Starting phenix.real_space_refine on Fri Mar 14 00:56:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gs8_34225/03_2025/8gs8_34225_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gs8_34225/03_2025/8gs8_34225.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gs8_34225/03_2025/8gs8_34225.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gs8_34225/03_2025/8gs8_34225.map" model { file = "/net/cci-nas-00/data/ceres_data/8gs8_34225/03_2025/8gs8_34225_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gs8_34225/03_2025/8gs8_34225_neut.cif" } resolution = 2.86 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= 0.029 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Fe 10 7.16 5 P 3 5.49 5 S 79 5.16 5 C 5466 2.51 5 N 1487 2.21 5 O 1592 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 87 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8637 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4727 Classifications: {'peptide': 614} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 588} Chain: "B" Number of atoms: 1920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1920 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 13, 'TRANS': 225} Chain: "C" Number of atoms: 1051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1051 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "D" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 757 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 98} Chain: "A" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'FAD': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 19 Unusual residues: {'F3S': 1, 'FES': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'UQ1': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 92 Unusual residues: {'HEM': 1, 'PEV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5204 SG CYS B 93 43.801 37.764 58.973 1.00 41.50 S ATOM 5242 SG CYS B 98 41.315 39.982 59.756 1.00 30.16 S ATOM 5258 SG CYS B 101 41.268 34.324 63.367 1.00 33.48 S ATOM 5337 SG CYS B 113 44.271 34.217 61.940 1.00 41.16 S ATOM 5991 SG CYS B 192 42.604 43.447 74.670 1.00 26.07 S ATOM 6498 SG CYS B 253 48.028 41.334 72.212 1.00 30.41 S ATOM 5952 SG CYS B 186 44.521 46.574 69.839 1.00 31.46 S ATOM 5974 SG CYS B 189 42.699 40.372 69.142 1.00 27.29 S ATOM 6420 SG CYS B 243 43.785 46.963 84.788 1.00 31.02 S ATOM 6016 SG CYS B 196 39.596 43.285 82.490 1.00 31.55 S ATOM 6467 SG CYS B 249 45.470 43.095 80.345 1.00 32.57 S Time building chain proxies: 6.24, per 1000 atoms: 0.72 Number of scatterers: 8637 At special positions: 0 Unit cell: (80.3, 83.22, 138.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 10 26.01 S 79 16.00 P 3 15.00 O 1592 8.00 N 1487 7.00 C 5466 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.65 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" F3S B 303 " pdb="FE4 F3S B 303 " - pdb=" SG CYS B 249 " pdb="FE3 F3S B 303 " - pdb=" SG CYS B 196 " pdb="FE1 F3S B 303 " - pdb=" SG CYS B 243 " pdb=" FES B 301 " pdb="FE2 FES B 301 " - pdb=" SG CYS B 101 " pdb="FE1 FES B 301 " - pdb=" SG CYS B 93 " pdb="FE2 FES B 301 " - pdb=" SG CYS B 113 " pdb="FE1 FES B 301 " - pdb=" SG CYS B 98 " pdb=" SF4 B 302 " pdb="FE1 SF4 B 302 " - pdb=" SG CYS B 192 " pdb="FE4 SF4 B 302 " - pdb=" SG CYS B 189 " pdb="FE3 SF4 B 302 " - pdb=" SG CYS B 186 " pdb="FE2 SF4 B 302 " - pdb=" SG CYS B 253 " Number of angles added : 27 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1988 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 11 sheets defined 48.3% alpha, 9.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'A' and resid 51 through 55 removed outlier: 3.611A pdb=" N GLN A 54 " --> pdb=" O ILE A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 84 Processing helix chain 'A' and resid 94 through 102 removed outlier: 6.574A pdb=" N HIS A 99 " --> pdb=" O THR A 96 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N THR A 100 " --> pdb=" O ARG A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 131 removed outlier: 3.651A pdb=" N HIS A 122 " --> pdb=" O ASN A 118 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASP A 131 " --> pdb=" O VAL A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 155 Proline residue: A 147 - end of helix Processing helix chain 'A' and resid 195 through 209 Processing helix chain 'A' and resid 259 through 263 Processing helix chain 'A' and resid 274 through 282 Processing helix chain 'A' and resid 308 through 315 removed outlier: 4.145A pdb=" N ARG A 312 " --> pdb=" O THR A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 331 removed outlier: 3.602A pdb=" N TYR A 330 " --> pdb=" O PHE A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 352 removed outlier: 3.648A pdb=" N ILE A 351 " --> pdb=" O MET A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 379 Processing helix chain 'A' and