Starting phenix.real_space_refine on Thu Mar 5 12:04:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lc6_23269/03_2026/7lc6_23269_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lc6_23269/03_2026/7lc6_23269.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7lc6_23269/03_2026/7lc6_23269_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lc6_23269/03_2026/7lc6_23269_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7lc6_23269/03_2026/7lc6_23269.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lc6_23269/03_2026/7lc6_23269.map" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians K 1 8.98 5 P 1 5.49 5 Mg 1 5.21 5 S 60 5.16 5 C 6954 2.51 5 N 1814 2.21 5 O 1954 1.98 5 H 11106 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21891 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 8445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 557, 8445 Classifications: {'peptide': 557} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 25, 'TRANS': 531} Chain: "B" Number of atoms: 10166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 672, 10166 Classifications: {'peptide': 672} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 646} Chain: "C" Number of atoms: 2815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 2815 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 13, 'TRANS': 171} Chain: "D" Number of atoms: 402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 402 Classifications: {'peptide': 26} Link IDs: {'TRANS': 25} Chain: "A" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 50 Unusual residues: {' K': 1, '9Y0': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 12 Classifications: {'water': 4} Link IDs: {None: 3} Time building chain proxies: 3.60, per 1000 atoms: 0.16 Number of scatterers: 21891 At special positions: 0 Unit cell: (82.004, 105.742, 169.403, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) K 1 19.00 S 60 16.00 P 1 15.00 Mg 1 11.99 O 1954 8.00 N 1814 7.00 C 6954 6.00 H 11106 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.88 Conformation dependent library (CDL) restraints added in 770.5 milliseconds 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2620 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 8 sheets defined 63.7% alpha, 4.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 1 through 31 removed outlier: 3.534A pdb=" N LEU A 7 " --> pdb=" O ALA A 3 " (cutoff:3.500A) Proline residue: A 22 - end of helix Processing helix chain 'A' and resid 41 through 51 Processing helix chain 'A' and resid 58 through 83 Processing helix chain 'A' and resid 98 through 111 Processing helix chain 'A' and resid 127 through 157 removed outlier: 3.699A pdb=" N THR A 134 " --> pdb=" O MET A 130 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N VAL A 135 " --> pdb=" O ALA A 131 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLN A 136 " --> pdb=" O GLY A 132 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA A 141 " --> pdb=" O ASN A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 176 Processing helix chain 'A' and resid 177 through 193 removed outlier: 4.200A pdb=" N VAL A 181 " --> pdb=" O VAL A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 229 Processing helix chain 'A' and resid 248 through 274 removed outlier: 4.938A pdb=" N ILE A 262 " --> pdb=" O ALA A 258 " (cutoff:3.500A) Proline residue: A 263 - end of helix removed outlier: 3.706A pdb=" N MET A 274 " --> pdb=" O PHE A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 305 removed outlier: 4.156A pdb=" N GLY A 280 " --> pdb=" O ASP A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 313 removed outlier: 4.078A pdb=" N ALA A 311 " --> pdb=" O PRO A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 342 Processing helix chain 'A' and resid 350 through 354 Processing helix chain 'A' and resid 355 through 368 Proline residue: A 362 - end of helix Processing helix chain 'A' and resid 377 through 399 Processing helix chain 'A' and resid 410 through 437 removed outlier: 3.753A pdb=" N THR A 424 " --> pdb=" O ALA A 420 " (cutoff:3.500A) Proline residue: A 425 - end of helix Processing helix chain 'A' and resid 438 through 444 removed outlier: 3.615A pdb=" N ALA A 444 " --> pdb=" O ALA A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 465 removed outlier: 3.899A pdb=" N PHE A 453 " --> pdb=" O GLY A 449 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL A 456 " --> pdb=" O GLY A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 510 Proline residue: A 499 - end of helix removed outlier: 3.801A pdb=" N SER A 509 " --> pdb=" O GLY A 505 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS A 510 " --> pdb=" O SER A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 550 Proline residue: A 545 - end of helix Processing helix chain 'A' and resid 550 through 557 Processing helix chain 'B' and resid 12 through 24 Processing helix chain 'B' and resid 26 through 31 removed outlier: 3.884A pdb=" N TRP B 31 " --> pdb=" O PRO B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 55 Processing helix chain 'B' and resid 61 through 99 removed outlier: 3.573A pdb=" N SER B 65 " --> pdb=" O ASN B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 126 Processing helix chain 'B' and resid 155 through 160 removed outlier: 3.807A pdb=" N THR B 159 " --> pdb=" O GLU B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 