Starting phenix.real_space_refine on Sat Oct 11 21:28:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8usx_42522/10_2025/8usx_42522.cif Found real_map, /net/cci-nas-00/data/ceres_data/8usx_42522/10_2025/8usx_42522.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8usx_42522/10_2025/8usx_42522.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8usx_42522/10_2025/8usx_42522.map" model { file = "/net/cci-nas-00/data/ceres_data/8usx_42522/10_2025/8usx_42522.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8usx_42522/10_2025/8usx_42522.cif" } resolution = 4.1 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= 0.037 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 60 5.16 5 C 11048 2.51 5 N 3325 2.21 5 O 3493 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17926 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 741, 4477 Classifications: {'peptide': 741} Incomplete info: {'truncation_to_alanine': 408} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 708} Chain breaks: 2 Unresolved chain link angles: 19 Unresolved non-hydrogen bonds: 1478 Unresolved non-hydrogen angles: 1901 Unresolved non-hydrogen dihedrals: 1245 Unresolved non-hydrogen chiralities: 138 Planarities with less than four sites: {'ASN:plan1': 26, 'ARG:plan': 27, 'HIS:plan': 14, 'GLU:plan': 28, 'GLN:plan1': 15, 'PHE:plan': 14, 'TRP:plan': 10, 'ASP:plan': 19, 'TYR:plan': 15} Unresolved non-hydrogen planarities: 791 Chain: "B" Number of atoms: 4500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 745, 4500 Classifications: {'peptide': 745} Incomplete info: {'truncation_to_alanine': 415} Link IDs: {'PCIS': 3, 'PTRANS': 33, 'TRANS': 708} Chain breaks: 4 Unresolved chain link angles: 20 Unresolved non-hydrogen bonds: 1433 Unresolved non-hydrogen angles: 1856 Unresolved non-hydrogen dihedrals: 1186 Unresolved non-hydrogen chiralities: 158 Planarities with less than four sites: {'GLN:plan1': 21, 'ARG:plan': 19, 'HIS:plan': 12, 'ASP:plan': 19, 'PHE:plan': 24, 'ASN:plan1': 23, 'GLU:plan': 25, 'TYR:plan': 7, 'TRP:plan': 9} Unresolved non-hydrogen planarities: 739 Chain: "C" Number of atoms: 4495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 738, 4495 Classifications: {'peptide': 738} Incomplete info: {'truncation_to_alanine': 399} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 705} Chain breaks: 2 Unresolved chain link angles: 22 Unresolved non-hydrogen bonds: 1440 Unresolved non-hydrogen angles: 1859 Unresolved non-hydrogen dihedrals: 1212 Unresolved non-hydrogen chiralities: 137 Planarities with less than four sites: {'ASN:plan1': 24, 'ARG:plan': 25, 'HIS:plan': 13, 'GLU:plan': 27, 'GLN:plan1': 16, 'PHE:plan': 14, 'TRP:plan': 10, 'ASP:plan': 19, 'TYR:plan': 15} Unresolved non-hydrogen planarities: 770 Chain: "D" Number of atoms: 4454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 743, 4454 Classifications: {'peptide': 743} Incomplete info: {'truncation_to_alanine': 423} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 706} Chain breaks: 4 Unresolved chain link angles: 20 Unresolved non-hydrogen bonds: 1466 Unresolved non-hydrogen angles: 1899 Unresolved non-hydrogen dihedrals: 1214 Unresolved non-hydrogen chiralities: 160 Planarities with less than four sites: {'GLN:plan1': 22, 'ARG:plan': 18, 'HIS:plan': 13, 'ASP:plan': 19, 'PHE:plan': 24, 'ASN:plan1': 23, 'GLU:plan': 28, 'TYR:plan': 8, 'TRP:plan': 9} Unresolved non-hydrogen planarities: 762 Time building chain proxies: 5.48, per 1000 atoms: 0.31 Number of scatterers: 17926 At special positions: 0 Unit cell: (146.376, 182.328, 189.176, 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 60 16.00 O 3493 8.00 N 3325 7.00 C 11048 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, 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 B 537 " - pdb=" SG CYS B 575 " distance=2.03 Simple disulfide: pdb=" SG CYS B 543 " - pdb=" SG CYS B 576 " distance=2.04 Simple disulfide: pdb=" SG CYS B 859 " - pdb=" SG CYS B 913 " 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 D 537 " - pdb=" SG CYS D 575 " distance=2.03 Simple disulfide: pdb=" SG CYS D 543 " - pdb=" SG CYS D 576 " distance=2.03 Simple disulfide: pdb=" SG CYS D 859 " - pdb=" SG CYS D 913 " 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: 2.06 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 953.7 nanoseconds 5870 Ramachandran restraints generated. 