Starting phenix.real_space_refine on Tue Mar 3 20:19:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7bw4_30226/03_2026/7bw4_30226.cif Found real_map, /net/cci-nas-00/data/ceres_data/7bw4_30226/03_2026/7bw4_30226.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7bw4_30226/03_2026/7bw4_30226.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7bw4_30226/03_2026/7bw4_30226.map" model { file = "/net/cci-nas-00/data/ceres_data/7bw4_30226/03_2026/7bw4_30226.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7bw4_30226/03_2026/7bw4_30226.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.002 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: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 63 5.16 5 C 5503 2.51 5 N 1430 2.21 5 O 1607 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 53 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8605 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 6541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 811, 6541 Classifications: {'peptide': 811} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 783} Chain breaks: 2 Chain: "B" Number of atoms: 890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 890 Classifications: {'peptide': 115} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 109} Chain: "C" Number of atoms: 496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 496 Classifications: {'peptide': 65} Link IDs: {'TRANS': 64} Chain: "D" Number of atoms: 676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 676 Classifications: {'peptide': 87} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 82} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1681 SG CYS A 301 37.606 64.202 36.311 1.00 60.22 S ATOM 1722 SG CYS A 306 37.746 61.966 32.323 1.00 54.47 S ATOM 1754 SG CYS A 310 40.444 62.538 35.190 1.00 51.56 S ATOM 3162 SG CYS A 487 18.959 60.096 44.561 1.00 74.40 S ATOM 4415 SG CYS A 645 18.857 59.240 41.138 1.00 73.86 S ATOM 4421 SG CYS A 646 21.336 61.568 42.144 1.00 71.79 S Time building chain proxies: 1.87, per 1000 atoms: 0.22 Number of scatterers: 8605 At special positions: 0 Unit cell: (80.8, 95.2, 124, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 2 29.99 S 63 16.00 O 1607 8.00 N 1430 7.00 C 5503 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: 0.56 Conformation dependent library (CDL) restraints added in 239.9 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 301 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 306 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 310 " pdb="ZN ZN A1001 " - pdb=" ND1 HIS A 295 " pdb=" ZN A1002 " pdb="ZN ZN A1002 " - pdb=" ND1 HIS A 642 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 487 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 646 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 645 " Number of angles added : 6 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2066 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 10 sheets defined 51.5% alpha, 10.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 123 through 133 Processing helix chain 'A' and resid 139 through 149 removed outlier: 4.058A pdb=" N TYR A 149 " --> pdb=" O ILE A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 159 removed outlier: 3.611A pdb=" N PHE A 157 " --> pdb=" O ASP A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 187 removed outlier: 3.590A pdb=" N TYR A 175 " --> pdb=" O ILE A 171 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN A 177 " --> pdb=" O ARG A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 197 removed outlier: 3.628A pdb=" N CYS A 193 " --> pdb=" O THR A 189 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ASP A 194 " --> pdb=" O VAL A 190 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ALA A 195 " --> pdb=" O GLN A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 210 removed outlier: 3.781A pdb=" N ASN A 209 " --> pdb=" O THR A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 242 removed outlier: 3.615A pdb=" N TYR A 238 " --> pdb=" O VAL A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 246 removed outlier: 4.200A pdb=" N THR A 246 " --> pdb=" O PRO A 243 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 243 through 246' Processing helix chain 'A' and resid 250 through 255 Processing helix chain 'A' and resid 275 through 287 Processing helix chain 'A' and resid 297 through 301 removed outlier: 3.710A pdb=" N ASN A 300 " --> pdb=" O ASN A 297 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N CYS A 301 " --> pdb=" O CYS A 298 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 297 through 301' Processing helix chain 'A' and resid 303 through 319 Processing helix chain 'A' and resid 367 through 377 Processing helix chain 'A' and resid 378 through 384 Processing helix chain 'A' and resid 416 through 426 removed outlier: 3.938A pdb=" N TYR A 420 " --> pdb=" O ASN A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 458 Processing helix chain 'A' and resid 466 through 480 Processing helix chain 'A' and resid 511 through 519 removed outlier: 3.735A pdb=" N TYR A 515 " --> pdb=" O LYS A 511 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N MET A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 532 Processing helix chain 'A' and resid 561 through 581 removed outlier: 3.649A pdb=" N THR A 565 " --> pdb=" O SER A 561 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA A 581 " --> pdb=" O LYS A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 607 Processing helix chain 'A' and resid 621 through 626 Processing helix chain 'A' and resid 627 through 641 removed outlier: 3.728A pdb=" N ARG A 631 " --> pdb=" O PRO A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 663 Processing helix chain 'A' and resid 684 through 709 removed outlier: 4.208A pdb=" N ALA A 688 " --> pdb=" O ASP A 684 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 733 Processing helix chain 'A' and resid 738 through 752 Processing helix chain 'A' and resid 768 through 774 Processing helix chain 'A' and resid 778 through 791 removed outlier: 3.952A pdb=" N PHE A 782 " --> pdb=" O SER A 778 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASN A 791 " --> pdb=" O TYR A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 795 through 799 removed outlier: 3.571A pdb=" N CYS A 799 " --> pdb=" O GLU A 796 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 