Starting phenix.real_space_refine on Sat Sep 12 05:45:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7aib_11794/09_2026/7aib_11794.cif Found real_map, /net/cci-nas-00/data/ceres_data/7aib_11794/09_2026/7aib_11794.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7aib_11794/09_2026/7aib_11794.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7aib_11794/09_2026/7aib_11794.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7aib_11794/09_2026/7aib_11794.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7aib_11794/09_2026/7aib_11794.cif" model { file = "/net/cci-nas-00/data/ceres_data/7aib_11794/09_2026/7aib_11794.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7aib_11794/09_2026/7aib_11794.cif" } resolution = 4.7 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= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 66 5.49 5 S 41 5.16 5 C 8493 2.51 5 N 2500 2.21 5 O 2739 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13839 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 5206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 661, 5206 Classifications: {'peptide': 661} Link IDs: {'PTRANS': 27, 'TRANS': 633} Chain breaks: 1 Chain: "B" Number of atoms: 5225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 663, 5225 Classifications: {'peptide': 663} Link IDs: {'PTRANS': 27, 'TRANS': 635} Chain breaks: 1 Chain: "C" Number of atoms: 2116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2116 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 9, 'TRANS': 257} Chain breaks: 3 Chain: "D" Number of atoms: 621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 621 Classifications: {'DNA': 30} Link IDs: {'rna3p': 29} Chain: "E" Number of atoms: 609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 609 Classifications: {'DNA': 30} Link IDs: {'rna3p': 29} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.58, per 1000 atoms: 0.26 Number of scatterers: 13839 At special positions: 0 Unit cell: (133.76, 110.88, 130.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 41 16.00 P 66 15.00 O 2739 8.00 N 2500 7.00 C 8493 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.06 Conformation dependent library (CDL) restraints added in 559.9 milliseconds 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2980 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 10 sheets defined 51.7% alpha, 13.8% beta 30 base pairs and 58 stacking pairs defined. Time for finding SS restraints: 1.80 Creating SS restraints... Processing helix chain 'A' and resid 162 through 174 removed outlier: 3.562A pdb=" N MET A 166 " --> pdb=" O ASP A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 190 removed outlier: 3.601A pdb=" N LEU A 189 " --> pdb=" O GLU A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 204 Processing helix chain 'A' and resid 205 through 218 Processing helix chain 'A' and resid 222 through 226 removed outlier: 3.507A pdb=" N PHE A 225 " --> pdb=" O LEU A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 248 removed outlier: 4.110A pdb=" N ALA A 236 " --> pdb=" O ARG A 232 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N CYS A 246 " --> pdb=" O GLN A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 278 removed outlier: 3.774A pdb=" N ARG A 274 " --> pdb=" O ASP A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 296 removed outlier: 3.648A pdb=" N VAL A 294 " --> pdb=" O THR A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 313 Processing helix chain 'A' and resid 317 through 332 Processing helix chain 'A' and resid 334 through 343 removed outlier: 3.516A pdb=" N LEU A 338 " --> pdb=" O PHE A 334 " (cutoff:3.500A) Proline residue: A 340 - end of helix Processing helix chain 'A' and resid 347 through 357 removed outlier: 3.514A pdb=" N ILE A 351 " --> pdb=" O ASP A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 373 Processing helix chain 'A' and resid 374 through 382 Processing helix chain 'A' and resid 387 through 398 Processing helix chain 'A' and resid 400 through 411 Processing helix chain 'A' and resid 430 through 442 removed outlier: 3.755A pdb=" N ALA A 440 " --> pdb=" O TRP A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 459 Processing helix chain 'A' and resid 479 through 483 removed outlier: 4.579A pdb=" N HIS A 483 " --> pdb=" O ARG A 479 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 479 through 483' Processing helix chain 'A' and resid 503 through 536 removed outlier: 3.865A pdb=" N PHE A 532 " --> pdb=" O TYR A 528 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASP A 533 " --> pdb=" O GLU A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 565 Processing helix chain 'A' and resid 587 through 592 Processing helix chain 'A' and resid 619 through 635 Processing helix chain 'A' and resid 673 through 684 removed outlier: 3.560A pdb=" N ASN A 679 " --> pdb=" O THR A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 700 through 718 removed outlier: 3.960A pdb=" N GLY A 704 " --> pdb=" O SER A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 729 through 735 Processing helix chain 'A' and resid 771 through 779 removed outlier: 3.941A pdb=" N ALA A 777 " --> pdb=" O LEU A 773 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU A 778 " --> pdb=" O ALA A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 782 through 797 removed outlier: 3.546A pdb=" N ILE A 786 " --> pdb=" O PRO A 782 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLU A 795 " --> pdb=" O GLN A 791 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 174 removed outlier: 3.561A pdb=" N MET B 166 " --> pdb=" O ASP B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 190 removed outlier: 3.606A pdb=" N LEU B 189 " --> pdb=" O GLU B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 204 Processing helix chain 'B' and resid 205 through 218 Processing helix chain 'B' and resid 222 through 226 Processing helix chain 'B' and resid 230 through 248 removed outlier: 4.092A pdb=" N ALA B 236 " --> pdb=" O ARG B 232 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N CYS B 246 " --> pdb=" O GLN B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 277 removed outlier: 3.515A pdb=" N ARG B 274 " --> pdb=" O ASP B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 296 removed outlier: 3.629A pdb=" N VAL B 294 " --> pdb=" O THR B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 313 Processing helix chain 'B' and resid 317 through 343 removed outlier: 4.991A pdb=" N ASP B 333 " --> pdb=" O GLY B 329 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N PHE B 334 " --> pdb=" O ALA B 330 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N ALA B 336 " --> pdb=" O GLN B 332 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N GLY B 337 " --> pdb=" O ASP B 333 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU B 338 " --> pdb=" O PHE B 334 " (cutoff:3.500A) Proline residue: B 340 - end of helix Processing helix chain 'B' and resid 347 through 357 Processing helix chain 'B' and resid 361 through 373 Processing helix chain 'B' and resid 374 through 382 Processing helix chain 'B' and resid 387 through 398 removed outlier: 3.573A pdb=" N GLY B 398 " --> pdb=" O ARG B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 411 Processing helix chain 'B' and resid 430 through 442 removed outlier: 3.732A pdb=" N ALA B 440 " --> pdb=" O TRP B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 459 Processing helix chain 'B' and resid 479 through 483 removed outlier: 4.559A pdb=" N HIS B 483 " --> pdb=" O ARG B 479 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 479 through 483' Processing helix chain 'B' and resid 503 through 536 removed outlier: 3.615A pdb=" N ASP B 511 " --> pdb=" O LYS B 507 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS B 512 " --> pdb=" O GLU B 508 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY B 518 " --> pdb=" O LEU B 514 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N PHE B 532 " --> pdb=" O TYR B 528 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ASP B 533 " --> pdb=" O GLU B 529 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 566 Processing helix chain 'B' and resid 587 through 592 Processing helix chain 'B' and resid 619 through 635 Processing helix chain 'B' and resid 672 through 684 removed outlier: 3.586A pdb=" N GLU B 676 " --> pdb=" O VAL B 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 702 through 718 removed outlier: 3.516A pdb=" N SER B 706 " --> pdb=" O TYR B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 729 through 735 Processing helix chain 'B' and resid 771 through 779 removed outlier: 3.923A pdb=" N ALA B 777 " --> pdb=" O LEU B 773 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU B 778 " --> pdb=" O ALA B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 782 through 797 removed outlier: 3.802A pdb=" N GLU B 795 " --> pdb=" O GLN B 791 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 37 removed outlier: 3.661A pdb=" N VAL C 26 " --> pdb=" O ARG C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 73 removed outlier: 3.919A pdb=" N ALA C 69 " --> pdb=" O LYS C 65 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N LEU C 70 " --> pdb=" O ASP C 66 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LEU C 72 " --> pdb=" O LEU C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 103 Processing helix chain 'C' and resid 155 through 161 removed outlier: 3.541A pdb=" N LYS C 159 " --> pdb=" O PRO C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 182 Processing helix chain 'C' and resid 208 through 223 removed outlier: 6.792A pdb=" N THR C 218 " --> pdb=" O ALA C 214 " (cutoff:3.500A) removed outlier: 9.120A pdb=" N ALA C 219 " --> pdb=" O ILE C 215 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N PHE C 220 " --> pdb=" O LEU C 216 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU C 221 " --> pdb=" O GLY C 217 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLN C 223 " --> pdb=" O ALA C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 246 removed outlier: 3.559A pdb=" N THR C 246 " --> pdb=" O PRO C 243 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 243 through 246' Processing helix chain 'C' and resid 249 through 252 removed outlier: 3.632A pdb=" N GLU C 252 " --> pdb=" O ALA C 249 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 249 through 252' Processing helix chain 'C' and resid 265 through 276 removed outlier: 4.052A pdb=" N ASN C 269 " --> pdb=" O ASP C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 331 removed outlier: 3.781A pdb=" N SER C 328 " --> pdb=" O GLN C 324 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL C 329 " --> pdb=" O GLY C 325 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLN C 331 " --> pdb=" O LEU C 327 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 155 through 158 removed outlier: 3.531A pdb=" N ARG A 156 " --> pdb=" O THR A 147 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N THR A 147 " --> pdb=" O ARG A 156 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ALA A 181 " --> pdb=" O ILE A 136 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N GLN A 138 " --> pdb=" O ALA A 181 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LEU A 178 " --> pdb=" O ARG A 197 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N ARG A 199 " --> pdb=" O LEU A 178 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N TYR A 180 " --> pdb=" O ARG A 199 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 268 through 269 removed outlier: 6.420A pdb=" N ILE A 268 " --> pdb=" O ILE A 653 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N THR A 655 " --> pdb=" O ILE A 268 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N ARG A 652 " --> pdb=" O LEU A 689 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N LEU A 691 " --> pdb=" O ARG A 652 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N PHE A 654 " --> pdb=" O LEU A 691 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N ASP A 693 " --> pdb=" O PHE A 654 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N LEU A 610 " --> pdb=" O PHE A 725 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N MET A 609 " --> pdb=" O ALA A 743 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N VAL A 745 " --> pdb=" O MET A 609 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N ILE A 611 " --> pdb=" O VAL A 745 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N LEU A 747 " --> pdb=" O ILE A 611 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N THR A 613 " --> pdb=" O LEU A 747 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N ALA A 749 " --> pdb=" O THR A 613 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASP A 748 " --> pdb=" O SER A 761 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N SER A 761 " --> pdb=" O ASP A 748 " (cutoff:3.500A) removed outlier: 8.629A pdb=" N LEU A 750 " --> pdb=" O MET A 759 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N MET A 759 " --> pdb=" O LEU A 750 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N HIS A 752 " --> pdb=" O ALA A 757 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ALA A 757 " --> pdb=" O HIS A 752 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 464 through 466 removed outlier: 5.882A pdb=" N ILE A 502 " --> pdb=" O ARG A 491 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N ARG A 491 " --> pdb=" O ILE A 502 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 571 through 572 removed outlier: 5.944A pdb=" N THR A 571 " --> pdb=" O ILE A 647 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N THR A 581 " --> pdb=" O LEU A 601 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N LEU A 601 " --> pdb=" O THR A 581 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 196 through 199 removed outlier: 6.495A pdb=" N LEU B 178 " --> pdb=" O ARG B 197 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N ARG B 199 " --> pdb=" O LEU B 178 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N TYR B 180 " --> pdb=" O ARG B 199 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ALA B 181 " --> pdb=" O ILE B 136 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N GLN B 138 " --> pdb=" O ALA B 181 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG B 156 " --> pdb=" O THR B 147 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 268 through 269 removed outlier: 7.090A pdb=" N ILE B 268 " --> pdb=" O ILE B 653 " (cutoff:3.500A) removed outlier: 8.343A pdb=" N THR B 655 " --> pdb=" O ILE B 268 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N LEU B 610 " --> pdb=" O PHE B 725 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N MET B 609 " --> pdb=" O ALA B 743 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N VAL B 745 " --> pdb=" O MET B 609 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N ILE B 611 " --> pdb=" O VAL B 745 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N LEU B 747 " --> pdb=" O ILE B 611 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N THR B 613 " --> pdb=" O LEU B 747 " (cutoff:3.500A) removed outlier: 8.523A pdb=" N ALA B 749 " --> pdb=" O THR B 613 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N SER B 761 " --> pdb=" O ASP B 748 " (cutoff:3.500A) removed outlier: 8.234A pdb=" N LEU B 750 " --> pdb=" O MET B 759 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N MET B 759 " --> pdb=" O LEU B 750 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N HIS B 752 " --> pdb=" O ALA B 757 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ALA