2935 Oldfield, 0 Emsley, 2935 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5554 Finding SS restraints... Secondary structure from input PDB file: 101 helices and 27 sheets defined 41.7% alpha, 11.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.97 Creating SS restraints... Processing helix chain 'A' and resid 34 through 53 removed outlier: 4.120A pdb=" N HIS A 38 " --> pdb=" O SER A 34 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU A 39 " --> pdb=" O THR A 35 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASN A 50 " --> pdb=" O VAL A 46 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LYS A 51 " --> pdb=" O ASN A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 82 removed outlier: 4.046A pdb=" N ALA A 75 " --> pdb=" O ALA A 71 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N LEU A 76 " --> pdb=" O ILE A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 111 removed outlier: 3.649A pdb=" N VAL A 107 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA A 111 " --> pdb=" O VAL A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 158 removed outlier: 3.712A pdb=" N GLN A 147 " --> pdb=" O PRO A 143 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N SER A 148 " --> pdb=" O TYR A 144 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER A 149 " --> pdb=" O SER A 145 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL A 150 " --> pdb=" O HIS A 146 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N GLU A 153 " --> pdb=" O SER A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 185 Processing helix chain 'A' and resid 186 through 188 No H-bonds generated for 'chain 'A' and resid 186 through 188' Processing helix chain 'A' and resid 208 through 214 removed outlier: 3.817A pdb=" N GLU A 213 " --> pdb=" O MET A 209 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU A 214 " --> pdb=" O GLU A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 238 removed outlier: 3.858A pdb=" N THR A 230 " --> pdb=" O ASP A 226 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL A 231 " --> pdb=" O ASP A 227 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA A 236 " --> pdb=" O TYR A 232 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N MET A 237 " --> pdb=" O ARG A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 260 removed outlier: 3.621A pdb=" N ARG A 260 " --> pdb=" O ASN A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 296 Processing helix chain 'A' and resid 318 through 326 removed outlier: 3.676A pdb=" N LYS A 322 " --> pdb=" O GLY A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 469 removed outlier: 3.656A pdb=" N LEU A 462 " --> pdb=" O PHE A 458 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N THR A 469 " --> pdb=" O LYS A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 507 Processing helix chain 'A' and resid 520 through 527 Processing helix chain 'A' and resid 561 through 578 Processing helix chain 'A' and resid 604 through 614 Processing helix chain 'A' and resid 629 through 655 Processing helix chain 'A' and resid 669 through 674 Processing helix chain 'A' and resid 687 through 696 Processing helix chain 'A' and resid 700 through 708 removed outlier: 3.726A pdb=" N LYS A 708 " --> pdb=" O ARG A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 715 through 724 Processing helix chain 'A' and resid 732 through 743 removed outlier: 3.519A pdb=" N LEU A 736 " --> pdb=" O ASP A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 783 Processing helix chain 'A' and resid 783 through 793 Processing helix chain 'B' and resid 39 through 45 Processing helix chain 'B' and resid 125 through 138 removed outlier: 3.547A pdb=" N VAL B 138 " --> pdb=" O ASN B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 192 removed outlier: 4.418A pdb=" N PHE B 180 " --> pdb=" O ASP B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 217 Processing helix chain 'B' and resid 245 through 258 removed outlier: 4.039A pdb=" N ASP B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 286 removed outlier: 4.428A pdb=" N ASN B 286 " --> pdb=" O LEU B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 320 removed outlier: 3.517A pdb=" N LEU B 307 " --> pdb=" O SER B 303 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ASN B 320 " --> pdb=" O GLU B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 345 removed outlier: 3.687A pdb=" N PHE B 345 " --> pdb=" O ILE B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 407 removed outlier: 