Starting phenix.real_space_refine on Sat Aug 23 00:52:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y94_39069/08_2025/8y94_39069.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y94_39069/08_2025/8y94_39069.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8y94_39069/08_2025/8y94_39069.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y94_39069/08_2025/8y94_39069.map" model { file = "/net/cci-nas-00/data/ceres_data/8y94_39069/08_2025/8y94_39069.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y94_39069/08_2025/8y94_39069.cif" } resolution = 3.29 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= 0.005 sd= 0.047 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: 4 Type Number sf(0) Gaussians S 40 5.16 5 C 6052 2.51 5 N 1412 2.21 5 O 1528 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9032 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 565, 4516 Classifications: {'peptide': 565} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 544} Chain: "C" Number of atoms: 4516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 565, 4516 Classifications: {'peptide': 565} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 544} Time building chain proxies: 2.36, per 1000 atoms: 0.26 Number of scatterers: 9032 At special positions: 0 Unit cell: (85.41, 116.07, 91.98, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 40 16.00 O 1528 8.00 N 1412 7.00 C 6052 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.87 Conformation dependent library (CDL) restraints added in 324.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2076 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 0 sheets defined 77.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 61 through 72 removed outlier: 3.692A pdb=" N PHE A 65 " --> pdb=" O LYS A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 78 removed outlier: 5.013A pdb=" N LEU A 76 " --> pdb=" O ALA A 73 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ALA A 77 " --> pdb=" O VAL A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 89 Processing helix chain 'A' and resid 94 through 121 Proline residue: A 108 - end of helix Processing helix chain 'A' and resid 131 through 133 No H-bonds generated for 'chain 'A' and resid 131 through 133' Processing helix chain 'A' and resid 134 through 167 removed outlier: 3.900A pdb=" N GLY A 138 " --> pdb=" O PHE A 134 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N TYR A 139 " --> pdb=" O LYS A 135 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ILE A 142 " --> pdb=" O GLY A 138 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA A 145 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N TYR A 151 " --> pdb=" O TYR A 147 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N VAL A 154 " --> pdb=" O PHE A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 204 Processing helix chain 'A' and resid 208 through 217 Processing helix chain 'A' and resid 220 through 224 removed outlier: 3.570A pdb=" N GLU A 223 " --> pdb=" O HIS A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 253 Processing helix chain 'A' and resid 255 through 267 removed outlier: 3.649A pdb=" N SER A 259 " --> pdb=" O GLY A 255 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ILE A 265 " --> pdb=" O LYS A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 284 removed outlier: 4.079A pdb=" N PHE A 272 " --> pdb=" O THR A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 295 removed outlier: 3.859A pdb=" N GLY A 290 " --> pdb=" O GLY A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 302 removed outlier: 3.758A pdb=" N LEU A 302 " --> pdb=" O PHE A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 320 removed outlier: 4.210A pdb=" N GLN A 314 " --> pdb=" O ASP A 310 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE A 315 " --> pdb=" O ALA A 311 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE A 316 " --> pdb=" O ALA A 312 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY A 320 " --> pdb=" O PHE A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 332 removed outlier: 3.898A pdb=" N TYR A 332 " --> pdb=" O ALA A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 372 Processing helix chain 'A' and resid 385 through 398 removed outlier: 3.939A pdb=" N TYR A 391 " --> pdb=" O VAL A 387 " (cutoff:3.500A) Proline residue: A 392 - end of helix Processing helix chain 'A' and resid 400 through 435 removed outlier: 3.623A pdb=" N TRP A 404 " --> pdb=" O GLY A 400 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N SER A 419 " --> pdb=" O LEU A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 441 removed outlier: 4.008A pdb=" N ARG A 440 " --> pdb=" O GLN A 436 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N HIS A 441 " --> pdb=" O VAL A 437 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 436 through 441' Processing helix chain 'A' and resid 441 through 457 Processing helix chain 'A' and resid 457 through 462 removed outlier: 3.508A pdb=" N THR A 462 " --> pdb=" O LEU A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 494 removed outlier: 4.045A pdb=" N VAL A 468 " --> pdb=" O GLY A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 509 removed outlier: 3.501A pdb=" N PHE A 501 " --> pdb=" O GLY A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 523 Processing helix chain 'A' and resid 523 through 539 removed outlier: 3.788A pdb=" N ALA A 527 " --> pdb=" O PHE A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 567 removed outlier: 3.776A pdb=" N ASN A 555 " --> pdb=" O PRO A 551 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TRP A 556 " --> pdb=" O PRO A 552 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N SER A 565 " --> pdb=" O ILE A 561 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N MET A 566 " --> pdb=" O ALA A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 579 Processing helix chain 'A' and resid 583 through 593 Processing helix chain 'A' and resid 597 through 604 removed outlier: 3.767A pdb=" N VAL A 601 " --> pdb=" O GLU A 597 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ALA A 602 " --> pdb=" O HIS A 598 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLN A 603 " --> pdb=" O HIS A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 615 removed outlier: 4.014A pdb=" N TRP A 614 " --> pdb=" O GLN A 610 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 72 removed outlier: 3.690A pdb=" N PHE C 65 " --> pdb=" O LYS C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 78 removed outlier: 5.018A pdb=" N LEU C 76 " --> pdb=" O ALA C 73 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ALA C 77 " --> pdb=" O VAL C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 94 through 121 Proline residue: C 108 - end of helix Processing helix chain 'C' and resid 131 through 133 No H-bonds generated for 'chain 'C' and resid 131 through 133' Processing helix chain 'C' and resid 134 through 167 removed outlier: 3.894A pdb=" N GLY C 138 " --> pdb=" O PHE C 134 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TYR C 139 " --> pdb=" O LYS C 135 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ILE C 142 " --> pdb=" O GLY C 138 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA C 145 " --> pdb=" O VAL C 141 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TYR C 151 " --> pdb=" O TYR C 147 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N VAL C 154 " --> pdb=" O PHE C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 204 Processing helix chain 'C' and resid 208 through 217 Processing helix chain 'C' and resid 220 through 224 removed outlier: 3.570A pdb=" N GLU C 223 " --> pdb=" O HIS C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 253 Processing helix chain 'C' and resid 255 through 267 removed outlier: 3.652A pdb=" N SER C 259 " --> pdb=" O GLY C 255 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ILE C 265 " --> pdb=" O LYS C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 284 removed outlier: 4.086A pdb=" N PHE C 272 " --> pdb=" O THR C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 295 removed outlier: 3.860A pdb=" N GLY C 290 " --> pdb=" O GLY C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 302 removed outlier: 3.758A pdb=" N LEU C 302 " --> pdb=" O PHE C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 320 removed outlier: 4.209A pdb=" N GLN C 314 " --> pdb=" O ASP C 310 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ILE C 315 " --> pdb=" O ALA C 311 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE C 316 " --> pdb=" O ALA C 312 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY C 320 " --> pdb=" O PHE C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 332 removed outlier: 3.908A pdb=" N TYR C 332 " --> pdb=" O ALA C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 372 Processing helix chain 'C' and resid 385 through 398 removed outlier: 3.939A pdb=" N TYR C 391 " --> pdb=" O VAL C 387 " (cutoff:3.500A) Proline residue: C 392 - end of helix Processing helix chain 'C' and resid 400 through 435 removed outlier: 3.623A pdb=" N TRP C 404 " --> pdb=" O GLY C 400 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N SER C 419 " --> pdb=" O LEU C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 436 through 441 removed outlier: 4.005A pdb=" N ARG C 440 " --> pdb=" O GLN C 436 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N HIS C 441 " --> pdb=" O VAL C 437 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 436 through 441' Processing helix chain 'C' and resid 441 through 457 Processing helix chain 'C' and resid 457 through 462 removed outlier: 3.507A pdb=" N THR C 462 " --> pdb=" O LEU C 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 464 through 494 removed outlier: 4.045A pdb=" N VAL C 468 " --> pdb=" O GLY C 464 " (cutoff:3.500A) Processing helix chain 'C' and resid 497 through 509 removed outlier: 3.501A pdb=" N PHE C 501 " --> pdb=" O GLY C 497 " (cutoff:3.500A) Processing helix chain 'C' and resid 514 through 523 Processing helix chain 'C' and resid 523 through 539 removed outlier: 3.789A pdb=" N ALA C 527 " --> pdb=" O PHE C 523 " (cutoff:3.500A) Processing helix chain 'C' and resid 551 through 567 removed outlier: 3.775A pdb=" N ASN C 555 " --> pdb=" O PRO C 551 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TRP C 556 " --> pdb=" O PRO C 552 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N SER C 565 " --> pdb=" O ILE C 561 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N MET C 566 " --> pdb=" O ALA C 562 " (cutoff:3.500A) Processing helix chain 'C' and resid 567 through 579 Processing helix chain 'C' and resid 583 through 593 Processing helix chain 'C' and resid 597 through 604 removed outlier: 3.761A pdb=" N VAL C 601 " --> pdb=" O GLU C 597 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ALA C 602 " --> pdb=" O HIS C 598 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLN C 603 " --> pdb=" O HIS C 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 610 through 615 removed outlier: 4.013A pdb=" N TRP C 614 " --> pdb=" O GLN C 610 " (cutoff:3.500A) 550 hydrogen bonds defined for protein. 1620 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: 1.44 Time building geometry restraints manager: 1.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2658 1.34 - 1.46: 2276 1.46 - 1.58: 4330 1.58 - 1.69: 0 1.69 - 1.81: 62 Bond restraints: 9326 Sorted by residual: bond pdb=" C LEU C 269 " pdb=" N PRO C 270 " ideal model delta sigma weight residual 1.335 1.348 -0.013 1.28e-02 6.10e+03 1.10e+00 bond pdb=" C VAL A 379 " pdb=" O VAL A 379 " ideal model delta sigma weight residual 1.241 1.231 0.010 1.03e-02 9.43e+03 9.55e-01 bond pdb=" C ILE C 549 " pdb=" N PHE C 550 " ideal model delta sigma weight residual 1.331 1.359 -0.028 3.12e-02 1.03e+03 8.29e-01 bond pdb=" C ILE A 549 " pdb=" N PHE A 550 " ideal model delta sigma weight residual 1.331 1.359 -0.028 3.12e-02 1.03e+03 8.24e-01 bond pdb=" C LEU A 269 " pdb=" N PRO A 270 " ideal model delta sigma weight residual 1.335 1.346 -0.012 1.28e-02 6.10e+03 8.16e-01 ... (remaining 9321 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.14: 12326 1.14 - 2.28: 325 2.28 - 3.42: 59 3.42 - 4.55: 4 4.55 - 5.69: 12 Bond angle restraints: 12726 Sorted by residual: angle pdb=" N ILE C 265 " pdb=" CA ILE C 265 " pdb=" C ILE C 265 " ideal model delta sigma