Starting phenix.real_space_refine on Tue Nov 18 06:52:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6e14_8953/11_2025/6e14_8953.cif Found real_map, /net/cci-nas-00/data/ceres_data/6e14_8953/11_2025/6e14_8953.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6e14_8953/11_2025/6e14_8953.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6e14_8953/11_2025/6e14_8953.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6e14_8953/11_2025/6e14_8953.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6e14_8953/11_2025/6e14_8953.map" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 37 5.16 5 C 7508 2.51 5 N 2078 2.21 5 O 2372 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11995 Number of models: 1 Model: "" Number of chains: 5 Chain: "H" Number of atoms: 2051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2051 Classifications: {'peptide': 279} Link IDs: {'PTRANS': 16, 'TRANS': 262} Chain: "D" Number of atoms: 6167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 805, 6167 Classifications: {'peptide': 805} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 31, 'TRANS': 773} Chain breaks: 2 Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 3, 'ASP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 33 Chain: "F" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1137 Classifications: {'peptide': 154} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 145} Chain: "G" Number of atoms: 1038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1038 Classifications: {'peptide': 143} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 139} Chain: "C" Number of atoms: 1602 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 205, 1598 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 190} Conformer: "B" Number of residues, atoms: 205, 1598 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 190} bond proxies already assigned to first conformer: 1623 Time building chain proxies: 2.93, per 1000 atoms: 0.24 Number of scatterers: 11995 At special positions: 0 Unit cell: (92.65, 104.64, 200.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 37 16.00 O 2372 8.00 N 2078 7.00 C 7508 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS H 3 " - pdb=" SG CYS H 44 " distance=2.03 Simple disulfide: pdb=" SG CYS H 161 " - pdb=" SG CYS H 187 " distance=2.03 Simple disulfide: pdb=" SG CYS D 63 " - pdb=" SG CYS D 90 " distance=2.03 Simple disulfide: pdb=" SG CYS D 810 " - pdb=" SG CYS D 832 " distance=2.04 Simple disulfide: pdb=" SG CYS F 16 " - pdb=" SG CYS F 56 " distance=2.02 Simple disulfide: pdb=" SG CYS G 16 " - pdb=" SG CYS G 54 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.92 Conformation dependent library (CDL) restraints added in 784.4 milliseconds 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2888 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 30 sheets defined 2.1% alpha, 35.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'D' and resid 19 through 24 removed outlier: 4.644A pdb=" N GLU D 23 " --> pdb=" O LEU D 19 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASN D 24 " --> pdb=" O SER D 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 19 through 24' Processing helix chain 'D' and resid 92 through 97 Processing helix chain 'D' and resid 246 through 250 removed outlier: 3.624A pdb=" N ARG D 250 " --> pdb=" O ASP D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 443 through 449 removed outlier: 3.856A pdb=" N THR D 447 " --> pdb=" O ASN D 443 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR D 448 " --> pdb=" O PHE D 444 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 112 removed outlier: 3.651A pdb=" N ALA F 111 " --> pdb=" O PRO F 108 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LEU F 112 " --> pdb=" O SER F 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 108 through 112' Processing helix chain 'C' and resid 123 through 127 removed outlier: 3.756A pdb=" N GLN C 126 " --> pdb=" O PRO C 123 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA C 127 " --> pdb=" O PRO C 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 123 through 127' Processing sheet with id=AA1, first strand: chain 'H' and resid 2 through 4 removed outlier: 3.557A pdb=" N PHE H 43 " --> pdb=" O LYS H 4 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 19 through 21 removed outlier: 6.575A pdb=" N VAL H 20 " --> pdb=" O TYR H 149 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N PHE H 142 " --> pdb=" O GLN H 133 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLN H 133 " --> pdb=" O PHE H 142 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N PHE H 144 " --> pdb=" O LEU H 131 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU H 129 " --> pdb=" O TRP H 146 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL H 56 " --> pdb=" O VAL H 93 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL H 93 " --> pdb=" O VAL H 56 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 33 through 37 removed outlier: 6.040A pdb=" N LEU H 34 " --> pdb=" O LEU H 109 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N LEU H 109 " --> pdb=" O LEU H 34 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL H 36 " --> pdb=" O LEU H 107 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N THR H 74 " --> pdb=" O TYR H 108 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N GLY H 73 " --> pdb=" O PHE H 84 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 117 through 118 Processing sheet with id=AA5, first strand: chain 'H' and resid 161 through 163 removed outlier: 3.658A pdb=" N VAL H 248 " --> pdb=" O VAL H 185 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 167 through 171 removed outlier: 6.463A pdb=" N VAL H 168 " --> pdb=" O THR G 6 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N ASN G 8 " --> pdb=" O VAL H 168 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N VAL H 170 " --> pdb=" O ASN G 8 " (cutoff:3.500A) removed outlier: 8.825A pdb=" N LYS G 10 " --> pdb=" O VAL H 170 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE H 272 " --> pdb=" O ILE G 5 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N VAL G 7 " --> pdb=" O SER H 270 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N SER H 270 " --> pdb=" O VAL G 7 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N GLY H 273 " --> pdb=" O SER H 198 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N SER H 198 " --> pdb=" O GLY H 273 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 179 through 180 removed outlier: 4.367A pdb=" N VAL H 179 " --> pdb=" O ALA H 254 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALA H 254 " --> pdb=" O VAL H 179 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 194 through 195 Processing sheet with id=AA9, first strand: chain 'D' and resid 36 through 38 removed outlier: 3.942A pdb=" N ALA D 45 " --> pdb=" O ILE D 37 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 51 through 53 Processing sheet with id=AB2, first strand: chain 'D' and resid 102 through 105 removed outlier: 3.689A pdb=" N HIS D 103 " --> pdb=" O ASN D 112 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 198 through 202 removed outlier: 3.814A pdb=" N GLN D 199 " --> pdb=" O THR D 182 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR D 182 " --> pdb=" O GLN D 199 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N ASN D 180 " --> pdb=" O ILE D 201 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE D 172 " --> pdb=" O TRP D 175 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N TYR D 161 " --> pdb=" O ASN D 149 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLY D 140 " --> pdb=" O ALA D 658 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N ALA D 658 " --> pdb=" O GLY D 140 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU D 142 " --> pdb=" O VAL D 656 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TYR D 144 " --> pdb=" O GLY D 654 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLY D 654 " --> pdb=" O TYR D 144 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N TYR D 650 " --> pdb=" O GLY D 148 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 175 through 185 removed outlier: 3.698A pdb=" N ARG D 178 " --> pdb=" O TRP D 204 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N TRP D 204 " --> pdb=" O ARG D 178 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA D 239 " --> pdb=" O ARG D 215 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG D 234 " --> pdb=" O GLU D 337 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N TYR D 331 " --> pdb=" O SER D 240 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N GLY D 336 " --> pdb=" O PHE D 350 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N PHE D 350 " --> pdb=" O GLY D 336 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU D 355 " --> pdb=" O GLY D 367 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLY D 367 " --> pdb=" O LEU D 355 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TRP D 363 " --> pdb=" O LEU D 359 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY D 368 " --> pdb=" O ASN D 379 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA D 377 " --> pdb=" O