Starting phenix.real_space_refine on Thu Jul 31 13:24:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ytj_34090/07_2025/7ytj_34090.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ytj_34090/07_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_34090/07_2025/7ytj_34090.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ytj_34090/07_2025/7ytj_34090.map" model { file = "/net/cci-nas-00/data/ceres_data/7ytj_34090/07_2025/7ytj_34090.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ytj_34090/07_2025/7ytj_34090.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 8.54, per 1000 atoms: 0.65 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: 3.62 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.44 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: 4.42 Time building geometry restraints manager: 4.28 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: 4.450 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: 0.410 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 33.660 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.820 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (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 TRP 0.014 0.001 TRP D 268 HIS 0.002 0.001 HIS E 160 PHE 0.029 0.002 PHE E 183 TYR 0.026 0.001 TYR E 198 ARG 0.012 0.000 ARG D 443 Details of bonding type rmsd hydrogen bonds : bond 0.11472 ( 860) hydrogen bonds : angle 5.45833 ( 2628) covalent geometry : bond 0.00448 (13432) covalent geometry : angle 0.81215 (18183) *********************** 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 : 1.561 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: 0.7905 (p0) outliers start: 20 outliers final: 15 residues processed: 159 average time/residue: 1.0509 time to fit residues: 186.8752 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 : 1.522 ------------------------------------------------------------------------------- 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 131 optimal weight: 0.9980 chunk 118 optimal weight: 0.8980 chunk 65 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 chunk 79 optimal weight: 4.9990 chunk 63 optimal weight: 0.5980 chunk 122 optimal weight: 0.4980 chunk 47 optimal weight: 0.6980 chunk 74 optimal weight: 0.5980 chunk 91 optimal weight: 0.6980 chunk 141 optimal weight: 3.9990 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 15 GLN D 160 ASN D 198 GLN D 264 HIS D 335 ASN D 427 ASN D 605 GLN E 101 ASN E 185 ASN E 433 ASN E 462 GLN E 527 ASN E 602 GLN ** E 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.194782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.140969 restraints weight = 14840.882| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 2.74 r_work: 0.3614 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.0838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 13432 Z= 0.137 Angle : 0.610 10.819 18183 Z= 0.292 Chirality : 0.044 0.477 2001 Planarity : 0.004 0.047 2267 Dihedral : 12.507 107.761 1979 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.03 % Allowed : 16.42 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.22), residues: 1554 helix: 2.42 (0.17), residues: 918 sheet: 0.41 (0.38), residues: 178 loop : -0.44 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 268 HIS 0.003 0.001 HIS E 256 PHE 0.020 0.001 PHE E 145 TYR 0.034 0.001 TYR E 198 ARG 0.005 0.000 ARG E 509 Details of bonding type rmsd hydrogen bonds : bond 0.04412 ( 860) hydrogen bonds : angle 4.23521 ( 2628) covalent geometry : bond 0.00308 (13432) covalent geometry : angle 0.61050 (18183) *********************** 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 190 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 147 time to evaluate : 1.745 Fit side-chains revert: symmetry clash REVERT: D 51 GLU cc_start: 0.7535 (OUTLIER) cc_final: 0.7241 (mt-10) REVERT: D 77 GLU cc_start: 0.7209 (tm-30) cc_final: 0.6957 (pp20) REVERT: D 163 GLU cc_start: 0.7709 (tp30) cc_final: 0.7334 (tp30) REVERT: D 383 MET cc_start: 0.8344 (OUTLIER) cc_final: 0.7405 (mtt) REVERT: D 440 GLU cc_start: 0.7460 (OUTLIER) cc_final: 0.6965 (tm-30) REVERT: A 47 LYS cc_start: 0.8222 (mmpt) cc_final: 0.7970 (mmpt) REVERT: A 108 ILE cc_start: 0.7306 (mm) cc_final: 0.6984 (mt) REVERT: A 153 ARG cc_start: 0.8302 (OUTLIER) cc_final: 0.7584 (tpp-160) REVERT: