Starting phenix.real_space_refine on Fri Jul 3 12:08:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7aib_11794/07_2026/7aib_11794.cif Found real_map, /net/cci-nas-00/data/ceres_data/7aib_11794/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/7aib_11794/07_2026/7aib_11794.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7aib_11794/07_2026/7aib_11794.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7aib_11794/07_2026/7aib_11794.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7aib_11794/07_2026/7aib_11794.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7aib_11794/07_2026/7aib_11794.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7aib_11794/07_2026/7aib_11794.map" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/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: 2.56, per 1000 atoms: 0.18 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: 1.12 Conformation dependent library (CDL) restraints added in 605.3 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: 1.64 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: 2.15 Time building geometry restraints manager: 1.46 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: 0.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 12.680 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.030 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:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.760 ------------------------------------------------------------------------------- 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 : 1.845 12.159 19480 Z= 1.350 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 1.84525 / 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 : 0.502 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: 0.1555 time to fit residues: 46.2440 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 : 0.479 ------------------------------------------------------------------------------- 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 B 214 ASN B 312 HIS B 468 ASN ** B 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 122 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.053676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.041122 restraints weight = 119359.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.042459 restraints weight = 77158.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.043390 restraints weight = 55873.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.044016 restraints weight = 43792.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.044515 restraints weight = 36564.663| |-----------------------------------------------------------------------------| r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.2867 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= 0.180 Angle : 0.734 9.997 19480 Z= 0.388 Chirality : 0.046 0.429 2218 Planarity : 0.006 0.105 2319 Dihedral : 20.034 157.753 2427 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.15 % Allowed : 3.19 % Favored : 96.66 % 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: -1.68 (0.20), residues: 1575 helix: -0.40 (0.18), residues: 749 sheet: -1.41 (0.33), residues: 216 loop : -1.79 (0.24), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.040 0.001 ARG A 697 TYR 0.022 0.002 TYR B 623 PHE 0.022 0.003 PHE C 168 TRP 0.016 0.002 TRP A 709 HIS 0.011 0.002 HIS B 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.18 (14194) covalent geometry : angle 0.73405 / 0.39 (19480) hydrogen bonds : bond 0.05872 / 3.90 ( 699) hydrogen bonds : angle 5.74314 / 4.11 ( 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 138 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 136 time to evaluate : 0.488 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: 0.9532 (tpt) cc_final: 0.9146 (tpt) REVERT: A 306 MET cc_start: 0.9040 (ttm) cc_final: 0.8612 (ttt) REVERT: A 313 MET cc_start: 0.9446 (ttm) cc_final: 0.9222 (ttp) REVERT: A 348 LEU cc_start: 0.9258 (mt) cc_final: 0.8505 (mt) REVERT: A 368 MET cc_start: 0.9507 (mmp) cc_final: 0.9067 (mmp) REVERT: A 490 MET cc_start: 0.8797 (mpp) cc_final: 0.8583 (mpp) REVERT: A 552 LEU cc_start: 0.9655 (mt) cc_final: 0.9221 (mt) REVERT: A 574 ASP cc_start: 0.8394 (p0) cc_final: 0.7783 (p0) REVERT: A 633 MET cc_start: 0.8091 (mtp) cc_final: 0.7743 (tpp) REVERT: A 687 TYR cc_start: 0.8895 (m-80) cc_final: 0.8148 (m-10) REVERT: A 739 MET cc_start: 0.8063 (ttm) cc_final: 0.7350 (ttm) REVERT: A 759 MET cc_start: 0.8934 (mmp) cc_final: 0.8550 (mpp) REVERT: B 215 LEU cc_start: 0.8903 (pp) cc_final: 0.8167 (pp) REVERT: B 260 MET cc_start: 0.8810 (ttt) cc_final: 0.7024 (tmm) REVERT: B 313 MET cc_start: 0.8946 (tmm) cc_final: 0.8649 (tmm) REVERT: B 386 ASP cc_start: 0.8941 (t0) cc_final: 0.8258 (m-30) REVERT: B 397 MET cc_start: 0.9003 (ttm) cc_final: 0.8726 (ttm) REVERT: B 490 MET cc_start: 0.9363 (mmp) cc_final: 0.9089 (mmm) REVERT: C 26 VAL cc_start: 0.9578 (t) cc_final: 0.9133 (t) REVERT: C 28 LYS cc_start: 0.9411 (tttt) cc_final: 0.9147 (ttmm) REVERT: C 29 GLU cc_start: 0.9042 (mt-10) cc_final: 0.8505 (pt0) REVERT: C 133 THR cc_start: 0.9343 (p) cc_final: 0.9109 (p) REVERT: C 160 PHE cc_start: 0.8895 (m-10) cc_final: 0.8586 (m-80) REVERT: C 233 ASP cc_start: 0.8894 (p0) cc_final: 0.7853 (t70) REVERT: C 255 TYR cc_start: 0.8257 (m-80) cc_final: 0.8002 (m-80) outliers start: 2 outliers final: 0 residues processed: 138 average time/residue: 0.1387 time to fit residues: 26.5322 Evaluate side-chains 89 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.428 ------------------------------------------------------------------------------- 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: 9.9990 chunk 24 optimal weight: 0.9980 chunk 120 optimal weight: 5.9990 chunk 44 optimal weight: 9.9990 chunk 144 optimal weight: 4.9990 chunk 147 optimal weight: 8.9990 chunk 118 optimal weight: 3.9990 chunk 5 optimal weight: 10.0000 chunk 47 optimal weight: 0.0070 chunk 66 optimal weight: 9.9990 chunk 121 optimal weight: 0.7980 overall best weight: 2.1602 ------------------------------------------------------------------------------- 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** ** B 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 468 ASN ** B 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 714 ASN ** C 198 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 = 0.3497 r_free = 0.3497 target = 0.052065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.039558 restraints weight = 123370.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.040830 restraints weight = 79705.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.041716 restraints weight = 57669.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.042349 restraints weight = 45242.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.042802 restraints weight = 37645.935| |-----------------------------------------------------------------------------| r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.3592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14194 Z= 0.185 Angle : 0.665 7.992 19480 Z= 0.350 Chirality : 0.042 0.199 2218 Planarity : 0.005 0.065 2319 Dihedral : 20.095 152.034 2427 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % 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: -1.03 (0.20), residues: 1575 helix: 0.21 (0.18), residues: 759 sheet: -1.14 (0.34), residues: 214 loop : -1.58 (0.24), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG C 237 TYR 0.027 0.002 TYR A 509 PHE 0.037 0.002 PHE A 725 TRP 0.011 0.002 TRP B 202 HIS 0.006 0.001 HIS B 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.18 (14194) covalent geometry : angle 0.66523 / 0.35 (19480) hydrogen bonds : bond 0.05153 / 3.43 ( 699) hydrogen bonds : angle 5.41717 / 3.84 ( 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 109 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.520 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: 0.9600 (tpt) cc_final: 0.9240 (tpt) REVERT: A 306 MET cc_start: 0.8964 (ttm) cc_final: 0.8500 (ttt) REVERT: A 348 LEU cc_start: 0.9587 (mt) cc_final: 0.9141 (mt) REVERT: A 368 MET cc_start: 0.9475 (mmp) cc_final: 0.9115 (mmp) REVERT: A 574 ASP cc_start: 0.8481 (p0) cc_final: 0.7794 (p0) REVERT: A 617 MET cc_start: 0.7006 (mpp) cc_final: 0.6762 (ttm) REVERT: A 633 MET cc_start: 0.8216 (mtp) cc_final: 0.7684 (tpp) REVERT: A 687 TYR cc_start: 0.8921 (m-80) cc_final: 0.8226 (m-80) REVERT: A 739 MET cc_start: 0.7993 (ttm) cc_final: 0.7591 (ttm) REVERT: A 759 MET cc_start: 0.9051 (mmp) cc_final: 0.8525 (mpp) REVERT: B 166 MET cc_start: 0.9052 (mmm) cc_final: 0.8847 (mmm) REVERT: B 260 MET cc_start: 0.8453 (ttt) cc_final: 0.8221 (tmm) REVERT: B 269 MET cc_start: 0.8069 (ttm) cc_final: 0.7447 (ttm) REVERT: B 302 MET cc_start: 0.9596 (ptm) cc_final: 0.9363 (ptm) REVERT: B 306 MET cc_start: 0.9183 (tpp) cc_final: 0.8409 (tmm) REVERT: B 313 MET cc_start: 0.9106 (tmm) cc_final: 0.8738 (tmm) REVERT: B 386 ASP cc_start: 0.9012 (t0) cc_final: 0.8346 (m-30) REVERT: B 397 MET cc_start: 0.9002 (ttm) cc_final: 0.8628 (ttm) REVERT: B 490 MET cc_start: 0.9415 (mmp) cc_final: 0.9166 (mmm) REVERT: B 574 ASP cc_start: 0.8981 (t70) cc_final: 0.8731 (t0) REVERT: B 624 MET cc_start: 0.9003 (mtp) cc_final: 0.8610 (mtp) REVERT: B 692 MET cc_start: 0.8500 (mtp) cc_final: 0.8094 (mtp) REVERT: C 28 LYS cc_start: 0.9402 (tttt) cc_final: 0.9150 (ttmm) REVERT: C 29 GLU cc_start: 0.9059 (mt-10) cc_final: 0.8577 (mt-10) REVERT: C 160 PHE cc_start: 0.8898 (m-10) cc_final: 0.8589 (m-80) REVERT: C 168 PHE cc_start: 0.9199 (t80) cc_final: 0.8969 (t80) REVERT: C 233 ASP cc_start: 0.8967 (p0) cc_final: 0.7901 (t0) outliers start: 0 outliers final: 0 residues processed: 109 average time/residue: 0.1502 time to fit residues: 22.9771 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 : 0.508 ------------------------------------------------------------------------------- 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: 6.9990 chunk 107 optimal weight: 7.9990 chunk 42 optimal weight: 9.9990 chunk 128 optimal weight: 10.0000 chunk 140 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 12 optimal weight: 9.9990 chunk 149 optimal weight: 7.9990 chunk 51 optimal weight: 0.3980 chunk 119 optimal weight: 2.9990 chunk 48 optimal weight: 10.0000 overall best weight: 3.