842 removed outlier: 3.648A pdb=" N ILE A 837 " --> pdb=" O ASP A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 851 through 866 removed outlier: 4.046A pdb=" N MET A 855 " --> pdb=" O ASP A 851 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 872 Processing helix chain 'A' and resid 874 through 895 removed outlier: 4.166A pdb=" N ALA A 878 " --> pdb=" O ASN A 874 " (cutoff:3.500A) Processing helix chain 'A' and resid 918 through 923 Processing helix chain 'A' and resid 924 through 926 No H-bonds generated for 'chain 'A' and resid 924 through 926' Processing helix chain 'B' and resid 79 through 97 removed outlier: 3.648A pdb=" N LYS B 97 " --> pdb=" O THR B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 109 Processing helix chain 'B' and resid 119 through 124 Processing helix chain 'B' and resid 134 through 142 removed outlier: 3.608A pdb=" N TYR B 138 " --> pdb=" O ASP B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 172 removed outlier: 3.601A pdb=" N ILE B 172 " --> pdb=" O LEU B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 180 Processing helix chain 'C' and resid 3 through 20 removed outlier: 4.020A pdb=" N LYS C 7 " --> pdb=" O MET C 3 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 24 removed outlier: 3.563A pdb=" N SER C 24 " --> pdb=" O ARG C 21 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 21 through 24' Processing helix chain 'C' and resid 25 through 40 Processing helix chain 'C' and resid 46 through 62 removed outlier: 3.649A pdb=" N GLU C 50 " --> pdb=" O THR C 46 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N MET C 62 " --> pdb=" O VAL C 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 99 removed outlier: 3.775A pdb=" N ASP D 99 " --> pdb=" O LEU D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 113 removed outlier: 3.576A pdb=" N ASN D 104 " --> pdb=" O ASN D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 134 through 141 Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 38 removed outlier: 4.178A pdb=" N ILE A 37 " --> pdb=" O GLY A 44 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLY A 44 " --> pdb=" O ILE A 37 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 223 through 224 removed outlier: 5.836A pdb=" N ILE A 201 " --> pdb=" O VAL A 231 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N VAL A 233 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N GLY A 203 " --> pdb=" O VAL A 233 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 353 through 355 removed outlier: 6.320A pdb=" N LEU A 329 " --> pdb=" O THR A 344 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N TYR A 346 " --> pdb=" O GLY A 327 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N GLY A 327 " --> pdb=" O TYR A 346 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 387 through 390 removed outlier: 3.567A pdb=" N VAL B 131 " --> pdb=" O LEU A 389 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N THR B 187 " --> pdb=" O GLN B 158 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N GLN B 158 " --> pdb=" O THR B 187 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N LEU B 189 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N ILE B 156 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ALA B 191 " --> pdb=" O TRP B 154 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N TRP B 154 " --> pdb=" O ALA B 191 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 414 through 415 Processing sheet with id=AA6, first strand: chain 'A' and resid 556 through 559 removed outlier: 6.427A pdb=" N THR A 540 " --> pdb=" O MET A 668 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 753 through 758 Processing sheet with id=AA8, first strand: chain 'A' and resid 816 through 821 Processing sheet with id=AA9, first strand: chain 'D' and resid 115 through 116 removed outlier: 4.120A pdb=" N VAL D 115 " --> pdb=" O VAL D 131 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA D 188 " --> pdb=" O LEU D 128 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL D 130 " --> pdb=" O VAL D 186 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL D 186 " --> pdb=" O VAL D 130 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N LEU D 189 " --> pdb=" O GLU D 155 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLU D 155 " --> pdb=" O LEU D 189 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 142 through 143 396 hydrogen bonds defined for protein. 1131 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.23 Time building geometry restraints manager: 0.79 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: 2411 1.33 - 1.45: 1541 1.45 - 1.57: 4746 1.57 - 1.69: 0 1.69 - 1.81: 96 Bond restraints: 8794 Sorted by residual: bond pdb=" N LEU A 401 " pdb=" CA LEU A 401 " ideal model delta sigma weight residual 1.458 1.499 -0.041 1.37e-02 5.33e+03 8.89e+00 bond pdb=" N THR A 248 " pdb=" CA THR A 248 " ideal model delta sigma weight residual 1.455 1.495 -0.041 1.37e-02 5.33e+03 8.86e+00 bond pdb=" N ARG A 249 " pdb=" CA ARG A 249 " ideal model delta sigma weight residual 1.457 1.495 -0.037 1.29e-02 6.01e+03 8.36e+00 bond pdb=" N VAL A 166 " pdb=" CA VAL A 166 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.18e+00 bond pdb=" N VAL A 174 " pdb=" CA VAL A 174 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.84e+00 ... (remaining 8789 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 11592 1.73 - 3.46: 293 3.46 - 5.19: 48 5.19 - 6.92: 3 6.92 - 8.65: 2 Bond angle restraints: 11938 Sorted by residual: angle pdb=" C THR A 248 " pdb=" CA THR A 248 " pdb=" CB THR A 248 " ideal model delta sigma weight residual 109.55 116.90 -7.35 1.68e+00 3.54e-01 1.91e+01 angle pdb=" C VAL A 166 " pdb=" CA VAL A 166 " pdb=" CB VAL A 166 " ideal model delta sigma weight residual 111.29 104.38 6.91 1.64e+00 3.72e-01 1.78e+01 angle pdb=" N VAL A 166 " pdb=" CA VAL A 166 " pdb=" C VAL A 166 " ideal model delta sigma weight residual 109.34 117.99 -8.65 2.08e+00 2.31e-01 1.73e+01 angle pdb=" N ASN A 447 " pdb=" CA ASN A 447 " pdb=" C ASN A 447 " ideal model delta sigma weight residual 111.71 106.96 4.75 1.15e+00 7.56e-01 1.71e+01 angle pdb=" N LEU A 247 " pdb=" CA LEU A 247 " pdb=" C LEU A 247 " ideal model delta sigma weight residual 111.82 107.38 4.44 1.16e+00 7.43e-01 1.47e+01 ... (remaining 11933 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 4637 17.99 - 35.98: 495 