Starting phenix.real_space_refine on Thu Feb 13 01:10:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7bw4_30226/02_2025/7bw4_30226.cif Found real_map, /net/cci-nas-00/data/ceres_data/7bw4_30226/02_2025/7bw4_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_30226/02_2025/7bw4_30226.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7bw4_30226/02_2025/7bw4_30226.map" model { file = "/net/cci-nas-00/data/ceres_data/7bw4_30226/02_2025/7bw4_30226.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7bw4_30226/02_2025/7bw4_30226.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 5.06, per 1000 atoms: 0.59 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: 2.42 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.99 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: 2.67 Time building geometry restraints manager: 2.61 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: 0.960 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: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 24.300 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.970 ------------------------------------------------------------------------------- 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 : 0.004 0.041 8794 Z= 0.245 Angle : 0.655 8.651 11938 Z= 0.421 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.50 (0.22), residues: 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 TRP 0.005 0.001 TRP D 154 HIS 0.004 0.001 HIS A 309 PHE 0.017 0.001 PHE A 571 TYR 0.013 0.001 TYR A 453 ARG 0.002 0.000 ARG A 457 *********************** 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 : 0.948 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: 0.2537 time to fit residues: 87.9968 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 : 0.983 ------------------------------------------------------------------------------- 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 89 optimal weight: 2.9990 chunk 80 optimal weight: 8.9990 chunk 44 optimal weight: 0.9990 chunk 27 optimal weight: 6.9990 chunk 54 optimal weight: 5.9990 chunk 42 optimal weight: 10.0000 chunk 83 optimal weight: 9.9990 chunk 32 optimal weight: 0.6980 chunk 50 optimal weight: 4.9990 chunk 61 optimal weight: 0.9990 chunk 96 optimal weight: 0.0970 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 = 0.4032 r_free = 0.4032 target = 0.140501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.114361 restraints weight = 16840.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.117654 restraints weight = 9381.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.119933 restraints weight = 6393.529| |-----------------------------------------------------------------------------| r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8794 Z= 0.201 Angle : 0.643 9.441 11938 Z= 0.345 Chirality : 0.046 0.193 1350 Planarity : 0.004 0.044 1517 Dihedral : 6.782 89.082 1187 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.77 % Favored : 96.13 % Rotamer: Outliers : 2.31 % Allowed : 13.46 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.24), residues: 1060 helix: -0.01 (0.23), residues: 508 sheet: -1.71 (0.57), residues: 66 loop : -2.16 (0.24), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 617 HIS 0.005 0.001 HIS A 309 PHE 0.012 0.001 PHE B 147 TYR 0.018 0.001 TYR A 887 ARG 0.006 0.001 ARG A 457 *********************** 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 222 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 200 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 PHE cc_start: 0.7285 (m-80) cc_final: 0.6731 (m-80) REVERT: A 316 LEU cc_start: 0.7790 (tp) cc_final: 0.7533 (tt) REVERT: A 456 TYR cc_start: 0.8118 (OUTLIER) cc_final: 0.7029 (t80) REVERT: A 500 LYS cc_start: 0.6060 (mttp) cc_final: 0.5737 (tttm) REVERT: A 889 ARG cc_start: 0.8187 (mtt90) cc_final: 0.7393 (mmt90) REVERT: C 21 ARG cc_start: 0.8517 (OUTLIER) cc_final: 0.8268 (mtm-85) REVERT: C 31 GLN cc_start: 0.7248 (mt0) cc_final: 0.6984 (mt0) REVERT: D 87 MET cc_start: 0.6447 (tpt) cc_final: 0.6235 (tpt) outliers start: 22 outliers final: 12 residues processed: 212 average time/residue: 0.2158 time to fit residues: 62.7680 Evaluate side-chains 188 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 174 time to evaluate : 1.012 ------------------------------------------------------------------------------- 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 21 ARG 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 65 optimal weight: 0.9990 chunk 33 optimal weight: 4.9990 chunk 52 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 13 optimal weight: 7.9990 chunk 78 optimal weight: 6.9990 chunk 36 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 86 optimal weight: 5.