Starting phenix.real_space_refine on Fri Feb 6 04:45:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9oop_70668/02_2026/9oop_70668.cif Found real_map, /net/cci-nas-00/data/ceres_data/9oop_70668/02_2026/9oop_70668.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9oop_70668/02_2026/9oop_70668.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9oop_70668/02_2026/9oop_70668.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9oop_70668/02_2026/9oop_70668.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9oop_70668/02_2026/9oop_70668.map" } resolution = 3.73 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= 0.034 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 118 5.16 5 C 14216 2.51 5 N 3868 2.21 5 O 4256 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22458 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 710, 5647 Classifications: {'peptide': 710} Link IDs: {'PTRANS': 23, 'TRANS': 686} Chain breaks: 1 Chain: "B" Number of atoms: 5582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 702, 5582 Classifications: {'peptide': 702} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 679} Chain breaks: 1 Chain: "C" Number of atoms: 5582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 702, 5582 Classifications: {'peptide': 702} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 21, 'TRANS': 678} Chain breaks: 1 Chain: "D" Number of atoms: 5647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 710, 5647 Classifications: {'peptide': 710} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 686} Chain breaks: 1 Time building chain proxies: 4.68, per 1000 atoms: 0.21 Number of scatterers: 22458 At special positions: 0 Unit cell: (198.925, 138.452, 171.871, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 118 16.00 O 4256 8.00 N 3868 7.00 C 14216 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 83 " - pdb=" SG CYS A 355 " distance=2.03 Simple disulfide: pdb=" SG CYS A 99 " - pdb=" SG CYS A 131 " distance=2.03 Simple disulfide: pdb=" SG CYS A 298 " - pdb=" SG CYS A 310 " distance=2.04 Simple disulfide: pdb=" SG CYS B 83 " - pdb=" SG CYS B 355 " distance=2.04 Simple disulfide: pdb=" SG CYS B 99 " - pdb=" SG CYS B 131 " distance=2.03 Simple disulfide: pdb=" SG CYS B 298 " - pdb=" SG CYS B 310 " distance=2.03 Simple disulfide: pdb=" SG CYS C 83 " - pdb=" SG CYS C 355 " distance=2.03 Simple disulfide: pdb=" SG CYS C 99 " - pdb=" SG CYS C 131 " distance=2.03 Simple disulfide: pdb=" SG CYS C 298 " - pdb=" SG CYS C 310 " distance=2.03 Simple disulfide: pdb=" SG CYS D 83 " - pdb=" SG CYS D 355 " distance=2.04 Simple disulfide: pdb=" SG CYS D 99 " - pdb=" SG CYS D 131 " distance=2.03 Simple disulfide: pdb=" SG CYS D 298 " - pdb=" SG CYS D 310 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.72 Conformation dependent library (CDL) restraints added in 720.6 milliseconds 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5244 Finding SS restraints... Secondary structure from input PDB file: 110 helices and 33 sheets defined 44.9% alpha, 13.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 37 through 54 Processing helix chain 'A' and resid 74 through 89 removed outlier: 3.503A pdb=" N ALA A 78 " --> pdb=" O ASN A 74 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU A 84 " --> pdb=" O GLN A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 113 removed outlier: 4.183A pdb=" N GLY A 103 " --> pdb=" O CYS A 99 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N SER A 104 " --> pdb=" O THR A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 removed outlier: 3.659A pdb=" N GLY A 125 " --> pdb=" O SER A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 163 removed outlier: 3.657A pdb=" N ILE A 156 " --> pdb=" O LEU A 152 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N LEU A 157 " --> pdb=" O HIS A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 191 removed outlier: 3.597A pdb=" N VAL A 188 " --> pdb=" O PHE A 184 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N SER A 189 " --> pdb=" O LEU A 185 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLN A 190 " --> pdb=" O ASP A 186 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLN A 191 " --> pdb=" O LYS A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 213 removed outlier: 3.517A pdb=" N LEU A 211 " --> pdb=" O MET A 207 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE A 212 " --> pdb=" O ILE A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 227 removed outlier: 4.365A pdb=" N ARG A 222 " --> pdb=" O GLU A 218 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ASP A 225 " --> pdb=" O ASN A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 249 removed outlier: 3.835A pdb=" N LYS A 240 " --> pdb=" O PRO A 236 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N SER A 241 " --> pdb=" O ALA A 237 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU A 248 " --> pdb=" O THR A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 277 removed outlier: 3.590A pdb=" N VAL A 274 " --> pdb=" O VAL A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 298 removed outlier: 4.269A pdb=" N CYS A 298 " --> pdb=" O ILE A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 311 Processing helix chain 'A' and resid 316 through 320 removed outlier: 4.152A pdb=" N MET A 320 " --> pdb=" O ALA A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 344 removed outlier: 3.949A pdb=" N LEU A 325 " --> pdb=" O GLU A 321 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N TYR A 326 " --> pdb=" O ILE A 322 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL A 331 " --> pdb=" O ILE A 327 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU A 332 " --> pdb=" O TYR A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 374 removed outlier: 4.218A pdb=" N ARG A 367 " --> pdb=" O TRP A 363 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N SER A 368 " --> pdb=" O GLN A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 483 removed outlier: 3.610A pdb=" N TYR A 481 " --> pdb=" O ALA A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 514 removed outlier: 3.760A pdb=" N LEU A 512 " --> pdb=" O LEU A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 659 removed outlier: 4.774A pdb=" N LEU A 639 " --> pdb=" O GLY A 635 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N LEU A 642 " --> pdb=" O TRP A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 669 through 674 Processing helix chain 'A' and resid 685 through 697 removed outlier: 3.683A pdb=" N LEU A 696 " --> pdb=" O ARG A 692 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASN A 697 " --> pdb=" O MET A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 703 through 713 removed outlier: 3.789A pdb=" N GLN A 707 " --> pdb=" O SER A 703 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N MET A 708 " --> pdb=" O MET A 704 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N MET A 711 " --> pdb=" O GLN A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 734 Processing helix chain 'A' and resid 743 through 751 removed outlier: 4.298A pdb=" N TYR A 748 " --> pdb=" O ALA A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 780 through 795 removed outlier: 3.738A pdb=" N GLN A 793 " --> pdb=" O LEU A 789 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLY A 795 " --> pdb=" O LEU A 791 " (cutoff:3.500A) Processing helix chain 'A' and resid 795 through 804 removed outlier: 3.570A pdb=" N TRP A 804 " --> pdb=" O LEU A 800 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 53 removed outlier: 3.517A pdb=" N GLU B 42 " --> pdb=" O LYS B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 87 removed outlier: 3.530A pdb=" N ALA B 78 " --> pdb=" O ASN B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 103 removed outlier: 4.072A pdb=" N GLY B 103 " --> pdb=" O CYS B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 110 removed outlier: 4.176A pdb=" N ASP B 110 " --> pdb=" O GLN B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 126 removed outlier: 3.618A pdb=" N GLY B 125 " --> pdb=" O SER B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 156 Processing helix chain 'B' and resid 158 through 163 Processing helix chain 'B' and resid 177 through 182 Processing helix chain 'B' and resid 186 through 191 Processing helix chain 'B' and resid 203 through 215 removed outlier: 3.542A pdb=" N MET B 207 " --> pdb=" O ASN B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 221 Processing helix chain 'B' and resid 222 through 227 removed outlier: 4.399A pdb=" N THR B 226 " --> pdb=" O ARG B 222 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU B 227 " --> pdb=" O TYR B 223 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 222 through 227' Processing helix chain 'B' and resid 235 through 249 removed outlier: 4.145A pdb=" N SER B 241 " --> pdb=" O ALA B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 277 Processing helix chain 'B' and resid 293 through 297 Processing helix chain 'B' and resid 306 through 311 Processing helix chain 'B' and resid 321 through 344 removed outlier: 4.190A pdb=" N LEU B 325 " --> pdb=" O GLU B 321 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TYR B 326 " --> pdb=" O ILE B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 375 Processing helix chain 'B' and resid 469 through 483 removed outlier: 4.370A pdb=" N TYR B 481 " --> pdb=" O ALA B 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 514 Processing helix chain 'B' and resid 529 through 533 Processing helix chain 'B' and resid 628 through 659 removed outlier: 3.605A pdb=" N MET B 634 " --> pdb=" O THR B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 667 through 674 Processing helix chain 'B' and resid 685 through 697 Processing helix chain 'B' and resid 704 through 713 Processing helix chain 'B' and resid 724 through 734 removed outlier: 3.861A pdb=" N GLY