B 757 " --> pdb=" O HIS B 752 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 464 through 466 removed outlier: 5.902A pdb=" N ILE B 502 " --> pdb=" O ARG B 491 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N ARG B 491 " --> pdb=" O ILE B 502 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 571 through 572 removed outlier: 5.896A pdb=" N THR B 571 " --> pdb=" O ILE B 647 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N THR B 581 " --> pdb=" O LEU B 601 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N LEU B 601 " --> pdb=" O THR B 581 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 135 through 136 removed outlier: 4.139A pdb=" N THR C 143 " --> pdb=" O ASP C 58 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ILE C 42 " --> pdb=" O ASN C 188 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N SER C 190 " --> pdb=" O ILE C 42 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ILE C 44 " --> pdb=" O SER C 190 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N HIS C 191 " --> pdb=" O ILE C 195 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N ILE C 195 " --> pdb=" O HIS C 191 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 224 through 231 removed outlier: 3.507A pdb=" N LEU C 290 " --> pdb=" O TYR C 255 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG C 261 " --> pdb=" O VAL C 258 " (cutoff:3.500A) 623 hydrogen bonds defined for protein. 1776 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 76 hydrogen bonds 152 hydrogen bond angles 0 basepair planarities 30 basepair parallelities 58 stacking parallelities Total time for adding SS restraints: 2.38 Time building geometry restraints manager: 1.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 2240 1.31 - 1.44: 3805 1.44 - 1.57: 7941 1.57 - 1.70: 128 1.70 - 1.83: 80 Bond restraints: 14194 Sorted by residual: bond pdb=" N3B ANP B1801 " pdb=" PG ANP B1801 " ideal model delta sigma weight residual 1.795 1.632 0.163 2.00e-02 2.50e+03 6.63e+01 bond pdb=" N3B ANP A1801 " pdb=" PG ANP A1801 " ideal model delta sigma weight residual 1.795 1.634 0.161 2.00e-02 2.50e+03 6.47e+01 bond pdb=" CE1 HIS A 682 " pdb=" NE2 HIS A 682 " ideal model delta sigma weight residual 1.321 1.373 -0.052 1.00e-02 1.00e+04 2.75e+01 bond pdb=" N ILE A 503 " pdb=" CA ILE A 503 " ideal model delta sigma weight residual 1.462 1.506 -0.044 8.70e-03 1.32e+04 2.57e+01 bond pdb=" O3A ANP B1801 " pdb=" PB ANP B1801 " ideal model delta sigma weight residual 1.700 1.603 0.097 2.00e-02 2.50e+03 2.35e+01 ... (remaining 14189 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.43: 15878 2.43 - 4.86: 3272 4.86 - 7.30: 303 7.30 - 9.73: 23 9.73 - 12.16: 4 Bond angle restraints: 19480 Sorted by residual: angle pdb=" C PHE A 143 " pdb=" N GLY A 144 " pdb=" CA GLY A 144 " ideal model delta sigma weight residual 121.65 127.06 -5.41 6.80e-01 2.16e+00 6.32e+01 angle pdb=" N LEU C 150 " pdb=" CA LEU C 150 " pdb=" C LEU C 150 " ideal model delta sigma weight residual 111.07 102.93 8.14 1.07e+00 8.73e-01 5.78e+01 angle pdb=" N ASP A 265 " pdb=" CA ASP A 265 " pdb=" C ASP A 265 " ideal model delta sigma weight residual 111.33 103.23 8.10 1.21e+00 6.83e-01 4.48e+01 angle pdb=" N ILE A 695 " pdb=" CA ILE A 695 " pdb=" C ILE A 695 " ideal model delta sigma weight residual 109.37 100.49 8.88 1.35e+00 5.49e-01 4.32e+01 angle pdb=" C PHE B 143 " pdb=" N GLY B 144 " pdb=" CA GLY B 144 " ideal model delta sigma weight residual 121.65 126.09 -4.44 6.80e-01 2.16e+00 4.26e+01 ... (remaining 19475 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.66: 7853 31.66 - 63.31: 593 63.31 - 94.97: 25 94.97 - 126.63: 0 126.63 - 158.28: 2 Dihedral angle restraints: 8473 sinusoidal: 3862 harmonic: 4611 Sorted by residual: dihedral pdb=" N TYR C 152 " pdb=" C TYR C 152 " pdb=" CA TYR C 152 " pdb=" CB TYR C 152 " ideal model delta harmonic sigma weight residual 122.80 134.39 -11.59 0 2.50e+00 1.60e-01 2.15e+01 dihedral pdb=" C THR C 109 " pdb=" N THR C 109 " pdb=" CA THR C 109 " pdb=" CB THR C 109 " ideal model delta harmonic sigma weight residual -122.00 -133.58 11.58 0 2.50e+00 1.60e-01 2.15e+01 dihedral pdb=" C TYR C 152 " pdb=" N TYR C 152 " pdb=" CA TYR C 152 " pdb=" CB TYR C 152 " ideal model delta harmonic sigma weight residual -122.60 -133.98 11.38 0 2.50e+00 1.60e-01 2.07e+01 ... (remaining 8470 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 1239 0.082 - 0.164: 808 0.164 - 0.247: 149 0.247 - 0.329: 19 0.329 - 0.411: 3 Chirality restraints: 2218 Sorted by residual: chirality pdb=" CA TYR C 152 " pdb=" N TYR C 152 " pdb=" C TYR C 152 " pdb=" CB TYR C 152 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.22e+00 chirality pdb=" C3' DG D 31 " pdb=" C4' DG D 31 " pdb=" O3' DG D 31 " pdb=" C2' DG D 31 " both_signs ideal model delta sigma weight residual False -2.73 -2.34 -0.39 2.00e-01 2.50e+01 3.74e+00 chirality pdb=" C3' ANP A1801 " pdb=" C2' ANP A1801 " pdb=" C4' ANP A1801 " pdb=" O3' ANP A1801 " both_signs ideal model delta sigma weight residual False -2.36 -2.70 0.35 2.00e-01 2.50e+01 3.01e+00 ... (remaining 2215 not shown) Planarity restraints: 2319 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE C 168 " -0.018 2.00e-02 2.50e+03 3.66e-02 1.34e+01 pdb=" C PHE C 168 " 0.063 2.00e-02 2.50e+03 pdb=" O PHE C 168 " -0.024 2.00e-02 2.50e+03 pdb=" N ASN C 169 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 623 " 0.034 2.00e-02 2.50e+03 2.38e-02 1.13e+01 pdb=" CG TYR A 623 " 0.003 2.00e-02 2.50e+03 pdb=" CD1 TYR A 623 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TYR A 623 " -0.018 2.00e-02 2.50e+03 pdb=" CE1 TYR A 623 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR A 623 " -0.014 2.00e-02 2.50e+03 pdb=" CZ TYR A 623 " -0.020 2.00e-02 2.50e+03 pdb=" OH TYR A 623 " 0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 215 " -0.016 2.00e-02 2.50e+03 3.20e-02 1.03e+01 pdb=" C LEU A 215 " 0.055 2.00e-02 2.50e+03 pdb=" O LEU A 215 " -0.021 2.00e-02 2.50e+03 pdb=" N GLN A 216 " -0.019 2.00e-02 2.50e+03 ... (remaining 2316 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 2457 2.84 - 3.36: 14179 3.36 - 3.87: 23177 3.87 - 4.39: 30108 4.39 - 4.90: 45552 Nonbonded interactions: 115473 Sorted by model distance: nonbonded pdb=" O LEU B 295 " pdb=" ND2 ASN B 557 " model vdw 2.329 3.120 nonbonded pdb=" O PHE B 730 " pdb=" OG1 THR B 733 " model vdw 2.330 3.040 nonbonded pdb=" OG SER C 112 " pdb=" O GLY C 142 " model vdw 2.336 3.040 nonbonded pdb=" O LEU A 295 " pdb=" ND2 ASN A 557 " model vdw 2.351 3.120 nonbonded pdb=" O ARG B 232 " pdb=" OG SER B 235 " model vdw 2.351 3.040 ... (remaining 115468 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 128 through 659 or resid 672 through 1801)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.030 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7203 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 : 0.014 0.163 14194 Z= 1.042 Angle : 1.846 12.159 19480 Z= 1.351 Chirality : 0.098 0.411 2218 Planarity : 0.006 0.037 2319 Dihedral : 18.857 158.283 5493 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 1.14 % Allowed : 6.68 % Favored : 92.19 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.64 (0.17), residues: 1575 helix: -2.22 (0.15), residues: 704 sheet: -2.30 (0.36), residues: 156 loop : -2.55 (0.20), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.034 0.002 ARG A 790 TYR 0.044 0.005 TYR A 623 PHE 0.032 0.006 PHE A 758 TRP 0.022 0.004 TRP A 709 HIS 0.010 0.002 HIS B 254 Details of bonding type rmsd/Z covalent geometry : bond 0.01387 / 1.04 (14194) covalent geometry : angle 1.84601 / 1.35 (19480) hydrogen bonds : bond 0.25273 / 16.82 ( 699) hydrogen bonds : angle 9.38479 / 6.59 ( 1928) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 210 