Starting phenix.real_space_refine on Fri Jun 5 14:41:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9obx_70302/06_2026/9obx_70302.cif Found real_map, /net/cci-nas-00/data/ceres_data/9obx_70302/06_2026/9obx_70302.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9obx_70302/06_2026/9obx_70302.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9obx_70302/06_2026/9obx_70302.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9obx_70302/06_2026/9obx_70302.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9obx_70302/06_2026/9obx_70302.map" } resolution = 2.59 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= -0.000 sd= 0.013 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 100 5.16 5 C 13334 2.51 5 N 3660 2.21 5 O 3923 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-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21017 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 791, 5388 Classifications: {'peptide': 791} Incomplete info: {'truncation_to_alanine': 248} Link IDs: {'PTRANS': 34, 'TRANS': 756} Chain breaks: 2 Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 899 Unresolved non-hydrogen angles: 1138 Unresolved non-hydrogen dihedrals: 739 Unresolved non-hydrogen chiralities: 63 Planarities with less than four sites: {'ASN:plan1': 18, 'ARG:plan': 21, 'HIS:plan': 7, 'GLU:plan': 29, 'GLN:plan1': 10, 'PHE:plan': 8, 'ASP:plan': 21, 'TYR:plan': 10, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 540 Chain: "B" Number of atoms: 5353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 785, 5353 Classifications: {'peptide': 785} Incomplete info: {'truncation_to_alanine': 242} Link IDs: {'PTRANS': 27, 'TRANS': 757} Chain breaks: 2 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 890 Unresolved non-hydrogen angles: 1122 Unresolved non-hydrogen dihedrals: 746 Unresolved non-hydrogen chiralities: 60 Planarities with less than four sites: {'ASP:plan': 25, 'GLU:plan': 28, 'HIS:plan': 8, 'PHE:plan': 13, 'ARG:plan': 12, 'ASN:plan1': 10, 'GLN:plan1': 13, 'TYR:plan': 9, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 528 Chain: "C" Number of atoms: 5015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 792, 5015 Classifications: {'peptide': 792} Incomplete info: {'truncation_to_alanine': 358} Link IDs: {'PTRANS': 34, 'TRANS': 757} Chain breaks: 2 Unresolved chain link angles: 19 Unresolved non-hydrogen bonds: 1307 Unresolved non-hydrogen angles: 1671 Unresolved non-hydrogen dihedrals: 1082 Unresolved non-hydrogen chiralities: 113 Planarities with less than four sites: {'ASN:plan1': 22, 'ARG:plan': 29, 'HIS:plan': 11, 'GLU:plan': 32, 'GLN:plan1': 16, 'PHE:plan': 12, 'ASP:plan': 23, 'TYR:plan': 13, 'TRP:plan': 5} Unresolved non-hydrogen planarities: 735 Chain: "D" Number of atoms: 5231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 788, 5231 Classifications: {'peptide': 788} Incomplete info: {'truncation_to_alanine': 285} Link IDs: {'PTRANS': 28, 'TRANS': 759} Chain breaks: 2 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 1044 Unresolved non-hydrogen angles: 1323 Unresolved non-hydrogen dihedrals: 871 Unresolved non-hydrogen chiralities: 77 Planarities with less than four sites: {'ASP:plan': 28, 'GLU:plan': 33, 'HIS:plan': 8, 'PHE:plan': 15, 'ARG:plan': 13, 'ASN:plan1': 13, 'GLN:plan1': 13, 'TYR:plan': 13, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 611 Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "D" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Time building chain proxies: 5.61, per 1000 atoms: 0.27 Number of scatterers: 21017 At special positions: 0 Unit cell: (147, 116.76, 173.88, 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 100 16.00 O 3923 8.00 N 3660 7.00 C 13334 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 420 " - pdb=" SG CYS A 454 " distance=2.03 Simple disulfide: pdb=" SG CYS A 436 " - pdb=" SG CYS A 455 " distance=2.03 Simple disulfide: pdb=" SG CYS A 744 " - pdb=" SG CYS A 798 " distance=2.03 Simple disulfide: pdb=" SG CYS B 429 " - pdb=" SG CYS B 456 " distance=2.03 Simple disulfide: pdb=" SG CYS B 436 " - pdb=" SG CYS B 457 " distance=2.03 Simple disulfide: pdb=" SG CYS B 746 " - pdb=" SG CYS B 801 " distance=2.03 Simple disulfide: pdb=" SG CYS C 420 " - pdb=" SG CYS C 454 " distance=2.03 Simple disulfide: pdb=" SG CYS C 436 " - pdb=" SG CYS C 455 " distance=2.03 Simple disulfide: pdb=" SG CYS C 744 " - pdb=" SG CYS C 798 " distance=2.03 Simple disulfide: pdb=" SG CYS D 429 " - pdb=" SG CYS D 456 " distance=2.03 Simple disulfide: pdb=" SG CYS D 436 " - pdb=" SG CYS D 457 " distance=2.03 Simple disulfide: pdb=" SG CYS D 746 " - pdb=" SG CYS D 801 " 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: 1.79 Conformation dependent library (CDL) restraints added in 1.1 seconds 6264 Ramachandran restraints generated. 3132 Oldfield, 0 Emsley, 3132 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5900 Finding SS restraints... Secondary structure from input PDB file: 111 helices and 34 sheets defined 44.5% alpha, 11.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'A' and resid 35 through 52 removed outlier: 3.505A pdb=" N ASN A 47 " --> pdb=" O ARG A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 86 removed outlier: 3.753A pdb=" N SER A 85 " --> pdb=" O ASP A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 115 removed outlier: 3.886A pdb=" N PHE A 113 " --> pdb=" O TYR A 109 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N TYR A 114 " --> pdb=" O THR A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 130 Processing helix chain 'A' and resid 147 through 159 removed outlier: 3.512A pdb=" N TRP A 151 " --> pdb=" O GLN A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 187 removed outlier: 3.897A pdb=" N GLU A 186 " --> pdb=" O THR A 182 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ARG A 187 " --> pdb=" O LEU A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 213 removed outlier: 3.592A pdb=" N GLU A 210 " --> pdb=" O ALA A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 238 removed outlier: 3.524A pdb=" N THR A 230 " --> pdb=" O ASP A 226 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N MET A 237 " --> pdb=" O ARG A 233 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU A 238 " --> pdb=" O ALA A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 255 removed outlier: 3.548A pdb=" N ILE A 254 " --> pdb=" O GLY A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 261 Processing helix chain 'A' and resid 276 through 298 removed outlier: 3.726A pdb=" N HIS A 293 " --> pdb=" O ALA A 289 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU A 294 " --> pdb=" O GLN A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 328 Processing helix chain 'A' and resid 381 through 385 removed outlier: 4.004A pdb=" N GLU A 385 " --> pdb=" O PRO A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 471 Processing helix chain 'A' and resid 499 through 507 Processing helix chain 'A' and resid 520 through 525 Processing helix chain 'A' and resid 559 through 583 removed outlier: 4.341A pdb=" N HIS A 571 " --> pdb=" O GLY A 567 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL A 572 " --> pdb=" O LEU A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 616 Processing helix chain 'A' and resid 626 through 657 removed outlier: 3.542A pdb=" N LEU A 632 " --> pdb=" O SER A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 669 through 674 Processing helix chain 'A' and resid 687 through 696 removed outlier: 3.829A pdb=" N GLN A 696 " --> pdb=" O TYR A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 708 removed outlier: 4.024A pdb=" N LYS A 708 " --> pdb=" O ARG A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 723 Processing helix chain 'A' and resid 733 through 743 removed outlier: 4.080A pdb=" N PHE A 738 " --> pdb=" O ALA A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 782 Processing helix chain 'A' and resid 783 through 793 Processing helix chain 'A' and resid 813 through 838 removed outlier: 3.624A pdb=" N VAL A 825 " --> pdb=" O ALA A 821 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA A 826 " --> pdb=" O GLY A 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 53 Processing helix chain 'B' and resid 54 through 56 No H-bonds generated for 'chain 'B' and resid 54 through 56' Processing helix chain 'B' and resid 77 through 90 Processing helix chain 'B' and resid 106 through 119 removed outlier: 4.090A pdb=" N GLN B 110 " --> pdb=" O GLU B 106 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR B 119 " --> pdb=" O ILE B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 132 removed outlier: 3.625A pdb=" N SER B 130 " --> pdb=" O HIS B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 164 removed outlier: 3.585A pdb=" N MET B 161 " --> pdb=" O MET B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 191 removed outlier: 3.586A pdb=" N PHE B 182 " --> pdb=" O GLY B 178 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL B 183 " --> pdb=" O TYR B 179 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE B 186 " --> pdb=" O PHE B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 221 Processing helix chain 'B' and resid 235 through 248 removed outlier: 3.685A pdb=" N TYR B 239 " --> pdb=" O GLU B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 264 removed outlier: 3.950A pdb=" N ALA B 263 " --> pdb=" O PRO B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 311 removed outlier: 3.540A pdb=" N ARG B 294 " --> pdb=" O PRO B 290 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ILE B 300 " --> pdb=" O GLY B 296 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N THR B 301 " --> pdb=" O ILE B 297 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N HIS B 311 " --> pdb=" O MET B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 338 removed outlier: 4.324A pdb=" N TYR B 338 " --> pdb=" O MET B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 473 Processing helix chain 'B' and resid 495 through 503 Processing helix chain 'B' and resid 516 through 521 removed outlier: 3.600A pdb=" N GLU B 521 " --> pdb=" O GLU B 517 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 579 Processing helix chain 'B' and resid 601 through 614 removed outlier: 3.576A pdb=" N VAL B 613 " --> pdb=" O LEU B 609 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHE B 614 " --> pdb=" O TRP B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 656 Processing helix chain 'B' and resid 668 through 673 Processing helix chain 'B' and resid 689 through 699 Processing helix chain 'B' and resid 699 through 707 removed outlier: 3.779A pdb=" N GLY B 707 " --> pdb=" O HIS B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 708 through 710 No H-bonds generated for 'chain 'B' and resid 708 through 710' Processing helix chain 