210 Processing helix chain 'B' and resid 215 through 247 removed outlier: 3.570A pdb=" N LEU B 221 " --> pdb=" O ASN B 217 " (cutoff:3.500A) Proline residue: B 241 - end of helix removed outlier: 3.578A pdb=" N GLY B 246 " --> pdb=" O PHE B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 263 Processing helix chain 'B' and resid 265 through 284 removed outlier: 4.173A pdb=" N GLY B 269 " --> pdb=" O THR B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 299 Processing helix chain 'B' and resid 329 through 341 Processing helix chain 'B' and resid 346 through 360 Processing helix chain 'B' and resid 397 through 408 Processing helix chain 'B' and resid 414 through 426 Processing helix chain 'B' and resid 452 through 463 Processing helix chain 'B' and resid 474 through 486 Processing helix chain 'B' and resid 495 through 508 Processing helix chain 'B' and resid 522 through 529 Processing helix chain 'B' and resid 539 through 544 Processing helix chain 'B' and resid 555 through 595 removed outlier: 4.066A pdb=" N ILE B 559 " --> pdb=" O PRO B 555 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU B 560 " --> pdb=" O THR B 556 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE B 580 " --> pdb=" O THR B 576 " (cutoff:3.500A) Proline residue: B 592 - end of helix Processing helix chain 'B' and resid 599 through 605 removed outlier: 3.849A pdb=" N ASN B 603 " --> pdb=" O TYR B 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 638 Proline residue: B 633 - end of helix removed outlier: 3.528A pdb=" N GLY B 638 " --> pdb=" O LEU B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 645 through 680 Proline residue: B 665 - end of helix Processing helix chain 'C' and resid 5 through 20 Processing helix chain 'C' and resid 20 through 34 removed outlier: 3.571A pdb=" N LEU C 24 " --> pdb=" O GLY C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 39 Processing helix chain 'C' and resid 91 through 109 removed outlier: 3.923A pdb=" N ASP C 95 " --> pdb=" O ASN C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 122 removed outlier: 3.772A pdb=" N VAL C 121 " --> pdb=" O PRO C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 140 removed outlier: 3.581A pdb=" N GLN C 140 " --> pdb=" O ALA C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 149 removed outlier: 3.636A pdb=" N VAL C 144 " --> pdb=" O GLN C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 162 Processing helix chain 'C' and resid 178 through 188 Processing helix chain 'D' and resid 3 through 25 Processing sheet with id=AA1, first strand: chain 'A' and resid 204 through 205 Processing sheet with id=AA2, first strand: chain 'A' and resid 403 through 404 Processing sheet with id=AA3, first strand: chain 'B' and resid 119 through 121 removed outlier: 4.019A pdb=" N ARG B 107 " --> pdb=" O LEU B 133 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N VAL B 188 " --> pdb=" O ILE B 147 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE B 147 " --> pdb=" O VAL B 188 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 165 through 167 removed outlier: 3.910A pdb=" N ARG B 181 " --> pdb=" O ASP B 154 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 466 through 470 removed outlier: 5.789A pdb=" N LEU B 304 " --> pdb=" O VAL B 468 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N ILE B 470 " --> pdb=" O LEU B 304 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N LEU B 306 " --> pdb=" O ILE B 470 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N VAL B 303 " --> pdb=" O ALA B 514 " (cutoff:3.500A) removed outlier: 8.321A pdb=" N THR B 516 " --> pdb=" O VAL B 303 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N LEU B 305 " --> pdb=" O THR B 516 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N VAL B 513 " --> pdb=" O VAL B 531 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N VAL B 533 " --> pdb=" O VAL B 513 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N MET B 515 " --> pdb=" O VAL B 533 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 323 through 324 removed outlier: 6.631A pdb=" N VAL B 433 " --> pdb=" O LEU B 440 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N VAL B 442 " --> pdb=" O LEU B 431 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N LEU B 431 " --> pdb=" O VAL B 442 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N ALA B 444 " --> pdb=" O THR B 429 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N THR B 429 " --> pdb=" O ALA B 444 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 42 through 45 removed outlier: 6.964A pdb=" N ILE C 43 " --> pdb=" O ARG C 50 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 131 through 132 removed outlier: 3.552A pdb=" N ILE C 132 " --> pdb=" O VAL C 176 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL C 175 " --> pdb=" O GLN C 164 " (cutoff:3.500A) 673 hydrogen bonds defined for protein. 1974 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: 5.11 Time building geometry restraints manager: 2.