Starting phenix.real_space_refine on Wed Sep 25 08:18:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pqu_20453/09_2024/6pqu_20453.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pqu_20453/09_2024/6pqu_20453.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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pqu_20453/09_2024/6pqu_20453.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pqu_20453/09_2024/6pqu_20453.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pqu_20453/09_2024/6pqu_20453.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pqu_20453/09_2024/6pqu_20453.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: 8 Type Number sf(0) Gaussians K 2 8.98 5 Zn 2 6.06 5 P 124 5.49 5 Mg 2 5.21 5 S 34 5.16 5 C 5962 2.51 5 N 1728 2.21 5 O 2150 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 10004 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3728 Classifications: {'peptide': 468} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 17, 'TRANS': 450} Chain breaks: 3 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'HIS:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 305 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} 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: 633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 633 Classifications: {'DNA': 31} Link IDs: {'rna3p': 30} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' K': 1, ' MG': 1, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1629 SG CYS A 240 84.803 102.677 59.207 1.00119.06 S ATOM 1655 SG CYS A 243 87.305 102.753 61.798 1.00116.38 S Restraints were copied for chains: F, E, G, H Time building chain proxies: 8.08, per 1000 atoms: 0.81 Number of scatterers: 10004 At special positions: 0 Unit cell: (110.25, 118.65, 114.45, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 2 29.99 K 2 19.00 S 34 16.00 P 124 15.00 Mg 2 11.99 O 2150 8.00 N 1728 7.00 C 5962 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: 2.79 Conformation dependent library (CDL) restraints added in 883.5 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 602 " pdb="ZN ZN A 602 " - pdb=" NE2 HIS A 408 " pdb="ZN ZN A 602 " - pdb=" NE2 HIS A 413 " pdb="ZN ZN A 602 " - pdb=" SG CYS A 243 " pdb="ZN ZN A 602 " - pdb=" SG CYS A 240 " pdb=" ZN E 602 " pdb="ZN ZN E 602 " - pdb=" NE2 HIS E 408 " pdb="ZN ZN E 602 " - pdb=" NE2 HIS E 413 " pdb="ZN ZN E 602 " - pdb=" SG CYS E 243 " pdb="ZN ZN E 602 " - pdb=" SG CYS E 240 " Number of angles added : 4 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1792 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 4 sheets defined 52.4% alpha, 12.8% beta 61 base pairs and 100 stacking pairs defined. Time for finding SS restraints: 4.32 Creating SS restraints... Processing helix chain 'A' and resid 25 through 36 removed outlier: 3.860A pdb=" N GLY A 31 " --> pdb=" O GLU A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 53 Processing helix chain 'A' and resid 61 through 72 removed outlier: 3.698A pdb=" N GLN A 71 " --> pdb=" O LYS A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 106 removed outlier: 3.618A pdb=" N PHE A 102 " --> pdb=" O VAL A 98 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG A 106 " --> pdb=" O PHE A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 175 removed outlier: 3.948A pdb=" N TYR A 174 " --> pdb=" O SER A 171 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N CYS A 175 " --> pdb=" O PRO A 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 171 through 175' Processing helix chain 'A' and resid 186 through 204 removed outlier: 3.633A pdb=" N VAL A 190 " --> pdb=" O THR A 186 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU A 202 " --> pdb=" O ASP A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 233 Processing helix chain 'A' and resid 264 through 272 removed outlier: 3.671A pdb=" N THR A 272 " --> pdb=" O PHE A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 290 removed outlier: 4.052A pdb=" N ILE A 286 " --> pdb=" O CYS A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 321 removed outlier: 3.748A pdb=" N LEU A 305 " --> pdb=" O GLY A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 346 removed outlier: 3.650A pdb=" N ALA A 341 " --> pdb=" O ASP A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 356 removed outlier: 4.061A pdb=" N THR A 351 " --> pdb=" O PHE A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 375 removed outlier: 3.815A pdb=" N ILE A 362 " --> pdb=" O ASP A 358 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N GLY A 375 " --> pdb=" O ALA A 371 " (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 414 through 422 removed outlier: 3.965A pdb=" N ILE A 418 " --> pdb=" O GLY A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 447 Processing