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 543 GLN ** A 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 GLN B 242 GLN B 289 ASN B 332 GLN B 544 GLN ** B 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 682 HIS B 717 ASN ** B 728 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 198 GLN ** C 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.049283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.036687 restraints weight = 130964.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.037849 restraints weight = 86042.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.038690 restraints weight = 63114.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.039254 restraints weight = 50050.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.039655 restraints weight = 42336.319| |-----------------------------------------------------------------------------| r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.4555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 14194 Z= 0.291 Angle : 0.804 10.292 19480 Z= 0.411 Chirality : 0.045 0.301 2218 Planarity : 0.006 0.062 2319 Dihedral : 20.168 148.094 2427 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 21.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 0.15 % Allowed : 3.26 % Favored : 96.59 % 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: -0.98 (0.20), residues: 1575 helix: 0.33 (0.18), residues: 768 sheet: -1.38 (0.32), residues: 249 loop : -1.57 (0.25), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 158 TYR 0.023 0.003 TYR C 124 PHE 0.021 0.003 PHE C 151 TRP 0.013 0.002 TRP B 202 HIS 0.010 0.002 HIS B 760 Details of bonding type rmsd/Z covalent geometry : bond 0.00590 / 0.29 (14194) covalent geometry : angle 0.80400 / 0.41 (19480) hydrogen bonds : bond 0.05787 / 3.86 ( 699) hydrogen bonds : angle 5.34537 / 3.78 ( 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 107 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 105 time to evaluate : 0.520 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: 0.9697 (tpt) cc_final: 0.9299 (tpt) REVERT: A 187 MET cc_start: 0.9037 (mmp) cc_final: 0.8680 (mmm) REVERT: A 306 MET cc_start: 0.8897 (ttm) cc_final: 0.8474 (ttt) REVERT: A 368 MET cc_start: 0.9537 (mmp) cc_final: 0.9205 (mmp) REVERT: A 397 MET cc_start: 0.8826 (mtm) cc_final: 0.8406 (mtt) REVERT: A 574 ASP cc_start: 0.8617 (p0) cc_final: 0.7893 (p0) REVERT: A 617 MET cc_start: 0.7159 (mpp) cc_final: 0.6865 (ttp) REVERT: A 633 MET cc_start: 0.8303 (mtp) cc_final: 0.7768 (tpp) REVERT: A 687 TYR cc_start: 0.8972 (m-80) cc_final: 0.8482 (m-10) REVERT: B 166 MET cc_start: 0.9255 (mmm) cc_final: 0.8936 (mmm) REVERT: B 260 MET cc_start: 0.8744 (ttt) cc_final: 0.8290 (tmm) REVERT: B 269 MET cc_start: 0.7813 (ttm) cc_final: 0.7514 (ttm) REVERT: B 302 MET cc_start: 0.9683 (ptm) cc_final: 0.9335 (ptm) REVERT: B 368 MET cc_start: 0.9657 (ptm) cc_final: 0.9330 (ptt) REVERT: B 386 ASP cc_start: 0.9007 (t0) cc_final: 0.8359 (m-30) REVERT: B 552 LEU cc_start: 0.9563 (mt) cc_final: 0.9341 (tt) REVERT: B 692 MET cc_start: 0.8556 (mtp) cc_final: 0.8164 (mtp) REVERT: C 28 LYS cc_start: 0.9310 (tttt) cc_final: 0.9099 (ttmm) REVERT: C 29 GLU cc_start: 0.9015 (mt-10) cc_final: 0.8533 (mt-10) REVERT: C 160 PHE cc_start: 0.9111 (m-10) cc_final: 0.8741 (m-80) REVERT: C 168 PHE cc_start: 0.9346 (t80) cc_final: 0.9053 (t80) REVERT: C 227 ILE cc_start: 0.8301 (OUTLIER) cc_final: 0.8027 (tt) REVERT: C 233 ASP cc_start: 0.9090 (p0) cc_final: 0.8327 (t70) outliers start: 2 outliers final: 0 residues processed: 106 average time/residue: 0.1519 time to fit residues: 22.6186 Evaluate side-chains 82 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 81 time to evaluate : 0.512 ------------------------------------------------------------------------------- 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: 7.9990 chunk 119 optimal weight: 3.9990 chunk 33 optimal weight: 10.0000 chunk 128 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 145 optimal weight: 1.9990 chunk 159 optimal weight: 30.0000 chunk 122 optimal weight: 0.6980 chunk 147 optimal weight: 6.9990 chunk 151 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 171 GLN A 211 GLN ** A 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 289 ASN B 481 GLN ** B 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 223 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.050369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.037782 restraints weight = 123420.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.039082 restraints weight = 78349.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.039988 restraints weight = 55950.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.040592 restraints weight = 43465.