Starting phenix.real_space_refine on Sat Aug 23 17:05:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ytj_34090/08_2025/7ytj_34090.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ytj_34090/08_2025/7ytj_34090.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ytj_34090/08_2025/7ytj_34090.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ytj_34090/08_2025/7ytj_34090.map" model { file = "/net/cci-nas-00/data/ceres_data/7ytj_34090/08_2025/7ytj_34090.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ytj_34090/08_2025/7ytj_34090.cif" } resolution = 3.0 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= 0.002 sd= 0.089 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: 5 Type Number sf(0) Gaussians P 22 5.49 5 S 34 5.16 5 C 8474 2.51 5 N 2194 2.21 5 O 2413 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 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: 13137 Number of models: 1 Model: "" Number of chains: 7 Chain: "D" Number of atoms: 4940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 601, 4940 Classifications: {'peptide': 601} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 574} Chain breaks: 2 Chain: "A" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 941 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 6, 'TRANS': 112} Chain: "B" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 811 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "C" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 811 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "E" Number of atoms: 5408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 650, 5408 Classifications: {'peptide': 650} Link IDs: {'PTRANS': 28, 'TRANS': 621} Chain breaks: 3 Chain: "D" Number of atoms: 172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 172 Unusual residues: {'IHP': 3, 'PC1': 1, 'PO4': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "E" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 54 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.59, per 1000 atoms: 0.20 Number of scatterers: 13137 At special positions: 0 Unit cell: (111.28, 93.09, 169.06, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 34 16.00 P 22 15.00 O 2413 8.00 N 2194 7.00 C 8474 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: 0.97 Conformation dependent library (CDL) restraints added in 396.0 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2996 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 6 sheets defined 63.3% alpha, 15.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'D' and resid 3 through 11 Processing helix chain 'D' and resid 22 through 37 Processing helix chain 'D' and resid 42 through 88 Processing helix chain 'D' and resid 89 through 91 No H-bonds generated for 'chain 'D' and resid 89 through 91' Processing helix chain 'D' and resid 95 through 139 removed outlier: 3.830A pdb=" N ASP D 99 " --> pdb=" O PRO D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 154 Processing helix chain 'D' and resid 161 through 180 Processing helix chain 'D' and resid 205 through 207 No H-bonds generated for 'chain 'D' and resid 205 through 207' Processing helix chain 'D' and resid 208 through 218 Processing helix chain 'D' and resid 248 through 256 Processing helix chain 'D' and resid 302 through 310 removed outlier: 4.488A pdb=" N ASN D 306 " --> pdb=" O GLU D 302 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N ASP D 307 " --> pdb=" O ARG D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 314 through 319 Processing helix chain 'D' and resid 319 through 326 removed outlier: 3.564A pdb=" N ARG D 323 " --> pdb=" O PHE D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 329 through 351 Processing helix chain 'D' and resid 439 through 447 Processing helix chain 'D' and resid 458 through 468 Processing helix chain 'D' and resid 469 through 472 Processing helix chain 'D' and resid 478 through 482 removed outlier: 3.543A pdb=" N MET D 482 " --> pdb=" O LEU D 479 " (cutoff:3.500A) Processing helix chain 'D' and resid 623 through 652 removed outlier: 3.951A pdb=" N GLU D 629 " --> pdb=" O TYR D 625 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TYR D 632 " --> pdb=" O THR D 628 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE D 638 " --> pdb=" O SER D 634 " (cutoff:3.500A) Processing helix chain 'D' and resid 656 through 687 removed outlier: 4.204A pdb=" N GLY D 660 " --> pdb=" O THR D 656 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLY D 663 " --> pdb=" O ILE D 659 " (cutoff:3.500A) Processing helix chain 'D' and resid 688 through 690 No H-bonds generated for 'chain 'D' and resid 688 through 690' Processing helix chain 'D' and resid 698 through 724 Processing helix chain 'A' and resid 56 through 88 removed outlier: 4.460A pdb=" N PHE A 60 " --> pdb=" O GLU A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 124 removed outlier: 4.147A pdb=" N GLY A 97 " --> pdb=" O ARG A 93 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N LEU A 98 " --> pdb=" O VAL A 94 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N PHE A 99 " --> pdb=" O SER A 95 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N VAL A 102 " --> pdb=" O LEU A 98 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG A 123 " --> pdb=" O ALA A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 156 Processing helix chain 'B' and resid 56 through 88 removed outlier: 3.634A pdb=" N PHE B 60 " --> pdb=" O GLU B 56 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N PHE B 73 " --> pdb=" O SER B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 124 removed outlier: 3.661A pdb=" N SER B 95 " --> pdb=" O ILE B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 156 removed outlier: 3.874A pdb=" N THR B 136 " --> pdb=" O ARG B 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 88 removed outlier: 3.533A pdb=" N PHE C 87 " --> pdb=" O GLY C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 124 Processing helix chain 'C' and resid 133 through 156 Processing helix chain 'E' and resid 32 through 39 Processing helix chain 'E' and resid 41 through 48 removed outlier: 5.267A pdb=" N ASP E 46 " --> pdb=" O PRO E 43 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N TYR E 48 " --> pdb=" O LYS E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 64 removed outlier: 4.430A pdb=" N SER E 61 " --> pdb=" O LEU E 57 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N VAL E 62 " --> pdb=" O LEU E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 112 Processing helix chain 'E' and resid 116 through 122 Processing helix chain 'E' and resid 124 through 164 Processing helix chain 'E' and resid 170 through 180 removed outlier: 3.667A pdb=" N LEU E 174 " --> pdb=" O VAL E 170 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 207 removed outlier: 3.551A pdb=" N TYR E 194 " --> pdb=" O SER E 190 " (cutoff:3.500A) Processing helix chain 'E' and resid 242 through 255 removed outlier: 4.427A pdb=" N