C 122 ARG cc_start: 0.6081 (mpt180) cc_final: 0.5802 (mmp-170) REVERT: E 112 GLU cc_start: 0.7816 (pp20) cc_final: 0.7504 (pp20) REVERT: E 189 TYR cc_start: 0.7738 (m-80) cc_final: 0.7399 (m-80) REVERT: E 522 GLU cc_start: 0.8359 (tt0) cc_final: 0.8044 (tp30) REVERT: E 573 ASN cc_start: 0.8013 (p0) cc_final: 0.7778 (p0) outliers start: 43 outliers final: 15 residues processed: 173 average time/residue: 1.5263 time to fit residues: 294.6794 Evaluate side-chains 155 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 136 time to evaluate : 1.481 ------------------------------------------------------------------------------- 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 209 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 697 LYS Chi-restraints excluded: chain D residue 712 LEU Chi-restraints excluded: chain A residue 153 ARG Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain E residue 467 THR 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 143 optimal weight: 10.0000 chunk 103 optimal weight: 1.9990 chunk 97 optimal weight: 8.9990 chunk 112 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 47 optimal weight: 2.9990 chunk 99 optimal weight: 7.9990 chunk 123 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 19 optimal weight: 0.5980 chunk 94 optimal weight: 0.7980 overall best weight: 1.2786 ------------------------------------------------------------------------------- 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 D 718 ASN E 185 ASN E 535 ASN ** E 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 844 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.191926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.137598 restraints weight = 15049.718| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 2.70 r_work: 0.3570 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.1127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 13432 Z= 0.184 Angle : 0.592 9.865 18183 Z= 0.292 Chirality : 0.043 0.382 2001 Planarity : 0.005 0.061 2267 Dihedral : 12.018 103.758 1958 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.38 % Allowed : 16.28 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.22), residues: 1554 helix: 2.30 (0.16), residues: 929 sheet: 0.45 (0.39), residues: 177 loop : -0.58 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 268 HIS 0.004 0.001 HIS D 135 PHE 0.020 0.002 PHE E 762 TYR 0.026 0.001 TYR D 679 ARG 0.020 0.001 ARG E 738 Details of bonding type rmsd hydrogen bonds : bond 0.04502 ( 860) hydrogen bonds : angle 4.15295 ( 2628) covalent geometry : bond 0.00444 (13432) covalent geometry : angle 0.59249 (18183) *********************** 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 195 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 147 time to evaluate : 1.431 Fit side-chains revert: symmetry clash REVERT: D 51 GLU cc_start: 0.7506 (OUTLIER) cc_final: 0.7255 (mt-10) REVERT: D 163 GLU cc_start: 0.7693 (tp30) cc_final: 0.7297 (tp30) REVERT: D 383 MET cc_start: 0.8576 (OUTLIER) cc_final: 0.7369 (mtt) REVERT: D 440 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7374 (tm-30) REVERT: D 712 LEU cc_start: 0.7601 (OUTLIER) cc_final: 0.7147 (mp) REVERT: A 47 LYS cc_start: 0.8302 (mmpt) cc_final: 0.8031 (mmpt) REVERT: A 108 ILE cc_start: 0.7342 (mm) cc_final: 0.7050 (mt) REVERT: C 122 ARG cc_start: 0.6182 (mpt180) cc_final: 0.5925 (mmp-170) REVERT: E 112 GLU cc_start: 0.7569 (pp20) cc_final: 0.7242 (pp20) REVERT: E 189 TYR cc_start: 0.7750 (m-80) cc_final: 0.7435 (m-80) REVERT: E 268 GLU cc_start: 0.6611 (OUTLIER) cc_final: 0.5874 (tp30) REVERT: E 503 ASN cc_start: 0.8050 (m110) cc_final: 0.7422 (p0) REVERT: E 522 GLU cc_start: 0.8418 (tt0) cc_final: 0.8081 (tp30) REVERT: E 533 MET cc_start: 0.3179 (tpp) cc_final: 0.2777 (tpp) REVERT: E 573 ASN cc_start: 0.8070 (p0) cc_final: 0.7832 (p0) REVERT: E 738 ARG cc_start: 0.7866 (mtt90) cc_final: 0.7664 (mtt180) outliers start: 48 outliers final: 18 residues processed: 177 average time/residue: 1.5949 time to fit residues: 314.2189 Evaluate side-chains 160 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 137 time to evaluate : 1.908 ------------------------------------------------------------------------------- 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 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 697 LYS Chi-restraints excluded: chain D residue 712 LEU Chi-restraints excluded: chain D residue 723 LEU Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 54 LEU 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 15 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 40 optimal weight: 0.3980 chunk 76 optimal weight: 0.7980 chunk 123 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 46 optimal weight: 0.5980 chunk 77 optimal weight: 1.9990 chunk 96 optimal weight: 6.