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 MET cc_start: 0.8272 (tpt) cc_final: 0.7972 (tpt) REVERT: A 306 MET cc_start: 0.8625 (ttm) cc_final: 0.8144 (ttt) REVERT: A 534 LEU cc_start: 0.9130 (mt) cc_final: 0.8490 (mt) REVERT: A 552 LEU cc_start: 0.9372 (mt) cc_final: 0.9149 (mt) REVERT: A 633 MET cc_start: 0.7882 (mtp) cc_final: 0.7579 (tpp) REVERT: A 674 MET cc_start: 0.8519 (mmp) cc_final: 0.8262 (mpp) REVERT: A 679 ASN cc_start: 0.8367 (t0) cc_final: 0.7778 (m-40) REVERT: A 750 LEU cc_start: 0.8416 (mt) cc_final: 0.7477 (mm) REVERT: B 213 LEU cc_start: 0.9597 (mt) cc_final: 0.9268 (mm) REVERT: B 222 LEU cc_start: 0.8148 (mt) cc_final: 0.7593 (mt) REVERT: B 260 MET cc_start: 0.8995 (ttt) cc_final: 0.7698 (ttp) REVERT: B 269 MET cc_start: 0.7955 (ttm) cc_final: 0.7085 (ttm) REVERT: B 386 ASP cc_start: 0.7718 (t0) cc_final: 0.7508 (m-30) REVERT: B 609 MET cc_start: 0.8231 (ttm) cc_final: 0.7576 (mtm) REVERT: B 691 LEU cc_start: 0.8748 (mt) cc_final: 0.8415 (mp) REVERT: C 28 LYS cc_start: 0.9574 (tttt) cc_final: 0.9255 (ttmm) REVERT: C 29 GLU cc_start: 0.8983 (mt-10) cc_final: 0.8632 (mt-10) outliers start: 15 outliers final: 1 residues processed: 222 average time/residue: 0.1554 time to fit residues: 46.6564 Evaluate side-chains 117 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 116 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 10.0000 chunk 149 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 616 ASN ** A 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 ASN ** B 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 468 ASN ** B 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 122 GLN ** C 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 324 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 = 0.3543 r_free = 0.3543 target = 0.053695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.041138 restraints weight = 118372.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.042473 restraints weight = 76690.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.043425 restraints weight = 55590.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.044095 restraints weight = 43415.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.044562 restraints weight = 36017.183| |-----------------------------------------------------------------------------| r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14194 Z= 0.178 Angle : 0.724 8.832 19480 Z= 0.386 Chirality : 0.045 0.412 2218 Planarity : 0.006 0.119 2319 Dihedral : 19.995 158.337 2427 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.15 % Allowed : 2.81 % Favored : 97.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.77 (0.20), residues: 1575 helix: -0.45 (0.18), residues: 750 sheet: -1.56 (0.32), residues: 222 loop : -1.81 (0.24), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.038 0.001 ARG A 697 TYR 0.022 0.002 TYR C 276 PHE 0.020 0.002 PHE C 168 TRP 0.017 0.002 TRP A 709 HIS 0.012 0.001 HIS B 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.18 (14194) covalent geometry : angle 0.72416 / 0.39 (19480) hydrogen bonds : bond 0.06234 / 4.13 ( 699) hydrogen bonds : angle 5.80343 / 4.15 ( 1928) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 135 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 MET cc_start: 0.9510 (tpt) cc_final: 0.9129 (tpt) REVERT: A 306 MET cc_start: 0.9039 (ttm) cc_final: 0.8606 (ttt) REVERT: A 313 MET cc_start: 0.9443 (ttm) cc_final: 0.9224 (ttp) REVERT: A 348 LEU cc_start: 0.9288 (mt) cc_final: 0.8540 (mt) REVERT: A 368 MET cc_start: 0.9496 (mmp) cc_final: 0.9056 (mmp) REVERT: A 490 MET cc_start: 0.8791 (mpp) cc_final: 0.8576 (mpp) REVERT: A 552 LEU cc_start: 0.9660 (mt) cc_final: 0.9232 (mt) REVERT: A 574 ASP cc_start: 0.8377 (p0) cc_final: 0.7768 (p0) REVERT: A 633 MET cc_start: 0.8093 (mtp) cc_final: 0.7761 (tpp) REVERT: A 687 TYR cc_start: 0.8910 (m-80) cc_final: 0.8166 (m-10) REVERT: A 739 MET cc_start: 0.8065 (ttm) cc_final: 0.7291 (ttm) REVERT: A 759 MET cc_start: 0.8899 (mmp) cc_final: 0.8527 (mpp) REVERT: B 215 LEU cc_start: 0.8912 (pp) cc_final: 0.8186 (pp) REVERT: B 260 MET cc_start: 0.8825 (ttt) cc_final: 0.8135 (ttp) REVERT: B 313 MET cc_start: 0.8940 (tmm) cc_final: 0.8658 (tmm) REVERT: B 386 ASP cc_start: 0.8946 (t0) cc_final: 0.8259 (m-30) REVERT: B 397 MET cc_start: 0.9050 (ttm) cc_final: 0.8754 (ttm) REVERT: B 421 ASP cc_start: 0.8255 (p0) cc_final: 0.7967 (p0) REVERT: B 490 MET cc_start: 0.9342 (mmp) cc_final: 0.9056 (mmm) REVERT: B 633 MET cc_start: 0.9319 (ttt) cc_final: 0.9094 (ttm) REVERT: B 739 MET cc_start: 0.6811 (tpp) cc_final: 0.6222 (tpp) REVERT: C 26 VAL cc_start: 0.9530 (t) cc_final: 0.9100 (t) REVERT: C 28 LYS cc_start: 0.9413 (tttt) cc_final: 0.9152 (ttmm) REVERT: C 29 GLU cc_start: 0.9041 (mt-10) cc_final: 0.8487 (pt0) REVERT: C 133 THR cc_start: 0.9359 (p) cc_final: 0.9129 (p) REVERT: C 160 PHE cc_start: 0.8899 (m-10) cc_final: 0.8691 (m-80) REVERT: C 233 ASP cc_start: 0.8897 (p0) cc_final: 0.7871 (t70) REVERT: C 255 TYR cc_start: 0.8197 (m-80) cc_final: 0.7959 (m-80) outliers start: 2 outliers final: 0 residues processed: 137 average time/residue: 0.1347 time to fit residues: 25.9404 Evaluate side-chains 91 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 6 optimal weight: 0.9990 chunk 24 optimal weight: 4.9990 chunk 120 optimal weight: 6.9990 chunk 44 optimal weight: 0.7980 chunk 144 optimal weight: 4.9990 chunk 147 optimal weight: 8.9990 chunk 118 optimal weight: 5.9990 chunk 5 optimal weight: 20.0000 chunk 47 optimal weight: 9.9990 chunk 66 optimal weight: 9.9990 chunk 121 optimal weight: 0.7980 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 312 HIS B 468 ASN B 544 GLN ** B 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 682 HIS C 198 GLN C 223 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.051461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.039048 restraints weight = 124136.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.040289 restraints weight = 80441.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.041178 restraints weight = 58496.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.041790 restraints weight = 45957.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.042240 restraints weight = 38333.009| |-----------------------------------------------------------------------------| r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.3737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 14194 Z= 0.209 Angle : 0.707 8.369 19480 Z= 0.369 Chirality : 0.043 0.204 2218 Planarity : 0.005 0.065 2319 Dihedral : 20.086 149.509 2427 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.20), residues: 1575 helix: 0.23 (0.18), residues: 759 sheet: -1.19 (0.33), residues: 222 loop : -1.62 (0.24), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG C 237 TYR 0.030 0.003 TYR A 509 PHE 0.019 0.002 PHE A 155 TRP 0.013 0.002 TRP A 709 HIS 0.009 0.002 HIS B 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.21 (14194) covalent geometry : angle 0.70750 / 0.37 (19480) hydrogen bonds : bond 0.05290 / 3.51 ( 699) hydrogen bonds : angle 5.47550 / 3.87 ( 1928) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 MET cc_start: 0.9627 (tpt) cc_final: 0.9234 (tpt) REVERT: A 306 MET cc_start: 0.8924 (ttm) cc_final: 0.8462 (ttt) REVERT: A 348 LEU cc_start: 0.9560 (mt) cc_final: 0.9327 (mt) REVERT: A 368 MET cc_start: 0.9460 (mmp) cc_final: 0.9138 (mmp) REVERT: A 397 MET cc_start: 0.8477 (mtm) cc_final: 0.8190 (mtp) REVERT: A 507 LYS cc_start: 0.9736 (tmmt) cc_final: 0.9534 (tppt) REVERT: A 574 ASP cc_start: 0.8539 (p0) cc_final: 0.8248 (p0) REVERT: A 617 MET cc_start: 0.7022 (mpp) cc_final: 0.6753 (ttm) REVERT: A 633 MET cc_start: 0.8267 (mtp) cc_final: 0.7659 (tpp) REVERT: A 739 MET cc_start: 0.8026 (ttm) cc_final: 