B 728 " --> pdb=" O GLU B 724 " (cutoff:3.500A) Processing helix chain 'B' and resid 743 through 752 removed outlier: 4.186A pdb=" N TYR B 748 " --> pdb=" O ALA B 744 " (cutoff:3.500A) Processing helix chain 'B' and resid 780 through 794 removed outlier: 3.663A pdb=" N SER B 785 " --> pdb=" O ARG B 781 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N GLN B 786 " --> pdb=" O ASP B 782 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ARG B 787 " --> pdb=" O VAL B 783 " (cutoff:3.500A) Processing helix chain 'B' and resid 795 through 804 removed outlier: 3.969A pdb=" N LYS B 801 " --> pdb=" O MET B 797 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 53 removed outlier: 3.893A pdb=" N GLU C 42 " --> pdb=" O LYS C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 89 removed outlier: 3.503A pdb=" N LEU C 85 " --> pdb=" O GLU C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 113 removed outlier: 3.509A pdb=" N ALA C 102 " --> pdb=" O GLY C 98 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLY C 103 " --> pdb=" O CYS C 99 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N SER C 104 " --> pdb=" O THR C 100 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEU C 108 " --> pdb=" O SER C 104 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA C 109 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASP C 110 " --> pdb=" O GLN C 106 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ALA C 111 " --> pdb=" O SER C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 removed outlier: 3.630A pdb=" N GLY C 125 " --> pdb=" O SER C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 156 Processing helix chain 'C' and resid 158 through 163 Processing helix chain 'C' and resid 177 through 182 Processing helix chain 'C' and resid 183 through 191 removed outlier: 3.721A pdb=" N LYS C 187 " --> pdb=" O GLU C 183 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N SER C 189 " --> pdb=" O LEU C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 215 removed outlier: 3.608A pdb=" N MET C 207 " --> pdb=" O ASN C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 227 removed outlier: 4.172A pdb=" N ARG C 222 " --> pdb=" O GLU C 218 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASP C 225 " --> pdb=" O ASN C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 249 Processing helix chain 'C' and resid 266 through 277 Processing helix chain 'C' and resid 293 through 298 removed outlier: 4.780A pdb=" N CYS C 298 " --> pdb=" O ILE C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 311 Processing helix chain 'C' and resid 314 through 319 Processing helix chain 'C' and resid 321 through 344 removed outlier: 4.122A pdb=" N LEU C 325 " --> pdb=" O GLU C 321 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N TYR C 326 " --> pdb=" O ILE C 322 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASP C 329 " --> pdb=" O LEU C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 375 Processing helix chain 'C' and resid 469 through 482 Processing helix chain 'C' and resid 506 through 514 removed outlier: 3.605A pdb=" N LEU C 512 " --> pdb=" O LEU C 508 " (cutoff:3.500A) Processing helix chain 'C' and resid 529 through 534 Processing helix chain 'C' and resid 628 through 659 removed outlier: 3.886A pdb=" N MET C 632 " --> pdb=" O LEU C 628 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N MET C 634 " --> pdb=" O THR C 630 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLY C 635 " --> pdb=" O ARG C 631 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N TRP C 637 " --> pdb=" O MET C 633 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N PHE C 640 " --> pdb=" O ALA C 636 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA C 641 " --> pdb=" O TRP C 637 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU C 642 " --> pdb=" O TRP C 638 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ILE C 643 " --> pdb=" O LEU C 639 " (cutoff:3.500A) Processing helix chain 'C' and resid 667 through 674 Processing helix chain 'C' and resid 685 through 697 removed outlier: 3.907A pdb=" N VAL C 691 " --> pdb=" O VAL C 687 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ARG C 692 " --> pdb=" O TYR C 688 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N MET C 693 " --> pdb=" O GLU C 689 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LYS C 694 " --> pdb=" O HIS C 690 " (cutoff:3.500A) Processing helix chain 'C' and resid 703 through 713 Processing helix chain 'C' and resid 724 through 734 removed outlier: 3.612A pdb=" N GLY C 728 " --> pdb=" O GLU C 724 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N LYS C 731 " --> pdb=" O ALA C 727 " (cutoff:3.500A) Processing helix chain 'C' and resid 742 through 753 removed outlier: 3.560A pdb=" N LEU C 746 " --> pdb=" O ASP C 742 " (cutoff:3.500A) Processing helix chain 'C' and resid 779 through 795 removed outlier: 4.119A pdb=" N VAL C 783 " --> pdb=" O PRO C 779 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N GLN C 786 " --> pdb=" O ASP C 782 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N ARG C 787 " --> pdb=" O VAL C 783 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ILE C 788 " --> pdb=" O PHE C 784 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N LEU C 789 " --> pdb=" O SER C 785 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU C 790 " --> pdb=" O GLN C 786 " (cutoff:3.500A) Processing helix chain 'C' and resid 795 through 803 Processing helix chain 'D' and resid 37 through 52 Processing helix chain 'D' and resid 74 through 89 Processing helix chain 'D' and resid 98 through 113 removed outlier: 4.015A pdb=" N GLY D 103 " --> pdb=" O CYS D 99 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N SER D 104 " --> pdb=" O THR D 100 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ALA D 109 " --> pdb=" O LEU D 105 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA D 111 " --> pdb=" O SER D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 126 removed outlier: 3.619A pdb=" N GLY D 125 " --> pdb=" O SER D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 164 removed outlier: 3.581A pdb=" N ILE D 156 " --> pdb=" O LEU D 152 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LEU D 157 " --> pdb=" O HIS D 153 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL D 160 " --> pdb=" O ILE D 156 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU D 162 " --> pdb=" O ARG D 158 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 191 removed outlier: 3.587A pdb=" N LYS D 187 " --> pdb=" O GLU D 183 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL D 188 " --> pdb=" O PHE D 184 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N SER D 189 " --> pdb=" O LEU D 185 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLN D 190 " --> pdb=" O ASP D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 213 removed outlier: 4.067A pdb=" N LEU D 211 " --> pdb=" O MET D 207 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N PHE D 212 " --> pdb=" O ILE D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 227 Processing helix chain 'D' and resid 235 through 248 removed outlier: 3.546A pdb=" N ALA D 239 " --> pdb=" O ASN D 235 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LYS D 240 " --> pdb=" O PRO D 236 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N SER D 241 " --> pdb=" O ALA D 237 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU D 248 " --> pdb=" O THR D 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 277 removed outlier: 3.666A pdb=" N VAL D 274 " --> pdb=" O VAL D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 297 Processing helix chain 'D' and resid 306 through 311 Processing helix chain 'D' and resid 316 through 320 removed outlier: 3.949A pdb=" N MET D 320 " --> pdb=" O ALA D 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 344 removed outlier: 3.868A pdb=" N LEU D 325 " --> pdb=" O GLU D 321 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N TYR D 326 " --> pdb=" O ILE D 322 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASP D 329 " --> pdb=" O LEU D 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 375 Processing helix chain 'D' and resid 459 through 463 removed outlier: 3.666A pdb=" N LYS D 463 " --> pdb=" O VAL D 460 " (cutoff:3.500A) Processing helix chain 'D' and resid 469 through 483 Processing helix chain 'D' and resid 506 through 514 removed outlier: 3.960A pdb=" N LEU D 512 " --> pdb=" O LEU D 508 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 533 removed outlier: 3.620A pdb=" N ASN D 532 " --> pdb=" O ASP D 529 " (cutoff:3.500A) Processing helix chain 'D' and resid 628 through 657 removed outlier: 4.659A pdb=" N MET D 634 " --> pdb=" O THR D 630 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N GLY D 635 " --> pdb=" O ARG D 631 " (cutoff:3.500A) Processing helix chain 'D' and resid 667 through 674 Processing helix chain 'D' and resid 685 through 695 removed outlier: 3.651A pdb=" N LYS D 694 " --> pdb=" O HIS D 690 " (cutoff:3.500A) Processing helix chain 'D' and resid 703 through 713 removed outlier: 3.829A pdb=" N GLN D 707 " --> pdb=" O SER D 703 " (cutoff:3.500A) Processing helix chain 'D' and resid 724 through 734 Processing helix chain 'D' and resid 743 through 751 removed outlier: 5.295A pdb=" N TYR D 748 " --> pdb=" O ALA D 744 " (cutoff:3.500A) Processing helix chain 'D' and resid 780 through 795 removed outlier: 3.956A pdb=" N GLN D 793 " --> pdb=" O LEU D 789 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN D 794 " --> pdb=" O GLU D 790 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLY D 795 " --> pdb=" O LEU D 791 " (cutoff:3.500A) Processing helix chain 'D' and resid 795 through 804 removed outlier: 3.646A pdb=" N TRP D 804 " --> pdb=" O LEU D 800 " (cutoff:3.500A) Processing helix chain 'D' and resid 807 through 811 removed outlier: 4.216A pdb=" N