GLN D 370 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 376 through 387 removed outlier: 3.779A pdb=" N MET D 386 " --> pdb=" O GLY D 390 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N GLY D 390 " --> pdb=" O MET D 386 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASN D 419 " --> pdb=" O ALA D 391 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER D 393 " --> pdb=" O LEU D 417 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU D 417 " --> pdb=" O SER D 393 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ASP D 395 " --> pdb=" O ARG D 415 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ARG D 415 " --> pdb=" O ASP D 395 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLY D 411 " --> pdb=" O ALA D 399 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL D 432 " --> pdb=" O TYR D 418 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N ILE D 429 " --> pdb=" O THR D 489 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N THR D 489 " --> pdb=" O ILE D 429 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N LEU D 431 " --> pdb=" O THR D 487 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N THR D 487 " --> pdb=" O LEU D 431 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY D 433 " --> pdb=" O GLN D 485 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N ARG D 481 " --> pdb=" O SER D 437 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLN D 516 " --> pdb=" O SER D 503 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 529 through 537 removed outlier: 3.620A pdb=" N ALA D 550 " --> pdb=" O SER D 533 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N MET D 578 " --> pdb=" O LEU D 551 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ALA D 572 " --> pdb=" O PHE D 557 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N TYR D 610 " --> pdb=" O ASN D 588 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL D 606 " --> pdb=" O VAL D 592 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLY D 594 " --> pdb=" O TYR D 604 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N TYR D 604 " --> pdb=" O GLY D 594 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ASN D 634 " --> pdb=" O SER D 653 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASN D 636 " --> pdb=" O GLY D 651 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLY D 651 " --> pdb=" O ASN D 636 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLN D 647 " --> pdb=" O SER D 640 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLY D 655 " --> pdb=" O GLY D 666 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLY D 666 " --> pdb=" O GLY D 655 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 256 through 260 removed outlier: 4.062A pdb=" N ILE D 256 " --> pdb=" O ILE D 287 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ILE D 287 " --> pdb=" O ILE D 256 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLY D 258 " --> pdb=" O PHE D 285 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 273 through 280 removed outlier: 6.713A pdb=" N ILE D 268 " --> pdb=" O ILE D 275 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ASN D 277 " --> pdb=" O VAL D 266 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N VAL D 266 " --> pdb=" O ASN D 277 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N THR D 279 " --> pdb=" O ALA D 264 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N ALA D 264 " --> pdb=" O THR D 279 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N THR D 267 " --> pdb=" O THR D 302 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N THR D 302 " --> pdb=" O THR D 267 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL D 301 " --> pdb=" O PHE D 313 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N PHE D 313 " --> pdb=" O VAL D 301 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 402 through 403 removed outlier: 3.540A pdb=" N LEU D 403 " --> pdb=" O SER D 407 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N SER D 407 " --> pdb=" O LEU D 403 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'D' and resid 699 through 701 Processing sheet with id=AC2, first strand: chain 'D' and resid 751 through 756 removed outlier: 3.623A pdb=" N ILE D 751 " --> pdb=" O MET D 792 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N LEU D 753 " --> pdb=" O SER D 790 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N SER D 790 " --> pdb=" O LEU D 753 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N MET D 755 " --> pdb=" O TYR D 788 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N TYR D 788 " --> pdb=" O MET D 755 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLN D 786 " --> pdb=" O ALA D 782 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N TYR D 788 " --> pdb=" O ILE D 780 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ILE D 780 " --> pdb=" O TYR D 788 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N SER D 790 " --> pdb=" O SER D 778 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N SER D 778 " --> pdb=" O SER D 790 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL D 770 " --> pdb=" O GLY D 779 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N MET D 769 " --> pdb=" O LYS D 801 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N CYS D 810 " --> pdb=" O VAL D 800 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 25 through 30 removed outlier: 3.701A pdb=" N ARG F 8 " --> pdb=" O VAL G 25 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N TYR F 10 " --> pdb=" O LEU G 27 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ASP G 29 " --> pdb=" O TYR F 10 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N SER F 3 " --> pdb=" O ILE G 139 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE F 5 " --> pdb=" O ILE G 137 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE G 137 " --> pdb=" O ILE F 5 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA G 135 " --> pdb=" O ILE F 7 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N SER G 144 " --> pdb=" O ARG G 60 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ARG G 60 " --> pdb=" O SER G 144 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N VAL G 61 " --> pdb=" O VAL G 104 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL G 104 " --> pdb=" O VAL G 61 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 18 through 19 removed outlier: 3.784A pdb=" N ALA F 129 " --> pdb=" O VAL F 47 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 62 through 63 Processing sheet with id=AC6, first strand: chain 'F' and resid 67 through 68 removed outlier: 3.631A pdb=" N ILE C 108 " --> pdb=" O PHE F 149 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N VAL C 9 " --> pdb=" O TYR C 114 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 67 through 68 removed outlier: 3.631A pdb=" N ILE C 108 " --> pdb=" O PHE F 149 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE C 107 " --> pdb=" O ALA C 89 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL C 87 " --> pdb=" O SER C 109 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N TRP C 84 " --> pdb=" O GLU C 38 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ASN C 86 " --> pdb=" O TRP C 36 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N TRP C 36 " --> pdb=" O ASN C 86 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N PHE C 55 " --> pdb=" O ILE C 33 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 17 through 18 removed outlier: 3.799A pdb=" N THR G 17 " --> pdb=" O THR G 52 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N THR G 52 " --> pdb=" O THR G 17 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 46 through 47 removed outlier: 3.822A pdb=" N GLN G 118 " --> pdb=" O GLN G 89 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLN G 89 " --> pdb=" O GLN G 118 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 2 through 3 removed outlier: 3.673A pdb=" N GLU C 18 " --> pdb=" O ILE C 67 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ILE C 67 " --> pdb=" O GLU C 18 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ARG C 66 " --> pdb=" O THR C 51 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 132 through 135 removed outlier: 3.505A pdb=" N LEU C 142 " --> pdb=" O SER C 173 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N SER C 173 " --> pdb=" O LEU C 142 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 165 through 167 removed outlier: 4.079A pdb=" N ALA C 165 " --> pdb=" O VAL C 152 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N VAL C 152 " --> pdb=" O ALA C 165 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N VAL C 167 " --> pdb=" O LEU C 150 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N LEU C 150 " --> pdb=" O VAL C 167 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N GLU C 154 " --> pdb=" O ARG C 188 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N ARG C 188 " --> pdb=" O GLU C 154 " (cutoff:3.500A) 307 hydrogen bonds defined for protein. 834 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: 2.36 Time building geometry restraints manager: 1.