Starting phenix.real_space_refine on Thu Mar 5 13:31:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7bgy_12184/03_2026/7bgy_12184_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7bgy_12184/03_2026/7bgy_12184.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7bgy_12184/03_2026/7bgy_12184.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7bgy_12184/03_2026/7bgy_12184.map" model { file = "/net/cci-nas-00/data/ceres_data/7bgy_12184/03_2026/7bgy_12184_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7bgy_12184/03_2026/7bgy_12184_trim.cif" } resolution = 2.9 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= 0.001 sd= 0.084 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 P 2 5.49 5 Mg 2 5.21 5 S 62 5.16 5 C 7043 2.51 5 N 1825 2.21 5 O 1989 1.98 5 F 4 1.80 5 H 11192 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 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: 22119 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 8444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 557, 8444 Classifications: {'peptide': 557} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 25, 'TRANS': 531} Chain: "B" Number of atoms: 10201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 674, 10201 Classifications: {'peptide': 674} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 26, 'TRANS': 647} Chain: "C" Number of atoms: 2879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 2879 Classifications: {'peptide': 190} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 13, 'TRANS': 176} Chain: "D" Number of atoms: 452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 452 Classifications: {'peptide': 29} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 28} Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 98 Unusual residues: {'9Y0': 1, 'PEV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 6 Unusual residues: {' MG': 1, 'MF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 18 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 18 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Classifications: {'water': 1} Time building chain proxies: 3.58, per 1000 atoms: 0.16 Number of scatterers: 22119 At special positions: 0 Unit cell: (74.13, 97.428, 173.676, 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) S 62 16.00 P 2 15.00 Mg 2 11.99 F 4 9.00 O 1989 8.00 N 1825 7.00 C 7043 6.00 H 11192 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: 1.87 Conformation dependent library (CDL) restraints added in 530.0 milliseconds 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2638 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 9 sheets defined 63.5% alpha, 5.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 1 through 32 Proline residue: A 22 - end of helix removed outlier: 3.846A pdb=" N ARG A 29 " --> pdb=" O SER A 25 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU A 30 " --> pdb=" O GLY A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 50 removed outlier: 3.779A pdb=" N ARG A 44 " --> pdb=" O THR A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 83 Processing helix chain 'A' and resid 98 through 111 Processing helix chain 'A' and resid 125 through 132 Processing helix chain 'A' and resid 132 through 157 Processing helix chain 'A' and resid 165 through 177 Processing helix chain 'A' and resid 177 through 193 Processing helix chain 'A' and resid 218 through 229 removed outlier: 4.207A pdb=" N GLN A 222 " --> pdb=" O PRO A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 274 removed outlier: 4.412A pdb=" N ILE A 262 " --> pdb=" O ALA A 258 " (cutoff:3.500A) Proline residue: A 263 - end of helix removed outlier: 3.599A pdb=" N MET A 274 " --> pdb=" O PHE A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 305 removed outlier: 4.199A pdb=" N GLY A 280 " --> pdb=" O ASP A 276 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE A 290 " --> pdb=" O ALA A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 314 removed outlier: 4.473A pdb=" N LEU A 310 " --> pdb=" O ASN A 306 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ALA A 311 " --> pdb=" O PRO A 307 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N THR A 314 " --> pdb=" O LEU A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 342 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: 3.755A pdb=" N MET A 414 " --> pdb=" O ASP A 410 " (cutoff:3.500A) removed outlier: 4.361A 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 443 Processing helix chain 'A' and resid 449 through 465 removed outlier: 3.859A pdb=" N PHE A 453 " --> pdb=" O GLY A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 509 Proline residue: A 499 - end of helix removed outlier: 3.917A pdb=" N SER A 509 " --> pdb=" O GLY A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 549 removed outlier: 4.168A pdb=" N PHE A 527 " --> pdb=" O HIS A 523 " (cutoff:3.500A) Proline residue: A 545 - end of helix Processing helix chain 'A' and resid 550 through 557 Processing helix chain 'B' and resid 