MET E 247 " --> pdb=" O ASP E 243 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N GLU E 248 " --> pdb=" O ASP E 244 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA E 251 " --> pdb=" O MET E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 343 Processing helix chain 'E' and resid 358 through 362 Processing helix chain 'E' and resid 394 through 400 Processing helix chain 'E' and resid 404 through 417 removed outlier: 4.110A pdb=" N ASN E 408 " --> pdb=" O PRO E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 420 through 442 Processing helix chain 'E' and resid 503 through 508 Processing helix chain 'E' and resid 536 through 544 Processing helix chain 'E' and resid 555 through 566 Processing helix chain 'E' and resid 578 through 582 Processing helix chain 'E' and resid 590 through 594 Processing helix chain 'E' and resid 596 through 618 removed outlier: 3.706A pdb=" N THR E 600 " --> pdb=" O GLU E 596 " (cutoff:3.500A) Processing helix chain 'E' and resid 723 through 755 Processing helix chain 'E' and resid 762 through 797 Processing helix chain 'E' and resid 806 through 828 Processing helix chain 'E' and resid 829 through 833 removed outlier: 3.838A pdb=" N ARG E 833 " --> pdb=" O GLU E 830 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 290 through 301 removed outlier: 7.208A pdb=" N THR D 276 " --> pdb=" O TYR D 269 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N TYR D 269 " --> pdb=" O THR D 276 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ALA D 261 " --> pdb=" O HIS D 284 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N HIS D 264 " --> pdb=" O PHE D 243 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N VAL D 356 " --> pdb=" O TYR D 242 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N ASP D 244 " --> pdb=" O PRO D 354 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N VAL D 355 " --> pdb=" O ARG D 385 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ARG D 385 " --> pdb=" O VAL D 355 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N ARG D 357 " --> pdb=" O MET D 383 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N MET D 383 " --> pdb=" O ARG D 357 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N PHE D 359 " --> pdb=" O LEU D 381 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N LEU D 381 " --> pdb=" O PHE D 359 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 290 through 301 removed outlier: 7.208A pdb=" N THR D 276 " --> pdb=" O TYR D 269 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N TYR D 269 " --> pdb=" O THR D 276 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ALA D 261 " --> pdb=" O HIS D 284 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N HIS D 264 " --> pdb=" O PHE D 243 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N VAL D 356 " --> pdb=" O TYR D 242 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N ASP D 244 " --> pdb=" O PRO D 354 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N VAL D 355 " --> pdb=" O ARG D 385 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ARG D 385 " --> pdb=" O VAL D 355 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N ARG D 357 " --> pdb=" O MET D 383 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N MET D 383 " --> pdb=" O ARG D 357 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N PHE D 359 " --> pdb=" O LEU D 381 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N LEU D 381 " --> pdb=" O PHE D 359 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 222 through 224 removed outlier: 6.084A pdb=" N VAL D 222 " --> pdb=" O VAL E 261 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N ALA E 455 " --> pdb=" O LEU E 260 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N TYR E 262 " --> pdb=" O ARG E 453 " (cutoff:3.500A) removed outlier: 11.258A pdb=" N ARG E 453 " --> pdb=" O TYR E 262 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N VAL E 446 " --> pdb=" O ARG E 476 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N ARG E 476 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ARG E 448 " --> pdb=" O TYR E 474 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N TYR E 474 " --> pdb=" O ARG E 448 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N THR E 450 " --> pdb=" O ILE E 472 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ILE E 472 " --> pdb=" O THR E 450 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 383 through 390 removed outlier: 4.207A pdb=" N ILE E 365 " --> pdb=" O MET E 390 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N LEU E 351 " --> pdb=" O PHE E 330 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILE E 325 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N THR E 450 " --> pdb=" O ILE E 325 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N THR E 327 " --> pdb=" O ARG E 448 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ARG E 448 " --> pdb=" O THR E 327 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N TYR E 329 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N VAL E 446 " --> pdb=" O ARG E 476 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N ARG E 476 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ARG E 448 " --> pdb=" O TYR E 474 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N TYR E 474 " --> pdb=" O ARG E 448 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N THR E 450 " --> pdb=" O ILE E 472 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ILE E 472 " --> pdb=" O THR E 450 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 474 through 475 Processing sheet with id=AA6, first strand: chain 'A' and resid 41 through 42 901 hydrogen bonds defined for protein. 2628 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: 1.77 Time building geometry restraints manager: 1.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2082 1.31 - 1.44: 3642 1.44 - 1.56: 7624 1.56 - 1.69: 25 1.69 - 1.82: 59 Bond restraints: 13432 Sorted by residual: bond pdb=" C21 PC1 E 901 " pdb=" O21 PC1 E 901 " ideal model delta sigma weight residual 1.331 1.400 -0.069 2.00e-02 2.50e+03 1.19e+01 bond pdb=" C31 PC1 E 901 " pdb=" O31 PC1 E 901 " ideal model delta sigma weight residual 1.330 1.399 -0.069 2.00e-02 2.50e+03 1.19e+01 bond pdb=" C31 PC1 D1003 " pdb=" O31 PC1 D1003 " ideal model delta sigma weight residual 1.330 1.397 -0.067 2.00e-02 2.50e+03 1.13e+01 bond pdb=" C21 PC1 D1003 " pdb=" O21 PC1 D1003 " ideal model delta sigma weight residual 1.331 1.396 -0.065 2.00e-02 2.50e+03 1.05e+01 bond pdb=" O3 PO4 D1005 " pdb=" P PO4 D1005 " ideal model delta sigma weight residual 1.569 1.509 0.060 2.00e-02 2.50e+03 8.94e+00 ... (remaining 13427 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.89: 17879 2.89 - 5.77: 253 5.77 - 8.66: 35 8.66 - 11.54: 11 11.54 - 14.43: 5 Bond angle restraints: 18183 Sorted by residual: angle pdb=" CA PRO E 502 " pdb=" N PRO E 502 " pdb=" CD PRO E 502 " ideal model delta sigma weight residual 112.00 98.48 13.52 