helix chain 'A' and resid 454 through 468 removed outlier: 3.533A pdb=" N ASN A 458 " --> pdb=" O ARG A 454 " (cutoff:3.500A) Processing helix chain 'E' and resid 25 through 36 removed outlier: 3.859A pdb=" N GLY E 31 " --> pdb=" O GLU E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 53 Processing helix chain 'E' and resid 61 through 72 removed outlier: 3.698A pdb=" N GLN E 71 " --> pdb=" O LYS E 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 106 removed outlier: 3.618A pdb=" N PHE E 102 " --> pdb=" O VAL E 98 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG E 106 " --> pdb=" O PHE E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 171 through 175 removed outlier: 3.949A pdb=" N TYR E 174 " --> pdb=" O SER E 171 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N CYS E 175 " --> pdb=" O PRO E 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 171 through 175' Processing helix chain 'E' and resid 186 through 204 removed outlier: 3.632A pdb=" N VAL E 190 " --> pdb=" O THR E 186 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU E 202 " --> pdb=" O ASP E 198 " (cutoff:3.500A) Processing helix chain 'E' and resid 224 through 233 Processing helix chain 'E' and resid 264 through 272 removed outlier: 3.670A pdb=" N THR E 272 " --> pdb=" O PHE E 268 " (cutoff:3.500A) Processing helix chain 'E' and resid 276 through 290 removed outlier: 4.051A pdb=" N ILE E 286 " --> pdb=" O CYS E 282 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 321 removed outlier: 3.747A pdb=" N LEU E 305 " --> pdb=" O GLY E 301 " (cutoff:3.500A) Processing helix chain 'E' and resid 337 through 346 removed outlier: 3.650A pdb=" N ALA E 341 " --> pdb=" O ASP E 337 " (cutoff:3.500A) Processing helix chain 'E' and resid 347 through 356 removed outlier: 4.062A pdb=" N THR E 351 " --> pdb=" O PHE E 347 " (cutoff:3.500A) Processing helix chain 'E' and resid 358 through 375 removed outlier: 3.815A pdb=" N ILE E 362 " --> pdb=" O ASP E 358 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N GLY E 375 " --> pdb=" O ALA E 371 " (cutoff:3.500A) Processing helix chain 'E' and resid 379 through 398 Processing helix chain 'E' and resid 404 through 412 Processing helix chain 'E' and resid 414 through 422 removed outlier: 3.966A pdb=" N ILE E 418 " --> pdb=" O GLY E 414 " (cutoff:3.500A) Processing helix chain 'E' and resid 430 through 447 Processing helix chain 'E' and resid 454 through 468 removed outlier: 3.519A pdb=" N ASN E 458 " --> pdb=" O ARG E 454 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 79 through 82 removed outlier: 4.250A pdb=" N GLN A 179 " --> pdb=" O THR A 149 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N LEU A 154 " --> pdb=" O VAL A 165 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N VAL A 165 " --> pdb=" O LEU A 154 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LEU A 156 " --> pdb=" O VAL A 163 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 127 through 128 removed outlier: 5.040A pdb=" N LEU A 151 " --> pdb=" O GLY A 123 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N GLY A 123 " --> pdb=" O LEU A 151 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N LYS A 121 " --> pdb=" O PRO A 153 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LEU A 116 " --> pdb=" O GLU A 213 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS A 217 " --> pdb=" O LEU A 118 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N PHE A 124 " --> pdb=" O THR A 221 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N ILE A 223 " --> pdb=" O PHE A 124 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 79 through 82 removed outlier: 4.249A pdb=" N GLN E 179 " --> pdb=" O THR E 149 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N LEU E 154 " --> pdb=" O VAL E 165 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N VAL E 165 " --> pdb=" O LEU E 154 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N LEU E 156 " --> pdb=" O VAL E 163 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 127 through 128 removed outlier: 5.039A pdb=" N LEU E 151 " --> pdb=" O GLY E 123 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N GLY E 123 " --> pdb=" O LEU E 151 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LYS E 121 " --> pdb=" O PRO E 153 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LEU E 116 " --> pdb=" O GLU E 213 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS E 217 " --> pdb=" O LEU E 118 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N PHE E 124 " --> pdb=" O THR E 221 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N ILE E 223 " --> pdb=" O PHE E 124 " (cutoff:3.500A) 370 hydrogen bonds defined for protein. 