10 through 25 Processing helix chain 'B' and resid 26 through 31 Processing helix chain 'B' and resid 33 through 56 Processing helix chain 'B' and resid 61 through 86 removed outlier: 3.952A pdb=" N SER B 65 " --> pdb=" O ASN B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 103 Processing helix chain 'B' and resid 124 through 126 No H-bonds generated for 'chain 'B' and resid 124 through 126' Processing helix chain 'B' and resid 155 through 160 removed outlier: 3.792A pdb=" N THR B 159 " --> pdb=" O GLU B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 208 Processing helix chain 'B' and resid 215 through 246 removed outlier: 4.174A pdb=" N TRP B 240 " --> pdb=" O THR B 236 " (cutoff:3.500A) Proline residue: B 241 - end of helix Processing helix chain 'B' and resid 251 through 263 Processing helix chain 'B' and resid 264 through 285 removed outlier: 3.568A pdb=" N GLY B 268 " --> pdb=" O PRO B 264 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N LEU B 271 " --> pdb=" O ILE B 267 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N SER B 272 " --> pdb=" O GLY B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 300 removed outlier: 4.042A pdb=" N GLU B 296 " --> pdb=" O GLY B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 341 Processing helix chain 'B' and resid 346 through 361 Processing helix chain 'B' and resid 397 through 408 Processing helix chain 'B' and resid 414 through 426 Processing helix chain 'B' and resid 453 through 463 Processing helix chain 'B' and resid 474 through 486 Processing helix chain 'B' and resid 495 through 509 removed outlier: 3.510A pdb=" N GLU B 509 " --> pdb=" O GLN B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 521 No H-bonds generated for 'chain 'B' and resid 519 through 521' Processing helix chain 'B' and resid 522 through 529 Processing helix chain 'B' and resid 539 through 546 Processing helix chain 'B' and resid 557 through 596 Proline residue: B 592 - end of helix removed outlier: 3.986A pdb=" N PHE B 595 " --> pdb=" O ILE B 591 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ALA B 596 " --> pdb=" O PRO B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 604 removed outlier: 3.593A pdb=" N ALA B 604 " --> pdb=" O GLN B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 637 removed outlier: 4.530A pdb=" N ILE B 632 " --> pdb=" O ILE B 628 " (cutoff:3.500A) Proline residue: B 633 - end of helix Processing helix chain 'B' and resid 645 through 680 Proline residue: B 665 - end of helix Processing helix chain 'C' and resid 3 through 20 Processing helix chain 'C' and resid 20 through 34 Processing helix chain 'C' and resid 78 through 82 removed outlier: 4.162A pdb=" N SER C 82 " --> pdb=" O PRO C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 109 removed outlier: 3.696A pdb=" N ASP C 95 " --> pdb=" O ASN C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 122 removed outlier: 3.713A pdb=" N VAL C 121 " --> pdb=" O PRO C 117 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR C 122 " --> pdb=" O VAL C 118 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 117 through 122' Processing helix chain 'C' and resid 133 through 139 Processing helix chain 'C' and resid 140 through 149 Processing helix chain 'C' and resid 151 through 162 Processing helix chain 'C' and resid 178 through 189 Processing helix chain 'D' and resid 2 through 25 Processing sheet with id=AA1, first strand: chain 'A' and resid 202 through 204 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 122 removed outlier: 3.953A pdb=" N ARG B 107 " --> pdb=" O LEU B 133 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N VAL B 188 " --> pdb=" O ILE B 147 " (cutoff:3.500A) removed outlier: 3.559A 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: 3.929A pdb=" N ARG B 181 " --> pdb=" O ASP B 154 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 287 through 289 removed outlier: 7.495A pdb=" N GLY B 517 " --> pdb=" O MET B 535 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 305 through 306 Processing sheet with id=AA7, first strand: chain 'B' and resid 319 through 324 removed outlier: 4.761A pdb=" N ALA B 319 " --> pdb=" O LYS B 446 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N LYS B 446 " --> pdb=" O ALA B 319 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLU B 321 " --> pdb=" O ALA B 444 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N VAL B 433 " --> pdb=" O LEU B 440 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N VAL B 442 " --> pdb=" O LEU B 431 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N LEU B 431 " --> pdb=" O VAL B 442 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N ALA B 444 " --> pdb=" O THR B 429 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N THR B 429 " --> pdb=" O ALA B 444 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 42 through 44 removed outlier: 4.121A pdb=" N GLY C 51 " --> pdb=" O ILE C 43 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 131 through 132 removed outlier: 3.587A pdb=" N VAL C 175 " --> pdb=" O GLN C 164 " (cutoff:3.500A) 682 hydrogen bonds defined for protein. 