0.7790 (ttm) REVERT: A 759 MET cc_start: 0.9050 (mmp) cc_final: 0.8521 (mpp) REVERT: B 166 MET cc_start: 0.9163 (mmm) cc_final: 0.8895 (mmm) REVERT: B 260 MET cc_start: 0.9331 (ttt) cc_final: 0.7759 (tmm) REVERT: B 269 MET cc_start: 0.8106 (ttm) cc_final: 0.7520 (ttm) REVERT: B 302 MET cc_start: 0.9609 (ptm) cc_final: 0.9351 (ptm) REVERT: B 306 MET cc_start: 0.9236 (tpp) cc_final: 0.8443 (tmm) REVERT: B 313 MET cc_start: 0.9017 (tmm) cc_final: 0.8690 (tmm) REVERT: B 386 ASP cc_start: 0.9005 (t0) cc_final: 0.8353 (m-30) REVERT: B 397 MET cc_start: 0.9001 (ttm) cc_final: 0.8632 (ttm) REVERT: B 449 ARG cc_start: 0.9606 (mtt90) cc_final: 0.9395 (ptp90) REVERT: B 453 ARG cc_start: 0.9721 (tpt90) cc_final: 0.9519 (tpm170) REVERT: B 490 MET cc_start: 0.9447 (mmp) cc_final: 0.9221 (mmm) REVERT: B 609 MET cc_start: 0.7732 (mtm) cc_final: 0.7262 (ptp) REVERT: B 624 MET cc_start: 0.8944 (mtp) cc_final: 0.8645 (mtp) REVERT: B 692 MET cc_start: 0.8415 (mtp) cc_final: 0.8078 (mtp) REVERT: C 28 LYS cc_start: 0.9389 (tttt) cc_final: 0.9139 (ttmm) REVERT: C 29 GLU cc_start: 0.8962 (mt-10) cc_final: 0.8493 (mt-10) REVERT: C 160 PHE cc_start: 0.8995 (m-10) cc_final: 0.8658 (m-80) REVERT: C 168 PHE cc_start: 0.9227 (t80) cc_final: 0.8963 (t80) REVERT: C 233 ASP cc_start: 0.8980 (p0) cc_final: 0.7949 (t70) outliers start: 0 outliers final: 0 residues processed: 110 average time/residue: 0.1344 time to fit residues: 20.9572 Evaluate side-chains 84 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 120 optimal weight: 7.9990 chunk 107 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 128 optimal weight: 9.9990 chunk 140 optimal weight: 3.9990 chunk 2 optimal weight: 9.9990 chunk 12 optimal weight: 2.9990 chunk 149 optimal weight: 6.9990 chunk 51 optimal weight: 7.9990 chunk 119 optimal weight: 2.9990 chunk 48 optimal weight: 7.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 171 GLN ** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 543 GLN ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 274 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.050263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.037747 restraints weight = 125355.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.038939 restraints weight = 81153.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.039866 restraints weight = 59097.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.040484 restraints weight = 46019.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.040921 restraints weight = 38339.119| |-----------------------------------------------------------------------------| r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.4319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14194 Z= 0.211 Angle : 0.661 8.876 19480 Z= 0.346 Chirality : 0.042 0.244 2218 Planarity : 0.005 0.055 2319 Dihedral : 20.097 145.608 2427 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.21), residues: 1575 helix: 0.61 (0.18), residues: 764 sheet: -1.18 (0.32), residues: 239 loop : -1.48 (0.25), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 158 TYR 0.017 0.002 TYR C 124 PHE 0.017 0.002 PHE B 725 TRP 0.012 0.001 TRP B 202 HIS 0.006 0.001 HIS B 760 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.21 (14194) covalent geometry : angle 0.66072 / 0.35 (19480) hydrogen bonds : bond 0.04660 / 3.10 ( 699) hydrogen bonds : angle 5.16273 / 3.66 ( 1928) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 MET cc_start: 0.9658 (tpt) cc_final: 0.9227 (tpt) REVERT: A 260 MET cc_start: 0.9031 (tmm) cc_final: 0.8556 (tmm) REVERT: A 302 MET cc_start: 0.9281 (ptm) cc_final: 0.8963 (ptt) REVERT: A 306 MET cc_start: 0.8909 (ttm) cc_final: 0.8474 (ttt) REVERT: A 368 MET cc_start: 0.9528 (mmp) cc_final: 0.9148 (mmp) REVERT: A 397 MET cc_start: 0.8569 (mtm) cc_final: 0.8366 (mtt) REVERT: A 574 ASP cc_start: 0.8593 (p0) cc_final: 0.7830 (p0) REVERT: A 617 MET cc_start: 0.7143 (mpp) cc_final: 0.6865 (ttm) REVERT: A 633 MET cc_start: 0.8340 (mtp) cc_final: 0.7790 (tpp) REVERT: A 687 TYR cc_start: 0.8949 (m-80) cc_final: 0.8454 (m-10) REVERT: A 739 MET cc_start: 0.7898 (ttm) cc_final: 0.7607 (ttp) REVERT: A 759 MET cc_start: 0.9055 (mmp) cc_final: 0.8472 (mpp) REVERT: B 166 MET cc_start: 0.9232 (mmm) cc_final: 0.8880 (mmm) REVERT: B 260 MET cc_start: 0.9274 (ttt) cc_final: 0.7583 (tmm) REVERT: B 269 MET cc_start: 0.8145 (ttm) cc_final: 0.7596 (ttm) REVERT: B 302 MET cc_start: 0.9673 (ptm) cc_final: 0.9380 (ptm) REVERT: B 313 MET cc_start: 0.9160 (tmm) cc_final: 0.8849 (tmm) REVERT: B 386 ASP cc_start: 0.8971 (t0) cc_final: 0.8325 (m-30) REVERT: B 449 ARG cc_start: 0.9669 (mtt90) cc_final: 0.9440 (ptp-170) REVERT: B 552 LEU cc_start: 0.9508 (mt) cc_final: 0.9271 (tt) REVERT: B 566 ASN cc_start: 0.8982 (m110) cc_final: 0.8766 (m110) REVERT: B 609 MET cc_start: 0.7820 (mtm) cc_final: 0.7523 (ptm) REVERT: B 633 MET cc_start: 0.9293 (ttt) cc_final: 0.8931 (ppp) REVERT: C 29 GLU cc_start: 0.8965 (mt-10) cc_final: 0.8462 (mt-10) REVERT: C 160 PHE cc_start: 0.9204 (m-10) cc_final: 0.8825 (m-80) REVERT: C 168 PHE cc_start: 0.9285 (t80) cc_final: 0.8970 (t80) REVERT: C 233 ASP cc_start: 0.8911 (p0) cc_final: 0.8286 (t70) outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.1426 time to fit residues: 20.9134 Evaluate side-chains 79 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 73 optimal weight: 5.9990 chunk 119 optimal weight: 0.8980 chunk 33 optimal weight: 0.1980 chunk 128 optimal weight: 10.0000 chunk 77 optimal weight: 1.9990 chunk 145 optimal weight: 0.9990 chunk 159 optimal weight: 20.0000 chunk 122 optimal weight: 3.9990 chunk 147 optimal weight: 0.4980 chunk 151 optimal weight: 3.9990 chunk 24 optimal weight: 0.0980 overall best weight: 0.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 GLN B 481 GLN ** B 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.051784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.039103 restraints weight = 122577.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.040410 restraints weight = 78374.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.041343 restraints weight = 56126.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.041996 restraints weight = 43550.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.042424 restraints weight = 36088.265| |-----------------------------------------------------------------------------| r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.4444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14194 Z= 0.120 Angle : 0.574 7.278 19480 Z= 0.301 Chirality : 0.041 0.176 2218 Planarity : 0.004 0.047 2319 Dihedral : 19.954 139.657 2427 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.21), residues: 1575 helix: 0.91 (0.19), residues: 761 sheet: -1.13 (0.33), residues: 227 loop : -1.29 (0.25), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 449 TYR 0.018 0.002 TYR C 255 PHE 0.019 0.002 PHE A 155 TRP 0.012 0.001 TRP B 202 HIS 0.004 0.001 HIS C 319 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.12 (14194) covalent geometry : angle 0.57440 / 0.30 (19480) hydrogen bonds : bond 0.03927 / 2.61 ( 699) hydrogen bonds : angle 4.96848 / 3.54 ( 1928) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 MET cc_start: 0.9619 (tpt) cc_final: 0.9189 (tpt) REVERT: A 302 MET cc_start: 0.9571 (ptm) cc_final: 0.9212 (ptm) REVERT: A 306 MET cc_start: 0.8895 (ttm) cc_final: 0.8424 (ttt) REVERT: A 313 MET cc_start: 0.9423 (ttp) cc_final: 0.9025 (mmt) REVERT: A 348 LEU cc_start: 0.9196 (mt) cc_final: 0.8665 (mm) REVERT: A 368 MET cc_start: 0.9518 (mmp) cc_final: 0.9225 (mmp) REVERT: A 490 MET cc_start: 0.8748 (mpp) cc_final: 0.8497 (mpp) REVERT: A 574 ASP cc_start: 0.8612 (p0) cc_final: 0.7939 (p0) REVERT: A 609 MET cc_start: 0.8260 (mmm) cc_final: 0.8024 (mmm) REVERT: A 617 MET cc_start: 0.7323 (mpp) cc_final: 0.6679 (tmm) REVERT: A 633 MET cc_start: 0.8240 (mtp) cc_final: 0.7687 (tpp) REVERT: A 687 TYR cc_start: 0.8888 (m-80) cc_final: 0.8389 (m-10) REVERT: A 759 MET cc_start: 0.9016 (mmp) cc_final: 0.8534 (mpp) REVERT: A 775 VAL cc_start: 0.9018 (t) cc_final: 0.8718 (t) REVERT: B 166 MET cc_start: 0.9190 (mmm) cc_final: 0.8876 (mmm) REVERT: B 260 MET cc_start: 0.9299 (ttt) cc_final: 0.8014 (tmm) REVERT: B 269 MET cc_start: 0.8024 (ttm) cc_final: 0.7772 (ttm) REVERT: B 302 MET cc_start: 0.9680 (ptm) cc_final: 0.9435 (ptm) REVERT: B 306 MET cc_start: 0.9220 (tpp) cc_final: 0.8481 (tmm) REVERT: B 386 ASP cc_start: 0.9016 (t0) cc_final: 0.8464 (m-30) REVERT: B 449 ARG cc_start: 0.9682 (mtt90) cc_final: 0.9420 (ptp-170) REVERT: B 566 ASN cc_start: 0.8921 (m110) cc_final: 0.8631 (m110) REVERT: B 609 MET cc_start: 0.7751 (mtm) cc_final: 0.6413 (ptp) REVERT: B 633 MET cc_start: 0.9243 (ttt) cc_final: 0.8976 (tmm) REVERT: C 29 GLU cc_start: 0.8940 (mt-10) cc_final: 0.8363 (pt0) REVERT: C 160 PHE cc_start: 0.8994 (m-10) cc_final: 0.8691 (m-80) REVERT: C 168 PHE cc_start: 0.9150 (t80) cc_final: 0.8843 (t80) REVERT: C 233 ASP cc_start: 0.8906 (p0) cc_final: 0.8252 (t70) REVERT: C 270 HIS cc_start: 0.9595 (t-90) cc_final: 0.9356 (t-90) outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.1232 time to fit residues: 17.7517 Evaluate side-chains 81 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 155 optimal weight: 7.9990 chunk 40 optimal weight: 1.9990 chunk 130 optimal weight: 10.0000 chunk 151 optimal weight: 3.9990 chunk 20 optimal weight: 10.0000 chunk 74 optimal weight: 5.9990 chunk 94 optimal weight: 10.0000 chunk 14 optimal weight: 8.9990 chunk 10 optimal weight: 0.8980 chunk 157 optimal weight: 5.9990 chunk 46 optimal weight: 0.6980 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 481 GLN ** B 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 122 GLN ** 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 = 0.3452 r_free = 0.3452 target = 0.050238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.037664 restraints weight = 130147.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.038857 restraints weight = 85018.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.039711 restraints weight = 62164.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.040308 restraints weight = 49088.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.040698 restraints weight = 41249.044| |-----------------------------------------------------------------------------| r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.4793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14194 Z= 0.208 Angle : 0.646 7.665 19480 Z= 0.334 Chirality : 0.041 0.212 2218 Planarity : 0.005 0.064 2319 Dihedral : 19.896 136.320 2427 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 15.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.21), residues: 1575 helix: 0.99 (0.19), residues: 762 sheet: -1.05 (0.33), residues: 232 loop : -1.18 (0.26), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 48 TYR 0.025 0.002 TYR C 257 PHE 0.013 0.002 PHE A 467 TRP 0.011 0.001 TRP B 202 HIS 0.006 0.001 HIS B 746 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.21 (14194) covalent geometry : angle 0.64567 / 0.33 (19480) hydrogen bonds : bond 0.04622 / 3.11 ( 699) hydrogen bonds : angle 5.02812 / 3.58 ( 1928) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 MET cc_start: 0.9642 (tpt) cc_final: 0.9171 (tpt) REVERT: A 260 MET cc_start: 0.9150 (tmm) cc_final: 0.8693 (tmm) REVERT: A 306 MET cc_start: 0.8804 (ttm) cc_final: 0.8411 (ttt) REVERT: A 313 MET cc_start: 0.9388 (ttp) cc_final: 0.9085 (mmt) REVERT: A 348 LEU cc_start: 0.9061 (mt) cc_final: 0.8250 (mt) REVERT: A 368 MET cc_start: 0.9489 (mmp) cc_final: 0.9137 (mmp) REVERT: A 397 MET cc_start: 0.8863 (mtm) cc_final: 0.8630 (mtp) REVERT: A 490 MET cc_start: 0.8846 (mpp) cc_final: 0.8638 (mpp) REVERT: A 507 LYS cc_start: 0.9668 (tptp) cc_final: 0.9455 (tppt) REVERT: A 574 ASP cc_start: 0.8559 (p0) cc_final: 0.7920 (p0) REVERT: A 617 MET cc_start: 0.7475 (mpp) cc_final: 0.7154 (ttm) REVERT: A 633 MET cc_start: 0.8454 (mtp) cc_final: 0.7797 (tpp) REVERT: A 687 TYR cc_start: 0.8891 (m-80) cc_final: 0.8280 (m-80) REVERT: B 166 MET cc_start: 0.9213 (mmm) cc_final: 0.8908 (mmm) REVERT: B 260 MET cc_start: 0.9171 (ttt) cc_final: 0.7832 (tmm) REVERT: B 269 MET cc_start: 0.8152 (ttm) cc_final: 0.7719 (ttm) REVERT: B 302 MET cc_start: 0.9709 (ptm) cc_final: 0.9450 (ptm) REVERT: B 306 MET cc_start: 0.9222 (tpp) cc_final: 0.8504 (tmm) REVERT: B 386 ASP cc_start: 0.8943 (t0) cc_final: 0.8435 (m-30) REVERT: B 449 ARG cc_start: 0.9699 (mtt90) cc_final: 0.9311 (ptp90) REVERT: B 453 ARG cc_start: 0.9566 (tpm170) cc_final: 0.9361 (tpp-160) REVERT: B 609 MET cc_start: 0.7835 (mtm) cc_final: 0.7204 (ptm) REVERT: B 633 MET cc_start: 0.9238 (ttt) cc_final: 0.8977 (tmm) REVERT: B 674 MET cc_start: 0.8322 (mmt) cc_final: 0.8049 (mmp) REVERT: B 692 MET cc_start: 0.8435 (mtp) cc_final: 0.8119 (mtp) REVERT: C 29 GLU cc_start: 0.8973 (mt-10) cc_final: 0.8423 (mt-10) REVERT: C 160 PHE cc_start: 0.8739 (m-10) cc_final: 0.8392 (m-80) REVERT: C 168 PHE cc_start: 0.9213 (t80) cc_final: 0.8947 (t80) REVERT: C 233 ASP cc_start: 0.8822 (p0) cc_final: 0.8164 (t70) REVERT: C 270 HIS cc_start: 0.9602 (t-90) cc_final: 0.9390 (t-90) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.1336 time to fit residues: 16.5072 Evaluate side-chains 79 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 18 optimal weight: 6.9990 chunk 113 optimal weight: 1.9990 chunk 20 optimal weight: 7.9990 chunk 34 optimal weight: 9.9990 chunk 144 optimal weight: 5.9990 chunk 155 optimal weight: 7.9990 chunk 33 optimal weight: 3.9990 chunk 57 optimal weight: 0.8980 chunk 1 optimal weight: 10.0000 chunk 158 optimal weight: 20.0000 chunk 109 optimal weight: 5.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 339 GLN A 381 GLN ** A 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 242 GLN B 276 ASN B 289 ASN ** B 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 483 HIS ** B 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 122 GLN ** 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 = 0.3387 r_free = 0.3387 target = 0.047992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.035670 restraints weight = 131125.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.036818 restraints weight = 85670.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.037624 restraints weight = 62565.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.038197 restraints weight = 49364.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.038562 restraints weight = 41592.282| |-----------------------------------------------------------------------------| r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.5458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 14194 Z= 0.271 Angle : 0.731 8.470 19480 Z= 0.380 Chirality : 0.044 0.253 2218 Planarity : 0.005 0.065 2319 Dihedral : 19.997 132.582 2427 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 22.