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.041065 restraints weight = 36144.304| |-----------------------------------------------------------------------------| r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.4645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 14194 Z= 0.157 Angle : 0.618 16.540 19480 Z= 0.322 Chirality : 0.041 0.169 2218 Planarity : 0.005 0.048 2319 Dihedral : 20.098 145.642 2427 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 16.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.15 % Allowed : 1.37 % Favored : 98.48 % 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: -0.59 (0.21), residues: 1575 helix: 0.72 (0.18), residues: 762 sheet: -1.23 (0.33), residues: 227 loop : -1.45 (0.25), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 158 TYR 0.015 0.002 TYR A 509 PHE 0.017 0.002 PHE A 155 TRP 0.014 0.001 TRP B 202 HIS 0.005 0.001 HIS A 760 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.16 (14194) covalent geometry : angle 0.61808 / 0.32 (19480) hydrogen bonds : bond 0.04375 / 2.91 ( 699) hydrogen bonds : angle 5.11163 / 3.63 ( 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 100 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 98 time to evaluate : 0.517 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: A 166 MET cc_start: 0.9640 (tpt) cc_final: 0.9198 (tpt) REVERT: A 260 MET cc_start: 0.9033 (tmm) cc_final: 0.8632 (tmm) REVERT: A 306 MET cc_start: 0.8808 (ttm) cc_final: 0.8397 (ttt) REVERT: A 368 MET cc_start: 0.9462 (mmp) cc_final: 0.9207 (mmm) REVERT: A 397 MET cc_start: 0.8761 (mtm) cc_final: 0.8469 (mtt) REVERT: A 449 ARG cc_start: 0.9367 (mtm180) cc_final: 0.9157 (ptt-90) REVERT: A 574 ASP cc_start: 0.8607 (p0) cc_final: 0.7974 (p0) REVERT: A 617 MET cc_start: 0.7224 (mpp) cc_final: 0.6760 (ttm) REVERT: A 633 MET cc_start: 0.8288 (mtp) cc_final: 0.7883 (tpp) REVERT: A 687 TYR cc_start: 0.8970 (m-80) cc_final: 0.8353 (m-80) REVERT: A 739 MET cc_start: 0.7015 (ttm) cc_final: 0.6701 (ttm) REVERT: A 759 MET cc_start: 0.8969 (mmp) cc_final: 0.8750 (mmp) REVERT: B 166 MET cc_start: 0.9192 (mmm) cc_final: 0.8836 (mmm) REVERT: B 269 MET cc_start: 0.8274 (ttm) cc_final: 0.7856 (ttm) REVERT: B 302 MET cc_start: 0.9669 (ptm) cc_final: 0.9377 (ptm) REVERT: B 306 MET cc_start: 0.9263 (tpp) cc_final: 0.8494 (tmm) REVERT: B 313 MET cc_start: 0.9024 (tmm) cc_final: 0.8789 (tmm) REVERT: B 386 ASP cc_start: 0.9003 (t0) cc_final: 0.8404 (m-30) REVERT: B 674 MET cc_start: 0.8258 (mmt) cc_final: 0.7822 (mmp) REVERT: B 692 MET cc_start: 0.8610 (mtp) cc_final: 0.8294 (mtp) REVERT: C 29 GLU cc_start: 0.8932 (mt-10) cc_final: 0.8404 (mt-10) REVERT: C 160 PHE cc_start: 0.9172 (m-10) cc_final: 0.8827 (m-80) REVERT: C 168 PHE cc_start: 0.9188 (t80) cc_final: 0.8935 (t80) REVERT: C 233 ASP cc_start: 0.8884 (p0) cc_final: 0.8181 (t70) REVERT: C 316 ARG cc_start: 0.9284 (pmt170) cc_final: 0.8742 (ttp80) outliers start: 2 outliers final: 0 residues processed: 99 average time/residue: 0.1484 time to fit residues: 21.7703 Evaluate side-chains 80 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.397 ------------------------------------------------------------------------------- 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: 5.9990 chunk 40 optimal weight: 0.9990 chunk 130 optimal weight: 1.9990 chunk 151 optimal weight: 8.9990 chunk 20 optimal weight: 5.9990 chunk 74 optimal weight: 5.9990 chunk 94 optimal weight: 10.0000 chunk 14 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 chunk 157 optimal weight: 4.9990 chunk 46 optimal weight: 0.0980 overall best weight: 2.8188 ------------------------------------------------------------------------------- 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 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 289 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.049288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.036866 restraints weight = 125109.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.038066 restraints weight = 80745.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.038927 restraints weight = 58552.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.039525 restraints weight = 45784.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.039942 restraints weight = 38199.495| |-----------------------------------------------------------------------------| r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.4987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 14194 Z= 0.214 Angle : 0.645 12.483 19480 Z= 0.337 Chirality : 0.041 0.186 2218 Planarity : 0.005 0.046 2319 Dihedral : 20.030 143.656 2427 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 17.