2010 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: 5.52 Time building geometry restraints manager: 2.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.80 - 1.00: 11180 1.00 - 1.20: 16 1.20 - 1.41: 4301 1.41 - 1.61: 6686 1.61 - 1.81: 120 Bond restraints: 22303 Sorted by residual: bond pdb=" C13 9Y0 A 802 " pdb=" C14 9Y0 A 802 " ideal model delta sigma weight residual 1.333 1.561 -0.228 2.00e-02 2.50e+03 1.29e+02 bond pdb=" C21 9Y0 A 802 " pdb=" O7 9Y0 A 802 " ideal model delta sigma weight residual 1.330 1.428 -0.098 2.00e-02 2.50e+03 2.39e+01 bond pdb=" C5 9Y0 A 802 " pdb=" O5 9Y0 A 802 " ideal model delta sigma weight residual 1.326 1.420 -0.094 2.00e-02 2.50e+03 2.19e+01 bond pdb=" C31 PEV A 801 " pdb=" O2 PEV A 801 " ideal model delta sigma weight residual 1.330 1.399 -0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" C14 9Y0 A 802 " pdb=" C15 9Y0 A 802 " ideal model delta sigma weight residual 1.497 1.561 -0.064 2.00e-02 2.50e+03 1.04e+01 ... (remaining 22298 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.22: 40341 6.22 - 12.45: 45 12.45 - 18.67: 7 18.67 - 24.90: 6 24.90 - 31.12: 4 Bond angle restraints: 40403 Sorted by residual: angle pdb="HD22 LEU B 85 " pdb=" CD2 LEU B 85 " pdb="HD23 LEU B 85 " ideal model delta sigma weight residual 110.00 78.88 31.12 3.00e+00 1.11e-01 1.08e+02 angle pdb="HD21 LEU B 85 " pdb=" CD2 LEU B 85 " pdb="HD22 LEU B 85 " ideal model delta sigma weight residual 110.00 80.03 29.97 3.00e+00 1.11e-01 9.98e+01 angle pdb=" CG LEU B 85 " pdb=" CD2 LEU B 85 " pdb="HD23 LEU B 85 " ideal model delta sigma weight residual 109.00 79.78 29.22 3.00e+00 1.11e-01 9.49e+01 angle pdb=" CG LEU B 85 " pdb=" CD2 LEU B 85 " pdb="HD21 LEU B 85 " ideal model delta sigma weight residual 109.00 82.69 26.31 3.00e+00 1.11e-01 7.69e+01 angle pdb=" CG ASN D 25 " pdb=" ND2 ASN D 25 " pdb="HD22 ASN D 25 " ideal model delta sigma weight residual 120.00 143.96 -23.96 3.00e+00 1.11e-01 6.38e+01 ... (remaining 40398 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.70: 9920 28.70 - 57.40: 484 57.40 - 86.10: 50 86.10 - 114.81: 3 114.81 - 143.51: 3 Dihedral angle restraints: 10460 sinusoidal: 5779 harmonic: 4681 Sorted by residual: dihedral pdb=" C3 PEV A 801 " pdb=" C1 PEV A 801 " pdb=" C2 PEV A 801 " pdb=" O3P PEV A 801 " ideal model delta sinusoidal sigma weight residual 292.80 149.29 143.51 1 3.00e+01 1.11e-03 1.92e+01 dihedral pdb=" N 9Y0 A 802 " pdb=" C3 9Y0 A 802 " pdb=" C4 9Y0 A 802 " pdb=" O1 9Y0 A 802 " ideal model delta sinusoidal sigma weight residual -62.65 72.78 -135.43 1 3.00e+01 1.11e-03 1.83e+01 dihedral pdb=" C3 9Y0 A 802 " pdb=" O1 9Y0 A 802 " pdb=" P 9Y0 A 802 " pdb=" O3 9Y0 A 802 " ideal model delta sinusoidal sigma weight residual 291.93 172.04 119.89 1 3.00e+01 1.11e-03 1.60e+01 ... (remaining 10457 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1454 0.060 - 0.120: 307 0.120 - 0.180: 42 0.180 - 0.240: 4 0.240 - 0.300: 1 Chirality restraints: 1808 Sorted by residual: chirality pdb=" CA ILE B 591 " pdb=" N ILE B 591 " pdb=" C ILE B 591 " pdb=" CB ILE B 591 " both_signs ideal model delta sigma weight residual False 2.43 2.13 0.30 2.00e-01 2.50e+01 2.24e+00 chirality pdb=" CB THR B 516 " pdb=" CA THR B 516 " pdb=" OG1 THR B 516 " pdb=" CG2 THR B 516 " both_signs ideal model delta sigma weight residual False 2.55 2.32 0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CB THR A 251 " pdb=" CA THR A 251 " pdb=" OG1 THR A 251 " pdb=" CG2 THR A 251 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.23 2.00e-01 2.50e+01 1.28e+00 ... (remaining 1805 not shown) Planarity restraints: 3292 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C12 9Y0 A 802 " 0.167 2.00e-02 2.50e+03 2.93e-01 8.60e+02 pdb=" C13 9Y0 A 802 " -0.405 2.00e-02 2.50e+03 pdb=" C14 9Y0 A 802 " 0.368 2.00e-02 2.50e+03 pdb=" C15 9Y0 A 802 " -0.130 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 25 " -0.054 2.00e-02 2.50e+03 9.34e-02 1.31e+02 pdb=" CG ASN D 25 " 0.006 2.00e-02 2.50e+03 pdb=" OD1 ASN D 25 " 0.000 2.00e-02 2.50e+03 pdb=" ND2 ASN D 25 " 0.160 2.00e-02 2.50e+03 pdb="HD21 ASN D 25 " 0.038 2.00e-02 2.50e+03 pdb="HD22 ASN D 25 " -0.150 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 93 " -0.065 2.00e-02 2.50e+03 8.82e-02 1.17e+02 pdb=" CD GLN A 93 " 0.041 2.00e-02 2.50e+03 pdb=" OE1 GLN A 93 " 0.002 2.00e-02 2.50e+03 pdb=" NE2 GLN A 93 " 0.144 2.00e-02 2.50e+03 pdb="HE21 GLN A 93 " 0.018 2.00e-02 2.50e+03 pdb="HE22 GLN A 93 " -0.140 2.00e-02 2.50e+03 ... (remaining 3289 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.21: 1737 2.21 - 2.81: 48509 2.81 - 3.41: 63165 3.41 - 4.00: 85304 4.00 - 4.60: 134116 Nonbonded interactions: 332831 Sorted by model distance: nonbonded pdb=" OD1 ASP B 473 " pdb=" H ASN B 474 " model vdw 1.615 2.450 nonbonded pdb=" OD1 ASP B 143 " pdb=" H GLY B 178 " model vdw 1.618 2.450 nonbonded pdb=" OD2 ASP B 552 " pdb=" HZ2 LYS B 557 " model vdw 1.636 2.450 nonbonded pdb=" O GLY C 61 " pdb=" HE2 HIS C 66 " model vdw 1.637 2.450 nonbonded pdb=" O ARG A 157 " pdb=" HZ3 LYS A 407 " model vdw 1.638 2.450 ... (remaining 332826 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: 2.040 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: 0.080 Extract box with map and model: 0.280 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 20.320 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 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: 0.010 Load rotamer database and sin/cos tables:8.