resid 380 through 390 removed outlier: 3.702A pdb=" N SER A 384 " --> pdb=" O LEU A 380 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU A 385 " --> pdb=" O PRO A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 475 removed outlier: 3.809A pdb=" N LEU A 458 " --> pdb=" O ALA A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 501 removed outlier: 3.543A pdb=" N VAL A 493 " --> pdb=" O GLY A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 523 Processing helix chain 'A' and resid 528 through 545 removed outlier: 4.267A pdb=" N GLU A 534 " --> pdb=" O SER A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 585 removed outlier: 3.664A pdb=" N LEU A 573 " --> pdb=" O GLN A 569 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN A 577 " --> pdb=" O LEU A 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 83 removed outlier: 3.718A pdb=" N ALA B 75 " --> pdb=" O MET B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 153 Processing helix chain 'B' and resid 173 through 178 Processing helix chain 'B' and resid 179 through 181 No H-bonds generated for 'chain 'B' and resid 179 through 181' Processing helix chain 'B' and resid 192 through 195 Processing helix chain 'B' and resid 196 through 202 Processing helix chain 'B' and resid 207 through 220 removed outlier: 4.432A pdb=" N VAL B 211 " --> pdb=" O LEU B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 235 Processing helix chain 'B' and resid 247 through 253 removed outlier: 4.094A pdb=" N ARG B 251 " --> pdb=" O MET B 247 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N THR B 252 " --> pdb=" O ASN B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 272 Processing helix chain 'C' and resid 35 through 48 removed outlier: 3.848A pdb=" N GLY C 47 " --> pdb=" O ASN C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 92 removed outlier: 3.625A pdb=" N HIS C 71 " --> pdb=" O MET C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 106 removed outlier: 4.079A pdb=" N LEU C 106 " --> pdb=" O LEU C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 139 removed outlier: 3.591A pdb=" N ILE C 113 " --> pdb=" O GLY C 109 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N HIS C 114 " --> pdb=" O PRO C 110 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N PHE C 118 " --> pdb=" O HIS C 114 " (cutoff:3.500A) Proline residue: C 123 - end of helix Processing helix chain 'C' and resid 144 through 168 removed outlier: 3.754A pdb=" N TYR C 149 " --> pdb=" O ILE C 145 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLN C 150 " --> pdb=" O PRO C 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 80 Processing helix chain 'D' and resid 80 through 86 removed outlier: 3.625A pdb=" N TYR D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 115 Processing helix chain 'D' and resid 117 through 146 removed outlier: 3.610A pdb=" N ALA D 123 " --> pdb=" O ALA D 119 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ALA D 137 " --> pdb=" O ALA D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 157 removed outlier: 4.026A pdb=" N LYS D 151 " --> pdb=" O VAL D 147 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 57 through 61 removed outlier: 6.726A pdb=" N VAL A 58 " --> pdb=" O ARG A 246 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N ARG A 248 " --> pdb=" O VAL A 58 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N HIS A 60 " --> pdb=" O ARG A 248 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N CYS A 231 " --> pdb=" O MET A 226 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N MET A 226 " --> pdb=" O CYS A 231 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N GLY A 233 " --> pdb=" O LEU A 224 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N LEU A 224 " --> pdb=" O GLY A 233 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ILE A 235 " --> pdb=" O LEU A 222 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 87 through 90 removed outlier: 4.873A pdb=" N VAL A 421 " --> pdb=" O VAL A 432 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 107 through 108 Processing sheet with id=AA4, first strand: chain 'A' and resid 287 through 288 removed outlier: 3.684A pdb=" N LYS A 636 " --> pdb=" O ASP A 631 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 293 through 294 Processing sheet with id=AA6, first strand: chain 'A' and resid 299 through 300 Processing sheet with id=AA7, first strand: chain 'A' and resid 413 through 414 removed outlier: 5.851A pdb=" N ILE A 413 " --> pdb=" O CYS A 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 506 through 507 removed outlier: 6.328A pdb=" N ILE A 506 " --> pdb=" O LYS A 550 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 526 through 527 Processing sheet with id=AB1, first strand: chain 'B' and resid 57 through 64 removed outlier: 3.620A pdb=" N MET B 103 " --> pdb=" O THR B 110 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 135 through 137 removed outlier: 6.762A pdb=" N VAL B 140 " --> pdb=" O ILE B 136 " (cutoff:3.500A) 405 hydrogen bonds defined for protein. 