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 11094 1.02 - 1.22: 17 1.22 - 1.42: 4344 1.42 - 1.62: 6518 1.62 - 1.82: 110 Bond restraints: 22083 Sorted by residual: bond pdb=" C13 9Y0 A 602 " pdb=" C14 9Y0 A 602 " ideal model delta sigma weight residual 1.333 1.545 -0.212 2.00e-02 2.50e+03 1.12e+02 bond pdb=" ND2 ASN B 624 " pdb="HD22 ASN B 624 " ideal model delta sigma weight residual 0.860 0.977 -0.117 2.00e-02 2.50e+03 3.41e+01 bond pdb=" ND2 ASN B 624 " pdb="HD21 ASN B 624 " ideal model delta sigma weight residual 0.860 0.976 -0.116 2.00e-02 2.50e+03 3.38e+01 bond pdb=" C5 9Y0 A 602 " pdb=" O5 9Y0 A 602 " ideal model delta sigma weight residual 1.326 1.421 -0.095 2.00e-02 2.50e+03 2.25e+01 bond pdb=" C21 9Y0 A 602 " pdb=" O7 9Y0 A 602 " ideal model delta sigma weight residual 1.330 1.419 -0.089 2.00e-02 2.50e+03 2.00e+01 ... (remaining 22078 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.27: 39975 5.27 - 10.54: 84 10.54 - 15.82: 7 15.82 - 21.09: 0 21.09 - 26.36: 1 Bond angle restraints: 40067 Sorted by residual: angle pdb=" C11 9Y0 A 602 " pdb=" C12 9Y0 A 602 " pdb=" C13 9Y0 A 602 " ideal model delta sigma weight residual 111.77 85.41 26.36 3.00e+00 1.11e-01 7.72e+01 angle pdb=" C12 9Y0 A 602 " pdb=" C13 9Y0 A 602 " pdb=" C14 9Y0 A 602 " ideal model delta sigma weight residual 127.16 112.84 14.32 3.00e+00 1.11e-01 2.28e+01 angle pdb=" CD1 ILE C 141 " pdb=" CG1 ILE C 141 " pdb="HG13 ILE C 141 " ideal model delta sigma weight residual 108.00 94.49 13.51 3.00e+00 1.11e-01 2.03e+01 angle pdb=" CB ILE C 141 " pdb=" CG1 ILE C 141 " pdb=" CD1 ILE C 141 " ideal model delta sigma weight residual 113.80 122.90 -9.10 2.10e+00 2.27e-01 1.88e+01 angle pdb=" N ASN A 32 " pdb=" CA ASN A 32 " pdb=" C ASN A 32 " ideal model delta sigma weight residual 112.59 107.49 5.10 1.22e+00 6.72e-01 1.75e+01 ... (remaining 40062 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.91: 9918 28.91 - 57.83: 379 57.83 - 86.74: 39 86.74 - 115.65: 4 115.65 - 144.57: 5 Dihedral angle restraints: 10345 sinusoidal: 5701 harmonic: 4644 Sorted by residual: dihedral pdb=" C23 9Y0 A 602 " pdb=" C21 9Y0 A 602 " pdb=" C22 9Y0 A 602 " pdb=" O7 9Y0 A 602 " ideal model delta sinusoidal sigma weight residual 181.02 36.45 144.57 1 3.00e+01 1.11e-03 1.94e+01 dihedral pdb=" C23 9Y0 A 602 " pdb=" C21 9Y0 A 602 " pdb=" C22 9Y0 A 602 " pdb=" O6 9Y0 A 602 " ideal model delta sinusoidal sigma weight residual 0.61 -143.51 144.12 1 3.00e+01 1.11e-03 1.93e+01 dihedral pdb=" C3 9Y0 A 602 " pdb=" O1 9Y0 A 602 " pdb=" P 9Y0 A 602 " pdb=" O3 9Y0 A 602 " ideal model delta sinusoidal sigma weight residual 291.93 150.21 141.72 1 3.00e+01 1.11e-03 1.90e+01 ... (remaining 10342 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1323 0.060 - 0.120: 395 0.120 - 0.180: 65 0.180 - 0.240: 11 0.240 - 0.300: 4 Chirality restraints: 1798 Sorted by residual: chirality pdb=" CG LEU B 225 " pdb=" CB LEU B 225 " pdb=" CD1 LEU B 225 " pdb=" CD2 LEU B 225 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.25e+00 chirality pdb=" CB ILE A 148 " pdb=" CA ILE A 148 " pdb=" CG1 ILE A 148 " pdb=" CG2 ILE A 148 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 1.98e+00 chirality pdb=" CA THR A 424 " pdb=" N THR A 424 " pdb=" C THR A 424 " pdb=" CB THR A 424 " both_signs ideal model delta sigma weight residual False 2.53 2.28 0.25 2.00e-01 2.50e+01 1.57e+00 ... (remaining 1795 not shown) Planarity restraints: 3264 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 624 " -0.313 2.00e-02 2.50e+03 3.84e-01 2.21e+03 pdb=" CG ASN B 624 " 0.024 2.00e-02 2.50e+03 pdb=" OD1 ASN B 624 " 0.303 2.00e-02 2.50e+03 pdb=" ND2 ASN B 624 " 0.000 2.00e-02 2.50e+03 pdb="HD21 ASN B 624 " -0.595 2.00e-02 2.50e+03 pdb="HD22 ASN B 624 " 0.581 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C12 9Y0 A 602 " 0.039 2.00e-02 2.50e+03 3.09e-01 9.57e+02 pdb=" C13 9Y0 A 602 " 0.203 2.00e-02 2.50e+03 pdb=" C14 9Y0 A 602 " -0.515 2.00e-02 2.50e+03 pdb=" C15 9Y0 A 602 " 0.274 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 86 " 0.048 2.00e-02 2.50e+03 8.93e-02 1.20e+02 pdb=" CG ASN C 86 " -0.096 2.00e-02 2.50e+03 pdb=" OD1 ASN C 86 " -0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN C 86 " 0.152 2.00e-02 2.50e+03 pdb="HD21 ASN C 86 " 0.022 2.00e-02 2.50e+03 pdb="HD22 ASN C 86 " -0.112 2.00e-02 2.50e+03 ... (remaining 3261 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.33: 6078 2.33 - 3.03: 62479 3.03 - 3.73: 79473 3.73 - 4.44: 122643 4.44 - 5.14: 191216 Nonbonded interactions: 461889 Sorted by model distance: nonbonded pdb=" O ASP B 329 " pdb=" H THR B 332 " model vdw 1.626 2.450 nonbonded pdb=" HZ1 LYS B 499 " pdb=" OD2 ASP B 522 " model vdw 1.644 2.450 nonbonded pdb=" OE1 GLN B 601 " pdb=" H GLN B 601 " model vdw 1.651 2.450 nonbonded pdb=" O ARG C 68 " pdb=" HH TYR C 77 " model vdw 1.667 2.450 nonbonded pdb=" OE2 GLU A 121 " pdb=" HG SER C 82 " model vdw 1.670 2.450 ... (remaining 461884 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.870 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: 0.120 Extract box with map and model: 0.290 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 20.910 Find NCS groups from input model: 0.060 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:1.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 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 : 0.010 0.212 10977 Z= 0.439 Angle : 1.124 26.360 14930 Z= 0.623 Chirality : 0.058 0.300 1798 Planarity : 0.011 0.309 1891 Dihedral : 12.510 144.567 3923 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 1.51 % Allowed : 5.15 % Favored : 93.