1080 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 152 hydrogen bonds 304 hydrogen bond angles 0 basepair planarities 61 basepair parallelities 100 stacking parallelities Total time for adding SS restraints: 3.80 Time building geometry restraints manager: 3.20 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: 2297 1.33 - 1.45: 2825 1.45 - 1.58: 5025 1.58 - 1.70: 241 1.70 - 1.82: 52 Bond restraints: 10440 Sorted by residual: bond pdb=" C CYS A 175 " pdb=" N ARG A 176 " ideal model delta sigma weight residual 1.331 1.377 -0.046 1.63e-02 3.76e+03 7.92e+00 bond pdb=" C CYS E 175 " pdb=" N ARG E 176 " ideal model delta sigma weight residual 1.331 1.376 -0.045 1.63e-02 3.76e+03 7.48e+00 bond pdb=" N SER E 453 " pdb=" CA SER E 453 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.29e-02 6.01e+03 6.11e+00 bond pdb=" N SER A 453 " pdb=" CA SER A 453 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.29e-02 6.01e+03 5.81e+00 bond pdb=" N ARG E 454 " pdb=" CA ARG E 454 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.29e-02 6.01e+03 5.40e+00 ... (remaining 10435 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.68: 14375 2.68 - 5.37: 211 5.37 - 8.05: 34 8.05 - 10.73: 2 10.73 - 13.41: 2 Bond angle restraints: 14624 Sorted by residual: angle pdb=" N SER A 453 " pdb=" CA SER A 453 " pdb=" C SER A 453 " ideal model delta sigma weight residual 110.80 124.21 -13.41 2.13e+00 2.20e-01 3.97e+01 angle pdb=" N SER E 453 " pdb=" CA SER E 453 " pdb=" C SER E 453 " ideal model delta sigma weight residual 110.80 124.19 -13.39 2.13e+00 2.20e-01 3.95e+01 angle pdb=" C SER E 453 " pdb=" N ARG E 454 " pdb=" CA ARG E 454 " ideal model delta sigma weight residual 121.54 132.13 -10.59 1.91e+00 2.74e-01 3.08e+01 angle pdb=" C SER A 453 " pdb=" N ARG A 454 " pdb=" CA ARG A 454 " ideal model delta sigma weight residual 121.54 132.00 -10.46 1.91e+00 2.74e-01 3.00e+01 angle pdb=" O3' DA H 11 " pdb=" C3' DA H 11 " pdb=" C2' DA H 11 " ideal model delta sigma weight residual 111.50 103.56 7.94 1.50e+00 4.44e-01 2.80e+01 ... (remaining 14619 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.97: 5100 27.97 - 55.94: 784 55.94 - 83.91: 114 83.91 - 111.88: 0 111.88 - 139.85: 2 Dihedral angle restraints: 6000 sinusoidal: 3248 harmonic: 2752 Sorted by residual: dihedral pdb=" CA GLN A 499 " pdb=" C GLN A 499 " pdb=" N ASP A 500 " pdb=" CA ASP A 500 " ideal model delta harmonic sigma weight residual -180.00 -150.88 -29.12 0 5.00e+00 4.00e-02 3.39e+01 dihedral pdb=" CA GLN E 499 " pdb=" C GLN E 499 " pdb=" N ASP E 500 " pdb=" CA ASP E 500 " ideal model delta harmonic sigma weight residual -180.00 -150.89 -29.11 0 5.00e+00 4.00e-02 3.39e+01 dihedral pdb=" N ARG A 454 " pdb=" C ARG A 454 " pdb=" CA ARG A 454 " pdb=" CB ARG A 454 " ideal model delta harmonic sigma weight residual 122.80 134.17 -11.37 0 2.50e+00 1.60e-01 2.07e+01 ... (remaining 5997 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 1469 0.077 - 0.154: 183 0.154 - 0.231: 10 0.231 - 0.308: 0 0.308 - 0.385: 4 Chirality restraints: 1666 Sorted by residual: chirality pdb=" CA SER A 453 " pdb=" N SER A 453 " pdb=" C SER A 453 " pdb=" CB SER A 453 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.70e+00 chirality pdb=" CA SER E 453 " pdb=" N SER E 453 " pdb=" C SER E 453 " pdb=" CB SER E 453 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.68e+00 chirality pdb=" CA ARG A 454 " pdb=" N ARG A 454 " pdb=" C ARG A 454 " pdb=" CB ARG A 454 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.44e+00 ... (remaining 1663 not shown) Planarity restraints: 1416 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG G 20 " -0.030 2.00e-02 2.50e+03 1.23e-02 4.57e+00 pdb=" N9 DG G 20 " 0.027 2.00e-02 2.50e+03 pdb=" C8 DG G 20 " 0.005 2.00e-02 2.50e+03 pdb=" N7 DG G 20 " -0.002 2.00e-02 2.50e+03 pdb=" C5 DG G 20 " 0.004 2.00e-02 2.50e+03 pdb=" C6 DG G 20 " -0.002 2.00e-02 2.50e+03 pdb=" O6 DG G 20 " -0.010 2.00e-02 2.50e+03 pdb=" N1 DG G 20 " -0.003 2.00e-02 2.50e+03 pdb=" C2 DG G 20 " 0.001 2.00e-02 2.50e+03 pdb=" N2 DG G 20 " 0.002 2.00e-02 2.50e+03 pdb=" N3 DG G 20 " 0.004 2.00e-02 2.50e+03 pdb=" C4 DG G 20 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG C 20 " -0.030 2.00e-02 2.50e+03 1.22e-02 4.44e+00 pdb=" N9 DG C 20 " 0.026 2.00e-02 2.50e+03 pdb=" C8 DG C 20 " 0.005 2.00e-02 2.50e+03 pdb=" N7 DG C 20 " -0.002 2.00e-02 2.50e+03 pdb=" C5 DG C 20 " 0.003 2.00e-02 2.50e+03 pdb=" C6 DG C 20 " -0.003 2.00e-02 2.50e+03 pdb=" O6 DG C 20 " -0.010 2.00e-02 2.50e+03 pdb=" N1 DG C 20 " -0.003 2.00e-02 2.50e+03 pdb=" C2 DG C 20 " 0.002 2.00e-02 2.50e+03 pdb=" N2 DG C 20 " 0.001 2.00e-02 2.50e+03 pdb=" N3 DG C 20 " 0.005 2.00e-02 2.50e+03 pdb=" C4 DG C 20 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL E 380 " 0.030 5.00e-02 4.00e+02 4.58e-02 3.35e+00 pdb=" N PRO E 381 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO E 