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % 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: -0.44 (0.21), residues: 1575 helix: 0.81 (0.18), residues: 764 sheet: -1.16 (0.33), residues: 232 loop : -1.33 (0.25), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 158 TYR 0.021 0.002 TYR C 257 PHE 0.017 0.002 PHE B 725 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 0.00436 / 0.21 (14194) covalent geometry : angle 0.64502 / 0.34 (19480) hydrogen bonds : bond 0.04858 / 3.24 ( 699) hydrogen bonds : angle 5.09016 / 3.62 ( 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 91 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.540 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: 0.9657 (tpt) cc_final: 0.9205 (tpt) REVERT: A 260 MET cc_start: 0.9172 (tmm) cc_final: 0.8784 (tmm) REVERT: A 306 MET cc_start: 0.8565 (ttm) cc_final: 0.8260 (ttt) REVERT: A 368 MET cc_start: 0.9481 (mmp) cc_final: 0.9197 (mmm) REVERT: A 397 MET cc_start: 0.8717 (mtm) cc_final: 0.8294 (mtp) REVERT: A 449 ARG cc_start: 0.9337 (mtm180) cc_final: 0.9090 (ptt-90) REVERT: A 490 MET cc_start: 0.8841 (mpp) cc_final: 0.8611 (mpp) REVERT: A 574 ASP cc_start: 0.8691 (p0) cc_final: 0.7978 (p0) REVERT: A 617 MET cc_start: 0.7294 (mpp) cc_final: 0.7012 (ttm) REVERT: A 633 MET cc_start: 0.8399 (mtp) cc_final: 0.8003 (tpp) REVERT: A 687 TYR cc_start: 0.9030 (m-80) cc_final: 0.8413 (m-80) REVERT: A 759 MET cc_start: 0.8977 (mmp) cc_final: 0.8738 (mmp) REVERT: B 166 MET cc_start: 0.9253 (mmm) cc_final: 0.8869 (mmm) REVERT: B 269 MET cc_start: 0.7916 (ttm) cc_final: 0.7633 (ttm) REVERT: B 302 MET cc_start: 0.9677 (ptm) cc_final: 0.9363 (ptm) REVERT: B 306 MET cc_start: 0.9259 (tpp) cc_final: 0.8520 (tmm) REVERT: B 313 MET cc_start: 0.9058 (tmm) cc_final: 0.8821 (tmm) REVERT: B 386 ASP cc_start: 0.9099 (t0) cc_final: 0.8453 (m-30) REVERT: B 624 MET cc_start: 0.9165 (mtp) cc_final: 0.8686 (mtp) REVERT: B 674 MET cc_start: 0.8349 (mmt) cc_final: 0.7779 (mmp) REVERT: B 692 MET cc_start: 0.8610 (mtp) cc_final: 0.7978 (mtp) REVERT: C 29 GLU cc_start: 0.8970 (mt-10) cc_final: 0.8451 (mt-10) REVERT: C 160 PHE cc_start: 0.8712 (m-10) cc_final: 0.8463 (m-80) REVERT: C 168 PHE cc_start: 0.9246 (t80) cc_final: 0.8982 (t80) REVERT: C 233 ASP cc_start: 0.8876 (p0) cc_final: 0.8194 (t70) REVERT: C 316 ARG cc_start: 0.9279 (pmt170) cc_final: 0.8708 (ttp80) outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.1545 time to fit residues: 19.9868 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 : 0.558 ------------------------------------------------------------------------------- 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: 0.7980 chunk 113 optimal weight: 0.8980 chunk 20 optimal weight: 7.9990 chunk 34 optimal weight: 2.9990 chunk 144 optimal weight: 0.0370 chunk 155 optimal weight: 0.0470 chunk 33 optimal weight: 9.9990 chunk 57 optimal weight: 0.7980 chunk 1 optimal weight: 10.0000 chunk 158 optimal weight: 20.0000 chunk 109 optimal weight: 5.9990 overall best weight: 0.5156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 289 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 = 0.3465 r_free = 0.3465 target = 0.050572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.038101 restraints weight = 121465.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.039386 restraints weight = 76586.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.040303 restraints weight = 54588.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.040951 restraints weight = 42300.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.041430 restraints weight = 34802.201| |-----------------------------------------------------------------------------| r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.5006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 14194 Z= 0.125 Angle : 0.600 14.190 19480 Z= 0.310 Chirality : 0.040 0.178 2218 Planarity : 0.005 0.103 2319 Dihedral : 19.983 139.896 2427 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % 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: 1.00 (0.19), residues: 753 sheet: -1.14 (0.32), residues: 237 loop : -1.14 (0.26), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG A 379 TYR 0.016 0.002 TYR C 255 PHE 0.033 0.002 PHE A 372 TRP 0.014 0.001 TRP B 202 HIS 0.004 0.001 HIS B 728 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (14194) covalent geometry : angle 0.59963 / 0.31 (19480) hydrogen bonds : bond 0.03876 / 2.59 ( 699) hydrogen bonds : angle 4.91913 / 3.48 ( 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 96 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.471 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: 0.9608 (tpt) cc_final: 0.9153 (tpt) REVERT: A 187 MET cc_start: 0.9299 (mmp) cc_final: 0.9028 (tpp) REVERT: A 260 MET cc_start: 0.9133 (tmm) cc_final: 0.8686 (tmm) REVERT: A 306 MET cc_start: 0.8608 (ttm) cc_final: 0.8252 (ttt) REVERT: A 313 MET cc_start: 0.9429 (ttp) cc_final: 0.9075 (mmt) REVERT: A 368 MET cc_start: 0.9579 (mmp) cc_final: 0.9324 (mmm) REVERT: A 449 ARG cc_start: 0.9300 (mtm180) cc_final: 0.9052 (ptt-90) REVERT: A 490 MET cc_start: 0.8736 (mpp) cc_final: 0.8478 (mpp) REVERT: A 507 LYS cc_start: 0.9734 (tptp) cc_final: 0.9530 (tppt) REVERT: A 574 ASP cc_start: 0.8495 (p0) cc_final: 0.7788 (p0) REVERT: A 609 MET cc_start: 0.8222 (mmm) cc_final: 0.7063 (mmm) REVERT: A 617 MET cc_start: 0.7212 (mpp) cc_final: 0.7009 (ttm) REVERT: A 633 MET cc_start: 0.8281 (mtp) cc_final: 0.7861 (tpp) REVERT: A 687 TYR cc_start: 0.9070 (m-80) cc_final: 0.8411 (m-80) REVERT: A 759 MET cc_start: 0.8835 (mmp) cc_final: 0.8617 (mmp) REVERT: A 775 VAL cc_start: 0.9060 (t) cc_final: 0.8764 (t) REVERT: B 166 MET cc_start: 0.9216 (mmm) cc_final: 0.8891 (mmm) REVERT: B 269 MET cc_start: 0.8163 (ttm) cc_final: 0.7509 (ttm) REVERT: B 289 ASN cc_start: 0.8240 (m-40) cc_final: 0.7879 (t0) REVERT: B 302 MET cc_start: 0.9686 (ptm) cc_final: 0.9440 (ptm) REVERT: B 306 MET cc_start: 0.9254 (tpp) cc_final: 0.8490 (tmm) REVERT: B 313 MET cc_start: 0.9065 (tmm) cc_final: 0.8840 (tmm) REVERT: B 386 ASP cc_start: 0.9103 (t0) cc_final: 0.8544 (m-30) REVERT: B 453 ARG cc_start: 0.9688 (tpt90) cc_final: 0.9460 (tpm170) REVERT: B 624 MET cc_start: 0.9137 (mtp) cc_final: 0.8868 (mmm) REVERT: B 692 MET cc_start: 0.8499 (mtp) cc_final: 0.8194 (mtp) REVERT: B 759 MET cc_start: 0.8335 (mpp) cc_final: 0.7907 (mpp) REVERT: C 29 GLU cc_start: 0.8922 (mt-10) cc_final: 0.8327 (pt0) REVERT: C 160 PHE cc_start: 0.8583 (m-10) cc_final: 0.8323 (m-80) REVERT: C 168 PHE cc_start: 0.9233 (t80) cc_final: 0.9009 (t80) REVERT: C 233 ASP cc_start: 0.8836 (p0) cc_final: 0.8138 (t70) outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.1502 time to fit residues: 20.5184 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 : 0.600 ------------------------------------------------------------------------------- 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: 10.0000 chunk 119 optimal weight: 0.7980 chunk 143 optimal weight: 3.9990 chunk 3 optimal weight: 0.6980 chunk 77 optimal weight: 3.9990 chunk 62 optimal weight: 0.2980 chunk 157 optimal weight: 5.9990 chunk 98 optimal weight: 4.9990 chunk 124 optimal weight: 0.7980 chunk 110 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- 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** B 289 ASN B 312 HIS B 370 HIS ** B 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.050613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.038155 restraints weight = 128416.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.039362 restraints weight = 83487.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.040196 restraints weight = 60649.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.040789 restraints weight = 47980.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.041196 restraints weight = 40251.592| |-----------------------------------------------------------------------------| r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.5187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14194 Z= 0.139 Angle : 0.594 12.262 19480 Z= 0.308 Chirality : 0.040 0.194 2218 Planarity : 0.004 0.067 2319 Dihedral : 19.907 136.802 2427 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 15.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.08 % Allowed : 0.68 % Favored : 99.24 % 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: -0.10 (0.21), residues: 1575 helix: 1.09 (0.19), residues: 754 sheet: -1.16 (0.33), residues: 233 loop : -1.03 (0.26), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 379 TYR 0.023 0.002 TYR C 255 PHE 0.036 0.002 PHE A 725 TRP 0.013 0.001 TRP B 202 HIS 0.003 0.001 HIS B 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 (14194) covalent geometry : angle 0.59397 / 0.31 (19480) hydrogen bonds : bond 0.03984 / 2.66 ( 699) hydrogen bonds : angle 4.83466 / 3.43 ( 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 88 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 87 time to evaluate : 0.526 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: 0.9605 (tpt) cc_final: 0.9148 (tpt) REVERT: A 260 MET cc_start: 0.9185 (tmm) cc_final: 0.8555 (tmm) REVERT: A 306 MET cc_start: 0.8464 (ttm) cc_final: 0.8131 (ttt) REVERT: A 313 MET cc_start: 0.9366 (ttp) cc_final: 0.9077 (mmt) REVERT: A 449 ARG cc_start: 0.9292 (mtm180) cc_final: 0.9060 (ptt-90) REVERT: A 490 MET cc_start: 0.8744 (mpp) cc_final: 0.8490 (mpp) REVERT: A 507 LYS cc_start: 0.9718 (tptp) cc_final: 0.9504 (tppt) REVERT: A 508 GLU cc_start: 0.9666 (mp0) cc_final: 0.9230 (tp30) REVERT: A 574 ASP cc_start: 0.8460 (p0) cc_final: 0.7768 (p0) REVERT: A 609 MET cc_start: 0.8407 (mmm) cc_final: 0.7297 (mmm) REVERT: A 617 MET cc_start: 0.7329 (mpp) cc_final: 0.7116 (ttm) REVERT: A 633 MET cc_start: 0.8322 (mtp) cc_final: 0.7874 (tpp) REVERT: A 687 TYR cc_start: 0.9007 (m-80) cc_final: 0.8355 (m-80) REVERT: A 759 MET cc_start: 0.8830 (mmp) cc_final: 0.8606 (mmp) REVERT: A 775 VAL cc_start: 0.9076 (t) cc_final: 0.8780 (t) REVERT: B 166 MET cc_start: 0.9227 (mmm) cc_final: 0.8909 (mmm) REVERT: B 269 MET cc_start: 0.8073 (ttm) cc_final: 0.7411 (ttm) REVERT: B 289 ASN cc_start: 0.8041 (OUTLIER) cc_final: 0.7738 (t0) REVERT: B 302 MET cc_start: 0.9697 (ptm) cc_final: 0.9450 (ptm) REVERT: B 306 MET cc_start: 0.9333 (tpp) cc_final: 0.8555 (tmm) REVERT: B 386 ASP cc_start: 0.9042 (t0) cc_final: 0.8518 (m-30) REVERT: B 609 MET cc_start: 0.8844 (mmm) cc_final: 0.8491 (mmm) REVERT: B 624 MET cc_start: 0.9112 (mtp) cc_final: 