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.96 (0.18), residues: 1432 helix: -1.05 (0.15), residues: 857 sheet: -3.62 (0.38), residues: 97 loop : -3.13 (0.22), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 107 TYR 0.035 0.004 TYR C 22 PHE 0.036 0.005 PHE A 392 TRP 0.027 0.003 TRP A 176 HIS 0.009 0.002 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00986 (10977) covalent geometry : angle 1.12418 (14930) hydrogen bonds : bond 0.13335 ( 673) hydrogen bonds : angle 6.53817 ( 1974) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 175 time to evaluate : 0.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 321 GLU cc_start: 0.7800 (tp30) cc_final: 0.7295 (tm-30) REVERT: B 190 GLU cc_start: 0.7016 (tt0) cc_final: 0.6370 (tp30) REVERT: B 192 SER cc_start: 0.7970 (t) cc_final: 0.7449 (m) REVERT: B 350 ARG cc_start: 0.8421 (mtm-85) cc_final: 0.7633 (mmm160) REVERT: C 48 THR cc_start: 0.6938 (p) cc_final: 0.6505 (p) REVERT: C 111 ASP cc_start: 0.7698 (m-30) cc_final: 0.7314 (t0) outliers start: 17 outliers final: 5 residues processed: 190 average time/residue: 0.3001 time to fit residues: 76.0419 Evaluate side-chains 104 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 99 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 PHE Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 497 ILE Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 453 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 6.9990 chunk 55 optimal weight: 0.9980 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 61 GLN A 112 ASN ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 246 ASN B 316 ASN B 390 ASN B 582 ASN C 58 ASN C 135 GLN C 164 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.116159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.092511 restraints weight = 91366.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.093979 restraints weight = 39021.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.094645 restraints weight = 23445.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.094693 restraints weight = 19550.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.094913 restraints weight = 19218.183| |-----------------------------------------------------------------------------| r_work (final): 0.4042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10977 Z= 0.158 Angle : 0.614 6.403 14930 Z= 0.326 Chirality : 0.039 0.153 1798 Planarity : 0.005 0.071 1891 Dihedral : 11.605 177.381 1569 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 0.71 % Allowed : 8.52 % Favored : 90.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.64 (0.20), residues: 1432 helix: 0.04 (0.16), residues: 866 sheet: -3.34 (0.45), residues: 81 loop : -2.72 (0.23), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 504 TYR 0.027 0.001 TYR A 381 PHE 0.013 0.002 PHE A 260 TRP 0.012 0.001 TRP A 364 HIS 0.005 0.001 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00323 (10977) covalent geometry : angle 0.61359 (14930) hydrogen bonds : bond 0.06184 ( 673) hydrogen bonds : angle 5.13304 ( 1974) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 115 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 191 CYS cc_start: 0.6725 (m) cc_final: 0.6213 (t) REVERT: B 279 MET cc_start: 0.6061 (mmp) cc_final: 0.5815 (mmp) REVERT: B 350 ARG cc_start: 0.8318 (mtm-85) cc_final: 0.7758 (mmm160) outliers start: 8 outliers final: 8 residues processed: 121 average time/residue: 0.2523 time to fit residues: 43.0847 Evaluate side-chains 104 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 96 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 327 PHE Chi-restraints excluded: chain A residue 497 ILE Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 516 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 100 optimal weight: 8.9990 chunk 10 optimal weight: 2.9990 chunk 117 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 109 optimal weight: 6.9990 chunk 5 optimal weight: 0.5980 chunk 65 optimal weight: 8.9990 chunk 28 optimal weight: 2.9990 chunk 98 optimal weight: 8.9990 chunk 110 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 205 ASN C 86 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.113911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.090220 restraints weight = 90633.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.091483 restraints weight = 44415.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.091734 restraints weight = 26480.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.091814 restraints weight = 23575.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.092246 restraints weight = 21553.901| |-----------------------------------------------------------------------------| r_work (final): 0.3973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10977 Z= 0.169 Angle : 0.577 6.437 14930 Z= 0.306 Chirality : 0.039 0.170 1798 Planarity : 0.004 0.057 1891 Dihedral : 10.524 153.090 1567 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 1.42 % Allowed : 9.14 % Favored : 89.