processing helix chain 'E' and resid 379 through 398 Processing helix chain 'E' and resid 404 through 412 Processing helix chain 'E' and resid 413 through 421 Processing helix chain 'E' and resid 431 through 448 removed outlier: 3.808A pdb=" N LYS E 439 " --> pdb=" O GLU E 435 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ARG E 443 " --> pdb=" O LYS E 439 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N HIS E 447 " --> pdb=" O ARG E 443 " (cutoff:3.500A) Processing helix chain 'E' and resid 453 through 469 Processing helix chain 'E' and resid 470 through 476 removed outlier: 3.665A pdb=" N THR E 476 " --> pdb=" O LEU E 472 " (cutoff:3.500A) Processing helix chain 'E' and resid 491 through 495 Processing sheet with id=AA1, first strand: chain 'A' and resid 79 through 81 removed outlier: 6.340A pdb=" N VAL A 178 " --> pdb=" O ILE A 88 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N THR A 149 " --> pdb=" O VAL A 178 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N PHE A 180 " --> pdb=" O PHE A 147 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N PHE A 147 " --> pdb=" O PHE A 180 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N TRP A 164 " --> pdb=" O LEU A 156 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ALA A 158 " --> pdb=" O THR A 162 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N THR A 162 " --> pdb=" O ALA A 158 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 79 through 81 removed outlier: 6.340A pdb=" N VAL A 178 " --> pdb=" O ILE A 88 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N THR A 149 " --> pdb=" O VAL A 178 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N PHE A 180 " --> pdb=" O PHE A 147 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N PHE A 147 " --> pdb=" O PHE A 180 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N PHE A 147 " --> pdb=" O ALA A 127 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N ALA A 127 " --> pdb=" O PHE A 147 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N THR A 149 " --> pdb=" O ASP A 125 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N ASP A 125 " --> pdb=" O THR A 149 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N LEU A 151 " --> pdb=" O GLY A 123 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N GLY A 123 " --> pdb=" O LEU A 151 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N LYS A 121 " --> pdb=" O PRO A 153 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LEU A 116 " --> pdb=" O SER A 215 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N LYS A 217 " --> pdb=" O LEU A 116 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N LEU A 118 " --> pdb=" O LYS A 217 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N MET A 219 " --> pdb=" O LEU A 118 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N SER A 120 " --> pdb=" O MET A 219 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 377 through 378 removed outlier: 4.128A pdb=" N ILE A 377 " --> pdb=" O GLN A 497 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 79 through 82 removed outlier: 3.723A pdb=" N SER E 85 " --> pdb=" O THR E 82 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N VAL E 178 " --> pdb=" O ILE E 88 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N THR E 149 " --> pdb=" O VAL E 178 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N PHE E 180 " --> pdb=" O PHE E 147 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N PHE E 147 " --> pdb=" O PHE E 180 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N TRP E 164 " --> pdb=" O LEU E 156 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ALA E 158 " --> pdb=" O THR E 162 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N THR E 162 " --> pdb=" O ALA E 158 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 79 through 82 removed outlier: 3.723A pdb=" N SER E 85 " --> pdb=" O THR E 82 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N VAL E 178 " --> pdb=" O ILE E 88 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N THR E 149 " --> pdb=" O VAL E 178 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N PHE E 180 " --> pdb=" O PHE E 147 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N PHE E 147 " --> pdb=" O PHE E 180 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ILE E 119 " --> pdb=" O LEU E 154 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N LEU E 156 " --> pdb=" O ILE E 117 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ILE E 117 " --> pdb=" O LEU E 156 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N LEU E 116 " --> pdb=" O SER E 215 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N LYS E 217 " --> pdb=" O LEU E 116 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N LEU E 118 " --> pdb=" O LYS E 217 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N MET E 219 " --> pdb=" O LEU E 118 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N SER E 120 " --> pdb=" O MET E 219 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 328 through 329 Processing sheet with id=AA7, first strand: chain 'E' and resid 377 through 378 removed outlier: 4.145A pdb=" N ILE E 377 " --> pdb=" O GLN E 497 " (cutoff:3.500A) 388 hydrogen bonds defined for protein. 1113 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 149 hydrogen bonds 298 hydrogen bond angles 0 basepair planarities 60 basepair parallelities 96 stacking parallelities Total time for adding SS restraints: 4.03 Time building geometry restraints manager: 3.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2124 1.33 - 1.45: 2836 1.45 - 1.57: 5380 1.57 - 1.69: 242 1.69 - 1.81: 56 Bond restraints: 10638 Sorted by residual: bond pdb=" C TYR A 73 " pdb=" N PRO A 74 " ideal model delta sigma weight residual 1.329 1.367 -0.038 1.18e-02 7.18e+03 1.05e+01 bond pdb=" N GLN A 330 " pdb=" CA GLN A 330 " ideal model delta sigma weight residual 1.459 1.420 0.039 1.23e-02 6.61e+03 1.00e+01 bond pdb=" N CYS A 72 " pdb=" CA CYS A 72 " ideal model delta sigma weight residual 1.457 1.424 0.032 1.32e-02 5.74e+03 6.00e+00 bond pdb=" CB VAL A 152 " pdb=" CG1 VAL A 152 " ideal model delta sigma weight residual 1.521 1.467 0.054 3.30e-02 9.18e+02 2.67e+00 bond pdb=" CB VAL E 152 " pdb=" CG1 VAL E 152 " ideal model delta sigma weight residual 1.521 1.468 0.053 3.30e-02 9.18e+02 2.62e+00 ... (remaining 10633 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.11: 14508 2.11 - 4.21: 347 4.21 - 6.32: 25 6.32 - 8.43: 9 8.43 - 10.53: 3 Bond angle restraints: 14892 Sorted by residual: angle pdb=" O3' DT F 2 " pdb=" C3' DT F 2 " pdb=" C2' DT F 2 " ideal model delta sigma weight residual 111.50 102.43 9.07 1.50e+00 4.44e-01 3.66e+01 angle pdb=" C ASP E 379 " pdb=" N VAL E 380 " pdb=" CA VAL E 380 " ideal model delta sigma weight residual 120.24 123.50 -3.26 6.30e-01 2.52e+00 2.68e+01 angle pdb=" O3' DG H 31 " pdb=" C3' DG H 31 " pdb=" C2' DG H 31 " ideal model delta sigma weight residual 111.50 104.64 6.86 1.50e+00 4.44e-01 2.09e+01 angle pdb=" O3' DG B 12 " pdb=" C3' DG B 12 " pdb=" C2' DG B 12 " ideal model delta sigma weight residual 111.50 105.18 6.32 1.50e+00 4.44e-01 1.77e+01 angle pdb=" N GLU E 138 " pdb=" CA GLU E 138 " pdb=" C GLU E 138 " ideal model delta sigma weight residual 110.80 119.50 -8.70 2.13e+00 2.20e-01 1.67e+01 ... (remaining 14887 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.04: 5430 32.04 - 64.08: 673 64.08 - 96.12: 24 96.12 - 128.15: 1 128.15 - 160.19: 2 Dihedral angle restraints: 6130 sinusoidal: 3302 harmonic: 2828 Sorted by residual: dihedral pdb=" CA GLY E 427 " pdb=" C GLY E 427 " pdb=" N SER E 428 " pdb=" CA SER E 428 " ideal model delta harmonic sigma weight residual 180.00 155.55 24.45 0 5.00e+00 4.00e-02 2.39e+01 dihedral pdb=" CA GLY A 427 " pdb=" C GLY A 427 " pdb=" N SER A 428 " pdb=" CA SER A 428 " ideal model delta harmonic sigma weight residual 180.00 156.17 23.83 0 5.00e+00 4.00e-02 2.27e+01 dihedral pdb=" CA GLU A 138 " pdb=" C GLU A 138 " pdb=" N SER A 139 " pdb=" CA SER A 139 " ideal model delta harmonic sigma weight residual 180.00 -156.34 -23.66 0 5.00e+00 4.00e-02 2.24e+01 ... (remaining 6127 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1369 0.058 - 0.117: 285 0.117 - 0.175: 31 0.175 - 0.233: 3 0.233 - 0.291: 2 Chirality restraints: 1690 Sorted by residual: chirality pdb=" CA GLU E 138 " pdb=" N GLU E 138 " pdb=" C GLU E 138 " pdb=" CB GLU E 138 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" CB