GLN D 810 " --> pdb=" O LYS D 807 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N CYS D 811 " --> pdb=" O ASN D 808 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 807 through 811' Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 70 removed outlier: 7.632A pdb=" N HIS A 28 " --> pdb=" O ALA A 92 " (cutoff:3.500A) removed outlier: 8.774A pdb=" N VAL A 94 " --> pdb=" O HIS A 28 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N GLY A 30 " --> pdb=" O VAL A 94 " (cutoff:3.500A) removed outlier: 8.493A pdb=" N SER A 96 " --> pdb=" O GLY A 30 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N ILE A 32 " --> pdb=" O SER A 96 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N LEU A 93 " --> pdb=" O LEU A 117 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N HIS A 116 " --> pdb=" O LEU A 144 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 194 through 196 removed outlier: 3.756A pdb=" N PHE A 168 " --> pdb=" O ASP A 194 " (cutoff:3.500A) removed outlier: 8.817A pdb=" N ILE A 231 " --> pdb=" O LYS A 167 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N ILE A 169 " --> pdb=" O ILE A 231 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ALA A 230 " --> pdb=" O ILE A 259 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 299 through 300 Processing sheet with id=AA4, first strand: chain 'A' and resid 377 through 380 removed outlier: 3.545A pdb=" N GLY A 383 " --> pdb=" O GLY A 380 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 417 through 418 Processing sheet with id=AA6, first strand: chain 'A' and resid 487 through 490 removed outlier: 3.673A pdb=" N ILE A 519 " --> pdb=" O ARG A 444 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 455 through 456 Processing sheet with id=AA8, first strand: chain 'A' and resid 459 through 460 removed outlier: 3.735A pdb=" N LYS A 463 " --> pdb=" O VAL A 460 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 679 through 680 removed outlier: 6.926A pdb=" N GLY A 680 " --> pdb=" O VAL A 740 " (cutoff:3.500A) removed outlier: 9.378A pdb=" N ASP A 742 " --> pdb=" O GLY A 680 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N PHE A 739 " --> pdb=" O LEU A 548 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N TYR A 543 " --> pdb=" O VAL A 765 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N VAL A 545 " --> pdb=" O ASN A 763 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ASN A 763 " --> pdb=" O VAL A 545 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE A 761 " --> pdb=" O VAL A 547 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 64 through 70 removed outlier: 8.612A pdb=" N VAL B 94 " --> pdb=" O HIS B 28 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N GLY B 30 " --> pdb=" O VAL B 94 " (cutoff:3.500A) removed outlier: 8.330A pdb=" N SER B 96 " --> pdb=" O GLY B 30 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ILE B 32 " --> pdb=" O SER B 96 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LEU B 93 " --> pdb=" O LEU B 117 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N ILE B 119 " --> pdb=" O LEU B 93 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N SER B 95 " --> pdb=" O ILE B 119 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 194 through 200 removed outlier: 3.543A pdb=" N PHE B 168 " --> pdb=" O ASP B 194 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALA B 196 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N TYR B 172 " --> pdb=" O GLN B 198 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N LYS B 167 " --> pdb=" O ARG B 229 " (cutoff:3.500A) removed outlier: 8.588A pdb=" N ILE B 231 " --> pdb=" O LYS B 167 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ILE B 169 " --> pdb=" O ILE B 231 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N VAL B 233 " --> pdb=" O ILE B 169 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N PHE B 171 " --> pdb=" O VAL B 233 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA B 230 " --> pdb=" O HIS B 257 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR B 282 " --> pdb=" O TRP B 258 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLY B 417 " --> pdb=" O ILE B 400 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N GLY B 402 " --> pdb=" O LYS B 415 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N LYS B 415 " --> pdb=" O GLY B 402 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASN B 420 " --> pdb=" O GLY B 424 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 299 through 300 Processing sheet with id=AB4, first strand: chain 'B' and resid 378 through 380 removed outlier: 3.529A pdb=" N VAL B 378 " --> pdb=" O LEU B 385 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 405 through 406 removed outlier: 4.443A pdb=" N GLY B 406 " --> pdb=" O GLY B 410 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 485 through 490 Processing sheet with id=AB7, first strand: chain 'B' and resid 455 through 460 removed outlier: 6.271A pdb=" N LYS B 466 " --> pdb=" O SER B 457 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ASN B 459 " --> pdb=" O PRO B 464 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 679 through 680 removed outlier: 6.688A pdb=" N GLY B 680 " --> pdb=" O VAL B 740 " (cutoff:3.500A) removed outlier: 9.200A pdb=" N ASP B 742 " --> pdb=" O GLY B 680 " (cutoff:3.500A) removed outlier: 12.024A pdb=" N MET B 541 " --> pdb=" O ASP B 767 " (cutoff:3.500A) removed outlier: 10.180A pdb=" N ASP B 767 " --> pdb=" O MET B 541 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N TYR B 543 " --> pdb=" O VAL B 765 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N VAL B 765 " --> pdb=" O TYR B 543 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL B 545 " --> pdb=" O ASN B 763 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 64 through 70 removed outlier: 8.573A pdb=" N VAL C 94 " --> pdb=" O HIS C 28 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N GLY C 30 " --> pdb=" O VAL C 94 " (cutoff:3.500A) removed outlier: 8.366A pdb=" N SER C 96 " --> pdb=" O GLY C 30 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ILE C 32 " --> pdb=" O SER C 96 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N LEU C 93 " --> pdb=" O LEU C 117 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 194 through 200 removed outlier: 3.651A pdb=" N PHE C 168 " --> pdb=" O ASP C 194 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA C 196 " --> pdb=" O PHE C 168 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N TYR C 172 " --> pdb=" O GLN C 198 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N ARG C 229 " --> pdb=" O LYS C 167 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ASP C 173 " --> pdb=" O VAL C 233 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA C 230 " --> pdb=" O HIS C 257 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR C 282 " --> pdb=" O TRP C 258 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLY C 417 " --> pdb=" O ILE C 400 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 299 through 300 Processing sheet with id=AC3, first strand: chain 'C' and resid 379 through 380 Processing sheet with id=AC4, first strand: chain 'C' and resid 485 through 490 Processing sheet with id=AC5, first strand: chain 'C' and resid 455 through 456 Processing sheet with id=AC6, first strand: chain 'C' and resid 679 through 680 removed outlier: 6.628A pdb=" N GLY C 680 " --> pdb=" O VAL C 740 " (cutoff:3.500A) removed outlier: 11.391A pdb=" N MET C 541 " --> pdb=" O ASP C 767 " (cutoff:3.500A) removed outlier: 9.173A pdb=" N ASP C 767 " --> pdb=" O MET C 541 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N TYR C 543 " --> pdb=" O VAL C 765 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 64 through 70 removed outlier: 6.560A pdb=" N ILE D 29 " --> pdb=" O SER D 66 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N THR D 68 " --> pdb=" O ILE D 29 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ALA D 31 " --> pdb=" O THR D 68 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N VAL D 70 " --> pdb=" O ALA D 31 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N PHE D 33 " --> pdb=" O VAL D 70 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N HIS D 28 " --> pdb=" O ALA D 92 " (cutoff:3.500A) removed outlier: 8.666A pdb=" N VAL D 94 " --> pdb=" O HIS D 28 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N GLY D 30 " --> pdb=" O VAL D 94 " (cutoff:3.500A) removed outlier: 8.336A pdb=" N SER D 96 " --> pdb=" O GLY D 30 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N ILE D 32 " --> pdb=" O SER D 96 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LEU D 93 " --> pdb=" O LEU D 117 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N HIS D 116 " --> pdb=" O LEU D 144 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'D' and resid 194 through 200 removed outlier: 3.644A pdb=" N PHE D 168 " --> pdb=" O ASP D 194 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ASP D 173 " --> pdb=" O VAL D 233 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 284 through 286 Processing sheet with id=AD1, first strand: chain 'D' and resid 299 through 300 Processing sheet with id=AD2, first strand: chain 'D' and resid 377 through 380 removed outlier: 3.651A pdb=" N GLY D 383 " --> pdb=" O GLY D 380 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 403 through 406 Processing sheet with id=AD4, first strand: chain 'D' and resid 485 through 490 removed outlier: 3.671A pdb=" N ILE D 519 " --> pdb=" O ARG D 444 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 455 through 456 Processing sheet with id=AD6, first strand: chain 'D' and resid 679 through 680 removed outlier: 6.839A pdb=" N GLY D 680 " --> pdb=" O VAL D 740 " (cutoff:3.500A) removed outlier: 9.339A pdb=" N ASP D 742 " --> pdb=" O GLY D 680 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N TRP D 741 " --> pdb=" O GLY D 546 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N VAL D 547 " --> pdb=" O ILE D 761 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ILE D 761 " --> pdb=" O VAL D 547 " (cutoff:3.500A) 894 hydrogen bonds defined for protein. 