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 4015 1.35 - 1.47: 2946 1.47 - 1.59: 5215 1.59 - 1.71: 0 1.71 - 1.83: 62 Bond restraints: 12238 Sorted by residual: bond pdb=" C ILE D 210 " pdb=" N PRO D 211 " ideal model delta sigma weight residual 1.336 1.376 -0.040 1.20e-02 6.94e+03 1.13e+01 bond pdb=" C PRO D 29 " pdb=" N PRO D 30 " ideal model delta sigma weight residual 1.334 1.369 -0.035 1.11e-02 8.12e+03 9.95e+00 bond pdb=" CB PRO F 137 " pdb=" CG PRO F 137 " ideal model delta sigma weight residual 1.492 1.358 0.134 5.00e-02 4.00e+02 7.23e+00 bond pdb=" CB PRO F 55 " pdb=" CG PRO F 55 " ideal model delta sigma weight residual 1.492 1.380 0.112 5.00e-02 4.00e+02 5.04e+00 bond pdb=" N PRO H 85 " pdb=" CA PRO H 85 " ideal model delta sigma weight residual 1.469 1.442 0.027 1.28e-02 6.10e+03 4.41e+00 ... (remaining 12233 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.73: 16674 7.73 - 15.46: 22 15.46 - 23.19: 2 23.19 - 30.92: 4 30.92 - 38.66: 4 Bond angle restraints: 16706 Sorted by residual: angle pdb=" C THR C 51 " pdb=" N PRO C 52 " pdb=" CA PRO C 52 " ideal model delta sigma weight residual 120.38 153.72 -33.34 1.03e+00 9.43e-01 1.05e+03 angle pdb=" C VAL F 136 " pdb=" N PRO F 137 " pdb=" CA PRO F 137 " ideal model delta sigma weight residual 119.84 158.50 -38.66 1.25e+00 6.40e-01 9.56e+02 angle pdb=" C SER F 54 " pdb=" N PRO F 55 " pdb=" CA PRO F 55 " ideal model delta sigma weight residual 119.84 158.04 -38.20 1.25e+00 6.40e-01 9.34e+02 angle pdb=" C PHE H 84 " pdb=" N PRO H 85 " pdb=" CA PRO H 85 " ideal model delta sigma weight residual 119.84 154.63 -34.79 1.25e+00 6.40e-01 7.75e+02 angle pdb=" C LYS F 35 " pdb=" N GLN F 36 " pdb=" CA GLN F 36 " ideal model delta sigma weight residual 121.54 141.44 -19.90 1.91e+00 2.74e-01 1.09e+02 ... (remaining 16701 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.92: 7142 26.92 - 53.84: 77 53.84 - 80.77: 12 80.77 - 107.69: 2 107.69 - 134.61: 3 Dihedral angle restraints: 7236 sinusoidal: 2694 harmonic: 4542 Sorted by residual: dihedral pdb=" CA PRO D 30 " pdb=" C PRO D 30 " pdb=" N GLY D 31 " pdb=" CA GLY D 31 " ideal model delta harmonic sigma weight residual 180.00 45.39 134.61 0 5.00e+00 4.00e-02 7.25e+02 dihedral pdb=" CA LYS F 35 " pdb=" C LYS F 35 " pdb=" N GLN F 36 " pdb=" CA GLN F 36 " ideal model delta harmonic sigma weight residual 180.00 55.61 124.39 0 5.00e+00 4.00e-02 6.19e+02 dihedral pdb=" CA TYR H 175 " pdb=" C TYR H 175 " pdb=" N PRO H 176 " pdb=" CA PRO H 176 " ideal model delta harmonic sigma weight residual 180.00 56.60 123.40 0 5.00e+00 4.00e-02 6.09e+02 ... (remaining 7233 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1526 0.065 - 0.130: 312 0.130 - 0.195: 57 0.195 - 0.261: 13 0.261 - 0.326: 4 Chirality restraints: 1912 Sorted by residual: chirality pdb=" CB ILE D 382 " pdb=" CA ILE D 382 " pdb=" CG1 ILE D 382 " pdb=" CG2 ILE D 382 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.33 2.00e-01 2.50e+01 2.65e+00 chirality pdb=" CA VAL F 136 " pdb=" N VAL F 136 " pdb=" C VAL F 136 " pdb=" CB VAL F 136 " both_signs ideal model delta sigma weight residual False 2.44 2.76 -0.32 2.00e-01 2.50e+01 2.56e+00 chirality pdb=" CA ASP D 722 " pdb=" N ASP D 722 " pdb=" C ASP D 722 " pdb=" CB ASP D 722 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.39e+00 ... (remaining 1909 not shown) Planarity restraints: 2200 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR H 175 " 0.037 2.00e-02 2.50e+03 7.37e-02 5.42e+01 pdb=" C TYR H 175 " -0.127 2.00e-02 2.50e+03 pdb=" O TYR H 175 " 0.046 2.00e-02 2.50e+03 pdb=" N PRO H 176 " 0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO D 30 " -0.034 2.00e-02 2.50e+03 6.87e-02 4.72e+01 pdb=" C PRO D 30 " 0.119 2.00e-02 2.50e+03 pdb=" O PRO D 30 " -0.045 2.00e-02 2.50e+03 pdb=" N GLY D 31 " -0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS F 35 " -0.031 2.00e-02 2.50e+03 6.01e-02 3.61e+01 pdb=" C LYS F 35 " 0.104 2.00e-02 2.50e+03 pdb=" O LYS F 35 " -0.038 2.00e-02 2.50e+03 pdb=" N GLN F 36 " -0.035 2.00e-02 2.50e+03 ... (remaining 2197 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.86: 3866 2.86 - 3.37: 8561 3.37 - 3.88: 18589 3.88 - 4.39: 17536 4.39 - 4.90: 32878 Nonbonded interactions: 81430 Sorted by model distance: nonbonded pdb=" OD1 ASP D 564 " pdb=" OG SER D 567 " model vdw 2.345 3.040 nonbonded pdb=" O THR G 62 " pdb=" OG1 THR G 142 " model vdw 2.354 3.040 nonbonded pdb=" O LEU C 122 " pdb=" OH TYR C 148 " model vdw 2.358 3.040 nonbonded pdb=" OG1 THR H 201 " pdb=" OD1 ASP H 203 " model vdw 2.361 3.040 nonbonded pdb=" O THR H 210 " pdb=" OG SER H 270 " model vdw 2.369 3.040 ... (remaining 81425 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.670 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6430 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 : 0.006 0.134 12244 Z= 0.318 Angle : 1.370 38.655 16718 Z= 0.864 Chirality : 0.058 0.326 1912 Planarity : 0.008 0.074 2200 Dihedral : 9.492 134.608 4330 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.64 % Favored : 95.10 % Rotamer: Outliers : 0.23 % Allowed : 1.87 % Favored : 97.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.94 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.72 (0.18), residues: 1572 helix: -5.35 (0.25), residues: 18 sheet: -1.76 (0.21), residues: 546 loop : -2.99 (0.15), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 34 TYR 0.022 0.002 TYR H 64 PHE 0.027 0.003 PHE C 55 TRP 0.031 0.002 TRP H 103 HIS 0.010 0.002 HIS D 409 Details of bonding type rmsd covalent geometry : bond 0.00649 (12238) covalent geometry : angle 1.36993 (16706) SS BOND : bond 0.00628 ( 6) SS BOND : angle 1.69401 ( 12) hydrogen bonds : bond 0.30399 ( 303) hydrogen bonds : angle 11.82697 ( 834) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 1299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 379 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 64 TYR cc_start: 0.6248 (m-80) cc_final: 0.6027 (m-80) REVERT: H 84 PHE cc_start: 0.6407 (t80) cc_final: 0.5664 (t80) REVERT: H 102 PRO cc_start: 0.6520 (Cg_exo) cc_final: 0.6186 (Cg_endo) REVERT: H 107 LEU cc_start: 0.8538 (mt) cc_final: 0.8172 (mt) REVERT: H 130 ILE cc_start: 0.8040 (mt) cc_final: 0.7775 (mt) REVERT: H 206 ASN cc_start: 0.7807 (m-40) cc_final: 0.7159 (m-40) REVERT: D 151 VAL cc_start: 0.7672 (t) cc_final: 0.7367 (t) REVERT: D 208 ASP cc_start: 0.5946 (p0) cc_final: 0.5484 (m-30) REVERT: D 303 ILE cc_start: 0.7400 (mt) cc_final: 0.7032 (tt) REVERT: D 346 GLU cc_start: 0.7748 (mm-30) cc_final: 0.7381 (mp0) REVERT: D 481 ARG cc_start: 0.7081 (ttt180) cc_final: 0.6439 (ttt90) REVERT: D 708 TYR cc_start: 0.7324 (m-80) cc_final: 0.6922 (m-10) REVERT: D 725 ASP cc_start: 0.7690 (t0) cc_final: 0.7195 (m-30) REVERT: D 769 MET cc_start: 0.6481 (mmm) cc_final: 0.6207 (tmm) REVERT: D 793 PRO cc_start: 0.6131 (Cg_endo) cc_final: 0.5146 (Cg_exo) REVERT: F 4 THR cc_start: 0.7803 (p) cc_final: 0.7568 (p) REVERT: F 6 THR cc_start: 0.7855 (m) cc_final: 0.7567 (t) REVERT: F 16 CYS cc_start: 0.8144 (m) cc_final: 0.7711 (m) REVERT: F 79 LEU cc_start: 0.8468 (tp) cc_final: 0.8238 (tt) REVERT: F 116 THR cc_start: 0.7867 (p) cc_final: 0.7586 (t) REVERT: G 24 THR cc_start: 0.7937 (m) cc_final: 0.7664 (p) REVERT: C 72 ASN cc_start: 0.8665 (m110) cc_final: 0.8457 (t0) REVERT: C 104 GLN cc_start: 0.7678 (mt0) cc_final: 0.7452 (mt0) REVERT: C 160 ARG cc_start: 0.8108 (mmm160) cc_final: 0.7275 (mmt-90) outliers start: 1 outliers final: 0 residues processed: 380 average time/residue: 0.1152 time to fit residues: 61.6925 Evaluate side-chains 213 residues out of total 1299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 213 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 30.0000 chunk 66 optimal weight: 0.0170 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.0170 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 7.9990 overall best weight: 1.4062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 45 HIS H 59 GLN H 279 GLN D 103 HIS D 112 ASN D 295 ASN D 328 HIS D 344 GLN D 370 GLN D 580 HIS D 661 ASN D 718 ASN F 77 ASN F 123 ASN G 78 GLN G 82 GLN C 101 ASN C 164 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.184297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.158523 restraints weight = 16884.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.155577 restraints weight = 32845.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.154981 restraints weight = 34516.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.153242 restraints weight = 29079.