1.40e+00 5.10e-01 9.33e+01 angle pdb=" CA PRO E 168 " pdb=" N PRO E 168 " pdb=" CD PRO E 168 " ideal model delta sigma weight residual 112.00 100.68 11.32 1.40e+00 5.10e-01 6.54e+01 angle pdb=" O12 PC1 E 901 " pdb=" P PC1 E 901 " pdb=" O14 PC1 E 901 " ideal model delta sigma weight residual 123.67 109.24 14.43 3.00e+00 1.11e-01 2.31e+01 angle pdb=" O12 PC1 D1003 " pdb=" P PC1 D1003 " pdb=" O14 PC1 D1003 " ideal model delta sigma weight residual 123.67 109.48 14.19 3.00e+00 1.11e-01 2.24e+01 angle pdb=" CA LEU E 57 " pdb=" CB LEU E 57 " pdb=" CG LEU E 57 " ideal model delta sigma weight residual 116.30 130.72 -14.42 3.50e+00 8.16e-02 1.70e+01 ... (remaining 18178 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.66: 7795 35.66 - 71.32: 312 71.32 - 106.98: 18 106.98 - 142.63: 18 142.63 - 178.29: 3 Dihedral angle restraints: 8146 sinusoidal: 3520 harmonic: 4626 Sorted by residual: dihedral pdb=" C4 IHP D1001 " pdb=" C2 IHP D1001 " pdb=" C3 IHP D1001 " pdb=" O12 IHP D1001 " ideal model delta sinusoidal sigma weight residual 60.90 -117.39 178.29 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O12 IHP D1001 " pdb=" C2 IHP D1001 " pdb=" C3 IHP D1001 " pdb=" O13 IHP D1001 " ideal model delta sinusoidal sigma weight residual 64.08 -121.46 -174.46 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C6 IHP D1004 " pdb=" C1 IHP D1004 " pdb=" C2 IHP D1004 " pdb=" O12 IHP D1004 " ideal model delta sinusoidal sigma weight residual 61.05 -153.70 -145.25 1 3.00e+01 1.11e-03 1.94e+01 ... (remaining 8143 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.044: 1992 1.044 - 2.088: 0 2.088 - 3.132: 0 3.132 - 4.176: 0 4.176 - 5.221: 9 Chirality restraints: 2001 Sorted by residual: chirality pdb=" C4 IHP D1002 " pdb=" C3 IHP D1002 " pdb=" C5 IHP D1002 " pdb=" O14 IHP D1002 " both_signs ideal model delta sigma weight residual False 2.48 -2.74 5.22 2.00e-01 2.50e+01 6.81e+02 chirality pdb=" C4 IHP D1004 " pdb=" C3 IHP D1004 " pdb=" C5 IHP D1004 " pdb=" O14 IHP D1004 " both_signs ideal model delta sigma weight residual False 2.48 -2.66 5.14 2.00e-01 2.50e+01 6.61e+02 chirality pdb=" C1 IHP D1002 " pdb=" C2 IHP D1002 " pdb=" C6 IHP D1002 " pdb=" O11 IHP D1002 " both_signs ideal model delta sigma weight residual False 2.32 -2.74 5.06 2.00e-01 2.50e+01 6.39e+02 ... (remaining 1998 not shown) Planarity restraints: 2267 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR E 167 " -0.095 5.00e-02 4.00e+02 1.35e-01 2.91e+01 pdb=" N PRO E 168 " 0.233 5.00e-02 4.00e+02 pdb=" CA PRO E 168 " -0.067 5.00e-02 4.00e+02 pdb=" CD PRO E 168 " -0.071 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE E 501 " 0.084 5.00e-02 4.00e+02 1.17e-01 2.20e+01 pdb=" N PRO E 502 " -0.202 5.00e-02 4.00e+02 pdb=" CA PRO E 502 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO E 502 " 0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B 56 " 0.040 5.00e-02 4.00e+02 5.99e-02 5.74e+00 pdb=" N PRO B 57 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO B 57 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 57 " 0.033 5.00e-02 4.00e+02 ... (remaining 2264 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1167 2.74 - 3.28: 12900 3.28 - 3.82: 22513 3.82 - 4.36: 25668 4.36 - 4.90: 45301 Nonbonded interactions: 107549 Sorted by model distance: nonbonded pdb=" OH TYR E 409 " pdb=" O45 IHP D1004 " model vdw 2.203 3.040 nonbonded pdb=" OE2 GLU E 90 " pdb=" OG1 THR E 94 " model vdw 2.245 3.040 nonbonded pdb=" O PRO D 95 " pdb=" OG1 THR D 96 " model vdw 2.253 3.040 nonbonded pdb=" O GLY D 644 " pdb=" OG1 THR D 648 " model vdw 2.275 3.040 nonbonded pdb=" OH TYR D 23 " pdb=" O32 IHP D1001 " model vdw 2.288 3.040 ... (remaining 107544 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 55 through 156) selection = chain 'B' 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: 1.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 10.410 Find NCS groups from input model: 0.070 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:6.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 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 : 0.004 0.139 13432 Z= 0.202 Angle : 0.812 14.426 18183 Z= 0.373 Chirality : 0.332 5.221 2001 Planarity : 0.006 0.135 2267 Dihedral : 18.798 178.292 5150 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.41 % Allowed : 19.31 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % 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: 1.69 (0.22), residues: 1554 helix: 2.06 (0.17), residues: 920 sheet: 0.41 (0.38), residues: 180 loop : -0.51 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 443 TYR 0.026 0.001 TYR E 198 PHE 0.029 0.002 PHE E 183 TRP 0.014 0.001 TRP D 268 HIS 0.002 0.001 HIS E 160 Details of bonding type rmsd covalent geometry : bond 0.00448 (13432) covalent geometry : angle 0.81215 (18183) hydrogen bonds : bond 0.11472 ( 860) hydrogen bonds : angle 5.45833 ( 2628) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 142 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 9 SER cc_start: 0.7566 (m) cc_final: 0.7326 (t) REVERT: D 383 MET cc_start: 0.8431 (OUTLIER) cc_final: 0.7695 (mtt) REVERT: D 443 ARG cc_start: 0.7976 (ttm-80) cc_final: 0.7705 (mtm180) REVERT: E 112 GLU cc_start: 0.7764 (pp20) cc_final: 0.7509 (pp20) REVERT: E 189 TYR cc_start: 0.7870 (m-80) cc_final: 0.7569 (m-80) REVERT: E 533 MET cc_start: 0.2802 (tpp) cc_final: 0.2522 (tpp) REVERT: E 573 ASN cc_start: 0.8132 (p0) cc_final: 0.7904 (p0) outliers start: 20 outliers final: 15 residues processed: 159 average time/residue: 0.4036 time to fit residues: 71.3608 Evaluate side-chains 145 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 129 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 316 ASP Chi-restraints excluded: chain D residue 341 SER Chi-restraints excluded: chain D residue 383 MET Chi-restraints excluded: chain D residue 723 LEU Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain E residue 183 PHE Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 556 LEU Chi-restraints excluded: chain E residue 807 VAL Chi-restraints excluded: chain E residue 825 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 2.