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 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 0.228 11111 Z= 0.421 Angle : 0.970 23.957 15099 Z= 0.471 Chirality : 0.050 0.300 1808 Planarity : 0.009 0.293 1910 Dihedral : 14.148 143.508 3998 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 0.44 % Allowed : 7.14 % Favored : 92.42 % 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: -2.73 (0.19), residues: 1442 helix: -0.92 (0.16), residues: 862 sheet: -3.76 (0.41), residues: 90 loop : -2.90 (0.24), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 21 TYR 0.027 0.003 TYR A 381 PHE 0.026 0.003 PHE A 109 TRP 0.029 0.003 TRP B 73 HIS 0.006 0.001 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00967 (11111) covalent geometry : angle 0.96981 (15099) hydrogen bonds : bond 0.12101 ( 682) hydrogen bonds : angle 6.33698 ( 2010) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 151 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 MET cc_start: 0.8235 (mmt) cc_final: 0.7634 (mmt) REVERT: A 112 ASN cc_start: 0.8836 (OUTLIER) cc_final: 0.8449 (t0) REVERT: A 211 GLN cc_start: 0.8227 (mm110) cc_final: 0.7987 (mm-40) REVERT: A 316 SER cc_start: 0.8481 (m) cc_final: 0.8096 (p) REVERT: B 300 ASP cc_start: 0.6710 (m-30) cc_final: 0.6407 (m-30) REVERT: B 383 MET cc_start: 0.8265 (ptp) cc_final: 0.7884 (ptm) REVERT: B 515 MET cc_start: 0.8747 (ttt) cc_final: 0.8545 (ttt) outliers start: 5 outliers final: 2 residues processed: 156 average time/residue: 1.0792 time to fit residues: 184.5846 Evaluate side-chains 125 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 122 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ASN Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain B residue 628 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.1980 chunk 55 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN A 306 ASN B 603 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.116108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.087424 restraints weight = 44168.041| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 1.82 r_work: 0.2919 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.1228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11111 Z= 0.145 Angle : 0.588 6.017 15099 Z= 0.307 Chirality : 0.040 0.158 1808 Planarity : 0.004 0.041 1910 Dihedral : 10.590 148.464 1621 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 1.06 % Allowed : 10.75 % Favored : 88.19 % 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: -1.17 (0.21), residues: 1442 helix: 0.45 (0.17), residues: 874 sheet: -3.51 (0.46), residues: 80 loop : -2.54 (0.24), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 48 TYR 0.025 0.001 TYR A 381 PHE 0.011 0.001 PHE A 109 TRP 0.011 0.001 TRP B 245 HIS 0.002 0.000 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00318 (11111) covalent geometry : angle 0.58784 (15099) hydrogen bonds : bond 0.04840 ( 682) hydrogen bonds : angle 5.07055 ( 2010) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 131 time to evaluate : 0.574 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: A 316 SER cc_start: 0.8407 (m) cc_final: 0.7794 (p) REVERT: B 300 ASP cc_start: 0.6108 (m-30) cc_final: 0.5825 (m-30) REVERT: B 338 GLN cc_start: 0.7693 (tm-30) cc_final: 0.7387 (tm130) REVERT: B 383 MET cc_start: 0.7832 (ptp) cc_final: 0.7559 (ptm) REVERT: B 392 MET cc_start: 0.8032 (ptp) cc_final: 0.7681 (ptm) REVERT: C 68 ARG cc_start: 0.8177 (mmt180) cc_final: 0.7887 (mtt180) outliers start: 12 outliers final: 6 residues processed: 139 average time/residue: 1.0585 time to fit residues: 161.8162 Evaluate side-chains 123 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 117 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain B residue 142 CYS Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 628 ILE Chi-restraints excluded: chain B residue 649 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 98 optimal weight: 0.6980 chunk 120 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 8 optimal weight: 0.3980 chunk 26 optimal weight: 0.3980 chunk 41 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 128 optimal weight: 1.9990 chunk 94 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 86 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.116883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.088139 restraints weight = 43547.937| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 1.86 