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.21), residues: 1575 helix: 0.68 (0.18), residues: 769 sheet: -1.34 (0.31), residues: 258 loop : -1.24 (0.26), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 158 TYR 0.025 0.003 TYR C 255 PHE 0.022 0.003 PHE B 725 TRP 0.011 0.002 TRP B 202 HIS 0.014 0.002 HIS A 760 Details of bonding type rmsd/Z covalent geometry : bond 0.00544 / 0.27 (14194) covalent geometry : angle 0.73054 / 0.38 (19480) hydrogen bonds : bond 0.05442 / 3.66 ( 699) hydrogen bonds : angle 5.20854 / 3.67 ( 1928) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 MET cc_start: 0.9702 (tpt) cc_final: 0.9213 (tpt) REVERT: A 260 MET cc_start: 0.9128 (tmm) cc_final: 0.8878 (tmm) REVERT: A 306 MET cc_start: 0.8532 (ttm) cc_final: 0.8187 (ttt) REVERT: A 313 MET cc_start: 0.9415 (ttp) cc_final: 0.9107 (mmt) REVERT: A 348 LEU cc_start: 0.9471 (mt) cc_final: 0.9193 (mt) REVERT: A 368 MET cc_start: 0.9503 (mmp) cc_final: 0.9233 (mmp) REVERT: A 397 MET cc_start: 0.8961 (mtm) cc_final: 0.8690 (mtt) REVERT: A 609 MET cc_start: 0.9013 (mmm) cc_final: 0.8135 (mmm) REVERT: A 617 MET cc_start: 0.7364 (mpp) cc_final: 0.7138 (ttp) REVERT: A 633 MET cc_start: 0.8459 (mtp) cc_final: 0.7993 (tpp) REVERT: A 687 TYR cc_start: 0.9064 (m-80) cc_final: 0.8442 (m-80) REVERT: B 166 MET cc_start: 0.9244 (mmm) cc_final: 0.8888 (mmm) REVERT: B 260 MET cc_start: 0.9203 (ttt) cc_final: 0.8310 (tpt) REVERT: B 302 MET cc_start: 0.9676 (ptm) cc_final: 0.9356 (ptm) REVERT: B 306 MET cc_start: 0.9256 (tpp) cc_final: 0.8529 (tmm) REVERT: B 386 ASP cc_start: 0.9058 (t0) cc_final: 0.8468 (m-30) REVERT: B 609 MET cc_start: 0.8192 (mtm) cc_final: 0.7270 (ptm) REVERT: B 633 MET cc_start: 0.9237 (ttt) cc_final: 0.8983 (tmm) REVERT: B 692 MET cc_start: 0.8093 (mtp) cc_final: 0.7864 (mtp) REVERT: C 26 VAL cc_start: 0.9471 (t) cc_final: 0.9091 (t) REVERT: C 29 GLU cc_start: 0.8943 (mt-10) cc_final: 0.8423 (mt-10) REVERT: C 160 PHE cc_start: 0.8964 (m-10) cc_final: 0.8628 (m-80) REVERT: C 168 PHE cc_start: 0.9340 (t80) cc_final: 0.9092 (t80) REVERT: C 233 ASP cc_start: 0.8836 (p0) cc_final: 0.8140 (t0) outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1346 time to fit residues: 15.9592 Evaluate side-chains 71 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 146 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 chunk 143 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 157 optimal weight: 6.9990 chunk 98 optimal weight: 4.9990 chunk 124 optimal weight: 4.9990 chunk 110 optimal weight: 8.9990 chunk 65 optimal weight: 3.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 211 GLN A 381 GLN ** A 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 717 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 122 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 = 0.3399 r_free = 0.3399 target = 0.048252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.035951 restraints weight = 125445.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.037154 restraints weight = 80471.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.038001 restraints weight = 58103.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.038625 restraints weight = 45518.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.039042 restraints weight = 37723.330| |-----------------------------------------------------------------------------| r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.5595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14194 Z= 0.208 Angle : 0.635 7.401 19480 Z= 0.333 Chirality : 0.042 0.244 2218 Planarity : 0.005 0.044 2319 Dihedral : 19.950 135.381 2427 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 18.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.08 % Allowed : 0.46 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.21), residues: 1575 helix: 0.90 (0.19), residues: 759 sheet: -1.44 (0.32), residues: 239 loop : -1.14 (0.26), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 158 TYR 0.018 0.002 TYR A 771 PHE 0.027 0.002 PHE A 372 TRP 0.013 0.001 TRP B 202 HIS 0.007 0.001 HIS A 760 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.21 (14194) covalent geometry : angle 0.63479 / 0.33 (19480) hydrogen bonds : bond 0.04662 / 3.14 ( 699) hydrogen bonds : angle 5.05014 / 3.55 ( 1928) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 80 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 MET cc_start: 0.9680 (tpt) cc_final: 0.9182 (tpt) REVERT: A 260 MET cc_start: 0.9136 (tmm) cc_final: 0.8682 (tmm) REVERT: A 306 MET cc_start: 0.8565 (ttm) cc_final: 0.8221 (ttt) REVERT: A 313 MET cc_start: 0.9446 (ttp) cc_final: 0.9090 (mmt) REVERT: A 348 LEU cc_start: 0.9393 (mt) cc_final: 0.8622 (mt) REVERT: A 368 MET cc_start: 0.9634 (mmp) cc_final: 0.9317 (mmp) REVERT: A 397 MET cc_start: 0.9102 (mtm) cc_final: 0.8847 (mtp) REVERT: A 574 ASP cc_start: 0.8521 (p0) cc_final: 0.7838 (p0) REVERT: A 633 MET cc_start: 0.8556 (mtp) cc_final: 0.7861 (tpp) REVERT: A 687 TYR cc_start: 0.9144 (m-80) cc_final: 0.8470 (m-80) REVERT: B 166 MET cc_start: 0.9259 (mmm) cc_final: 0.8870 (mmm) REVERT: B 260 MET cc_start: 0.9222 (ttt) cc_final: 0.8311 (tpt) REVERT: B 269 MET cc_start: 0.8288 (ttm) cc_final: 0.7757 (ttm) REVERT: B 302 MET cc_start: 0.9662 (ptm) cc_final: 0.9339 (ptm) REVERT: B 306 MET cc_start: 0.9260 (tpp) cc_final: 0.8511 (tmm) REVERT: B 386 ASP cc_start: 0.9111 (t0) cc_final: 0.8538 (m-30) REVERT: B 453 ARG cc_start: 0.9704 (tpt90) cc_final: 0.9492 (tpm170) REVERT: B 609 MET cc_start: 0.8122 (mtm) cc_final: 0.7781 (mpp) REVERT: B 692 MET cc_start: 0.8225 (mtp) cc_final: 0.7857 (mtp) REVERT: C 28 LYS cc_start: 0.9623 (ptmt) cc_final: 0.9404 (ptmm) REVERT: C 29 GLU cc_start: 0.8968 (mt-10) cc_final: 0.8444 (mt-10) REVERT: C 160 PHE cc_start: 0.8969 (m-10) cc_final: 0.8493 (m-80) REVERT: C 168 PHE cc_start: 0.9335 (t80) cc_final: 0.9103 (t80) REVERT: C 233 ASP cc_start: 0.8863 (p0) cc_final: 0.8152 (t0) outliers start: 1 outliers final: 0 residues processed: 81 average time/residue: 0.1433 time to fit residues: 16.4892 Evaluate side-chains 71 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 129 optimal weight: 5.9990 chunk 22 optimal weight: 6.9990 chunk 7 optimal weight: 0.4980 chunk 35 optimal weight: 0.9990 chunk 67 optimal weight: 9.9990 chunk 118 optimal weight: 6.9990 chunk 122 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 161 optimal weight: 30.0000 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 683 ASN ** A 717 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 HIS ** B 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 122 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 = 0.3419 r_free = 0.3419 target = 0.048796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.036486 restraints weight = 125383.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.037724 restraints weight = 79427.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.038597 restraints weight = 56971.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.039222 restraints weight = 44391.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.039652 restraints weight = 36825.415| |-----------------------------------------------------------------------------| r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.5689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14194 Z= 0.154 Angle : 0.595 7.601 19480 Z= 0.312 Chirality : 0.040 0.218 2218 Planarity : 0.005 0.044 2319 Dihedral : 19.897 135.521 2427 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 17.