Starting phenix.real_space_refine on Wed Sep 25 03:30:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gs8_34225/09_2024/8gs8_34225_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gs8_34225/09_2024/8gs8_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gs8_34225/09_2024/8gs8_34225.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gs8_34225/09_2024/8gs8_34225.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gs8_34225/09_2024/8gs8_34225_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gs8_34225/09_2024/8gs8_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-5461/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: 6.32, per 1000 atoms: 0.73 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: 2.53 Conformation dependent library (CDL) restraints added in 1.0 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: 0.89 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: 2.46 Time building geometry restraints manager: 2.89 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: 2.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 25.510 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.250 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 6 poor density : 114 time to evaluate : 0.919 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: 1.2212 time to fit residues: 154.0772 Evaluate side-chains 95 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 92 time to evaluate : 0.930 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 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 fitting. rotamer outliers: 13 poor density : 97 time to evaluate : 0.967 Fit side-chains REVERT: A 104 GLN cc_start: 0.7828 (mt0) cc_final: 0.6874 (mp10) REVERT: A 164 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7407 (mm-30) REVERT: A 497 ASP cc_start: 0.8134 (t70) cc_final: 0.7605 (t70) REVERT: A 619 GLU cc_start: 0.7986 (mp0) cc_final: 0.7564 (tp30) outliers start: 13 outliers final: 4 residues processed: 102 average time/residue: 1.1968 time to fit residues: 130.8904 Evaluate side-chains 92 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 87 time to evaluate : 0.944 ------------------------------------------------------------------------------- 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 54 optimal weight: 7.9990 chunk 30 optimal weight: 10.0000 chunk 80 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 97 optimal weight: 3.9990 chunk 105 optimal weight: 4.9990 chunk 86 optimal weight: 4.9990 chunk 96 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 78 optimal weight: 0.6980 overall best weight: 2.7186 ------------------------------------------------------------------------------- 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 548 HIS A 650 ASN B 81 ASN B 120 ASN ** B 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.162 8843 Z= 0.577 Angle : 1.308 78.295 11994 Z= 0.515 Chirality : 0.052 0.526 1296 Planarity : 0.006 0.061 1518 Dihedral : 9.242 129.981 1301 Min Nonbonded Distance : 1.537 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.33 % Allowed : 8.67 % Favored : 89.00 % 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: -0.56 (0.25), residues: 1082 helix: 0.46 (0.23), residues: 505 sheet: -1.12 (0.48), residues: 96 loop : -1.05 (0.29), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP A 558 HIS 0.007 0.002 HIS A 407 PHE 0.020 0.002 PHE B 146 TYR 0.017 0.002 TYR C 59 ARG 0.011 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 113 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 92 time to evaluate : 0.942 Fit side-chains REVERT: A 619 GLU cc_start: 0.7984 (mp0) cc_final: 0.7523 (tp30) REVERT: B 85 SER cc_start: 0.9165 (t) cc_final: 0.8812 (t) REVERT: B 133 MET cc_start: 0.8264 (OUTLIER) cc_final: 0.8030 (mmt) REVERT: B 165 GLU cc_start: 0.7144 (OUTLIER) cc_final: 0.6537 (tp30) outliers start: 21 outliers final: 11 residues processed: 103 average time/residue: 1.1411 time to fit residues: 126.3543 Evaluate side-chains 98 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 85 time to evaluate : 0.837 ------------------------------------------------------------------------------- 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 511 LEU Chi-restraints excluded: chain A residue 515 MET Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain A residue 628 SER Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 133 MET Chi-restraints excluded: chain B residue 165 GLU 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 96 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 97 optimal weight: 0.6980 chunk 103 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 92 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 81 ASN ** B 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.172 8843 Z= 0.294 Angle : 1.180 74.356 11994 Z= 0.445 Chirality : 0.048 0.865 1296 Planarity : 0.004 0.056 1518 Dihedral : 8.791 127.634 1301 Min Nonbonded Distance : 1.540 