r_work: 0.2925 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2815 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11111 Z= 0.129 Angle : 0.531 5.650 15099 Z= 0.276 Chirality : 0.039 0.149 1808 Planarity : 0.004 0.037 1910 Dihedral : 10.298 148.661 1619 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 1.15 % Allowed : 11.01 % 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: -0.48 (0.22), residues: 1442 helix: 0.96 (0.17), residues: 885 sheet: -3.23 (0.48), residues: 80 loop : -2.24 (0.25), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 48 TYR 0.024 0.001 TYR A 381 PHE 0.010 0.001 PHE A 392 TRP 0.009 0.001 TRP B 240 HIS 0.003 0.001 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00286 (11111) covalent geometry : angle 0.53054 (15099) hydrogen bonds : bond 0.04408 ( 682) hydrogen bonds : angle 4.74234 ( 2010) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 122 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 MET cc_start: 0.7914 (mmt) cc_final: 0.7425 (mmt) REVERT: A 316 SER cc_start: 0.8322 (m) cc_final: 0.7740 (p) REVERT: A 366 MET cc_start: 0.8232 (mtp) cc_final: 0.8029 (mtm) REVERT: A 439 ASP cc_start: 0.8079 (t0) cc_final: 0.7874 (t0) REVERT: B 300 ASP cc_start: 0.6125 (m-30) cc_final: 0.5846 (m-30) REVERT: B 338 GLN cc_start: 0.7623 (tm-30) cc_final: 0.7232 (tm130) REVERT: B 383 MET cc_start: 0.7642 (ptp) cc_final: 0.7174 (ptp) outliers start: 13 outliers final: 5 residues processed: 131 average time/residue: 1.0534 time to fit residues: 152.3507 Evaluate side-chains 121 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 116 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain B residue 142 CYS Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 628 ILE Chi-restraints excluded: chain B residue 649 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 41 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 135 optimal weight: 0.5980 chunk 86 optimal weight: 0.7980 chunk 78 optimal weight: 0.7980 chunk 119 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 82 optimal weight: 0.9990 chunk 95 optimal weight: 8.9990 chunk 2 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 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 306 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.116731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.087848 restraints weight = 43881.580| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 1.80 r_work: 0.2928 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11111 Z= 0.146 Angle : 0.527 5.651 15099 Z= 0.274 Chirality : 0.039 0.147 1808 Planarity : 0.004 0.038 1910 Dihedral : 9.772 158.648 1617 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 0.97 % Allowed : 12.07 % Favored : 86.96 % 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: 1442 helix: 1.17 (0.17), residues: 884 sheet: -3.00 (0.50), residues: 80 loop : -2.08 (0.25), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 212 TYR 0.023 0.001 TYR A 381 PHE 0.010 0.001 PHE A 109 TRP 0.009 0.001 TRP B 240 HIS 0.003 0.000 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00331 (11111) covalent geometry : angle 0.52667 (15099) hydrogen bonds : bond 0.04328 ( 682) hydrogen bonds : angle 4.59755 ( 2010) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 118 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 SER cc_start: 0.8322 (m) cc_final: 0.7782 (p) REVERT: B 338 GLN cc_start: 0.7534 (tm-30) cc_final: 0.7241 (tm130) REVERT: B 383 MET cc_start: 0.7757 (ptp) cc_final: 0.7400 (ptp) REVERT: B 392 MET cc_start: 0.8010 (ptp) cc_final: 0.7688 (ptm) outliers start: 11 outliers final: 7 residues processed: 124 average time/residue: 1.0301 time to fit residues: 140.7509 Evaluate side-chains 122 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 115 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain B residue 142 CYS Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 489 ASP Chi-restraints excluded: chain B residue 628 ILE Chi-restraints excluded: chain B residue 649 MET Chi-restraints excluded: chain C residue 189 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 1 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 95 optimal weight: 0.7980 chunk 114 optimal weight: 0.0020 chunk 85 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 121 optimal weight: 0.8980 chunk 116 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 overall best weight: 0.7388 ------------------------------------------------------------------------------- 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 = 0.3491 r_free = 0.3491 target = 0.118457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.089358 restraints weight = 43915.694| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 1.85 r_work: 0.2950 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2842 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11111 Z= 0.135 Angle : 0.515 5.593 15099 Z= 0.267 Chirality : 0.039 0.147 1808 Planarity : 0.004 0.039 1910 Dihedral : 9.609 165.547 1617 