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 E 844 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.191469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.143722 restraints weight = 14942.214| |-----------------------------------------------------------------------------| r_work (start): 0.3838 rms_B_bonded: 2.57 r_work: 0.3593 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.1326 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= 0.138 Angle : 0.552 13.299 18183 Z= 0.273 Chirality : 0.041 0.364 2001 Planarity : 0.004 0.048 2267 Dihedral : 11.700 102.256 1958 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.24 % Allowed : 16.70 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.21), residues: 1554 helix: 2.38 (0.16), residues: 931 sheet: 0.44 (0.38), residues: 177 loop : -0.57 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 268 HIS 0.002 0.001 HIS D 462 PHE 0.016 0.001 PHE E 95 TYR 0.023 0.001 TYR E 198 ARG 0.007 0.000 ARG E 738 Details of bonding type rmsd hydrogen bonds : bond 0.04157 ( 860) hydrogen bonds : angle 4.03313 ( 2628) covalent geometry : bond 0.00319 (13432) covalent geometry : angle 0.55245 (18183) *********************** 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 : 2.777 Fit side-chains revert: symmetry clash REVERT: D 26 LEU cc_start: 0.8298 (mt) cc_final: 0.8081 (mp) REVERT: D 51 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.7392 (mt-10) REVERT: D 77 GLU cc_start: 0.7287 (tm-30) cc_final: 0.6993 (pp20) REVERT: D 163 GLU cc_start: 0.7786 (tp30) cc_final: 0.7375 (tp30) REVERT: D 383 MET cc_start: 0.8562 (OUTLIER) cc_final: 0.8008 (mpt) REVERT: D 712 LEU cc_start: 0.7726 (OUTLIER) cc_final: 0.7316 (mp) REVERT: A 44 THR cc_start: 0.6850 (OUTLIER) cc_final: 0.6635 (p) REVERT: A 47 LYS cc_start: 0.8270 (mmpt) cc_final: 0.8027 (mmpt) REVERT: A 147 ILE cc_start: 0.8519 (mm) cc_final: 0.8314 (mm) REVERT: C 122 ARG cc_start: 0.6070 (mpt180) cc_final: 0.5766 (mmp-170) REVERT: E 112 GLU cc_start: 0.7564 (pp20) cc_final: 0.7193 (pp20) REVERT: E 189 TYR cc_start: 0.7712 (m-80) cc_final: 0.7370 (m-80) REVERT: E 268 GLU cc_start: 0.6711 (OUTLIER) cc_final: 0.5960 (tp30) REVERT: E 358 LYS cc_start: 0.8074 (OUTLIER) cc_final: 0.7704 (mtmm) REVERT: E 522 GLU cc_start: 0.8326 (tt0) cc_final: 0.8071 (tp30) REVERT: E 573 ASN cc_start: 0.8040 (p0) cc_final: 0.7830 (p0) REVERT: E 598 LYS cc_start: 0.4392 (OUTLIER) cc_final: 0.3865 (ptmt) REVERT: E 738 ARG cc_start: 0.8052 (mtt90) cc_final: 0.7800 (mtt180) outliers start: 46 outliers final: 20 residues processed: 167 average time/residue: 1.8084 time to fit residues: 333.8741 Evaluate side-chains 156 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 129 time to evaluate : 1.585 ------------------------------------------------------------------------------- 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 347 MET Chi-restraints excluded: chain D residue 355 VAL Chi-restraints excluded: chain D residue 383 MET 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 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 54 LEU 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 144 optimal weight: 0.5980 chunk 114 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 chunk 57 optimal weight: 0.0670 chunk 59 optimal weight: 2.9990 chunk 154 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 84 optimal weight: 0.8980 chunk 137 optimal weight: 0.0570 overall best weight: 0.4436 ------------------------------------------------------------------------------- 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 A 149 ASN E 185 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 = 0.4349 r_free = 0.4349 target = 0.193074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.145044 restraints weight = 