'B' and resid 713 through 723 Processing helix chain 'B' and resid 733 through 741 Processing helix chain 'B' and resid 771 through 786 removed outlier: 4.464A pdb=" N GLN B 775 " --> pdb=" O GLY B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 787 through 797 Processing helix chain 'B' and resid 819 through 843 Processing helix chain 'C' and resid 35 through 52 removed outlier: 3.804A pdb=" N ARG C 43 " --> pdb=" O GLU C 39 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLU C 44 " --> pdb=" O GLN C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 86 removed outlier: 3.929A pdb=" N SER C 85 " --> pdb=" O ASP C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 115 removed outlier: 3.504A pdb=" N THR C 110 " --> pdb=" O PRO C 106 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N PHE C 113 " --> pdb=" O TYR C 109 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N TYR C 114 " --> pdb=" O THR C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 130 Processing helix chain 'C' and resid 143 through 146 Processing helix chain 'C' and resid 147 through 159 removed outlier: 3.799A pdb=" N ARG C 156 " --> pdb=" O PHE C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 187 removed outlier: 3.601A pdb=" N ARG C 187 " --> pdb=" O LEU C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 213 removed outlier: 3.560A pdb=" N ALA C 211 " --> pdb=" O LEU C 207 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLU C 213 " --> pdb=" O MET C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 238 removed outlier: 3.879A pdb=" N ALA C 229 " --> pdb=" O GLU C 225 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N THR C 230 " --> pdb=" O ASP C 226 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL C 231 " --> pdb=" O ASP C 227 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N MET C 237 " --> pdb=" O ARG C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 255 Processing helix chain 'C' and resid 257 through 262 removed outlier: 4.464A pdb=" N TYR C 261 " --> pdb=" O ASN C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 298 removed outlier: 3.509A pdb=" N GLY C 286 " --> pdb=" O SER C 282 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N HIS C 293 " --> pdb=" O ALA C 289 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU C 297 " --> pdb=" O HIS C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 328 removed outlier: 3.583A pdb=" N VAL C 324 " --> pdb=" O LEU C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 385 removed outlier: 4.222A pdb=" N GLU C 385 " --> pdb=" O PRO C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 457 through 471 Processing helix chain 'C' and resid 499 through 507 Processing helix chain 'C' and resid 520 through 525 Processing helix chain 'C' and resid 559 through 582 removed outlier: 3.564A pdb=" N VAL C 570 " --> pdb=" O VAL C 566 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N HIS C 571 " --> pdb=" O GLY C 567 " (cutoff:3.500A) Processing helix chain 'C' and resid 603 through 616 Processing helix chain 'C' and resid 626 through 657 removed outlier: 3.511A pdb=" N VAL C 635 " --> pdb=" O ILE C 631 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE C 642 " --> pdb=" O GLY C 638 " (cutoff:3.500A) Processing helix chain 'C' and resid 669 through 674 Processing helix chain 'C' and resid 687 through 695 Processing helix chain 'C' and resid 696 through 698 No H-bonds generated for 'chain 'C' and resid 696 through 698' Processing helix chain 'C' and resid 699 through 708 removed outlier: 3.911A pdb=" N LYS C 708 " --> pdb=" O ARG C 704 " (cutoff:3.500A) Processing helix chain 'C' and resid 713 through 723 Processing helix chain 'C' and resid 733 through 743 removed outlier: 4.024A pdb=" N PHE C 738 " --> pdb=" O ALA C 734 " (cutoff:3.500A) Processing helix chain 'C' and resid 768 through 782 Processing helix chain 'C' and resid 783 through 793 Processing helix chain 'C' and resid 813 through 838 removed outlier: 3.517A pdb=" N PHE C 817 " --> pdb=" O MET C 813 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL C 825 " --> pdb=" O ALA C 821 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ALA C 826 " --> pdb=" O GLY C 822 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ILE C 828 " --> pdb=" O ILE C 824 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N PHE C 829 " --> pdb=" O VAL C 825 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 53 Processing helix chain 'D' and resid 54 through 57 removed outlier: 4.164A pdb=" N ASP D 57 " --> pdb=" O HIS D 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 54 through 57' Processing helix chain 'D' and resid 77 through 90 Processing helix chain 'D' and resid 107 through 119 Processing helix chain 'D' and resid 127 through 132 removed outlier: 3.818A pdb=" N SER D 130 " --> pdb=" O HIS D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 164 Processing helix chain 'D' and resid 178 through 191 removed outlier: 4.071A pdb=" N VAL D 183 " --> pdb=" O TYR D 179 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE D 186 " --> pdb=" O PHE D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 221 Processing helix chain 'D' and resid 235 through 248 removed outlier: 3.621A pdb=" N TYR D 239 " --> pdb=" O GLU D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 264 removed outlier: 3.900A pdb=" N ALA D 263 " --> pdb=" O PRO D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 311 removed outlier: 3.723A pdb=" N HIS D 311 " --> pdb=" O MET D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 327 Processing helix chain 'D' and resid 332 through 338 removed outlier: 4.397A pdb=" N TYR D 338 " --> pdb=" O MET D 334 " (cutoff:3.500A) Processing helix chain 'D' and resid 459 through 473 Processing helix chain 'D' and resid 495 through 503 Processing helix chain 'D' and resid 518 through 522 removed outlier: 3.558A pdb=" N GLU D 521 " --> pdb=" O GLU D 518 " (cutoff:3.500A) Processing helix chain 'D' and resid 555 through 579 removed outlier: 3.645A pdb=" N TYR D 579 " --> pdb=" O PHE D 575 " (cutoff:3.500A) Processing helix chain 'D' and resid 601 through 614 removed outlier: 3.511A pdb=" N LEU D 612 " --> pdb=" O LEU D 608 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL D 613 " --> pdb=" O LEU D 609 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE D 614 " --> pdb=" O TRP D 610 " (cutoff:3.500A) Processing helix chain 'D' and resid 625 through 656 Processing helix chain 'D' and resid 668 through 673 Processing helix chain 'D' and resid 689 through 699 Processing helix chain 'D' and resid 699 through 707 removed outlier: 3.669A pdb=" N GLY D 707 " --> pdb=" O HIS D 703 " (cutoff:3.500A) Processing helix chain 'D' and resid 708 through 710 No H-bonds generated for 'chain 'D' and resid 708 through 710' Processing helix chain 'D' and resid 713 through 723 Processing helix chain 'D' and resid 733 through 741 Processing helix chain 'D' and resid 771 through 786 removed outlier: 4.377A pdb=" N GLN D 775 " --> pdb=" O GLY D 771 " (cutoff:3.500A) Processing helix chain 'D' and resid 787 through 797 removed outlier: 3.608A pdb=" N GLU D 791 " --> pdb=" O GLY D 787 " (cutoff:3.500A) Processing helix chain 'D' and resid 819 through 843 Processing sheet with id=AA1, first strand: chain 'A' and resid 90 through 91 removed outlier: 7.000A pdb=" N ILE A 90 " --> pdb=" O LEU A 119 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N VAL A 118 " --> pdb=" O LEU A 138 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 193 through 197 removed outlier: 4.030A pdb=" N LYS A 193 " --> pdb=" O ILE A 163 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE A 197 " --> pdb=" O VAL A 167 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 267 through 271 removed outlier: 6.550A pdb=" N TYR A 351 " --> pdb=" O ILE A 366 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ILE A 366 " --> pdb=" O TYR A 351 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ILE A 353 " --> pdb=" O VAL A 364 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 339 through 340 removed outlier: 4.227A pdb=" N GLU A 339 " --> pdb=" O LYS A 347 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 410 through 413 removed outlier: 8.114A pdb=" N ILE A 435 " --> pdb=" O TYR A 474 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N VAL A 476 " --> pdb=" O ILE A 435 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU A 478 " --> pdb=" O THR A 437 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 487 through 489 Processing sheet with id=AA7, first strand: chain 'A' and resid 527 through 529 Processing sheet with id=AA8, first strand: chain 'A' and resid 681 through 682 removed outlier: 6.815A pdb=" N ALA A 682 " --> pdb=" O ILE A 730 " (cutoff:3.500A) removed outlier: 9.201A pdb=" N ASP A 732 " --> pdb=" O ALA A 682 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LEU A 538 " --> pdb=" O GLU A 751 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N GLU A 751 " --> pdb=" O LEU A 538 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE A 540 " --> pdb=" O THR A 749 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 67 through 73 removed outlier: 6.647A pdb=" N GLY B 36 " --> pdb=" O ILE B 94 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLY B 96 " --> pdb=" O GLY B 36 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 123 through 124 removed outlier: 6.466A pdb=" N ILE B 123 " --> pdb=" O PHE B 144 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 198 through 199 removed outlier: 3.972A pdb=" N ILE B 227 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LEU B 277 " --> pdb=" O LEU B 367 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N LEU B 362 " --> pdb=" O LYS B 378 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N LYS B 378 " --> pdb=" O LEU B 362 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ILE B 364 " --> pdb=" O VAL B 376 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 343 through 344 Processing sheet with id=AB4, first strand: chain 'B' and resid 475 through 480 removed outlier: 3.887A pdb=" N MET B 508 " --> pdb=" O SER B 407 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 418 through 420 Processing sheet with id=AB6, first strand: chain 'B' and resid 489 through 490 Processing sheet with id=AB7, first strand: chain 'B' and resid 530 through 532 removed outlier: 4.324A pdb=" N ILE B 530 " --> pdb=" O TYR B 762 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 683 through 684 removed outlier: 6.489A pdb=" N GLY B 684 " --> pdb=" O ILE B 730 " (cutoff:3.500A) removed outlier: 8.891A pdb=" N ASP B 732 " --> pdb=" O GLY B 684 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 28 through 31 removed outlier: 6.642A pdb=" N ASN C 28 " --> pdb=" O ALA C 89 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N