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 572 HIS A 599 HIS A 882 HIS B 158 GLN ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.135244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.108248 restraints weight = 17172.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.111435 restraints weight = 9691.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.113585 restraints weight = 6681.801| |-----------------------------------------------------------------------------| r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8794 Z= 0.276 Angle : 0.661 8.943 11938 Z= 0.358 Chirality : 0.046 0.233 1350 Planarity : 0.004 0.042 1517 Dihedral : 5.622 52.011 1177 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.34 % Favored : 95.57 % Rotamer: Outliers : 4.00 % Allowed : 15.67 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.24), residues: 1060 helix: 0.27 (0.23), residues: 504 sheet: -1.77 (0.51), residues: 79 loop : -2.02 (0.25), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 154 HIS 0.016 0.001 HIS A 882 PHE 0.015 0.002 PHE A 766 TYR 0.022 0.002 TYR A 453 ARG 0.006 0.000 ARG A 836 *********************** 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 220 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 182 time to evaluate : 0.960 Fit side-chains revert: symmetry clash REVERT: A 35 PHE cc_start: 0.7301 (m-80) cc_final: 0.6732 (m-80) REVERT: A 456 TYR cc_start: 0.8324 (OUTLIER) cc_final: 0.7007 (t80) REVERT: A 500 LYS cc_start: 0.6306 (mttp) cc_final: 0.5829 (tttm) REVERT: A 575 LEU cc_start: 0.7958 (tp) cc_final: 0.7633 (tt) REVERT: A 889 ARG cc_start: 0.8195 (mtt90) cc_final: 0.7480 (mmt90) REVERT: B 90 MET cc_start: 0.8250 (tmm) cc_final: 0.7886 (tmm) REVERT: C 31 GLN cc_start: 0.7492 (mt0) cc_final: 0.7166 (mt0) REVERT: C 38 ASP cc_start: 0.7561 (t0) cc_final: 0.7336 (t0) outliers start: 38 outliers final: 21 residues processed: 204 average time/residue: 0.2231 time to fit residues: 62.0277 Evaluate side-chains 184 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 162 time to evaluate : 0.903 ------------------------------------------------------------------------------- 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 271 LEU 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 662 VAL Chi-restraints excluded: chain A residue 681 SER Chi-restraints excluded: chain A residue 804 ASP 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 13 LEU Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 159 VAL 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 0 optimal weight: 10.0000 chunk 54 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 102 optimal weight: 0.0000 chunk 27 optimal weight: 5.9990 chunk 81 optimal weight: 0.2980 chunk 72 optimal weight: 7.9990 chunk 67 optimal weight: 3.9990 chunk 104 optimal weight: 0.0870 chunk 64 optimal weight: 5.9990 chunk 105 optimal weight: 0.9990 overall best weight: 1.0766 ------------------------------------------------------------------------------- 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** B 158 GLN ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 109 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.138667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.112058 restraints weight = 17028.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.115386 restraints weight = 9585.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.117615 restraints weight = 6533.978| |-----------------------------------------------------------------------------| r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.3133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8794 Z= 0.192 Angle : 0.605 8.821 11938 Z= 0.325 Chirality : 0.044 0.161 1350 Planarity : 0.004 0.045 1517 Dihedral : 5.237 55.689 1174 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 3.47 % Allowed : 17.98 % Favored : 78.