2523 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.92 Time building geometry restraints manager: 2.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7482 1.34 - 1.46: 5027 1.46 - 1.58: 10205 1.58 - 1.70: 0 1.70 - 1.82: 198 Bond restraints: 22912 Sorted by residual: bond pdb=" CB ARG A 660 " pdb=" CG ARG A 660 " ideal model delta sigma weight residual 1.520 1.579 -0.059 3.00e-02 1.11e+03 3.83e+00 bond pdb=" CA ARG A 660 " pdb=" CB ARG A 660 " ideal model delta sigma weight residual 1.541 1.563 -0.022 1.20e-02 6.94e+03 3.33e+00 bond pdb=" N ARG A 660 " pdb=" CA ARG A 660 " ideal model delta sigma weight residual 1.456 1.474 -0.018 1.23e-02 6.61e+03 2.17e+00 bond pdb=" CA SER C 522 " pdb=" CB SER C 522 " ideal model delta sigma weight residual 1.542 1.530 0.013 8.90e-03 1.26e+04 2.09e+00 bond pdb=" CB VAL C 188 " pdb=" CG2 VAL C 188 " ideal model delta sigma weight residual 1.521 1.476 0.045 3.30e-02 9.18e+02 1.84e+00 ... (remaining 22907 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.79: 31040 5.79 - 11.58: 8 11.58 - 17.36: 1 17.36 - 23.15: 0 23.15 - 28.94: 1 Bond angle restraints: 31050 Sorted by residual: angle pdb=" CA ARG A 660 " pdb=" CB ARG A 660 " pdb=" CG ARG A 660 " ideal model delta sigma weight residual 114.10 128.86 -14.76 2.00e+00 2.50e-01 5.45e+01 angle pdb=" C GLU A 451 " pdb=" N PRO A 452 " pdb=" CD PRO A 452 " ideal model delta sigma weight residual 125.00 96.06 28.94 4.10e+00 5.95e-02 4.98e+01 angle pdb=" C SER A 664 " pdb=" N ILE A 665 " pdb=" CA ILE A 665 " ideal model delta sigma weight residual 121.97 128.24 -6.27 1.80e+00 3.09e-01 1.21e+01 angle pdb=" N ASP A 767 " pdb=" CA ASP A 767 " pdb=" C ASP A 767 " ideal model delta sigma weight residual 110.80 118.14 -7.34 2.13e+00 2.20e-01 1.19e+01 angle pdb=" CB ARG A 660 " pdb=" CG ARG A 660 " pdb=" CD ARG A 660 " ideal model delta sigma weight residual 111.30 119.10 -7.80 2.30e+00 1.89e-01 1.15e+01 ... (remaining 31045 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 12757 17.91 - 35.81: 788 35.81 - 53.72: 107 53.72 - 71.63: 30 71.63 - 89.54: 28 Dihedral angle restraints: 13710 sinusoidal: 5546 harmonic: 8164 Sorted by residual: dihedral pdb=" CA GLU A 451 " pdb=" C GLU A 451 " pdb=" N PRO A 452 " pdb=" CA PRO A 452 " ideal model delta harmonic sigma weight residual -180.00 -151.06 -28.94 0 5.00e+00 4.00e-02 3.35e+01 dihedral pdb=" CA GLN D 666 " pdb=" C GLN D 666 " pdb=" N SER D 667 " pdb=" CA SER D 667 " ideal model delta harmonic sigma weight residual 180.00 151.65 28.35 0 5.00e+00 4.00e-02 3.22e+01 dihedral pdb=" CA ILE C 356 " pdb=" C ILE C 356 " pdb=" N ARG C 357 " pdb=" CA ARG C 357 " ideal model delta harmonic sigma weight residual 180.00 151.66 28.34 0 5.00e+00 4.00e-02 3.21e+01 ... (remaining 13707 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 3003 0.072 - 0.143: 437 0.143 - 0.215: 13 0.215 - 0.286: 3 0.286 - 0.358: 2 Chirality restraints: 3458 Sorted by residual: chirality pdb=" CA PRO A 452 " pdb=" N PRO A 452 " pdb=" C PRO A 452 " pdb=" CB PRO A 452 " both_signs ideal model delta sigma weight residual False 2.72 2.36 0.36 2.00e-01 2.50e+01 3.20e+00 chirality pdb=" CA ARG A 660 " pdb=" N ARG A 660 " pdb=" C ARG A 660 " pdb=" CB ARG A 660 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.77e+00 chirality pdb=" CB ILE A 661 " pdb=" CA ILE A 661 " pdb=" CG1 ILE A 661 " pdb=" CG2 ILE A 661 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 1.99e+00 ... (remaining 3455 not shown) Planarity restraints: 4022 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 451 " 0.135 5.00e-02 4.00e+02 2.10e-01 7.03e+01 pdb=" N PRO A 452 " -0.362 5.00e-02 4.00e+02 pdb=" CA PRO A 452 " 0.135 5.00e-02 4.00e+02 pdb=" CD PRO A 452 " 0.092 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA C 102 " -0.016 2.00e-02 2.50e+03 3.25e-02 1.06e+01 pdb=" C ALA C 102 " 0.056 2.00e-02 2.50e+03 pdb=" O ALA C 102 " -0.021 2.00e-02 2.50e+03 pdb=" N GLY C 103 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 798 " 0.013 2.00e-02 2.50e+03 2.67e-02 7.15e+00 pdb=" C ASP A 798 " -0.046 2.00e-02 2.50e+03 pdb=" O ASP A 798 " 0.017 2.00e-02 2.50e+03 pdb=" N ILE A 799 " 0.016 2.00e-02 2.50e+03 ... (remaining 4019 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 604 2.71 - 3.26: 22976 3.26 - 3.80: 32380 3.80 - 4.35: 42653 4.35 - 4.90: 70301 Nonbonded interactions: 168914 Sorted by model distance: nonbonded pdb=" OD1 ASN D 420 " pdb=" OG1 THR D 423 " model vdw 2.160 3.040 nonbonded pdb=" NZ LYS C 240 " pdb=" OD1 ASP C 269 " model vdw 2.242 3.120 nonbonded pdb=" OH TYR B 543 " pdb=" OD1 ASP B 742 " model vdw 2.266 3.040 nonbonded pdb=" O ALA A 517 " pdb=" NE2 GLN A 775 " model vdw 2.277 3.120 nonbonded pdb=" NH2 ARG C 135 " pdb=" O ASP C 140 " model vdw 2.287 3.120 ... (remaining 168909 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and resid 27 through 804) selection = chain 'B' selection = chain 'C' selection = (chain 'D' and resid 27 through 804) } 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: 1.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 18.250 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7121 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 : 0.003 0.059 22924 Z= 0.146 Angle : 0.712 28.940 31074 Z= 0.410 Chirality : 0.048 0.358 3458 Planarity : 0.009 0.210 4022 Dihedral : 12.900 89.535 8430 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.53 % Allowed : 5.56 % Favored : 93.91 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.04 % 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: -2.12 (0.14), residues: 2808 helix: -1.69 (0.13), residues: 1106 sheet: -0.92 (0.26), residues: 385 loop : -1.14 (0.17), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.003 ARG A 414 TYR 0.025 0.005 TYR A 486 PHE 0.030 0.002 PHE A 171 TRP 0.026 0.002 TRP B 419 HIS 0.003 0.001 HIS B 116 Details of bonding type rmsd covalent geometry : bond 0.00301 (22912) covalent geometry : angle 0.71109 (31050) SS BOND : bond 0.00334 ( 12) SS BOND : angle 1.23544 ( 24) hydrogen bonds : bond 0.19397 ( 894) hydrogen bonds : angle 7.44770 ( 2523) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 2470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 461 time to evaluate : 0.652 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 207 MET cc_start: 0.8233 (ttp) cc_final: 0.8032 (ttt) REVERT: A 455 MET cc_start: 0.7009 (mtm) cc_final: 0.6704 (mtp) REVERT: A 486 TYR cc_start: 0.7748 (p90) cc_final: 0.7524 (p90) REVERT: A 633 MET cc_start: 0.4621 (ttm) cc_final: 0.3735 (ttp) REVERT: A 797 MET cc_start: 0.8107 (tpp) cc_final: 0.7906 (tpp) REVERT: B 303 HIS cc_start: 0.6413 (t70) cc_final: 0.6207 (t-90) REVERT: B 455 MET cc_start: 0.5331 (mpp) cc_final: 0.4881 (mtm) REVERT: C 303 HIS cc_start: 0.6107 (t70) cc_final: 0.5875 (t-90) REVERT: C 371 GLU cc_start: 0.7770 (tp30) cc_final: 0.7461 (tp30) REVERT: C 541 MET cc_start: 0.4256 (ttp) cc_final: 0.3516 (ttm) REVERT: C 632 MET cc_start: 0.2820 (tpt) cc_final: -0.0122 (mtt) REVERT: D 143 THR cc_start: 0.9203 (m) cc_final: 0.8992 (p) REVERT: D 472 ILE cc_start: 0.7693 (mm) cc_final: 0.7270 (mm) REVERT: D 705 TYR cc_start: 0.7679 (m-80) cc_final: 0.7043 (m-80) outliers start: 0 outliers final: 0 residues processed: 461 average time/residue: 0.1528 time to fit residues: 105.0114 Evaluate side-chains 245 residues out of total 2470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 245 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 30.0000 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 10.0000 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN ** A 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 106 GLN B 324 ASN C 324 ASN C 397 HIS ** C 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 GLN D 205 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.185533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.156674 restraints weight = 35960.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.149936 restraints weight = 50092.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.146760 restraints weight = 46767.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.146805 restraints weight = 43176.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.145371 restraints weight = 34850.902| |-----------------------------------------------------------------------------| r_work (final): 0.3932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 22924 Z= 0.180 Angle : 0.681 12.812 31074 Z= 0.367 Chirality : 0.047 0.316 3458 Planarity : 0.005 0.156 4022 Dihedral : 5.736 32.844 3076 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.74 % Favored : 96.05 % Rotamer: Outliers : 1.70 % Allowed : 7.85 % Favored : 90.