LEU C 91 " --> pdb=" O ASN C 28 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N GLY C 30 " --> pdb=" O LEU C 91 " (cutoff:3.500A) removed outlier: 9.456A pdb=" N LEU C 119 " --> pdb=" O TYR C 88 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N ILE C 90 " --> pdb=" O LEU C 119 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'C' and resid 194 through 197 removed outlier: 6.318A pdb=" N LEU C 165 " --> pdb=" O LEU C 195 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N PHE C 197 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N VAL C 167 " --> pdb=" O PHE C 197 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N SER C 168 " --> pdb=" O SER C 222 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N TRP C 247 " --> pdb=" O ILE C 267 " (cutoff:3.500A) removed outlier: 8.324A pdb=" N LEU C 269 " --> pdb=" O TRP C 247 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N VAL C 249 " --> pdb=" O LEU C 269 " (cutoff:3.500A) removed outlier: 9.388A pdb=" N LEU C 271 " --> pdb=" O VAL C 249 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 365 through 367 removed outlier: 3.581A pdb=" N ILE C 373 " --> pdb=" O ILE C 366 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 473 through 478 Processing sheet with id=AC4, first strand: chain 'C' and resid 410 through 413 Processing sheet with id=AC5, first strand: chain 'C' and resid 487 through 489 Processing sheet with id=AC6, first strand: chain 'C' and resid 527 through 529 Processing sheet with id=AC7, first strand: chain 'C' and resid 681 through 682 removed outlier: 6.802A pdb=" N ALA C 682 " --> pdb=" O ILE C 730 " (cutoff:3.500A) removed outlier: 9.213A pdb=" N ASP C 732 " --> pdb=" O ALA C 682 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N LEU C 538 " --> pdb=" O GLU C 751 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N GLU C 751 " --> pdb=" O LEU C 538 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ILE C 540 " --> pdb=" O THR C 749 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 68 through 73 removed outlier: 4.135A pdb=" N GLU D 69 " --> pdb=" O ILE D 37 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N MET D 73 " --> pdb=" O LEU D 41 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N GLY D 36 " --> pdb=" O ILE D 94 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLY D 96 " --> pdb=" O GLY D 36 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 123 through 124 removed outlier: 6.047A pdb=" N ILE D 123 " --> pdb=" O PHE D 144 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'D' and resid 198 through 199 removed outlier: 3.901A pdb=" N ILE D 227 " --> pdb=" O ILE D 168 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY D 377 " --> pdb=" O ILE D 364 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N LEU D 366 " --> pdb=" O ARG D 375 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N ARG D 375 " --> pdb=" O LEU D 366 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 343 through 344 Processing sheet with id=AD3, first strand: chain 'D' and resid 475 through 480 removed outlier: 4.085A pdb=" N MET D 508 " --> pdb=" O SER D 407 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 418 through 421 Processing sheet with id=AD5, first strand: chain 'D' and resid 489 through 490 Processing sheet with id=AD6, first strand: chain 'D' and resid 530 through 532 removed outlier: 4.391A pdb=" N ILE D 530 " --> pdb=" O TYR D 762 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 683 through 684 removed outlier: 6.437A pdb=" N GLY D 684 " --> pdb=" O ILE D 730 " (cutoff:3.500A) removed outlier: 8.903A pdb=" N ASP D 732 " --> pdb=" O GLY D 684 " (cutoff:3.500A) 1101 hydrogen bonds defined for protein. 3177 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: 3.80 Time building geometry restraints manager: 2.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5594 1.33 - 1.45: 3755 1.45 - 1.57: 11857 1.57 - 1.69: 0 1.69 - 1.81: 169 Bond restraints: 21375 Sorted by residual: bond pdb=" N SER C 443 " pdb=" CA SER C 443 " ideal model delta sigma weight residual 1.455 1.486 -0.031 9.60e-03 1.09e+04 1.05e+01 bond pdb=" CA SER C 446 " pdb=" CB SER C 446 " ideal model delta sigma weight residual 1.536 1.512 0.024 9.10e-03 1.21e+04 7.10e+00 bond pdb=" N THR C 442 " pdb=" CA THR C 442 " ideal model delta sigma weight residual 1.457 1.486 -0.029 1.10e-02 8.26e+03 6.99e+00 bond pdb=" N HIS C 449 " pdb=" CA HIS C 449 " ideal model delta sigma weight residual 1.457 1.491 -0.033 1.29e-02 6.01e+03 6.59e+00 bond pdb=" N CYS C 436 " pdb=" CA CYS C 436 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.23e-02 6.61e+03 6.57e+00 ... (remaining 21370 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.24: 28637 1.24 - 2.48: 482 2.48 - 3.73: 112 3.73 - 4.97: 25 4.97 - 6.21: 3 Bond angle restraints: 29259 Sorted by residual: angle pdb=" CA PRO C 444 " pdb=" C PRO C 444 " pdb=" O PRO C 444 " ideal model delta sigma weight residual 121.31 118.48 2.83 7.40e-01 1.83e+00 1.46e+01 angle pdb=" CA THR C 437 " pdb=" C THR C 437 " pdb=" O THR C 437 " ideal model delta sigma weight residual 121.58 117.95 3.63 1.12e+00 7.97e-01 1.05e+01 angle pdb=" CA SER C 443 " pdb=" C SER C 443 " pdb=" N PRO C 444 " ideal model delta sigma weight residual 117.95 120.40 -2.45 7.70e-01 1.69e+00 1.01e+01 angle pdb=" N THR C 442 " pdb=" CA THR C 442 " pdb=" C THR C 442 " ideal model delta sigma weight residual 114.16 109.50 4.66 1.48e+00 4.57e-01 9.94e+00 angle pdb=" CA ASN C 440 " pdb=" C ASN C 440 " pdb=" O ASN C 440 " ideal model delta sigma weight residual 121.94 118.33 3.61 1.15e+00 7.56e-01 9.84e+00 ... (remaining 29254 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.91: 12085 16.91 - 33.81: 364 33.81 - 50.71: 75 50.71 - 67.62: 11 67.62 - 84.52: 8 Dihedral angle restraints: 12543 sinusoidal: 3432 harmonic: 9111 Sorted by residual: dihedral pdb=" CA GLN A 405 " pdb=" C GLN A 405 " pdb=" N GLU A 406 " pdb=" CA GLU A 406 " ideal model delta harmonic sigma weight residual -180.00 -156.56 -23.44 0 5.00e+00 4.00e-02 2.20e+01 dihedral pdb=" CA GLN C 405 " pdb=" C GLN C 405 " pdb=" N GLU C 406 " pdb=" CA GLU C 406 " ideal model delta harmonic sigma weight residual -180.00 -159.67 -20.33 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CA GLY D 754 " pdb=" C GLY D 754 " pdb=" N LYS D 755 " pdb=" CA LYS D 755 " ideal model delta harmonic sigma weight residual -180.00 -160.29 -19.71 0 5.00e+00 4.00e-02 1.55e+01 ... (remaining 12540 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 2321 0.033 - 0.067: 857 0.067 - 0.100: 225 0.100 - 0.134: 142 0.134 - 0.167: 6 Chirality restraints: 3551 Sorted by residual: chirality pdb=" CA CYS C 436 " pdb=" N CYS C 436 " pdb=" C CYS C 436 " pdb=" CB CYS C 436 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.00e-01 chirality pdb=" CA VAL B 527 " pdb=" N VAL B 527 " pdb=" C VAL B 527 " pdb=" CB VAL B 527 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.84e-01 chirality pdb=" CA VAL D 527 " pdb=" N VAL D 527 " pdb=" C VAL D 527 " pdb=" CB VAL D 527 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.66e-01 ... (remaining 3548 not shown) Planarity restraints: 3816 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 176 " 0.024 5.00e-02 4.00e+02 3.56e-02 2.03e+00 pdb=" N PRO B 177 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO B 177 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 177 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU D 552 " -0.021 5.00e-02 4.00e+02 3.09e-02 1.52e+00 pdb=" N PRO D 553 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO D 553 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO D 553 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 443 " 0.020 5.00e-02 4.00e+02 3.00e-02 1.44e+00 pdb=" N PRO A 444 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO A 444 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 444 " 0.017 5.00e-02 4.00e+02 ... (remaining 3813 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 2562 2.75 - 3.29: 20027 3.29 - 3.83: 32983 3.83 - 4.36: 37872 4.36 - 4.90: 65757 Nonbonded interactions: 159201 Sorted by model distance: nonbonded pdb=" OH TYR B 167 " pdb=" OG1 THR B 428 " model vdw 2.216 3.040 nonbonded pdb=" OD2 ASP D 732 " pdb=" OH TYR D 762 " model vdw 2.254 3.040 nonbonded pdb=" OD2 ASP B 732 " pdb=" OH TYR B 762 " model vdw 2.279 3.040 nonbonded pdb=" O ASP A 198 " pdb=" OG1 THR A 201 " model vdw 2.307 3.040 nonbonded pdb=" N GLY C 120 " pdb=" O LEU C 138 " model vdw 2.330 3.120 ... (remaining 159196 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 26 through 172 and (name N or name CA or name C or name O \ or name CB )) or (resid 173 through 199 and (name N or name CA or name C or nam \ e O or name CB )) or resid 200 or (resid 201 through 241 and (name N or name CA \ or name C or name O or name CB )) or resid 242 or (resid 243 and (name N or name \ CA or name C or name O or name CB )) or resid 244 or (resid 245 through 249 and \ (name N or name CA or name C or name O or name CB )) or (resid 250 through 255 \ and (name N or name CA or name C or name O or name CB )) or (resid 256 through 2 \ 64 and (name N or name CA or name C or name O or name CB )) or resid 265 or (res \ id 266 through 267 and (name N or name CA or name C or name O or name CB )) or r \ esid 268 or (resid 269 through 273 and (name N or name CA or name C or name O or \ name CB )) or (resid 274 through 343 and (name N or name CA or name C or name O \ or name CB )) or (resid 344 through 364 and (name N or name CA or name C or nam \ e O or name CB )) or resid 365 or (resid 366 through 368 and (name N or name CA \ or name C or name O or name CB )) or (resid 369 through 382 and (name N or name \ CA or name C or name O or name CB )) or (resid 383 through 390 and (name N or na \ me CA or name C or name O or name CB )) or resid 391 through 420 or (resid 421 a \ nd (name N or name CA or name C or name O or name CB )) or resid 422 through 546 \ or (resid 547 through 550 and (name N or name CA or name C or name O or name CB \ )) or resid 551 or (resid 552 and (name N or name CA or name C or name O or nam \ e CB )) or resid 553 through 563 or (resid 564 and (name N or name CA or name C \ or name O or name CB )) or resid 565 through 580 or (resid 581 through 583 and ( \ name N or name CA or name C or name O or name CB )) or resid 584 through 694 or \ (resid 695 and (name N or name CA or name C or name O or name CB )) or resid 696 \ through 763 or (resid 764 through 765 and (name N or name CA or name C or name \ O or name CB )) or resid 766 through 769 or (resid 770 and (name N or name CA or \ name C or name O or name CB )) or resid 771 through 817 or (resid 818 and (name \ N or name CA or name C or name O or name CB )) or resid 819 through 827 or (res \ id 828 through 830 and (name N or name CA or name C or