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 15 GLN D 160 ASN D 198 GLN D 264 HIS D 335 ASN D 427 ASN D 605 GLN D 718 ASN A 149 ASN E 101 ASN E 185 ASN E 462 GLN E 527 ASN E 602 GLN ** E 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 844 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.188670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.139389 restraints weight = 15145.506| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 2.47 r_work: 0.3546 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.1084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 13432 Z= 0.249 Angle : 0.692 11.356 18183 Z= 0.331 Chirality : 0.047 0.478 2001 Planarity : 0.005 0.048 2267 Dihedral : 12.672 108.248 1979 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 4.37 % Allowed : 15.22 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % 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: 1.76 (0.21), residues: 1554 helix: 2.12 (0.17), residues: 918 sheet: 0.59 (0.40), residues: 170 loop : -0.53 (0.30), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 117 TYR 0.031 0.002 TYR E 198 PHE 0.022 0.002 PHE D 460 TRP 0.015 0.002 TRP D 268 HIS 0.006 0.001 HIS D 135 Details of bonding type rmsd covalent geometry : bond 0.00604 (13432) covalent geometry : angle 0.69207 (18183) hydrogen bonds : bond 0.05033 ( 860) hydrogen bonds : angle 4.36073 ( 2628) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 144 time to evaluate : 0.421 Fit side-chains revert: symmetry clash REVERT: D 51 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.7323 (mt-10) REVERT: D 77 GLU cc_start: 0.7185 (tm-30) cc_final: 0.6837 (pp20) REVERT: D 163 GLU cc_start: 0.7685 (tp30) cc_final: 0.7321 (tp30) REVERT: D 383 MET cc_start: 0.8568 (OUTLIER) cc_final: 0.7404 (mtt) REVERT: D 440 GLU cc_start: 0.7523 (OUTLIER) cc_final: 0.7099 (tm-30) REVERT: D 690 ARG cc_start: 0.7769 (OUTLIER) cc_final: 0.7504 (mmm-85) REVERT: D 712 LEU cc_start: 0.7714 (OUTLIER) cc_final: 0.7396 (mp) REVERT: A 108 ILE cc_start: 0.7372 (mm) cc_final: 0.7072 (mt) REVERT: B 138 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8525 (tp) REVERT: C 122 ARG cc_start: 0.6099 (mpt180) cc_final: 0.5824 (mmp-170) REVERT: E 112 GLU cc_start: 0.7809 (pp20) cc_final: 0.7493 (pp20) REVERT: E 189 TYR cc_start: 0.7751 (m-80) cc_final: 0.7467 (m-80) REVERT: E 268 GLU cc_start: 0.6690 (OUTLIER) cc_final: 0.5908 (tp30) REVERT: E 503 ASN cc_start: 0.7999 (m110) cc_final: 0.7465 (p0) REVERT: E 522 GLU cc_start: 0.8458 (tt0) cc_final: 0.8106 (tp30) REVERT: E 573 ASN cc_start: 0.8111 (p0) cc_final: 0.7828 (p0) outliers start: 62 outliers final: 19 residues processed: 187 average time/residue: 0.4928 time to fit residues: 101.5289 Evaluate side-chains 159 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 133 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 51 GLU Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 333 ILE Chi-restraints excluded: chain D residue 347 MET Chi-restraints excluded: chain D residue 355 VAL Chi-restraints excluded: chain D residue 383 MET Chi-restraints excluded: chain D residue 440 GLU Chi-restraints excluded: chain D residue 456 LYS Chi-restraints excluded: chain D residue 613 THR Chi-restraints excluded: chain D residue 690 ARG Chi-restraints excluded: chain D residue 697 LYS Chi-restraints excluded: chain D residue 712 LEU Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 268 GLU Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 753 ILE Chi-restraints excluded: chain E residue 801 LYS Chi-restraints excluded: chain E residue 807 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 144 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 117 optimal weight: 0.8980 chunk 148 optimal weight: 0.9980 chunk 126 optimal weight: 3.9990 chunk 90 optimal weight: 0.8980 chunk 105 optimal weight: 5.9990 chunk 14 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 48 optimal weight: 0.0270 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 15 GLN D 160 ASN D 335 ASN E 185 ASN E 535 ASN E 844 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.191259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.142703 restraints weight = 15185.632| |-----------------------------------------------------------------------------| r_work (start): 0.3839 rms_B_bonded: 2.31 r_work: 0.3602 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.1182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13432 Z= 0.136 Angle : 0.574 13.328 18183 Z= 0.281 Chirality : 0.042 0.384 2001 Planarity : 0.004 0.049 2267 Dihedral : 12.024 104.312 1959 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.45 % Allowed : 16.77 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % 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: 1.89 (0.22), residues: 1554 helix: 2.28 (0.16), residues: 929 sheet: 0.45 (0.39), residues: 177 loop : -0.63 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 53 TYR 0.026 0.001 TYR E 198 PHE 0.022 0.002 PHE E 762 TRP 0.014 0.001 TRP D 268 HIS 0.003 0.001 HIS D 135 Details of bonding type rmsd covalent geometry : bond 0.00311 (13432) covalent geometry : angle 0.57410 (18183) hydrogen bonds : bond 0.04296 ( 860) hydrogen bonds : angle 4.11225 ( 2628) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 148 time to evaluate : 0.426 Fit side-chains revert: symmetry clash REVERT: D 26 LEU cc_start: 0.8214 (mt) cc_final: 0.7993 (mp) REVERT: D 51 GLU cc_start: 0.7527 (OUTLIER) cc_final: 0.7299 (mt-10) REVERT: D 163 GLU cc_start: 0.7671 (tp30) cc_final: 0.7285 (tp30) REVERT: D 440 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.7432 (tm-30) REVERT: D 712 LEU cc_start: 0.7700 (OUTLIER) cc_final: 0.7289 (mp) REVERT: C 122 ARG cc_start: 0.6142 (mpt180) cc_final: 0.5862 (mmp-170) REVERT: E 112 GLU cc_start: 0.7582 (pp20) cc_final: 0.7245 (pp20) REVERT: E 189 TYR cc_start: 0.7734 (m-80) cc_final: 0.7427 (m-80) REVERT: E 358 LYS cc_start: 0.8058 (OUTLIER) cc_final: 0.7602 (mtmm) REVERT: E 503 ASN cc_start: 0.8061 (m110) cc_final: 0.7439 (p0) REVERT: E 522 GLU cc_start: 0.8353 (tt0) cc_final: 0.8049 (tp30) REVERT: E 573 ASN cc_start: 0.8109 (p0) cc_final: 0.7843 (p0) outliers start: 49 outliers final: 20 residues processed: 180 average time/residue: 0.4399 time to fit residues: 88.1058 Evaluate side-chains 156 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 132 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 51 GLU Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 347 MET Chi-restraints excluded: chain D residue 355 VAL Chi-restraints excluded: chain D residue 440 GLU Chi-restraints excluded: chain D residue 456 LYS Chi-restraints excluded: chain D residue 613 THR Chi-restraints excluded: chain D residue 697 LYS Chi-restraints excluded: chain D residue 712 LEU Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 358 LYS Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 556 LEU Chi-restraints excluded: chain E residue 753 ILE Chi-restraints excluded: chain E residue 767 ASP Chi-restraints excluded: chain E residue 807 VAL Chi-restraints excluded: chain E residue 825 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 99 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 chunk 115 optimal weight: 0.5980 chunk 133 optimal weight: 2.9990 chunk 109 optimal weight: 0.3980 chunk 98 optimal weight: 0.9990 chunk 78 optimal weight: 0.6980 chunk 106 optimal weight: 0.7980 chunk 154 optimal weight: 4.9990 chunk 2 optimal weight: 0.9990 chunk 51 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 160 ASN D 335 ASN A 149 ASN E 185 ASN E 535 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.193192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.139090 restraints weight = 15114.587| |-----------------------------------------------------------------------------| r_work (start): 0.3780 rms_B_bonded: 2.73 r_work: 0.3587 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.1447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13432 Z= 0.127 Angle : 0.541 8.434 18183 Z= 0.269 Chirality : 0.041 0.308 2001 Planarity : 0.004 0.048 2267 Dihedral : 11.493 101.333 1956 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 3.24 % Allowed : 16.56 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % 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: 2.00 (0.21), residues: 1554 helix: 2.36 (0.16), residues: 934 sheet: 0.44 (0.38), residues: 177 loop : -0.56 (0.30), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 197 TYR 0.021 0.001 TYR E 198 PHE 0.019 0.002 PHE E 95 TRP 0.014 0.001 TRP D 268 HIS 0.003 0.001 HIS E 160 Details of bonding type rmsd covalent geometry : bond 0.00290 (13432) covalent geometry : angle 0.54125 (18183) hydrogen bonds : bond 0.04052 ( 860) hydrogen bonds : angle 3.95924 ( 2628) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 141 time to evaluate : 0.340 Fit side-chains revert: symmetry clash REVERT: D 26 LEU cc_start: 0.8223 (mt) cc_final: 0.7998 (mp) REVERT: D 163 GLU cc_start: 0.7757 (tp30) cc_final: 0.7369 (tp30) REVERT: D 341 SER cc_start: 0.8038 (m) cc_final: 0.7792 (m) REVERT: D 383 MET cc_start: 0.8847 (mpp) cc_final: 0.8089 (mpt) REVERT: D 712 LEU cc_start: 0.7663 (OUTLIER) cc_final: 0.7278 (mp) REVERT: A 44 THR cc_start: 0.6810 (OUTLIER) cc_final: 0.6593 (p) REVERT: A 47 LYS cc_start: 0.8235 (mmpt) cc_final: 0.7866 (mmpt) REVERT: A 85 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.8101 (mt) REVERT: C 122 ARG cc_start: 0.6169 (mpt180) cc_final: 0.5922 (mmp-170) REVERT: E 112 GLU cc_start: 0.7537 (pp20) cc_final: 0.7151 (pp20) REVERT: E 189 TYR cc_start: 0.7742 (m-80) cc_final: 0.7358 (m-80) REVERT: E 268 GLU cc_start: 0.6672 (OUTLIER) cc_final: 0.5919 (tp30) REVERT: E 358 LYS cc_start: 0.8080 (OUTLIER) cc_final: 0.7634 (mtmm) REVERT: E 503 ASN cc_start: 0.8162 (m110) cc_final: 0.7467 (p0) REVERT: E 522 GLU cc_start: 0.8345 (tt0) cc_final: 0.8047 (tp30) REVERT: E 533 MET cc_start: 0.3656 (tpp) cc_final: 0.3262 (tpp) REVERT: E 573 ASN cc_start: 0.8051 (p0) cc_final: 0.7813 (p0) REVERT: E 598 LYS cc_start: 0.4445 (OUTLIER) cc_final: 0.3911 (ptmt) REVERT: E 738 ARG cc_start: 0.8021 (mtt-85) cc_final: 0.7791 (mtt-85) outliers start: 46 outliers final: 22 residues processed: 171 average time/residue: 0.4471 time to fit residues: 84.7156 Evaluate side-chains 159 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 131 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 347 MET Chi-restraints excluded: chain D residue 355 VAL Chi-restraints excluded: chain D residue 456 LYS Chi-restraints excluded: chain D residue 613 THR Chi-restraints excluded: chain D residue 697 LYS Chi-restraints excluded: chain D residue 712 LEU Chi-restraints excluded: chain D residue 723 LEU Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 234 PHE Chi-restraints excluded: chain E residue 268 GLU Chi-restraints excluded: chain E residue 358 LYS Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 598 LYS Chi-restraints excluded: chain E residue 776 LEU Chi-restraints excluded: chain E residue 807 VAL Chi-restraints excluded: chain E residue 825 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 145 optimal weight: 1.9990 chunk 46 optimal weight: 0.2980 chunk 101 optimal weight: 6.9990 chunk 52 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 152 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 90 optimal weight: 0.6980 chunk 3 optimal weight: 3.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 160 ASN D 335 ASN E 185 ASN E 535 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.191463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.143266 restraints weight = 15177.406| |-----------------------------------------------------------------------------| r_work (start): 0.3854 rms_B_bonded: 2.36 r_work: 0.3637 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.3487 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.1513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13432 Z= 0.130 Angle : 0.544 13.281 18183 Z= 0.268 Chirality : 0.040 0.321 2001 Planarity : 0.004 0.049 2267 Dihedral : 11.290 100.132 1956 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.96 % Allowed : 17.12 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % 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: 2.05 (0.22), residues: 1554 helix: 2.40 (0.16), residues: 935 sheet: 0.44 (0.38), residues: 180 loop : -0.53 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 197 TYR 0.020 0.001 TYR D 679 PHE 0.020 0.001 PHE E 762 TRP 0.013 0.001 TRP D 268 HIS 0.002 0.001 HIS D 135 Details of bonding type rmsd covalent geometry : bond 0.00300 (13432) covalent geometry : angle 0.54359 (18183) hydrogen bonds : bond 0.03990 ( 860) hydrogen bonds : angle 3.93351 ( 2628) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 138 time to evaluate : 0.331 Fit side-chains revert: symmetry clash REVERT: D 26 LEU cc_start: 0.8330 (mt) cc_final: 0.8111 (mp) REVERT: D 72 PHE cc_start: 0.7830 (m-10) cc_final: 0.7605 (m-10) REVERT: D 163 GLU cc_start: 0.7827 (tp30) cc_final: 0.7423 (tp30) REVERT: D 341 SER cc_start: 0.8197 (m) cc_final: 0.7977 (m) REVERT: D 383 MET cc_start: 0.8913 (mpp) cc_final: 0.8078 (mpt) REVERT: D 712 LEU cc_start: 0.7761 (OUTLIER) cc_final: 0.7366 (mp) REVERT: A 44 THR cc_start: 0.6837 (OUTLIER) cc_final: 0.6627 (p) REVERT: A 47 LYS cc_start: 0.8251 (mmpt) cc_final: 0.7860 (mmpt) REVERT: A 152 LEU cc_start: 0.7901 (mm) cc_final: 0.7588 (mp) REVERT: C 122 ARG cc_start: 0.6264 (OUTLIER) cc_final: 0.5980 (mmp-170) REVERT: E 112 GLU cc_start: 0.7487 (pp20) cc_final: 0.7072 (pp20) REVERT: E 189 TYR cc_start: 0.7728 (m-80) cc_final: 0.7348 (m-80) REVERT: E 358 LYS cc_start: 0.8080 (OUTLIER) cc_final: 0.7647 (mtmm) REVERT: E 503 ASN cc_start: 0.8132 (m110) cc_final: 0.7383 (p0) REVERT: E 522 GLU cc_start: 0.8467 (tt0) cc_final: 0.8184 (tp30) REVERT: E 533 MET cc_start: 0.3511 (tpp) cc_final: 0.3111 (tpp) REVERT: E 573 ASN cc_start: 0.8088 (p0) cc_final: 0.7876 (p0) REVERT: E 598 LYS cc_start: 0.4444 (OUTLIER) cc_final: 0.3869 (ptmt) REVERT: E 738 ARG cc_start: 0.8264 (mtt-85) cc_final: 0.8028 (mtt-85) outliers start: 42 outliers final: 24 residues processed: 167 average time/residue: 0.4037 time to fit residues: 75.1198 Evaluate side-chains 163 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 134 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 347 MET Chi-restraints excluded: chain D residue 355 VAL Chi-restraints excluded: chain D residue 419 CYS Chi-restraints excluded: chain D residue 456 LYS Chi-restraints excluded: chain D residue 613 THR Chi-restraints excluded: chain D residue 697 LYS Chi-restraints excluded: chain D residue 712 LEU Chi-restraints excluded: chain D residue 723 