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.21), residues: 1575 helix: 1.03 (0.19), residues: 757 sheet: -1.42 (0.32), residues: 237 loop : -1.06 (0.26), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 409 TYR 0.015 0.002 TYR A 771 PHE 0.031 0.002 PHE A 372 TRP 0.014 0.001 TRP B 202 HIS 0.004 0.001 HIS A 682 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.15 (14194) covalent geometry : angle 0.59500 / 0.31 (19480) hydrogen bonds : bond 0.04115 / 2.75 ( 699) hydrogen bonds : angle 4.89161 / 3.43 ( 1928) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 MET cc_start: 0.9646 (tpt) cc_final: 0.9159 (tpt) REVERT: A 260 MET cc_start: 0.9139 (tmm) cc_final: 0.8700 (tmm) REVERT: A 306 MET cc_start: 0.8566 (ttm) cc_final: 0.8182 (ttt) REVERT: A 348 LEU cc_start: 0.9533 (mt) cc_final: 0.9162 (mt) REVERT: A 368 MET cc_start: 0.9585 (mmp) cc_final: 0.9308 (mmp) REVERT: A 397 MET cc_start: 0.9057 (mtm) cc_final: 0.8781 (mtp) REVERT: A 574 ASP cc_start: 0.8633 (p0) cc_final: 0.8000 (p0) REVERT: A 609 MET cc_start: 0.8978 (mmm) cc_final: 0.7999 (mmm) REVERT: A 633 MET cc_start: 0.8526 (mtp) cc_final: 0.7844 (tpp) REVERT: A 687 TYR cc_start: 0.9096 (m-80) cc_final: 0.8343 (m-80) REVERT: A 739 MET cc_start: 0.6908 (ttm) cc_final: 0.5007 (tmm) REVERT: B 166 MET cc_start: 0.9255 (mmm) cc_final: 0.8864 (mmm) REVERT: B 260 MET cc_start: 0.9197 (ttt) cc_final: 0.8369 (tpt) REVERT: B 269 MET cc_start: 0.8248 (ttm) cc_final: 0.7960 (ttm) REVERT: B 302 MET cc_start: 0.9682 (ptm) cc_final: 0.9427 (ptm) REVERT: B 306 MET cc_start: 0.9267 (tpp) cc_final: 0.8558 (tmm) REVERT: B 386 ASP cc_start: 0.9080 (t0) cc_final: 0.8536 (m-30) REVERT: B 609 MET cc_start: 0.7928 (mtm) cc_final: 0.7679 (mpp) REVERT: B 624 MET cc_start: 0.8601 (mmm) cc_final: 0.8150 (mmt) REVERT: B 643 GLN cc_start: 0.9469 (tm-30) cc_final: 0.9078 (tm-30) REVERT: B 692 MET cc_start: 0.8229 (mtp) cc_final: 0.7687 (mtp) REVERT: B 724 LEU cc_start: 0.8670 (mt) cc_final: 0.8376 (mt) REVERT: C 28 LYS cc_start: 0.9606 (ptmt) cc_final: 0.9394 (ptmm) REVERT: C 29 GLU cc_start: 0.8931 (mt-10) cc_final: 0.8407 (mt-10) REVERT: C 160 PHE cc_start: 0.8790 (m-10) cc_final: 0.8489 (m-80) REVERT: C 168 PHE cc_start: 0.9340 (t80) cc_final: 0.9090 (t80) REVERT: C 233 ASP cc_start: 0.8862 (p0) cc_final: 0.8066 (t0) outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.1194 time to fit residues: 14.7384 Evaluate side-chains 75 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 140 optimal weight: 6.9990 chunk 72 optimal weight: 1.9990 chunk 103 optimal weight: 9.9990 chunk 25 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 chunk 138 optimal weight: 3.9990 chunk 95 optimal weight: 8.9990 chunk 120 optimal weight: 6.9990 chunk 20 optimal weight: 0.6980 chunk 88 optimal weight: 5.9990 chunk 145 optimal weight: 0.6980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 717 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 HIS ** B 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 122 GLN ** 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 = 0.3438 r_free = 0.3438 target = 0.049518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.037005 restraints weight = 130145.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.038227 restraints weight = 83444.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.039082 restraints weight = 60301.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.039685 restraints weight = 47462.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.040099 restraints weight = 39785.551| |-----------------------------------------------------------------------------| r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.5769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14194 Z= 0.139 Angle : 0.590 7.350 19480 Z= 0.310 Chirality : 0.040 0.181 2218 Planarity : 0.004 0.043 2319 Dihedral : 19.836 135.207 2427 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 16.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.00 % Allowed : 0.08 % Favored : 99.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.21), residues: 1575 helix: 1.10 (0.19), residues: 756 sheet: -1.41 (0.32), residues: 236 loop : -0.97 (0.26), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 158 TYR 0.014 0.002 TYR A 771 PHE 0.028 0.002 PHE A 372 TRP 0.014 0.001 TRP B 202 HIS 0.003 0.001 HIS B 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.14 (14194) covalent geometry : angle 0.58977 / 0.31 (19480) hydrogen bonds : bond 0.03839 / 2.58 ( 699) hydrogen bonds : angle 4.85701 / 3.42 ( 1928) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 MET cc_start: 0.9546 (tpt) cc_final: 0.9104 (tpt) REVERT: A 260 MET cc_start: 0.9077 (tmm) cc_final: 0.8623 (tmm) REVERT: A 302 MET cc_start: 0.9298 (mtm) cc_final: 0.8484 (mpp) REVERT: A 306 MET cc_start: 0.8581 (ttm) cc_final: 0.8202 (ttt) REVERT: A 348 LEU cc_start: 0.9328 (mt) cc_final: 0.8827 (mt) REVERT: A 368 MET cc_start: 0.9574 (mmp) cc_final: 0.9297 (mmp) REVERT: A 507 LYS cc_start: 0.9728 (tptp) cc_final: 0.9520 (tppt) REVERT: A 508 GLU cc_start: 0.9716 (mp0) cc_final: 0.9321 (tp30) REVERT: A 574 ASP cc_start: 0.8571 (p0) cc_final: 0.7962 (p0) REVERT: A 609 MET cc_start: 0.8996 (mmm) cc_final: 0.8028 (mmm) REVERT: A 624 MET cc_start: 0.7481 (mmm) cc_final: 0.6444 (mmt) REVERT: A 633 MET cc_start: 0.8529 (mtp) cc_final: 0.7829 (tpp) REVERT: A 687 TYR cc_start: 0.9067 (m-80) cc_final: 0.8376 (m-80) REVERT: A 739 MET cc_start: 0.6884 (ttm) cc_final: 0.5102 (tmm) REVERT: B 166 MET cc_start: 0.9252 (mmm) cc_final: 0.8869 (mmm) REVERT: B 260 MET cc_start: 0.9161 (ttt) cc_final: 0.8319 (tpt) REVERT: B 269 MET cc_start: 0.8169 (ttm) cc_final: 0.7904 (ttm) REVERT: B 302 MET cc_start: 0.9662 (ptm) cc_final: 0.9402 (ptm) REVERT: B 306 MET cc_start: 0.9246 (tpp) cc_final: 0.8563 (tmm) REVERT: B 386 ASP cc_start: 0.9021 (t0) cc_final: 0.8520 (m-30) REVERT: B 624 MET cc_start: 0.8566 (mmm) cc_final: 0.8110 (mmt) REVERT: B 633 MET cc_start: 0.9167 (ptm) cc_final: 0.8583 (ppp) REVERT: B 643 GLN cc_start: 0.9446 (tm-30) cc_final: 0.9038 (tm-30) REVERT: B 692 MET cc_start: 0.8207 (mtp) cc_final: 0.7655 (mtp) REVERT: B 724 LEU cc_start: 0.8756 (mt) cc_final: 0.8463 (mt) REVERT: C 28 LYS cc_start: 0.9613 (ptmt) cc_final: 0.9363 (ptmm) REVERT: C 29 GLU cc_start: 0.8927 (mt-10) cc_final: 0.8412 (mt-10) REVERT: C 160 PHE cc_start: 0.8822 (m-10) cc_final: 0.8523 (m-80) REVERT: C 168 PHE cc_start: 0.9311 (t80) cc_final: 0.9059 (t80) REVERT: C 233 ASP cc_start: 0.8765 (p0) cc_final: 0.7925 (t0) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.1237 time to fit residues: 15.5744 Evaluate side-chains 76 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 146 optimal weight: 8.9990 chunk 93 optimal weight: 9.9990 chunk 122 optimal weight: 8.9990 chunk 144 optimal weight: 3.9990 chunk 3 optimal weight: 10.0000 chunk 52 optimal weight: 5.9990 chunk 126 optimal weight: 1.9990 chunk 75 optimal weight: 5.9990 chunk 109 optimal weight: 4.9990 chunk 90 optimal weight: 0.9990 chunk 121 optimal weight: 0.7980 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 717 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.048402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.036209 restraints weight = 131588.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.037387 restraints weight = 84711.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.038211 restraints weight = 61474.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.038789 restraints weight = 48452.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.039196 restraints weight = 40663.536| |-----------------------------------------------------------------------------| r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.6021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14194 Z= 0.193 Angle : 0.630 7.003 19480 Z= 0.328 Chirality : 0.040 0.164 2218 Planarity : 0.005 0.042 2319 Dihedral : 19.842 136.099 2427 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 19.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.21), residues: 1575 helix: 1.05 (0.19), residues: 760 sheet: -1.23 (0.34), residues: 225 loop : -1.03 (0.26), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 158 TYR 0.018 0.002 TYR A 771 PHE 0.024 0.002 PHE A 372 TRP 0.014 0.002 TRP B 202 HIS 0.009 0.001 HIS A 760 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.19 (14194) covalent geometry : angle 0.62958 / 0.33 (19480) hydrogen bonds : bond 0.04403 / 2.97 ( 699) hydrogen bonds : angle 4.92606 / 3.46 ( 1928) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2072.82 seconds wall clock time: 36 minutes 48.16 seconds (2208.16 seconds total)