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.154210 restraints weight = 26615.349| |-----------------------------------------------------------------------------| r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3779 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3779 r_free = 0.3779 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3777 r_free = 0.3777 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3777 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7137 moved from start: 0.4032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12244 Z= 0.159 Angle : 0.675 9.724 16718 Z= 0.353 Chirality : 0.045 0.233 1912 Planarity : 0.007 0.100 2200 Dihedral : 5.296 60.707 1719 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.45 % Favored : 95.48 % Rotamer: Outliers : 2.88 % Allowed : 10.42 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.33 % Twisted General : 0.27 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.80 (0.19), residues: 1572 helix: -4.84 (0.46), residues: 24 sheet: -0.93 (0.22), residues: 545 loop : -2.46 (0.16), residues: 1003 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 116 TYR 0.020 0.002 TYR F 10 PHE 0.022 0.002 PHE D 525 TRP 0.017 0.002 TRP D 530 HIS 0.006 0.001 HIS D 200 Details of bonding type rmsd covalent geometry : bond 0.00341 (12238) covalent geometry : angle 0.67367 (16706) SS BOND : bond 0.00841 ( 6) SS BOND : angle 1.53345 ( 12) hydrogen bonds : bond 0.04753 ( 303) hydrogen bonds : angle 7.05419 ( 834) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 247 time to evaluate : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 12 ASP cc_start: 0.6865 (p0) cc_final: 0.6558 (t0) REVERT: D 396 MET cc_start: 0.7348 (tmm) cc_final: 0.7103 (tmm) REVERT: D 397 THR cc_start: 0.8316 (m) cc_final: 0.7269 (p) REVERT: D 413 SER cc_start: 0.8810 (OUTLIER) cc_final: 0.8579 (m) REVERT: D 452 MET cc_start: 0.5453 (OUTLIER) cc_final: 0.5107 (ptp) REVERT: D 481 ARG cc_start: 0.7777 (ttt180) cc_final: 0.7434 (ttt90) REVERT: D 653 SER cc_start: 0.8779 (p) cc_final: 0.8558 (t) REVERT: D 707 GLU cc_start: 0.7930 (pm20) cc_final: 0.7719 (pm20) REVERT: D 708 TYR cc_start: 0.7863 (m-80) cc_final: 0.7568 (m-10) REVERT: F 77 ASN cc_start: 0.6214 (OUTLIER) cc_final: 0.5396 (m-40) REVERT: F 81 LEU cc_start: 0.6439 (mm) cc_final: 0.6124 (tp) REVERT: F 99 GLN cc_start: 0.7430 (mm-40) cc_final: 0.7169 (mp10) REVERT: G 14 LYS cc_start: 0.8514 (mmpt) cc_final: 0.7987 (mtmt) REVERT: G 24 THR cc_start: 0.8027 (m) cc_final: 0.7709 (p) REVERT: G 103 THR cc_start: 0.8912 (OUTLIER) cc_final: 0.8688 (p) REVERT: C 126 GLN cc_start: 0.7144 (OUTLIER) cc_final: 0.6929 (tm-30) REVERT: C 130 LYS cc_start: 0.8094 (mmtm) cc_final: 0.7577 (mmtm) outliers start: 35 outliers final: 18 residues processed: 272 average time/residue: 0.1011 time to fit residues: 40.4362 Evaluate side-chains 213 residues out of total 1299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 190 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 69 SER Chi-restraints excluded: chain H residue 183 LEU Chi-restraints excluded: chain D residue 122 ASN Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain D residue 234 ARG Chi-restraints excluded: chain D residue 248 SER Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 328 HIS Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 413 SER Chi-restraints excluded: chain D residue 452 MET Chi-restraints excluded: chain D residue 523 THR Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain F residue 77 ASN Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 123 ASN Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 91 ASP Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 126 GLN Chi-restraints excluded: chain C residue 185 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 14 optimal weight: 9.9990 chunk 42 optimal weight: 8.9990 chunk 45 optimal weight: 2.9990 chunk 109 optimal weight: 0.0020 chunk 87 optimal weight: 9.9990 chunk 85 optimal weight: 0.8980 chunk 2 optimal weight: 9.9990 chunk 19 optimal weight: 3.9990 chunk 37 optimal weight: 7.9990 chunk 93 optimal weight: 6.9990 chunk 90 optimal weight: 3.9990 overall best weight: 2.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 40 ASN D 328 HIS D 490 GLN F 142 HIS G 105 GLN C 72 ASN ** C 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.171236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 97)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.138505 restraints weight = 20286.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.134188 restraints weight = 21054.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.134394 restraints weight = 24621.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.136069 restraints weight = 18613.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.136221 restraints weight = 13629.847| |-----------------------------------------------------------------------------| r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3502 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3502 r_free = 0.3502 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3501 r_free = 0.3501 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3501 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.5554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 12244 Z= 0.198 Angle : 0.692 9.502 16718 Z= 0.365 Chirality : 0.046 0.208 1912 Planarity : 0.006 0.111 2200 Dihedral : 5.430 61.536 1719 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.09 % Favored : 94.85 % Rotamer: Outliers : 3.97 % Allowed : 12.75 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.56 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.51 (0.19), residues: 1572 helix: -5.01 (0.40), residues: 30 sheet: -0.62 (0.22), residues: 580 loop : -2.35 (0.17), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 134 TYR 0.017 0.002 TYR H 278 PHE 0.023 0.002 PHE D 525 TRP 0.015 0.002 TRP D 802 HIS 0.026 0.002 HIS D 328 Details of bonding type rmsd covalent geometry : bond 0.00450 (12238) covalent geometry : angle 0.68981 (16706) SS BOND : bond 0.00781 ( 6) SS BOND : angle 2.02439 ( 12) hydrogen bonds : bond 0.05097 ( 303) hydrogen bonds : angle 6.52897 ( 834) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 223 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 46 ASN cc_start: 0.4077 (t0) cc_final: 0.3753 (m110) REVERT: D 300 GLN cc_start: 0.7933 (tm-30) cc_final: 0.7516 (tm-30) REVERT: D 396 MET cc_start: 0.7522 (tmm) cc_final: 0.7265 (tmm) REVERT: D 397 THR cc_start: 0.8487 (m) cc_final: 0.8055 (m) REVERT: D 413 SER cc_start: 0.8871 (OUTLIER) cc_final: 0.8650 (m) REVERT: D 481 ARG cc_start: 0.7770 (ttt180) cc_final: 0.7360 (ttt90) REVERT: F 81 LEU cc_start: 0.7010 (mm) cc_final: 0.6685 (tp) REVERT: F 123 ASN cc_start: 0.7428 (OUTLIER) cc_final: 0.7195 (m-40) REVERT: G 14 LYS cc_start: 0.8653 (mmpt) cc_final: 0.8017 (mtmt) REVERT: G 31 TYR cc_start: 0.7937 (m-10) cc_final: 0.7618 (m-80) REVERT: G 105 GLN cc_start: 0.7051 (mm110) cc_final: 0.6800 (mp10) REVERT: C 16 LYS cc_start: 0.8714 (tptt) cc_final: 0.8296 (ttpp) REVERT: C 126 GLN cc_start: 0.7697 (OUTLIER) cc_final: 0.7414 (pp30) REVERT: C 200 MET cc_start: 0.7754 (ppp) cc_final: 0.7518 (ppp) REVERT: C 204 MET cc_start: 0.1380 (mmm) cc_final: -0.2111 (ttp) outliers start: 49 outliers final: 28 residues processed: 257 average time/residue: 0.1055 time to fit residues: 39.4410 Evaluate side-chains 223 residues out of total 1299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 192 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 69 SER Chi-restraints excluded: chain H residue 183 LEU Chi-restraints excluded: chain H residue 186 TYR Chi-restraints excluded: chain H residue 206 ASN Chi-restraints excluded: chain H residue 250 LEU Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 122 ASN Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain D residue 234 ARG Chi-restraints excluded: chain D residue 248 SER Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 413 SER Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 575 SER Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain D residue 770 VAL Chi-restraints excluded: chain F residue 16 CYS Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 97 ASN Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 123 ASN Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 110 SER Chi-restraints excluded: chain G residue 129 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 112 LYS Chi-restraints excluded: chain C residue 126 GLN Chi-restraints excluded: chain C residue 185 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 106 optimal weight: 0.0070 chunk 14 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 chunk 45 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 88 optimal weight: 9.9990 chunk 40 optimal weight: 2.9990 chunk 29 optimal weight: 0.0270 chunk 95 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 83 optimal weight: 3.9990 overall best weight: 1.0058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 33 ASN ** H 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 809 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 102 GLN ** C 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.172793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.151825 restraints weight = 20144.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.146892 restraints weight = 46558.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.143305 restraints weight = 31985.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.141472 restraints weight = 38209.