35.98 - 53.97: 78 53.97 - 71.95: 12 71.95 - 89.94: 8 Dihedral angle restraints: 5230 sinusoidal: 2035 harmonic: 3195 Sorted by residual: dihedral pdb=" CA ASP D 161 " pdb=" C ASP D 161 " pdb=" N ALA D 162 " pdb=" CA ALA D 162 " ideal model delta harmonic sigma weight residual 180.00 150.73 29.27 0 5.00e+00 4.00e-02 3.43e+01 dihedral pdb=" CA THR A 462 " pdb=" C THR A 462 " pdb=" N MET A 463 " pdb=" CA MET A 463 " ideal model delta harmonic sigma weight residual 180.00 152.65 27.35 0 5.00e+00 4.00e-02 2.99e+01 dihedral pdb=" CA TRP A 617 " pdb=" C TRP A 617 " pdb=" N ASP A 618 " pdb=" CA ASP A 618 " ideal model delta harmonic sigma weight residual 180.00 153.05 26.95 0 5.00e+00 4.00e-02 2.91e+01 ... (remaining 5227 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 988 0.055 - 0.111: 295 0.111 - 0.166: 53 0.166 - 0.221: 11 0.221 - 0.276: 3 Chirality restraints: 1350 Sorted by residual: chirality pdb=" CA LEU A 251 " pdb=" N LEU A 251 " pdb=" C LEU A 251 " pdb=" CB LEU A 251 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" CA THR A 248 " pdb=" N THR A 248 " pdb=" C THR A 248 " pdb=" CB THR A 248 " both_signs ideal model delta sigma weight residual False 2.53 2.25 0.27 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" CA SER B 177 " pdb=" N SER B 177 " pdb=" C SER B 177 " pdb=" CB SER B 177 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.49e+00 ... (remaining 1347 not shown) Planarity restraints: 1517 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 686 " -0.018 2.00e-02 2.50e+03 3.66e-02 1.34e+01 pdb=" C THR A 686 " 0.063 2.00e-02 2.50e+03 pdb=" O THR A 686 " -0.024 2.00e-02 2.50e+03 pdb=" N THR A 687 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS A 572 " -0.016 2.00e-02 2.50e+03 3.28e-02 1.08e+01 pdb=" C HIS A 572 " 0.057 2.00e-02 2.50e+03 pdb=" O HIS A 572 " -0.021 2.00e-02 2.50e+03 pdb=" N GLN A 573 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 570 " -0.016 2.00e-02 2.50e+03 3.22e-02 1.04e+01 pdb=" C GLN A 570 " 0.056 2.00e-02 2.50e+03 pdb=" O GLN A 570 " -0.021 2.00e-02 2.50e+03 pdb=" N PHE A 571 " -0.019 2.00e-02 2.50e+03 ... (remaining 1514 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 148 2.64 - 3.21: 8024 3.21 - 3.77: 13095 3.77 - 4.34: 17510 4.34 - 4.90: 28137 Nonbonded interactions: 66914 Sorted by model distance: nonbonded pdb=" O ASN A 168 " pdb=" ND2 ASN A 168 " model vdw 2.078 3.120 nonbonded pdb=" N LYS D 127 " pdb=" O ALA D 188 " model vdw 2.159 3.120 nonbonded pdb=" OG1 THR A 120 " pdb=" O TYR A 122 " model vdw 2.180 3.040 nonbonded pdb=" OH TYR A 122 " pdb=" OE1 GLU A 144 " model vdw 2.185 3.040 nonbonded pdb=" O VAL A 174 " pdb=" N ASN A 177 " model vdw 2.193 3.120 ... (remaining 66909 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 group one per residue 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: 1.160 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.190 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 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 : 0.007 0.472 8802 Z= 0.279 Angle : 0.791 32.606 11944 Z= 0.436 Chirality : 0.055 0.276 1350 Planarity : 0.004 0.042 1517 Dihedral : 15.164 89.943 3164 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 16.25 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.34 % Favored : 95.47 % Rotamer: Outliers : 1.68 % Allowed : 4.73 % Favored : 93.59 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.50 (0.22), residues: 1060 helix: -0.74 (0.21), residues: 493 sheet: -1.63 (0.55), residues: 76 loop : -2.66 (0.22), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 457 TYR 0.013 0.001 TYR A 453 PHE 0.017 0.001 PHE A 571 TRP 0.005 0.001 TRP D 154 HIS 0.004 0.001 HIS A 309 Details of bonding type rmsd covalent geometry : bond 0.00372 ( 8794) covalent geometry : angle 0.65530 (11938) hydrogen bonds : bond 0.15721 ( 396) hydrogen bonds : angle 6.09662 ( 1131) metal coordination : bond 0.19302 ( 8) metal coordination : angle 19.77167 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 256 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 PHE cc_start: 0.7484 (m-80) cc_final: 0.7121 (m-80) REVERT: A 191 GLN cc_start: 0.7581 (OUTLIER) cc_final: 0.7216 (tm-30) REVERT: A 217 TYR cc_start: 0.6078 (p90) cc_final: 0.5854 (p90) REVERT: A 316 LEU cc_start: 0.7504 (tp) cc_final: 0.7298 (tt) REVERT: A 500 LYS cc_start: 0.6395 (mttp) cc_final: 0.5666 (tttm) REVERT: A 548 ILE cc_start: 0.8426 (mp) cc_final: 0.8121 (mp) REVERT: A 575 LEU cc_start: 0.7481 (tp) cc_final: 0.7233 (tt) REVERT: A 868 PRO cc_start: 0.8302 (Cg_exo) cc_final: 0.8011 (Cg_endo) REVERT: A 882 HIS cc_start: 0.8059 (m-70) cc_final: 0.7858 (m90) REVERT: A 889 ARG cc_start: 0.8152 (mtt90) cc_final: 0.7325 (mmt90) REVERT: B 91 LEU cc_start: 0.9249 (mt) cc_final: 0.8839 (mt) REVERT: C 18 GLN cc_start: 0.7945 (tm-30) cc_final: 0.7730 (tm-30) REVERT: C 31 GLN cc_start: 0.7389 (mt0) cc_final: 0.7078 (mt0) REVERT: C 51 LYS cc_start: 0.8731 (mttm) cc_final: 0.8482 (mmtp) outliers start: 16 outliers final: 7 residues processed: 268 average time/residue: 0.1183 time to fit residues: 41.4413 Evaluate side-chains 192 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 184 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 191 GLN Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain A residue 196 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 10.0000 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 6.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 ASN A 191 GLN A 210 GLN A 213 ASN ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 386 ASN A 439 HIS A 447 ASN A 497 ASN A 568 ASN A 572 HIS A 650 HIS A 703 ASN A 713 ASN A 722 ASN A 789 GLN A 928 HIS B 104 ASN B 118 ASN ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 104 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.140627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.114365 restraints weight = 17209.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.117789 restraints weight = 9546.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.120022 restraints weight = 6439.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.121528 restraints weight = 4955.