THR E 334 " pdb=" CA THR E 334 " pdb=" OG1 THR E 334 " pdb=" CG2 THR E 334 " both_signs ideal model delta sigma weight residual False 2.55 2.31 0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" CA CYS A 72 " pdb=" N CYS A 72 " pdb=" C CYS A 72 " pdb=" CB CYS A 72 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.21 2.00e-01 2.50e+01 1.05e+00 ... (remaining 1687 not shown) Planarity restraints: 1452 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT F 2 " -0.008 2.00e-02 2.50e+03 1.57e-02 6.19e+00 pdb=" N1 DT F 2 " -0.011 2.00e-02 2.50e+03 pdb=" C2 DT F 2 " -0.020 2.00e-02 2.50e+03 pdb=" O2 DT F 2 " 0.024 2.00e-02 2.50e+03 pdb=" N3 DT F 2 " 0.000 2.00e-02 2.50e+03 pdb=" C4 DT F 2 " -0.021 2.00e-02 2.50e+03 pdb=" O4 DT F 2 " 0.010 2.00e-02 2.50e+03 pdb=" C5 DT F 2 " -0.002 2.00e-02 2.50e+03 pdb=" C7 DT F 2 " 0.000 2.00e-02 2.50e+03 pdb=" C6 DT F 2 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA D 11 " -0.027 2.00e-02 2.50e+03 1.44e-02 5.73e+00 pdb=" N9 DA D 11 " 0.039 2.00e-02 2.50e+03 pdb=" C8 DA D 11 " -0.001 2.00e-02 2.50e+03 pdb=" N7 DA D 11 " -0.003 2.00e-02 2.50e+03 pdb=" C5 DA D 11 " -0.003 2.00e-02 2.50e+03 pdb=" C6 DA D 11 " -0.003 2.00e-02 2.50e+03 pdb=" N6 DA D 11 " -0.005 2.00e-02 2.50e+03 pdb=" N1 DA D 11 " 0.000 2.00e-02 2.50e+03 pdb=" C2 DA D 11 " 0.002 2.00e-02 2.50e+03 pdb=" N3 DA D 11 " 0.001 2.00e-02 2.50e+03 pdb=" C4 DA D 11 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT B 16 " -0.001 2.00e-02 2.50e+03 1.49e-02 5.55e+00 pdb=" N1 DT B 16 " -0.012 2.00e-02 2.50e+03 pdb=" C2 DT B 16 " -0.001 2.00e-02 2.50e+03 pdb=" O2 DT B 16 " 0.000 2.00e-02 2.50e+03 pdb=" N3 DT B 16 " 0.012 2.00e-02 2.50e+03 pdb=" C4 DT B 16 " -0.000 2.00e-02 2.50e+03 pdb=" O4 DT B 16 " -0.000 2.00e-02 2.50e+03 pdb=" C5 DT B 16 " -0.034 2.00e-02 2.50e+03 pdb=" C7 DT B 16 " 0.010 2.00e-02 2.50e+03 pdb=" C6 DT B 16 " 0.026 2.00e-02 2.50e+03 ... (remaining 1449 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 95 2.55 - 3.14: 8049 3.14 - 3.73: 17032 3.73 - 4.31: 23758 4.31 - 4.90: 37759 Nonbonded interactions: 86693 Sorted by model distance: nonbonded pdb=" O3' DC F 9 " pdb="MG MG E 601 " model vdw 1.963 2.170 nonbonded pdb=" OD1 ASP E 125 " pdb="MG MG E 601 " model vdw 2.123 2.170 nonbonded pdb=" OD2 ASP E 125 " pdb="MG MG E 602 " model vdw 2.133 2.170 nonbonded pdb=" OD2 ASP E 224 " pdb="MG MG E 601 " model vdw 2.138 2.170 nonbonded pdb=" OE1 GLU E 435 " pdb="MG MG E 602 " model vdw 2.149 2.170 ... (remaining 86688 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'G' } 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: 1.250 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: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 30.270 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.054 10638 Z= 0.491 Angle : 0.776 10.532 14892 Z= 0.447 Chirality : 0.047 0.291 1690 Planarity : 0.004 0.039 1452 Dihedral : 22.941 160.193 4294 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.31 % Allowed : 1.36 % Favored : 98.33 % Rotamer: Outliers : 0.71 % Allowed : 10.47 % Favored : 88.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.27 (0.21), residues: 956 helix: -1.83 (0.19), residues: 506 sheet: -1.05 (0.60), residues: 64 loop : -2.71 (0.23), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 41 HIS 0.006 0.001 HIS A 483 PHE 0.015 0.002 PHE A 292 TYR 0.012 0.002 TYR E 394 ARG 0.007 0.001 ARG A 477 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 111 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 ASP cc_start: 0.8418 (p0) cc_final: 0.8170 (p0) REVERT: A 212 HIS cc_start: 0.7805 (m90) cc_final: 0.7395 (m170) REVERT: E 173 MET cc_start: 0.7295 (mtp) cc_final: 0.6998 (mtp) REVERT: E 184 LYS cc_start: 0.8311 (tttt) cc_final: 0.7833 (tppt) REVERT: E 295 TRP cc_start: 0.8549 (t60) cc_final: 0.8314 (t-100) REVERT: E 423 ILE cc_start: 0.8351 (OUTLIER) cc_final: 0.8102 (tt) outliers start: 6 outliers final: 4 residues processed: 116 average time/residue: 0.2541 time to fit residues: 40.6932 Evaluate side-chains 80 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 75 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 355 THR Chi-restraints excluded: chain E residue 423 