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.142547 restraints weight = 26909.054| |-----------------------------------------------------------------------------| r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3602 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3602 r_free = 0.3602 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3602 r_free = 0.3602 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3602 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.5963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12244 Z= 0.115 Angle : 0.590 8.788 16718 Z= 0.303 Chirality : 0.044 0.182 1912 Planarity : 0.005 0.120 2200 Dihedral : 4.769 57.386 1719 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.95 % Allowed : 15.09 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.56 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.20 (0.20), residues: 1572 helix: -4.58 (0.55), residues: 25 sheet: -0.36 (0.22), residues: 602 loop : -2.23 (0.17), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 116 TYR 0.015 0.001 TYR D 436 PHE 0.020 0.001 PHE D 146 TRP 0.012 0.001 TRP D 198 HIS 0.003 0.001 HIS D 809 Details of bonding type rmsd covalent geometry : bond 0.00259 (12238) covalent geometry : angle 0.58881 (16706) SS BOND : bond 0.00410 ( 6) SS BOND : angle 1.33050 ( 12) hydrogen bonds : bond 0.03503 ( 303) hydrogen bonds : angle 5.92620 ( 834) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 208 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 12 ASP cc_start: 0.6944 (p0) cc_final: 0.6686 (t0) REVERT: D 333 ILE cc_start: 0.8528 (OUTLIER) cc_final: 0.8299 (mp) REVERT: D 396 MET cc_start: 0.7482 (tmm) cc_final: 0.7214 (tmm) REVERT: D 397 THR cc_start: 0.8494 (m) cc_final: 0.8228 (m) REVERT: D 481 ARG cc_start: 0.7663 (ttt180) cc_final: 0.7269 (ttt90) REVERT: G 14 LYS cc_start: 0.8729 (mmpt) cc_final: 0.8079 (mtmt) REVERT: G 31 TYR cc_start: 0.7916 (m-10) cc_final: 0.7554 (m-80) REVERT: G 36 MET cc_start: 0.8323 (mtt) cc_final: 0.8108 (mtt) REVERT: G 105 GLN cc_start: 0.7013 (mm110) cc_final: 0.6803 (mp10) REVERT: G 110 SER cc_start: 0.8043 (OUTLIER) cc_final: 0.7734 (t) REVERT: G 141 TYR cc_start: 0.8781 (m-80) cc_final: 0.8544 (m-10) REVERT: C 16 LYS cc_start: 0.8747 (tptt) cc_final: 0.8279 (ttpp) REVERT: C 100 GLU cc_start: 0.7791 (mm-30) cc_final: 0.7506 (mm-30) REVERT: C 204 MET cc_start: 0.1044 (mmm) cc_final: 0.0477 (mmm) outliers start: 36 outliers final: 25 residues processed: 237 average time/residue: 0.1071 time to fit residues: 37.1820 Evaluate side-chains 216 residues out of total 1299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 189 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 69 SER Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 130 ILE Chi-restraints excluded: chain H residue 183 LEU Chi-restraints excluded: chain H residue 186 TYR Chi-restraints excluded: chain H residue 206 ASN Chi-restraints excluded: chain H residue 269 GLN Chi-restraints excluded: chain D residue 122 ASN Chi-restraints excluded: chain D residue 138 ASN Chi-restraints excluded: chain D residue 234 ARG Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 333 ILE Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 589 LEU Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain F residue 16 CYS Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 77 ASN Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain G residue 110 SER Chi-restraints excluded: chain G residue 133 ILE Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 185 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 48 optimal weight: 0.8980 chunk 20 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 64 optimal weight: 5.9990 chunk 78 optimal weight: 5.9990 chunk 99 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 80 optimal weight: 0.9990 chunk 137 optimal weight: 0.0070 chunk 90 optimal weight: 4.9990 chunk 85 optimal weight: 9.9990 overall best weight: 1.1804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 46 ASN ** H 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 40 ASN ** D 809 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 36 GLN F 126 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.172207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.151513 restraints weight = 17113.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.144245 restraints weight = 40547.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.140874 restraints weight = 37047.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.140504 restraints weight = 34130.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.141408 restraints weight = 24788.174| |-----------------------------------------------------------------------------| r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3589 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3589 r_free = 0.3589 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3589 r_free = 0.3589 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3589 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.6376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12244 Z= 0.118 Angle : 0.575 8.309 16718 Z= 0.294 Chirality : 0.043 0.152 1912 Planarity : 0.005 0.111 2200 Dihedral : 4.530 54.567 1719 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 4.28 % Allowed : 14.70 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.56 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.99 (0.20), residues: 1572 helix: -4.58 (0.51), residues: 31 sheet: -0.03 (0.22), residues: 561 loop : -2.13 (0.17), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 79 TYR 0.013 0.001 TYR D 144 PHE 0.027 0.002 PHE D 525 TRP 0.013 0.001 TRP D 198 HIS 0.002 0.001 HIS D 571 Details of bonding type rmsd covalent geometry : bond 0.00267 (12238) covalent geometry : angle 0.57406 (16706) SS BOND : bond 0.00257 ( 6) SS BOND : angle 1.07388 ( 12) hydrogen bonds : bond 0.03547 ( 303) hydrogen bonds : angle 5.56749 ( 834) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 200 time to evaluate : 0.522 Fit side-chains revert: symmetry clash REVERT: D 12 ASP cc_start: 0.6933 (p0) cc_final: 0.6662 (t0) REVERT: D 44 MET cc_start: 0.6782 (ttt) cc_final: 0.6314 (ttp) REVERT: D 237 GLN cc_start: 0.8934 (OUTLIER) cc_final: 0.7943 (tt0) REVERT: D 333 ILE cc_start: 0.8558 (OUTLIER) cc_final: 0.8255 (mp) REVERT: D 396 MET cc_start: 0.7589 (tmm) cc_final: 0.7336 (tmm) REVERT: D 481 ARG cc_start: 0.7752 (ttt180) cc_final: 0.7304 (ttt90) REVERT: D 512 ASN cc_start: 0.6590 (m-40) cc_final: 0.5773 (m-40) REVERT: F 17 SER cc_start: 0.8889 (t) cc_final: 0.8371 (p) REVERT: F 132 MET cc_start: 0.7245 (tpp) cc_final: 0.6825 (tpp) REVERT: G 14 LYS cc_start: 0.8789 (mmpt) cc_final: 0.8142 (mtmt) REVERT: G 105 GLN cc_start: 0.7073 (mm110) cc_final: 0.6851 (mp10) REVERT: G 141 TYR cc_start: 0.8801 (m-80) cc_final: 0.8513 (m-10) REVERT: C 16 LYS cc_start: 0.8667 (tptt) cc_final: 0.8361 (ttpp) REVERT: C 100 GLU cc_start: 0.7843 (mm-30) cc_final: 0.7530 (mm-30) REVERT: C 126 GLN cc_start: 0.7723 (OUTLIER) cc_final: 0.7353 (pp30) REVERT: C 204 MET cc_start: 0.0658 (mmm) cc_final: -0.2211 (ttm) outliers start: 53 outliers final: 33 residues processed: 241 average time/residue: 0.0925 time to fit residues: 34.3469 Evaluate side-chains 223 residues out of total 1299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 187 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 46 ASN Chi-restraints excluded: chain H residue 69 SER Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 130 ILE Chi-restraints excluded: chain H residue 183 LEU Chi-restraints excluded: chain H residue 186 TYR Chi-restraints excluded: chain H residue 193 LEU Chi-restraints excluded: chain H residue 206 ASN Chi-restraints excluded: chain H residue 250 LEU Chi-restraints excluded: chain D residue 122 ASN Chi-restraints excluded: chain D residue 138 ASN Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain D residue 234 ARG Chi-restraints excluded: chain D residue 237 GLN Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 333 ILE Chi-restraints excluded: chain D residue 518 GLN Chi-restraints excluded: chain D residue 589 LEU Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain D residue 811 VAL Chi-restraints excluded: chain F residue 16 CYS Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 77 ASN Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 32 SER Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain G residue 133 ILE Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 126 GLN Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 185 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 10 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 154 optimal weight: 8.9990 chunk 57 optimal weight: 8.9990 chunk 69 optimal weight: 2.9990 chunk 116 optimal weight: 10.0000 chunk 8 optimal weight: 10.0000 chunk 70 optimal weight: 0.9980 chunk 132 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 46 ASN ** H 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 324 GLN ** D 809 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 815 GLN F 102 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.176168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.164996 restraints weight = 16235.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.162040 restraints weight = 35091.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.160964 restraints weight = 44451.