15034.349| |-----------------------------------------------------------------------------| r_work (start): 0.3868 rms_B_bonded: 2.48 r_work: 0.3599 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.1485 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= 0.116 Angle : 0.531 11.078 18183 Z= 0.263 Chirality : 0.040 0.325 2001 Planarity : 0.004 0.047 2267 Dihedral : 11.307 100.431 1958 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.45 % Allowed : 16.42 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.15 (0.22), residues: 1554 helix: 2.51 (0.17), residues: 932 sheet: 0.54 (0.38), residues: 177 loop : -0.57 (0.30), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 268 HIS 0.001 0.000 HIS E 256 PHE 0.017 0.001 PHE E 762 TYR 0.022 0.001 TYR E 198 ARG 0.004 0.000 ARG D 197 Details of bonding type rmsd hydrogen bonds : bond 0.03895 ( 860) hydrogen bonds : angle 3.91901 ( 2628) covalent geometry : bond 0.00256 (13432) covalent geometry : angle 0.53066 (18183) *********************** 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 192 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 143 time to evaluate : 1.957 Fit side-chains revert: symmetry clash REVERT: D 163 GLU cc_start: 0.7707 (tp30) cc_final: 0.7336 (tp30) REVERT: D 341 SER cc_start: 0.8072 (m) cc_final: 0.7854 (m) REVERT: D 712 LEU cc_start: 0.7695 (OUTLIER) cc_final: 0.7285 (mp) REVERT: A 44 THR cc_start: 0.6760 (OUTLIER) cc_final: 0.6552 (p) REVERT: A 47 LYS cc_start: 0.8225 (mmpt) cc_final: 0.7876 (mmpt) REVERT: A 147 ILE cc_start: 0.8430 (mm) cc_final: 0.8219 (mm) REVERT: C 122 ARG cc_start: 0.6152 (OUTLIER) cc_final: 0.5883 (mmp-170) REVERT: E 112 GLU cc_start: 0.7563 (pp20) cc_final: 0.7172 (pp20) REVERT: E 177 ARG cc_start: 0.7687 (OUTLIER) cc_final: 0.7482 (tpp-160) REVERT: E 189 TYR cc_start: 0.7682 (m-80) cc_final: 0.7298 (m-80) REVERT: E 268 GLU cc_start: 0.6675 (OUTLIER) cc_final: 0.5959 (tp30) REVERT: E 503 ASN cc_start: 0.8161 (m110) cc_final: 0.7397 (p0) REVERT: E 522 GLU cc_start: 0.8336 (tt0) cc_final: 0.8105 (tp30) REVERT: E 573 ASN cc_start: 0.8038 (p0) cc_final: 0.7835 (p0) REVERT: E 598 LYS cc_start: 0.4237 (OUTLIER) cc_final: 0.3712 (ptmt) REVERT: E 738 ARG cc_start: 0.8107 (mtt90) cc_final: 0.7837 (mtt90) outliers start: 49 outliers final: 23 residues processed: 173 average time/residue: 1.5581 time to fit residues: 310.2308 Evaluate side-chains 160 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 131 time to evaluate : 1.267 ------------------------------------------------------------------------------- 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 146 VAL Chi-restraints excluded: chain B residue 100 THR 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 54 LEU Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 177 ARG 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 807 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 141 optimal weight: 0.6980 chunk 3 optimal weight: 5.9990 chunk 154 optimal weight: 2.9990 chunk 120 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 63 optimal weight: 0.7980 chunk 40 optimal weight: 0.3980 chunk 60 optimal weight: 3.9990 chunk 88 optimal weight: 6.9990 chunk 102 optimal weight: 9.9990 chunk 65 optimal weight: 3.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- 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 = 0.4333 r_free = 0.4333 target = 0.191538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.143171 restraints weight = 15156.611| |-----------------------------------------------------------------------------| r_work (start): 0.3854 rms_B_bonded: 2.36 r_work: 0.3636 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.1597 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= 0.136 Angle : 0.548 10.982 18183 Z= 0.271 Chirality : 0.041 0.327 2001 Planarity : 0.004 0.047 2267 Dihedral : 11.122 98.956 1955 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.03 % Allowed : 17.41 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.12 (0.21), residues: 1554 helix: 2.46 (0.16), residues: 935 sheet: 0.51 (0.38), residues: 180 loop : -0.54 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 268 HIS 0.002 0.001 HIS E 546 PHE 0.017 0.001 PHE E 145 TYR 0.027 0.001 TYR D 679 ARG 0.004 0.000 ARG D 197 Details of bonding type rmsd hydrogen bonds : bond 0.03985 ( 860) hydrogen bonds : angle 