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.21), residues: 1432 helix: 0.48 (0.16), residues: 869 sheet: -3.16 (0.46), residues: 82 loop : -2.54 (0.25), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 363 TYR 0.023 0.001 TYR A 381 PHE 0.012 0.001 PHE A 244 TRP 0.009 0.001 TRP A 176 HIS 0.003 0.001 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00371 (10977) covalent geometry : angle 0.57661 (14930) hydrogen bonds : bond 0.05562 ( 673) hydrogen bonds : angle 4.90519 ( 1974) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 99 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 279 MET cc_start: 0.5888 (mmp) cc_final: 0.5585 (mmp) REVERT: B 350 ARG cc_start: 0.8226 (mtm-85) cc_final: 0.7765 (mmm160) REVERT: B 535 MET cc_start: 0.8287 (pmm) cc_final: 0.7870 (pmm) outliers start: 16 outliers final: 11 residues processed: 112 average time/residue: 0.2363 time to fit residues: 37.3148 Evaluate side-chains 106 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 95 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 302 GLU Chi-restraints excluded: chain A residue 327 PHE Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 516 THR Chi-restraints excluded: chain B residue 664 VAL Chi-restraints excluded: chain D residue 15 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 13 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 97 optimal weight: 3.9990 chunk 115 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 139 optimal weight: 0.6980 chunk 61 optimal weight: 5.9990 chunk 135 optimal weight: 0.5980 chunk 49 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 211 GLN C 86 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.113167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.088023 restraints weight = 90453.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.090538 restraints weight = 36099.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.091957 restraints weight = 20487.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.092502 restraints weight = 15115.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.092806 restraints weight = 13456.966| |-----------------------------------------------------------------------------| r_work (final): 0.3993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.3131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10977 Z= 0.156 Angle : 0.561 7.551 14930 Z= 0.293 Chirality : 0.038 0.142 1798 Planarity : 0.004 0.047 1891 Dihedral : 9.370 116.183 1565 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 1.33 % Allowed : 9.94 % Favored : 88.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.21), residues: 1432 helix: 0.82 (0.17), residues: 870 sheet: -2.51 (0.50), residues: 77 loop : -2.49 (0.25), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 363 TYR 0.024 0.001 TYR A 381 PHE 0.015 0.001 PHE B 78 TRP 0.008 0.001 TRP A 176 HIS 0.005 0.001 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00340 (10977) covalent geometry : angle 0.56059 (14930) hydrogen bonds : bond 0.05101 ( 673) hydrogen bonds : angle 4.68886 ( 1974) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 96 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 279 MET cc_start: 0.5937 (mmp) cc_final: 0.5562 (mmp) REVERT: B 350 ARG cc_start: 0.8263 (mtm-85) cc_final: 0.7865 (mmm160) REVERT: B 535 MET cc_start: 0.8329 (pmm) cc_final: 0.7941 (pmm) outliers start: 15 outliers final: 13 residues processed: 106 average time/residue: 0.2219 time to fit residues: 33.3367 Evaluate side-chains 106 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 93 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 302 GLU Chi-restraints excluded: chain A residue 327 PHE Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 516 THR Chi-restraints excluded: chain B residue 664 VAL Chi-restraints excluded: chain D residue 15 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 120 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 121 optimal weight: 6.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 205 ASN B 248 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.110387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.086309 restraints weight = 90338.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.087318 restraints weight = 37790.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.087952 restraints weight = 25433.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.087934 restraints weight = 21247.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.088098 restraints weight = 20469.758| |-----------------------------------------------------------------------------| r_work (final): 0.3913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.3565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10977 Z= 0.180 Angle : 0.572 7.566 14930 Z= 0.302 Chirality : 0.039 0.140 1798 Planarity : 0.004 0.050 1891 Dihedral : 8.926 116.471 1565 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 1.77 % Allowed : 10.03 % Favored : 88.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.22), residues: 1432 helix: 0.99 (0.17), residues: 874 sheet: -2.43 (0.51), residues: 82 loop : -2.35 (0.26), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 68 TYR 0.021 0.002 TYR A 381 PHE 0.018 0.002 PHE A 260 TRP 0.010 0.001 TRP A 176 HIS 0.003 0.001 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00403 (10977) covalent geometry : angle 0.57187 (14930) hydrogen bonds : bond 0.05013 ( 673) hydrogen bonds : angle 4.65471 ( 1974) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 96 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 321 GLU cc_start: 0.7551 (tp30) cc_final: 0.7228 (tm-30) REVERT: B 74 ILE cc_start: 0.9495 (OUTLIER) cc_final: 0.9239 (tt) REVERT: B 78 PHE cc_start: 0.7917 (m-10) cc_final: 0.7637 (m-10) REVERT: B 279 MET cc_start: 