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.94 % Favored : 97.97 % Rotamer: Outliers : 2.22 % Allowed : 10.33 % Favored : 87.44 % 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: 0.17 (0.26), residues: 1082 helix: 1.27 (0.24), residues: 504 sheet: -0.82 (0.49), residues: 96 loop : -0.91 (0.29), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 132 HIS 0.008 0.001 HIS C 55 PHE 0.017 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 111 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 91 time to evaluate : 0.962 Fit side-chains REVERT: A 164 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7448 (mm-30) REVERT: A 388 MET cc_start: 0.6750 (tpt) cc_final: 0.6314 (mmp) REVERT: A 619 GLU cc_start: 0.8014 (mp0) cc_final: 0.7486 (tp30) REVERT: B 85 SER cc_start: 0.9191 (t) cc_final: 0.8827 (t) REVERT: B 165 GLU cc_start: 0.7037 (OUTLIER) cc_final: 0.6576 (tp30) REVERT: C 92 LEU cc_start: 0.7110 (tp) cc_final: 0.6803 (tp) REVERT: C 164 MET cc_start: 0.6593 (mtp) cc_final: 0.5424 (ptt) outliers start: 20 outliers final: 9 residues processed: 100 average time/residue: 1.3408 time to fit residues: 143.4103 Evaluate side-chains 96 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 85 time to evaluate : 0.965 ------------------------------------------------------------------------------- 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 164 GLU 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 165 GLU Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain C residue 121 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 86 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 1 optimal weight: 0.9990 chunk 77 optimal weight: 0.6980 chunk 42 optimal weight: 5.9990 chunk 88 optimal weight: 4.9990 chunk 71 optimal weight: 0.0870 chunk 0 optimal weight: 5.9990 chunk 52 optimal weight: 0.9990 chunk 92 optimal weight: 4.9990 chunk 26 optimal weight: 10.0000 overall best weight: 1.3564 ------------------------------------------------------------------------------- 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 548 HIS A 650 ASN ** B 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.170 8843 Z= 0.384 Angle : 1.165 69.043 11994 Z= 0.446 Chirality : 0.055 1.221 1296 Planarity : 0.004 0.059 1518 Dihedral : 8.677 128.299 1301 Min Nonbonded Distance : 1.532 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.56 % Allowed : 11.78 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.26), residues: 1082 helix: 1.37 (0.24), residues: 506 sheet: -0.64 (0.51), residues: 96 loop : -0.84 (0.30), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 132 HIS 0.007 0.001 HIS C 55 PHE 0.018 0.002 PHE B 146 TYR 0.015 0.002 TYR B 45 ARG 0.006 0.001 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 106 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 92 time to evaluate : 0.869 Fit side-chains REVERT: A 164 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7461 (mm-30) REVERT: A 430 GLN cc_start: 0.7912 (tt0) cc_final: 0.7672 (tt0) REVERT: A 619 GLU cc_start: 0.8006 (mp0) cc_final: 0.7482 (tp30) REVERT: B 165 GLU cc_start: 0.7085 (OUTLIER) cc_final: 0.6580 (tp30) REVERT: C 55 HIS cc_start: 0.7530 (p90) cc_final: 0.7193 (p90) REVERT: C 92 LEU cc_start: 0.7110 (tp) cc_final: 0.6832 (tp) REVERT: C 164 MET cc_start: 0.6610 (mtp) cc_final: 0.5437 (ptt) outliers start: 14 outliers final: 11 residues processed: 102 average time/residue: 1.1180 time to fit residues: 122.6697 Evaluate side-chains 99 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 86 time to evaluate : 0.942 ------------------------------------------------------------------------------- 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 155 ASN Chi-restraints excluded: chain A residue 164 GLU 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 Chi-restraints excluded: chain D residue 159 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 34 optimal weight: 4.9990 chunk 93 optimal weight: 0.6980 chunk 20 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 8 optimal weight: 0.9980 chunk 54 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.093 8843 Z= 0.372 Angle : 1.077 86.710 11994 Z= 0.425 Chirality : 0.059 1.368 1296 Planarity : 0.005 0.058 1518 Dihedral : 8.699 128.094 1301 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.50 % Favored : 97.41 % Rotamer: Outliers : 1.78 % Allowed : 12.22 % Favored : 86.00 % 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: 0.33 (0.26), residues: 1082 helix: 1.36 (0.23), residues: 506 sheet: -0.53 (0.52), residues: 96 loop : -0.84 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 132 HIS 0.007 0.002 HIS C 55 PHE 0.018 0.002 PHE B 146 TYR 0.016 0.002 TYR B 45 ARG 0.006 0.001 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 104 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 88 time to evaluate : 0.897 Fit side-chains REVERT: A 142 MET cc_start: 0.8717 (ttp) cc_final: 0.8455 (ttm) REVERT: A 430 GLN