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.92 (0.15), residues: 2808 helix: -0.05 (0.15), residues: 1150 sheet: -0.75 (0.25), residues: 405 loop : -0.98 (0.17), residues: 1253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 367 TYR 0.020 0.002 TYR A 486 PHE 0.027 0.002 PHE A 65 TRP 0.032 0.002 TRP A 638 HIS 0.005 0.001 HIS A 690 Details of bonding type rmsd covalent geometry : bond 0.00413 (22912) covalent geometry : angle 0.68068 (31050) SS BOND : bond 0.01058 ( 12) SS BOND : angle 1.11305 ( 24) hydrogen bonds : bond 0.05331 ( 894) hydrogen bonds : angle 5.34371 ( 2523) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 269 time to evaluate : 1.173 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: A 121 ARG cc_start: 0.8174 (OUTLIER) cc_final: 0.7949 (ttm-80) REVERT: A 486 TYR cc_start: 0.7897 (p90) cc_final: 0.7647 (p90) REVERT: A 633 MET cc_start: 0.3858 (ttm) cc_final: 0.3153 (ttp) REVERT: A 638 TRP cc_start: 0.6296 (m-10) cc_final: 0.5981 (m-90) REVERT: B 303 HIS cc_start: 0.6337 (t70) cc_final: 0.5972 (t-90) REVERT: B 763 ASN cc_start: 0.6093 (p0) cc_final: 0.5884 (p0) REVERT: C 112 MET cc_start: 0.8379 (mmt) cc_final: 0.7452 (mmm) REVERT: C 429 LEU cc_start: 0.7762 (OUTLIER) cc_final: 0.7538 (mt) REVERT: C 543 TYR cc_start: 0.6271 (t80) cc_final: 0.5846 (t80) REVERT: C 632 MET cc_start: 0.2209 (tpt) cc_final: 0.0033 (mtt) REVERT: C 758 PHE cc_start: 0.2244 (m-80) cc_final: 0.1846 (m-80) REVERT: D 112 MET cc_start: 0.8169 (mmt) cc_final: 0.7842 (mmp) REVERT: D 114 ILE cc_start: 0.9194 (mt) cc_final: 0.8962 (mp) REVERT: D 472 ILE cc_start: 0.7423 (mm) cc_final: 0.7154 (mm) REVERT: D 702 ASP cc_start: 0.6478 (t0) cc_final: 0.6197 (t0) REVERT: D 705 TYR cc_start: 0.8045 (m-80) cc_final: 0.7418 (m-80) outliers start: 42 outliers final: 29 residues processed: 293 average time/residue: 0.1290 time to fit residues: 60.9375 Evaluate side-chains 253 residues out of total 2470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 222 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ARG Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 452 PRO Chi-restraints excluded: chain A residue 681 THR Chi-restraints excluded: chain A residue 693 MET Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 760 THR Chi-restraints excluded: chain A residue 761 ILE Chi-restraints excluded: chain A residue 781 ARG Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain C residue 382 THR Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain D residue 40 ASP Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 455 MET Chi-restraints excluded: chain D residue 729 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 247 optimal weight: 0.0980 chunk 204 optimal weight: 6.9990 chunk 128 optimal weight: 6.9990 chunk 223 optimal weight: 3.9990 chunk 43 optimal weight: 8.9990 chunk 133 optimal weight: 8.9990 chunk 190 optimal weight: 30.0000 chunk 26 optimal weight: 7.9990 chunk 151 optimal weight: 5.9990 chunk 40 optimal weight: 0.9990 chunk 99 optimal weight: 3.9990 overall best weight: 3.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 532 ASN B 775 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.182065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.148750 restraints weight = 36087.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.142246 restraints weight = 58345.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.139643 restraints weight = 51251.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.139800 restraints weight = 45770.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.139852 restraints weight = 36227.286| |-----------------------------------------------------------------------------| r_work (final): 0.3821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.3505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.086 22924 Z= 0.288 Angle : 0.754 11.195 31074 Z= 0.402 Chirality : 0.050 0.323 3458 Planarity : 0.005 0.149 4022 Dihedral : 5.795 31.374 3076 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.20 % Favored : 94.59 % Rotamer: Outliers : 3.08 % Allowed : 9.92 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.15), residues: 2808 helix: 0.14 (0.15), residues: 1168 sheet: -1.08 (0.25), residues: 417 loop : -1.22 (0.17), residues: 1223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 787 TYR 0.029 0.002 TYR A 328 PHE 0.034 0.003 PHE D 171 TRP 0.022 0.002 TRP A 805 HIS 0.009 0.001 HIS A 690 Details of bonding type rmsd covalent geometry : bond 0.00698 (22912) covalent geometry : angle 0.75296 (31050) SS BOND : bond 0.00331 ( 12) SS BOND : angle 1.53589 ( 24) hydrogen bonds : bond 0.05716 ( 894) hydrogen bonds : angle 5.43564 ( 2523) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 244 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 MET cc_start: 0.8228 (mmt) cc_final: 0.7644 (mmp) REVERT: A 121 ARG cc_start: 0.8179 (OUTLIER) cc_final: 0.7895 (ttm-80) REVERT: A 633 MET cc_start: 0.3748 (ttm) cc_final: 0.3003 (ttp) REVERT: A 638 TRP cc_start: 0.7321 (m-10) cc_final: 0.6798 (m-90) REVERT: A 705 TYR cc_start: 0.7778 (m-80) cc_final: 0.7208 (m-80) REVERT: B 182 GLN cc_start: 0.8575 (OUTLIER) cc_final: 0.8295 (tt0) REVERT: B 303 HIS cc_start: 0.6670 (t70) cc_final: 0.6135 (t-90) REVERT: B 453 PHE cc_start: 0.6466 (m-80) cc_final: 0.6230 (m-80) REVERT: C 314 ASP cc_start: 0.6799 (t0) cc_final: 0.6402 (t0) REVERT: C 632 MET cc_start: 0.1734 (tpt) cc_final: -0.0680 (mtt) REVERT: C 704 MET cc_start: 0.4206 (ttt) cc_final: 0.2489 (tmm) REVERT: C 758 PHE cc_start: 0.1936 (m-80) cc_final: 0.1360 (m-80) REVERT: D 112 MET cc_start: 0.8340 (mmt) cc_final: 0.7950 (mmp) REVERT: D 472 ILE cc_start: 0.7529 (mm) cc_final: 0.7314 (mm) REVERT: D 702 ASP cc_start: 0.6812 (t0) cc_final: 0.6573 (t0) REVERT: D 705 TYR cc_start: 0.8340 (m-80) cc_final: 0.7811 (m-80) outliers start: 76 outliers final: 49 residues processed: 290 average time/residue: 0.1223 time to fit residues: 57.9823 Evaluate side-chains 270 residues out of total 2470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 219 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 GLU Chi-restraints excluded: chain A residue 121 ARG Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 681 THR Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 760 THR Chi-restraints excluded: chain A residue 761 ILE Chi-restraints excluded: chain A residue 772 ILE Chi-restraints excluded: chain A residue 781 ARG Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 182 GLN Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 395 ASN Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 789 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 138 ARG Chi-restraints excluded: chain C residue 193 MET Chi-restraints excluded: chain C residue 243 ILE Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain C residue 382 THR Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain D residue 256 CYS Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 384 GLU Chi-restraints excluded: chain D residue 675 THR Chi-restraints excluded: chain D residue 729 ILE Chi-restraints excluded: chain D residue 732 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 16 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 72 optimal weight: 2.9990 chunk 34 optimal weight: 8.9990 chunk 181 optimal weight: 6.9990 chunk 52 optimal weight: 10.0000 chunk 59 optimal weight: 0.9990 chunk 266 optimal weight: 4.9990 chunk 259 optimal weight: 0.6980 chunk 39 optimal weight: 4.9990 chunk 164 optimal weight: 0.9980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 257 HIS A 674 GLN ** B 721 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 674 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 = 0.4371 r_free = 0.4371 target = 0.186218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.156664 restraints weight = 36203.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.152450 restraints weight = 53479.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.149403 restraints weight = 38633.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.149282 restraints weight = 45115.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.149137 restraints weight = 33759.768| |-----------------------------------------------------------------------------| r_work (final): 0.3930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.3845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22924 Z= 0.144 Angle : 0.614 17.938 31074 Z= 0.319 Chirality : 0.045 0.381 3458 Planarity : 0.005 0.172 4022 Dihedral : 5.162 35.528 3076 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.31 % Favored : 95.48 % Rotamer: Outliers : 2.51 % Allowed : 11.70 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.04 % Twisted Proline : 1.11 % Twisted General : 0.11 % 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: -0.60 (0.16), residues: 2808 helix: 0.58 (0.15), residues: 1162 sheet: -1.01 (0.25), residues: 416 loop : -1.05 (0.17), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 304 TYR 0.019 0.001 TYR A 328 PHE 0.028 0.002 PHE A 65 TRP 0.021 0.001 TRP A 637 HIS 0.004 0.001 HIS A 690 Details of bonding type rmsd covalent geometry : bond 0.00334 (22912) covalent geometry : angle 0.61339 (31050) SS BOND : bond 0.00239 ( 12) SS BOND : angle 0.85543 ( 24) hydrogen bonds : bond 0.04163 ( 894) hydrogen bonds : angle 4.91640 ( 2523) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 243 time to evaluate : 0.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ARG cc_start: 0.8227 (OUTLIER) cc_final: 0.7878 (ttm-80) REVERT: A 486 TYR cc_start: 0.7775 (p90) cc_final: 0.7430 (p90) REVERT: A 539 ARG cc_start: 0.7912 (ptp90) cc_final: 0.7696 (ptp-170) REVERT: A 633 MET cc_start: 0.3143 (ttm) cc_final: 0.2431 (ttp) REVERT: A 705 TYR cc_start: 0.7540 (m-80) cc_final: 0.7051 (m-80) REVERT: B 197 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.7810 (pp) REVERT: B 303 HIS cc_start: 0.6012 (t70) cc_final: 0.5732 (t-90) REVERT: C 112 MET cc_start: 0.8360 (mmt) cc_final: 0.8004 (mmm) REVERT: C 314 ASP cc_start: 0.6560 (t0) cc_final: 0.6317 (t0) REVERT: C 443 LEU cc_start: 0.5544 (mt) cc_final: 0.5308 (mt) REVERT: C 632 MET cc_start: 0.1830 (tpt) cc_final: -0.0705 (mtt) REVERT: C 704 MET cc_start: 0.4381 (ttt) cc_final: 0.2307 (tmm) REVERT: C 758 PHE cc_start: 0.1837 (m-80) cc_final: 0.1290 (m-80) REVERT: D 112 MET cc_start: 0.8291 (mmt) cc_final: 0.8012 (mmp) REVERT: D 660 ARG cc_start: 0.6529 (tpp-160) cc_final: 0.6314 (tpp-160) REVERT: D 705 TYR cc_start: 0.8269 (m-80) cc_final: 0.7763 (m-10) REVERT: D 708 MET cc_start: 0.8126 (mtp) cc_final: 0.7903 (mtp) outliers start: 62 outliers final: 37 residues processed: 287 average time/residue: 0.1304 time to fit residues: 60.4155 Evaluate side-chains 258 residues out of total 2470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 219 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ARG Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 359 ASN Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 674 GLN Chi-restraints excluded: chain A residue 681 THR Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 243 ILE Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 382 THR Chi-restraints excluded: chain C residue 655 PHE Chi-restraints excluded: chain D residue 40 ASP Chi-restraints excluded: chain D residue 193 MET Chi-restraints excluded: chain D residue 256 CYS Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 675 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 123 optimal weight: 40.0000 chunk 206 optimal weight: 1.9990 chunk 198 optimal weight: 1.9990 chunk 226 optimal weight: 0.8980 chunk 151 optimal weight: 1.9990 chunk 170 optimal weight: 2.9990 chunk 103 optimal weight: 0.0470 chunk 73 optimal weight: 10.0000 chunk 128 optimal weight: 8.9990 chunk 216 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 overall best weight: 1.1882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 674 GLN D 303 HIS ** D 674 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 = 0.4372 r_free = 0.4372 target = 0.186193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.156094 restraints weight = 36006.