3.90781 ( 2628) covalent geometry : bond 0.00315 (13432) covalent geometry : angle 0.54756 (18183) *********************** 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 178 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 135 time to evaluate : 1.606 Fit side-chains revert: symmetry clash REVERT: D 163 GLU cc_start: 0.7673 (tp30) cc_final: 0.7293 (tp30) REVERT: D 341 SER cc_start: 0.8045 (m) cc_final: 0.7810 (m) REVERT: D 712 LEU cc_start: 0.7671 (OUTLIER) cc_final: 0.7268 (mp) REVERT: A 44 THR cc_start: 0.6774 (OUTLIER) cc_final: 0.6566 (p) REVERT: A 47 LYS cc_start: 0.8215 (mmpt) cc_final: 0.7835 (mmpt) REVERT: A 147 ILE cc_start: 0.8367 (mm) cc_final: 0.8160 (mm) REVERT: A 152 LEU cc_start: 0.7914 (mm) cc_final: 0.7640 (mp) REVERT: C 122 ARG cc_start: 0.6186 (OUTLIER) cc_final: 0.5918 (mmp-170) REVERT: E 112 GLU cc_start: 0.7557 (pp20) cc_final: 0.7156 (pp20) REVERT: E 177 ARG cc_start: 0.7744 (OUTLIER) cc_final: 0.7515 (tpp-160) REVERT: E 189 TYR cc_start: 0.7769 (m-80) cc_final: 0.7368 (m-80) REVERT: E 268 GLU cc_start: 0.6605 (OUTLIER) cc_final: 0.5873 (tp30) REVERT: E 503 ASN cc_start: 0.8117 (m110) cc_final: 0.7358 (p0) REVERT: E 522 GLU cc_start: 0.8298 (tt0) cc_final: 0.8032 (tp30) REVERT: E 568 ASP cc_start: 0.7057 (m-30) cc_final: 0.6819 (m-30) REVERT: E 573 ASN cc_start: 0.8054 (p0) cc_final: 0.7840 (p0) REVERT: E 598 LYS cc_start: 0.4271 (OUTLIER) cc_final: 0.3794 (ptmt) REVERT: E 738 ARG cc_start: 0.8050 (mtt90) cc_final: 0.7804 (mtt-85) outliers start: 43 outliers final: 23 residues processed: 162 average time/residue: 1.0585 time to fit residues: 191.7550 Evaluate side-chains 157 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 128 time to evaluate : 1.458 ------------------------------------------------------------------------------- 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 712 LEU Chi-restraints excluded: chain D residue 723 LEU Chi-restraints excluded: chain A residue 44 THR 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 54 LEU Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 177 ARG 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 97 optimal weight: 5.9990 chunk 69 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 42 optimal weight: 0.0980 chunk 39 optimal weight: 0.1980 chunk 133 optimal weight: 1.9990 chunk 115 optimal weight: 0.7980 chunk 147 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 87 optimal weight: 4.9990 chunk 127 optimal weight: 0.0980 overall best weight: 0.4380 ------------------------------------------------------------------------------- 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 535 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.193305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.145412 restraints weight = 15019.257| |-----------------------------------------------------------------------------| r_work (start): 0.3869 rms_B_bonded: 2.36 r_work: 0.3628 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.1736 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= 0.112 Angle : 0.528 10.767 18183 Z= 0.261 Chirality : 0.040 0.290 2001 Planarity : 0.004 0.047 2267 Dihedral : 10.769 96.428 1955 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.96 % Allowed : 17.90 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.27 (0.21), residues: 1554 helix: 2.55 (0.16), residues: 936 sheet: 0.60 (0.38), residues: 179 loop : -0.45 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 268 HIS 0.002 0.000 HIS E 242 PHE 0.024 0.001 PHE C 101 TYR 0.021 0.001 TYR E 198 ARG 0.003 0.000 ARG D 197 Details of bonding type rmsd hydrogen bonds : bond 0.03760 ( 860) hydrogen bonds : angle 3.81528 ( 2628) covalent geometry : bond 0.00248 (13432) covalent geometry : angle 0.52790 (18183) *********************** 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 184 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 142 time to evaluate : 1.484 Fit side-chains revert: symmetry clash REVERT: D 163 GLU cc_start: 0.7701 (tp30) cc_final: 0.7331 (tp30) REVERT: D 341 SER cc_start: 0.8062 (m) cc_final: 0.7850 (m) REVERT: D 712 LEU cc_start: 0.7692 (OUTLIER) cc_final: 0.7314 (mp) REVERT: A 44 THR cc_start: 0.6778 (OUTLIER) cc_final: 0.6562 (p) REVERT: A 47 LYS cc_start: 0.8184 (mmpt) cc_final: 0.7815 (mmpt) REVERT: A 76 MET cc_start: 0.8320 (OUTLIER) cc_final: 0.8113 (mtm) REVERT: A 147 ILE cc_start: 0.8409 (mm) cc_final: 0.8194 (mm) REVERT: C 122 ARG cc_start: 0.6265 (OUTLIER) cc_final: 0.6023 (mmp-170) REVERT: E 45 LYS cc_start: 0.8258 (mttp) cc_final: 0.7688 (ptmm) REVERT: E 112 GLU cc_start: 0.7599 (pp20) cc_final: 0.7160 (pp20) REVERT: E 177 ARG cc_start: 0.7728 (OUTLIER) cc_final: 0.7503 (tpp-160) REVERT: E 189 TYR cc_start: 0.7728 (m-80) cc_final: 0.7326 (m-80) REVERT: E 268 GLU cc_start: 0.6636 (OUTLIER) cc_final: 0.5938 (tp30) REVERT: E 358 LYS cc_start: 0.8117 (OUTLIER) cc_final: 0.7721 (mtmm) REVERT: E 503 ASN cc_start: 0.8114 (m110) cc_final: 0.7332 (p0) REVERT: E 522 GLU cc_start: 0.8354 (tt0) cc_final: 0.8127 (tp30) REVERT: E 568 ASP cc_start: 0.7032 (m-30) cc_final: 0.6806 (m-30) REVERT: E 573 ASN cc_start: 0.8083 (p0) cc_final: 0.7877 (p0) REVERT: E 598 LYS cc_start: 0.4099 (OUTLIER) cc_final: 0.3552 (ptmt) outliers start: 42 outliers final: 20 residues processed: 168 average time/residue: 1.0434 time to fit residues: 195.7054 Evaluate side-chains 162 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 134 time to evaluate : 1.558 ------------------------------------------------------------------------------- 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 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 A residue 44 THR Chi-restraints excluded: chain A residue 76 MET 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 A residue 148 ILE Chi-restraints excluded: chain C residue 122 ARG Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 177 ARG 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 776 LEU Chi-restraints excluded: chain E residue 807 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 73 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 106 optimal weight: 6.9990 chunk 107 optimal weight: 7.9990 chunk 103 optimal weight: 0.9980 chunk 131 optimal weight: 0.9980 chunk 90 optimal weight: 0.8980 chunk 61 optimal weight: 0.5980 chunk 137 optimal weight: 0.0970 chunk 16 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 overall best weight: 0.6378 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.192269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.144377 restraints weight = 15064.438| |-----------------------------------------------------------------------------| r_work (start): 0.3850 rms_B_bonded: 2.37 r_work: 0.3635 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3484 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.1822 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= 0.125 Angle : 0.542 12.246 18183 Z= 0.267 Chirality : 0.040 0.297 2001 Planarity : 0.004 0.047 2267 Dihedral : 10.589 94.838 1955 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.75 % Allowed : 18.04 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.26 (0.21), residues: 1554 helix: 2.54 (0.16), residues: 935 sheet: 0.69 (0.38), residues: 179 loop : -0.48 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 268 HIS 0.002 0.000 HIS E 242 PHE 0.015 0.001 PHE D 147 TYR 0.022 0.001 TYR D 679 ARG 0.004 0.000 ARG D 630 Details of bonding type rmsd hydrogen bonds : bond 0.03823 ( 860) hydrogen bonds : angle 3.81219 ( 2628) covalent geometry : bond 0.00288 (13432) covalent geometry : angle 0.54151 (18183) *********************** 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 178 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 139 time to evaluate : 1.463 Fit side-chains revert: symmetry clash REVERT: D 72 PHE cc_start: 0.7816 (m-10) cc_final: 0.7584 (m-10) REVERT: D 163 GLU cc_start: 0.7834 (tp30) cc_final: 0.7435 (tp30) REVERT: D 341 SER cc_start: 0.8209 (m) cc_final: 0.8003 (m) REVERT: D 712 LEU cc_start: 0.7702 (OUTLIER) cc_final: 0.7297 (mp) REVERT: A 47 LYS cc_start: 0.8216 (mmpt) cc_final: 0.7439 (mmpt) REVERT: A 147 ILE cc_start: 0.8419 (mm) cc_final: 0.8190 (mm) REVERT: C 122 ARG cc_start: 0.6304 (OUTLIER) cc_final: 0.6051 (mmp-170) REVERT: E 45 LYS cc_start: 0.8250 (mttp) cc_final: 0.7687 (ptmm) REVERT: E 112 GLU cc_start: 0.7578 (pp20) cc_final: 0.7121 (pp20) REVERT: E 189 TYR cc_start: 0.7751 (m-80) cc_final: 0.7334 (m-80) REVERT: E 268 GLU cc_start: 0.6748 (OUTLIER) cc_final: 0.6040 (tp30) REVERT: E 358 LYS cc_start: 0.8098 (OUTLIER) cc_final: 0.7674 (mtmm) REVERT: E 503 ASN cc_start: 0.8104 (m110) cc_final: 0.7267 (p0) REVERT: E 522 GLU cc_start: 0.8584 (tt0) cc_final: 0.8302 (tp30) REVERT: E 568 ASP cc_start: 0.7123 (m-30) cc_final: 0.6883 (m-30) REVERT: E 598 LYS cc_start: 0.4234 (OUTLIER) cc_final: 0.3712 (ptmt) outliers start: 39 outliers final: 21 residues processed: 164 average time/residue: 1.0551 time to fit residues: 192.7635 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 : 1.404 ------------------------------------------------------------------------------- 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 333 ILE 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 613 THR Chi-restraints excluded: chain D residue 712 LEU Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain C residue 122 ARG Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 54 LEU 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 25 optimal weight: 1.9990 chunk 123 optimal weight: 0.0050 chunk 75 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 140 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 93 optimal weight: 5.9990 chunk 73 optimal weight: 1.9990 chunk 146 optimal weight: 0.1980 chunk 108 optimal weight: 0.0030 overall best weight: 0.5606 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.194287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.143596 restraints weight = 14930.756| |-----------------------------------------------------------------------------| r_work (start): 0.3836 rms_B_bonded: 2.49 r_work: 0.3603 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.1883 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= 0.120 Angle : 0.551 14.006 18183 Z= 0.267 Chirality : 0.040 0.289 2001 Planarity : 0.004 0.047 2267 Dihedral : 10.331 92.686 1955 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.40 % Allowed : 18.68 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.30 (0.21), residues: 1554 helix: 2.56 (0.16), residues: 935 sheet: 0.77 (0.39), residues: 178 loop : -0.47 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 268 HIS 0.002 0.000 HIS E 242 PHE 0.022 0.001 PHE E 762 TYR 0.021 0.001 TYR D 679 ARG 0.005 0.000 ARG E 738 Details of bonding type rmsd hydrogen bonds : bond 0.03775 ( 860) hydrogen bonds : angle 3.79324 ( 2628) covalent geometry : bond 0.00273 (13432) covalent geometry : angle 0.55061 (18183) *********************** 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 173 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 139 time to evaluate : 1.556 Fit side-chains revert: symmetry clash REVERT: D 341 SER cc_start: 0.8087 (m) cc_final: 0.7870 (m) REVERT: D 630 ARG cc_start: 0.7415 (mtt180) cc_final: 0.7202 (tmm160) REVERT: D 712 LEU cc_start: 0.7606 (OUTLIER) cc_final: 0.7225 (mp) REVERT: A 147 ILE cc_start: 0.8421 (mm) cc_final: 0.8214 (mm) REVERT: C 122 ARG cc_start: 0.6284 (OUTLIER) cc_final: 0.6048 (mmp-170) REVERT: E 45 LYS cc_start: 0.8285 (mttp) cc_final: 0.7730 (ptmm) REVERT: E 112 GLU cc_start: 0.7621 (pp20) cc_final: 0.7072 (pp20) REVERT: E 189 TYR cc_start: 0.7734 (m-80) cc_final: 0.7323 (m-80) REVERT: E 268 GLU cc_start: 0.6648 (OUTLIER) cc_final: 0.5931 (tp30) REVERT: E 358 LYS cc_start: 0.8098 (OUTLIER) cc_final: 0.7723 (mtmm) REVERT: E 503 ASN cc_start: 0.8077 (m110) cc_final: 0.7305 (p0) REVERT: E 522 GLU cc_start: 0.8407 (tt0) cc_final: 0.8153 (tp30) REVERT: E 568 ASP cc_start: 0.7025 (m-30) cc_final: 0.6795 (m-30) REVERT: E 598 LYS cc_start: 0.4185 (OUTLIER) cc_final: 0.3605 (ptmt) outliers start: 34 outliers final: 19 residues processed: 159 average time/residue: 1.0137 time to fit residues: 180.3214 Evaluate side-chains 159 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 135 time to evaluate : 1.366 ------------------------------------------------------------------------------- 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 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 A residue 100 THR Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain C residue 122 ARG Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 54 LEU 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 80 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 44 optimal weight: 0.0980 chunk 128 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 115 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 81 optimal weight: 5.9990 chunk 104 optimal weight: 8.