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.122531 restraints weight = 4158.912| |-----------------------------------------------------------------------------| r_work (final): 0.3776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8802 Z= 0.152 Angle : 0.648 9.543 11944 Z= 0.346 Chirality : 0.046 0.196 1350 Planarity : 0.004 0.044 1517 Dihedral : 6.797 89.213 1187 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.77 % Favored : 96.13 % Rotamer: Outliers : 2.21 % Allowed : 13.46 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.62 (0.24), residues: 1060 helix: -0.02 (0.23), residues: 509 sheet: -1.71 (0.57), residues: 66 loop : -2.15 (0.24), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 457 TYR 0.017 0.001 TYR A 887 PHE 0.011 0.001 PHE B 147 TRP 0.006 0.001 TRP A 617 HIS 0.005 0.001 HIS A 309 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 8794) covalent geometry : angle 0.64411 (11938) hydrogen bonds : bond 0.05373 ( 396) hydrogen bonds : angle 5.29984 ( 1131) metal coordination : bond 0.01008 ( 8) metal coordination : angle 3.09119 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 197 time to evaluate : 0.322 Fit side-chains revert: symmetry clash REVERT: A 35 PHE cc_start: 0.7227 (m-80) cc_final: 0.6734 (m-80) REVERT: A 316 LEU cc_start: 0.7765 (tp) cc_final: 0.7511 (tt) REVERT: A 456 TYR cc_start: 0.8114 (OUTLIER) cc_final: 0.7044 (t80) REVERT: A 500 LYS cc_start: 0.5985 (mttp) cc_final: 0.5731 (tttm) REVERT: A 889 ARG cc_start: 0.8087 (mtt90) cc_final: 0.7347 (mmt90) REVERT: C 21 ARG cc_start: 0.8484 (ptp90) cc_final: 0.8255 (mtm-85) REVERT: C 31 GLN cc_start: 0.7232 (mt0) cc_final: 0.6975 (mt0) outliers start: 21 outliers final: 12 residues processed: 209 average time/residue: 0.0931 time to fit residues: 27.3872 Evaluate side-chains 188 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 175 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 196 MET Chi-restraints excluded: chain A residue 428 PHE Chi-restraints excluded: chain A residue 456 TYR Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 818 MET Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 45 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 94 optimal weight: 10.0000 chunk 50 optimal weight: 4.9990 chunk 88 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 93 optimal weight: 3.9990 chunk 36 optimal weight: 0.0970 chunk 70 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 40 optimal weight: 0.5980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 ASN A 191 GLN ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 882 HIS C 19 GLN ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.140655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.113955 restraints weight = 16923.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.117281 restraints weight = 9460.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.119525 restraints weight = 6427.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.121000 restraints weight = 4972.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.121813 restraints weight = 4189.172| |-----------------------------------------------------------------------------| r_work (final): 0.3787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.2832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8802 Z= 0.132 Angle : 0.600 8.950 11944 Z= 0.323 Chirality : 0.044 0.155 1350 Planarity : 0.004 0.046 1517 Dihedral : 5.413 52.520 1177 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.94 % Allowed : 15.98 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (0.25), residues: 1060 helix: 0.28 (0.23), residues: 516 sheet: -1.68 (0.53), residues: 76 loop : -1.91 (0.25), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 836 TYR 0.018 0.001 TYR A 453 PHE 0.019 0.001 PHE A 504 TRP 0.007 0.001 TRP B 154 HIS 0.015 0.001 HIS A 882 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 8794) covalent geometry : angle 0.59851 (11938) hydrogen bonds : bond 0.04869 ( 396) hydrogen bonds : angle 5.16885 ( 1131) metal coordination : bond 0.00816 ( 8) metal coordination : angle 2.00872 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 199 time to evaluate : 0.347 Fit side-chains REVERT: A 35 PHE cc_start: 0.7229 (m-80) cc_final: 0.6688 (m-80) REVERT: A 217 TYR cc_start: 0.5848 (p90) cc_final: 0.5195 (p90) REVERT: A 456 TYR cc_start: 0.8037 (OUTLIER) cc_final: 0.7032 (t80) REVERT: A 500 LYS cc_start: 0.6076 (mttp) cc_final: 0.5783 (tttm) REVERT: A 548 ILE cc_start: 0.8431 (mp) cc_final: 0.8202 (mm) REVERT: A 575 LEU cc_start: 0.7295 (tp) cc_final: 0.6397 (tt) REVERT: A 608 ASP cc_start: 0.7592 (m-30) cc_final: 0.7369 (m-30) REVERT: A 665 GLU cc_start: 0.6955 (pm20) cc_final: 0.6654 (pm20) REVERT: A 811 GLU cc_start: 0.6807 (tp30) cc_final: 0.6548 (tp30) REVERT: A 889 ARG cc_start: 0.8074 (mtt90) cc_final: 0.7357 (mmt90) REVERT: C 18 GLN cc_start: 0.8054 (tm-30) cc_final: 0.7735 (tm-30) REVERT: C 31 GLN cc_start: 0.7416 (mt0) cc_final: 0.7123 (mt0) REVERT: D 129 MET cc_start: 0.7194 (tpp) cc_final: 0.6981 (tpt) outliers start: 28 outliers final: 17 residues processed: 213 average time/residue: 0.0903 time to fit residues: 26.6531 Evaluate side-chains 188 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 170 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 428 PHE Chi-restraints excluded: chain A residue 456 TYR Chi-restraints excluded: chain A residue 468 GLN Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 681 SER Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 804 ASP Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 880 VAL Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 27 LYS Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 184 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 21 optimal weight: 3.9990 chunk 96 optimal weight: 8.9990 chunk 36 optimal weight: 0.5980 chunk 58 optimal weight: 0.2980 chunk 88 optimal weight: 6.9990 chunk 20 optimal weight: 0.9980 chunk 53 optimal weight: 0.6980 chunk 80 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 10 optimal weight: 0.0870 chunk 76 optimal weight: 10.0000 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 GLN ** C 36 HIS ** 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 = 0.4064 r_free = 0.4064 target = 0.142644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.116362 restraints weight = 16982.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.119802 restraints weight = 9447.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.122101 restraints weight = 6358.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.123589 restraints weight = 4896.