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 0.97 % Allowed : 12.25 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.09 (0.22), residues: 1442 helix: 1.36 (0.17), residues: 885 sheet: -2.85 (0.50), residues: 85 loop : -1.92 (0.26), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 212 TYR 0.022 0.001 TYR A 381 PHE 0.011 0.001 PHE A 392 TRP 0.009 0.001 TRP B 240 HIS 0.003 0.001 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00306 (11111) covalent geometry : angle 0.51524 (15099) hydrogen bonds : bond 0.04174 ( 682) hydrogen bonds : angle 4.48563 ( 2010) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 123 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 MET cc_start: 0.7991 (mmt) cc_final: 0.7509 (mmt) REVERT: A 316 SER cc_start: 0.8392 (m) cc_final: 0.7878 (p) REVERT: B 316 ASN cc_start: 0.7778 (m-40) cc_final: 0.7494 (m-40) REVERT: B 338 GLN cc_start: 0.7429 (tm-30) cc_final: 0.7140 (tm130) REVERT: B 383 MET cc_start: 0.7766 (ptp) cc_final: 0.7408 (ptp) REVERT: B 392 MET cc_start: 0.8049 (ptp) cc_final: 0.7743 (ptm) REVERT: B 649 MET cc_start: 0.8018 (OUTLIER) cc_final: 0.7770 (tpt) outliers start: 11 outliers final: 3 residues processed: 131 average time/residue: 0.9857 time to fit residues: 143.2826 Evaluate side-chains 120 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 116 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 142 CYS Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 628 ILE Chi-restraints excluded: chain B residue 649 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 137 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 ASN D 25 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.116642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.087598 restraints weight = 44896.405| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 1.81 r_work: 0.2925 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2815 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 11111 Z= 0.202 Angle : 0.549 5.708 15099 Z= 0.287 Chirality : 0.040 0.146 1808 Planarity : 0.004 0.041 1910 Dihedral : 9.704 168.999 1617 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 1.32 % Allowed : 12.51 % Favored : 86.17 % 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: 0.04 (0.22), residues: 1442 helix: 1.30 (0.17), residues: 880 sheet: -2.76 (0.54), residues: 79 loop : -1.91 (0.25), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 212 TYR 0.022 0.002 TYR A 381 PHE 0.016 0.001 PHE B 322 TRP 0.010 0.001 TRP B 240 HIS 0.004 0.001 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00474 (11111) covalent geometry : angle 0.54943 (15099) hydrogen bonds : bond 0.04545 ( 682) hydrogen bonds : angle 4.55485 ( 2010) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 119 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 SER cc_start: 0.8384 (m) cc_final: 0.7867 (p) REVERT: B 316 ASN cc_start: 0.7788 (m-40) cc_final: 0.7510 (m-40) REVERT: B 338 GLN cc_start: 0.7368 (tm-30) cc_final: 0.7050 (tm130) REVERT: B 383 MET cc_start: 0.7823 (ptp) cc_final: 0.7448 (ptp) REVERT: B 392 MET cc_start: 0.8067 (ptp) cc_final: 0.7805 (ptm) REVERT: B 649 MET cc_start: 0.8071 (OUTLIER) cc_final: 0.7822 (tpt) outliers start: 15 outliers final: 7 residues processed: 128 average time/residue: 1.0730 time to fit residues: 151.5310 Evaluate side-chains 125 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 117 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 410 ASP Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain B residue 142 CYS Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain B residue 628 ILE Chi-restraints excluded: chain B residue 649 MET Chi-restraints excluded: chain C residue 189 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 104 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 118 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 102 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 101 optimal weight: 0.6980 chunk 124 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 = 0.3479 r_free = 0.3479 target = 0.117553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.088552 restraints weight = 44320.013| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 1.80 r_work: 0.2940 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 11111 Z= 0.153 Angle : 0.524 5.610 15099 Z= 0.273 Chirality : 0.039 0.146 1808 Planarity : 0.004 0.050 1910 Dihedral : 9.628 174.440 1617 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 1.59 % Allowed : 12.60 % Favored : 85.81 % 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: 0.16 (0.22), residues: 1442 helix: 1.40 (0.17), residues: 880 sheet: -2.75 (0.51), residues: 86 loop : -1.80 (0.26), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 48 TYR 0.022 0.001 TYR A 381 PHE 0.015 0.001 PHE A 392 TRP 0.010 0.001 TRP B 240 HIS 0.003 0.001 HIS A 85 Details of bonding type rmsd covalent geometry : bond 0.00352 (11111) covalent geometry : angle 0.52415 (15099) hydrogen bonds : bond 0.04313 ( 682) hydrogen bonds : angle 4.47391 ( 2010) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 117 time to evaluate : 0.