0.5962 (mmp) cc_final: 0.5651 (mmt) REVERT: B 535 MET cc_start: 0.8217 (pmm) cc_final: 0.7837 (pmm) outliers start: 20 outliers final: 14 residues processed: 110 average time/residue: 0.2310 time to fit residues: 36.3119 Evaluate side-chains 103 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 88 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 PHE Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 302 GLU Chi-restraints excluded: chain A residue 327 PHE Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 516 THR Chi-restraints excluded: chain B residue 664 VAL Chi-restraints excluded: chain D residue 15 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 52 optimal weight: 0.5980 chunk 120 optimal weight: 4.9990 chunk 56 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 139 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 chunk 47 optimal weight: 0.7980 chunk 123 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 chunk 76 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.111136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.087372 restraints weight = 91048.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.088561 restraints weight = 39922.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.089336 restraints weight = 24887.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.089365 restraints weight = 20491.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.089520 restraints weight = 20114.085| |-----------------------------------------------------------------------------| r_work (final): 0.3944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.3821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10977 Z= 0.117 Angle : 0.522 7.856 14930 Z= 0.268 Chirality : 0.037 0.138 1798 Planarity : 0.004 0.042 1891 Dihedral : 8.632 112.672 1565 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 1.24 % Allowed : 10.91 % Favored : 87.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.22), residues: 1432 helix: 1.28 (0.17), residues: 874 sheet: -2.05 (0.55), residues: 77 loop : -2.27 (0.26), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 363 TYR 0.023 0.001 TYR A 381 PHE 0.013 0.001 PHE A 260 TRP 0.006 0.001 TRP A 176 HIS 0.003 0.000 HIS A 85 Details of bonding type rmsd covalent geometry : bond 0.00252 (10977) covalent geometry : angle 0.52214 (14930) hydrogen bonds : bond 0.04559 ( 673) hydrogen bonds : angle 4.40881 ( 1974) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 97 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 321 GLU cc_start: 0.7490 (tp30) cc_final: 0.7174 (tm-30) REVERT: A 327 PHE cc_start: 0.8645 (OUTLIER) cc_final: 0.8107 (p90) REVERT: B 74 ILE cc_start: 0.9462 (OUTLIER) cc_final: 0.9030 (tt) REVERT: B 78 PHE cc_start: 0.7902 (m-10) cc_final: 0.7534 (m-10) REVERT: B 279 MET cc_start: 0.5878 (mmp) cc_final: 0.5573 (mmt) REVERT: B 535 MET cc_start: 0.8226 (pmm) cc_final: 0.7849 (pmm) outliers start: 14 outliers final: 9 residues processed: 105 average time/residue: 0.2391 time to fit residues: 36.6584 Evaluate side-chains 101 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 90 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 PHE Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 327 PHE Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 516 THR Chi-restraints excluded: chain B residue 664 VAL Chi-restraints excluded: chain D residue 15 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 64 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 129 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.108897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.083381 restraints weight = 92017.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.085808 restraints weight = 37198.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.087131 restraints weight = 21771.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.087851 restraints weight = 16344.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.088005 restraints weight = 14228.163| |-----------------------------------------------------------------------------| r_work (final): 0.3926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.4023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10977 Z= 0.192 Angle : 0.567 7.464 14930 Z= 0.301 Chirality : 0.039 0.143 1798 Planarity : 0.004 0.046 1891 Dihedral : 8.512 115.510 1563 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 1.60 % Allowed : 11.27 % Favored : 87.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.22), residues: 1432 helix: 1.18 (0.17), residues: 878 sheet: -1.94 (0.59), residues: 74 loop : -2.33 (0.26), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 278 TYR 0.020 0.002 TYR A 381 PHE 0.014 0.002 PHE A 127 TRP 0.010 0.001 TRP A 176 HIS 0.004 0.001 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00433 (10977) covalent geometry : angle 0.56687 (14930) hydrogen bonds : bond 0.04876 ( 673) hydrogen bonds : angle 4.57531 ( 1974) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 87 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 321 GLU cc_start: 0.7622 (tp30) cc_final: 0.7273 (tm-30) REVERT: B 279 MET cc_start: 0.5759 (mmp) cc_final: 0.5530 (mmp) REVERT: B 535 MET cc_start: 0.8258 (pmm) cc_final: 0.7916 (pmm) outliers start: 18 outliers final: 16 residues processed: 102 average time/residue: 0.2324 time to fit residues: 33.9275 Evaluate side-chains 100 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 84 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 GLN Chi-restraints excluded: chain A residue 155 PHE Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 302 GLU Chi-restraints excluded: chain A residue 327 PHE Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 516 THR Chi-restraints excluded: chain B residue 664 VAL Chi-restraints excluded: chain D residue 15 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 99 optimal weight: 6.9990 chunk 113 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 98 optimal weight: 3.9990 chunk 95 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 137 optimal weight: 2.