3.511A pdb=" N ILE B 406 " --> pdb=" O THR B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 413 Processing helix chain 'B' and resid 428 through 439 Processing helix chain 'B' and resid 550 through 562 removed outlier: 3.779A pdb=" N LEU B 554 " --> pdb=" O ASP B 550 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 571 No H-bonds generated for 'chain 'B' and resid 569 through 571' Processing helix chain 'B' and resid 578 through 591 Processing helix chain 'B' and resid 614 through 621 removed outlier: 3.507A pdb=" N GLY B 618 " --> pdb=" O THR B 614 " (cutoff:3.500A) Processing helix chain 'B' and resid 744 through 770 removed outlier: 3.743A pdb=" N GLY B 770 " --> pdb=" O ALA B 766 " (cutoff:3.500A) Processing helix chain 'B' and resid 782 through 787 removed outlier: 3.868A pdb=" N HIS B 786 " --> pdb=" O ASP B 782 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N HIS B 787 " --> pdb=" O PRO B 783 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 782 through 787' Processing helix chain 'B' and resid 803 through 810 Processing helix chain 'B' and resid 811 through 813 No H-bonds generated for 'chain 'B' and resid 811 through 813' Processing helix chain 'B' and resid 814 through 820 removed outlier: 3.800A pdb=" N TYR B 820 " --> pdb=" O TYR B 816 " (cutoff:3.500A) Processing helix chain 'B' and resid 824 through 833 removed outlier: 3.555A pdb=" N LYS B 833 " --> pdb=" O VAL B 829 " (cutoff:3.500A) Processing helix chain 'B' and resid 846 through 854 removed outlier: 3.745A pdb=" N SER B 854 " --> pdb=" O ASP B 850 " (cutoff:3.500A) Processing helix chain 'B' and resid 883 through 897 removed outlier: 3.984A pdb=" N ILE B 887 " --> pdb=" O LEU B 883 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER B 888 " --> pdb=" O THR B 884 " (cutoff:3.500A) Processing helix chain 'B' and resid 898 through 905 removed outlier: 3.545A pdb=" N MET B 902 " --> pdb=" O GLY B 898 " (cutoff:3.500A) Processing helix chain 'B' and resid 928 through 955 Processing helix chain 'C' and resid 34 through 53 removed outlier: 4.264A pdb=" N HIS C 38 " --> pdb=" O SER C 34 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU C 39 " --> pdb=" O THR C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 82 removed outlier: 3.896A pdb=" N ALA C 75 " --> pdb=" O ALA C 71 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N LEU C 76 " --> pdb=" O ILE C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 111 removed outlier: 3.635A pdb=" N ALA C 111 " --> pdb=" O VAL C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 115 Processing helix chain 'C' and resid 145 through 158 removed outlier: 3.641A pdb=" N VAL C 150 " --> pdb=" O HIS C 146 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N PHE C 152 " --> pdb=" O SER C 148 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N GLU C 153 " --> pdb=" O SER C 149 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N TYR C 158 " --> pdb=" O MET C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 185 Processing helix chain 'C' and resid 186 through 188 No H-bonds generated for 'chain 'C' and resid 186 through 188' Processing helix chain 'C' and resid 204 through 213 removed outlier: 3.531A pdb=" N MET C 209 " --> pdb=" O THR C 205 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLU C 210 " --> pdb=" O ALA C 206 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ALA C 211 " --> pdb=" O LEU C 207 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLU C 213 " --> pdb=" O MET C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 238 removed outlier: 4.248A pdb=" N THR C 230 " --> pdb=" O ASP C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 261 Processing helix chain 'C' and resid 276 through 296 removed outlier: 3.755A pdb=" N GLN C 290 " --> pdb=" O GLY C 286 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N HIS C 293 " --> pdb=" O ALA C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 326 removed outlier: 3.504A pdb=" N LYS C 322 " --> pdb=" O GLY C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 471 Processing helix chain 'C' and resid 501 through 507 Processing helix chain 'C' and resid 522 through 526 removed outlier: 3.993A pdb=" N GLN C 525 " --> pdb=" O GLU C 522 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N TYR C 526 " --> pdb=" O ARG C 523 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 522 through 526' Processing helix chain 'C' and resid 