1155 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: 2.63 Time building geometry restraints manager: 3.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.77: 8721 1.77 - 2.33: 119 2.33 - 2.90: 0 2.90 - 3.46: 0 3.46 - 4.03: 3 Bond restraints: 8843 Sorted by residual: bond pdb=" S1 F3S B 303 " pdb="FE4 F3S B 303 " ideal model delta sigma weight residual 2.258 4.027 -1.769 2.00e-02 2.50e+03 7.82e+03 bond pdb=" S4 F3S B 303 " pdb="FE1 F3S B 303 " ideal model delta sigma weight residual 2.233 3.770 -1.537 2.00e-02 2.50e+03 5.91e+03 bond pdb=" S2 F3S B 303 " pdb="FE3 F3S B 303 " ideal model delta sigma weight residual 2.300 3.834 -1.534 2.00e-02 2.50e+03 5.89e+03 bond pdb=" C HIS A 99 " pdb=" N THR A 100 " ideal model delta sigma weight residual 1.335 1.230 0.104 1.25e-02 6.40e+03 6.97e+01 bond pdb=" C LEU D 101 " pdb=" N HIS D 102 " ideal model delta sigma weight residual 1.334 1.411 -0.077 1.27e-02 6.20e+03 3.66e+01 ... (remaining 8838 not shown) Histogram of bond angle deviations from ideal: 0.00 - 10.63: 11962 10.63 - 21.26: 22 21.26 - 31.89: 4 31.89 - 42.52: 4 42.52 - 53.15: 2 Bond angle restraints: 11994 Sorted by residual: angle pdb=" S1 F3S B 303 " pdb="FE4 F3S B 303 " pdb=" S3 F3S B 303 " ideal model delta sigma weight residual 114.75 61.60 53.15 3.00e+00 1.11e-01 3.14e+02 angle pdb=" S3 F3S B 303 " pdb="FE1 F3S B 303 " pdb=" S4 F3S B 303 " ideal model delta sigma weight residual 112.59 66.77 45.82 3.00e+00 1.11e-01 2.33e+02 angle pdb=" S2 F3S B 303 " pdb="FE3 F3S B 303 " pdb=" S4 F3S B 303 " ideal model delta sigma weight residual 103.26 65.93 37.33 3.00e+00 1.11e-01 1.55e+02 angle pdb=" S1 F3S B 303 " pdb="FE4 F3S B 303 " pdb=" S2 F3S B 303 " ideal model delta sigma weight residual 103.63 67.39 36.24 3.00e+00 1.11e-01 1.46e+02 angle pdb=" S2 F3S B 303 " pdb="FE1 F3S B 303 " pdb=" S4 F3S B 303 " ideal model delta sigma weight residual 102.84 67.25 35.59 3.00e+00 1.11e-01 1.41e+02 ... (remaining 11989 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.00: 5025 28.00 - 56.00: 207 56.00 - 83.99: 31 83.99 - 111.99: 3 111.99 - 139.99: 1 Dihedral angle restraints: 5267 sinusoidal: 2145 harmonic: 3122 Sorted by residual: dihedral pdb=" C2C HEM D 201 " pdb=" C3C HEM D 201 " pdb=" CAC HEM D 201 " pdb=" CBC HEM D 201 " ideal model delta sinusoidal sigma weight residual 180.00 111.96 68.04 2 1.00e+01 1.00e-02 4.13e+01 dihedral pdb=" C3 PEV D 202 " pdb=" C1 PEV D 202 " pdb=" C2 PEV D 202 " pdb=" O3P PEV D 202 " ideal model delta sinusoidal sigma weight residual 292.80 152.81 139.99 1 3.00e+01 1.11e-03 1.88e+01 dihedral pdb=" CA PHE A 463 " pdb=" C PHE A 463 " pdb=" N GLY A 464 " pdb=" CA GLY A 464 " ideal model delta harmonic sigma weight residual 180.00 159.14 20.86 0 5.00e+00 4.00e-02 1.74e+01 ... (remaining 5264 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 3.694: 1295 3.694 - 7.387: 0 7.387 - 11.080: 0 11.080 - 14.774: 0 14.774 - 18.467: 1 Chirality restraints: 1296 Sorted by residual: chirality pdb=" S2 F3S B 303 " pdb="FE1 F3S B 303 " pdb="FE3 F3S B 303 " pdb="FE4 F3S B 303 " both_signs ideal model delta sigma weight residual False 10.77 -7.70 18.47 2.00e-01 2.50e+01 8.53e+03 chirality pdb="FE1 SF4 B 302 " pdb=" S2 SF4 B 302 " pdb=" S3 SF4 B 302 " pdb=" S4 SF4 B 302 " both_signs ideal model delta sigma weight residual False -10.55 -9.50 -1.06 2.00e-01 2.50e+01 2.80e+01 chirality pdb="FE3 SF4 B 302 " pdb=" S1 SF4 B 302 " pdb=" S2 SF4 B 302 " pdb=" S4 SF4 B 302 " both_signs ideal model delta sigma weight residual False -10.55 -9.56 -1.00 2.00e-01 2.50e+01 2.49e+01 ... (remaining 1293 not shown) Planarity restraints: 1518 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 UQ1 C 201 " -0.036 2.00e-02 2.50e+03 5.08e-02 7.75e+01 pdb=" C2 UQ1 C 201 " -0.019 2.00e-02 2.50e+03 pdb=" C3 UQ1 C 201 " 0.030 2.00e-02 2.50e+03 pdb=" C4 UQ1 C 201 " -0.044 2.00e-02 2.50e+03 pdb=" C5 UQ1 C 201 " -0.013 2.00e-02 2.50e+03 pdb=" C6 UQ1 C 201 " 0.014 2.00e-02 2.50e+03 pdb=" C7 UQ1 C 201 " 0.079 2.00e-02 2.50e+03 pdb=" CM5 UQ1 C 201 " -0.002 2.00e-02 2.50e+03 pdb=" O1 UQ1 C 201 " -0.027 2.00e-02 2.50e+03 pdb=" O2 UQ1 C 201 " -0.035 2.00e-02 2.50e+03 pdb=" O3 UQ1 C 201 " 0.117 2.00e-02 2.50e+03 pdb=" O4 UQ1 C 201 " -0.065 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CBA HEM D 201 " 0.036 2.00e-02 2.50e+03 7.81e-02 6.11e+01 pdb=" CGA HEM D 201 " -0.135 2.00e-02 2.50e+03 pdb=" O1A HEM D 201 " 0.050 2.00e-02 2.50e+03 pdb=" O2A HEM D 201 " 0.049 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CBD HEM D 201 " 0.029 2.00e-02 2.50e+03 5.87e-02 3.45e+01 pdb=" CGD HEM D 201 " -0.102 2.00e-02 2.50e+03 pdb=" O1D HEM D 201 " 0.036 2.00e-02 2.50e+03 pdb=" O2D HEM D 201 " 0.036 2.00e-02 2.50e+03 ... (remaining 1515 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 502 2.71 - 3.26: 8776 3.26 - 3.81: 14674 3.81 - 4.35: 20028 4.35 - 4.90: 32613 Nonbonded interactions: 76593 Sorted by model distance: nonbonded pdb=" O GLN A 104 " pdb=" O4 FAD A 701 " model vdw 2.168 3.040 nonbonded pdb=" NE2 HIS C 127 " pdb="FE HEM D 201 " model vdw 2.224 3.080 nonbonded pdb=" S3 F3S B 303 " pdb="FE3 F3S B 303 " model vdw 2.256 2.688 nonbonded pdb=" S1 F3S B 303 " pdb="FE1 F3S B 303 " model vdw 2.256 2.688 nonbonded pdb=" S4 F3S B 303 " pdb="FE4 F3S B 303 " model vdw 2.265 2.688 ... (remaining 76588 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.360 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: 0.420 Check model and map are aligned: 0.060 Set scattering table: 0.100 Process input model: 27.320 Find NCS groups from input model: 0.080 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:14.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 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 : 0.032 1.769 8843 Z= 2.258 Angle : 1.670 53.152 11994 Z= 0.853 Chirality : 0.520 18.467 1296 Planarity : 0.013 0.135 1518 Dihedral : 14.956 139.988 3279 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.86 % Favored : 92.05 % Rotamer: Outliers : 0.67 % Allowed : 1.11 % Favored : 98.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.22 (0.21), residues: 1082 helix: -3.21 (0.17), residues: 487 sheet: -2.15 (0.46), residues: 97 loop : -2.35 (0.25), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.004 TRP C 129 HIS 0.023 0.003 HIS A 296 PHE 0.029 0.004 PHE A 526 TYR 0.030 0.003 TYR C 59 ARG 0.092 0.013 ARG A 246 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 114 time to evaluate : 0.944 Fit side-chains revert: symmetry clash REVERT: A 497 ASP cc_start: 0.8198 (t70) cc_final: 0.7772 (t70) REVERT: A 619 GLU cc_start: 0.7955 (mp0) cc_final: 0.7545 (tp30) REVERT: B 91 ARG cc_start: 0.8388 (OUTLIER) cc_final: 0.8083 (ptt-90) REVERT: B 123 LYS cc_start: 0.7462 (mtpp) cc_final: 0.7212 (mttp) outliers start: 6 outliers final: 2 residues processed: 118 average time/residue: 1.3023 time to fit residues: 164.1535 Evaluate side-chains 95 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 92 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 91 ARG Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 65 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 83 optimal weight: 0.7980 chunk 32 optimal weight: 3.9990 chunk 50 optimal weight: 0.0870 chunk 62 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 overall best weight: 0.7562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 ASN A 155 ASN A 185 GLN A 650 ASN B 66 ASN B 81 ASN ** B 132 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 = 0.3679 r_free = 0.3679 target = 0.155461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.110639 restraints weight = 9045.455| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 1.84 r_work: 0.2965 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.1272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.174 8843 Z= 0.301 Angle : 1.213 74.642 11994 Z= 0.469 Chirality : 0.045 0.573 1296 Planarity : 0.005 0.062 1518 Dihedral : 9.525 131.569 1310 Min Nonbonded Distance : 1.498 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.68 % Favored : 97.23 % Rotamer: Outliers : 1.44 % Allowed : 6.33 % Favored : 92.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.24), residues: 1082 helix: -0.29 (0.22), residues: 487 sheet: -1.43 (0.47), residues: 96 loop : -1.41 (0.27), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 132 HIS 0.011 0.002 HIS C 55 PHE 0.016 0.002 PHE A 463 TYR 0.014 0.001 TYR B 45 ARG 0.007 0.001 ARG C 133 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 97 time to evaluate : 1.004 Fit side-chains REVERT: A 104 GLN cc_start: 0.8374 (mt0) cc_final: 0.7155 (mp10) REVERT: A 164 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.8082 (mm-30) REVERT: A 497 ASP cc_start: 0.8361 (t70) cc_final: 0.7846 (t70) REVERT: A 619 GLU cc_start: 0.8209 (mp0) cc_final: 0.7563 (tp30) REVERT: B 123 LYS cc_start: 0.7611 (mtpp) cc_final: 0.7319 (mttp) outliers start: 13 outliers final: 4 residues processed: 102 average time/residue: 1.2572 time to fit residues: 137.5500 Evaluate side-chains 92 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 87 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 173 PHE Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 204 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 6 optimal weight: 5.9990 chunk 35 optimal weight: 6.9990 chunk 86 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 55 optimal weight: 6.9990 chunk 14 optimal weight: 