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.109957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.084654 restraints weight = 91674.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.087152 restraints weight = 37013.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.088502 restraints weight = 21424.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.089240 restraints weight = 15981.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.089400 restraints weight = 13900.423| |-----------------------------------------------------------------------------| r_work (final): 0.3953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.4176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10977 Z= 0.131 Angle : 0.533 8.141 14930 Z= 0.275 Chirality : 0.037 0.134 1798 Planarity : 0.004 0.043 1891 Dihedral : 8.248 112.942 1563 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 1.33 % Allowed : 11.80 % Favored : 86.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.00 (0.22), residues: 1432 helix: 1.36 (0.17), residues: 878 sheet: -2.37 (0.52), residues: 86 loop : -2.22 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 68 TYR 0.022 0.001 TYR A 381 PHE 0.010 0.001 PHE A 373 TRP 0.007 0.001 TRP A 176 HIS 0.003 0.000 HIS A 85 Details of bonding type rmsd covalent geometry : bond 0.00289 (10977) covalent geometry : angle 0.53294 (14930) hydrogen bonds : bond 0.04565 ( 673) hydrogen bonds : angle 4.39416 ( 1974) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 90 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 321 GLU cc_start: 0.7563 (tp30) cc_final: 0.7221 (tm-30) REVERT: A 327 PHE cc_start: 0.8765 (OUTLIER) cc_final: 0.8489 (p90) REVERT: B 279 MET cc_start: 0.5612 (mmp) cc_final: 0.5395 (mmp) REVERT: B 388 ILE cc_start: 0.4959 (pt) cc_final: 0.4640 (tt) REVERT: B 392 MET cc_start: 0.4596 (ttp) cc_final: 0.3987 (tmm) REVERT: B 535 MET cc_start: 0.8246 (pmm) cc_final: 0.7896 (pmm) outliers start: 15 outliers final: 12 residues processed: 100 average time/residue: 0.2060 time to fit residues: 31.1706 Evaluate side-chains 100 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 87 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 GLN Chi-restraints excluded: chain A residue 155 PHE Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 302 GLU Chi-restraints excluded: chain A residue 327 PHE Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 516 THR Chi-restraints excluded: chain B residue 664 VAL Chi-restraints excluded: chain D residue 15 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 125 optimal weight: 0.8980 chunk 3 optimal weight: 0.1980 chunk 114 optimal weight: 4.9990 chunk 9 optimal weight: 0.7980 chunk 68 optimal weight: 0.0670 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 108 optimal weight: 10.0000 chunk 41 optimal weight: 0.7980 chunk 75 optimal weight: 0.9990 chunk 80 optimal weight: 0.9980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.111965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.088871 restraints weight = 91359.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.090526 restraints weight = 38764.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.090667 restraints weight = 23489.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.090624 restraints weight = 22105.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.091032 restraints weight = 21119.147| |-----------------------------------------------------------------------------| r_work (final): 0.3958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.4301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10977 Z= 0.106 Angle : 0.512 6.946 14930 Z= 0.261 Chirality : 0.037 0.133 1798 Planarity : 0.004 0.041 1891 Dihedral : 7.910 111.189 1563 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 1.33 % Allowed : 11.54 % Favored : 87.