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 SER cc_start: 0.8448 (m) cc_final: 0.7933 (p) REVERT: B 186 TRP cc_start: 0.8241 (OUTLIER) cc_final: 0.7226 (p90) REVERT: B 316 ASN cc_start: 0.7789 (m-40) cc_final: 0.7507 (m-40) REVERT: B 329 ASP cc_start: 0.7221 (OUTLIER) cc_final: 0.7011 (t70) REVERT: B 338 GLN cc_start: 0.7341 (tm-30) cc_final: 0.7032 (tm130) REVERT: B 383 MET cc_start: 0.7808 (ptp) cc_final: 0.7368 (ptp) REVERT: B 392 MET cc_start: 0.8079 (ptp) cc_final: 0.7754 (ptm) outliers start: 18 outliers final: 9 residues processed: 127 average time/residue: 1.0423 time to fit residues: 146.3116 Evaluate side-chains 128 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 117 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 410 ASP Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain B residue 142 CYS Chi-restraints excluded: chain B residue 186 TRP Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 329 ASP Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 608 MET Chi-restraints excluded: chain B residue 628 ILE Chi-restraints excluded: chain B residue 649 MET Chi-restraints excluded: chain C residue 189 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 40 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 36 optimal weight: 0.0870 chunk 3 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 88 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 overall best weight: 1.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.116360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.087294 restraints weight = 44435.522| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 1.79 r_work: 0.2921 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 11111 Z= 0.213 Angle : 0.555 5.693 15099 Z= 0.291 Chirality : 0.040 0.147 1808 Planarity : 0.004 0.042 1910 Dihedral : 9.761 179.223 1617 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 1.67 % Allowed : 12.69 % Favored : 85.64 % 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: 1442 helix: 1.30 (0.17), residues: 880 sheet: -2.59 (0.52), residues: 85 loop : -1.84 (0.26), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 48 TYR 0.021 0.002 TYR A 381 PHE 0.012 0.001 PHE A 109 TRP 0.010 0.001 TRP B 240 HIS 0.004 0.001 HIS A 85 Details of bonding type rmsd covalent geometry : bond 0.00504 (11111) covalent geometry : angle 0.55519 (15099) hydrogen bonds : bond 0.04640 ( 682) hydrogen bonds : angle 4.56754 ( 2010) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 116 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 SER cc_start: 0.8392 (m) cc_final: 0.7886 (p) REVERT: B 186 TRP cc_start: 0.8244 (OUTLIER) cc_final: 0.7316 (p90) REVERT: B 316 ASN cc_start: 0.7792 (m-40) cc_final: 0.7514 (m-40) REVERT: B 338 GLN cc_start: 0.7371 (tm-30) cc_final: 0.7043 (tm130) REVERT: B 392 MET cc_start: 0.8121 (ptp) cc_final: 0.7839 (ptm) outliers start: 19 outliers final: 13 residues processed: 129 average time/residue: 1.1024 time to fit residues: 156.9663 Evaluate side-chains 130 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 116 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 410 ASP Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain B residue 142 CYS Chi-restraints excluded: chain B residue 186 TRP Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain B residue 608 MET Chi-restraints excluded: chain B residue 628 ILE Chi-restraints excluded: chain B residue 649 MET Chi-restraints excluded: chain C residue 189 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 28 optimal weight: 1.9990 chunk 115 optimal weight: 0.9990 chunk 102 optimal weight: 0.4980 chunk 89 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 30 optimal weight: 0.5980 chunk 129 optimal weight: 0.3980 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 239 ASN ** 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 = 0.3480 r_free = 0.3480 target = 0.117510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.088609 restraints weight = 44243.275| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 1.80 r_work: 0.2941 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11111 Z= 0.136 Angle : 0.524 5.578 15099 Z= 0.272 Chirality : 0.039 0.145 1808 Planarity : 0.004 0.054 1910 Dihedral : 9.568 173.918 1617 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 1.41 % Allowed : 13.22 % Favored : 85.37 % 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: 0.22 (0.22), residues: 1442 helix: 1.44 (0.17), residues: 880 sheet: -2.43 (0.51), residues: 91 loop : -1.82 (0.26), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 48 TYR 0.022 0.001 TYR A 381 PHE 0.010 0.001 PHE A 494 TRP 0.010 0.001 TRP B 240 HIS 0.003 0.001 HIS A 85 Details of bonding type rmsd covalent geometry : bond 0.00310 (11111) covalent geometry : angle 0.52384 (15099) hydrogen bonds : bond 0.04300 ( 682) hydrogen bonds : angle 4.46367 ( 