weight residual 111.90 109.56 2.34 8.10e-01 1.52e+00 8.34e+00 angle pdb=" N ILE A 265 " pdb=" CA ILE A 265 " pdb=" C ILE A 265 " ideal model delta sigma weight residual 111.90 109.57 2.33 8.10e-01 1.52e+00 8.25e+00 angle pdb=" C PHE A 388 " pdb=" N ILE A 389 " pdb=" CA ILE A 389 " ideal model delta sigma weight residual 123.08 120.24 2.84 1.01e+00 9.80e-01 7.90e+00 angle pdb=" C PHE C 388 " pdb=" N ILE C 389 " pdb=" CA ILE C 389 " ideal model delta sigma weight residual 123.08 120.29 2.79 1.01e+00 9.80e-01 7.63e+00 angle pdb=" N GLY A 231 " pdb=" CA GLY A 231 " pdb=" C GLY A 231 " ideal model delta sigma weight residual 111.21 113.74 -2.53 1.04e+00 9.25e-01 5.91e+00 ... (remaining 12721 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.99: 4833 11.99 - 23.98: 255 23.98 - 35.97: 85 35.97 - 47.96: 32 47.96 - 59.95: 9 Dihedral angle restraints: 5214 sinusoidal: 1950 harmonic: 3264 Sorted by residual: dihedral pdb=" N PHE A 359 " pdb=" CA PHE A 359 " pdb=" CB PHE A 359 " pdb=" CG PHE A 359 " ideal model delta sinusoidal sigma weight residual -60.00 -119.95 59.95 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" N PHE C 359 " pdb=" CA PHE C 359 " pdb=" CB PHE C 359 " pdb=" CG PHE C 359 " ideal model delta sinusoidal sigma weight residual -60.00 -119.94 59.94 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" N LEU A 190 " pdb=" CA LEU A 190 " pdb=" CB LEU A 190 " pdb=" CG LEU A 190 " ideal model delta sinusoidal sigma weight residual -60.00 -117.24 57.24 3 1.50e+01 4.44e-03 9.43e+00 ... (remaining 5211 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.022: 796 0.022 - 0.045: 360 0.045 - 0.067: 205 0.067 - 0.090: 36 0.090 - 0.112: 21 Chirality restraints: 1418 Sorted by residual: chirality pdb=" CA PRO C 270 " pdb=" N PRO C 270 " pdb=" C PRO C 270 " pdb=" CB PRO C 270 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 3.15e-01 chirality pdb=" CA ILE A 606 " pdb=" N ILE A 606 " pdb=" C ILE A 606 " pdb=" CB ILE A 606 " both_signs ideal model delta sigma weight residual False 2.43 2.54 -0.11 2.00e-01 2.50e+01 3.10e-01 chirality pdb=" CA ILE C 606 " pdb=" N ILE C 606 " pdb=" C ILE C 606 " pdb=" CB ILE C 606 " both_signs ideal model delta sigma weight residual False 2.43 2.54 -0.11 2.00e-01 2.50e+01 3.02e-01 ... (remaining 1415 not shown) Planarity restraints: 1552 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE C 103 " 0.006 2.00e-02 2.50e+03 1.11e-02 1.24e+00 pdb=" C ILE C 103 " -0.019 2.00e-02 2.50e+03 pdb=" O ILE C 103 " 0.007 2.00e-02 2.50e+03 pdb=" N ILE C 104 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 103 " -0.006 2.00e-02 2.50e+03 1.11e-02 1.24e+00 pdb=" C ILE A 103 " 0.019 2.00e-02 2.50e+03 pdb=" O ILE A 103 " -0.007 2.00e-02 2.50e+03 pdb=" N ILE A 104 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA C 477 " 0.005 2.00e-02 2.50e+03 1.09e-02 1.20e+00 pdb=" C ALA C 477 " -0.019 2.00e-02 2.50e+03 pdb=" O ALA C 477 " 0.007 2.00e-02 2.50e+03 pdb=" N GLY C 478 " 0.006 2.00e-02 2.50e+03 ... (remaining 1549 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 2669 2.82 - 3.34: 9057 3.34 - 3.86: 15119 3.86 - 4.38: 17356 4.38 - 4.90: 29697 Nonbonded interactions: 73898 Sorted by model distance: nonbonded pdb=" O LYS A 88 " pdb=" NH2 ARG A 301 " model vdw 2.295 3.120 nonbonded pdb=" O LYS C 88 " pdb=" NH2 ARG C 301 " model vdw 2.296 3.120 nonbonded pdb=" O SER C 251 " pdb=" OG1 THR C 258 " model vdw 2.309 3.040 nonbonded pdb=" O SER A 251 " pdb=" OG1 THR A 258 " model vdw 2.312 3.040 nonbonded pdb=" OG1 THR C 462 " pdb=" N LYS C 463 " model vdw 2.361 3.120 ... (remaining 73893 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } 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: 1.090 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: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.920 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6284 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 : 0.002 0.028 9326 Z= 0.107 Angle : 0.463 5.693 12726 Z= 0.278 Chirality : 0.033 0.112 1418 Planarity : 0.003 0.026 1552 Dihedral : 9.274 59.949 3138 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.15 % Allowed : 6.09 % Favored : 90.76 % 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 aren not related in a simple way. whole: -1.50 (0.22), residues: 1126 helix: -0.56 (0.18), residues: 732 sheet: None (None), residues: 0 loop : -1.63 (0.27), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 607 TYR 0.008 0.001 TYR A 151 PHE 0.005 0.001 PHE A 362 TRP 0.005 0.000 TRP C 235 HIS 0.002 0.000 HIS A 296 Details of bonding type rmsd covalent geometry : bond 0.00173 ( 9326) covalent geometry : angle 0.46322 (12726) hydrogen bonds : bond 0.14882 ( 550) hydrogen bonds : angle 6.27347 ( 1620) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 352 time to evaluate : 0.340 Fit side-chains REVERT: A 122 GLU cc_start: 0.7397 (mt-10) cc_final: 0.7176 (mt-10) REVERT: A 126 THR cc_start: 0.8786 (p) cc_final: 0.8563 (p) REVERT: A 173 TRP cc_start: 0.7971 (OUTLIER) cc_final: 0.7657 (p90) REVERT: A 278 LEU cc_start: 0.6509 (mt) cc_final: 0.6248 (mt) REVERT: A 332 TYR cc_start: 0.8246 (m-80) cc_final: 0.8016 (m-10) REVERT: A 337 ASN cc_start: 0.6205 (m110) cc_final: 0.5223 (m110) REVERT: A 480 SER cc_start: 0.8365 (m) cc_final: 0.8164 (t) REVERT: A 559 TRP cc_start: 0.6645 (m100) cc_final: 0.5925 (t60) REVERT: C 126 THR cc_start: 0.8757 (p) cc_final: 0.8548 (p) REVERT: C 173 TRP cc_start: 0.7888 (OUTLIER) cc_final: 0.7582 (p90) REVERT: C 425 GLU cc_start: 0.7237 (tt0) cc_final: 0.6952 (tt0) REVERT: C 453 THR cc_start: 0.5477 (m) cc_final: 0.4735 (p) REVERT: C 480 SER cc_start: 0.8374 (m) cc_final: 0.8168 (t) REVERT: C 559 TRP cc_start: 0.6649 (m100) cc_final: 0.5894 (t60) outliers start: 30 outliers final: 9 residues processed: 372 average time/residue: 0.0873 time to fit residues: 46.5517 Evaluate side-chains 229 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 218 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 173 TRP Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 173 TRP Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 359 PHE Chi-restraints excluded: chain C residue 390 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 7.9990 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 0.4980 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 0.7980 chunk 106 optimal weight: 0.