551 through 556 Processing helix chain 'C' and resid 559 through 579 removed outlier: 3.742A pdb=" N LEU C 579 " --> pdb=" O VAL C 575 " (cutoff:3.500A) Processing helix chain 'C' and resid 604 through 614 Processing helix chain 'C' and resid 629 through 657 removed outlier: 3.610A pdb=" N LEU C 657 " --> pdb=" O ALA C 653 " (cutoff:3.500A) Processing helix chain 'C' and resid 669 through 674 Processing helix chain 'C' and resid 687 through 696 removed outlier: 3.511A pdb=" N ILE C 691 " --> pdb=" O SER C 687 " (cutoff:3.500A) Processing helix chain 'C' and resid 702 through 707 removed outlier: 3.904A pdb=" N MET C 706 " --> pdb=" O MET C 702 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU C 707 " --> pdb=" O TYR C 703 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 702 through 707' Processing helix chain 'C' and resid 713 through 723 removed outlier: 3.551A pdb=" N ALA C 717 " --> pdb=" O SER C 713 " (cutoff:3.500A) Processing helix chain 'C' and resid 733 through 743 Processing helix chain 'C' and resid 768 through 780 removed outlier: 3.512A pdb=" N SER C 773 " --> pdb=" O LYS C 769 " (cutoff:3.500A) Processing helix chain 'C' and resid 783 through 792 Processing helix chain 'D' and resid 39 through 44 Processing helix chain 'D' and resid 125 through 138 Processing helix chain 'D' and resid 142 through 146 removed outlier: 4.046A pdb=" N ASN D 145 " --> pdb=" O LEU D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 192 removed outlier: 4.027A pdb=" N PHE D 180 " --> pdb=" O ASP D 176 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL D 190 " --> pdb=" O HIS D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 217 Processing helix chain 'D' and resid 246 through 260 Processing helix chain 'D' and resid 276 through 286 removed outlier: 4.085A pdb=" N ASN D 286 " --> pdb=" O LEU D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 320 removed outlier: 3.571A pdb=" N LEU D 307 " --> pdb=" O SER D 303 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN D 320 " --> pdb=" O GLU D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 331 through 345 Processing helix chain 'D' and resid 384 through 405 Processing helix chain 'D' and resid 407 through 413 removed outlier: 3.562A pdb=" N ILE D 413 " --> pdb=" O GLU D 409 " (cutoff:3.500A) Processing helix chain 'D' and resid 428 through 439 Processing helix chain 'D' and resid 552 through 562 removed outlier: 3.706A pdb=" N SER D 556 " --> pdb=" O SER D 552 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 573 Processing helix chain 'D' and resid 578 through 592 Processing helix chain 'D' and resid 614 through 622 Processing helix chain 'D' and resid 635 through 642 removed outlier: 4.083A pdb=" N VAL D 641 " --> pdb=" O ALA D 637 " (cutoff:3.500A) Processing helix chain 'D' and resid 741 through 769 removed outlier: 3.559A pdb=" N VAL D 769 " --> pdb=" O ALA D 765 " (cutoff:3.500A) Processing helix chain 'D' and resid 800 through 810 Processing helix chain 'D' and resid 810 through 820 removed outlier: 3.911A pdb=" N HIS D 814 " --> pdb=" O PHE D 810 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLU D 815 " --> pdb=" O PRO D 811 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N TYR D 820 " --> pdb=" O TYR D 816 " (cutoff:3.500A) Processing helix chain 'D' and resid 824 through 826 No H-bonds generated for 'chain 'D' and resid 824 through 826' Processing helix chain 'D' and resid 827 through 832 removed outlier: 3.535A pdb=" N LEU D 832 " --> pdb=" O GLY D 828 " (cutoff:3.500A) Processing helix chain 'D' and resid 846 through 856 Processing helix chain 'D' and resid 883 through 898 Processing helix chain 'D' and resid 898 through 908 Processing helix chain 'D' and resid 927 through 954 removed outlier: 3.777A pdb=" N ILE D 954 " --> pdb=" O ILE D 950 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 59 through 65 removed outlier: 3.894A pdb=" N THR A 63 " --> pdb=" O ILE A 29 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N VAL A 118 " --> pdb=" O LEU A 138 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 194 through 196 removed outlier: 7.059A pdb=" N LEU A 165 " --> pdb=" O LEU A 195 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N ILE A 219 " --> pdb=" O LEU A 248 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 270 through 271 removed outlier: 6.653A pdb=" N TYR A 351 " --> pdb=" O ILE A 366 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ILE