2010) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 117 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 SER cc_start: 0.8454 (m) cc_final: 0.7927 (p) REVERT: B 186 TRP cc_start: 0.8232 (OUTLIER) cc_final: 0.7303 (p90) REVERT: B 316 ASN cc_start: 0.7796 (m-40) cc_final: 0.7513 (m-40) REVERT: B 338 GLN cc_start: 0.7352 (tm-30) cc_final: 0.7041 (tm130) REVERT: B 383 MET cc_start: 0.7995 (ptp) cc_final: 0.7657 (ptp) REVERT: B 392 MET cc_start: 0.8097 (ptp) cc_final: 0.7825 (ptm) outliers start: 16 outliers final: 12 residues processed: 127 average time/residue: 1.0712 time to fit residues: 149.6290 Evaluate side-chains 128 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 115 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 410 ASP Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain B residue 142 CYS Chi-restraints excluded: chain B residue 186 TRP Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain B residue 608 MET Chi-restraints excluded: chain B residue 628 ILE Chi-restraints excluded: chain B residue 649 MET Chi-restraints excluded: chain C residue 189 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 85 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 133 optimal weight: 0.0070 chunk 103 optimal weight: 0.9980 chunk 127 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 overall best weight: 0.8002 ------------------------------------------------------------------------------- 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 = 0.3486 r_free = 0.3486 target = 0.117951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.089121 restraints weight = 44393.772| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 1.80 r_work: 0.2950 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11111 Z= 0.142 Angle : 0.518 5.560 15099 Z= 0.269 Chirality : 0.038 0.143 1808 Planarity : 0.004 0.049 1910 Dihedral : 9.243 158.496 1617 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 1.15 % Allowed : 13.39 % Favored : 85.46 % 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: 0.34 (0.22), residues: 1442 helix: 1.54 (0.17), residues: 880 sheet: -2.38 (0.52), residues: 91 loop : -1.80 (0.26), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 48 TYR 0.022 0.001 TYR A 381 PHE 0.019 0.001 PHE A 392 TRP 0.010 0.001 TRP B 245 HIS 0.004 0.001 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00325 (11111) covalent geometry : angle 0.51819 (15099) hydrogen bonds : bond 0.04203 ( 682) hydrogen bonds : angle 4.40163 ( 2010) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 116 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 SER cc_start: 0.8412 (m) cc_final: 0.7917 (p) REVERT: B 186 TRP cc_start: 0.8240 (OUTLIER) cc_final: 0.7312 (p90) REVERT: B 316 ASN cc_start: 0.7818 (m-40) cc_final: 0.7526 (m-40) REVERT: B 338 GLN cc_start: 0.7369 (tm-30) cc_final: 0.7037 (tm130) REVERT: B 383 MET cc_start: 0.7991 (ptp) cc_final: 0.7678 (ptp) REVERT: B 392 MET cc_start: 0.8103 (ptp) cc_final: 0.7829 (ptm) REVERT: C 74 GLU cc_start: 0.8448 (mt-10) cc_final: 0.8079 (mp0) outliers start: 13 outliers final: 10 residues processed: 123 average time/residue: 1.0601 time to fit residues: 143.1020 Evaluate side-chains 127 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 116 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 410 ASP Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain B residue 142 CYS Chi-restraints excluded: chain B residue 186 TRP Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 628 ILE Chi-restraints excluded: chain B residue 649 MET Chi-restraints excluded: chain C residue 189 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 77 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 54 optimal weight: 0.5980 chunk 91 optimal weight: 0.0770 chunk 35 optimal weight: 0.5980 chunk 84 optimal weight: 0.9980 chunk 135 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.117826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.089205 restraints weight = 43631.934| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 1.83 r_work: 0.2946 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2837 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11111 Z= 0.125 Angle : 0.515 5.512 15099 Z= 0.267 Chirality : 0.038 0.143 1808 Planarity : 0.004 0.044 1910 Dihedral : 9.066 148.484 1617 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 0.97 % Allowed : 13.48 % Favored : 85.55 % 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: 1442 helix: 1.61 (0.17), residues: 880 sheet: -2.36 (0.53), residues: 91 loop : -1.75 (0.26), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 48 TYR 0.022 0.001 TYR A 381 PHE 0.009 0.001 PHE A 494 TRP 0.010 0.001 TRP B 245 HIS 0.003 0.001 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00281 (11111) covalent geometry : angle 0.51515 (15099) hydrogen bonds : bond 0.04100 ( 682) hydrogen bonds : angle 4.36687 ( 2010) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6205.74 seconds wall clock time: 105 minutes 35.16 seconds (6335.16 seconds total)