name O or name CB )) or r \ esid 831 through 901)) selection = (chain 'C' and ((resid 26 through 392 and (name N or name CA or name C or name O \ or name CB )) or resid 393 through 426 or (resid 427 and (name N or name CA or \ name C or name O or name CB )) or resid 428 through 567 or (resid 568 and (name \ N or name CA or name C or name O or name CB )) or resid 569 through 764 or (resi \ d 765 and (name N or name CA or name C or name O or name CB )) or resid 766 thro \ ugh 793 or (resid 794 and (name N or name CA or name C or name O or name CB )) o \ r resid 795 or (resid 796 through 797 and (name N or name CA or name C or name O \ or name CB )) or resid 798 through 799 or (resid 800 through 806 and (name N or \ name CA or name C or name O or name CB )) or resid 807 through 832 or (resid 83 \ 3 through 838 and (name N or name CA or name C or name O or name CB )) or resid \ 901)) } ncs_group { reference = (chain 'B' and (resid 34 through 171 or (resid 172 and (name N or name CA or nam \ e C or name O or name CB )) or resid 173 through 174 or (resid 175 through 176 a \ nd (name N or name CA or name C or name O or name CB )) or resid 177 through 190 \ or (resid 191 through 192 and (name N or name CA or name C or name O or name CB \ )) or resid 193 through 201 or (resid 202 through 211 and (name N or name CA or \ name C or name O or name CB )) or (resid 212 through 224 and (name N or name CA \ or name C or name O or name CB )) or resid 225 through 231 or (resid 232 throug \ h 247 and (name N or name CA or name C or name O or name CB )) or resid 248 or ( \ resid 249 through 250 and (name N or name CA or name C or name O or name CB )) o \ r (resid 251 through 254 and (name N or name CA or name C or name O or name CB ) \ ) or resid 255 through 260 or (resid 261 and (name N or name CA or name C or nam \ e O or name CB )) or resid 262 through 264 or (resid 265 and (name N or name CA \ or name C or name O or name CB )) or resid 266 through 267 or (resid 268 and (na \ me N or name CA or name C or name O or name CB )) or resid 269 through 285 or (r \ esid 286 through 287 and (name N or name CA or name C or name O or name CB )) or \ resid 288 or (resid 289 through 295 and (name N or name CA or name C or name O \ or name CB )) or (resid 296 through 345 and (name N or name CA or name C or name \ O or name CB )) or (resid 346 through 359 and (name N or name CA or name C or n \ ame O or name CB )) or resid 360 or (resid 361 and (name N or name CA or name C \ or name O or name CB )) or resid 362 through 369 or (resid 370 and (name N or na \ me CA or name C or name O or name CB )) or resid 371 or (resid 372 and (name N o \ r name CA or name C or name O or name CB )) or resid 373 through 374 or (resid 3 \ 75 and (name N or name CA or name C or name O or name CB )) or resid 376 through \ 377 or (resid 378 and (name N or name CA or name C or name O or name CB )) or r \ esid 379 through 440 or (resid 441 and (name N or name CA or name C or name O or \ name CB )) or resid 442 through 545 or (resid 546 through 547 and (name N or na \ me CA or name C or name O or name CB )) or resid 548 through 564 or (resid 565 a \ nd (name N or name CA or name C or name O or name CB )) or resid 566 through 573 \ or (resid 574 through 575 and (name N or name CA or name C or name O or name CB \ )) or resid 576 through 577 or (resid 578 through 579 and (name N or name CA or \ name C or name O or name CB )) or resid 599 through 676 or (resid 677 and (name \ N or name CA or name C or name O or name CB )) or resid 678 through 700 or (res \ id 701 and (name N or name CA or name C or name O or name CB )) or resid 702 thr \ ough 815 or (resid 816 and (name N or name CA or name C or name O or name CB )) \ or resid 817 through 901)) selection = (chain 'D' and (resid 34 through 445 or (resid 446 through 449 and (name N or na \ me CA or name C or name O or name CB )) or resid 450 through 502 or (resid 503 a \ nd (name N or name CA or name C or name O or name CB )) or resid 504 through 576 \ or (resid 577 through 579 and (name N or name CA or name C or name O or name CB \ )) or resid 599 through 630 or (resid 631 and (name N or name CA or name C or n \ ame O or name CB )) or resid 632 through 655 or (resid 656 through 662 and (name \ N or name CA or name C or name O or name CB )) or resid 663 through 809 or (res \ id 810 and (name N or name CA or name C or name O or name CB )) or resid 811 thr \ ough 828 or (resid 829 through 830 and (name N or name CA or name C or name O or \ name CB )) or resid 831 through 839 or (resid 840 through 845 and (name N or na \ me CA or name C or name O or name CB )) or resid 901)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.990 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: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 21.300 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 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 : 0.002 0.033 21387 Z= 0.123 Angle : 0.445 6.209 29283 Z= 0.261 Chirality : 0.041 0.167 3551 Planarity : 0.003 0.036 3816 Dihedral : 9.466 84.524 6607 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.90 % Favored : 96.01 % Rotamer: Outliers : 0.81 % Allowed : 3.35 % Favored : 95.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.15), residues: 3132 helix: 0.08 (0.14), residues: 1289 sheet: 0.04 (0.30), residues: 340 loop : -0.91 (0.16), residues: 1503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 397 TYR 0.012 0.001 TYR A 410 PHE 0.017 0.001 PHE C 458 TRP 0.008 0.001 TRP A 381 HIS 0.007 0.001 HIS C 449 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.12 (21375) covalent geometry : angle 0.44496 / 0.26 (29259) SS BOND : bond 0.00188 / 0.13 ( 12) SS BOND : angle 0.69962 / 0.48 ( 24) hydrogen bonds : bond 0.26340 / 19.36 ( 1101) hydrogen bonds : angle 7.24616 / 5.35 ( 3177) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6264 Ramachandran restraints generated. 3132 Oldfield, 0 Emsley, 3132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6264 Ramachandran restraints generated. 3132 Oldfield, 0 Emsley, 3132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 362 time to evaluate : 0.517 Fit side-chains REVERT: A 182 THR cc_start: 0.7997 (m) cc_final: 0.7716 (p) REVERT: A 252 ARG cc_start: 0.7152 (mtm180) cc_final: 0.6705 (mtt90) REVERT: A 394 MET cc_start: 0.8200 (ttp) cc_final: 0.7923 (ttm) REVERT: A 488 GLU cc_start: 0.7397 (mt-10) cc_final: 0.7087 (pm20) REVERT: A 522 GLU cc_start: 0.8564 (mp0) cc_final: 0.8342 (mp0) REVERT: A 654 PHE cc_start: 0.8523 (t80) cc_final: 0.8302 (t80) REVERT: B 372 LYS cc_start: 0.8125 (ptmt) cc_final: 0.7908 (ttmt) REVERT: B 606 ILE cc_start: 0.8213 (tt) cc_final: 0.7929 (mm) REVERT: B 693 ARG cc_start: 0.8496 (tpp-160) cc_final: 0.7896 (ttp-110) REVERT: B 742 ARG cc_start: 0.7979 (mmm-85) cc_final: 0.7319 (mmt90) REVERT: C 423 GLU cc_start: 0.7536 (mt-10) cc_final: 0.7202 (mm-30) REVERT: C 451 VAL cc_start: 0.8255 (m) cc_final: 0.8005 (p) REVERT: C 501 MET cc_start: 0.9192 (mtm) cc_final: 0.8807 (mtm) REVERT: C 704 ARG cc_start: 0.7446 (ttm110) cc_final: 0.7083 (mtt90) REVERT: D 385 GLN cc_start: 0.7189 (mt0) cc_final: 0.6862 (mt0) REVERT: D 388 TYR cc_start: 0.7197 (m-10) cc_final: 0.6929 (m-80) REVERT: D 420 GLU cc_start: 0.7108 (pt0) cc_final: 0.6714 (pm20) REVERT: D 453 ILE cc_start: 0.8189 (tt) cc_final: 0.7977 (pt) REVERT: D 693 ARG cc_start: 0.8264 (tpp-160) cc_final: 0.7677 (tmm160) REVERT: D 814 ASP cc_start: 0.7351 (p0) cc_final: 0.6623 (t0) outliers start: 13 outliers final: 4 residues processed: 369 average time/residue: 0.5946 time to fit residues: 250.2739 Evaluate side-chains 321 residues out of total 2744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 317 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 773 SER Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 440 ILE Chi-restraints excluded: chain C residue 791 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 197 optimal weight: 0.0060 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 50.0000 chunk 183 optimal weight: 50.0000 chunk 298 optimal weight: 0.1980 overall best weight: 0.8398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 GLN ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 393 GLN ** B 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 219 GLN ** B 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 385 GLN B 767 GLN C 393 GLN C 440 ASN C 509 GLN ** D 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 656 GLN D 662 GLN D 767 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.228016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.166088 restraints weight = 22119.247| |-----------------------------------------------------------------------------| r_work (start): 0.3821 rms_B_bonded: 1.96 r_work: 0.3456 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3349 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.1421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 21387 Z= 0.126 Angle : 0.496 6.510 29283 Z= 0.275 Chirality : 0.043 0.150 3551 Planarity : 0.004 0.057 3816 Dihedral : 4.270 44.536 3282 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.09 % Favored : 95.82 % Rotamer: Outliers : 2.67 % Allowed : 8.75 % Favored : 88.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.15), residues: 3132 helix: 1.32 (0.14), residues: 1329 sheet: 0.06 (0.29), residues: 364 loop : -0.96 (0.17), residues: 1439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 359 TYR 0.016 0.001 TYR A 410 PHE 0.020 0.002 PHE A 458 TRP 0.009 0.001 TRP C 563 HIS 0.004 0.001 HIS B 486 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.13 (21375) covalent geometry : angle 0.49575 / 0.28 (29259) SS BOND : bond 0.00336 / 0.24 ( 12) SS BOND : angle 0.87725 / 0.63 ( 24) hydrogen bonds : bond 0.05292 / 3.89 ( 1101) hydrogen bonds : angle 4.75764 / 3.48 ( 3177) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6264 Ramachandran restraints generated. 3132 Oldfield, 0 Emsley, 3132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6264 Ramachandran restraints generated. 