0.7980 chunk 81 optimal weight: 0.7980 chunk 104 optimal weight: 3.9990 chunk 68 optimal weight: 0.8980 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 GLN A 155 ASN A 185 GLN ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 650 ASN B 81 ASN ** B 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.153574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.108931 restraints weight = 9185.907| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 1.83 r_work: 0.2870 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2728 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.165 8843 Z= 0.430 Angle : 1.266 78.312 11994 Z= 0.490 Chirality : 0.048 0.505 1296 Planarity : 0.005 0.058 1518 Dihedral : 9.126 130.650 1301 Min Nonbonded Distance : 1.536 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.00 % Allowed : 8.67 % Favored : 89.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.26), residues: 1082 helix: 0.70 (0.23), residues: 503 sheet: -1.12 (0.48), residues: 96 loop : -1.00 (0.29), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 558 HIS 0.006 0.002 HIS C 55 PHE 0.020 0.002 PHE B 146 TYR 0.015 0.002 TYR B 45 ARG 0.009 0.001 ARG B 217 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 97 time to evaluate : 0.895 Fit side-chains REVERT: A 619 GLU cc_start: 0.8220 (mp0) cc_final: 0.7484 (tp30) REVERT: B 85 SER cc_start: 0.9147 (t) cc_final: 0.8757 (t) REVERT: B 123 LYS cc_start: 0.7749 (mtpp) cc_final: 0.7339 (mttp) REVERT: B 133 MET cc_start: 0.8667 (mtp) cc_final: 0.8447 (mmt) outliers start: 18 outliers final: 11 residues processed: 104 average time/residue: 1.1768 time to fit residues: 131.4929 Evaluate side-chains 101 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 90 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 173 PHE Chi-restraints excluded: chain A residue 228 ASN Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 515 MET Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain D residue 159 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 8 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 chunk 82 optimal weight: 0.5980 chunk 99 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 chunk 93 optimal weight: 0.9990 chunk 52 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 chunk 87 optimal weight: 0.9990 chunk 30 optimal weight: 10.0000 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 HIS A 155 ASN A 185 GLN ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 650 ASN B 81 ASN ** B 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.153042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.107510 restraints weight = 9244.890| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 1.83 r_work: 0.2926 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2784 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.169 8843 Z= 0.285 Angle : 1.203 76.719 11994 Z= 0.452 Chirality : 0.045 0.662 1296 Planarity : 0.004 0.058 1518 Dihedral : 8.746 129.908 1301 Min Nonbonded Distance : 1.545 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.03 % Favored : 97.87 % Rotamer: Outliers : 2.22 % Allowed : 10.56 % Favored : 87.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.26), residues: 1082 helix: 1.34 (0.24), residues: 504 sheet: -0.80 (0.49), residues: 96 loop : -0.87 (0.30), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 132 HIS 0.009 0.001 HIS C 55 PHE 0.016 0.001 PHE A 463 TYR 0.014 0.001 TYR B 45 ARG 0.005 0.000 ARG A 120 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 93 time to evaluate : 1.008 Fit side-chains REVERT: A 164 GLU cc_start: 0.8673 (OUTLIER) cc_final: 0.8136 (mm-30) REVERT: A 388 MET cc_start: 0.6210 (tpt) cc_final: 0.5854 (mmp) REVERT: A 619 GLU cc_start: 0.8236 (mp0) cc_final: 0.7472 (tp30) REVERT: B 85 SER cc_start: 0.9194 (t) cc_final: 0.8802 (t) REVERT: B 123 LYS cc_start: 0.7815 (mtpp) cc_final: 0.7398 (mttt) REVERT: C 92 LEU cc_start: 0.6985 (tp) cc_final: 0.6686 (tp) REVERT: C 164 MET cc_start: 0.6766 (mtp) cc_final: 0.5596 (ptt) outliers start: 20 outliers final: 8 residues processed: 102 average time/residue: 1.1822 time to fit residues: 129.2309 Evaluate side-chains 96 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 87 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 173 PHE Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain D residue 159 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 32 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 95 optimal weight: 0.5980 chunk 54 optimal weight: 10.0000 chunk 83 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 chunk 99 optimal weight: 0.3980 chunk 71 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 chunk 84 optimal weight: 0.0670 chunk 57 optimal weight: 3.9990 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 ASN A 185 