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.159900 restraints weight = 41725.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.159291 restraints weight = 42185.418| |-----------------------------------------------------------------------------| r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3794 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3794 r_free = 0.3794 target_work(ls_wunit_k1) = 0.157 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3794 r_free = 0.3794 target_work(ls_wunit_k1) = 0.157 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3794 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.7018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 12244 Z= 0.199 Angle : 0.674 9.346 16718 Z= 0.349 Chirality : 0.046 0.198 1912 Planarity : 0.006 0.129 2200 Dihedral : 5.159 56.802 1719 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 3.81 % Allowed : 16.56 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.17 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.15 (0.19), residues: 1572 helix: -4.47 (0.55), residues: 31 sheet: -0.12 (0.22), residues: 554 loop : -2.25 (0.17), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 79 TYR 0.020 0.002 TYR D 436 PHE 0.019 0.002 PHE G 33 TRP 0.016 0.002 TRP D 198 HIS 0.010 0.001 HIS H 45 Details of bonding type rmsd covalent geometry : bond 0.00461 (12238) covalent geometry : angle 0.67373 (16706) SS BOND : bond 0.00352 ( 6) SS BOND : angle 1.04314 ( 12) hydrogen bonds : bond 0.04735 ( 303) hydrogen bonds : angle 5.96789 ( 834) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 188 time to evaluate : 0.453 Fit side-chains revert: symmetry clash REVERT: D 12 ASP cc_start: 0.7349 (p0) cc_final: 0.6414 (t0) REVERT: D 138 ASN cc_start: 0.8371 (OUTLIER) cc_final: 0.8161 (p0) REVERT: D 237 GLN cc_start: 0.8964 (OUTLIER) cc_final: 0.7476 (tp40) REVERT: D 333 ILE cc_start: 0.8673 (OUTLIER) cc_final: 0.8398 (mp) REVERT: D 396 MET cc_start: 0.7664 (tmm) cc_final: 0.7380 (tmm) REVERT: D 481 ARG cc_start: 0.7982 (ttt180) cc_final: 0.7258 (ttt90) REVERT: F 17 SER cc_start: 0.9008 (t) cc_final: 0.8418 (p) REVERT: G 14 LYS cc_start: 0.8690 (mmpt) cc_final: 0.8081 (mtmt) REVERT: G 78 GLN cc_start: 0.7688 (mt0) cc_final: 0.7434 (mt0) REVERT: G 105 GLN cc_start: 0.7224 (mm110) cc_final: 0.6991 (mp10) REVERT: C 16 LYS cc_start: 0.8756 (tptt) cc_final: 0.8341 (ttpp) REVERT: C 82 LEU cc_start: 0.8144 (tp) cc_final: 0.7931 (tp) REVERT: C 204 MET cc_start: 0.0730 (mmm) cc_final: -0.1530 (tmm) outliers start: 47 outliers final: 41 residues processed: 226 average time/residue: 0.0979 time to fit residues: 33.4232 Evaluate side-chains 218 residues out of total 1299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 174 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 46 ASN Chi-restraints excluded: chain H residue 69 SER Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 130 ILE Chi-restraints excluded: chain H residue 183 LEU Chi-restraints excluded: chain H residue 186 TYR Chi-restraints excluded: chain H residue 206 ASN Chi-restraints excluded: chain H residue 250 LEU Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 122 ASN Chi-restraints excluded: chain D residue 138 ASN Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain D residue 234 ARG Chi-restraints excluded: chain D residue 237 GLN Chi-restraints excluded: chain D residue 248 SER Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 333 ILE Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 518 GLN Chi-restraints excluded: chain D residue 537 THR Chi-restraints excluded: chain D residue 581 ASP Chi-restraints excluded: chain D residue 589 LEU Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain D residue 770 VAL Chi-restraints excluded: chain D residue 811 VAL Chi-restraints excluded: chain F residue 16 CYS Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 77 ASN Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 32 SER Chi-restraints excluded: chain G residue 91 ASP Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain G residue 133 ILE Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 126 GLN Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 185 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 65 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 35 optimal weight: 0.1980 chunk 61 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 chunk 137 optimal weight: 1.9990 chunk 101 optimal weight: 10.0000 chunk 116 optimal weight: 9.9990 chunk 82 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 overall best weight: 2.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 46 ASN ** H 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 809 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.175308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.162962 restraints weight = 18541.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 67)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.153024 restraints weight = 42546.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.150005 restraints weight = 39487.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.148460 restraints weight = 29643.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.148593 restraints weight = 25057.961| |-----------------------------------------------------------------------------| r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3529 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3529 r_free = 0.3529 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3528 r_free = 0.3528 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3528 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.7306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12244 Z= 0.175 Angle : 0.656 13.392 16718 Z= 0.334 Chirality : 0.045 0.189 1912 Planarity : 0.006 0.122 2200 Dihedral : 5.099 55.040 1719 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 4.35 % Allowed : 16.95 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.17 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.16 (0.19), residues: 1572 helix: -4.27 (0.61), residues: 31 sheet: -0.17 (0.22), residues: 569 loop : -2.26 (0.17), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 160 TYR 0.022 0.002 TYR D 436 PHE 0.028 0.002 PHE D 766 TRP 0.016 0.002 TRP D 198 HIS 0.008 0.001 HIS H 45 Details of bonding type rmsd covalent geometry : bond 0.00402 (12238) covalent geometry : angle 0.65565 (16706) SS BOND : bond 0.00256 ( 6) SS BOND : angle 0.87441 ( 12) hydrogen bonds : bond 0.04344 ( 303) hydrogen bonds : angle 5.88493 ( 834) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 192 time to evaluate : 0.497 Fit side-chains revert: symmetry clash REVERT: D 12 ASP cc_start: 0.7289 (OUTLIER) cc_final: 0.6587 (t0) REVERT: D 138 ASN cc_start: 0.8374 (OUTLIER) cc_final: 0.8125 (p0) REVERT: D 237 GLN cc_start: 0.8955 (OUTLIER) cc_final: 0.7804 (tt0) REVERT: D 333 ILE cc_start: 0.8653 (OUTLIER) cc_final: 0.8277 (mp) REVERT: D 396 MET cc_start: 0.7514 (tmm) cc_final: 0.7273 (tmm) REVERT: D 481 ARG cc_start: 0.7964 (ttt180) cc_final: 0.7231 (ttt90) REVERT: G 14 LYS cc_start: 0.8775 (mmpt) cc_final: 0.8136 (mtmt) REVERT: G 78 GLN cc_start: 0.7777 (mt0) cc_final: 0.7536 (mt0) REVERT: G 105 GLN cc_start: 0.7366 (mm110) cc_final: 0.7128 (mp10) REVERT: C 16 LYS cc_start: 0.8831 (tptt) cc_final: 0.8502 (ttpt) REVERT: C 204 MET cc_start: 0.1573 (mmm) cc_final: -0.1214 (ttp) outliers start: 54 outliers final: 46 residues processed: 235 average time/residue: 0.0939 time to fit residues: 33.6149 Evaluate side-chains 228 residues out of total 1299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 178 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 46 ASN Chi-restraints excluded: chain H residue 69 SER Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 130 ILE Chi-restraints excluded: chain H residue 183 LEU Chi-restraints excluded: chain H residue 186 TYR Chi-restraints excluded: chain H residue 206 ASN Chi-restraints excluded: chain H residue 214 SER Chi-restraints excluded: chain H residue 250 LEU Chi-restraints excluded: chain H residue 275 THR Chi-restraints excluded: chain D residue 12 ASP Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 122 ASN Chi-restraints excluded: chain D residue 138 ASN Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain D residue 234 ARG Chi-restraints excluded: chain D residue 237 GLN Chi-restraints excluded: chain D residue 248 SER Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 333 ILE Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 499 TYR Chi-restraints excluded: chain D residue 518 GLN Chi-restraints excluded: chain D residue 537 THR Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 581 ASP Chi-restraints excluded: chain D residue 589 LEU Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain D residue 770 VAL Chi-restraints excluded: chain D residue 811 VAL Chi-restraints excluded: chain F residue 16 CYS Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 77 ASN Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 32 SER Chi-restraints excluded: chain G residue 91 ASP Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain G residue 133 ILE Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 126 GLN Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 185 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 103 optimal weight: 7.9990 chunk 102 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 chunk 109 optimal weight: 0.9980 chunk 154 optimal weight: 0.7980 chunk 136 optimal weight: 3.9990 chunk 151 optimal weight: 6.9990 chunk 15 optimal weight: 5.9990 chunk 62 optimal weight: 0.9980 chunk 74 optimal weight: 5.9990 chunk 4 optimal weight: 20.0000 overall best weight: 2.