0.8798 (mmm) REVERT: B 692 MET cc_start: 0.8388 (mtp) cc_final: 0.8137 (mtp) REVERT: B 759 MET cc_start: 0.8321 (mpp) cc_final: 0.7858 (mpp) REVERT: C 29 GLU cc_start: 0.8949 (mt-10) cc_final: 0.8303 (pt0) REVERT: C 160 PHE cc_start: 0.8606 (m-10) cc_final: 0.8342 (m-80) REVERT: C 233 ASP cc_start: 0.8803 (p0) cc_final: 0.8153 (t70) outliers start: 1 outliers final: 0 residues processed: 87 average time/residue: 0.1470 time to fit residues: 18.2727 Evaluate side-chains 75 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 74 time to evaluate : 0.528 ------------------------------------------------------------------------------- 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: 0.9980 chunk 22 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 chunk 35 optimal weight: 5.9990 chunk 67 optimal weight: 10.0000 chunk 118 optimal weight: 0.7980 chunk 122 optimal weight: 10.0000 chunk 20 optimal weight: 6.9990 chunk 114 optimal weight: 6.9990 chunk 79 optimal weight: 8.9990 chunk 161 optimal weight: 30.0000 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 339 GLN A 381 GLN ** A 557 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 122 GLN ** 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 = 0.3418 r_free = 0.3418 target = 0.049017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.036677 restraints weight = 131378.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.037840 restraints weight = 85118.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.038657 restraints weight = 61958.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.039236 restraints weight = 49079.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.039614 restraints weight = 41209.067| |-----------------------------------------------------------------------------| r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.5543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 14194 Z= 0.213 Angle : 0.667 14.546 19480 Z= 0.347 Chirality : 0.042 0.280 2218 Planarity : 0.005 0.044 2319 Dihedral : 19.951 136.815 2427 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 19.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % 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: 0.97 (0.19), residues: 763 sheet: -1.19 (0.32), residues: 239 loop : -1.07 (0.27), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 48 TYR 0.024 0.002 TYR C 255 PHE 0.024 0.002 PHE A 725 TRP 0.012 0.002 TRP B 202 HIS 0.010 0.001 HIS A 760 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.21 (14194) covalent geometry : angle 0.66681 / 0.35 (19480) hydrogen bonds : bond 0.04745 / 3.21 ( 699) hydrogen bonds : angle 4.96122 / 3.52 ( 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 82 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.530 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: 0.9641 (tpt) cc_final: 0.9178 (tpt) REVERT: A 306 MET cc_start: 0.8478 (ttm) cc_final: 0.8141 (ttt) REVERT: A 313 MET cc_start: 0.9396 (ttp) cc_final: 0.9079 (mmt) REVERT: A 368 MET cc_start: 0.9576 (mmp) cc_final: 0.9333 (mmp) REVERT: A 507 LYS cc_start: 0.9715 (tptp) cc_final: 0.9503 (tppt) REVERT: A 508 GLU cc_start: 0.9666 (mp0) cc_final: 0.9264 (tp30) REVERT: A 574 ASP cc_start: 0.8406 (p0) cc_final: 0.7699 (p0) REVERT: A 609 MET cc_start: 0.8646 (mmm) cc_final: 0.7552 (mmm) REVERT: A 633 MET cc_start: 0.8632 (mtp) cc_final: 0.8014 (tpp) REVERT: A 687 TYR cc_start: 0.8989 (m-80) cc_final: 0.8265 (m-80) REVERT: B 166 MET cc_start: 0.9185 (mmm) cc_final: 0.8912 (mmm) REVERT: B 269 MET cc_start: 0.7560 (ttm) cc_final: 0.7246 (ttm) REVERT: B 302 MET cc_start: 0.9697 (ptm) cc_final: 0.9427 (ptm) REVERT: B 306 MET cc_start: 0.9350 (tpp) cc_final: 0.8583 (tmm) REVERT: B 386 ASP cc_start: 0.9052 (t0) cc_final: 0.8488 (m-30) REVERT: B 692 MET cc_start: 0.8387 (mtp) cc_final: 0.7936 (mtp) REVERT: B 759 MET cc_start: 0.8227 (mpp) cc_final: 0.7887 (mpp) REVERT: C 26 VAL cc_start: 0.9460 (t) cc_final: 0.9162 (t) REVERT: C 29 GLU cc_start: 0.8965 (mt-10) cc_final: 0.8436 (mt-10) REVERT: C 160 PHE cc_start: 0.8684 (m-10) cc_final: 0.8426 (m-80) REVERT: C 168 PHE cc_start: 0.9357 (t80) cc_final: 0.9007 (t80) REVERT: C 233 ASP cc_start: 0.8838 (p0) cc_final: 0.8145 (t0) outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1554 time to fit residues: 17.9917 Evaluate side-chains 69 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.472 ------------------------------------------------------------------------------- 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: 0.9980 chunk 72 optimal weight: 1.9990 chunk 103 optimal weight: 8.9990 chunk 25 optimal weight: 0.5980 chunk 39 optimal weight: 0.7980 chunk 138 optimal weight: 6.9990 chunk 95 optimal weight: 9.9990 chunk 120 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 88 optimal weight: 4.9990 chunk 145 optimal weight: 0.2980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 381 GLN ** A 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 679 ASN 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.050559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.038099 restraints weight = 127663.