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 0.9980 chunk 79 optimal weight: 5.9990 chunk 44 optimal weight: 0.9980 chunk 27 optimal weight: 9.9990 chunk 53 optimal weight: 3.9990 chunk 42 optimal weight: 0.7980 chunk 82 optimal weight: 0.6980 chunk 31 optimal weight: 5.9990 chunk 50 optimal weight: 0.8980 chunk 61 optimal weight: 0.6980 chunk 95 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 ASN ** A 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 216 HIS A 339 ASN A 448 HIS A 486 GLN E 71 GLN E 91 GLN E 130 GLN E 136 ASN ** E 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 216 HIS E 322 ASN E 330 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.139573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.113618 restraints weight = 15887.794| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 1.97 r_work: 0.3402 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3262 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10638 Z= 0.194 Angle : 0.588 10.246 14892 Z= 0.328 Chirality : 0.038 0.178 1690 Planarity : 0.004 0.039 1452 Dihedral : 25.901 160.012 2392 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.62 % Favored : 97.28 % Rotamer: Outliers : 2.00 % Allowed : 13.18 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.25), residues: 956 helix: 0.12 (0.23), residues: 498 sheet: -0.98 (0.59), residues: 64 loop : -2.05 (0.27), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 41 HIS 0.002 0.001 HIS A 408 PHE 0.012 0.002 PHE A 180 TYR 0.014 0.001 TYR E 241 ARG 0.002 0.000 ARG E 437 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 106 time to evaluate : 0.978 Fit side-chains revert: symmetry clash REVERT: A 145 SER cc_start: 0.8889 (p) cc_final: 0.8638 (m) REVERT: A 219 MET cc_start: 0.8941 (ptm) cc_final: 0.8714 (ptm) REVERT: A 442 ARG cc_start: 0.8642 (mpt-90) cc_final: 0.8403 (mtt90) REVERT: A 470 ASP cc_start: 0.9031 (t70) cc_final: 0.8829 (t70) REVERT: E 173 MET cc_start: 0.8054 (mtp) cc_final: 0.7680 (mtp) REVERT: E 184 LYS cc_start: 0.8520 (tttt) cc_final: 0.7640 (tppt) REVERT: E 307 HIS cc_start: 0.8293 (m90) cc_final: 0.7949 (m-70) outliers start: 17 outliers final: 12 residues processed: 118 average time/residue: 0.2339 time to fit residues: 39.1516 Evaluate side-chains 93 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 81 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 124 PHE Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 487 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 74 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 12 optimal weight: 5.9990 chunk 92 optimal weight: 0.8980 chunk 41 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 103 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 chunk 58 optimal weight: 9.9990 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 GLN ** A 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 ASN A 499 GLN ** E 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.138488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.112521 restraints weight = 16048.330| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 1.95 r_work: 0.3385 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10638 Z= 0.237 Angle : 0.590 9.291 14892 Z= 0.328 Chirality : 0.039 0.186 1690 Planarity : 0.004 0.035 1452 Dihedral : 25.982 163.265 2389 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.35 % Favored : 96.55 % Rotamer: Outliers : 2.12 % Allowed : 16.94 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.26), residues: 956 helix: 0.80 (0.23), residues: 498 sheet: -0.88 (0.57), residues: 64 loop : -1.83 (0.28), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 41 HIS 0.003 0.001 HIS E 408 PHE 0.015 0.001 PHE A 292 TYR 0.012 0.001 TYR A 62 ARG 0.004 0.000 ARG E 437 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 85 time to evaluate : 1.235 Fit side-chains REVERT: A 145 SER cc_start: 0.8918 (p) cc_final: 0.8482 (m) REVERT: A 219 MET cc_start: 0.9017 (ptm) cc_final: 0.8774 (ptm) REVERT: A 315 ASP cc_start: 0.8355 (m-30) cc_final: 0.8032 (m-30) REVERT: E 173 MET cc_start: 0.8104 (mtp) cc_final: 0.7723 (mtp) REVERT: E 184 LYS cc_start: 0.8521 (tttt) cc_final: 0.7622 (tppt) REVERT: E 307 HIS cc_start: 0.8296 (m90) cc_final: 0.8033 (m90) outliers start: 18 outliers final: 14 residues processed: 100 average time/residue: 0.2040 time to fit residues: 30.8699 Evaluate side-chains 93 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 79 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain A residue 499 GLN Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 124 PHE Chi-restraints excluded: chain E residue 150 SER Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 487 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 65 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 chunk 27 optimal weight: 9.9990 chunk 97 optimal weight: 5.9990 chunk 22 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 chunk 79 optimal weight: 9.9990 chunk 30 optimal weight: 6.9990 chunk 67 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 499 GLN ** E 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.137575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.111558 restraints weight = 16041.530| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 1.95 r_work: 0.3375 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10638 Z= 0.270 Angle : 0.596 9.700 14892 Z= 0.329 Chirality : 0.039 0.208 1690 Planarity : 0.004 0.038 1452 Dihedral : 26.038 164.011 2389 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.77 % Favored : 96.13 % Rotamer: Outliers : 2.00 % Allowed : 18.24 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.27), residues: 956 helix: 1.02 (0.24), residues: 498 sheet: -0.82 (0.58), residues: 64 loop : -1.75 (0.28), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 41 HIS 0.003 0.001 HIS E 408 PHE 0.012 0.001 PHE A 180 TYR 0.016 0.001 TYR E 241 ARG 0.004 0.000 ARG E 106 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 79 time to evaluate : 1.147 Fit side-chains REVERT: A 145 SER cc_start: 0.8945 (p) cc_final: 0.8461 (m) REVERT: A 219 MET cc_start: 0.9043 (ptm) cc_final: 0.8810 (ptm) REVERT: A 315 ASP cc_start: 0.8436 (m-30) cc_final: 0.8088 (m-30) REVERT: E 173 MET cc_start: 0.8159 (mtp) cc_final: 0.7791 (mtp) REVERT: E 184 LYS cc_start: 0.8511 (tttt) cc_final: 0.7610 (tppt) REVERT: E 307 HIS cc_start: 0.8293 (m90) cc_final: 0.8030 (m90) REVERT: E 470 ASP cc_start: 0.8616 (t70) cc_final: 0.8343 (t0) outliers start: 17 outliers final: 16 residues processed: 94 average time/residue: 0.2070 time to fit residues: 29.2424 Evaluate side-chains 88 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 72 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain A residue 499 GLN Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 124 PHE Chi-restraints excluded: chain E residue 150 SER Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 487 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 16 optimal weight: 0.9990 chunk 21 optimal weight: 7.9990 chunk 104 optimal weight: 8.9990 chunk 20 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 62 optimal weight: 5.9990 chunk 47 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 336 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 = 0.3850 r_free = 0.3850 target = 0.138649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.112665 restraints weight = 15831.991| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 1.94 r_work: 0.3393 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10638 Z= 0.221 Angle : 0.576 9.307 14892 Z= 0.320 Chirality : 0.038 0.203 1690 Planarity : 0.004 0.039 1452 Dihedral : 26.000 164.263 2389 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.66 % Favored : 96.23 % Rotamer: Outliers : 2.59 % Allowed : 19.06 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.27), residues: 956 helix: 1.22 (0.24), residues: 500 sheet: -0.68 (0.58), residues: 64 loop : -1.65 (0.29), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 41 HIS 0.003 0.001 HIS E 408 PHE 0.014 0.001 PHE A 292 TYR 0.016 0.001 TYR E 241 ARG 0.003 0.000 ARG E 437 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 84 time to evaluate : 0.985 Fit side-chains revert: symmetry clash REVERT: A 124 PHE cc_start: 0.9268 (OUTLIER) cc_final: 0.8941 (p90) REVERT: A 219 MET cc_start: 0.9061 (ptm) cc_final: 0.8836 (ptm) REVERT: E 173 MET cc_start: 0.8134 (mtp) cc_final: 0.7762 (mtp) REVERT: E 184 LYS cc_start: 0.8507 (tttt) cc_final: 0.7592 (tppt) REVERT: E 307 HIS cc_start: 0.8291 (m90) cc_final: 0.8079 (m90) REVERT: E 470 ASP cc_start: 0.8563 (t70) cc_final: 0.8176 (t0) outliers start: 22 outliers final: 16 residues processed: 103 average time/residue: 0.1915 time to fit residues: 29.7476 Evaluate side-chains 88 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 71 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 124 PHE Chi-restraints excluded: chain E residue 150 SER Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 487 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 97 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 31 optimal weight: 9.9990 chunk 51 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 64 optimal weight: 6.9990 chunk 4 optimal weight: 2.9990 chunk 102 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 42 optimal weight: 0.6980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 336 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 = 0.3831 r_free = 0.3831 target = 0.137625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.111880 restraints weight = 16207.076| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 1.90 r_work: 0.3374 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3236 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 10638 Z= 0.269 Angle : 0.592 9.756 14892 Z= 0.327 Chirality : 0.039 0.222 1690 Planarity : 0.004 0.039 1452 Dihedral : 26.034 164.957 2389 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.39 % Favored : 95.50 % Rotamer: Outliers : 2.94 % Allowed : 19.18 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.27), residues: 956 helix: 1.26 (0.24), residues: 500 sheet: -0.67 (0.59), residues: 64 loop : -1.63 (0.29), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 41 HIS 0.004 0.001 HIS E 408 PHE 0.011 0.001 PHE A 180 TYR 0.016 0.001 TYR E 241 ARG 0.003 0.000 ARG E 437 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 72 time to evaluate : 0.997 Fit side-chains REVERT: A 124 PHE cc_start: 0.9280 (OUTLIER) cc_final: 0.8969 (p90) REVERT: A 219 MET cc_start: 0.9134 (ptm) cc_final: 0.8893 (ptm) REVERT: A 270 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8340 (tp) REVERT: E 173 MET cc_start: 0.8122 (mtp) cc_final: 0.7773 (mtp) REVERT: E 184 LYS cc_start: 0.8531 (tttt) cc_final: 0.7689 (tppt) outliers start: 25 outliers final: 21 residues processed: 93 average time/residue: 0.1885 time to fit residues: 27.0294 Evaluate side-chains 96 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 73 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 117 ILE Chi-restraints excluded: chain E residue 124 PHE Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 150 SER Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 328 VAL Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 487 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 44 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 45 optimal weight: 0.0270 chunk 68 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 78 optimal weight: 7.9990 chunk 64 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 overall best weight: 1.1242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 336 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 = 0.3849 r_free = 0.3849 target = 0.139674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.112387 restraints weight = 16157.970| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 2.04 r_work: 0.3399 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10638 Z= 0.198 Angle : 0.555 9.237 14892 Z= 0.309 Chirality : 0.037 0.209 1690 Planarity : 0.004 0.040 1452 Dihedral : 25.898 165.297 2389 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.94 % Allowed : 20.12 % Favored : 76.