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 46 ASN ** H 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 279 GLN D 270 GLN D 728 ASN D 809 HIS G 114 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.172707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.156472 restraints weight = 18601.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.154405 restraints weight = 42262.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.149733 restraints weight = 45362.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.146014 restraints weight = 38376.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.145699 restraints weight = 39715.141| |-----------------------------------------------------------------------------| r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3501 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3501 r_free = 0.3501 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3501 r_free = 0.3501 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3501 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.7592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12244 Z= 0.183 Angle : 0.669 12.218 16718 Z= 0.344 Chirality : 0.045 0.218 1912 Planarity : 0.006 0.124 2200 Dihedral : 5.208 53.464 1719 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 4.51 % Allowed : 17.81 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.17 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.23 (0.19), residues: 1572 helix: -4.09 (0.69), residues: 31 sheet: -0.22 (0.22), residues: 566 loop : -2.30 (0.17), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 116 TYR 0.024 0.002 TYR D 436 PHE 0.030 0.002 PHE D 525 TRP 0.017 0.002 TRP D 198 HIS 0.011 0.001 HIS H 45 Details of bonding type rmsd covalent geometry : bond 0.00422 (12238) covalent geometry : angle 0.66925 (16706) SS BOND : bond 0.00251 ( 6) SS BOND : angle 0.80860 ( 12) hydrogen bonds : bond 0.04495 ( 303) hydrogen bonds : angle 5.93816 ( 834) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 182 time to evaluate : 0.529 Fit side-chains revert: symmetry clash REVERT: H 101 LYS cc_start: 0.6566 (OUTLIER) cc_final: 0.5685 (tptt) REVERT: D 12 ASP cc_start: 0.7326 (OUTLIER) cc_final: 0.6589 (t0) REVERT: D 138 ASN cc_start: 0.8358 (OUTLIER) cc_final: 0.8051 (p0) REVERT: D 237 GLN cc_start: 0.8996 (OUTLIER) cc_final: 0.7825 (tt0) REVERT: D 333 ILE cc_start: 0.8699 (OUTLIER) cc_final: 0.8326 (mp) REVERT: D 396 MET cc_start: 0.7577 (tmm) cc_final: 0.7195 (tmm) REVERT: D 481 ARG cc_start: 0.7941 (ttt180) cc_final: 0.7236 (ttt90) REVERT: G 14 LYS cc_start: 0.8734 (mmpt) cc_final: 0.8025 (mtmt) REVERT: G 105 GLN cc_start: 0.7332 (mm110) cc_final: 0.7047 (mp10) REVERT: G 144 SER cc_start: 0.7883 (p) cc_final: 0.7464 (t) REVERT: C 16 LYS cc_start: 0.8882 (tptt) cc_final: 0.8551 (ttpp) REVERT: C 204 MET cc_start: 0.1887 (mmm) cc_final: -0.1328 (tmm) outliers start: 56 outliers final: 45 residues processed: 225 average time/residue: 0.0942 time to fit residues: 32.6282 Evaluate side-chains 227 residues out of total 1299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 177 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 46 ASN Chi-restraints excluded: chain H residue 69 SER Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 101 LYS Chi-restraints excluded: chain H residue 130 ILE Chi-restraints excluded: chain H residue 183 LEU Chi-restraints excluded: chain H residue 186 TYR Chi-restraints excluded: chain H residue 206 ASN Chi-restraints excluded: chain H residue 214 SER Chi-restraints excluded: chain H residue 250 LEU Chi-restraints excluded: chain D residue 12 ASP Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 122 ASN Chi-restraints excluded: chain D residue 138 ASN Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain D residue 234 ARG Chi-restraints excluded: chain D residue 237 GLN Chi-restraints excluded: chain D residue 248 SER Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 333 ILE Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain D residue 499 TYR Chi-restraints excluded: chain D residue 518 GLN Chi-restraints excluded: chain D residue 537 THR Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 581 ASP Chi-restraints excluded: chain D residue 589 LEU Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain D residue 770 VAL Chi-restraints excluded: chain D residue 811 VAL Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 77 ASN Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 32 SER Chi-restraints excluded: chain G residue 36 MET Chi-restraints excluded: chain G residue 91 ASP Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain G residue 133 ILE Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 185 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 62 optimal weight: 6.9990 chunk 73 optimal weight: 4.9990 chunk 18 optimal weight: 8.9990 chunk 109 optimal weight: 0.0980 chunk 1 optimal weight: 10.0000 chunk 26 optimal weight: 4.9990 chunk 55 optimal weight: 7.9990 chunk 28 optimal weight: 1.9990 chunk 120 optimal weight: 8.9990 chunk 67 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 overall best weight: 3.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 46 ASN ** H 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.171581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.159642 restraints weight = 25299.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.150801 restraints weight = 50629.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.145869 restraints weight = 32621.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.145611 restraints weight = 24766.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.145779 restraints weight = 17949.526| |-----------------------------------------------------------------------------| r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3479 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3479 r_free = 0.3479 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3479 r_free = 0.3479 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| r_final: 0.3479 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.7912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 12244 Z= 0.225 Angle : 0.722 11.470 16718 Z= 0.374 Chirality : 0.047 0.214 1912 Planarity : 0.006 0.131 2200 Dihedral : 5.596 58.265 1719 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 4.35 % Allowed : 18.66 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.17 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.31 (0.19), residues: 1572 helix: -3.73 (0.79), residues: 25 sheet: -0.25 (0.22), residues: 554 loop : -2.39 (0.17), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 176 TYR 0.025 0.002 TYR D 436 PHE 0.027 0.003 PHE D 766 TRP 0.021 0.002 TRP D 198 HIS 0.012 0.002 HIS H 45 Details of bonding type rmsd covalent geometry : bond 0.00522 (12238) covalent geometry : angle 0.72239 (16706) SS BOND : bond 0.00338 ( 6) SS BOND : angle 0.72524 ( 12) hydrogen bonds : bond 0.05090 ( 303) hydrogen bonds : angle 6.13331 ( 834) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 186 time to evaluate : 0.317 Fit side-chains revert: symmetry clash REVERT: H 101 LYS cc_start: 0.6674 (OUTLIER) cc_final: 0.5692 (tptt) REVERT: H 156 VAL cc_start: 0.8840 (t) cc_final: 0.8451 (m) REVERT: D 12 ASP cc_start: 0.7270 (OUTLIER) cc_final: 0.6424 (t0) REVERT: D 51 PHE cc_start: 0.4279 (m-80) cc_final: 0.4062 (m-10) REVERT: D 138 ASN cc_start: 0.8399 (OUTLIER) cc_final: 0.8009 (p0) REVERT: D 237 GLN cc_start: 0.9001 (OUTLIER) cc_final: 0.7384 (tp40) REVERT: D 333 ILE cc_start: 0.8659 (OUTLIER) cc_final: 0.8339 (mp) REVERT: D 396 MET cc_start: 0.7583 (tmm) cc_final: 0.7340 (tmm) REVERT: G 14 LYS cc_start: 0.8683 (mmpt) cc_final: 0.8004 (mtmt) REVERT: G 144 SER cc_start: 0.7993 (p) cc_final: 0.7525 (t) REVERT: C 16 LYS cc_start: 0.8934 (tptt) cc_final: 0.8535 (ttpp) REVERT: C 204 MET cc_start: 0.2308 (mmm) cc_final: -0.0937 (tmm) outliers start: 54 outliers final: 48 residues processed: 225 average time/residue: 0.0964 time to fit residues: 32.7899 Evaluate side-chains 231 residues out of total 1299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 178 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 46 ASN Chi-restraints excluded: chain H residue 69 SER Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 101 LYS Chi-restraints excluded: chain H residue 130 ILE Chi-restraints excluded: chain H residue 183 LEU Chi-restraints excluded: chain H residue 187 CYS Chi-restraints excluded: chain H residue 193 LEU Chi-restraints excluded: chain H residue 206 ASN Chi-restraints excluded: chain H residue 214 SER