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.124412 restraints weight = 4105.306| |-----------------------------------------------------------------------------| r_work (final): 0.3818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.3190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8802 Z= 0.121 Angle : 0.575 8.679 11944 Z= 0.308 Chirality : 0.044 0.232 1350 Planarity : 0.004 0.049 1517 Dihedral : 5.027 55.054 1174 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.94 % Allowed : 17.67 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.25), residues: 1060 helix: 0.52 (0.23), residues: 509 sheet: -1.41 (0.55), residues: 76 loop : -1.73 (0.26), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 190 TYR 0.025 0.001 TYR A 453 PHE 0.014 0.001 PHE A 504 TRP 0.007 0.001 TRP A 617 HIS 0.005 0.001 HIS A 309 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 8794) covalent geometry : angle 0.57380 (11938) hydrogen bonds : bond 0.04588 ( 396) hydrogen bonds : angle 5.02294 ( 1131) metal coordination : bond 0.00529 ( 8) metal coordination : angle 1.49578 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 200 time to evaluate : 0.237 Fit side-chains revert: symmetry clash REVERT: A 35 PHE cc_start: 0.7294 (m-80) cc_final: 0.6716 (m-80) REVERT: A 217 TYR cc_start: 0.5730 (p90) cc_final: 0.5176 (p90) REVERT: A 456 TYR cc_start: 0.7978 (OUTLIER) cc_final: 0.7004 (t80) REVERT: A 497 ASN cc_start: 0.7887 (t0) cc_final: 0.6938 (t0) REVERT: A 500 LYS cc_start: 0.6125 (mttp) cc_final: 0.5749 (tttm) REVERT: A 608 ASP cc_start: 0.7642 (m-30) cc_final: 0.7436 (m-30) REVERT: A 703 ASN cc_start: 0.7213 (m-40) cc_final: 0.7008 (m110) REVERT: A 759 SER cc_start: 0.8721 (p) cc_final: 0.8339 (m) REVERT: A 822 GLN cc_start: 0.7392 (tm-30) cc_final: 0.6942 (pp30) REVERT: A 889 ARG cc_start: 0.8014 (mtt90) cc_final: 0.7300 (mmt90) REVERT: C 18 GLN cc_start: 0.7877 (tm-30) cc_final: 0.7513 (tm-30) REVERT: C 31 GLN cc_start: 0.7537 (mt0) cc_final: 0.7175 (mt0) REVERT: C 38 ASP cc_start: 0.7675 (t0) cc_final: 0.7386 (t0) REVERT: D 90 MET cc_start: 0.8650 (mpp) cc_final: 0.8406 (mpp) REVERT: D 92 PHE cc_start: 0.8274 (m-80) cc_final: 0.7971 (m-80) outliers start: 28 outliers final: 17 residues processed: 220 average time/residue: 0.0871 time to fit residues: 26.7058 Evaluate side-chains 197 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 179 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 428 PHE Chi-restraints excluded: chain A residue 456 TYR Chi-restraints excluded: chain A residue 468 GLN Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 681 SER Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 27 LYS Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 159 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 0 optimal weight: 10.0000 chunk 63 optimal weight: 0.5980 chunk 65 optimal weight: 3.9990 chunk 29 optimal weight: 7.9990 chunk 70 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 99 optimal weight: 8.9990 chunk 98 optimal weight: 0.9990 chunk 61 optimal weight: 10.0000 chunk 87 optimal weight: 6.9990 chunk 80 optimal weight: 0.5980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 524 GLN B 158 GLN ** C 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.139240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.112636 restraints weight = 17152.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.115857 restraints weight = 9676.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.118067 restraints weight = 6644.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.119524 restraints weight = 5131.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.120346 restraints weight = 4313.480| |-----------------------------------------------------------------------------| r_work (final): 0.3769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.3403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8802 Z= 0.151 Angle : 0.617 8.506 11944 Z= 0.329 Chirality : 0.045 0.345 1350 Planarity : 0.004 0.048 1517 Dihedral : 5.074 54.533 1174 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 3.47 % Allowed : 19.98 % Favored : 76.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.25), residues: 1060 helix: 0.60 (0.23), residues: 508 sheet: -1.10 (0.54), residues: 74 loop : -1.71 (0.26), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 836 TYR 0.025 0.001 TYR A 453 PHE 0.014 0.001 PHE B 147 TRP 0.007 0.001 TRP B 154 HIS 0.005 0.001 HIS A 572 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 8794) covalent geometry : angle 0.61667 (11938) hydrogen bonds : bond 0.05049 ( 396) hydrogen bonds : angle 5.06235 ( 1131) metal coordination : bond 0.01359 ( 8) metal coordination : angle 1.17755 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 186 time to evaluate : 0.330 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 PHE cc_start: 0.7310 (m-80) cc_final: 0.6778 (m-80) REVERT: A 217 TYR cc_start: 0.5893 (p90) cc_final: 0.5316 (p90) REVERT: A 456 TYR cc_start: 0.8235 (OUTLIER) cc_final: 0.7088 (t80) REVERT: A 500 LYS cc_start: 0.6224 (mttp) cc_final: 0.5842 (tttm) REVERT: A 822 GLN cc_start: 0.7542 (tm-30) cc_final: 0.6891 (pp30) REVERT: A 889 ARG cc_start: 0.7967 (mtt90) cc_final: 0.7280 (mmt90) outliers start: 33 outliers final: 21 residues processed: 207 average time/residue: 0.0981 time to fit residues: 27.6856 Evaluate side-chains 190 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 168 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 ASP Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 428 PHE Chi-restraints excluded: chain A residue 456 TYR Chi-restraints excluded: chain A residue 468 GLN Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 681 SER Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 804 ASP Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 27 LYS Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 189 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 36 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 93 optimal weight: 0.6980 chunk 92 optimal weight: 7.9990 chunk 2 optimal weight: 8.9990 chunk 19 optimal weight: 0.0030 chunk 3 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 overall best weight: 0.