LEU Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 122 ARG Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 234 PHE Chi-restraints excluded: chain E residue 358 LYS Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 556 LEU Chi-restraints excluded: chain E residue 598 LYS Chi-restraints excluded: chain E residue 776 LEU Chi-restraints excluded: chain E residue 807 VAL Chi-restraints excluded: chain E residue 825 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 136 optimal weight: 0.0670 chunk 34 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 108 optimal weight: 0.9980 chunk 113 optimal weight: 7.9990 chunk 31 optimal weight: 2.9990 chunk 129 optimal weight: 3.9990 chunk 42 optimal weight: 0.4980 chunk 152 optimal weight: 0.0770 chunk 131 optimal weight: 0.4980 chunk 71 optimal weight: 6.9990 overall best weight: 0.3676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 160 ASN D 304 HIS D 335 ASN E 185 ASN E 433 ASN E 535 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.192907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.143504 restraints weight = 15008.450| |-----------------------------------------------------------------------------| r_work (start): 0.3837 rms_B_bonded: 2.55 r_work: 0.3622 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 13432 Z= 0.111 Angle : 0.517 8.311 18183 Z= 0.258 Chirality : 0.039 0.279 2001 Planarity : 0.004 0.048 2267 Dihedral : 10.978 97.762 1955 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.75 % Allowed : 17.83 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % 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: 2.21 (0.22), residues: 1554 helix: 2.52 (0.17), residues: 934 sheet: 0.52 (0.38), residues: 179 loop : -0.45 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 177 TYR 0.023 0.001 TYR D 679 PHE 0.023 0.001 PHE E 153 TRP 0.014 0.001 TRP D 268 HIS 0.001 0.000 HIS E 242 Details of bonding type rmsd covalent geometry : bond 0.00242 (13432) covalent geometry : angle 0.51718 (18183) hydrogen bonds : bond 0.03765 ( 860) hydrogen bonds : angle 3.82036 ( 2628) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 147 time to evaluate : 0.515 Fit side-chains revert: symmetry clash REVERT: D 163 GLU cc_start: 0.7746 (tp30) cc_final: 0.7386 (tp30) REVERT: D 327 LYS cc_start: 0.8607 (OUTLIER) cc_final: 0.8089 (mttt) REVERT: D 341 SER cc_start: 0.8136 (m) cc_final: 0.7914 (m) REVERT: D 712 LEU cc_start: 0.7712 (OUTLIER) cc_final: 0.7353 (mp) REVERT: A 47 LYS cc_start: 0.8142 (mmpt) cc_final: 0.7471 (mmpt) REVERT: A 85 LEU cc_start: 0.8166 (mt) cc_final: 0.7957 (mt) REVERT: B 140 PHE cc_start: 0.7740 (t80) cc_final: 0.7184 (t80) REVERT: C 122 ARG cc_start: 0.6269 (OUTLIER) cc_final: 0.6015 (mmp-170) REVERT: C 124 ARG cc_start: 0.5076 (OUTLIER) cc_final: 0.4768 (ttm170) REVERT: E 45 LYS cc_start: 0.8222 (mttp) cc_final: 0.7662 (ptmm) REVERT: E 112 GLU cc_start: 0.7574 (pp20) cc_final: 0.7166 (pp20) REVERT: E 189 TYR cc_start: 0.7752 (m-80) cc_final: 0.7353 (m-80) REVERT: E 268 GLU cc_start: 0.6666 (OUTLIER) cc_final: 0.5943 (tp30) REVERT: E 503 ASN cc_start: 0.8132 (m110) cc_final: 0.7366 (p0) REVERT: E 522 GLU cc_start: 0.8191 (tt0) cc_final: 0.7981 (tp30) REVERT: E 533 MET cc_start: 0.3801 (tpp) cc_final: 0.3409 (tpp) REVERT: E 598 LYS cc_start: 0.4275 (OUTLIER) cc_final: 0.3742 (ptmt) REVERT: E 738 ARG cc_start: 0.8003 (mtt-85) cc_final: 0.7787 (mtt-85) outliers start: 39 outliers final: 19 residues processed: 171 average time/residue: 0.3990 time to fit residues: 76.1111 Evaluate side-chains 161 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 136 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 327 LYS Chi-restraints excluded: chain D residue 347 MET Chi-restraints excluded: chain D residue 355 VAL Chi-restraints excluded: chain D residue 436 GLN Chi-restraints excluded: chain D residue 613 THR Chi-restraints excluded: chain D residue 712 LEU Chi-restraints excluded: chain D residue 723 LEU Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 122 ARG Chi-restraints excluded: chain C residue 124 ARG Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 234 PHE Chi-restraints excluded: chain E residue 268 GLU Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 556 LEU Chi-restraints excluded: chain E residue 598 LYS Chi-restraints excluded: chain E residue 767 ASP Chi-restraints excluded: chain E residue 776 LEU Chi-restraints excluded: chain E residue 807 VAL Chi-restraints excluded: chain E residue 825 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 114 optimal weight: 0.6980 chunk 130 optimal weight: 3.9990 chunk 60 optimal weight: 0.4980 chunk 40 optimal weight: 0.9980 chunk 152 optimal weight: 0.0060 chunk 27 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 76 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 15 GLN D 160 ASN D 335 ASN E 185 ASN E 535 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.192187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.144025 restraints weight = 14980.327| |-----------------------------------------------------------------------------| r_work (start): 0.3852 rms_B_bonded: 2.33 r_work: 0.3596 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13432 Z= 0.123 Angle : 0.533 8.507 18183 Z= 0.265 Chirality : 0.040 0.283 2001 Planarity : 0.004 0.048 2267 Dihedral : 10.851 96.335 1955 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.68 % Allowed : 18.25 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % 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: 2.21 (0.22), residues: 1554 helix: 2.51 (0.16), residues: 935 sheet: 0.60 (0.38), residues: 179 loop : -0.47 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 197 TYR 0.023 0.001 TYR E 198 PHE 0.022 0.001 PHE E 145 TRP 0.012 0.001 TRP D 268 HIS 0.002 0.000 HIS D 135 Details of bonding type rmsd covalent geometry : bond 0.00281 (13432) covalent geometry : angle 0.53286 (18183) hydrogen bonds : bond 0.03830 ( 860) hydrogen bonds : angle 3.82763 ( 2628) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 138 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 163 GLU cc_start: 0.7725 (tp30) cc_final: 0.7353 (tp30) REVERT: D 341 SER cc_start: 0.8169 (m) cc_final: 0.7951 (m) REVERT: D 712 LEU cc_start: 0.7686 (OUTLIER) cc_final: 0.7306 (mp) REVERT: A 85 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.8076 (mt) REVERT: C 122 ARG cc_start: 0.6264 (OUTLIER) cc_final: 0.6017 (mmp-170) REVERT: E 45 LYS cc_start: 0.8261 (mttp) cc_final: 0.7772 (ptmm) REVERT: E 112 GLU cc_start: 0.7602 (pp20) cc_final: 0.7174 (pp20) REVERT: E 189 TYR cc_start: 0.7743 (m-80) cc_final: 0.7372 (m-80) REVERT: E 268 GLU cc_start: 0.6727 (OUTLIER) cc_final: 0.6006 (tp30) REVERT: E 358 LYS cc_start: 0.8106 (OUTLIER) cc_final: 0.7738 (mtmm) REVERT: E 503 ASN cc_start: 0.8147 (m110) cc_final: 0.7346 (p0) REVERT: E 533 MET cc_start: 0.3781 (tpp) cc_final: 0.3518 (tpp) REVERT: E 568 ASP cc_start: 0.7086 (m-30) cc_final: 0.6863 (m-30) REVERT: E 598 LYS