Chi-restraints excluded: chain H residue 250 LEU Chi-restraints excluded: chain H residue 275 THR Chi-restraints excluded: chain D residue 12 ASP Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 122 ASN Chi-restraints excluded: chain D residue 138 ASN Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain D residue 234 ARG Chi-restraints excluded: chain D residue 237 GLN Chi-restraints excluded: chain D residue 248 SER Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 333 ILE Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 489 THR Chi-restraints excluded: chain D residue 499 TYR Chi-restraints excluded: chain D residue 518 GLN Chi-restraints excluded: chain D residue 537 THR Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 581 ASP Chi-restraints excluded: chain D residue 589 LEU Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain D residue 770 VAL Chi-restraints excluded: chain D residue 800 VAL Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 77 ASN Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 142 HIS Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 32 SER Chi-restraints excluded: chain G residue 36 MET Chi-restraints excluded: chain G residue 91 ASP Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain G residue 129 THR Chi-restraints excluded: chain G residue 133 ILE Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 185 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 84 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 36 optimal weight: 9.9990 chunk 144 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 119 optimal weight: 10.0000 chunk 83 optimal weight: 2.9990 chunk 115 optimal weight: 0.3980 chunk 101 optimal weight: 10.0000 chunk 152 optimal weight: 6.9990 chunk 85 optimal weight: 2.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 46 ASN ** H 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 277 ASN ** C 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.173745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.159217 restraints weight = 18702.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.155847 restraints weight = 39402.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.154129 restraints weight = 49681.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.153277 restraints weight = 42264.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.152626 restraints weight = 37848.078| |-----------------------------------------------------------------------------| r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3676 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3676 r_free = 0.3676 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3676 r_free = 0.3676 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3676 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.7943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12244 Z= 0.156 Angle : 0.679 11.588 16718 Z= 0.347 Chirality : 0.045 0.217 1912 Planarity : 0.006 0.129 2200 Dihedral : 5.365 61.509 1719 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 4.20 % Allowed : 19.91 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.17 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.20 (0.19), residues: 1572 helix: -3.68 (0.80), residues: 25 sheet: -0.22 (0.22), residues: 554 loop : -2.28 (0.17), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 66 TYR 0.025 0.002 TYR D 436 PHE 0.029 0.002 PHE D 766 TRP 0.019 0.002 TRP D 198 HIS 0.007 0.001 HIS H 45 Details of bonding type rmsd covalent geometry : bond 0.00362 (12238) covalent geometry : angle 0.67722 (16706) SS BOND : bond 0.00254 ( 6) SS BOND : angle 1.73058 ( 12) hydrogen bonds : bond 0.04238 ( 303) hydrogen bonds : angle 5.98253 ( 834) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 186 time to evaluate : 0.443 Fit side-chains REVERT: H 101 LYS cc_start: 0.6398 (pttt) cc_final: 0.5686 (tptt) REVERT: H 156 VAL cc_start: 0.8858 (t) cc_final: 0.8507 (m) REVERT: D 12 ASP cc_start: 0.7242 (OUTLIER) cc_final: 0.6618 (t0) REVERT: D 138 ASN cc_start: 0.8352 (OUTLIER) cc_final: 0.7934 (p0) REVERT: D 234 ARG cc_start: 0.7472 (OUTLIER) cc_final: 0.7042 (ttm-80) REVERT: D 237 GLN cc_start: 0.9041 (OUTLIER) cc_final: 0.7856 (tt0) REVERT: D 277 ASN cc_start: 0.7613 (OUTLIER) cc_final: 0.7324 (m-40) REVERT: D 333 ILE cc_start: 0.8573 (OUTLIER) cc_final: 0.8200 (mp) REVERT: D 396 MET cc_start: 0.7537 (tmm) cc_final: 0.7328 (tmm) REVERT: D 481 ARG cc_start: 0.7813 (ttt180) cc_final: 0.7037 (ttt90) REVERT: G 14 LYS cc_start: 0.8702 (mmpt) cc_final: 0.8049 (mtmt) REVERT: G 144 SER cc_start: 0.7948 (p) cc_final: 0.7452 (t) REVERT: C 16 LYS cc_start: 0.8881 (tptt) cc_final: 0.8581 (ttpp) REVERT: C 204 MET cc_start: 0.1444 (mmm) cc_final: -0.1359 (ttp) outliers start: 52 outliers final: 44 residues processed: 225 average time/residue: 0.0937 time to fit residues: 32.1330 Evaluate side-chains 226 residues out of total 1299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 176 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 69 SER Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 130 ILE Chi-restraints excluded: chain H residue 183 LEU Chi-restraints excluded: chain H residue 187 CYS Chi-restraints excluded: chain H residue 206 ASN Chi-restraints excluded: chain H residue 214 SER Chi-restraints excluded: chain H residue 250 LEU Chi-restraints excluded: chain D residue 12 ASP Chi-restraints excluded: chain D residue 122 ASN Chi-restraints excluded: chain D residue 138 ASN Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 234 ARG Chi-restraints excluded: chain D residue 237 GLN Chi-restraints excluded: chain D residue 248 SER Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 277 ASN Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 333 ILE Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 489 THR Chi-restraints excluded: chain D residue 499 TYR Chi-restraints excluded: chain D residue 518 GLN Chi-restraints excluded: chain D residue 537 THR Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 581 ASP Chi-restraints excluded: chain D residue 589 LEU Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain D residue 770 VAL Chi-restraints excluded: chain D residue 800 VAL Chi-restraints excluded: chain F residue 16 CYS Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 77 ASN Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 142 HIS Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 32 SER Chi-restraints excluded: chain G residue 36 MET Chi-restraints excluded: chain G residue 91 ASP Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain G residue 133 ILE Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 185 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 102 optimal weight: 5.9990 chunk 127 optimal weight: 2.9990 chunk 38 optimal weight: 10.0000 chunk 8 optimal weight: 0.0770 chunk 40 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 32 optimal weight: 9.9990 chunk 66 optimal weight: 6.9990 chunk 12 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 overall best weight: 3.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 46 ASN ** H 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 277 ASN G 130 GLN C 25 ASN ** C 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.170848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.157253 restraints weight = 19264.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.151895 restraints weight = 40119.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.149425 restraints weight = 45621.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.148335 restraints weight = 39740.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.147702 restraints weight = 31415.728| |-----------------------------------------------------------------------------| r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3526 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3526 r_free = 0.3526 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3526 r_free = 0.3526 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3526 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.8140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 12244 Z= 0.236 Angle : 0.743 10.917 16718 Z= 0.384 Chirality : 0.047 0.217 1912 Planarity : 0.006 0.126 2200 Dihedral : 5.700 58.484 1719 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer: Outliers : 4.82 % Allowed : 19.83 % Favored : 75.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.17 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.44 (0.19), residues: 1572 helix: -3.69 (0.72), residues: 27 sheet: -0.43 (0.21), residues: 564 loop : -2.44 (0.17), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 160 TYR 0.027 0.002 TYR D 436 PHE 0.057 0.003 PHE H 84 TRP 0.019 0.002 TRP D 198 HIS 0.006 0.001 HIS D 559 Details of bonding type rmsd covalent geometry : bond 0.00550 (12238) covalent geometry : angle 0.74257 (16706) SS BOND : bond 0.00323 ( 6) SS BOND : angle 1.45297 ( 12) hydrogen bonds : bond 0.05211 ( 303) hydrogen bonds : angle 6.17301 ( 834) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2086.87 seconds wall clock time: 36 minutes 45.79 seconds (2205.79 seconds total)