3132 Oldfield, 0 Emsley, 3132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 2744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 322 time to evaluate : 0.648 Fit side-chains REVERT: A 146 HIS cc_start: 0.7321 (OUTLIER) cc_final: 0.6829 (t-90) REVERT: A 182 THR cc_start: 0.7660 (m) cc_final: 0.7293 (p) REVERT: A 212 ARG cc_start: 0.7541 (ttp80) cc_final: 0.7331 (ttp80) REVERT: A 252 ARG cc_start: 0.6520 (mtm180) cc_final: 0.5818 (mtt90) REVERT: A 355 ASN cc_start: 0.6424 (p0) cc_final: 0.6093 (t0) REVERT: A 394 MET cc_start: 0.8039 (ttp) cc_final: 0.7773 (ttm) REVERT: A 488 GLU cc_start: 0.7598 (mt-10) cc_final: 0.6898 (pm20) REVERT: A 522 GLU cc_start: 0.8606 (mp0) cc_final: 0.8364 (mp0) REVERT: A 526 TYR cc_start: 0.9010 (m-80) cc_final: 0.8701 (m-80) REVERT: A 654 PHE cc_start: 0.8540 (t80) cc_final: 0.8338 (t80) REVERT: A 786 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.8141 (tt0) REVERT: B 191 GLU cc_start: 0.7152 (mt-10) cc_final: 0.6842 (tt0) REVERT: B 693 ARG cc_start: 0.8514 (tpp-160) cc_final: 0.7486 (tmm160) REVERT: B 742 ARG cc_start: 0.7914 (mmm-85) cc_final: 0.7163 (mmt180) REVERT: B 790 GLU cc_start: 0.7468 (OUTLIER) cc_final: 0.7166 (mt-10) REVERT: C 423 GLU cc_start: 0.7770 (mt-10) cc_final: 0.7393 (mt-10) REVERT: C 451 VAL cc_start: 0.7853 (m) cc_final: 0.7468 (p) REVERT: C 501 MET cc_start: 0.9041 (mtm) cc_final: 0.8722 (mtm) REVERT: C 556 GLN cc_start: 0.8274 (OUTLIER) cc_final: 0.7930 (tp40) REVERT: C 704 ARG cc_start: 0.7878 (ttm110) cc_final: 0.7357 (mtm-85) REVERT: D 385 GLN cc_start: 0.7172 (mt0) cc_final: 0.6818 (mt0) REVERT: D 388 TYR cc_start: 0.7308 (m-10) cc_final: 0.7054 (m-80) REVERT: D 420 GLU cc_start: 0.7547 (pt0) cc_final: 0.6866 (pm20) REVERT: D 453 ILE cc_start: 0.7985 (tt) cc_final: 0.7700 (pt) REVERT: D 491 ASN cc_start: 0.7986 (OUTLIER) cc_final: 0.7778 (m-40) REVERT: D 630 ILE cc_start: 0.7726 (OUTLIER) cc_final: 0.7493 (mm) REVERT: D 693 ARG cc_start: 0.8256 (tpp-160) cc_final: 0.7468 (ttp80) REVERT: D 814 ASP cc_start: 0.7544 (p0) cc_final: 0.6563 (t0) outliers start: 43 outliers final: 16 residues processed: 345 average time/residue: 0.5379 time to fit residues: 214.8875 Evaluate side-chains 322 residues out of total 2744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 300 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 773 SER Chi-restraints excluded: chain A residue 786 GLU Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 440 ILE Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 790 GLU Chi-restraints excluded: chain B residue 821 VAL Chi-restraints excluded: chain C residue 427 ASN Chi-restraints excluded: chain C residue 555 MET Chi-restraints excluded: chain C residue 556 GLN Chi-restraints excluded: chain C residue 569 SER Chi-restraints excluded: chain C residue 610 SER Chi-restraints excluded: chain C residue 748 THR Chi-restraints excluded: chain C residue 816 VAL Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 491 ASN Chi-restraints excluded: chain D residue 630 ILE Chi-restraints excluded: chain D residue 818 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 198 optimal weight: 20.0000 chunk 240 optimal weight: 8.9990 chunk 58 optimal weight: 0.6980 chunk 296 optimal weight: 6.9990 chunk 212 optimal weight: 0.0040 chunk 148 optimal weight: 0.7980 chunk 133 optimal weight: 0.6980 chunk 28 optimal weight: 6.9990 chunk 96 optimal weight: 6.9990 chunk 116 optimal weight: 2.9990 chunk 145 optimal weight: 1.9990 overall best weight: 0.8394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 393 GLN ** B 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 385 GLN C 440 ASN D 153 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4493 r_free = 0.4493 target = 0.228569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.167164 restraints weight = 22098.292| |-----------------------------------------------------------------------------| r_work (start): 0.3834 rms_B_bonded: 1.93 r_work: 0.3461 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3353 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21387 Z= 0.115 Angle : 0.473 8.599 29283 Z= 0.260 Chirality : 0.043 0.148 3551 Planarity : 0.003 0.052 3816 Dihedral : 4.125 40.881 3281 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.83 % Favored : 96.07 % Rotamer: Outliers : 2.79 % Allowed : 9.99 % Favored : 87.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.15), residues: 3132 helix: 1.80 (0.14), residues: 1333 sheet: 0.13 (0.28), residues: 356 loop : -0.93 (0.17), residues: 1443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 212 TYR 0.015 0.001 TYR A 410 PHE 0.019 0.001 PHE A 458 TRP 0.011 0.001 TRP D 256 HIS 0.004 0.001 HIS B 486 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.12 (21375) covalent geometry : angle 0.47217 / 0.26 (29259) SS BOND : bond 0.00273 / 0.20 ( 12) SS BOND : angle 0.87857 / 0.62 ( 24) hydrogen bonds : bond 0.04392 / 3.23 ( 1101) hydrogen bonds : angle 4.32079 / 3.16 ( 3177) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6264 Ramachandran restraints generated. 3132 Oldfield, 0 Emsley, 3132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6264 Ramachandran restraints generated. 3132 Oldfield, 0 Emsley, 3132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 2744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 314 time to evaluate : 0.813 Fit side-chains REVERT: A 146 HIS cc_start: 0.7412 (OUTLIER) cc_final: 0.6934 (t-90) REVERT: A 182 THR cc_start: 0.7533 (m) cc_final: 0.7155 (p) REVERT: A 252 ARG cc_start: 0.6544 (mtm180) cc_final: 0.5824 (mtt90) REVERT: A 394 MET cc_start: 0.8050 (ttp) cc_final: 0.7748 (ttm) REVERT: A 488 GLU cc_start: 0.7585 (mt-10) cc_final: 0.7026 (pm20) REVERT: A 522 GLU cc_start: 0.8628 (mp0) cc_final: 0.8357 (mp0) REVERT: A 526 TYR cc_start: 0.9012 (m-80) cc_final: 0.8675 (m-80) REVERT: A 786 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.8101 (tt0) REVERT: B 186 ILE cc_start: 0.7137 (OUTLIER) cc_final: 0.6689 (mt) REVERT: B 191 GLU cc_start: 0.7018 (mt-10) cc_final: 0.6735 (tt0) REVERT: B 606 ILE cc_start: 0.7995 (tt) cc_final: 0.7774 (mt) REVERT: B 693 ARG cc_start: 0.8492 (tpp-160) cc_final: 0.7504 (tmm160) REVERT: B 742 ARG cc_start: 0.7923 (mmm-85) cc_final: 0.7161 (mmt180) REVERT: C 423 GLU cc_start: 0.7794 (mt-10) cc_final: 0.7461 (mm-30) REVERT: C 451 VAL cc_start: 0.7747 (m) cc_final: 0.7416 (p) REVERT: C 556 GLN cc_start: 0.8288 (OUTLIER) cc_final: 0.7915 (tp40) REVERT: C 576 MET cc_start: 0.7729 (OUTLIER) cc_final: 0.7526 (ttt) REVERT: C 704 ARG cc_start: 0.7846 (ttm110) cc_final: 0.7565 (ttp-110) REVERT: D 385 GLN cc_start: 0.7199 (mt0) cc_final: 0.6856 (mt0) REVERT: D 388 TYR cc_start: 0.7165 (m-10) cc_final: 0.6963 (m-80) REVERT: D 420 GLU cc_start: 0.7403 (pt0) cc_final: 0.6934 (pm20) REVERT: D 453 ILE cc_start: 0.8034 (tt) cc_final: 0.7760 (pt) REVERT: D 630 ILE cc_start: 0.7643 (OUTLIER) cc_final: 0.7435 (mm) REVERT: D 693 ARG cc_start: 0.8217 (tpp-160) cc_final: 0.7423 (ttp80) REVERT: D 814 ASP cc_start: 0.7476 (p0) cc_final: 0.6549 (t0) outliers start: 45 outliers final: 22 residues processed: 339 average time/residue: 0.5426 time to fit residues: 212.6375 Evaluate side-chains 322 residues out of total 2744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 294 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 748 THR Chi-restraints excluded: chain A residue 786 GLU Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 440 ILE Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 821 VAL Chi-restraints excluded: chain C residue 427 ASN Chi-restraints excluded: chain C residue 555 MET Chi-restraints excluded: chain C residue 556 GLN Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 569 SER Chi-restraints excluded: chain C residue 576 MET Chi-restraints excluded: chain C residue 610 SER Chi-restraints excluded: chain C residue 748 THR Chi-restraints excluded: chain C residue 816 VAL Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 606 ILE Chi-restraints excluded: chain D residue 630 ILE Chi-restraints excluded: chain D residue 818 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 144 optimal weight: 0.5980 chunk 148 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 chunk 266 optimal weight: 9.9990 chunk 264 optimal weight: 5.9990 chunk 112 optimal weight: 3.9990 chunk 178 optimal weight: 50.0000 chunk 200 optimal weight: 1.9990 chunk 131 optimal weight: 3.9990 chunk 303 optimal weight: 2.9990 chunk 245 optimal weight: 6.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 GLN A 393 GLN A 616 ASN B 153 GLN B 385 GLN C 440 ASN C 509 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4462 r_free = 0.4462 target = 0.225027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.161680 restraints weight = 21960.796| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 1.96 r_work: 0.3397 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3285 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 21387 Z= 0.239 Angle : 0.610 7.148 29283 Z= 0.333 Chirality : 0.049 0.211 3551 Planarity : 0.004 0.054 3816 Dihedral : 4.608 45.317 3280 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.08 % Favored : 94.83 % Rotamer: Outliers : 3.79 % Allowed : 10.61 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.15), residues: 3132 helix: 1.56 (0.14), residues: 1325 sheet: -0.19 (0.27), residues: 381 loop : -1.07 (0.16), residues: 1426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 212 TYR 0.022 0.002 TYR A 410 PHE 0.031 0.003 PHE A 458 TRP 0.013 0.002 TRP A 768 HIS 0.006 0.002 HIS B 486 Details of bonding type rmsd/Z covalent geometry : bond 0.00573 / 0.24 (21375) covalent geometry : angle 0.60841 / 0.33 (29259) SS BOND : bond 0.00630 / 0.46 ( 12) SS BOND : angle 1.51119 / 1.13 ( 24) hydrogen bonds : bond 0.05708 / 4.17 ( 1101) hydrogen bonds : angle 4.54454 / 3.34 ( 3177) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6264 Ramachandran restraints generated. 3132 Oldfield, 0 Emsley, 3132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6264 Ramachandran restraints generated. 