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.25), residues: 1060 helix: 0.38 (0.23), residues: 509 sheet: -1.49 (0.50), residues: 84 loop : -1.92 (0.26), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 154 HIS 0.004 0.001 HIS A 309 PHE 0.010 0.001 PHE B 147 TYR 0.029 0.001 TYR A 453 ARG 0.005 0.000 ARG A 836 *********************** 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 224 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 191 time to evaluate : 0.937 Fit side-chains revert: symmetry clash REVERT: A 35 PHE cc_start: 0.7231 (m-80) cc_final: 0.6705 (m-80) REVERT: A 217 TYR cc_start: 0.5860 (p90) cc_final: 0.5185 (p90) REVERT: A 316 LEU cc_start: 0.7821 (tp) cc_final: 0.7560 (tt) REVERT: A 456 TYR cc_start: 0.8211 (OUTLIER) cc_final: 0.7199 (t80) REVERT: A 500 LYS cc_start: 0.6333 (mttp) cc_final: 0.5889 (tttm) REVERT: A 822 GLN cc_start: 0.7784 (tm-30) cc_final: 0.6764 (tm-30) REVERT: A 825 ASP cc_start: 0.6931 (p0) cc_final: 0.5831 (p0) REVERT: A 889 ARG cc_start: 0.8087 (mtt90) cc_final: 0.7388 (mmt90) REVERT: C 19 GLN cc_start: 0.8530 (mm-40) cc_final: 0.8214 (tp40) REVERT: C 27 LYS cc_start: 0.6343 (OUTLIER) cc_final: 0.6061 (pttt) REVERT: C 31 GLN cc_start: 0.7585 (mt0) cc_final: 0.7247 (mt0) REVERT: D 139 LYS cc_start: 0.8307 (mmtt) cc_final: 0.8074 (ptpt) outliers start: 33 outliers final: 19 residues processed: 214 average time/residue: 0.2054 time to fit residues: 60.3584 Evaluate side-chains 192 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 171 time to evaluate : 0.936 ------------------------------------------------------------------------------- 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 338 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 588 VAL Chi-restraints excluded: chain A residue 662 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 A residue 926 THR Chi-restraints excluded: chain B residue 79 LYS 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 159 VAL Chi-restraints excluded: chain D residue 189 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 47 optimal weight: 3.9990 chunk 94 optimal weight: 8.9990 chunk 16 optimal weight: 8.9990 chunk 61 optimal weight: 9.9990 chunk 88 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 46 optimal weight: 0.0670 chunk 90 optimal weight: 0.9990 chunk 26 optimal weight: 10.0000 chunk 50 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 overall best weight: 2.4126 ------------------------------------------------------------------------------- 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** 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 = 0.3952 r_free = 0.3952 target = 0.134463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.107737 restraints weight = 17094.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.110896 restraints weight = 9756.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.113017 restraints weight = 6740.236| |-----------------------------------------------------------------------------| r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.3360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 8794 Z= 0.289 Angle : 0.667 8.645 11938 Z= 0.358 Chirality : 0.046 0.187 1350 Planarity : 0.004 0.054 1517 Dihedral : 5.370 54.378 1174 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 3.79 % Allowed : 19.87 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.24), residues: 1060 helix: 0.36 (0.23), residues: 508 sheet: -1.51 (0.46), residues: 94 loop : -1.90 (0.26), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 154 HIS 0.004 0.001 HIS A 309 PHE 0.016 0.002 PHE B 147 TYR 0.029 0.002 TYR A 453 ARG 0.006 0.000 ARG A 836 *********************** 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 212 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 176 time to evaluate : 0.982 Fit side-chains REVERT: A 35 PHE cc_start: 0.7305 (m-80) cc_final: 0.6810 (m-80) REVERT: A 456 TYR cc_start: 0.8398 (OUTLIER) cc_final: 0.7062 (t80) REVERT: A 668 MET cc_start: 0.7487 (tpt) cc_final: 0.7119 (tpt) REVERT: A 822 GLN cc_start: 0.7892 (tm-30) cc_final: 0.7040 (tm-30) REVERT: A 825 ASP cc_start: 0.7094 (p0) cc_final: 0.6384 (p0) REVERT: A 889 ARG cc_start: 0.8138 (mtt90) cc_final: 0.7384 (mmt90) REVERT: C 27 LYS cc_start: 0.6525 (OUTLIER) cc_final: 0.6235 (pttt) REVERT: C 31 GLN cc_start: 0.7624 (mt0) cc_final: 0.7248 (mt0) REVERT: C 38 ASP cc_start: 0.7693 (t0) cc_final: 0.7380 (t0) REVERT: D 87 MET cc_start: 0.6317 (tpt) cc_final: 0.6032 (tpt) REVERT: D 139 LYS cc_start: 0.8314 (mmtt) cc_final: 0.8060 (ptpt) outliers start: 36 outliers final: 30 residues processed: 201 average time/residue: 0.2293 time to fit residues: 63.0630 Evaluate side-chains 192 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 