A 366 " --> pdb=" O TYR A 351 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ILE A 353 " --> pdb=" O VAL A 364 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE A 366 " --> pdb=" O ILE A 373 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 409 through 413 removed outlier: 3.618A pdb=" N TYR A 456 " --> pdb=" O TYR A 410 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ILE A 435 " --> pdb=" O VAL A 476 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N LEU A 478 " --> pdb=" O ILE A 435 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N THR A 437 " --> pdb=" O LEU A 478 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU A 475 " --> pdb=" O LEU A 398 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N THR A 402 " --> pdb=" O HIS A 477 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N MET A 512 " --> pdb=" O LYS A 399 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL A 401 " --> pdb=" O MET A 512 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 534 through 536 removed outlier: 3.840A pdb=" N LYS A 534 " --> pdb=" O PHE A 758 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 541 through 543 Processing sheet with id=AA7, first strand: chain 'A' and resid 681 through 682 removed outlier: 3.623A pdb=" N ALA A 682 " --> pdb=" O ALA A 728 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 147 through 152 removed outlier: 6.269A pdb=" N VAL B 48 " --> pdb=" O GLU B 149 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N VAL B 151 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N VAL B 50 " --> pdb=" O VAL B 151 " (cutoff:3.500A) removed outlier: 10.084A pdb=" N ALA B 195 " --> pdb=" O ALA B 47 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N ARG B 49 " --> pdb=" O ALA B 195 " (cutoff:3.500A) removed outlier: 8.371A pdb=" N LEU B 197 " --> pdb=" O ARG B 49 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N GLY B 51 " --> pdb=" O LEU B 197 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LEU B 196 " --> pdb=" O ILE B 221 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N ILE B 223 " --> pdb=" O LEU B 196 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ALA B 198 " --> pdb=" O ILE B 223 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N VAL B 457 " --> pdb=" O HIS B 237 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N GLN B 239 " --> pdb=" O VAL B 457 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N SER B 459 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N SER B 241 " --> pdb=" O SER B 459 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 290 through 296 removed outlier: 6.177A pdb=" N PHE B 265 " --> pdb=" O LEU B 291 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N SER B 293 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU B 267 " --> pdb=" O SER B 293 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR B 324 " --> pdb=" O ASN B 264 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 375 through 379 removed outlier: 6.505A pdb=" N PHE B 463 " --> pdb=" O SER B 483 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N SER B 483 " --> pdb=" O PHE B 463 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ILE B 465 " --> pdb=" O LEU B 481 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 593 through 599 removed outlier: 3.966A pdb=" N MET B 627 " --> pdb=" O ARG B 516 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 541 through 544 removed outlier: 3.695A pdb=" N GLN B 541 " --> pdb=" O CYS B 576 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N CYS B 576 " --> pdb=" O GLN B 541 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N CYS B 543 " --> pdb=" O LYS B 574 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 844 through 845 removed outlier: 4.174A pdb=" N ILE B 655 " --> pdb=" O VAL B 864 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 59 through 65 removed outlier: 7.297A pdb=" N VAL C 27 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N THR C 63 " --> pdb=" O VAL C 27 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ILE C 29 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N VAL C 65 " --> pdb=" O ILE C 29 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ALA C 31 " --> pdb=" O VAL C 65 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N TYR C 88 " --> pdb=" O ILE C 26 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ASN C 28 " --> pdb=" O TYR C 88 