381 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO E 381 " 0.026 5.00e-02 4.00e+02 ... (remaining 1413 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.60: 195 2.60 - 3.24: 10151 3.24 - 3.87: 20321 3.87 - 4.51: 26369 4.51 - 5.14: 39722 Nonbonded interactions: 96758 Sorted by model distance: nonbonded pdb=" OD1 ASP E 125 " pdb="MG MG E 601 " model vdw 1.970 2.170 nonbonded pdb=" OD2 ASP A 224 " pdb="MG MG A 601 " model vdw 1.996 2.170 nonbonded pdb=" OD1 ASP A 125 " pdb="MG MG A 601 " model vdw 2.015 2.170 nonbonded pdb=" OD2 ASP E 224 " pdb="MG MG E 601 " model vdw 2.027 2.170 nonbonded pdb=" OP2 DC D 5 " pdb=" OG SER E 61 " model vdw 2.202 3.040 ... (remaining 96753 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 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } 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: 1.080 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: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 32.470 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 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:2.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7063 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 0.060 10440 Z= 0.507 Angle : 0.898 13.413 14624 Z= 0.514 Chirality : 0.053 0.385 1666 Planarity : 0.005 0.046 1416 Dihedral : 23.511 139.846 4208 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 23.39 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.39 % Favored : 97.39 % Rotamer: Outliers : 1.21 % Allowed : 9.90 % Favored : 88.89 % Cbeta Deviations : 0.22 % 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: -4.67 (0.20), residues: 920 helix: -2.64 (0.17), residues: 464 sheet: -2.83 (0.57), residues: 58 loop : -3.66 (0.22), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 122 HIS 0.004 0.001 HIS E 483 PHE 0.022 0.003 PHE A 383 TYR 0.014 0.002 TYR E 394 ARG 0.004 0.001 ARG A 276 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 110 time to evaluate : 0.919 Fit side-chains revert: symmetry clash REVERT: A 99 ASN cc_start: 0.7061 (m-40) cc_final: 0.6593 (t0) REVERT: A 304 GLU cc_start: 0.7453 (OUTLIER) cc_final: 0.7093 (tm-30) REVERT: E 304 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.7531 (tm-30) REVERT: E 426 ILE cc_start: 0.7949 (tt) cc_final: 0.7723 (tt) outliers start: 10 outliers final: 4 residues processed: 120 average time/residue: 0.2103 time to fit residues: 36.2183 Evaluate side-chains 87 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 81 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain E residue 236 SER Chi-restraints excluded: chain E residue 304 GLU Chi-restraints excluded: chain E residue 404 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 2.9990 chunk 77 optimal weight: 10.0000 chunk 42 optimal weight: 0.4980 chunk 26 optimal weight: 20.0000 chunk 52 optimal weight: 0.5980 chunk 41 optimal weight: 0.8980 chunk 79 optimal weight: 0.0050 chunk 30 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 59 optimal weight: 0.6980 chunk 92 optimal weight: 0.8980 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 ASN A 129 ASN A 339 ASN E 113 ASN E 129 ASN E 339 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6916 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10440 Z= 0.216 Angle : 0.694 7.273 14624 Z= 0.383 Chirality : 0.042 0.171 1666 Planarity : 0.005 0.058 1416 Dihedral : 26.681 134.999 2366 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.80 % Favored : 95.98 % Rotamer: Outliers : 2.90 % Allowed : 11.96 % Favored : 85.14 % 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: -2.57 (0.24), residues: 920 helix: -0.61 (0.22), residues: 460 sheet: -1.99 (0.66), residues: 60 loop : -3.02 (0.24), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 122 HIS 0.003 0.001 HIS E 307 PHE 0.013 0.002 PHE A 345 TYR 0.016 0.002 TYR E 488 ARG 0.005 0.000 ARG A 454 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 102 time to evaluate : 0.968 Fit side-chains REVERT: A 116 LEU cc_start: 0.8436 (mt) cc_final: 0.8045 (mp) REVERT: A 199 ASP cc_start: 0.7363 (m-30) cc_final: 0.7106 (m-30) REVERT: A 236 SER cc_start: 0.2091 (OUTLIER) cc_final: 0.1783 (p) REVERT: A 304 GLU cc_start: 0.7365 (OUTLIER) cc_final: 0.7151 (tm-30) REVERT: E 199 ASP cc_start: 0.7253 (m-30) cc_final: 0.6965 (m-30) REVERT: E 236 SER cc_start: 0.2205 (OUTLIER) cc_final: 0.1905 (p) REVERT: E 291 ASP cc_start: 0.6972 (p0) cc_final: 0.6453 (p0) REVERT: E 304 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7390 (tm-30) outliers start: 24 outliers final: 10 residues processed: 119 average time/residue: 0.1982 time to fit residues: 34.4125 Evaluate side-chains 97 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 83 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 161 