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 524 GLN B 158 GLN ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 108 ASN D 109 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.142186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.115885 restraints weight = 17097.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.119228 restraints weight = 9617.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.121457 restraints weight = 6535.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.122722 restraints weight = 5042.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.123772 restraints weight = 4287.157| |-----------------------------------------------------------------------------| r_work (final): 0.3815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.3695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8802 Z= 0.126 Angle : 0.607 9.402 11944 Z= 0.317 Chirality : 0.044 0.186 1350 Planarity : 0.004 0.050 1517 Dihedral : 4.958 57.289 1174 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.15 % Allowed : 22.08 % Favored : 74.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.25), residues: 1060 helix: 0.65 (0.23), residues: 511 sheet: -0.68 (0.52), residues: 86 loop : -1.67 (0.26), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 836 TYR 0.022 0.001 TYR A 453 PHE 0.013 0.001 PHE A 287 TRP 0.008 0.001 TRP B 154 HIS 0.005 0.001 HIS A 309 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 8794) covalent geometry : angle 0.60651 (11938) hydrogen bonds : bond 0.04688 ( 396) hydrogen bonds : angle 5.02832 ( 1131) metal coordination : bond 0.00712 ( 8) metal coordination : angle 1.22629 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 193 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 PHE cc_start: 0.7342 (m-80) cc_final: 0.6775 (m-80) REVERT: A 456 TYR cc_start: 0.8123 (OUTLIER) cc_final: 0.7190 (t80) REVERT: A 576 LEU cc_start: 0.8674 (mt) cc_final: 0.8405 (mt) REVERT: A 615 MET cc_start: 0.5504 (ttt) cc_final: 0.5215 (ttt) REVERT: A 759 SER cc_start: 0.8613 (p) cc_final: 0.8380 (m) REVERT: A 822 GLN cc_start: 0.7547 (tm-30) cc_final: 0.6959 (pp30) REVERT: A 889 ARG cc_start: 0.7912 (mtt90) cc_final: 0.7209 (mmt90) REVERT: B 82 LYS cc_start: 0.8988 (mtpp) cc_final: 0.8672 (tptt) REVERT: C 62 MET cc_start: 0.6812 (ttp) cc_final: 0.6588 (tmm) REVERT: D 139 LYS cc_start: 0.8298 (mmtt) cc_final: 0.7936 (ptpp) outliers start: 30 outliers final: 24 residues processed: 210 average time/residue: 0.0956 time to fit residues: 27.5223 Evaluate side-chains 191 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 166 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 428 PHE Chi-restraints excluded: chain A residue 456 TYR Chi-restraints excluded: chain A residue 468 GLN Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 681 SER Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 804 ASP Chi-restraints excluded: chain A residue 818 MET Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 27 LYS Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 189 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 7.9990 chunk 3 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 32 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 92 optimal weight: 6.9990 chunk 103 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 99 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 GLN ** C 36 HIS ** 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 = 0.4002 r_free = 0.4002 target = 0.137724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.111523 restraints weight = 17112.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.114778 restraints weight = 9616.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.116927 restraints weight = 6535.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.118295 restraints weight = 5061.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.119089 restraints weight = 4282.617| |-----------------------------------------------------------------------------| r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.3746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8802 Z= 0.172 Angle : 0.670 9.340 11944 Z= 0.349 Chirality : 0.045 0.196 1350 Planarity : 0.004 0.052 1517 Dihedral : 5.084 55.740 1174 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 3.47 % Allowed : 22.40 % Favored : 74.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.25), residues: 1060 helix: 0.62 (0.23), residues: 510 sheet: -0.82 (0.47), residues: 104 loop : -1.70 (0.26), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 836 TYR 0.026 0.001 TYR A 453 PHE 0.015 0.001 PHE A 287 TRP 0.006 0.001 TRP B 154 HIS 0.007 0.001 HIS A 572 Details of bonding type rmsd covalent geometry : bond 0.00384 ( 8794) covalent geometry : angle 0.66896 (11938) hydrogen bonds : bond 0.05466 ( 396) hydrogen bonds : angle 5.20630 ( 1131) metal coordination : bond 0.01868 ( 8) metal coordination : angle 1.46287 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 174 time to evaluate : 0.313 Fit side-chains revert: symmetry clash REVERT: A 35 PHE cc_start: 0.7342 (m-80) cc_final: 0.6822 (m-80) REVERT: A 217 TYR cc_start: 0.5834 (p90) cc_final: 0.5283 (p90) REVERT: A 456 TYR cc_start: 0.8368 (OUTLIER) cc_final: 0.7140 (t80) REVERT: A 500 LYS cc_start: 0.6249 (mttp) cc_final: 0.5843 (tttm) REVERT: A 575 LEU cc_start: 0.7889 (tp) cc_final: 0.7630 (tt) REVERT: A 759 SER cc_start: 0.8774 (p) cc_final: 0.8559 (m) REVERT: A 822 GLN cc_start: 0.7577 (tm-30) cc_final: 0.6945 (pp30) REVERT: A 865 ASP cc_start: 0.7247 (t70) cc_final: 0.6383 (m-30) REVERT: A 889 ARG cc_start: 0.7897 (mtt90) cc_final: 0.7164 (mmt90) REVERT: B 82 LYS cc_start: 0.8961 (mtpp) cc_final: 0.8711 (tptt) REVERT: B 97 LYS cc_start: 0.8282 (tmtt) cc_final: 0.7747 (tttm) REVERT: C 31 GLN cc_start: 0.7600 (mt0) cc_final: 0.7321 (mt0) REVERT: D 139 LYS cc_start: 0.8270 (mmtt) cc_final: 0.7900 (ptpp) outliers start: 33 outliers final: 25 residues processed: 193 average time/residue: 0.0885 time to fit residues: 23.6732 Evaluate side-chains 190 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 164 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 428 PHE Chi-restraints excluded: chain A residue 456 TYR Chi-restraints excluded: chain A residue 468 GLN Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 681 SER Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 804 ASP Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 27 LYS Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 189 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 21 optimal weight: 1.9990 chunk 24 optimal weight: 8.9990 chunk 30 optimal weight: 6.9990 chunk 11 optimal weight: 0.9980 chunk 17 optimal weight: 5.9990 chunk 99 optimal weight: 2.9990 chunk 67 optimal weight: 6.9990 chunk 45 optimal weight: 0.4980 chunk 43 optimal weight: 0.8980 chunk 41 optimal weight: 7.9990 chunk 74 optimal weight: 0.0980 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 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 GLN ** C 36 HIS ** 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 = 0.3922 r_free = 0.3922 target = 0.134872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.107992 restraints weight = 16727.