cc_start: 0.7967 (tt0) cc_final: 0.7739 (tt0) REVERT: A 605 ASP cc_start: 0.7917 (t0) cc_final: 0.7653 (t0) REVERT: A 619 GLU cc_start: 0.7950 (mp0) cc_final: 0.7486 (tp30) REVERT: B 165 GLU cc_start: 0.7143 (OUTLIER) cc_final: 0.6636 (tp30) REVERT: C 55 HIS cc_start: 0.7485 (p90) cc_final: 0.7099 (p90) REVERT: C 92 LEU cc_start: 0.7110 (tp) cc_final: 0.6835 (tp) REVERT: C 164 MET cc_start: 0.6664 (mtp) cc_final: 0.5460 (ptt) outliers start: 16 outliers final: 10 residues processed: 100 average time/residue: 1.1875 time to fit residues: 127.5862 Evaluate side-chains 96 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 85 time to evaluate : 0.976 ------------------------------------------------------------------------------- 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 508 THR 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 Chi-restraints excluded: chain D residue 159 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 11 optimal weight: 0.7980 chunk 58 optimal weight: 5.9990 chunk 75 optimal weight: 0.4980 chunk 87 optimal weight: 5.9990 chunk 57 optimal weight: 0.5980 chunk 103 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 47 optimal weight: 4.9990 chunk 63 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.2229 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= 0.238 Angle : 1.019 83.382 11994 Z= 0.394 Chirality : 0.058 1.477 1296 Planarity : 0.004 0.057 1518 Dihedral : 8.530 129.144 1301 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.33 % Allowed : 12.89 % 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: 0.67 (0.27), residues: 1082 helix: 1.76 (0.24), residues: 498 sheet: -0.33 (0.52), residues: 94 loop : -0.77 (0.29), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 132 HIS 0.005 0.001 HIS C 55 PHE 0.017 0.001 PHE A 463 TYR 0.013 0.001 TYR B 45 ARG 0.007 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 103 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 91 time to evaluate : 0.988 Fit side-chains REVERT: A 142 MET cc_start: 0.8697 (ttp) cc_final: 0.8432 (ttm) REVERT: A 388 MET cc_start: 0.6754 (tpt) cc_final: 0.6477 (mmm) REVERT: A 564 GLU cc_start: 0.7586 (mt-10) cc_final: 0.7116 (mm-30) REVERT: A 605 ASP cc_start: 0.7895 (t0) cc_final: 0.7644 (t0) REVERT: A 619 GLU cc_start: 0.7970 (mp0) cc_final: 0.7486 (tp30) REVERT: B 123 LYS cc_start: 0.8217 (mttp) cc_final: 0.7205 (mtpp) REVERT: B 165 GLU cc_start: 0.7083 (OUTLIER) cc_final: 0.6660 (tp30) REVERT: C 92 LEU cc_start: 0.7107 (tp) cc_final: 0.6874 (tp) REVERT: C 164 MET cc_start: 0.6702 (mtp) cc_final: 0.5457 (ptt) outliers start: 12 outliers final: 8 residues processed: 97 average time/residue: 1.1122 time to fit residues: 116.1678 Evaluate side-chains 97 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 88 time to evaluate : 0.826 ------------------------------------------------------------------------------- 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 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 61 optimal weight: 6.9990 chunk 31 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 19 optimal weight: 0.0770 chunk 65 optimal weight: 0.9980 chunk 70 optimal weight: 0.0050 chunk 50 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 81 optimal weight: 0.5980 chunk 93 optimal weight: 0.5980 chunk 98 optimal weight: 2.9990 overall best weight: 0.4152 ------------------------------------------------------------------------------- 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 409 ASN ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 650 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.106 8843 Z= 0.202 Angle : 0.999 82.842 11994 Z= 0.383 Chirality : 0.057 1.475 1296 Planarity : 0.004 0.054 1518 Dihedral : 8.174 132.938 1301 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.00 % Allowed : 13.33 % Favored : 85.67 % 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: 0.91 (0.27), residues: 1082 helix: 1.99 (0.24), residues: 499 sheet: -0.19 (0.52), residues: 94 loop : -0.69 (0.30), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 132 HIS 0.004 0.001 HIS C 55 PHE 0.017 0.001 PHE A 463 TYR 0.011 0.001 TYR B 45 ARG 0.005 0.000 ARG A 120 *********************** 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 103 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 94 time to evaluate : 0.688 Fit side-chains REVERT: A 388 MET cc_start: 0.6804 (tpt) cc_final: 0.6461 (mmp) REVERT: A 564 GLU cc_start: 0.7539 (mt-10) cc_final: 0.7126 (mm-30) REVERT: A 619 GLU cc_start: 0.7997 (mp0) cc_final: 0.7505 (tp30) REVERT: B 165 GLU cc_start: 0.7015 (OUTLIER) cc_final: 0.6639 (tp30) REVERT: C 164 MET cc_start: 0.6747 (mtp) cc_final: 0.5492 (ptt) outliers start: 9 outliers final: 5 residues processed: 99 average time/residue: 0.7734 time to fit residues: 82.7920 Evaluate side-chains 98 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 92 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 