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 153 ASN A 220 HIS A 236 GLN A 280 HIS A 314 GLN A 555 ASN C 153 ASN C 236 GLN C 314 GLN ** C 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 372 HIS C 555 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.194003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.152594 restraints weight = 12851.134| |-----------------------------------------------------------------------------| r_work (start): 0.4016 rms_B_bonded: 3.09 r_work: 0.3865 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.3537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 9326 Z= 0.173 Angle : 0.620 9.759 12726 Z= 0.314 Chirality : 0.041 0.163 1418 Planarity : 0.004 0.034 1552 Dihedral : 5.802 58.584 1238 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 5.04 % Allowed : 16.60 % Favored : 78.36 % 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 aren not related in a simple way. whole: 0.21 (0.25), residues: 1126 helix: 0.78 (0.19), residues: 746 sheet: None (None), residues: 0 loop : -1.05 (0.30), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 440 TYR 0.019 0.002 TYR C 391 PHE 0.033 0.002 PHE A 82 TRP 0.014 0.001 TRP C 128 HIS 0.019 0.002 HIS C 222 Details of bonding type rmsd covalent geometry : bond 0.00387 ( 9326) covalent geometry : angle 0.61965 (12726) hydrogen bonds : bond 0.04515 ( 550) hydrogen bonds : angle 4.38129 ( 1620) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 222 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 121 ARG cc_start: 0.8564 (mmm-85) cc_final: 0.8303 (tpp80) REVERT: A 131 CYS cc_start: 0.8498 (t) cc_final: 0.8160 (m) REVERT: A 246 ILE cc_start: 0.7549 (OUTLIER) cc_final: 0.6906 (mp) REVERT: A 258 THR cc_start: 0.7667 (p) cc_final: 0.7441 (p) REVERT: A 261 LYS cc_start: 0.8179 (mmmt) cc_final: 0.7917 (mmmt) REVERT: A 278 LEU cc_start: 0.6828 (mt) cc_final: 0.6498 (mt) REVERT: A 280 HIS cc_start: 0.6719 (OUTLIER) cc_final: 0.6506 (t-170) REVERT: A 401 SER cc_start: 0.9109 (OUTLIER) cc_final: 0.8591 (t) REVERT: A 515 LEU cc_start: 0.7821 (tt) cc_final: 0.7495 (mt) REVERT: A 605 ASP cc_start: 0.7979 (m-30) cc_final: 0.7692 (m-30) REVERT: C 121 ARG cc_start: 0.8561 (mmm-85) cc_final: 0.8289 (tpp80) REVERT: C 131 CYS cc_start: 0.8527 (t) cc_final: 0.8132 (m) REVERT: C 246 ILE cc_start: 0.7556 (OUTLIER) cc_final: 0.6989 (mp) REVERT: C 258 THR cc_start: 0.7623 (p) cc_final: 0.7411 (p) REVERT: C 261 LYS cc_start: 0.8160 (mmmt) cc_final: 0.7901 (mmmt) REVERT: C 334 LYS cc_start: 0.8374 (OUTLIER) cc_final: 0.8127 (ptmm) REVERT: C 597 GLU cc_start: 0.8653 (mp0) cc_final: 0.8117 (mp0) outliers start: 48 outliers final: 23 residues processed: 257 average time/residue: 0.0833 time to fit residues: 31.0061 Evaluate side-chains 218 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 190 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 173 TRP Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 280 HIS Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 173 TRP Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 246 ILE Chi-restraints excluded: chain C residue 334 LYS Chi-restraints excluded: chain C residue 351 CYS Chi-restraints excluded: chain C residue 359 PHE Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 472 LEU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 557 VAL Chi-restraints excluded: chain C residue 593 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 54 optimal weight: 6.9990 chunk 56 optimal weight: 20.0000 chunk 8 optimal weight: 0.9980 chunk 75 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 82 optimal weight: 0.7980 chunk 2 optimal weight: 0.5980 chunk 69 optimal weight: 20.0000 chunk 22 optimal weight: 10.0000 chunk 18 optimal weight: 4.9990 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 HIS ** C 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 436 GLN C 599 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.186514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.145613 restraints weight = 13066.767| |-----------------------------------------------------------------------------| r_work (start): 0.3958 rms_B_bonded: 3.12 r_work: 0.3799 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.4266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9326 Z= 0.178 Angle : 0.593 10.391 12726 Z= 0.300 Chirality : 0.040 0.198 1418 Planarity : 0.004 0.035 1552 Dihedral : 5.496 56.343 1236 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 5.04 % Allowed : 16.70 % Favored : 78.26 % 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 aren not related in a simple way. whole: 0.49 (0.24), residues: 1126 helix: 0.96 (0.19), residues: 756 sheet: None (None), residues: 0 loop : -0.92 (0.31), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 81 TYR 0.020 0.002 TYR A 391 PHE 0.030 0.002 PHE C 409 TRP 0.012 0.001 TRP A 128 HIS 0.014 0.002 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00411 ( 9326) covalent geometry : angle 0.59329 (12726) hydrogen bonds : bond 0.04575 ( 550) hydrogen bonds : angle 4.34384 ( 1620) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 209 time to evaluate : 0.326 Fit side-chains REVERT: A 131 CYS cc_start: 0.8770 (t) cc_final: 0.8331 (m) REVERT: A 246 ILE cc_start: 0.7615 (OUTLIER) cc_final: 0.6977 (mp) REVERT: A 274 LEU cc_start: 0.9144 (mp) cc_final: 0.8892 (mp) REVERT: A 315 ILE cc_start: 0.5885 (OUTLIER) cc_final: 0.5652 (mp) REVERT: A 597 GLU cc_start: 0.8768 (OUTLIER) cc_final: 0.8258 (tp30) REVERT: A 605 ASP cc_start: 0.7883 (m-30) cc_final: 0.7627 (m-30) REVERT: C 129 LYS cc_start: 0.8642 (mmtp) cc_final: 0.8400 (mmmt) REVERT: C 246 ILE cc_start: 0.7703 (OUTLIER) cc_final: 0.7105 (mp) REVERT: C 250 PHE cc_start: 0.8402 (m-80) cc_final: 0.8177 (m-10) REVERT: C 315 ILE cc_start: 0.5832 (OUTLIER) cc_final: 0.5584 (mp) REVERT: C 597 GLU cc_start: 0.8724 (OUTLIER) cc_final: 0.8108 (mp0) outliers start: 48 outliers final: 35 residues processed: 241 average time/residue: 0.0857 time to fit residues: 