160 time to evaluate : 1.037 ------------------------------------------------------------------------------- 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 338 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 542 MET Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 662 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 A residue 845 ASP Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 27 LYS Chi-restraints excluded: chain D residue 101 ASP 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 104 optimal weight: 2.9990 chunk 103 optimal weight: 5.9990 chunk 97 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 80 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 24 optimal weight: 7.9990 chunk 76 optimal weight: 4.9990 chunk 64 optimal weight: 0.6980 chunk 58 optimal weight: 4.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 381 HIS ** A 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 GLN ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 108 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.133815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.107220 restraints weight = 16932.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.110344 restraints weight = 9705.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.112459 restraints weight = 6712.038| |-----------------------------------------------------------------------------| r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.3577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 8794 Z= 0.290 Angle : 0.678 8.824 11938 Z= 0.365 Chirality : 0.047 0.178 1350 Planarity : 0.004 0.049 1517 Dihedral : 5.450 54.413 1174 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 4.63 % Allowed : 22.08 % Favored : 73.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.24), residues: 1060 helix: 0.33 (0.23), residues: 510 sheet: -1.23 (0.55), residues: 74 loop : -1.89 (0.25), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 154 HIS 0.003 0.001 HIS A 309 PHE 0.015 0.002 PHE A 287 TYR 0.029 0.002 TYR A 453 ARG 0.006 0.001 ARG A 836 *********************** 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 217 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 173 time to evaluate : 1.014 Fit side-chains REVERT: A 35 PHE cc_start: 0.7379 (m-80) cc_final: 0.6875 (m-80) REVERT: A 217 TYR cc_start: 0.5918 (p90) cc_final: 0.5191 (p90) REVERT: A 456 TYR cc_start: 0.8471 (OUTLIER) cc_final: 0.7036 (t80) REVERT: A 668 MET cc_start: 0.7478 (tpt) cc_final: 0.7195 (tpt) REVERT: A 822 GLN cc_start: 0.7911 (tm-30) cc_final: 0.7016 (tm-30) REVERT: A 825 ASP cc_start: 0.7096 (p0) cc_final: 0.6359 (p0) REVERT: A 889 ARG cc_start: 0.8083 (mtt90) cc_final: 0.7448 (mtt-85) REVERT: C 27 LYS cc_start: 0.6543 (OUTLIER) cc_final: 0.6266 (pttt) REVERT: C 31 GLN cc_start: 0.7630 (mt0) cc_final: 0.7239 (mt0) REVERT: D 139 LYS cc_start: 0.8336 (mmtt) cc_final: 0.8080 (ptpt) outliers start: 44 outliers final: 33 residues processed: 202 average time/residue: 0.2196 time to fit residues: 60.2967 Evaluate side-chains 201 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 166 time to evaluate : 1.021 ------------------------------------------------------------------------------- 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 206 THR Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 338 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 542 MET Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 662 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 A residue 845 ASP Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain C residue 6 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 159 VAL Chi-restraints excluded: chain D residue 167 VAL 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 41 optimal weight: 2.9990 chunk 88 optimal weight: 6.9990 chunk 80 optimal weight: 0.9990 chunk 10 optimal weight: 6.9990 chunk 23 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 12 optimal weight: 6.9990 chunk 63 optimal weight: 5.9990 chunk 13 optimal weight: 0.3980 chunk 72 optimal weight: 7.9990 chunk 24 optimal weight: 0.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- 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 497 ASN ** 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 = 0.4012 r_free = 0.4012 target = 0.138632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.112673 restraints weight = 17070.