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.111484 restraints weight = 8975.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.113822 restraints weight = 5899.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.115216 restraints weight = 4442.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.116300 restraints weight = 3693.004| |-----------------------------------------------------------------------------| r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.3930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8802 Z= 0.138 Angle : 0.653 9.953 11944 Z= 0.336 Chirality : 0.045 0.184 1350 Planarity : 0.004 0.053 1517 Dihedral : 5.000 58.767 1174 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 3.05 % Allowed : 23.34 % Favored : 73.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.25), residues: 1060 helix: 0.71 (0.24), residues: 507 sheet: -0.79 (0.47), residues: 104 loop : -1.57 (0.27), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 836 TYR 0.023 0.001 TYR A 453 PHE 0.022 0.001 PHE D 92 TRP 0.010 0.001 TRP A 916 HIS 0.004 0.001 HIS A 309 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 8794) covalent geometry : angle 0.65271 (11938) hydrogen bonds : bond 0.04845 ( 396) hydrogen bonds : angle 5.10277 ( 1131) metal coordination : bond 0.00965 ( 8) metal coordination : angle 1.17183 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 178 time to evaluate : 0.340 Fit side-chains revert: symmetry clash REVERT: A 35 PHE cc_start: 0.7484 (m-80) cc_final: 0.6831 (m-80) REVERT: A 346 TYR cc_start: 0.7984 (t80) cc_final: 0.7704 (t80) REVERT: A 456 TYR cc_start: 0.8100 (OUTLIER) cc_final: 0.7065 (t80) REVERT: A 500 LYS cc_start: 0.6475 (mttp) cc_final: 0.5948 (tttm) REVERT: A 759 SER cc_start: 0.8658 (p) cc_final: 0.8433 (m) REVERT: A 822 GLN cc_start: 0.7771 (tm-30) cc_final: 0.7310 (pp30) REVERT: A 865 ASP cc_start: 0.7297 (t70) cc_final: 0.6328 (m-30) REVERT: A 889 ARG cc_start: 0.8060 (mtt90) cc_final: 0.7383 (mtt-85) REVERT: B 97 LYS cc_start: 0.8242 (tmtt) cc_final: 0.7822 (tttm) REVERT: D 139 LYS cc_start: 0.8268 (mmtt) cc_final: 0.7888 (ptpp) outliers start: 29 outliers final: 24 residues processed: 196 average time/residue: 0.0896 time to fit residues: 24.2153 Evaluate side-chains 197 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 172 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 ASP Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 428 PHE Chi-restraints excluded: chain A residue 456 TYR Chi-restraints excluded: chain A residue 468 GLN Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 681 SER Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 804 ASP Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 27 LYS Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 167 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 37 optimal weight: 0.4980 chunk 68 optimal weight: 0.6980 chunk 104 optimal weight: 0.0170 chunk 15 optimal weight: 9.9990 chunk 20 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 57 optimal weight: 7.9990 chunk 39 optimal weight: 8.9990 chunk 93 optimal weight: 2.9990 chunk 34 optimal weight: 0.0770 chunk 2 optimal weight: 7.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 524 GLN B 158 GLN C 19 GLN ** C 36 HIS ** 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 = 0.3939 r_free = 0.3939 target = 0.136080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.109327 restraints weight = 16721.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.112863 restraints weight = 8946.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.115205 restraints weight = 5873.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.116763 restraints weight = 4418.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.117835 restraints weight = 3632.749| |-----------------------------------------------------------------------------| r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.4096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8802 Z= 0.133 Angle : 0.658 12.751 11944 Z= 0.337 Chirality : 0.045 0.269 1350 Planarity : 0.004 0.055 1517 Dihedral : 4.929 59.599 1174 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.94 % Allowed : 23.97 % Favored : 73.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.25), residues: 1060 helix: 0.67 (0.23), residues: 507 sheet: -0.75 (0.48), residues: 104 loop : -1.47 (0.28), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 836 TYR 0.020 0.001 TYR A 453 PHE 0.023 0.001 PHE A 471 TRP 0.008 0.001 TRP A 916 HIS 0.007 0.001 HIS A 381 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 8794) covalent geometry : angle 0.65794 (11938) hydrogen bonds : bond 0.04691 ( 396) hydrogen bonds : angle 5.07657 ( 1131) metal coordination : bond 0.00739 ( 8) metal coordination : angle 1.02213 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 188 time to evaluate : 0.342 Fit side-chains revert: symmetry clash REVERT: A 35 PHE cc_start: 0.7440 (m-80) cc_final: 0.6779 (m-80) REVERT: A 346 TYR cc_start: 0.7997 (t80) cc_final: 0.7682 (t80) REVERT: A 456 TYR cc_start: 0.8084 (OUTLIER) cc_final: 0.7073 (t80) REVERT: A 500 LYS cc_start: 0.6491 (mttp) cc_final: 0.5922 (tttm) REVERT: A 615 MET cc_start: 0.5995 (tpp) cc_final: 0.5229 (ttt) REVERT: A 822 GLN cc_start: 0.7850 (tm-30) cc_final: 0.7366 (pp30) REVERT: A 865 ASP cc_start: 0.7282 (t70) cc_final: 0.6360 (m-30) REVERT: A 889 ARG cc_start: 0.8019 (mtt90) cc_final: 0.7339 (mtt-85) REVERT: B 94 MET cc_start: 0.7144 (ptm) cc_final: 0.6460 (ptm) REVERT: B 97 LYS cc_start: 0.8238 (tmtt) cc_final: 0.7852 (tttm) REVERT: C 18 GLN cc_start: 0.7511 (tm-30) cc_final: 0.6985 (tm-30) REVERT: D 139 LYS cc_start: 