3132 Oldfield, 0 Emsley, 3132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 305 time to evaluate : 0.763 Fit side-chains REVERT: A 146 HIS cc_start: 0.7388 (OUTLIER) cc_final: 0.6902 (t-90) REVERT: A 182 THR cc_start: 0.7620 (m) cc_final: 0.7250 (p) REVERT: A 252 ARG cc_start: 0.6669 (mtm180) cc_final: 0.5891 (mtt90) REVERT: A 394 MET cc_start: 0.8146 (ttp) cc_final: 0.7848 (ttm) REVERT: A 422 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7602 (mp0) REVERT: A 522 GLU cc_start: 0.8623 (mp0) cc_final: 0.8374 (mp0) REVERT: A 578 TYR cc_start: 0.8169 (t80) cc_final: 0.7865 (OUTLIER) REVERT: A 786 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.8140 (tt0) REVERT: B 186 ILE cc_start: 0.7258 (OUTLIER) cc_final: 0.6910 (mt) REVERT: B 191 GLU cc_start: 0.7151 (mt-10) cc_final: 0.6820 (tt0) REVERT: B 606 ILE cc_start: 0.8040 (tt) cc_final: 0.7787 (mt) REVERT: B 693 ARG cc_start: 0.8580 (tpp-160) cc_final: 0.7619 (ttp-110) REVERT: B 742 ARG cc_start: 0.7919 (mmm-85) cc_final: 0.7267 (mmt180) REVERT: C 423 GLU cc_start: 0.7779 (mt-10) cc_final: 0.7421 (mm-30) REVERT: C 451 VAL cc_start: 0.7794 (m) cc_final: 0.7431 (p) REVERT: C 556 GLN cc_start: 0.8251 (OUTLIER) cc_final: 0.7806 (tt0) REVERT: C 568 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8188 (tp) REVERT: C 704 ARG cc_start: 0.7931 (ttm110) cc_final: 0.7589 (ttp-110) REVERT: D 385 GLN cc_start: 0.7232 (mt0) cc_final: 0.6890 (mt0) REVERT: D 388 TYR cc_start: 0.7223 (m-10) cc_final: 0.6985 (m-80) REVERT: D 420 GLU cc_start: 0.7455 (pt0) cc_final: 0.6934 (pm20) REVERT: D 453 ILE cc_start: 0.8043 (tt) cc_final: 0.7764 (pt) REVERT: D 606 ILE cc_start: 0.8532 (OUTLIER) cc_final: 0.8322 (mp) REVERT: D 693 ARG cc_start: 0.8348 (tpp-160) cc_final: 0.7469 (tmm160) REVERT: D 814 ASP cc_start: 0.7557 (p0) cc_final: 0.6670 (t0) outliers start: 61 outliers final: 31 residues processed: 338 average time/residue: 0.5410 time to fit residues: 211.1146 Evaluate side-chains 337 residues out of total 2744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 300 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 422 GLU Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 555 MET Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 748 THR Chi-restraints excluded: chain A residue 786 GLU Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 440 ILE Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 557 ASP Chi-restraints excluded: chain B residue 821 VAL Chi-restraints excluded: chain C residue 555 MET Chi-restraints excluded: chain C residue 556 GLN Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 576 MET Chi-restraints excluded: chain C residue 610 SER Chi-restraints excluded: chain C residue 748 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 816 VAL Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 514 THR Chi-restraints excluded: chain D residue 601 THR Chi-restraints excluded: chain D residue 606 ILE Chi-restraints excluded: chain D residue 626 THR Chi-restraints excluded: chain D residue 818 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 43 optimal weight: 0.9980 chunk 304 optimal weight: 2.9990 chunk 190 optimal weight: 9.9990 chunk 151 optimal weight: 0.7980 chunk 279 optimal weight: 0.9990 chunk 220 optimal weight: 7.9990 chunk 245 optimal weight: 3.9990 chunk 177 optimal weight: 7.9990 chunk 230 optimal weight: 0.6980 chunk 63 optimal weight: 0.6980 chunk 228 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 GLN A 616 ASN B 385 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.227923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.169540 restraints weight = 22007.245| |-----------------------------------------------------------------------------| r_work (start): 0.3897 rms_B_bonded: 2.04 r_work: 0.3457 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3327 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21387 Z= 0.116 Angle : 0.478 8.436 29283 Z= 0.263 Chirality : 0.043 0.149 3551 Planarity : 0.003 0.055 3816 Dihedral : 4.229 42.093 3280 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.80 % Favored : 96.10 % Rotamer: Outliers : 2.61 % Allowed : 12.60 % Favored : 84.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.15), residues: 3132 helix: 1.88 (0.14), residues: 1340 sheet: -0.08 (0.28), residues: 364 loop : -1.06 (0.17), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 212 TYR 0.013 0.001 TYR C 578 PHE 0.019 0.001 PHE A 458 TRP 0.014 0.001 TRP D 256 HIS 0.004 0.001 HIS A 477 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (21375) covalent geometry : angle 0.47793 / 0.26 (29259) SS BOND : bond 0.00371 / 0.27 ( 12) SS BOND : angle 0.93042 / 0.71 ( 24) hydrogen bonds : bond 0.04076 / 2.99 ( 1101) hydrogen bonds : angle 4.24105 / 3.11 ( 3177) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6264 Ramachandran restraints generated. 3132 Oldfield, 0 Emsley, 3132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6264 Ramachandran restraints generated. 3132 Oldfield, 0 Emsley, 3132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 311 time to evaluate : 0.814 Fit side-chains REVERT: A 146 HIS cc_start: 0.7567 (OUTLIER) cc_final: 0.7092 (t-90) REVERT: A 182 THR cc_start: 0.7617 (m) cc_final: 0.7235 (p) REVERT: A 394 MET cc_start: 0.8137 (ttp) cc_final: 0.7812 (ttm) REVERT: A 422 GLU cc_start: 0.7946 (mp0) cc_final: 0.7690 (mp0) REVERT: A 526 TYR cc_start: 0.9105 (m-80) cc_final: 0.8803 (m-80) REVERT: A 578 TYR cc_start: 0.8118 (t80) cc_final: 0.7870 (OUTLIER) REVERT: A 786 GLU cc_start: 0.8482 (OUTLIER) cc_final: 0.8258 (tt0) REVERT: B 191 GLU cc_start: 0.7168 (mt-10) cc_final: 0.6874 (tt0) REVERT: B 606 ILE cc_start: 0.8077 (tt) cc_final: 0.7822 (mt) REVERT: B 693 ARG cc_start: 0.8627 (tpp-160) cc_final: 0.7775 (tmm160) REVERT: B 742 ARG cc_start: 0.8071 (mmm-85) cc_final: 0.7409 (mmt180) REVERT: C 423 GLU cc_start: 0.7822 (mt-10) cc_final: 0.7505 (mm-30) REVERT: C 451 VAL cc_start: 0.7872 (m) cc_final: 0.7577 (p) REVERT: C 556 GLN cc_start: 0.8360 (OUTLIER) cc_final: 0.7980 (tp40) REVERT: C 568 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8106 (tp) REVERT: C 579 LEU cc_start: 0.8086 (tt) cc_final: 0.7630 (mp) REVERT: C 812 ASN cc_start: 0.8131 (m110) cc_final: 0.7904 (m110) REVERT: D 159 ASN cc_start: 0.7899 (OUTLIER) cc_final: 0.7684 (t0) REVERT: D 187 ARG cc_start: 0.6736 (OUTLIER) cc_final: 0.6299 (mtt90) REVERT: D 385 GLN cc_start: 0.7379 (mt0) cc_final: 0.7041 (mt0) REVERT: D 420 GLU cc_start: 0.7542 (pt0) cc_final: 0.7151 (pm20) REVERT: D 453 ILE cc_start: 0.8141 (tt) cc_final: 0.7875 (pt) REVERT: D 693 ARG cc_start: 0.8420 (tpp-160) cc_final: 0.7762 (ttp80) REVERT: D 814 ASP cc_start: 0.7532 (p0) cc_final: 0.6663 (t0) outliers start: 42 outliers final: 21 residues processed: 330 average time/residue: 0.5398 time to fit residues: 205.7398 Evaluate side-chains 331 residues out of total 2744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 305 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 555 MET Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 748 THR Chi-restraints excluded: chain A residue 786 GLU Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 440 ILE Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 557 ASP Chi-restraints excluded: chain B residue 821 VAL Chi-restraints excluded: chain C residue 555 MET Chi-restraints excluded: chain C residue 556 GLN Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 610 SER Chi-restraints excluded: chain C residue 748 THR Chi-restraints excluded: chain C residue 816 VAL Chi-restraints excluded: chain D residue 159 ASN Chi-restraints excluded: chain D residue 187 ARG Chi-restraints excluded: chain D residue 606 ILE Chi-restraints excluded: chain D residue 818 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 90 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 308 optimal weight: 0.7980 chunk 281 optimal weight: 0.2980 chunk 258 optimal weight: 4.9990 chunk 16 optimal weight: 10.0000 chunk 153 optimal weight: 0.0170 chunk 63 optimal weight: 0.3980 chunk 94 optimal weight: 3.9990 chunk 234 optimal weight: 0.7980 chunk 262 optimal weight: 40.0000 overall best weight: 0.4618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 GLN A 616 ASN B 385 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.229519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.171211 restraints weight = 22182.771| |-----------------------------------------------------------------------------| r_work (start): 0.3918 rms_B_bonded: 2.05 r_work: 0.3490 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3369 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 21387 Z= 0.094 Angle : 0.445 6.488 29283 Z= 0.245 Chirality : 0.042 0.145 3551 Planarity : 0.003 0.052 3816 Dihedral : 3.971 38.896 3280 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.64 % Favored : 96.26 % Rotamer: Outliers : 2.11 % Allowed : 13.22 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.16), residues: 3132 helix: 2.14 (0.14), residues: 1341 sheet: 0.04 (0.28), residues: 369 loop : -0.99 (0.17), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 212 TYR 0.012 0.001 TYR C 578 PHE 0.015 0.001 PHE A 458 TRP 0.016 0.001 TRP D 256 HIS 0.003 0.001 HIS A 477 Details of bonding type rmsd/Z covalent geometry : bond 0.00198 / 0.09 (21375) covalent geometry : angle 0.44455 / 0.24 (29259) SS BOND : bond 0.00300 / 0.22 ( 12) SS BOND : angle 0.73312 / 0.55 ( 24) hydrogen bonds : bond 0.03445 / 2.53 ( 1101) hydrogen bonds : angle 4.06336 / 2.97 ( 3177) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6264 Ramachandran restraints generated. 3132 Oldfield, 0 Emsley, 3132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6264 Ramachandran restraints generated. 3132 Oldfield, 0 Emsley, 3132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 2744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 312 time to evaluate : 0.831 Fit side-chains REVERT: A 146 HIS cc_start: 0.7520 (OUTLIER) cc_final: 0.7050 (t-90) REVERT: A 394 MET cc_start: 0.8078 (ttp) cc_final: 0.7773 (ttm) REVERT: A 422 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7647 (mp0) REVERT: A 526 TYR cc_start: 0.9091 (m-80) cc_final: 0.8763 (m-80) REVERT: A 786 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.7930 (mp0) REVERT: B 191 GLU cc_start: 0.7095 (mt-10) cc_final: 0.6845 (tt0) REVERT: B 385 GLN cc_start: 0.8438 (mt0) cc_final: 0.8105 (mp10) REVERT: B 404 ASP cc_start: 0.7893 (m-30) cc_final: 0.7549 (p0) REVERT: B 606 ILE cc_start: 0.7995 (tt) cc_final: 0.7732 (mt) REVERT: B 693 ARG cc_start: 0.8579 (tpp-160) cc_final: 0.7705 (tmm160) REVERT: B 742 ARG cc_start: 0.7982 (mmm-85) cc_final: 0.7292 (mmt180) REVERT: C 423 GLU cc_start: 0.7797 (mt-10) cc_final: 0.7460 (mm-30) REVERT: C 451 VAL cc_start: 0.7822 (m) cc_final: 0.7524 (p) REVERT: C 556 GLN cc_start: 0.8359 (OUTLIER) cc_final: 0.8009 (tp40) REVERT: C 568 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8129 (tp) REVERT: C 579 LEU cc_start: 0.8059 (tt) cc_final: 0.7692 (mp) REVERT: C 704 ARG cc_start: 0.7935 (ttp-110) cc_final: 0.7680 (ttp-110) REVERT: D 187 ARG cc_start: 0.6662 (OUTLIER) cc_final: 0.6264 (mtt90) REVERT: D 228 ILE cc_start: 0.8478 (mt) cc_final: 0.8184 (mp) REVERT: D 385 GLN cc_start: 0.7341 (mt0) cc_final: 0.7049 (mt0) REVERT: D 420 GLU cc_start: 0.7464 (pt0) cc_final: 0.7061 (pm20) REVERT: D 453 ILE cc_start: 0.8031 (tt) cc_final: 0.7749 (pt) REVERT: D 473 LYS cc_start: 0.8567 (mptp) cc_final: 0.8142 (mtmm) REVERT: D 693 ARG cc_start: 0.8332 (tpp-160) cc_final: 0.7682 (ttp80) REVERT: D 814 ASP cc_start: 0.7433 (p0) cc_final: 0.6561 (t0) outliers start: 34 outliers final: 18 residues processed: 328 average time/residue: 0.5205 time to fit residues: 198.0572 Evaluate side-chains 323 residues out of total 2744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 299 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 422 GLU Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 786 GLU Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 557 ASP Chi-restraints excluded: chain B residue 821 VAL Chi-restraints excluded: chain C residue 555 MET Chi-restraints excluded: chain C residue 556 GLN Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 610 SER Chi-restraints excluded: chain C residue 748 THR Chi-restraints excluded: chain C residue 816 VAL Chi-restraints excluded: chain D residue 187 ARG Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 390 VAL Chi-restraints excluded: chain D residue 606 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 267 optimal weight: 20.0000 chunk 189 optimal weight: 6.9990 chunk 179 optimal weight: 40.0000 chunk 125 optimal weight: 1.9990 chunk 126 optimal weight: 0.2980 chunk 264 optimal weight: 20.0000 chunk 70 optimal weight: 0.6980 chunk 12 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 45 optimal weight: 5.9990 chunk 26 optimal weight: 6.