ASP Chi-restraints excluded: chain E residue 236 SER Chi-restraints excluded: chain E residue 304 GLU Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 377 ILE Chi-restraints excluded: chain E residue 404 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 51 optimal weight: 2.9990 chunk 28 optimal weight: 0.0870 chunk 77 optimal weight: 8.9990 chunk 63 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 92 optimal weight: 5.9990 chunk 100 optimal weight: 5.9990 chunk 82 optimal weight: 9.9990 chunk 31 optimal weight: 6.9990 chunk 74 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 overall best weight: 1.1764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 ASN E 278 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6924 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10440 Z= 0.242 Angle : 0.658 7.243 14624 Z= 0.362 Chirality : 0.042 0.194 1666 Planarity : 0.004 0.054 1416 Dihedral : 26.371 133.310 2365 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.09 % Favored : 93.70 % Rotamer: Outliers : 3.38 % Allowed : 15.58 % Favored : 81.04 % 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: -1.80 (0.26), residues: 920 helix: 0.04 (0.23), residues: 458 sheet: -1.44 (0.72), residues: 60 loop : -2.70 (0.25), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 122 HIS 0.003 0.001 HIS E 413 PHE 0.028 0.002 PHE A 345 TYR 0.017 0.002 TYR E 386 ARG 0.004 0.000 ARG E 289 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 95 time to evaluate : 0.960 Fit side-chains REVERT: A 99 ASN cc_start: 0.7190 (m-40) cc_final: 0.6676 (t0) REVERT: A 111 ILE cc_start: 0.5819 (pt) cc_final: 0.5594 (mm) REVERT: A 260 THR cc_start: 0.1651 (OUTLIER) cc_final: 0.1387 (t) REVERT: A 304 GLU cc_start: 0.7279 (OUTLIER) cc_final: 0.7012 (tm-30) REVERT: A 424 VAL cc_start: 0.7896 (OUTLIER) cc_final: 0.7661 (t) REVERT: A 488 TYR cc_start: 0.5411 (m-10) cc_final: 0.4716 (m-10) REVERT: E 116 LEU cc_start: 0.8399 (mt) cc_final: 0.8073 (mp) REVERT: E 260 THR cc_start: 0.1420 (OUTLIER) cc_final: 0.1148 (t) REVERT: E 291 ASP cc_start: 0.6868 (p0) cc_final: 0.6412 (p0) REVERT: E 304 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.7190 (tm-30) REVERT: E 424 VAL cc_start: 0.7842 (OUTLIER) cc_final: 0.7473 (t) outliers start: 28 outliers final: 12 residues processed: 115 average time/residue: 0.1853 time to fit residues: 31.9088 Evaluate side-chains 107 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 89 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 233 GLU Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain E residue 261 ILE Chi-restraints excluded: chain E residue 304 GLU Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 377 ILE Chi-restraints excluded: chain E residue 404 SER Chi-restraints excluded: chain E residue 424 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 69 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 62 optimal weight: 5.9990 chunk 93 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 88 optimal weight: 10.0000 chunk 26 optimal weight: 10.0000 chunk 82 optimal weight: 4.9990 chunk 55 optimal weight: 0.7980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 448 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6957 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 10440 Z= 0.282 Angle : 0.663 8.272 14624 Z= 0.363 Chirality : 0.042 0.203 1666 Planarity : 0.004 0.049 1416 Dihedral : 26.198 130.889 2363 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.41 % Favored : 93.37 % Rotamer: Outliers : 3.74 % Allowed : 16.67 % Favored : 79.59 % 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: -1.62 (0.26), residues: 920 helix: 0.15 (0.23), residues: 458 sheet: -1.43 (0.70), residues: 60 loop : -2.52 (0.26), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 122 HIS 0.003 0.001 HIS A 216 PHE 0.018 0.002 PHE A 345 TYR 0.023 0.002 TYR A 288 ARG 0.002 0.000 ARG A 309 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 97 time to evaluate : 0.947 Fit side-chains REVERT: A 99 ASN cc_start: 0.7199 (m-40) cc_final: 0.6638 (t0) REVERT: A 221 THR cc_start: 0.8346 (p) cc_final: 0.8105 (m) REVERT: A 304 GLU cc_start: 0.7112 (OUTLIER) cc_final: 0.6827 (tm-30) REVERT: A 424 VAL cc_start: 0.7892 (OUTLIER) cc_final: 0.7413 (t) REVERT: E 116 LEU cc_start: 0.8419 (mt) cc_final: 0.8072 (mp) REVERT: E 221 THR cc_start: 0.8312 (p) cc_final: 0.8047 (m) REVERT: E 291 ASP cc_start: 0.6999 (p0) cc_final: 0.6365 (p0) REVERT: E 304 GLU cc_start: 0.7670 (OUTLIER) cc_final: 0.7345 (tt0) REVERT: E 424 VAL cc_start: 0.7862 (OUTLIER) cc_final: 0.7418 (t) outliers start: 31 outliers final: 16 residues processed: 123 average time/residue: 0.1854 time to fit residues: 33.9678 Evaluate side-chains 109 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 89 