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.152530 restraints weight = 55963.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.149952 restraints weight = 39498.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.148376 restraints weight = 41602.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.147855 restraints weight = 32949.534| |-----------------------------------------------------------------------------| r_work (final): 0.3916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.4125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22924 Z= 0.136 Angle : 0.588 10.939 31074 Z= 0.307 Chirality : 0.045 0.287 3458 Planarity : 0.004 0.147 4022 Dihedral : 4.893 35.554 3076 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.70 % Favored : 95.09 % Rotamer: Outliers : 2.91 % Allowed : 11.82 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.04 % Twisted Proline : 1.11 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.16), residues: 2808 helix: 0.78 (0.16), residues: 1160 sheet: -0.92 (0.25), residues: 428 loop : -1.01 (0.17), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 660 TYR 0.014 0.001 TYR A 328 PHE 0.024 0.002 PHE A 65 TRP 0.023 0.001 TRP A 637 HIS 0.004 0.001 HIS A 690 Details of bonding type rmsd covalent geometry : bond 0.00317 (22912) covalent geometry : angle 0.58739 (31050) SS BOND : bond 0.00180 ( 12) SS BOND : angle 0.84793 ( 24) hydrogen bonds : bond 0.04015 ( 894) hydrogen bonds : angle 4.81470 ( 2523) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 223 time to evaluate : 0.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ARG cc_start: 0.8253 (OUTLIER) cc_final: 0.7893 (ttm-80) REVERT: A 486 TYR cc_start: 0.7833 (p90) cc_final: 0.7524 (p90) REVERT: A 633 MET cc_start: 0.2706 (ttm) cc_final: 0.2116 (ttp) REVERT: A 705 TYR cc_start: 0.7588 (m-80) cc_final: 0.7101 (m-80) REVERT: B 197 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.7977 (pp) REVERT: C 112 MET cc_start: 0.8360 (mmt) cc_final: 0.7917 (mmm) REVERT: C 632 MET cc_start: 0.1698 (tpt) cc_final: -0.0856 (mtt) REVERT: C 704 MET cc_start: 0.4396 (ttt) cc_final: 0.2156 (tmm) REVERT: C 758 PHE cc_start: 0.1741 (m-80) cc_final: 0.1291 (m-80) REVERT: D 705 TYR cc_start: 0.8279 (m-80) cc_final: 0.7798 (m-10) outliers start: 72 outliers final: 55 residues processed: 273 average time/residue: 0.1184 time to fit residues: 53.0322 Evaluate side-chains 264 residues out of total 2470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 207 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ARG Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 359 ASN Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 681 THR Chi-restraints excluded: chain A residue 693 MET Chi-restraints excluded: chain A residue 704 MET Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 760 THR Chi-restraints excluded: chain A residue 761 ILE Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 138 ARG Chi-restraints excluded: chain C residue 193 MET Chi-restraints excluded: chain C residue 212 PHE Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 243 ILE Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 382 THR Chi-restraints excluded: chain C residue 405 TYR Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 40 ASP Chi-restraints excluded: chain D residue 193 MET Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 675 THR Chi-restraints excluded: chain D residue 693 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 18 optimal weight: 1.9990 chunk 258 optimal weight: 0.0970 chunk 182 optimal weight: 8.9990 chunk 180 optimal weight: 2.9990 chunk 238 optimal weight: 2.9990 chunk 227 optimal weight: 2.9990 chunk 98 optimal weight: 20.0000 chunk 3 optimal weight: 0.0570 chunk 117 optimal weight: 9.9990 chunk 223 optimal weight: 3.9990 chunk 15 optimal weight: 0.5980 overall best weight: 1.1500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 721 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 485 ASN ** D 674 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 = 0.4377 r_free = 0.4377 target = 0.186598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.155102 restraints weight = 35955.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.149274 restraints weight = 57498.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.145753 restraints weight = 45054.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.146020 restraints weight = 45885.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.146335 restraints weight = 31798.343| |-----------------------------------------------------------------------------| r_work (final): 0.3895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.4285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22924 Z= 0.131 Angle : 0.576 10.726 31074 Z= 0.300 Chirality : 0.044 0.176 3458 Planarity : 0.004 0.096 4022 Dihedral : 4.832 55.360 3076 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.67 % Favored : 95.16 % Rotamer: Outliers : 2.91 % Allowed : 12.43 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.04 % Twisted Proline : 1.11 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.16), residues: 2808 helix: 0.86 (0.16), residues: 1161 sheet: -0.83 (0.25), residues: 430 loop : -1.03 (0.17), residues: 1217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 768 TYR 0.014 0.001 TYR A 328 PHE 0.021 0.001 PHE A 65 TRP 0.022 0.001 TRP A 637 HIS 0.004 0.001 HIS A 690 Details of bonding type rmsd covalent geometry : bond 0.00306 (22912) covalent geometry : angle 0.57585 (31050) SS BOND : bond 0.00174 ( 12) SS BOND : angle 0.80686 ( 24) hydrogen bonds : bond 0.03885 ( 894) hydrogen bonds : angle 4.73694 ( 2523) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 224 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 LEU cc_start: 0.7537 (mm) cc_final: 0.7235 (mm) REVERT: A 121 ARG cc_start: 0.8244 (OUTLIER) cc_final: 0.7921 (ttm-80) REVERT: A 486 TYR cc_start: 0.7856 (p90) cc_final: 0.7541 (p90) REVERT: A 633 MET cc_start: 0.2708 (ttm) cc_final: 0.2109 (ttp) REVERT: A 705 TYR cc_start: 0.7655 (m-80) cc_final: 0.7134 (m-80) REVERT: B 182 GLN cc_start: 0.8357 (OUTLIER) cc_final: 0.8070 (tt0) REVERT: B 438 MET cc_start: 0.4593 (ttm) cc_final: 0.4244 (ttp) REVERT: B 549 LEU cc_start: 0.7168 (OUTLIER) cc_final: 0.6399 (mp) REVERT: B 797 MET cc_start: 0.7334 (ppp) cc_final: 0.7131 (ppp) REVERT: C 112 MET cc_start: 0.8516 (mmt) cc_final: 0.8084 (mmm) REVERT: C 632 MET cc_start: 0.1595 (tpt) cc_final: -0.0902 (mtt) REVERT: C 704 MET cc_start: 0.4393 (ttt) cc_final: 0.2195 (tmm) REVERT: C 758 PHE cc_start: 0.1211 (m-80) cc_final: 0.0776 (m-80) REVERT: D 705 TYR cc_start: 0.8309 (m-80) cc_final: 0.7872 (m-10) outliers start: 72 outliers final: 56 residues processed: 274 average time/residue: 0.1217 time to fit residues: 55.0402 Evaluate side-chains 270 residues out of total 2470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 211 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 121 ARG Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 359 ASN Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 681 THR Chi-restraints excluded: chain A residue 693 MET Chi-restraints excluded: chain A residue 704 MET Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 760 THR Chi-restraints excluded: chain A residue 761 ILE Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 182 GLN Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 138 ARG Chi-restraints excluded: chain C residue 193 MET Chi-restraints excluded: chain C residue 212 PHE Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 243 ILE Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 382 THR Chi-restraints excluded: chain C residue 405 TYR Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 40 ASP Chi-restraints excluded: chain D residue 193 MET Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 378 VAL Chi-restraints excluded: chain D residue 519 ILE Chi-restraints excluded: chain D residue 675 THR Chi-restraints excluded: chain D residue 693 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 183 optimal weight: 6.9990 chunk 202 optimal weight: 9.9990 chunk 171 optimal weight: 0.9990 chunk 195 optimal weight: 8.9990 chunk 75 optimal weight: 0.5980 chunk 265 optimal weight: 1.9990 chunk 3 optimal weight: 0.0570 chunk 225 optimal weight: 0.0970 chunk 9 optimal weight: 2.9990 chunk 175 optimal weight: 5.9990 chunk 94 optimal weight: 2.9990 overall best weight: 0.7500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 ASN ** A 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 721 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 674 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 = 0.4388 r_free = 0.4388 target = 0.187734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.156508 restraints weight = 35713.