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.116056 restraints weight = 9514.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.118245 restraints weight = 6410.302| |-----------------------------------------------------------------------------| r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.3745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8794 Z= 0.192 Angle : 0.630 8.946 11938 Z= 0.334 Chirality : 0.045 0.201 1350 Planarity : 0.004 0.048 1517 Dihedral : 5.176 57.402 1174 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 3.68 % Allowed : 22.92 % Favored : 73.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.25), residues: 1060 helix: 0.52 (0.23), residues: 505 sheet: -1.36 (0.50), residues: 84 loop : -1.70 (0.26), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 154 HIS 0.004 0.001 HIS A 309 PHE 0.010 0.001 PHE A 287 TYR 0.024 0.001 TYR A 453 ARG 0.004 0.000 ARG B 190 *********************** 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 228 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 193 time to evaluate : 0.935 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 PHE cc_start: 0.7348 (m-80) cc_final: 0.6830 (m-80) REVERT: A 217 TYR cc_start: 0.5788 (p90) cc_final: 0.5185 (p90) REVERT: A 456 TYR cc_start: 0.8325 (OUTLIER) cc_final: 0.7206 (t80) REVERT: A 759 SER cc_start: 0.8778 (p) cc_final: 0.8505 (m) REVERT: A 822 GLN cc_start: 0.7883 (tm-30) cc_final: 0.7018 (tm-30) REVERT: A 889 ARG cc_start: 0.8005 (mtt90) cc_final: 0.7335 (mtt-85) REVERT: B 82 LYS cc_start: 0.8953 (mtpp) cc_final: 0.8671 (tptt) REVERT: B 94 MET cc_start: 0.6748 (ptm) cc_final: 0.6004 (ptm) REVERT: D 139 LYS cc_start: 0.8326 (mmtt) cc_final: 0.8093 (ptpt) outliers start: 35 outliers final: 27 residues processed: 214 average time/residue: 0.2113 time to fit residues: 61.7319 Evaluate side-chains 203 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 175 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU 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 380 MET 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 542 MET 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 829 LEU Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 165 LYS Chi-restraints excluded: chain D residue 167 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 89 optimal weight: 0.1980 chunk 96 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 104 optimal weight: 0.9990 chunk 22 optimal weight: 0.2980 chunk 21 optimal weight: 0.7980 chunk 33 optimal weight: 7.9990 chunk 14 optimal weight: 1.9990 chunk 79 optimal weight: 0.2980 chunk 31 optimal weight: 5.9990 chunk 87 optimal weight: 4.9990 overall best weight: 0.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 ASN A 497 ASN A 572 HIS A 810 HIS ** 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 = 0.4054 r_free = 0.4054 target = 0.141730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.115980 restraints weight = 17080.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.119378 restraints weight = 9516.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.121605 restraints weight = 6445.696| |-----------------------------------------------------------------------------| r_work (final): 0.3774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.4041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8794 Z= 0.174 Angle : 0.635 11.454 11938 Z= 0.331 Chirality : 0.044 0.219 1350 Planarity : 0.004 0.051 1517 Dihedral : 5.050 58.440 1174 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 3.26 % Allowed : 23.76 % Favored : 72.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.25), residues: 1060 helix: 0.57 (0.23), residues: 507 sheet: -0.94 (0.49), residues: 94 loop : -1.63 (0.27), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 154 HIS 0.005 0.001 HIS A 256 PHE 0.021 0.001 PHE D 92 TYR 0.020 0.001 TYR A 453 ARG 0.004 0.000 ARG B 190 *********************** 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 233 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 202 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 PHE cc_start: 0.7379 (m-80) cc_final: 0.6835 (m-80) REVERT: A 217 TYR cc_start: 0.5708 (p90) cc_final: 0.5185 (p90) REVERT: A 456 TYR cc_start: 0.8264 (OUTLIER) cc_final: 0.7243 (t80) REVERT: A 576 LEU cc_start: 0.8520 (mt) cc_final: 0.8302 (mt) REVERT: A 822 GLN cc_start: 0.7888 (tm-30) cc_final: 0.7099 (tm-30) REVERT: A 889 ARG cc_start: 0.7919 (mtt90) cc_final: 0.7202 (mmt90) REVERT: B 94 MET cc_start: 0.6543 (ptm) cc_final: 0.5945 (ptm) REVERT: B 97 LYS cc_start: 0.8230 (tmtt) cc_final: 0.7754 (tttm) REVERT: D 139 LYS cc_start: 0.8341 (mmtt) cc_final: 0.7989 (ptpp) REVERT: D 189 LEU cc_start: 0.4080 (OUTLIER) cc_final: 0.3879 (tt) outliers start: 31 outliers final: 25 residues processed: 224 average time/residue: 0.2152 time to fit residues: 65.3874 Evaluate side-chains 203 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 176 time to evaluate : 1.046 ------------------------------------------------------------------------------- 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 174 VAL Chi-restraints excluded: chain A residue 226 THR 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 380 MET 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 498 LEU Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 845 ASP Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 165 LYS Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 189 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 93 optimal weight: 0.7980 chunk 1 optimal weight: 7.9990 chunk 23 optimal weight: 0.9990 chunk 9 optimal weight: 10.0000 chunk 13 optimal weight: 5.9990 chunk 83 optimal weight: 10.0000 chunk 46 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 chunk 79 optimal weight: 8.9990 chunk 63 optimal weight: 5.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 381 HIS ** A 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 497 ASN A 572 HIS ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.135381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.109049 restraints weight = 17266.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.112257 restraints weight = 9951.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.114330 restraints weight = 6865.219| |-----------------------------------------------------------------------------| r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.4024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 8794 Z= 0.301 Angle : 0.734 9.805 11938 Z= 0.383 Chirality : 0.047 0.205 1350 Planarity : 0.004 0.058 1517 Dihedral : 5.224 55.947 1173 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 3.79 % Allowed : 24.40 % Favored : 71.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.25), residues: 1060 helix: 0.32 (0.23), residues: 509 sheet: -0.75 (0.55), residues: 84 loop : -1.85 (0.26), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 154 HIS 0.004 0.001 HIS A 810 PHE 0.017 0.002 PHE A 287 TYR 0.024 0.002 TYR A 453 ARG 0.009 0.001 ARG A 726 *********************** 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 221 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 185 time to evaluate : 0.921 Fit side-chains revert: symmetry clash REVERT: A 35 PHE cc_start: 0.7350 (m-80) cc_final: 0.6868 (m-80) REVERT: A 163 TYR cc_start: 0.8868 (p90) cc_final: 0.8666 (p90) REVERT: A 217 TYR cc_start: 0.5857 (p90) cc_final: 0.5255 (p90) REVERT: A 456 TYR cc_start: 0.8506 (OUTLIER) cc_final: 0.7059 (t80) REVERT: A 575 LEU cc_start: 0.7937 (OUTLIER) cc_final: 0.7714 (tt) REVERT: A 822 GLN cc_start: 0.7924 (tm-30) cc_final: 0.7094 (tm-30) REVERT: A 889 ARG cc_start: 0.8005 (mtt90) cc_final: 0.7372 (mtt-85) REVERT: B 94 MET cc_start: 0.6888 (ptm) cc_final: 0.6290 (ptm) REVERT: B 97 LYS cc_start: 0.8335 (tmtt) cc_final: 0.7822 (tttm) REVERT: C 31 GLN cc_start: 0.7648 (mt0) cc_final: 0.7388 (mt0) outliers start: 36 outliers final: 26 residues processed: 210 average time/residue: 0.2221 time to fit residues: 63.7347 Evaluate side-chains 205 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 177 time to evaluate : 0.941 ------------------------------------------------------------------------------- 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 174 VAL Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 456 TYR Chi-restraints excluded: chain A residue 468 GLN Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 609 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 829 LEU Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 165 LYS 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 9 optimal weight: 9.9990 chunk 21 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 23 optimal weight: 0.9990 chunk 102 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 45 optimal weight: 5.9990 chunk 20 optimal weight: 0.9980 chunk 54 optimal weight: 0.0570 chunk 61 optimal weight: 10.0000 overall best weight: 0.7500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 572 HIS A 781 ASN B 158 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 = 0.4038 r_free = 0.4038 target = 0.140470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.114730 restraints weight = 17106.