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.039333 restraints weight = 82148.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.040194 restraints weight = 59431.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.040780 restraints weight = 46772.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.041208 restraints weight = 39275.197| |-----------------------------------------------------------------------------| r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.5536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14194 Z= 0.122 Angle : 0.598 12.261 19480 Z= 0.310 Chirality : 0.041 0.305 2218 Planarity : 0.004 0.058 2319 Dihedral : 19.926 132.673 2427 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 14.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 1.08 (0.19), residues: 760 sheet: -1.33 (0.32), residues: 232 loop : -1.00 (0.26), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 379 TYR 0.020 0.002 TYR C 255 PHE 0.024 0.002 PHE A 725 TRP 0.013 0.001 TRP B 202 HIS 0.004 0.001 HIS A 728 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (14194) covalent geometry : angle 0.59786 / 0.31 (19480) hydrogen bonds : bond 0.03755 / 2.53 ( 699) hydrogen bonds : angle 4.79279 / 3.38 ( 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 84 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.467 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: 0.9588 (tpt) cc_final: 0.9137 (tpt) REVERT: A 306 MET cc_start: 0.8443 (ttm) cc_final: 0.8071 (ttt) REVERT: A 313 MET cc_start: 0.9355 (ttp) cc_final: 0.9087 (mmt) REVERT: A 508 GLU cc_start: 0.9662 (mp0) cc_final: 0.9241 (tp30) REVERT: A 574 ASP cc_start: 0.8450 (p0) cc_final: 0.7760 (p0) REVERT: A 609 MET cc_start: 0.8522 (mmm) cc_final: 0.7371 (mmm) REVERT: A 633 MET cc_start: 0.8518 (mtp) cc_final: 0.7846 (tpp) REVERT: A 687 TYR cc_start: 0.8977 (m-80) cc_final: 0.8335 (m-80) REVERT: A 692 MET cc_start: 0.8233 (ppp) cc_final: 0.7947 (ppp) REVERT: B 166 MET cc_start: 0.9194 (mmm) cc_final: 0.8925 (mmm) REVERT: B 269 MET cc_start: 0.7962 (ttm) cc_final: 0.7202 (ttm) REVERT: B 302 MET cc_start: 0.9669 (ptm) cc_final: 0.9424 (ptm) REVERT: B 306 MET cc_start: 0.9255 (tpp) cc_final: 0.8574 (tmm) REVERT: B 386 ASP cc_start: 0.9037 (t0) cc_final: 0.8561 (m-30) REVERT: B 692 MET cc_start: 0.8255 (mtp) cc_final: 0.8030 (mtp) REVERT: B 759 MET cc_start: 0.8771 (mpp) cc_final: 0.8482 (mpp) REVERT: C 29 GLU cc_start: 0.8878 (mt-10) cc_final: 0.8249 (pt0) REVERT: C 160 PHE cc_start: 0.8693 (m-10) cc_final: 0.8426 (m-80) REVERT: C 168 PHE cc_start: 0.9345 (t80) cc_final: 0.8940 (t80) REVERT: C 233 ASP cc_start: 0.8808 (p0) cc_final: 0.8007 (t0) outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.1429 time to fit residues: 17.3190 Evaluate side-chains 70 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.444 ------------------------------------------------------------------------------- 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: 10.0000 chunk 93 optimal weight: 5.9990 chunk 122 optimal weight: 10.0000 chunk 144 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 52 optimal weight: 7.9990 chunk 126 optimal weight: 3.9990 chunk 75 optimal weight: 6.9990 chunk 109 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 121 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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** B 276 ASN B 370 HIS B 483 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.048389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.036098 restraints weight = 132156.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.037247 restraints weight = 85486.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.038052 restraints weight = 62312.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.038610 restraints weight = 49312.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.039028 restraints weight = 41511.956| |-----------------------------------------------------------------------------| r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.5882 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= 0.217 Angle : 0.670 12.284 19480 Z= 0.347 Chirality : 0.042 0.271 2218 Planarity : 0.005 0.046 2319 Dihedral : 19.944 134.042 2427 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 20.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -0.18 (0.21), residues: 1575 helix: 0.96 (0.19), residues: 762 sheet: -1.29 (0.32), residues: 249 loop : -0.94 (0.27), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 158 TYR 0.025 0.002 TYR C 255 PHE 0.019 0.002 PHE A 725 TRP 0.013 0.002 TRP B 202 HIS 0.011 0.002 HIS A 760 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.22 (14194) covalent geometry : angle 0.67014 / 0.35 (19480) hydrogen bonds : bond 0.04836 / 3.28 ( 699) hydrogen bonds : angle 4.95506 / 3.49 ( 1928) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2210.54 seconds wall clock time: 39 minutes 11.11 seconds (2351.11 seconds total)