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.152736 restraints weight = 55151.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.149624 restraints weight = 41783.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.150063 restraints weight = 41423.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.149720 restraints weight = 32202.719| |-----------------------------------------------------------------------------| r_work (final): 0.3942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.4503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 22924 Z= 0.106 Angle : 0.548 10.534 31074 Z= 0.285 Chirality : 0.043 0.246 3458 Planarity : 0.004 0.073 4022 Dihedral : 4.585 53.361 3076 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.42 % Favored : 95.41 % Rotamer: Outliers : 3.04 % Allowed : 12.71 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.04 % Twisted Proline : 1.11 % Twisted General : 0.11 % 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: -0.16 (0.16), residues: 2808 helix: 1.04 (0.16), residues: 1162 sheet: -0.64 (0.25), residues: 423 loop : -0.98 (0.17), residues: 1223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 768 TYR 0.015 0.001 TYR A 328 PHE 0.019 0.001 PHE A 65 TRP 0.025 0.001 TRP A 638 HIS 0.003 0.001 HIS A 690 Details of bonding type rmsd covalent geometry : bond 0.00236 (22912) covalent geometry : angle 0.54830 (31050) SS BOND : bond 0.00177 ( 12) SS BOND : angle 0.69138 ( 24) hydrogen bonds : bond 0.03504 ( 894) hydrogen bonds : angle 4.65142 ( 2523) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 229 time to evaluate : 0.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 LEU cc_start: 0.7416 (mm) cc_final: 0.7150 (mm) REVERT: A 121 ARG cc_start: 0.8222 (OUTLIER) cc_final: 0.7897 (ttm-80) REVERT: A 486 TYR cc_start: 0.7851 (p90) cc_final: 0.7465 (p90) REVERT: A 633 MET cc_start: 0.2696 (ttm) cc_final: 0.2109 (ttp) REVERT: A 705 TYR cc_start: 0.7603 (m-80) cc_final: 0.7088 (m-80) REVERT: B 182 GLN cc_start: 0.8327 (OUTLIER) cc_final: 0.8073 (tt0) REVERT: B 197 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8240 (pt) REVERT: B 278 ILE cc_start: 0.8521 (OUTLIER) cc_final: 0.8172 (pt) REVERT: B 438 MET cc_start: 0.5038 (ttm) cc_final: 0.4627 (ttp) REVERT: B 549 LEU cc_start: 0.7027 (OUTLIER) cc_final: 0.6266 (mp) REVERT: C 112 MET cc_start: 0.8584 (mmt) cc_final: 0.8013 (mmm) REVERT: C 443 LEU cc_start: 0.6137 (mt) cc_final: 0.5450 (mp) REVERT: C 632 MET cc_start: 0.1787 (tpt) cc_final: -0.0707 (mtt) REVERT: C 704 MET cc_start: 0.4080 (ttt) cc_final: 0.2080 (tmm) REVERT: C 758 PHE cc_start: 0.1213 (m-80) cc_final: 0.0810 (m-80) REVERT: D 248 GLU cc_start: 0.7923 (tp30) cc_final: 0.7528 (tp30) REVERT: D 328 TYR cc_start: 0.6826 (t80) cc_final: 0.6568 (t80) REVERT: D 705 TYR cc_start: 0.8217 (m-80) cc_final: 0.7877 (m-10) REVERT: D 734 TYR cc_start: 0.7097 (m-10) cc_final: 0.6835 (m-10) outliers start: 75 outliers final: 53 residues processed: 282 average time/residue: 0.1263 time to fit residues: 58.4268 Evaluate side-chains 269 residues out of total 2470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 211 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 121 ARG Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 359 ASN Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 681 THR Chi-restraints excluded: chain A residue 693 MET Chi-restraints excluded: chain A residue 704 MET Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 760 THR Chi-restraints excluded: chain A residue 761 ILE Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 182 GLN Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 193 MET Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 212 PHE Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 243 ILE Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 382 THR Chi-restraints excluded: chain C residue 405 TYR Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 40 ASP Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 193 MET Chi-restraints excluded: chain D residue 269 ASP Chi-restraints excluded: chain D residue 299 PHE Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 327 ILE Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 378 VAL Chi-restraints excluded: chain D residue 519 ILE Chi-restraints excluded: chain D residue 675 THR Chi-restraints excluded: chain D residue 693 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 87 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 191 optimal weight: 20.0000 chunk 253 optimal weight: 0.9990 chunk 252 optimal weight: 4.9990 chunk 132 optimal weight: 20.0000 chunk 246 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 193 optimal weight: 30.0000 chunk 206 optimal weight: 2.9990 chunk 61 optimal weight: 0.5980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 721 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 74 ASN ** D 674 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 = 0.4386 r_free = 0.4386 target = 0.187509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.157016 restraints weight = 35407.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.153019 restraints weight = 54105.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.148878 restraints weight = 41006.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.149584 restraints weight = 43206.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.149197 restraints weight = 29728.350| |-----------------------------------------------------------------------------| r_work (final): 0.3939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.4643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 22924 Z= 0.116 Angle : 0.565 10.626 31074 Z= 0.292 Chirality : 0.043 0.183 3458 Planarity : 0.004 0.053 4022 Dihedral : 4.525 50.672 3076 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.38 % Favored : 95.44 % Rotamer: Outliers : 2.75 % Allowed : 13.36 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.04 % Twisted Proline : 1.11 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.16), residues: 2808 helix: 1.12 (0.16), residues: 1167 sheet: -0.61 (0.25), residues: 425 loop : -0.93 (0.17), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 768 TYR 0.032 0.001 TYR C 496 PHE 0.030 0.001 PHE A 65 TRP 0.033 0.001 TRP D 710 HIS 0.003 0.001 HIS A 690 Details of bonding type rmsd covalent geometry : bond 0.00266 (22912) covalent geometry : angle 0.56514 (31050) SS BOND : bond 0.00152 ( 12) SS BOND : angle 0.68418 ( 24) hydrogen bonds : bond 0.03576 ( 894) hydrogen bonds : angle 4.63548 ( 2523) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 224 time to evaluate : 0.776 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: A 91 LEU cc_start: 0.7292 (mm) cc_final: 0.6979 (mm) REVERT: A 121 ARG cc_start: 0.8242 (OUTLIER) cc_final: 0.7950 (ttm-80) REVERT: A 486 TYR cc_start: 0.7841 (p90) cc_final: 0.7444 (p90) REVERT: A 633 MET cc_start: 0.2687 (ttm) cc_final: 0.2124 (ttp) REVERT: A 705 TYR cc_start: 0.7764 (m-80) cc_final: 0.7314 (m-80) REVERT: B 182 GLN cc_start: 0.8363 (OUTLIER) cc_final: 0.8143 (tt0) REVERT: B 197 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8350 (pt) REVERT: B 438 MET cc_start: 0.4438 (ttm) cc_final: 0.4021 (ttp) REVERT: C 112 MET cc_start: 0.8644 (mmt) cc_final: 0.8262 (mmm) REVERT: C 632 MET cc_start: 0.2333 (tpt) cc_final: -0.0855 (mtt) REVERT: C 704 MET cc_start: 0.4067 (ttt) cc_final: 0.1987 (tmm) REVERT: C 758 PHE cc_start: 0.1270 (m-80) cc_final: 0.0877 (m-80) REVERT: D 328 TYR cc_start: 0.6850 (t80) cc_final: 0.6571 (t80) REVERT: D 705 TYR cc_start: 0.8225 (m-80) cc_final: 0.7920 (m-10) REVERT: D 734 TYR cc_start: 0.6972 (m-10) cc_final: 0.6684 (m-10) outliers start: 68 outliers final: 55 residues processed: 272 average time/residue: 0.1252 time to fit residues: 55.2386 Evaluate side-chains 274 residues out of total 2470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 216 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ARG Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 359 ASN Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 681 THR Chi-restraints excluded: chain A residue 693 MET Chi-restraints excluded: chain A residue 701 ARG Chi-restraints excluded: chain A residue 704 MET Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 760 THR Chi-restraints excluded: chain A residue 761 ILE Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 182 GLN Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 138 ARG Chi-restraints excluded: chain C residue 193 MET Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 212 PHE Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 243 ILE Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 382 THR Chi-restraints excluded: chain C residue 405 TYR Chi-restraints excluded: chain D residue 40 ASP Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 193 MET Chi-restraints excluded: chain D residue 299 PHE Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 519 ILE Chi-restraints excluded: chain D residue 675 THR Chi-restraints excluded: chain D residue 693 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 41 optimal weight: 3.9990 chunk 76 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 243 optimal weight: 10.0000 chunk 236 optimal weight: 0.0470 chunk 75 optimal weight: 4.9990 chunk 255 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 151 optimal weight: 0.2980 overall best weight: 0.5880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 721 ASN B 775 GLN ** C 720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 674 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 = 0.4400 r_free = 0.4400 target = 0.188993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.158322 restraints weight = 35550.