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.118097 restraints weight = 9591.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.120285 restraints weight = 6483.952| |-----------------------------------------------------------------------------| r_work (final): 0.3764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.4238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8794 Z= 0.198 Angle : 0.699 10.098 11938 Z= 0.357 Chirality : 0.046 0.242 1350 Planarity : 0.004 0.056 1517 Dihedral : 5.118 59.596 1173 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 3.26 % Allowed : 25.03 % Favored : 71.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.25), residues: 1060 helix: 0.47 (0.23), residues: 505 sheet: -0.82 (0.51), residues: 94 loop : -1.68 (0.27), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 154 HIS 0.006 0.001 HIS A 256 PHE 0.016 0.001 PHE A 287 TYR 0.021 0.001 TYR A 453 ARG 0.007 0.001 ARG A 836 ********************** 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 214 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 183 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 PHE cc_start: 0.7340 (m-80) cc_final: 0.6825 (m-80) REVERT: A 217 TYR cc_start: 0.5726 (p90) cc_final: 0.5166 (p90) REVERT: A 258 ASP cc_start: 0.7511 (m-30) cc_final: 0.7137 (p0) REVERT: A 456 TYR cc_start: 0.8322 (OUTLIER) cc_final: 0.7273 (t80) REVERT: A 805 LEU cc_start: 0.7896 (tt) cc_final: 0.7320 (pt) REVERT: A 822 GLN cc_start: 0.7938 (tm-30) cc_final: 0.7126 (tm-30) REVERT: A 889 ARG cc_start: 0.7896 (mtt90) cc_final: 0.7265 (mtt-85) REVERT: B 94 MET cc_start: 0.6785 (ptm) cc_final: 0.6323 (ptm) REVERT: B 97 LYS cc_start: 0.8227 (tmtt) cc_final: 0.7807 (tttm) REVERT: C 62 MET cc_start: 0.6856 (ttp) cc_final: 0.6606 (tmm) outliers start: 31 outliers final: 24 residues processed: 203 average time/residue: 0.2130 time to fit residues: 58.8747 Evaluate side-chains 202 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 177 time to evaluate : 0.949 ------------------------------------------------------------------------------- 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 174 VAL Chi-restraints excluded: chain A residue 226 THR 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 456 TYR Chi-restraints excluded: chain A residue 468 GLN Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 648 LEU 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 829 LEU Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 165 LYS 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 95 optimal weight: 9.9990 chunk 2 optimal weight: 6.9990 chunk 74 optimal weight: 9.9990 chunk 20 optimal weight: 4.9990 chunk 73 optimal weight: 0.8980 chunk 75 optimal weight: 4.9990 chunk 101 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 67 optimal weight: 0.0370 chunk 102 optimal weight: 8.9990 overall best weight: 1.5862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 497 ASN A 703 ASN 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 = 0.4009 r_free = 0.4009 target = 0.138170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.112232 restraints weight = 17079.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.115503 restraints weight = 9641.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.117688 restraints weight = 6571.454| |-----------------------------------------------------------------------------| r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.4283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8794 Z= 0.246 Angle : 0.736 9.817 11938 Z= 0.377 Chirality : 0.047 0.295 1350 Planarity : 0.004 0.058 1517 Dihedral : 5.217 59.771 1173 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.05 % Allowed : 25.55 % Favored : 71.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.25), residues: 1060 helix: 0.45 (0.23), residues: 507 sheet: -0.84 (0.53), residues: 94 loop : -1.73 (0.26), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 154 HIS 0.005 0.001 HIS A 381 PHE 0.030 0.002 PHE D 92 TYR 0.025 0.001 TYR A 453 ARG 0.008 0.001 ARG A 836 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2771.29 seconds wall clock time: 50 minutes 26.23 seconds (3026.23 seconds total)