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 GLN A 616 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4476 r_free = 0.4476 target = 0.226698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.165433 restraints weight = 22019.050| |-----------------------------------------------------------------------------| r_work (start): 0.3838 rms_B_bonded: 1.88 r_work: 0.3437 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3324 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 21387 Z= 0.166 Angle : 0.537 8.925 29283 Z= 0.291 Chirality : 0.045 0.152 3551 Planarity : 0.004 0.055 3816 Dihedral : 4.285 44.595 3278 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.53 % Favored : 95.37 % Rotamer: Outliers : 2.98 % Allowed : 13.41 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.15), residues: 3132 helix: 1.98 (0.14), residues: 1335 sheet: -0.07 (0.27), residues: 374 loop : -1.04 (0.17), residues: 1423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 212 TYR 0.026 0.002 TYR A 578 PHE 0.024 0.002 PHE C 458 TRP 0.015 0.001 TRP D 256 HIS 0.004 0.001 HIS D 486 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.17 (21375) covalent geometry : angle 0.53596 / 0.29 (29259) SS BOND : bond 0.00418 / 0.31 ( 12) SS BOND : angle 1.10597 / 0.81 ( 24) hydrogen bonds : bond 0.04594 / 3.35 ( 1101) hydrogen bonds : angle 4.23705 / 3.11 ( 3177) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6264 Ramachandran restraints generated. 3132 Oldfield, 0 Emsley, 3132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6264 Ramachandran restraints generated. 3132 Oldfield, 0 Emsley, 3132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 2744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 301 time to evaluate : 0.828 Fit side-chains REVERT: A 146 HIS cc_start: 0.7387 (OUTLIER) cc_final: 0.6906 (t-90) REVERT: A 182 THR cc_start: 0.7560 (m) cc_final: 0.7186 (p) REVERT: A 359 ARG cc_start: 0.5905 (mmp-170) cc_final: 0.5548 (mmp-170) REVERT: A 394 MET cc_start: 0.8058 (ttp) cc_final: 0.7741 (ttm) REVERT: A 488 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7075 (pm20) REVERT: A 526 TYR cc_start: 0.9077 (m-80) cc_final: 0.8742 (m-80) REVERT: A 786 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.8104 (tt0) REVERT: B 191 GLU cc_start: 0.7059 (mt-10) cc_final: 0.6783 (tt0) REVERT: B 606 ILE cc_start: 0.8031 (tt) cc_final: 0.7749 (mt) REVERT: B 693 ARG cc_start: 0.8526 (tpp-160) cc_final: 0.7375 (tmm160) REVERT: B 742 ARG cc_start: 0.7879 (mmm-85) cc_final: 0.7280 (mmt90) REVERT: C 423 GLU cc_start: 0.7780 (mt-10) cc_final: 0.7427 (mm-30) REVERT: C 451 VAL cc_start: 0.7758 (m) cc_final: 0.7403 (p) REVERT: C 556 GLN cc_start: 0.8263 (OUTLIER) cc_final: 0.7865 (tt0) REVERT: C 568 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8058 (tp) REVERT: C 704 ARG cc_start: 0.7851 (ttp-110) cc_final: 0.7625 (ttp-110) REVERT: D 385 GLN cc_start: 0.7300 (mt0) cc_final: 0.7013 (mt0) REVERT: D 420 GLU cc_start: 0.7388 (pt0) cc_final: 0.6922 (pm20) REVERT: D 440 ILE cc_start: 0.5982 (OUTLIER) cc_final: 0.5692 (tp) REVERT: D 453 ILE cc_start: 0.8015 (tt) cc_final: 0.7697 (pt) REVERT: D 693 ARG cc_start: 0.8272 (tpp-160) cc_final: 0.7388 (tmm160) REVERT: D 814 ASP cc_start: 0.7453 (p0) cc_final: 0.6573 (t0) REVERT: D 831 LEU cc_start: 0.7635 (tt) cc_final: 0.7434 (tp) outliers start: 48 outliers final: 28 residues processed: 330 average time/residue: 0.5418 time to fit residues: 206.8718 Evaluate side-chains 332 residues out of total 2744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 298 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 488 GLU Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 748 THR Chi-restraints excluded: chain A residue 786 GLU Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain A residue 818 MET Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 440 ILE Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 557 ASP Chi-restraints excluded: chain B residue 821 VAL Chi-restraints excluded: chain C residue 555 MET Chi-restraints excluded: chain C residue 556 GLN Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 569 SER Chi-restraints excluded: chain C residue 610 SER Chi-restraints excluded: chain C residue 748 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 816 VAL Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 390 VAL Chi-restraints excluded: chain D residue 440 ILE Chi-restraints excluded: chain D residue 514 THR Chi-restraints excluded: chain D residue 601 THR Chi-restraints excluded: chain D residue 606 ILE Chi-restraints excluded: chain D residue 818 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 258 optimal weight: 0.9990 chunk 37 optimal weight: 0.0370 chunk 73 optimal weight: 0.6980 chunk 44 optimal weight: 0.0980 chunk 39 optimal weight: 6.9990 chunk 118 optimal weight: 0.6980 chunk 228 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 251 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 overall best weight: 0.5060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 GLN A 616 ASN B 385 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4499 r_free = 0.4499 target = 0.229419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.169988 restraints weight = 21994.053| |-----------------------------------------------------------------------------| r_work (start): 0.3895 rms_B_bonded: 1.94 r_work: 0.3483 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3369 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 21387 Z= 0.095 Angle : 0.455 8.825 29283 Z= 0.247 Chirality : 0.042 0.145 3551 Planarity : 0.003 0.055 3816 Dihedral : 3.974 40.236 3278 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.51 % Favored : 96.39 % Rotamer: Outliers : 2.30 % Allowed : 13.78 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.16), residues: 3132 helix: 2.20 (0.14), residues: 1338 sheet: 0.04 (0.28), residues: 364 loop : -0.99 (0.17), residues: 1430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 212 TYR 0.034 0.001 TYR A 578 PHE 0.016 0.001 PHE A 458 TRP 0.023 0.001 TRP D 256 HIS 0.003 0.001 HIS A 477 Details of bonding type rmsd/Z covalent geometry : bond 0.00202 / 0.09 (21375) covalent geometry : angle 0.45441 / 0.25 (29259) SS BOND : bond 0.00299 / 0.21 ( 12) SS BOND : angle 0.75488 / 0.55 ( 24) hydrogen bonds : bond 0.03435 / 2.52 ( 1101) hydrogen bonds : angle 4.04459 / 2.96 ( 3177) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6264 Ramachandran restraints generated. 3132 Oldfield, 0 Emsley, 3132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6264 Ramachandran restraints generated. 3132 Oldfield, 0 Emsley, 3132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 303 time to evaluate : 0.906 Fit side-chains REVERT: A 146 HIS cc_start: 0.7431 (OUTLIER) cc_final: 0.6948 (t-90) REVERT: A 355 ASN cc_start: 0.6180 (p0) cc_final: 0.5140 (t0) REVERT: A 394 MET cc_start: 0.8040 (ttp) cc_final: 0.7770 (ttm) REVERT: A 526 TYR cc_start: 0.9055 (m-80) cc_final: 0.8730 (m-80) REVERT: A 786 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.7787 (mp0) REVERT: B 191 GLU cc_start: 0.6995 (mt-10) cc_final: 0.6774 (tt0) REVERT: B 385 GLN cc_start: 0.8330 (mt0) cc_final: 0.7948 (mp10) REVERT: B 606 ILE cc_start: 0.7963 (tt) cc_final: 0.7671 (mt) REVERT: B 693 ARG cc_start: 0.8507 (tpp-160) cc_final: 0.7542 (tmm160) REVERT: B 742 ARG cc_start: 0.7904 (mmm-85) cc_final: 0.7217 (mmt180) REVERT: C 423 GLU cc_start: 0.7762 (mt-10) cc_final: 0.7420 (mm-30) REVERT: C 451 VAL cc_start: 0.7816 (m) cc_final: 0.7494 (p) REVERT: C 556 GLN cc_start: 0.8319 (OUTLIER) cc_final: 0.7922 (tp40) REVERT: C 568 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8100 (tp) REVERT: C 579 LEU cc_start: 0.8016 (tt) cc_final: 0.7651 (mp) REVERT: C 704 ARG cc_start: 0.7895 (ttp-110) cc_final: 0.7657 (ttp-110) REVERT: D 187 ARG cc_start: 0.6637 (OUTLIER) cc_final: 0.6241 (mtt90) REVERT: D 228 ILE cc_start: 0.8342 (mt) cc_final: 0.8046 (mp) REVERT: D 385 GLN cc_start: 0.7290 (mt0) cc_final: 0.6986 (mt0) REVERT: D 420 GLU cc_start: 0.7404 (pt0) cc_final: 0.6958 (pm20) REVERT: D 440 ILE cc_start: 0.6005 (OUTLIER) cc_final: 0.5781 (tp) REVERT: D 453 ILE cc_start: 0.7967 (tt) cc_final: 0.7633 (pt) REVERT: D 473 LYS cc_start: 0.8562 (mptp) cc_final: 0.8087 (mtmm) REVERT: D 568 ILE cc_start: 0.8122 (OUTLIER) cc_final: 0.7913 (mt) REVERT: D 693 ARG cc_start: 0.8259 (tpp-160) cc_final: 0.7510 (ttp80) REVERT: D 814 ASP cc_start: 0.7384 (p0) cc_final: 0.6504 (t0) outliers start: 37 outliers final: 22 residues processed: 321 average time/residue: 0.5358 time to fit residues: 199.3659 Evaluate side-chains 330 residues out of total 2744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 301 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 748 THR Chi-restraints excluded: chain A residue 786 GLU Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 440 ILE Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 557 ASP Chi-restraints excluded: chain B residue 821 VAL Chi-restraints excluded: chain C residue 556 GLN Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 569 SER Chi-restraints excluded: chain C residue 610 SER Chi-restraints excluded: chain C residue 628 SER Chi-restraints excluded: chain C residue 697 VAL Chi-restraints excluded: chain C residue 748 THR Chi-restraints excluded: chain C residue 816 VAL Chi-restraints excluded: chain D residue 187 ARG Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 390 VAL Chi-restraints excluded: chain D residue 440 ILE Chi-restraints excluded: chain D residue 568 ILE Chi-restraints excluded: chain D residue 606 ILE Chi-restraints excluded: chain D residue 818 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 287 optimal weight: 0.6980 chunk 214 optimal weight: 0.0370 chunk 138 optimal weight: 0.6980 chunk 168 optimal weight: 50.0000 chunk 123 optimal weight: 0.8980 chunk 39 optimal weight: 6.9990 chunk 196 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 chunk 146 optimal weight: 0.1980 chunk 310 optimal weight: 0.6980 chunk 277 optimal weight: 4.9990 overall best weight: 0.4658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 GLN A 616 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4503 r_free = 0.4503 target = 0.229900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.170563 restraints weight = 22107.993| |-----------------------------------------------------------------------------| r_work (start): 0.3899 rms_B_bonded: 1.89 r_work: 0.3503 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3392 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 21387 Z= 0.092 Angle : 0.445 8.524 29283 Z= 0.242 Chirality : 0.042 0.143 3551 Planarity : 0.003 0.054 3816 Dihedral : 3.833 37.844 3278 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.64 % Favored : 96.26 % Rotamer: Outliers : 1.92 % Allowed : 14.71 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.16), residues: 3132 helix: 2.32 (0.14), residues: 1338 sheet: 0.17 (0.28), residues: 357 loop : -0.94 (0.17), residues: 1437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 212 TYR 0.012 0.001 TYR D 705 PHE 0.015 0.001 PHE A 458 TRP 0.024 0.001 TRP D 256 HIS 0.003 0.001 HIS A 477 Details of bonding type rmsd/Z covalent geometry : bond 0.00196 / 0.09 (21375) covalent geometry : angle 0.44495 / 0.24 (29259) SS BOND : bond 0.00272 / 0.20 ( 12) SS BOND : angle 0.71839 / 0.53 ( 24) hydrogen bonds : bond 0.03239 / 2.37 ( 1101) hydrogen bonds : angle 3.95204 / 2.89 ( 3177) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6264 Ramachandran restraints generated. 