29.7268 Evaluate side-chains 226 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 185 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 81 ARG Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 173 TRP Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 597 GLU Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 173 TRP Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 246 ILE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 334 LYS Chi-restraints excluded: chain C residue 351 CYS Chi-restraints excluded: chain C residue 359 PHE Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 490 ILE Chi-restraints excluded: chain C residue 557 VAL Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain C residue 597 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 99 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 14 optimal weight: 0.0040 chunk 90 optimal weight: 9.9990 chunk 57 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 87 optimal weight: 10.0000 chunk 1 optimal weight: 6.9990 overall best weight: 1.1796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 HIS A 370 HIS C 280 HIS ** C 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 337 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.186671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.146536 restraints weight = 13195.844| |-----------------------------------------------------------------------------| r_work (start): 0.3958 rms_B_bonded: 3.14 r_work: 0.3798 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.4628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9326 Z= 0.137 Angle : 0.584 14.290 12726 Z= 0.290 Chirality : 0.040 0.171 1418 Planarity : 0.004 0.038 1552 Dihedral : 5.525 56.845 1236 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 4.52 % Allowed : 19.33 % Favored : 76.16 % 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 aren not related in a simple way. whole: 0.69 (0.25), residues: 1126 helix: 1.06 (0.18), residues: 756 sheet: None (None), residues: 0 loop : -0.70 (0.33), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 81 TYR 0.023 0.001 TYR C 87 PHE 0.029 0.001 PHE C 82 TRP 0.017 0.001 TRP C 494 HIS 0.009 0.001 HIS A 370 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 9326) covalent geometry : angle 0.58356 (12726) hydrogen bonds : bond 0.04171 ( 550) hydrogen bonds : angle 4.26058 ( 1620) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 198 time to evaluate : 0.325 Fit side-chains REVERT: A 131 CYS cc_start: 0.8714 (t) cc_final: 0.8509 (m) REVERT: A 246 ILE cc_start: 0.7672 (OUTLIER) cc_final: 0.7068 (mp) REVERT: A 315 ILE cc_start: 0.6174 (OUTLIER) cc_final: 0.5911 (mp) REVERT: A 528 PHE cc_start: 0.7167 (t80) cc_final: 0.6941 (m-10) REVERT: A 597 GLU cc_start: 0.8755 (OUTLIER) cc_final: 0.8246 (tp30) REVERT: A 605 ASP cc_start: 0.7843 (m-30) cc_final: 0.7610 (m-30) REVERT: C 131 CYS cc_start: 0.8669 (t) cc_final: 0.8468 (m) REVERT: C 246 ILE cc_start: 0.7714 (OUTLIER) cc_final: 0.7166 (mp) REVERT: C 274 LEU cc_start: 0.9124 (mp) cc_final: 0.8923 (mp) REVERT: C 315 ILE cc_start: 0.6154 (OUTLIER) cc_final: 0.5865 (mp) REVERT: C 597 GLU cc_start: 0.8741 (OUTLIER) cc_final: 0.8114 (mp0) REVERT: C 611 LEU cc_start: 0.7781 (mm) cc_final: 0.7566 (mm) outliers start: 43 outliers final: 24 residues processed: 229 average time/residue: 0.0772 time to fit residues: 26.4264 Evaluate side-chains 213 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 183 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 81 ARG Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 173 TRP Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 597 GLU Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 173 TRP Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 246 ILE Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 334 LYS Chi-restraints excluded: chain C residue 359 PHE Chi-restraints excluded: chain C residue 490 ILE Chi-restraints excluded: chain C residue 519 LEU Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain C residue 597 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 16 optimal weight: 7.9990 chunk 26 optimal weight: 0.9980 chunk 74 optimal weight: 4.9990 chunk 34 optimal weight: 9.9990 chunk 58 optimal weight: 0.5980 chunk 54 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 chunk 108 optimal weight: 0.6980 chunk 53 optimal weight: 10.0000 chunk 85 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 HIS C 280 HIS ** C 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.185647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.145608 restraints weight = 13171.932| |-----------------------------------------------------------------------------| r_work (start): 0.3943 rms_B_bonded: 3.14 r_work: 0.3787 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.4895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9326 Z= 0.137 Angle : 0.581 14.957 12726 Z= 0.288 Chirality : 0.040 0.158 1418 Planarity : 0.004 0.037 1552 Dihedral : 5.323 56.941 1232 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 4.73 % Allowed : 19.64 % Favored : 75.63 % 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 aren not related in a simple way. whole: 0.89 (0.25), residues: 1126 helix: 1.23 (0.19), residues: 754 sheet: None (None), residues: 0 loop : -0.66 (0.34), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 81 TYR 0.025 0.002 TYR C 87 PHE 0.034 0.001 PHE C 82 TRP 0.012 0.001 TRP A 264 HIS 0.011 0.001 HIS A 370 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 9326) covalent geometry : angle 0.58055 (12726) hydrogen bonds : bond 0.04075 ( 550) hydrogen bonds : angle 4.26993 ( 1620) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 193 time to evaluate : 0.331 Fit side-chains REVERT: A 246 ILE cc_start: 0.7720 (OUTLIER) cc_final: 0.7262 (mp) REVERT: A 315 ILE cc_start: 0.6454 (OUTLIER) cc_final: 0.6068 (mp) REVERT: A 528 PHE cc_start: 0.7273 (t80) cc_final: 0.7033 (m-10) REVERT: A 597 GLU cc_start: 0.8771 (OUTLIER) cc_final: 0.8280 (tp30) REVERT: C 274 LEU cc_start: 0.9138 (mp) cc_final: 0.8898 (mp) REVERT: C 315 ILE cc_start: 0.6488 (OUTLIER) cc_final: 0.6089 (mp) REVERT: C 528 PHE cc_start: 0.7261 (t80) cc_final: 0.7023 (m-10) REVERT: C 597 GLU cc_start: 0.8738 (OUTLIER) cc_final: 0.8166 (mp0) outliers start: 45 outliers final: 31 residues processed: 219 average time/residue: 0.0836 time to fit residues: 26.7001 Evaluate side-chains 209 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 173 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 81 ARG Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 173 TRP Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 597 GLU Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 173 TRP Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 246 ILE Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 334 LYS Chi-restraints excluded: chain C residue 351 CYS Chi-restraints excluded: chain C residue 359 PHE Chi-restraints excluded: chain C residue 364 ILE Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain C residue 490 ILE Chi-restraints excluded: chain C residue 507 GLN Chi-restraints excluded: chain C residue 519 LEU Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain C residue 597 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 2 optimal weight: 0.9990 chunk 58 optimal weight: 0.8980 chunk 6 optimal weight: 5.9990 chunk 17 optimal weight: 10.0000 chunk 52 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 HIS C 280 HIS ** C 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 370 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.186135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.146192 restraints weight = 13209.860| |-----------------------------------------------------------------------------| r_work (start): 0.3959 rms_B_bonded: 3.10 r_work: 0.3801 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.5116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9326 Z= 0.126 Angle : 0.575 14.770 12726 Z= 0.280 Chirality : 0.039 0.165 1418 Planarity : 0.004 0.037 1552 Dihedral : 5.062 56.420 1230 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 4.20 % Allowed : 21.22 % Favored : 74.58 % 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 aren not related in a simple way. whole: 1.00 (0.26), residues: 1126 helix: 1.29 (0.19), residues: 766 sheet: None (None), residues: 0 loop : -0.62 (0.35), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 121 TYR 0.028 0.001 TYR A 87 PHE 0.034 0.001 PHE A 82 TRP 0.013 0.001 TRP A 264 HIS 0.010 0.001 HIS C 370 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 9326) covalent geometry : angle 0.57453 (12726) hydrogen bonds : bond 0.03870 ( 550) hydrogen bonds : angle 4.23760 ( 1620) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 193 time to evaluate : 0.346 Fit side-chains revert: symmetry clash REVERT: A 261 LYS cc_start: 0.8196 (mmmt) cc_final: 0.7499 (mttt) REVERT: A 277 LEU cc_start: 0.7766 (OUTLIER) cc_final: 0.7529 (mp) REVERT: A 278 LEU cc_start: 0.7105 (mt) cc_final: 0.6609 (mt) REVERT: A 315 ILE cc_start: 0.6523 (OUTLIER) cc_final: 0.6105 (mp) REVERT: A 528 PHE cc_start: 0.7356 (t80) cc_final: 0.7125 (m-10) REVERT: A 597 GLU cc_start: 0.8744 (OUTLIER) cc_final: 0.8275 (tp30) REVERT: C 401 SER cc_start: 0.8988 (p) cc_final: 0.8374 (t) REVERT: C 528 PHE cc_start: 0.7328 (t80) cc_final: 0.7072 (m-10) REVERT: C 597 GLU cc_start: 0.8719 (OUTLIER) cc_final: 0.8147 (mp0) outliers start: 40 outliers final: 26 residues processed: 217 average time/residue: 0.0877 time to fit residues: 27.9742 Evaluate side-chains 214 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 184 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 81 ARG Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 173 TRP Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 597 GLU Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 173 TRP Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 359 PHE Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain C residue 519 LEU Chi-restraints excluded: chain C residue 557 VAL Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain C residue 597 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 49 optimal weight: 0.0060 chunk 66 optimal weight: 4.9990 chunk 65 optimal weight: 0.7980 chunk 73 optimal weight: 9.9990 chunk 68 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 16 optimal weight: 7.9990 chunk 54 optimal weight: 4.9990 chunk 3 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 overall best weight: 1.5400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 ASN ** A 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 HIS ** C 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 370 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.183119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.142648 restraints weight = 13163.577| |-----------------------------------------------------------------------------| r_work (start): 0.3923 rms_B_bonded: 3.10 r_work: 0.3769 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.5389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9326 Z= 0.152 Angle : 0.596 14.328 12726 Z= 0.296 Chirality : 0.041 0.250 1418 Planarity : 0.004 0.037 1552 Dihedral : 5.070 55.771 1230 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 5.15 % Allowed : 21.01 % Favored : 73.84 % 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 aren not related in a simple way. whole: 0.96 (0.25), residues: 1126 helix: 1.26 (0.18), residues: 766 sheet: None (None), residues: 0 loop : -0.62 (0.35), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 121 TYR 0.025 0.002 TYR A 87 PHE 0.031 0.001 PHE A 82 TRP 0.015 0.001 TRP A 494 HIS 0.012 0.001 HIS C 370 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 9326) covalent geometry : angle 0.59598 (12726) hydrogen bonds : bond 0.04223 ( 550) hydrogen bonds : angle 4.30202 ( 1620) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 201 time to evaluate : 0.256 Fit side-chains revert: symmetry clash REVERT: A 129 LYS cc_start: 0.8595 (mmtp) cc_final: 0.8372 (mmmt) REVERT: A 261 LYS cc_start: 0.8108 (mmmt) cc_final: 0.7858 (mmmt) REVERT: A 528 PHE cc_start: 0.7364 (t80) cc_final: 0.7107 (m-10) REVERT: A 597 GLU cc_start: 0.8753 (OUTLIER) cc_final: 0.8291 (tp30) REVERT: C 401 SER cc_start: 0.9005 (p) cc_final: 0.8365 (t) REVERT: C 