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.191920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.143954 restraints weight = 15004.593| |-----------------------------------------------------------------------------| r_work (start): 0.3863 rms_B_bonded: 2.33 r_work: 0.3635 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13432 Z= 0.134 Angle : 0.563 15.507 18183 Z= 0.275 Chirality : 0.041 0.298 2001 Planarity : 0.004 0.047 2267 Dihedral : 10.231 91.503 1955 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.04 % Allowed : 19.10 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.26 (0.21), residues: 1554 helix: 2.52 (0.16), residues: 935 sheet: 0.78 (0.39), residues: 179 loop : -0.48 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 268 HIS 0.002 0.001 HIS D 462 PHE 0.014 0.001 PHE D 120 TYR 0.022 0.001 TYR D 679 ARG 0.004 0.000 ARG E 53 Details of bonding type rmsd hydrogen bonds : bond 0.03866 ( 860) hydrogen bonds : angle 3.80417 ( 2628) covalent geometry : bond 0.00314 (13432) covalent geometry : angle 0.56343 (18183) ********************** 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 160 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 131 time to evaluate : 1.382 Fit side-chains revert: symmetry clash REVERT: D 341 SER cc_start: 0.8077 (m) cc_final: 0.7849 (m) REVERT: D 712 LEU cc_start: 0.7574 (OUTLIER) cc_final: 0.7182 (mp) REVERT: A 147 ILE cc_start: 0.8329 (mm) cc_final: 0.8119 (mm) REVERT: B 140 PHE cc_start: 0.7683 (t80) cc_final: 0.7193 (t80) REVERT: C 122 ARG cc_start: 0.6280 (OUTLIER) cc_final: 0.6051 (mmp-170) REVERT: E 45 LYS cc_start: 0.8267 (mttp) cc_final: 0.7775 (ptmm) REVERT: E 112 GLU cc_start: 0.7708 (pp20) cc_final: 0.7130 (pp20) REVERT: E 189 TYR cc_start: 0.7689 (m-80) cc_final: 0.7301 (m-80) REVERT: E 268 GLU cc_start: 0.6613 (OUTLIER) cc_final: 0.5878 (tp30) REVERT: E 358 LYS cc_start: 0.8079 (OUTLIER) cc_final: 0.7660 (mtmm) REVERT: E 503 ASN cc_start: 0.8040 (m110) cc_final: 0.7221 (p0) REVERT: E 522 GLU cc_start: 0.8426 (tt0) cc_final: 0.8145 (tp30) REVERT: E 568 ASP cc_start: 0.7118 (m-30) cc_final: 0.6872 (m-30) REVERT: E 598 LYS cc_start: 0.4393 (OUTLIER) cc_final: 0.3828 (ptmt) outliers start: 29 outliers final: 21 residues processed: 149 average time/residue: 1.0616 time to fit residues: 177.3172 Evaluate side-chains 158 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 132 time to evaluate : 1.594 ------------------------------------------------------------------------------- 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 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 100 THR Chi-restraints excluded: chain A residue 146 VAL 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 54 LEU 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 10 optimal weight: 4.9990 chunk 101 optimal weight: 9.9990 chunk 87 optimal weight: 0.8980 chunk 124 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 chunk 49 optimal weight: 0.5980 chunk 32 optimal weight: 0.5980 chunk 83 optimal weight: 1.9990 chunk 116 optimal weight: 7.9990 chunk 79 optimal weight: 0.8980 chunk 74 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.193041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.141741 restraints weight = 15104.590| |-----------------------------------------------------------------------------| r_work (start): 0.3814 rms_B_bonded: 2.51 r_work: 0.3595 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13432 Z= 0.135 Angle : 0.574 15.384 18183 Z= 0.277 Chirality : 0.041 0.300 2001 Planarity : 0.004 0.047 2267 Dihedral : 10.159 90.396 1955 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.11 % Allowed : 19.17 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.26 (0.21), residues: 1554 helix: 2.51 (0.16), residues: 935 sheet: 0.82 (0.39), residues: 179 loop : -0.47 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 268 HIS 0.002 0.001 HIS E 242 PHE 0.023 0.001 PHE E 762 TYR 0.023 0.001 TYR D 679 ARG 0.004 0.000 ARG A 117 Details of bonding type rmsd hydrogen bonds : bond 0.03887 ( 860) hydrogen bonds : angle 3.80825 ( 2628) covalent geometry : bond 0.00317 (13432) covalent geometry : angle 0.57377 (18183) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9576.45 seconds wall clock time: 174 minutes 17.20 seconds (10457.20 seconds total)