3132 Oldfield, 0 Emsley, 3132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6264 Ramachandran restraints generated. 3132 Oldfield, 0 Emsley, 3132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 306 time to evaluate : 0.785 Fit side-chains REVERT: A 146 HIS cc_start: 0.7428 (OUTLIER) cc_final: 0.6912 (t-90) REVERT: A 215 GLU cc_start: 0.6917 (mt-10) cc_final: 0.6707 (mt-10) REVERT: A 355 ASN cc_start: 0.6031 (p0) cc_final: 0.5136 (t0) REVERT: A 526 TYR cc_start: 0.9039 (m-80) cc_final: 0.8694 (m-80) REVERT: A 786 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7755 (mp0) REVERT: B 191 GLU cc_start: 0.6956 (mt-10) cc_final: 0.6755 (tt0) REVERT: B 385 GLN cc_start: 0.8328 (mt0) cc_final: 0.7971 (mp10) REVERT: B 404 ASP cc_start: 0.7766 (m-30) cc_final: 0.7454 (p0) REVERT: B 606 ILE cc_start: 0.7929 (tt) cc_final: 0.7631 (mt) REVERT: B 642 PHE cc_start: 0.8559 (t80) cc_final: 0.8354 (t80) REVERT: B 693 ARG cc_start: 0.8437 (tpp-160) cc_final: 0.7454 (tmm160) REVERT: C 423 GLU cc_start: 0.7716 (mt-10) cc_final: 0.7377 (mm-30) REVERT: C 451 VAL cc_start: 0.7768 (m) cc_final: 0.7441 (p) REVERT: C 556 GLN cc_start: 0.8301 (OUTLIER) cc_final: 0.7866 (tp40) REVERT: C 568 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8084 (tp) REVERT: C 579 LEU cc_start: 0.7995 (tt) cc_final: 0.7642 (mp) REVERT: C 704 ARG cc_start: 0.7822 (ttp-110) cc_final: 0.7580 (ttp-110) REVERT: D 159 ASN cc_start: 0.7038 (OUTLIER) cc_final: 0.6752 (m-40) REVERT: D 187 ARG cc_start: 0.6596 (OUTLIER) cc_final: 0.6253 (mtt90) REVERT: D 228 ILE cc_start: 0.8272 (mt) cc_final: 0.7986 (mp) REVERT: D 385 GLN cc_start: 0.7311 (mt0) cc_final: 0.6990 (mt0) REVERT: D 420 GLU cc_start: 0.7347 (pt0) cc_final: 0.6901 (pm20) REVERT: D 453 ILE cc_start: 0.7904 (tt) cc_final: 0.7536 (pt) REVERT: D 473 LYS cc_start: 0.8530 (mptp) cc_final: 0.8059 (mtmm) REVERT: D 693 ARG cc_start: 0.8178 (tpp-160) cc_final: 0.7432 (ttp80) REVERT: D 814 ASP cc_start: 0.7313 (p0) cc_final: 0.6468 (t0) outliers start: 31 outliers final: 20 residues processed: 321 average time/residue: 0.4948 time to fit residues: 185.4350 Evaluate side-chains 327 residues out of total 2744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 301 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 786 GLU Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 557 ASP Chi-restraints excluded: chain B residue 821 VAL Chi-restraints excluded: chain C residue 427 ASN Chi-restraints excluded: chain C residue 556 GLN Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 569 SER Chi-restraints excluded: chain C residue 610 SER Chi-restraints excluded: chain C residue 628 SER Chi-restraints excluded: chain C residue 748 THR Chi-restraints excluded: chain C residue 816 VAL Chi-restraints excluded: chain D residue 159 ASN Chi-restraints excluded: chain D residue 187 ARG Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 390 VAL Chi-restraints excluded: chain D residue 606 ILE Chi-restraints excluded: chain D residue 818 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 255 optimal weight: 8.9990 chunk 305 optimal weight: 0.0060 chunk 143 optimal weight: 3.9990 chunk 109 optimal weight: 50.0000 chunk 182 optimal weight: 5.9990 chunk 303 optimal weight: 4.9990 chunk 145 optimal weight: 0.0870 chunk 191 optimal weight: 20.0000 chunk 124 optimal weight: 0.9990 chunk 177 optimal weight: 5.9990 chunk 149 optimal weight: 0.3980 overall best weight: 1.0978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.228141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.165675 restraints weight = 22029.247| |-----------------------------------------------------------------------------| r_work (start): 0.3814 rms_B_bonded: 1.94 r_work: 0.3449 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3339 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21387 Z= 0.129 Angle : 0.497 9.839 29283 Z= 0.269 Chirality : 0.044 0.164 3551 Planarity : 0.003 0.057 3816 Dihedral : 4.059 42.628 3278 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.99 % Favored : 95.91 % Rotamer: Outliers : 1.99 % Allowed : 14.59 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.16), residues: 3132 helix: 2.20 (0.14), residues: 1338 sheet: 0.05 (0.28), residues: 367 loop : -0.97 (0.17), residues: 1427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 212 TYR 0.026 0.001 TYR A 578 PHE 0.021 0.002 PHE A 458 TRP 0.028 0.001 TRP D 256 HIS 0.004 0.001 HIS B 486 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (21375) covalent geometry : angle 0.49657 / 0.27 (29259) SS BOND : bond 0.00346 / 0.25 ( 12) SS BOND : angle 0.92045 / 0.68 ( 24) hydrogen bonds : bond 0.03938 / 2.87 ( 1101) hydrogen bonds : angle 4.05615 / 2.97 ( 3177) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6264 Ramachandran restraints generated. 3132 Oldfield, 0 Emsley, 3132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6264 Ramachandran restraints generated. 3132 Oldfield, 0 Emsley, 3132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 295 time to evaluate : 0.802 Fit side-chains REVERT: A 146 HIS cc_start: 0.7405 (OUTLIER) cc_final: 0.6891 (t-90) REVERT: A 355 ASN cc_start: 0.6182 (p0) cc_final: 0.5117 (t0) REVERT: A 394 MET cc_start: 0.8009 (ttp) cc_final: 0.7724 (ttm) REVERT: A 526 TYR cc_start: 0.9055 (m-80) cc_final: 0.8720 (m-80) REVERT: A 786 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.7727 (mp0) REVERT: B 191 GLU cc_start: 0.7058 (mt-10) cc_final: 0.6772 (tt0) REVERT: B 606 ILE cc_start: 0.7963 (tt) cc_final: 0.7656 (mt) REVERT: B 693 ARG cc_start: 0.8510 (tpp-160) cc_final: 0.7502 (tmm160) REVERT: C 423 GLU cc_start: 0.7723 (mt-10) cc_final: 0.7389 (mm-30) REVERT: C 451 VAL cc_start: 0.7766 (m) cc_final: 0.7421 (p) REVERT: C 512 MET cc_start: 0.8930 (OUTLIER) cc_final: 0.8712 (ttp) REVERT: C 556 GLN cc_start: 0.8284 (OUTLIER) cc_final: 0.7890 (tp40) REVERT: C 568 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8109 (tp) REVERT: C 579 LEU cc_start: 0.8018 (tt) cc_final: 0.7610 (mp) REVERT: C 704 ARG cc_start: 0.7860 (ttp-110) cc_final: 0.7598 (ttp-110) REVERT: D 228 ILE cc_start: 0.8244 (mt) cc_final: 0.7961 (mp) REVERT: D 385 GLN cc_start: 0.7347 (mt0) cc_final: 0.7012 (mt0) REVERT: D 420 GLU cc_start: 0.7403 (pt0) cc_final: 0.6928 (pm20) REVERT: D 453 ILE cc_start: 0.7915 (tt) cc_final: 0.7620 (pt) REVERT: D 693 ARG cc_start: 0.8232 (tpp-160) cc_final: 0.7459 (ttp80) REVERT: D 814 ASP cc_start: 0.7343 (p0) cc_final: 0.6501 (t0) REVERT: D 831 LEU cc_start: 0.7610 (tt) cc_final: 0.7400 (tp) outliers start: 32 outliers final: 24 residues processed: 311 average time/residue: 0.5005 time to fit residues: 181.0071 Evaluate side-chains 324 residues out of total 2744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 295 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain A residue 748 THR Chi-restraints excluded: chain A residue 786 GLU Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 557 ASP Chi-restraints excluded: chain B residue 821 VAL Chi-restraints excluded: chain C residue 427 ASN Chi-restraints excluded: chain C residue 512 MET Chi-restraints excluded: chain C residue 556 GLN Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 569 SER Chi-restraints excluded: chain C residue 610 SER Chi-restraints excluded: chain C residue 628 SER Chi-restraints excluded: chain C residue 748 THR Chi-restraints excluded: chain C residue 816 VAL Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 390 VAL Chi-restraints excluded: chain D residue 606 ILE Chi-restraints excluded: chain D residue 818 MET Chi-restraints excluded: chain D residue 829 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 65 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 chunk 283 optimal weight: 0.0870 chunk 107 optimal weight: 30.0000 chunk 253 optimal weight: 0.0020 chunk 121 optimal weight: 0.9990 chunk 70 optimal weight: 0.0570 chunk 147 optimal weight: 0.9980 chunk 313 optimal weight: 0.9990 chunk 213 optimal weight: 1.9990 chunk 186 optimal weight: 0.9980 overall best weight: 0.4084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 GLN B 385 GLN D 812 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.230221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.170966 restraints weight = 22053.168| |-----------------------------------------------------------------------------| r_work (start): 0.3902 rms_B_bonded: 1.89 r_work: 0.3500 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3392 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 21387 Z= 0.090 Angle : 0.452 9.579 29283 Z= 0.244 Chirality : 0.042 0.143 3551 Planarity : 0.003 0.055 3816 Dihedral : 3.853 39.118 3278 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.48 % Favored : 96.42 % Rotamer: Outliers : 1.68 % Allowed : 15.15 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.16), residues: 3132 helix: 2.35 (0.14), residues: 1337 sheet: 0.19 (0.28), residues: 357 loop : -0.94 (0.17), residues: 1438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 212 TYR 0.021 0.001 TYR A 578 PHE 0.015 0.001 PHE B 460 TRP 0.029 0.001 TRP D 256 HIS 0.003 0.001 HIS A 477 Details of bonding type rmsd/Z covalent geometry : bond 0.00190 / 0.09 (21375) covalent geometry : angle 0.45193 / 0.24 (29259) SS BOND : bond 0.00302 / 0.20 ( 12) SS BOND : angle 0.73147 / 0.53 ( 24) hydrogen bonds : bond 0.03185 / 2.33 ( 1101) hydrogen bonds : angle 3.93887 / 2.88 ( 3177) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11191.22 seconds wall clock time: 189 minutes 49.72 seconds (11389.72 seconds total)