cc_start: 0.4318 (OUTLIER) cc_final: 0.3748 (ptmt) outliers start: 38 outliers final: 21 residues processed: 160 average time/residue: 0.4116 time to fit residues: 73.4222 Evaluate side-chains 161 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 134 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 347 MET Chi-restraints excluded: chain D residue 355 VAL Chi-restraints excluded: chain D residue 613 THR Chi-restraints excluded: chain D residue 712 LEU Chi-restraints excluded: chain D residue 723 LEU Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 122 ARG Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 234 PHE Chi-restraints excluded: chain E residue 268 GLU Chi-restraints excluded: chain E residue 358 LYS Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 556 LEU Chi-restraints excluded: chain E residue 598 LYS Chi-restraints excluded: chain E residue 767 ASP Chi-restraints excluded: chain E residue 776 LEU Chi-restraints excluded: chain E residue 807 VAL Chi-restraints excluded: chain E residue 825 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 44 optimal weight: 0.6980 chunk 87 optimal weight: 0.9980 chunk 50 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 8 optimal weight: 8.9990 chunk 14 optimal weight: 0.6980 chunk 34 optimal weight: 0.3980 chunk 25 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 160 ASN D 335 ASN E 185 ASN E 535 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.192225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.144298 restraints weight = 14906.686| |-----------------------------------------------------------------------------| r_work (start): 0.3856 rms_B_bonded: 2.32 r_work: 0.3613 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13432 Z= 0.123 Angle : 0.543 13.770 18183 Z= 0.266 Chirality : 0.040 0.274 2001 Planarity : 0.004 0.048 2267 Dihedral : 10.621 94.125 1955 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.47 % Allowed : 18.68 % Favored : 78.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % 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: 2.24 (0.22), residues: 1554 helix: 2.51 (0.16), residues: 935 sheet: 0.67 (0.38), residues: 179 loop : -0.45 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 117 TYR 0.022 0.001 TYR D 679 PHE 0.015 0.001 PHE D 120 TRP 0.012 0.001 TRP D 268 HIS 0.002 0.000 HIS E 242 Details of bonding type rmsd covalent geometry : bond 0.00280 (13432) covalent geometry : angle 0.54349 (18183) hydrogen bonds : bond 0.03810 ( 860) hydrogen bonds : angle 3.81432 ( 2628) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 136 time to evaluate : 0.496 Fit side-chains revert: symmetry clash REVERT: D 163 GLU cc_start: 0.7713 (tp30) cc_final: 0.7336 (tp30) REVERT: D 341 SER cc_start: 0.8062 (m) cc_final: 0.7830 (m) REVERT: D 712 LEU cc_start: 0.7611 (OUTLIER) cc_final: 0.7231 (mp) REVERT: A 85 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.8018 (mt) REVERT: C 122 ARG cc_start: 0.6261 (OUTLIER) cc_final: 0.6028 (mmp-170) REVERT: E 45 LYS cc_start: 0.8234 (mttp) cc_final: 0.7773 (ptmm) REVERT: E 112 GLU cc_start: 0.7617 (pp20) cc_final: 0.7151 (pp20) REVERT: E 189 TYR cc_start: 0.7730 (m-80) cc_final: 0.7307 (m-80) REVERT: E 268 GLU cc_start: 0.6671 (OUTLIER) cc_final: 0.5943 (tp30) REVERT: E 358 LYS cc_start: 0.8100 (OUTLIER) cc_final: 0.7683 (mtmm) REVERT: E 503 ASN cc_start: 0.8106 (m110) cc_final: 0.7325 (p0) REVERT: E 568 ASP cc_start: 0.7064 (m-30) cc_final: 0.6838 (m-30) REVERT: E 598 LYS cc_start: 0.4372 (OUTLIER) cc_final: 0.3789 (ptmt) REVERT: E 614 MET cc_start: 0.7901 (mpp) cc_final: 0.7318 (pp-130) REVERT: E 738 ARG cc_start: 0.7926 (mtt-85) cc_final: 0.7622 (mtt-85) outliers start: 35 outliers final: 23 residues processed: 158 average time/residue: 0.4273 time to fit residues: 75.0525 Evaluate side-chains 162 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 133 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 347 MET Chi-restraints excluded: chain D residue 355 VAL Chi-restraints excluded: chain D residue 419 CYS Chi-restraints excluded: chain D residue 436 GLN Chi-restraints excluded: chain D residue 613 THR Chi-restraints excluded: chain D residue 712 LEU Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 122 ARG Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 234 PHE Chi-restraints excluded: chain E residue 268 GLU Chi-restraints excluded: chain E residue 358 LYS Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 556 LEU Chi-restraints excluded: chain E residue 598 LYS Chi-restraints excluded: chain E residue 767 ASP Chi-restraints excluded: chain E residue 776 LEU Chi-restraints excluded: chain E residue 807 VAL Chi-restraints excluded: chain E residue 825 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 76 optimal weight: 4.9990 chunk 44 optimal weight: 0.0770 chunk 56 optimal weight: 0.4980 chunk 146 optimal weight: 0.5980 chunk 73 optimal weight: 0.8980 chunk 66 optimal weight: 0.6980 chunk 52 optimal weight: 0.7980 chunk 129 optimal weight: 3.9990 chunk 96 optimal weight: 10.0000 chunk 53 optimal weight: 0.8980 chunk 115 optimal weight: 0.7980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 160 ASN D 335 ASN E 185 ASN E 535 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.194109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.140204 restraints weight = 15077.413| |-----------------------------------------------------------------------------| r_work (start): 0.3795 rms_B_bonded: 2.72 r_work: 0.3605 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13432 Z= 0.119 Angle : 0.541 11.772 18183 Z= 0.266 Chirality : 0.040 0.269 2001 Planarity : 0.004 0.048 2267 Dihedral : 10.465 92.889 1955 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.61 % Allowed : 18.96 % Favored : 78.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % 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: 2.26 (0.22), residues: 1554 helix: 2.52 (0.16), residues: 935 sheet: 0.75 (0.39), residues: 178 loop : -0.45 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 117 TYR 0.021 0.001 TYR D 679 PHE 0.020 0.001 PHE E 762 TRP 0.013 0.001 TRP D 268 HIS 0.002 0.000 HIS E 256 Details of bonding type rmsd covalent geometry : bond 0.00271 (13432) covalent geometry : angle 0.54122 (18183) hydrogen bonds : bond 0.03770 ( 860) hydrogen bonds : angle 3.79831 ( 2628) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 134 time to evaluate : 0.319 Fit side-chains revert: symmetry clash REVERT: D 163 GLU cc_start: 0.7709 (tp30) cc_final: 0.7323 (tp30) REVERT: D 341 SER cc_start: 0.8067 (m) cc_final: 0.7833 (m) REVERT: D 712 LEU cc_start: 0.7584 (OUTLIER) cc_final: 0.7193 (mp) REVERT: A 85 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.8016 (mt) REVERT: C 122 ARG cc_start: 0.6272 (OUTLIER) cc_final: 0.6041 (mmp-170) REVERT: E 45 LYS cc_start: 0.8216 (mttp) cc_final: 0.7737 (ttpp) REVERT: E 112 GLU cc_start: 0.7704 (pp20) cc_final: 0.7179 (pp20) REVERT: E 189 TYR