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 165 GLU 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 90 optimal weight: 0.7980 chunk 96 optimal weight: 0.9990 chunk 98 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 chunk 41 optimal weight: 0.8980 chunk 75 optimal weight: 2.9990 chunk 29 optimal weight: 9.9990 chunk 86 optimal weight: 0.8980 chunk 95 optimal weight: 0.6980 chunk 63 optimal weight: 0.7980 chunk 101 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.105 8843 Z= 0.249 Angle : 1.020 83.097 11994 Z= 0.394 Chirality : 0.059 1.492 1296 Planarity : 0.004 0.054 1518 Dihedral : 8.156 133.629 1301 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.44 % Allowed : 14.00 % 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: 0.88 (0.27), residues: 1082 helix: 1.92 (0.24), residues: 504 sheet: -0.09 (0.52), residues: 94 loop : -0.73 (0.30), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 66 HIS 0.008 0.001 HIS C 55 PHE 0.016 0.001 PHE A 463 TYR 0.013 0.001 TYR B 45 ARG 0.004 0.000 ARG A 120 *********************** 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 105 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 92 time to evaluate : 1.052 Fit side-chains REVERT: A 388 MET cc_start: 0.6799 (tpt) cc_final: 0.6444 (mmp) REVERT: A 564 GLU cc_start: 0.7583 (mt-10) cc_final: 0.7159 (mm-30) REVERT: A 619 GLU cc_start: 0.7963 (mp0) cc_final: 0.7445 (tp30) REVERT: B 165 GLU cc_start: 0.7069 (OUTLIER) cc_final: 0.6655 (tp30) REVERT: C 164 MET cc_start: 0.6758 (mtp) cc_final: 0.5472 (ptt) outliers start: 13 outliers final: 7 residues processed: 99 average time/residue: 1.0313 time to fit residues: 110.3762 Evaluate side-chains 100 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 92 time to evaluate : 0.927 ------------------------------------------------------------------------------- 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 165 GLU 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 62 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 70 optimal weight: 0.5980 chunk 106 optimal weight: 6.9990 chunk 98 optimal weight: 3.9990 chunk 84 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 90 optimal weight: 0.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.2400 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= 0.275 Angle : 1.032 83.189 11994 Z= 0.401 Chirality : 0.059 1.497 1296 Planarity : 0.004 0.057 1518 Dihedral : 8.186 133.180 1301 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.11 % Allowed : 14.67 % Favored : 84.22 % 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: 0.84 (0.27), residues: 1082 helix: 1.88 (0.24), residues: 502 sheet: -0.06 (0.51), residues: 94 loop : -0.72 (0.30), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 132 HIS 0.008 0.001 HIS C 55 PHE 0.018 0.001 PHE A 463 TYR 0.014 0.001 TYR C 99 ARG 0.004 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 100 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 90 time to evaluate : 0.955 Fit side-chains REVERT: A 388 MET cc_start: 0.6786 (tpt) cc_final: 0.6578 (mmm) REVERT: A 564 GLU cc_start: 0.7597 (mt-10) cc_final: 0.7135 (mm-30) REVERT: A 619 GLU cc_start: 0.7984 (mp0) cc_final: 0.7434 (tp30) REVERT: B 133 MET cc_start: 0.8237 (mtp) cc_final: 0.8001 (mmt) REVERT: B 165 GLU cc_start: 0.7080 (OUTLIER) cc_final: 0.6663 (tp30) REVERT: C 164 MET cc_start: 0.6746 (mtp) cc_final: 0.5406 (ptt) outliers start: 10 outliers final: 7 residues processed: 96 average time/residue: 1.1359 time to fit residues: 117.2492 Evaluate side-chains 98 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 90 time to evaluate : 0.868 ------------------------------------------------------------------------------- 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 165 GLU 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 26 optimal weight: 4.9990 chunk 78 optimal weight: 0.6980 chunk 12 optimal weight: 6.9990 chunk 23 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 15 optimal weight: 0.5980 chunk 74 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3717 r_free = 0.3717 target = 0.158468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.115214 restraints weight = 9016.394| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 1.77 r_work: 0.2948 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.105 8843 Z= 0.244 Angle : 1.019 82.951 11994 Z= 0.393 Chirality : 0.059 1.496 1296 Planarity : 0.004 0.056 1518 Dihedral : 8.090 132.393 1301 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.11 % Allowed : 15.00 % Favored : 83.89 % 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: 0.91 (0.27), residues: 1082 helix: 1.95 (0.24), residues: 502 sheet: 0.03 (0.52), residues: 94 loop : -0.72 (0.30), residues: 486 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 0.018 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: 3008.72 seconds wall clock time: 54 minutes 59.43 seconds (3299.43 seconds total)