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.154194 restraints weight = 54533.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.149789 restraints weight = 41255.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.150858 restraints weight = 42904.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.150629 restraints weight = 29197.925| |-----------------------------------------------------------------------------| r_work (final): 0.3953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.4795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 22924 Z= 0.102 Angle : 0.561 10.787 31074 Z= 0.287 Chirality : 0.043 0.258 3458 Planarity : 0.003 0.046 4022 Dihedral : 4.378 48.436 3076 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.77 % Favored : 96.05 % Rotamer: Outliers : 1.94 % Allowed : 14.49 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.04 % Twisted Proline : 1.11 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.16), residues: 2808 helix: 1.19 (0.16), residues: 1167 sheet: -0.55 (0.25), residues: 435 loop : -0.85 (0.18), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 714 TYR 0.014 0.001 TYR A 405 PHE 0.026 0.001 PHE A 65 TRP 0.056 0.001 TRP A 638 HIS 0.003 0.001 HIS B 690 Details of bonding type rmsd covalent geometry : bond 0.00224 (22912) covalent geometry : angle 0.56094 (31050) SS BOND : bond 0.00280 ( 12) SS BOND : angle 0.66414 ( 24) hydrogen bonds : bond 0.03297 ( 894) hydrogen bonds : angle 4.56502 ( 2523) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 231 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 LEU cc_start: 0.7519 (mm) cc_final: 0.7254 (mm) REVERT: A 486 TYR cc_start: 0.7899 (p90) cc_final: 0.7503 (p90) REVERT: A 633 MET cc_start: 0.2691 (ttm) cc_final: 0.1971 (ttp) REVERT: A 705 TYR cc_start: 0.7738 (m-80) cc_final: 0.7318 (m-80) REVERT: B 438 MET cc_start: 0.4430 (ttm) cc_final: 0.4024 (ttp) REVERT: C 632 MET cc_start: 0.2074 (tpt) cc_final: -0.0928 (mtt) REVERT: C 693 MET cc_start: 0.4320 (mpp) cc_final: 0.3886 (mpp) REVERT: C 704 MET cc_start: 0.3955 (ttt) cc_final: 0.1929 (tmm) REVERT: C 758 PHE cc_start: 0.1549 (m-80) cc_final: 0.1324 (m-80) REVERT: D 705 TYR cc_start: 0.8213 (m-80) cc_final: 0.7930 (m-10) REVERT: D 734 TYR cc_start: 0.6966 (m-10) cc_final: 0.6665 (m-10) outliers start: 48 outliers final: 34 residues processed: 263 average time/residue: 0.1250 time to fit residues: 53.2365 Evaluate side-chains 253 residues out of total 2470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 219 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 660 ARG Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 693 MET Chi-restraints excluded: chain A residue 701 ARG Chi-restraints excluded: chain A residue 704 MET Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain C residue 138 ARG Chi-restraints excluded: chain C residue 212 PHE Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 382 THR Chi-restraints excluded: chain C residue 405 TYR Chi-restraints excluded: chain D residue 40 ASP Chi-restraints excluded: chain D residue 193 MET Chi-restraints excluded: chain D residue 299 PHE Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 675 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 196 optimal weight: 0.6980 chunk 105 optimal weight: 2.9990 chunk 198 optimal weight: 5.9990 chunk 44 optimal weight: 0.7980 chunk 199 optimal weight: 0.8980 chunk 248 optimal weight: 2.9990 chunk 128 optimal weight: 7.9990 chunk 142 optimal weight: 0.6980 chunk 96 optimal weight: 5.9990 chunk 145 optimal weight: 0.8980 chunk 166 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 674 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 = 0.4392 r_free = 0.4392 target = 0.188172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.157748 restraints weight = 35956.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.154229 restraints weight = 54637.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.150042 restraints weight = 41300.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.150874 restraints weight = 42842.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.150204 restraints weight = 31389.779| |-----------------------------------------------------------------------------| r_work (final): 0.3950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.4884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22924 Z= 0.113 Angle : 0.575 10.948 31074 Z= 0.293 Chirality : 0.043 0.231 3458 Planarity : 0.004 0.055 4022 Dihedral : 4.377 46.349 3076 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.20 % Favored : 95.62 % Rotamer: Outliers : 1.66 % Allowed : 14.94 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.04 % Twisted Proline : 1.11 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.16), residues: 2808 helix: 1.24 (0.16), residues: 1168 sheet: -0.48 (0.25), residues: 436 loop : -0.85 (0.18), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 714 TYR 0.017 0.001 TYR C 496 PHE 0.026 0.001 PHE A 65 TRP 0.060 0.001 TRP A 638 HIS 0.003 0.001 HIS A 690 Details of bonding type rmsd covalent geometry : bond 0.00258 (22912) covalent geometry : angle 0.57473 (31050) SS BOND : bond 0.00286 ( 12) SS BOND : angle 0.71566 ( 24) hydrogen bonds : bond 0.03406 ( 894) hydrogen bonds : angle 4.54264 ( 2523) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 225 time to evaluate : 0.848 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: A 91 LEU cc_start: 0.6870 (mm) cc_final: 0.6522 (mm) REVERT: A 486 TYR cc_start: 0.7937 (p90) cc_final: 0.7498 (p90) REVERT: A 633 MET cc_start: 0.2760 (ttm) cc_final: 0.1978 (ttp) REVERT: A 705 TYR cc_start: 0.7737 (m-80) cc_final: 0.7306 (m-80) REVERT: B 438 MET cc_start: 0.4396 (ttm) cc_final: 0.4013 (ttp) REVERT: B 549 LEU cc_start: 0.7306 (OUTLIER) cc_final: 0.6467 (mp) REVERT: B 711 MET cc_start: 0.4680 (tmm) cc_final: 0.4232 (tmm) REVERT: C 112 MET cc_start: 0.8507 (mmt) cc_final: 0.7516 (mmm) REVERT: C 138 ARG cc_start: 0.8080 (OUTLIER) cc_final: 0.7499 (mpp80) REVERT: C 632 MET cc_start: 0.2186 (tpt) cc_final: -0.0978 (mtt) REVERT: C 693 MET cc_start: 0.4189 (mpp) cc_final: 0.3801 (mpp) REVERT: C 704 MET cc_start: 0.4325 (ttt) cc_final: 0.2768 (tmm) REVERT: C 758 PHE cc_start: 0.1594 (m-80) cc_final: 0.1390 (m-80) REVERT: D 90 ILE cc_start: 0.7383 (mt) cc_final: 0.7068 (mp) REVERT: D 350 MET cc_start: 0.6299 (mmm) cc_final: 0.5794 (tpp) REVERT: D 705 TYR cc_start: 0.8239 (m-80) cc_final: 0.7956 (m-10) REVERT: D 734 TYR cc_start: 0.6955 (m-10) cc_final: 0.6621 (m-10) outliers start: 41 outliers final: 37 residues processed: 251 average time/residue: 0.1319 time to fit residues: 53.8545 Evaluate side-chains 254 residues out of total 2470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 215 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 359 ASN Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 693 MET Chi-restraints excluded: chain A residue 701 ARG Chi-restraints excluded: chain A residue 704 MET Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 760 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain C residue 138 ARG Chi-restraints excluded: chain C residue 212 PHE Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 382 THR Chi-restraints excluded: chain C residue 405 TYR Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain D residue 40 ASP Chi-restraints excluded: chain D residue 193 MET Chi-restraints excluded: chain D residue 299 PHE Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 675 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 76 optimal weight: 0.9980 chunk 223 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 71 optimal weight: 0.5980 chunk 279 optimal weight: 0.8980 chunk 245 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 136 optimal weight: 0.0270 chunk 112 optimal weight: 30.0000 chunk 109 optimal weight: 6.9990 chunk 32 optimal weight: 5.9990 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 674 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 = 0.4398 r_free = 0.4398 target = 0.188658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.158328 restraints weight = 35666.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.154709 restraints weight = 53703.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.150453 restraints weight = 40792.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.151239 restraints weight = 41463.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.150165 restraints weight = 31306.634| |-----------------------------------------------------------------------------| r_work (final): 0.3949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7259 moved from start: 0.4992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 22924 Z= 0.106 Angle : 0.585 14.136 31074 Z= 0.296 Chirality : 0.043 0.199 3458 Planarity : 0.004 0.046 4022 Dihedral : 4.320 45.302 3076 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.02 % Favored : 95.80 % Rotamer: Outliers : 1.86 % Allowed : 14.62 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.04 % Twisted Proline : 1.11 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.16), residues: 2808 helix: 1.27 (0.16), residues: 1168 sheet: -0.38 (0.25), residues: 434 loop : -0.84 (0.18), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 714 TYR 0.021 0.001 TYR B 648 PHE 0.026 0.001 PHE A 65 TRP 0.087 0.001 TRP A 638 HIS 0.003 0.001 HIS D 257 Details of bonding type rmsd covalent geometry : bond 0.00239 (22912) covalent geometry : angle 0.58544 (31050) SS BOND : bond 0.00228 ( 12) SS BOND : angle 0.62845 ( 24) hydrogen bonds : bond 0.03299 ( 894) hydrogen bonds : angle 4.51606 ( 2523) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3007.75 seconds wall clock time: 52 minutes 53.61 seconds (3173.61 seconds total)