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.22), residues: 1432 helix: 1.57 (0.17), residues: 885 sheet: -2.26 (0.51), residues: 86 loop : -2.09 (0.27), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 456 TYR 0.024 0.001 TYR A 381 PHE 0.011 0.001 PHE B 78 TRP 0.008 0.001 TRP B 655 HIS 0.002 0.000 HIS A 85 Details of bonding type rmsd covalent geometry : bond 0.00229 (10977) covalent geometry : angle 0.51234 (14930) hydrogen bonds : bond 0.04174 ( 673) hydrogen bonds : angle 4.20284 ( 1974) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 321 GLU cc_start: 0.7436 (tp30) cc_final: 0.7157 (tm-30) REVERT: A 327 PHE cc_start: 0.8753 (OUTLIER) cc_final: 0.8508 (p90) REVERT: B 279 MET cc_start: 0.5542 (mmp) cc_final: 0.5159 (mmt) REVERT: B 388 ILE cc_start: 0.4741 (pt) cc_final: 0.4441 (tt) REVERT: B 392 MET cc_start: 0.4588 (ttp) cc_final: 0.3903 (tmm) REVERT: B 535 MET cc_start: 0.8209 (pmm) cc_final: 0.7858 (pmm) REVERT: B 548 MET cc_start: 0.7572 (tpp) cc_final: 0.7342 (tpp) REVERT: C 93 GLU cc_start: 0.8471 (tp30) cc_final: 0.8235 (tp30) outliers start: 15 outliers final: 10 residues processed: 103 average time/residue: 0.2094 time to fit residues: 32.5143 Evaluate side-chains 100 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 89 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 PHE Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 302 GLU Chi-restraints excluded: chain A residue 327 PHE Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 516 THR Chi-restraints excluded: chain B residue 664 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 116 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 126 optimal weight: 0.2980 chunk 91 optimal weight: 0.4980 chunk 133 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 129 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 99 optimal weight: 5.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.111887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.087552 restraints weight = 91005.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.089976 restraints weight = 36963.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.091309 restraints weight = 21342.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.091807 restraints weight = 15977.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.091946 restraints weight = 14238.954| |-----------------------------------------------------------------------------| r_work (final): 0.3981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.4399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10977 Z= 0.109 Angle : 0.511 7.215 14930 Z= 0.262 Chirality : 0.037 0.133 1798 Planarity : 0.004 0.043 1891 Dihedral : 7.771 111.735 1563 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 1.15 % Allowed : 11.98 % Favored : 86.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.22), residues: 1432 helix: 1.63 (0.17), residues: 884 sheet: -2.24 (0.51), residues: 86 loop : -2.09 (0.27), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 363 TYR 0.022 0.001 TYR A 381 PHE 0.011 0.001 PHE B 78 TRP 0.006 0.001 TRP B 655 HIS 0.002 0.000 HIS A 85 Details of bonding type rmsd covalent geometry : bond 0.00240 (10977) covalent geometry : angle 0.51052 (14930) hydrogen bonds : bond 0.04135 ( 673) hydrogen bonds : angle 4.18176 ( 1974) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 88 time to evaluate : 0.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 321 GLU cc_start: 0.7458 (tp30) cc_final: 0.7160 (tm-30) REVERT: A 327 PHE cc_start: 0.8749 (OUTLIER) cc_final: 0.8496 (p90) REVERT: B 279 MET cc_start: 0.5460 (mmp) cc_final: 0.5241 (mmp) REVERT: B 388 ILE cc_start: 0.4894 (pt) cc_final: 0.4551 (tt) REVERT: B 392 MET cc_start: 0.4660 (ttp) cc_final: 0.3958 (tmm) REVERT: B 535 MET cc_start: 0.8203 (pmm) cc_final: 0.7841 (pmm) outliers start: 13 outliers final: 12 residues processed: 97 average time/residue: 0.2218 time to fit residues: 32.5199 Evaluate side-chains 98 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 PHE Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 260 PHE Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 302 GLU Chi-restraints excluded: chain A residue 327 PHE Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 516 THR Chi-restraints excluded: chain B residue 664 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 67 optimal weight: 5.9990 chunk 134 optimal weight: 3.9990 chunk 96 optimal weight: 8.9990 chunk 73 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 81 optimal weight: 6.9990 chunk 22 optimal weight: 0.8980 chunk 119 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.111037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.087868 restraints weight = 91366.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.089314 restraints weight = 40992.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.089370 restraints weight = 25915.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.089629 restraints weight = 22458.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.089807 restraints weight = 21617.578| |-----------------------------------------------------------------------------| r_work (final): 0.3939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.4481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10977 Z= 0.127 Angle : 0.519 7.197 14930 Z= 0.268 Chirality : 0.037 0.131 1798 Planarity : 0.004 0.044 1891 Dihedral : 7.675 112.472 1563 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 1.15 % Allowed : 11.98 % Favored : 86.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.22), residues: 1432 helix: 1.65 (0.17), residues: 884 sheet: -2.25 (0.51), residues: 86 loop : -2.09 (0.27), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 68 TYR 0.020 0.001 TYR A 381 PHE 0.017 0.001 PHE A 235 TRP 0.006 0.001 TRP A 176 HIS 0.002 0.001 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00281 (10977) covalent geometry : angle 0.51898 (14930) hydrogen bonds : bond 0.04212 ( 673) hydrogen bonds : angle 4.21665 ( 1974) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3432.76 seconds wall clock time: 59 minutes 8.95 seconds (3548.95 seconds total)