cc_start: 0.7734 (m-80) cc_final: 0.7330 (m-80) REVERT: E 268 GLU cc_start: 0.6659 (OUTLIER) cc_final: 0.5924 (tp30) REVERT: E 358 LYS cc_start: 0.8071 (OUTLIER) cc_final: 0.7635 (mtmm) REVERT: E 503 ASN cc_start: 0.8098 (m110) cc_final: 0.7295 (p0) REVERT: E 568 ASP cc_start: 0.7027 (m-30) cc_final: 0.6809 (m-30) REVERT: E 598 LYS cc_start: 0.4369 (OUTLIER) cc_final: 0.3777 (ptmt) REVERT: E 614 MET cc_start: 0.7867 (mpp) cc_final: 0.7323 (pp-130) REVERT: E 738 ARG cc_start: 0.7934 (mtt-85) cc_final: 0.7604 (mtt-85) outliers start: 37 outliers final: 24 residues processed: 157 average time/residue: 0.4463 time to fit residues: 78.2141 Evaluate side-chains 164 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 134 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 355 VAL Chi-restraints excluded: chain D residue 419 CYS Chi-restraints excluded: chain D residue 436 GLN Chi-restraints excluded: chain D residue 613 THR Chi-restraints excluded: chain D residue 712 LEU Chi-restraints excluded: chain D residue 723 LEU Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain C residue 122 ARG Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 234 PHE Chi-restraints excluded: chain E residue 268 GLU Chi-restraints excluded: chain E residue 358 LYS Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 535 ASN Chi-restraints excluded: chain E residue 556 LEU Chi-restraints excluded: chain E residue 598 LYS Chi-restraints excluded: chain E residue 767 ASP Chi-restraints excluded: chain E residue 776 LEU Chi-restraints excluded: chain E residue 807 VAL Chi-restraints excluded: chain E residue 825 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 111 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 155 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 chunk 83 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 147 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 160 ASN D 335 ASN E 185 ASN E 535 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.190493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.138227 restraints weight = 15045.327| |-----------------------------------------------------------------------------| r_work (start): 0.3773 rms_B_bonded: 2.85 r_work: 0.3548 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 13432 Z= 0.209 Angle : 0.626 14.744 18183 Z= 0.303 Chirality : 0.043 0.314 2001 Planarity : 0.005 0.049 2267 Dihedral : 10.572 92.140 1955 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.54 % Allowed : 19.24 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % 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: 2.01 (0.22), residues: 1554 helix: 2.29 (0.16), residues: 938 sheet: 0.69 (0.39), residues: 179 loop : -0.50 (0.31), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 117 TYR 0.031 0.002 TYR D 679 PHE 0.020 0.002 PHE D 460 TRP 0.010 0.001 TRP E 355 HIS 0.006 0.001 HIS D 135 Details of bonding type rmsd covalent geometry : bond 0.00511 (13432) covalent geometry : angle 0.62559 (18183) hydrogen bonds : bond 0.04326 ( 860) hydrogen bonds : angle 3.96427 ( 2628) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 135 time to evaluate : 0.498 Fit side-chains revert: symmetry clash REVERT: D 163 GLU cc_start: 0.7767 (tp30) cc_final: 0.7381 (tp30) REVERT: D 341 SER cc_start: 0.8175 (m) cc_final: 0.7931 (m) REVERT: D 712 LEU cc_start: 0.7812 (OUTLIER) cc_final: 0.7509 (mp) REVERT: A 85 LEU cc_start: 0.8363 (OUTLIER) cc_final: 0.8108 (mt) REVERT: B 140 PHE cc_start: 0.7774 (t80) cc_final: 0.7258 (t80) REVERT: C 122 ARG cc_start: 0.6319 (OUTLIER) cc_final: 0.6050 (mmp-170) REVERT: E 45 LYS cc_start: 0.8244 (mttp) cc_final: 0.7798 (ptmm) REVERT: E 112 GLU cc_start: 0.7717 (pp20) cc_final: 0.7165 (pp20) REVERT: E 189 TYR cc_start: 0.7784 (m-80) cc_final: 0.7397 (m-80) REVERT: E 268 GLU cc_start: 0.6841 (OUTLIER) cc_final: 0.6063 (tp30) REVERT: E 358 LYS cc_start: 0.8111 (OUTLIER) cc_final: 0.7745 (mtmm) REVERT: E 503 ASN cc_start: 0.8115 (m110) cc_final: 0.7345 (p0) REVERT: E 568 ASP cc_start: 0.7098 (m-30) cc_final: 0.6886 (m-30) REVERT: E 598 LYS cc_start: 0.4523 (OUTLIER) cc_final: 0.4053 (ptmt) REVERT: E 614 MET cc_start: 0.7899 (mpp) cc_final: 0.7329 (pp-130) REVERT: E 738 ARG cc_start: 0.8026 (mtt-85) cc_final: 0.7499 (mtp85) outliers start: 36 outliers final: 22 residues processed: 160 average time/residue: 0.4227 time to fit residues: 75.7827 Evaluate side-chains 158 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 130 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 355 VAL Chi-restraints excluded: chain D residue 419 CYS Chi-restraints excluded: chain D residue 613 THR Chi-restraints excluded: chain D residue 712 LEU Chi-restraints excluded: chain D residue 723 LEU Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain C residue 122 ARG Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 234 PHE Chi-restraints excluded: chain E residue 268 GLU Chi-restraints excluded: chain E residue 358 LYS Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 556 LEU Chi-restraints excluded: chain E residue 598 LYS Chi-restraints excluded: chain E residue 767 ASP Chi-restraints excluded: chain E residue 776 LEU Chi-restraints excluded: chain E residue 807 VAL Chi-restraints excluded: chain E residue 825 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 145 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 125 optimal weight: 0.7980 chunk 101 optimal weight: 9.9990 chunk 52 optimal weight: 0.1980 chunk 3 optimal weight: 0.8980 chunk 34 optimal weight: 0.5980 chunk 134 optimal weight: 0.5980 chunk 136 optimal weight: 1.9990 chunk 123 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 160 ASN D 335 ASN E 185 ASN E 535 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.191486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.143577 restraints weight = 15009.587| |-----------------------------------------------------------------------------| r_work (start): 0.3852 rms_B_bonded: 2.33 r_work: 0.3607 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13432 Z= 0.123 Angle : 0.562 14.979 18183 Z= 0.273 Chirality : 0.041 0.283 2001 Planarity : 0.004 0.048 2267 Dihedral : 10.284 90.700 1955 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.26 % Allowed : 19.45 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % 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: 2.19 (0.22), residues: 1554 helix: 2.45 (0.16), residues: 936 sheet: 0.85 (0.39), residues: 178 loop : -0.53 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 117 TYR 0.022 0.001 TYR D 679 PHE 0.033 0.001 PHE C 101 TRP 0.013 0.001 TRP D 268 HIS 0.002 0.000 HIS E 242 Details of bonding type rmsd covalent geometry : bond 0.00279 (13432) covalent geometry : angle 0.56211 (18183) hydrogen bonds : bond 0.03898 ( 860) hydrogen bonds : angle 3.84245 ( 2628) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3565.49 seconds wall clock time: 61 minutes 32.44 seconds (3692.44 seconds total)