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N ILE C 90 " --> pdb=" O ASN C 28 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N GLY C 30 " --> pdb=" O ILE C 90 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N VAL C 92 " --> pdb=" O GLY C 30 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N VAL C 32 " --> pdb=" O VAL C 92 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N VAL C 118 " --> pdb=" O LEU C 138 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 194 through 196 removed outlier: 6.643A pdb=" N ILE C 164 " --> pdb=" O ILE C 220 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N SER C 222 " --> pdb=" O ILE C 164 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N LEU C 166 " --> pdb=" O SER C 222 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 270 through 271 removed outlier: 3.630A pdb=" N SER C 352 " --> pdb=" O GLN C 270 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N TYR C 351 " --> pdb=" O ILE C 366 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N ILE C 366 " --> pdb=" O TYR C 351 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ILE C 353 " --> pdb=" O VAL C 364 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 397 through 398 Processing sheet with id=AB9, first strand: chain 'C' and resid 434 through 436 Processing sheet with id=AC1, first strand: chain 'C' and resid 485 through 489 Processing sheet with id=AC2, first strand: chain 'C' and resid 535 through 537 Processing sheet with id=AC3, first strand: chain 'C' and resid 710 through 711 removed outlier: 9.305A pdb=" N TYR C 711 " --> pdb=" O TYR C 681 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N THR C 683 " --> pdb=" O TYR C 711 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ALA C 682 " --> pdb=" O ILE C 730 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 147 through 152 removed outlier: 12.568A pdb=" N ALA D 47 " --> pdb=" O VAL D 193 " (cutoff:3.500A) removed outlier: 10.121A pdb=" N ALA D 195 " --> pdb=" O ALA D 47 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N ARG D 49 " --> pdb=" O ALA D 195 " (cutoff:3.500A) removed outlier: 8.725A pdb=" N LEU D 197 " --> pdb=" O ARG D 49 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N GLY D 51 " --> pdb=" O LEU D 197 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N ILE D 221 " --> pdb=" O SER D 194 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N LEU D 196 " --> pdb=" O ILE D 221 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N ILE D 223 " --> pdb=" O LEU D 196 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ALA D 198 " --> pdb=" O ILE D 223 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N VAL D 457 " --> pdb=" O HIS D 237 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N GLN D 239 " --> pdb=" O VAL D 457 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N SER D 459 " --> pdb=" O GLN D 239 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N SER D 241 " --> pdb=" O SER D 459 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 290 through 296 removed outlier: 6.294A pdb=" N PHE D 265 " --> pdb=" O LEU D 291 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N SER D 293 " --> pdb=" O PHE D 265 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N ASN D 264 " --> pdb=" O THR D 324 " (cutoff:3.500A) removed outlier: 8.222A pdb=" N VAL D 326 " --> pdb=" O ASN D 264 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N SER D 266 " --> pdb=" O VAL D 326 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N PHE D 328 " --> pdb=" O SER D 266 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N LEU D 268 " --> pdb=" O PHE D 328 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N MET D 327 " --> pdb=" O VAL D 355 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N TRP D 354 " --> pdb=" O ILE D 375 " (cutoff:3.500A) removed outlier: 8.830A pdb=" N HIS D 377 " --> pdb=" O TRP D 354 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N LEU D 356 " --> pdb=" O HIS D 377 " (cutoff:3.500A) removed outlier: 9.655A pdb=" N LYS D 379 " --> pdb=" O LEU D 356 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N PHE D 463 " --> pdb=" O SER D 483 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N SER D 483 " --> pdb=" O PHE D 463 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ILE D 465 " --> pdb=" O LEU D 481 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 595 through 596 removed outlier: 