0.8258 (mmtt) cc_final: 0.7845 (ptpp) outliers start: 28 outliers final: 24 residues processed: 206 average time/residue: 0.0905 time to fit residues: 25.6569 Evaluate side-chains 198 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 173 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 ASP Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 428 PHE Chi-restraints excluded: chain A residue 456 TYR Chi-restraints excluded: chain A residue 468 GLN Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 681 SER Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 788 TYR Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 27 LYS Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 167 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 32 optimal weight: 0.2980 chunk 22 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 chunk 49 optimal weight: 0.0050 chunk 20 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 chunk 98 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 76 optimal weight: 8.9990 chunk 71 optimal weight: 2.9990 chunk 53 optimal weight: 0.5980 overall best weight: 0.9798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 781 ASN B 158 GLN ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.135093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.108097 restraints weight = 16823.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.111540 restraints weight = 9059.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.113876 restraints weight = 6006.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.115389 restraints weight = 4545.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.116273 restraints weight = 3775.987| |-----------------------------------------------------------------------------| r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.4182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8802 Z= 0.143 Angle : 0.685 11.160 11944 Z= 0.349 Chirality : 0.046 0.235 1350 Planarity : 0.004 0.054 1517 Dihedral : 4.912 59.708 1174 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 3.05 % Allowed : 24.61 % Favored : 72.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.25), residues: 1060 helix: 0.69 (0.23), residues: 507 sheet: -1.14 (0.55), residues: 78 loop : -1.38 (0.27), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 836 TYR 0.020 0.001 TYR A 453 PHE 0.029 0.001 PHE D 92 TRP 0.007 0.001 TRP A 916 HIS 0.006 0.001 HIS A 381 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 8794) covalent geometry : angle 0.68429 (11938) hydrogen bonds : bond 0.04794 ( 396) hydrogen bonds : angle 5.10640 ( 1131) metal coordination : bond 0.01007 ( 8) metal coordination : angle 1.08737 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 177 time to evaluate : 0.196 Fit side-chains revert: symmetry clash REVERT: A 35 PHE cc_start: 0.7457 (m-80) cc_final: 0.6809 (m-80) REVERT: A 346 TYR cc_start: 0.8044 (t80) cc_final: 0.7682 (t80) REVERT: A 456 TYR cc_start: 0.8179 (OUTLIER) cc_final: 0.7100 (t80) REVERT: A 500 LYS cc_start: 0.6474 (mttp) cc_final: 0.5915 (tttm) REVERT: A 615 MET cc_start: 0.6161 (tpp) cc_final: 0.5713 (ttt) REVERT: A 822 GLN cc_start: 0.7872 (tm-30) cc_final: 0.7365 (pp30) REVERT: A 865 ASP cc_start: 0.7357 (t70) cc_final: 0.6388 (m-30) REVERT: A 889 ARG cc_start: 0.8024 (mtt90) cc_final: 0.7351 (mtt-85) REVERT: B 87 MET cc_start: 0.8333 (mtm) cc_final: 0.8131 (mtm) REVERT: B 94 MET cc_start: 0.7098 (ptm) cc_final: 0.6472 (ptm) REVERT: B 97 LYS cc_start: 0.8262 (tmtt) cc_final: 0.7892 (tttm) REVERT: D 139 LYS cc_start: 0.8277 (mmtt) cc_final: 0.7842 (ptpp) outliers start: 29 outliers final: 26 residues processed: 197 average time/residue: 0.0928 time to fit residues: 24.9715 Evaluate side-chains 197 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 170 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 126 ASP Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 428 PHE Chi-restraints excluded: chain A residue 456 TYR Chi-restraints excluded: chain A residue 468 GLN Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 681 SER Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 788 TYR Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 27 LYS Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 167 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 42 optimal weight: 3.9990 chunk 77 optimal weight: 8.9990 chunk 79 optimal weight: 0.0770 chunk 6 optimal weight: 5.9990 chunk 98 optimal weight: 0.9990 chunk 45 optimal weight: 9.9990 chunk 47 optimal weight: 0.4980 chunk 15 optimal weight: 8.9990 chunk 78 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 overall best weight: 0.7144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 GLN ** C 36 HIS ** 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 = 0.3940 r_free = 0.3940 target = 0.136391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.109668 restraints weight = 16656.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.113205 restraints weight = 8936.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.115525 restraints weight = 5891.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.117073 restraints weight = 4428.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.118104 restraints weight = 3652.586| |-----------------------------------------------------------------------------| r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.4305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8802 Z= 0.137 Angle : 0.691 13.247 11944 Z= 0.351 Chirality : 0.045 0.231 1350 Planarity : 0.004 0.053 1517 Dihedral : 4.848 58.273 1174 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.15 % Allowed : 24.50 % Favored : 72.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.25), residues: 1060 helix: 0.75 (0.23), residues: 507 sheet: -0.87 (0.53), residues: 90 loop : -1.36 (0.27), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 836 TYR 0.019 0.001 TYR A 453 PHE 0.033 0.001 PHE D 92 TRP 0.019 0.001 TRP A 509 HIS 0.005 0.001 HIS A 381 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 8794) covalent geometry : angle 0.69060 (11938) hydrogen bonds : bond 0.04593 ( 396) hydrogen bonds : angle 5.05325 ( 1131) metal coordination : bond 0.00774 ( 8) metal coordination : angle 1.06731 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1500.08 seconds wall clock time: 26 minutes 34.49 seconds (1594.49 seconds total)