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.27), residues: 956 helix: 1.39 (0.24), residues: 516 sheet: -0.65 (0.58), residues: 64 loop : -1.55 (0.29), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 41 HIS 0.002 0.000 HIS A 447 PHE 0.015 0.001 PHE A 292 TYR 0.013 0.001 TYR E 241 ARG 0.002 0.000 ARG A 477 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 84 time to evaluate : 1.019 Fit side-chains REVERT: A 124 PHE cc_start: 0.9229 (OUTLIER) cc_final: 0.8840 (p90) REVERT: A 145 SER cc_start: 0.8686 (OUTLIER) cc_final: 0.8339 (m) REVERT: A 219 MET cc_start: 0.9088 (ptm) cc_final: 0.8862 (ptm) REVERT: A 337 ASP cc_start: 0.7668 (m-30) cc_final: 0.7430 (m-30) REVERT: E 173 MET cc_start: 0.7843 (mtp) cc_final: 0.7505 (mtp) REVERT: E 184 LYS cc_start: 0.8438 (tttt) cc_final: 0.7580 (tppt) outliers start: 25 outliers final: 18 residues processed: 106 average time/residue: 0.1884 time to fit residues: 30.4053 Evaluate side-chains 93 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 73 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 117 ILE Chi-restraints excluded: chain E residue 124 PHE Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 487 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 93 optimal weight: 0.9990 chunk 29 optimal weight: 9.9990 chunk 4 optimal weight: 1.9990 chunk 83 optimal weight: 5.9990 chunk 95 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 54 optimal weight: 6.9990 chunk 46 optimal weight: 0.0980 chunk 19 optimal weight: 0.6980 chunk 0 optimal weight: 0.7980 chunk 62 optimal weight: 0.6980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 GLN ** A 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.141963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.115367 restraints weight = 15925.226| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 1.99 r_work: 0.3442 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10638 Z= 0.170 Angle : 0.541 7.473 14892 Z= 0.303 Chirality : 0.037 0.238 1690 Planarity : 0.004 0.041 1452 Dihedral : 25.708 166.625 2389 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.47 % Allowed : 20.59 % Favored : 76.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.27), residues: 956 helix: 1.61 (0.24), residues: 516 sheet: -0.69 (0.57), residues: 64 loop : -1.49 (0.30), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 41 HIS 0.003 0.001 HIS E 408 PHE 0.011 0.001 PHE A 180 TYR 0.010 0.001 TYR E 266 ARG 0.003 0.000 ARG A 289 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 96 time to evaluate : 1.008 Fit side-chains REVERT: A 291 ASP cc_start: 0.7224 (t70) cc_final: 0.6948 (t70) REVERT: E 173 MET cc_start: 0.7870 (mtp) cc_final: 0.7504 (mtp) REVERT: E 184 LYS cc_start: 0.8425 (tttt) cc_final: 0.7611 (tppt) REVERT: E 197 MET cc_start: 0.7658 (tpp) cc_final: 0.7297 (mpp) outliers start: 21 outliers final: 20 residues processed: 113 average time/residue: 0.1818 time to fit residues: 31.1558 Evaluate side-chains 97 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 77 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 117 ILE Chi-restraints excluded: chain E residue 124 PHE Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 330 GLN Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 487 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 64 optimal weight: 0.7980 chunk 3 optimal weight: 5.9990 chunk 58 optimal weight: 9.9990 chunk 61 optimal weight: 0.9980 chunk 71 optimal weight: 3.9990 chunk 23 optimal weight: 7.9990 chunk 0 optimal weight: 5.9990 chunk 17 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 chunk 78 optimal weight: 7.9990 chunk 72 optimal weight: 4.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 447 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.137026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.110085 restraints weight = 16340.516| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 2.04 r_work: 0.3348 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 10638 Z= 0.333 Angle : 0.636 10.387 14892 Z= 0.347 Chirality : 0.041 0.253 1690 Planarity : 0.004 0.038 1452 Dihedral : 26.003 167.454 2389 Min Nonbonded Distance : 1.611 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 2.82 % Allowed : 21.88 % Favored : 75.