528 PHE cc_start: 0.7350 (t80) cc_final: 0.7103 (m-10) REVERT: C 597 GLU cc_start: 0.8723 (OUTLIER) cc_final: 0.8181 (mp0) outliers start: 49 outliers final: 33 residues processed: 226 average time/residue: 0.0778 time to fit residues: 25.9237 Evaluate side-chains 218 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 183 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 81 ARG Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 597 GLU Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 112 MET Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 173 TRP Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 246 ILE Chi-restraints excluded: chain C residue 334 LYS Chi-restraints excluded: chain C residue 359 PHE Chi-restraints excluded: chain C residue 364 ILE Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain C residue 507 GLN Chi-restraints excluded: chain C residue 519 LEU Chi-restraints excluded: chain C residue 557 VAL Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain C residue 597 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 41 optimal weight: 2.9990 chunk 23 optimal weight: 0.0000 chunk 95 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 91 optimal weight: 7.9990 chunk 42 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 30 optimal weight: 6.9990 chunk 26 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 ASN ** A 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 HIS ** C 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 370 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.184957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.144571 restraints weight = 13087.236| |-----------------------------------------------------------------------------| r_work (start): 0.3941 rms_B_bonded: 3.09 r_work: 0.3790 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.5496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9326 Z= 0.130 Angle : 0.611 14.769 12726 Z= 0.297 Chirality : 0.040 0.170 1418 Planarity : 0.004 0.039 1552 Dihedral : 4.913 55.699 1228 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.99 % Allowed : 23.11 % Favored : 72.90 % 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 aren not related in a simple way. whole: 0.87 (0.26), residues: 1126 helix: 1.22 (0.19), residues: 778 sheet: None (None), residues: 0 loop : -0.81 (0.36), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 121 TYR 0.017 0.001 TYR A 575 PHE 0.029 0.001 PHE C 82 TRP 0.036 0.001 TRP C 494 HIS 0.012 0.001 HIS C 370 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 9326) covalent geometry : angle 0.61050 (12726) hydrogen bonds : bond 0.03963 ( 550) hydrogen bonds : angle 4.32652 ( 1620) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 196 time to evaluate : 0.367 Fit side-chains REVERT: A 87 TYR cc_start: 0.7003 (OUTLIER) cc_final: 0.6656 (m-80) REVERT: A 261 LYS cc_start: 0.8121 (mmmt) cc_final: 0.7901 (mmmt) REVERT: A 278 LEU cc_start: 0.7169 (mt) cc_final: 0.6672 (mt) REVERT: A 528 PHE cc_start: 0.7349 (t80) cc_final: 0.7084 (m-10) REVERT: A 597 GLU cc_start: 0.8728 (OUTLIER) cc_final: 0.8239 (tp30) REVERT: C 131 CYS cc_start: 0.8684 (t) cc_final: 0.8415 (m) REVERT: C 401 SER cc_start: 0.8987 (p) cc_final: 0.8359 (t) REVERT: C 528 PHE cc_start: 0.7350 (t80) cc_final: 0.7092 (m-10) REVERT: C 597 GLU cc_start: 0.8720 (OUTLIER) cc_final: 0.8182 (mp0) outliers start: 38 outliers final: 30 residues processed: 217 average time/residue: 0.0804 time to fit residues: 25.9543 Evaluate side-chains 220 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 187 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 81 ARG Chi-restraints excluded: chain A residue 87 TYR Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 597 GLU Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 112 MET Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 173 TRP Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain C residue 334 LYS Chi-restraints excluded: chain C residue 359 PHE Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain C residue 507 GLN Chi-restraints excluded: chain C residue 519 LEU Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain C residue 597 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 25 optimal weight: 1.9990 chunk 18 optimal weight: 0.0270 chunk 78 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 87 optimal weight: 9.9990 chunk 88 optimal weight: 4.9990 chunk 92 optimal weight: 0.8980 chunk 83 optimal weight: 0.7980 chunk 99 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 overall best weight: 0.7038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 ASN A 337 ASN A 370 HIS ** C 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 370 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.185449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.145736 restraints weight = 13104.930| |-----------------------------------------------------------------------------| r_work (start): 0.3952 rms_B_bonded: 3.14 r_work: 0.3798 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.5530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9326 Z= 0.126 Angle : 0.597 14.751 12726 Z= 0.292 Chirality : 0.040 0.167 1418 Planarity : 0.004 0.042 1552 Dihedral : 4.871 56.091 1228 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 4.20 % Allowed : 23.21 % Favored : 72.58 % 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 aren not related in a simple way. whole: 0.94 (0.25), residues: 1126 helix: 1.27 (0.18), residues: 776 sheet: None (None), residues: 0 loop : -0.78 (0.35), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 121 TYR 0.027 0.001 TYR A 391 PHE 0.032 0.001 PHE C 82 TRP 0.046 0.001 TRP A 494 HIS 0.013 0.001 HIS C 370 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 9326) covalent geometry : angle 0.59750 (12726) hydrogen bonds : bond 0.03769 ( 550) hydrogen bonds : angle 4.29810 ( 1620) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 195 time to evaluate : 0.338 Fit side-chains REVERT: A 87 TYR cc_start: 0.7068 (OUTLIER) cc_final: 0.6692 (m-80) REVERT: A 261 LYS cc_start: 0.8167 (mmmt) cc_final: 0.7954 (mmmt) REVERT: A 278 LEU cc_start: 0.7140 (mt) cc_final: 