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 304 GLU Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 377 ILE Chi-restraints excluded: chain E residue 404 SER Chi-restraints excluded: chain E residue 424 VAL Chi-restraints excluded: chain E residue 468 SER Chi-restraints excluded: chain E residue 492 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 1 optimal weight: 0.5980 chunk 73 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 84 optimal weight: 0.8980 chunk 68 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 chunk 50 optimal weight: 10.0000 chunk 88 optimal weight: 3.9990 chunk 24 optimal weight: 10.0000 chunk 33 optimal weight: 7.9990 chunk 19 optimal weight: 0.7980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6920 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10440 Z= 0.234 Angle : 0.639 7.909 14624 Z= 0.351 Chirality : 0.041 0.167 1666 Planarity : 0.004 0.047 1416 Dihedral : 26.059 129.167 2363 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 3.62 % Allowed : 17.75 % Favored : 78.62 % 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: -1.41 (0.26), residues: 920 helix: 0.27 (0.23), residues: 458 sheet: -1.26 (0.71), residues: 60 loop : -2.36 (0.27), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 122 HIS 0.005 0.001 HIS E 447 PHE 0.015 0.002 PHE A 344 TYR 0.020 0.002 TYR A 288 ARG 0.001 0.000 ARG E 289 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 95 time to evaluate : 1.085 Fit side-chains REVERT: A 99 ASN cc_start: 0.7123 (m-40) cc_final: 0.6611 (t0) REVERT: A 280 MET cc_start: 0.8404 (tpt) cc_final: 0.8049 (tpp) REVERT: A 304 GLU cc_start: 0.7171 (OUTLIER) cc_final: 0.6821 (tm-30) REVERT: A 424 VAL cc_start: 0.7878 (OUTLIER) cc_final: 0.7587 (t) REVERT: E 99 ASN cc_start: 0.7006 (m-40) cc_final: 0.6626 (t0) REVERT: E 304 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.7436 (tm-30) REVERT: E 424 VAL cc_start: 0.7897 (OUTLIER) cc_final: 0.7614 (t) outliers start: 30 outliers final: 22 residues processed: 120 average time/residue: 0.1895 time to fit residues: 34.0137 Evaluate side-chains 114 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 88 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 402 TYR Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 233 GLU Chi-restraints excluded: chain E residue 261 ILE Chi-restraints excluded: chain E residue 304 GLU Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 377 ILE Chi-restraints excluded: chain E residue 380 VAL Chi-restraints excluded: chain E residue 402 TYR Chi-restraints excluded: chain E residue 404 SER Chi-restraints excluded: chain E residue 424 VAL Chi-restraints excluded: chain E residue 468 SER Chi-restraints excluded: chain E residue 492 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 57 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 chunk 98 optimal weight: 3.9990 chunk 81 optimal weight: 0.9980 chunk 45 optimal weight: 0.2980 chunk 8 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 chunk 56 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 ASN E 278 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6856 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10440 Z= 0.193 Angle : 0.612 7.599 14624 Z= 0.335 Chirality : 0.039 0.162 1666 Planarity : 0.004 0.047 1416 Dihedral : 25.870 128.218 2363 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 2.90 % Allowed : 19.81 % Favored : 77.29 % 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: -1.00 (0.26), residues: 920 helix: 0.66 (0.24), residues: 446 sheet: -0.56 (0.76), residues: 58 loop : -2.23 (0.27), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 122 HIS 0.005 0.001 HIS E 447 PHE 0.015 0.001 PHE A 344 TYR 0.023 0.001 TYR E 386 ARG 0.002 0.000 ARG E 289 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 97 time to evaluate : 0.886 Fit side-chains REVERT: A 99 ASN cc_start: 0.7081 (m-40) cc_final: 0.6572 (t0) REVERT: A 280 MET cc_start: 0.8409 (tpt) cc_final: 0.8030 (tpp) REVERT: A 304 GLU cc_start: 0.7366 (OUTLIER) cc_final: 0.7031 (tm-30) REVERT: A 424 VAL cc_start: 0.7789 (OUTLIER) cc_final: 0.7582 (t) REVERT: E 99 ASN cc_start: 0.7024 (m-40) cc_final: 0.6603 (t0) REVERT: E 304 GLU cc_start: 0.7439 (OUTLIER) cc_final: 0.7135 (tm-30) outliers start: 24 outliers final: 18 residues processed: 115 average time/residue: 0.1838 time to fit residues: 31.2678 Evaluate side-chains 115 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 94 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 402 TYR Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 233 GLU Chi-restraints excluded: chain E residue 261 ILE Chi-restraints excluded: chain E residue 304 GLU Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 377 ILE Chi-restraints excluded: chain E