GLN A 202 HIS ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 650 ASN ** B 132 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 = 0.3731 r_free = 0.3731 target = 0.160130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.116863 restraints weight = 9096.371| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 1.79 r_work: 0.2972 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2830 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.176 8843 Z= 0.300 Angle : 1.092 63.395 11994 Z= 0.412 Chirality : 0.061 1.640 1296 Planarity : 0.004 0.051 1518 Dihedral : 8.344 133.249 1301 Min Nonbonded Distance : 1.539 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.67 % Allowed : 12.11 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.27), residues: 1082 helix: 1.73 (0.24), residues: 503 sheet: -0.47 (0.50), residues: 94 loop : -0.84 (0.30), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 132 HIS 0.005 0.001 HIS C 55 PHE 0.018 0.001 PHE A 463 TYR 0.012 0.001 TYR B 45 ARG 0.009 0.000 ARG A 120 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 99 time to evaluate : 0.883 Fit side-chains REVERT: A 104 GLN cc_start: 0.8007 (mt0) cc_final: 0.6743 (mp10) REVERT: A 347 MET cc_start: 0.6255 (mtp) cc_final: 0.5927 (ttm) REVERT: A 564 GLU cc_start: 0.7941 (mt-10) cc_final: 0.7409 (mm-30) REVERT: A 619 GLU cc_start: 0.8233 (mp0) cc_final: 0.7474 (tp30) REVERT: B 85 SER cc_start: 0.9219 (t) cc_final: 0.8872 (t) REVERT: B 123 LYS cc_start: 0.7753 (mtpp) cc_final: 0.7411 (mttm) REVERT: B 165 GLU cc_start: 0.7151 (OUTLIER) cc_final: 0.6722 (tp30) REVERT: C 92 LEU cc_start: 0.6977 (tp) cc_final: 0.6732 (tp) REVERT: C 164 MET cc_start: 0.6823 (mtp) cc_final: 0.5619 (ptt) outliers start: 15 outliers final: 6 residues processed: 109 average time/residue: 1.3420 time to fit residues: 156.7938 Evaluate side-chains 100 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 93 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 PHE Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 228 ASN Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain C residue 121 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 46 optimal weight: 3.9990 chunk 33 optimal weight: 8.9990 chunk 17 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 89 optimal weight: 7.9990 chunk 20 optimal weight: 0.8980 chunk 58 optimal weight: 5.9990 chunk 67 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 ASN A 185 GLN A 202 HIS ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 650 ASN ** B 132 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 = 0.3726 r_free = 0.3726 target = 0.159248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.116018 restraints weight = 8947.899| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 1.79 r_work: 0.2950 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.104 8843 Z= 0.273 Angle : 1.033 84.369 11994 Z= 0.401 Chirality : 0.058 1.427 1296 Planarity : 0.004 0.054 1518 Dihedral : 8.292 135.244 1301 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.00 % Allowed : 12.22 % Favored : 85.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.27), residues: 1082 helix: 1.74 (0.24), residues: 502 sheet: -0.30 (0.51), residues: 94 loop : -0.83 (0.29), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 66 HIS 0.006 0.001 HIS C 55 PHE 0.016 0.001 PHE A 463 TYR 0.020 0.001 TYR A 124 ARG 0.007 0.000 ARG A 120 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 93 time to evaluate : 0.814 Fit side-chains REVERT: A 347 MET cc_start: 0.6125 (mtp) cc_final: 0.5864 (ttm) REVERT: A 619 GLU cc_start: 0.8212 (mp0) cc_final: 0.7453 (tp30) REVERT: B 123 LYS cc_start: 0.7750 (mtpp) cc_final: 0.7473 (mttp) REVERT: B 165 GLU cc_start: 0.7132 (OUTLIER) cc_final: 0.6642 (tp30) REVERT: C 92 LEU cc_start: 0.6973 (tp) cc_final: 0.6746 (tp) REVERT: C 164 MET cc_start: 0.6858 (mtp) cc_final: 0.5645 (ptt) outliers start: 18 outliers final: 9 residues processed: 101 average time/residue: 1.1990 time to fit residues: 130.3542 Evaluate side-chains 97 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 87 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 PHE Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 173 PHE Chi-restraints excluded: chain A residue 228 ASN Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain C residue 121 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 22 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 100 optimal weight: 9.9990 chunk 24 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 102 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 50 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 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 155 ASN A 185 GLN ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 650 ASN ** B 132 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 = 0.3704 r_free = 0.3704 target = 0.157516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.113794 restraints weight = 9125.258| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 1.79 r_work: 0.2944 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.104 8843 Z= 0.252 Angle : 1.023 83.478 11994 Z= 0.396 Chirality : 0.059 1.484 1296 Planarity : 0.004 0.053 1518 Dihedral : 8.191 136.561 1301 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.67 % Allowed : 13.11 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.27), residues: 1082 helix: 1.83 (0.24), residues: 503 sheet: -0.21 (0.52), residues: 94 loop : -0.81 (0.30), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 132 HIS 0.009 0.001 HIS C 55 PHE 0.016 0.001 PHE A 463 TYR 0.014 0.001 TYR B 45 ARG 0.006 0.000 ARG A 120 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 0.872 Fit side-chains REVERT: A 347 MET cc_start: 0.6096 (mtp) cc_final: 0.5854 (ttm) REVERT: A 564 GLU cc_start: 0.8034 (mt-10) cc_final: 0.7448 (mm-30) REVERT: A 619 GLU cc_start: 0.8204 (mp0) cc_final: 0.7443 (tp30) REVERT: B 123 LYS cc_start: 0.7752 (mtpp) cc_final: 0.7461 (mttp) REVERT: B 165 GLU cc_start: 0.7121 (OUTLIER) cc_final: 0.6653 (tp30) REVERT: C 92 LEU cc_start: 0.6979 (tp) cc_final: 0.6778 (tp) REVERT: C 164 MET cc_start: 0.6827 (mtp) cc_final: 0.5626 (ptt) outliers start: 15 outliers final: 8 residues processed: 100 average time/residue: 1.1076 time to fit residues: 119.4663 Evaluate side-chains 99 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 90 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 ASN Chi-restraints excluded: chain A residue 173 PHE Chi-restraints excluded: chain A residue 228 ASN Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain C residue 121 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 2 optimal weight: 1.9990 chunk 28 optimal weight: 7.9990 chunk 78 optimal weight: 0.5980 chunk 84 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 4 optimal weight: 0.7980 chunk 12 optimal weight: 5.9990 chunk 24 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 ASN A 185 GLN ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 650 ASN ** B 132 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 = 0.3651 r_free = 0.3651 target = 0.153147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.107952 restraints weight = 9211.280| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 1.88 r_work: 0.2932 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2787 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.104 8843 Z= 0.271 Angle : 1.029 83.388 11994 Z= 0.399 Chirality : 0.059 1.493 1296 Planarity : 0.004 0.054 1518 Dihedral : 8.194 136.411 1301 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.56 % Allowed : 13.44 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.27), residues: 1082 helix: 1.82 (0.24), residues: 506 sheet: -0.13 (0.52), residues: 94 loop : -0.76 (0.30), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 132 HIS 0.009 0.001 HIS C 55 PHE 0.016 0.001 PHE B 146 TYR 0.014 0.001 TYR B 45 ARG 0.004 0.000 ARG B 217 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 88 time to evaluate : 1.009 Fit side-chains REVERT: A 347 MET cc_start: 0.6062 (mtp) cc_final: 0.5805 (ttm) REVERT: A 564 GLU cc_start: 0.8024 (mt-10) cc_final: 0.7425 (mm-30) REVERT: A 619 GLU cc_start: 0.8204 (mp0) cc_final: 0.7456 (tp30) REVERT: B 123 LYS cc_start: 0.7749 (mtpp) cc_final: 0.7494 (mtpp) REVERT: C 164 MET cc_start: 0.6860 (mtp) cc_final: 0.5634 (ptt) outliers start: 14 outliers final: 6 residues processed: 94 average time/residue: 1.1611 time to fit residues: 117.3371 Evaluate side-chains 92 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 86 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 PHE Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain C residue 121 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 84 optimal weight: 3.9990 chunk 54 optimal weight: 6.9990 chunk 86 optimal weight: 0.0570 chunk 102 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 chunk 88 optimal weight: 4.9990 chunk 60 optimal weight: 5.9990 chunk 41 optimal weight: 0.5980 chunk 94 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 overall best weight: 1.9304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 ASN A 185 GLN ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 548 HIS A 650 ASN ** B 132 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 = 0.3653 r_free = 0.3653 target = 0.152990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.108168 restraints weight = 9150.770| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 1.85 r_work: 0.2882 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2738 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.101 8843 Z= 0.424 Angle : 1.088 83.995 11994 Z= 0.433 Chirality : 0.062 1.502 1296 Planarity : 0.005 0.059 1518 Dihedral : 8.467 135.570 1301 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.33 % Allowed : 14.11 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.26), residues: 1082 helix: 1.52 (0.23), residues: 503 sheet: -0.35 (0.52), residues: 96 loop : -0.82 (0.30), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 558 HIS 0.012 0.002 HIS C 55 PHE 0.019 0.002 PHE B 146 TYR 0.017 0.002 TYR B 45 ARG 0.007 0.001 ARG B 217 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 90 time to evaluate : 0.988 Fit side-chains REVERT: A 347 MET cc_start: 0.6097 (mtp) cc_final: 0.5798 (ttm) REVERT: A 619 GLU cc_start: 0.8150 (mp0) cc_final: 0.7424 (tp30) REVERT: C 164 MET cc_start: 0.6841 (mtp) cc_final: 0.5632 (ptt) outliers start: 12 outliers final: 8 residues processed: 98 average time/residue: 1.0358 time to fit residues: 110.0061 Evaluate side-chains 95 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 87 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 PHE Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain D residue 159 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 0 optimal weight: 4.9990 chunk 62 optimal weight: 0.5980 chunk 58 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 59 optimal weight: 0.0010 chunk 105 optimal weight: 0.5980 chunk 42 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 96 optimal weight: 4.9990 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 ASN A 185 GLN A 202 HIS ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 650 ASN ** B 132 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 = 0.3669 r_free = 0.3669 target = 0.154697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.110452 restraints weight = 9048.460| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 1.79 r_work: 0.2950 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.105 8843 Z= 0.228 Angle : 1.019 83.012 11994 Z= 0.393 Chirality : 0.058 1.497 1296 Planarity : 0.004 0.054 1518 Dihedral : 8.119 135.261 1301 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.00 % Allowed : 14.67 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.27), residues: 1082 helix: 1.87 (0.24), residues: 504 sheet: -0.10 (0.51), residues: 94 loop : -0.75 (0.30), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 132 HIS 0.007 0.001 HIS C 55 PHE 0.017 0.001 PHE A 463 TYR 0.013 0.001 TYR B 45 ARG 0.005 0.000 ARG A 120 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 89 time to evaluate : 0.927 Fit side-chains REVERT: A 347 MET cc_start: 0.6054 (mtp) cc_final: 0.5814 (ttm) REVERT: A 388 MET cc_start: 0.6223 (tpt) cc_final: 0.5927 (mmp) REVERT: A 564 GLU cc_start: 0.7990 (mt-10) cc_final: 0.7368 (mm-30) REVERT: A 619 GLU cc_start: 0.8160 (mp0) cc_final: 0.7409 (tp30) REVERT: C 164 MET cc_start: 0.6857 (mtp) cc_final: 0.5646 (ptt) outliers start: 9 outliers final: 9 residues processed: 93 average time/residue: 1.4240 time to fit residues: 142.6584 Evaluate side-chains 96 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 87 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 PHE Chi-restraints excluded: chain A residue 155 ASN Chi-restraints excluded: chain A residue 173 PHE Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain C residue 121 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 49 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 chunk 99 optimal weight: 0.9990 chunk 46 optimal weight: 0.6980 chunk 62 optimal weight: 0.9980 chunk 28 optimal weight: 10.0000 chunk 60 optimal weight: 0.0170 chunk 61 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 overall best weight: 0.7420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 185 GLN A 202 HIS ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 650 ASN ** B 132 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 = 0.3667 r_free = 0.3667 target = 0.154579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.110237 restraints weight = 9060.966| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 1.79 r_work: 0.3015 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.104 8843 Z= 0.246 Angle : 1.024 82.971 11994 Z= 0.397 Chirality : 0.059 1.503 1296 Planarity : 0.004 0.054 1518 Dihedral : 8.113 134.967 1301 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.78 % Allowed : 14.89 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.27), residues: 1082 helix: 1.89 (0.24), residues: 504 sheet: -0.07 (0.51), residues: 94 loop : -0.74 (0.30), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 132 HIS 0.007 0.001 HIS C 55 PHE 0.017 0.001 PHE A 463 TYR 0.013 0.001 TYR B 45 ARG 0.004 0.000 ARG A 120 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6520.02 seconds wall clock time: 115 minutes 20.33 seconds (6920.33 seconds total)