0.6644 (mt) REVERT: A 528 PHE cc_start: 0.7356 (t80) cc_final: 0.7075 (m-10) REVERT: A 597 GLU cc_start: 0.8737 (OUTLIER) cc_final: 0.8254 (tp30) REVERT: C 131 CYS cc_start: 0.8680 (t) cc_final: 0.8402 (m) REVERT: C 261 LYS cc_start: 0.8256 (mmmt) cc_final: 0.7470 (mmtt) REVERT: C 401 SER cc_start: 0.8966 (p) cc_final: 0.8357 (t) REVERT: C 528 PHE cc_start: 0.7351 (t80) cc_final: 0.7092 (m-10) REVERT: C 597 GLU cc_start: 0.8704 (OUTLIER) cc_final: 0.8172 (mp0) outliers start: 40 outliers final: 31 residues processed: 218 average time/residue: 0.0801 time to fit residues: 25.8617 Evaluate side-chains 225 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 191 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 81 ARG Chi-restraints excluded: chain A residue 87 TYR Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 597 GLU Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain C residue 246 ILE Chi-restraints excluded: chain C residue 334 LYS Chi-restraints excluded: chain C residue 359 PHE Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain C residue 507 GLN Chi-restraints excluded: chain C residue 519 LEU Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain C residue 597 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 4 optimal weight: 0.9980 chunk 93 optimal weight: 0.0010 chunk 89 optimal weight: 6.9990 chunk 103 optimal weight: 0.8980 chunk 25 optimal weight: 0.5980 chunk 12 optimal weight: 6.9990 chunk 98 optimal weight: 0.6980 chunk 22 optimal weight: 6.9990 chunk 75 optimal weight: 1.9990 chunk 23 optimal weight: 0.0870 chunk 15 optimal weight: 8.9990 overall best weight: 0.4564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 ASN A 370 HIS ** C 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 370 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.187646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.148327 restraints weight = 12969.608| |-----------------------------------------------------------------------------| r_work (start): 0.3975 rms_B_bonded: 3.07 r_work: 0.3824 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.5569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9326 Z= 0.122 Angle : 0.615 14.947 12726 Z= 0.298 Chirality : 0.040 0.228 1418 Planarity : 0.004 0.038 1552 Dihedral : 4.696 56.253 1226 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.47 % Allowed : 23.74 % Favored : 72.79 % 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 aren not related in a simple way. whole: 1.03 (0.26), residues: 1126 helix: 1.37 (0.19), residues: 768 sheet: None (None), residues: 0 loop : -0.76 (0.35), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 121 TYR 0.052 0.001 TYR A 391 PHE 0.035 0.001 PHE C 82 TRP 0.057 0.001 TRP A 494 HIS 0.013 0.001 HIS C 370 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 9326) covalent geometry : angle 0.61489 (12726) hydrogen bonds : bond 0.03619 ( 550) hydrogen bonds : angle 4.32954 ( 1620) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 204 time to evaluate : 0.402 Fit side-chains REVERT: A 87 TYR cc_start: 0.7070 (OUTLIER) cc_final: 0.6734 (m-80) REVERT: A 118 GLN cc_start: 0.8850 (tt0) cc_final: 0.8648 (tt0) REVERT: A 370 HIS cc_start: 0.7410 (OUTLIER) cc_final: 0.7069 (m170) REVERT: A 528 PHE cc_start: 0.7319 (t80) cc_final: 0.7075 (m-10) REVERT: A 597 GLU cc_start: 0.8734 (OUTLIER) cc_final: 0.8242 (tp30) REVERT: C 131 CYS cc_start: 0.8616 (t) cc_final: 0.8353 (m) REVERT: C 156 ILE cc_start: 0.9025 (mt) cc_final: 0.8788 (mt) REVERT: C 261 LYS cc_start: 0.8211 (mmmt) cc_final: 0.7445 (mmtt) REVERT: C 401 SER cc_start: 0.8961 (p) cc_final: 0.8366 (t) REVERT: C 528 PHE cc_start: 0.7348 (t80) cc_final: 0.7098 (m-10) REVERT: C 597 GLU cc_start: 0.8689 (OUTLIER) cc_final: 0.8211 (mp0) outliers start: 33 outliers final: 24 residues processed: 225 average time/residue: 0.0799 time to fit residues: 26.8342 Evaluate side-chains 219 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 191 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 81 ARG Chi-restraints excluded: chain A residue 87 TYR Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 370 HIS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 597 GLU Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 112 MET Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 246 ILE Chi-restraints excluded: chain C residue 359 PHE Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain C residue 597 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 90 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 16 optimal weight: 0.6980 chunk 12 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 89 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 111 optimal weight: 10.0000 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 ASN A 370 HIS ** C 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 370 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.183930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.143825 restraints weight = 12979.734| |-----------------------------------------------------------------------------| r_work (start): 0.3930 rms_B_bonded: 3.06 r_work: 0.3778 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.5712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9326 Z= 0.167 Angle : 0.656 15.638 12726 Z= 0.324 Chirality : 0.041 0.161 1418 Planarity : 0.004 0.037 1552 Dihedral : 4.812 55.528 1226 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.89 % Allowed : 23.53 % Favored : 72.58 % 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 aren not related in a simple way. whole: 0.92 (0.26), residues: 1126 helix: 1.15 (0.19), residues: 782 sheet: None (None), residues: 0 loop : -0.50 (0.37), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 121 TYR 0.060 0.002 TYR A 391 PHE 0.033 0.001 PHE C 82 TRP 0.064 0.002 TRP A 494 HIS 0.014 0.001 HIS C 370 Details of bonding type rmsd covalent geometry : bond 0.00388 ( 9326) covalent geometry : angle 0.65623 (12726) hydrogen bonds : bond 0.04069 ( 550) hydrogen bonds : angle 4.38227 ( 1620) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2114.20 seconds wall clock time: 37 minutes 6.57 seconds (2226.57 seconds total)