residue 402 TYR Chi-restraints excluded: chain E residue 492 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 72 optimal weight: 9.9990 chunk 55 optimal weight: 0.6980 chunk 83 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 60 optimal weight: 6.9990 chunk 39 optimal weight: 0.9990 chunk 58 optimal weight: 0.7980 chunk 29 optimal weight: 0.0770 overall best weight: 0.7142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6843 moved from start: 0.3167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10440 Z= 0.188 Angle : 0.602 7.358 14624 Z= 0.327 Chirality : 0.039 0.147 1666 Planarity : 0.004 0.045 1416 Dihedral : 25.790 128.699 2362 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 3.02 % Allowed : 20.65 % Favored : 76.33 % 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: -0.84 (0.27), residues: 920 helix: 0.78 (0.24), residues: 446 sheet: -0.29 (0.78), residues: 58 loop : -2.18 (0.27), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 41 HIS 0.004 0.001 HIS E 447 PHE 0.014 0.001 PHE A 344 TYR 0.022 0.001 TYR A 386 ARG 0.001 0.000 ARG E 176 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 95 time to evaluate : 0.982 Fit side-chains REVERT: A 99 ASN cc_start: 0.7122 (m-40) cc_final: 0.6620 (t0) REVERT: A 280 MET cc_start: 0.8465 (tpt) cc_final: 0.8082 (tpp) REVERT: A 304 GLU cc_start: 0.6992 (OUTLIER) cc_final: 0.6693 (tm-30) REVERT: A 424 VAL cc_start: 0.7861 (OUTLIER) cc_final: 0.7621 (t) REVERT: E 99 ASN cc_start: 0.7000 (m-40) cc_final: 0.6609 (t0) REVERT: E 148 MET cc_start: 0.7269 (ptm) cc_final: 0.7048 (ptt) REVERT: E 304 GLU cc_start: 0.7232 (OUTLIER) cc_final: 0.6927 (tm-30) outliers start: 25 outliers final: 17 residues processed: 115 average time/residue: 0.1897 time to fit residues: 32.3470 Evaluate side-chains 109 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 89 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 402 TYR Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 233 GLU Chi-restraints excluded: chain E residue 261 ILE Chi-restraints excluded: chain E residue 304 GLU Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 377 ILE Chi-restraints excluded: chain E residue 402 TYR Chi-restraints excluded: chain E residue 492 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 19 optimal weight: 6.9990 chunk 62 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 77 optimal weight: 10.0000 chunk 89 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 0.4980 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6951 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 10440 Z= 0.322 Angle : 0.671 8.230 14624 Z= 0.364 Chirality : 0.042 0.198 1666 Planarity : 0.004 0.043 1416 Dihedral : 25.808 127.841 2362 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.80 % Favored : 91.20 % Rotamer: Outliers : 3.02 % Allowed : 20.89 % Favored : 76.09 % 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: -1.09 (0.27), residues: 920 helix: 0.55 (0.24), residues: 444 sheet: -0.47 (0.79), residues: 58 loop : -2.25 (0.27), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 122 HIS 0.008 0.002 HIS A 216 PHE 0.025 0.002 PHE A 345 TYR 0.014 0.002 TYR A 59 ARG 0.003 0.000 ARG A 106 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 89 time to evaluate : 0.981 Fit side-chains REVERT: A 99 ASN cc_start: 0.6984 (m-40) cc_final: 0.6586 (t0) REVERT: A 280 MET cc_start: 0.8470 (tpt) cc_final: 0.8120 (tpp) REVERT: E 99 ASN cc_start: 0.6973 (m-40) cc_final: 0.6553 (t0) REVERT: E 197 MET cc_start: 0.7669 (mtp) cc_final: 0.7230 (tpp) outliers start: 25 outliers final: 17 residues processed: 110 average time/residue: 0.1932 time to fit residues: 31.1445 Evaluate side-chains 102 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 85 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 402 TYR Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 233 GLU Chi-restraints excluded: chain E residue 261 ILE Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 377 ILE Chi-restraints excluded: chain E residue 402 TYR Chi-restraints excluded: chain E residue 468 SER Chi-restraints excluded: chain E residue 492 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 39 optimal weight: 4.9990 chunk 71 optimal weight: 0.6980 chunk 28 optimal weight: 8.9990 chunk 82 optimal weight: 0.0040 chunk 86 optimal weight: 7.9990 chunk 91 optimal weight: 0.5980 chunk 60 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 59 optimal weight: 0.0170 chunk 45 optimal weight: 0.0370 chunk 67 optimal weight: 0.7980 overall best weight: 0.2708 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6806 moved from start: 0.3452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10440 Z= 0.177 Angle : 0.608 6.852 14624 Z= 0.331 Chirality : 0.039 0.177 1666 Planarity : 0.004 