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.27), residues: 956 helix: 1.41 (0.24), residues: 514 sheet: -0.69 (0.58), residues: 64 loop : -1.46 (0.30), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 41 HIS 0.004 0.001 HIS E 408 PHE 0.012 0.002 PHE A 180 TYR 0.019 0.002 TYR E 241 ARG 0.005 0.001 ARG A 52 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 73 time to evaluate : 0.934 Fit side-chains REVERT: A 117 ILE cc_start: 0.8827 (OUTLIER) cc_final: 0.8221 (mt) REVERT: A 124 PHE cc_start: 0.9288 (OUTLIER) cc_final: 0.9058 (p90) REVERT: E 173 MET cc_start: 0.7911 (mtp) cc_final: 0.7569 (mtp) REVERT: E 184 LYS cc_start: 0.8443 (tttt) cc_final: 0.7632 (tppt) REVERT: E 197 MET cc_start: 0.7837 (tpp) cc_final: 0.7459 (mpp) REVERT: E 403 MET cc_start: 0.8001 (mtp) cc_final: 0.7688 (mtp) outliers start: 24 outliers final: 21 residues processed: 96 average time/residue: 0.2112 time to fit residues: 30.5118 Evaluate side-chains 94 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 71 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 117 ILE Chi-restraints excluded: chain E residue 124 PHE Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 150 SER Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 487 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 19 optimal weight: 4.9990 chunk 11 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 40 optimal weight: 3.9990 chunk 67 optimal weight: 8.9990 chunk 91 optimal weight: 0.6980 chunk 37 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 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 = 0.3863 r_free = 0.3863 target = 0.140165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.114027 restraints weight = 16047.125| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 1.98 r_work: 0.3383 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.2688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10638 Z= 0.201 Angle : 0.574 9.910 14892 Z= 0.318 Chirality : 0.038 0.242 1690 Planarity : 0.004 0.040 1452 Dihedral : 25.819 166.907 2389 Min Nonbonded Distance : 1.525 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 2.59 % Allowed : 22.00 % Favored : 75.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.27), residues: 956 helix: 1.53 (0.24), residues: 516 sheet: -0.66 (0.57), residues: 64 loop : -1.45 (0.30), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 41 HIS 0.003 0.001 HIS E 408 PHE 0.011 0.001 PHE A 180 TYR 0.019 0.001 TYR E 241 ARG 0.006 0.000 ARG A 52 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 78 time to evaluate : 0.955 Fit side-chains REVERT: A 124 PHE cc_start: 0.9214 (OUTLIER) cc_final: 0.8915 (p90) REVERT: E 173 MET cc_start: 0.7889 (mtp) cc_final: 0.7546 (mtp) REVERT: E 184 LYS cc_start: 0.8551 (tttt) cc_final: 0.7716 (tppt) REVERT: E 403 MET cc_start: 0.7906 (mtp) cc_final: 0.7520 (mtp) outliers start: 22 outliers final: 21 residues processed: 97 average time/residue: 0.1890 time to fit residues: 27.7666 Evaluate side-chains 97 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 75 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 117 ILE Chi-restraints excluded: chain E residue 124 PHE Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 150 SER Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 487 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 26 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 100 optimal weight: 10.0000 chunk 49 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 30 optimal weight: 7.9990 chunk 18 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 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 = 0.3871 r_free = 0.3871 target = 0.140854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.114661 restraints weight = 15951.352| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 1.97 r_work: 0.3422 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10638 Z= 0.190 Angle : 0.574 9.846 14892 Z= 0.318 Chirality : 0.037 0.253 1690 Planarity : 0.004 0.039 1452 Dihedral : 25.755 168.206 2389 Min Nonbonded Distance : 1.474 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 2.71 % Allowed : 22.47 % Favored : 74.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.28), residues: 956 helix: 1.56 (0.24), residues: 516 sheet: -0.46 (0.58), residues: 64 loop : -1.41 (0.30), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 41 HIS 0.003 0.001 HIS E 408 PHE 0.014 0.001 PHE A 292 TYR 0.018 0.001 TYR E 241 ARG 0.006 0.000 ARG A 52 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4136.90 seconds wall clock time: 74 minutes 27.55 seconds (4467.55 seconds total)