0.045 1416 Dihedral : 25.698 128.268 2356 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 2.05 % Allowed : 21.74 % Favored : 76.21 % 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: -0.73 (0.27), residues: 920 helix: 0.81 (0.23), residues: 448 sheet: -0.26 (0.80), residues: 58 loop : -2.05 (0.28), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 122 HIS 0.004 0.001 HIS A 447 PHE 0.015 0.001 PHE A 344 TYR 0.015 0.001 TYR A 386 ARG 0.012 0.000 ARG E 100 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 90 time to evaluate : 0.976 Fit side-chains REVERT: A 99 ASN cc_start: 0.6841 (m-40) cc_final: 0.6472 (t0) REVERT: A 106 ARG cc_start: 0.6321 (ttt90) cc_final: 0.6049 (ttt-90) REVERT: A 280 MET cc_start: 0.8474 (tpt) cc_final: 0.8117 (tpp) outliers start: 17 outliers final: 13 residues processed: 103 average time/residue: 0.2031 time to fit residues: 31.1252 Evaluate side-chains 104 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 91 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 402 TYR Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 233 GLU Chi-restraints excluded: chain E residue 261 ILE Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 402 TYR Chi-restraints excluded: chain E residue 492 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 101 optimal weight: 10.0000 chunk 93 optimal weight: 3.9990 chunk 80 optimal weight: 8.9990 chunk 8 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 49 optimal weight: 5.9990 chunk 64 optimal weight: 0.2980 chunk 86 optimal weight: 0.0870 chunk 24 optimal weight: 7.9990 chunk 74 optimal weight: 4.9990 chunk 11 optimal weight: 0.5980 overall best weight: 1.3962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6887 moved from start: 0.3359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10440 Z= 0.250 Angle : 0.636 8.060 14624 Z= 0.345 Chirality : 0.041 0.193 1666 Planarity : 0.004 0.044 1416 Dihedral : 25.703 128.401 2356 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 2.17 % Allowed : 21.86 % Favored : 75.97 % 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: -0.81 (0.27), residues: 920 helix: 0.73 (0.24), residues: 446 sheet: -0.24 (0.82), residues: 58 loop : -2.07 (0.28), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 41 HIS 0.009 0.002 HIS A 216 PHE 0.014 0.001 PHE A 344 TYR 0.015 0.002 TYR A 386 ARG 0.005 0.000 ARG A 100 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 92 time to evaluate : 1.001 Fit side-chains revert: symmetry clash REVERT: A 99 ASN cc_start: 0.6946 (m-40) cc_final: 0.6543 (t0) REVERT: A 280 MET cc_start: 0.8464 (tpt) cc_final: 0.8153 (tpt) REVERT: E 291 ASP cc_start: 0.6917 (p0) cc_final: 0.6333 (p0) outliers start: 18 outliers final: 16 residues processed: 106 average time/residue: 0.2118 time to fit residues: 32.5725 Evaluate side-chains 105 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 89 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 402 TYR Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 233 GLU Chi-restraints excluded: chain E residue 261 ILE Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 402 TYR Chi-restraints excluded: chain E residue 468 SER Chi-restraints excluded: chain E residue 492 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 22 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 33 optimal weight: 9.9990 chunk 83 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 4 optimal weight: 0.9990 chunk 58 optimal weight: 0.8980 chunk 92 optimal weight: 0.5980 chunk 54 optimal weight: 3.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5093 r_free = 0.5093 target = 0.239991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4607 r_free = 0.4607 target = 0.185084 restraints weight = 13858.533| |-----------------------------------------------------------------------------| r_work (start): 0.4541 rms_B_bonded: 2.48 r_work: 0.4338 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.4338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7129 moved from start: 0.3476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10440 Z= 0.216 Angle : 0.619 8.095 14624 Z= 0.336 Chirality : 0.040 0.183 1666 Planarity : 0.004 0.044 1416 Dihedral : 25.679 128.447 2356 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 2.29 % Allowed : 22.22 % Favored : 75.48 % 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: -0.77 (0.27), residues: 920 helix: 0.73 (0.23), residues: 448 sheet: -0.33 (0.80), residues: 58 loop : -2.00 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 41 HIS 0.010 0.001 HIS E 216 PHE 0.014 0.001 PHE A 344 TYR 0.015 0.001 TYR A 386 ARG 0.005 0.000 ARG A 100 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2038.31 seconds wall clock time: 37 minutes 16.15 seconds (2236.15 seconds total)