4.069A pdb=" N ASP D 596 " --> pdb=" O LEU D 515 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ARG D 516 " --> pdb=" O MET D 627 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 527 through 528 removed outlier: 3.676A pdb=" N TYR D 577 " --> pdb=" O PHE D 527 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 650 through 651 removed outlier: 3.517A pdb=" N THR D 651 " --> pdb=" O GLU D 871 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU D 871 " --> pdb=" O THR D 651 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'D' and resid 844 through 845 removed outlier: 3.845A pdb=" N ILE D 655 " --> pdb=" O VAL D 864 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N VAL D 657 " --> pdb=" O LEU D 862 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU D 862 " --> pdb=" O VAL D 657 " (cutoff:3.500A) 913 hydrogen bonds defined for protein. 2643 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: 4.19 Time building geometry restraints manager: 2.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6518 1.34 - 1.46: 3469 1.46 - 1.58: 8052 1.58 - 1.70: 0 1.70 - 1.82: 93 Bond restraints: 18132 Sorted by residual: bond pdb=" N LYS B 586 " pdb=" CA LYS B 586 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.19e-02 7.06e+03 6.33e+00 bond pdb=" CD GLU B 830 " pdb=" OE1 GLU B 830 " ideal model delta sigma weight residual 1.249 1.220 0.029 1.90e-02 2.77e+03 2.27e+00 bond pdb=" CA PHE B 794 " pdb=" CB PHE B 794 " ideal model delta sigma weight residual 1.530 1.555 -0.024 1.69e-02 3.50e+03 2.10e+00 bond pdb=" N GLU B 830 " pdb=" CA GLU B 830 " ideal model delta sigma weight residual 1.458 1.476 -0.018 1.26e-02 6.30e+03 2.00e+00 bond pdb=" N ARG B 622 " pdb=" CA ARG B 622 " ideal model delta sigma weight residual 1.458 1.477 -0.019 1.42e-02 4.96e+03 1.85e+00 ... (remaining 18127 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.35: 24606 2.35 - 4.70: 238 4.70 - 7.05: 37 7.05 - 9.40: 9 9.40 - 11.75: 3 Bond angle restraints: 24893 Sorted by residual: angle pdb=" N PRO C 447 " pdb=" CA PRO C 447 " pdb=" CB PRO C 447 " ideal model delta sigma weight residual 103.25 110.91 -7.66 1.05e+00 9.07e-01 5.33e+01 angle pdb=" C ARG B 793 " pdb=" N PHE B 794 " pdb=" CA PHE B 794 " ideal model delta sigma weight residual 121.54 133.29 -11.75 1.91e+00 2.74e-01 3.78e+01 angle pdb=" C GLU A 545 " pdb=" CA GLU A 545 " pdb=" CB GLU A 545 " ideal model delta sigma weight residual 115.79 110.08 5.71 1.19e+00 7.06e-01 2.30e+01 angle pdb=" C GLU B 830 " pdb=" CA GLU B 830 " pdb=" CB GLU B 830 " ideal model delta sigma weight residual 110.70 119.21 -8.51 1.83e+00 2.99e-01 2.16e+01 angle pdb=" N GLU B 830 " pdb=" CA GLU B 830 " pdb=" C GLU B 830 " ideal model delta sigma weight residual 111.69 106.08 5.61 1.23e+00 6.61e-01 2.08e+01 ... (remaining 24888 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 10170 17.87 - 35.74: 419 35.74 - 53.61: 90 53.61 - 71.48: 16 71.48 - 89.35: 8 Dihedral angle restraints: 10703 sinusoidal: 2155 harmonic: 8548 Sorted by residual: dihedral pdb=" CB CYS A 420 " pdb=" SG CYS A 420 " pdb=" SG CYS A 454 " pdb=" CB CYS A 454 " ideal model delta sinusoidal sigma weight residual 93.00 -179.36 -87.64 1 1.00e+01 1.00e-02 9.20e+01 dihedral pdb=" CB CYS B 543 " pdb=" SG CYS B 543 " pdb=" SG CYS B 576 " pdb=" CB CYS B 576 " ideal model delta sinusoidal sigma weight residual -86.00 -170.10 84.10 1 1.00e+01 1.00e-02 8.61e+01 dihedral pdb=" CB CYS C 436 " pdb=" SG CYS C 436 " pdb=" SG CYS C 455 " pdb=" CB CYS C 455 " ideal model delta sinusoidal sigma weight residual -86.00 -165.28 79.28 1 1.00e+01 1.00e-02 7.82e+01 ... (remaining 10700 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 2424 0.051 - 0.102: 502 0.102 - 0.153: 135 0.153 - 0.204: 9 0.204 - 0.256: 4 Chirality restraints: 3074 Sorted by residual: chirality pdb=" CA LYS B 586 " pdb=" N LYS B 586 " pdb=" C LYS B 586 " pdb=" CB LYS B 586 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" CA PRO C 447 " pdb=" N PRO C 447 " pdb=" C PRO C 447 " pdb=" CB PRO C 447 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CB VAL B 629 " pdb=" CA VAL B 629 " pdb=" CG1 VAL B 629 " pdb=" CG2 VAL B 629 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.09e+00 ... (remaining 3071 not shown) Planarity restraints: 3410 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS D 523 " -0.090 5.00e-02 4.00e+02 1.36e-01 2.97e+01 pdb=" N PRO D 524 " 0.236 5.00e-02 4.00e+02 pdb=" CA PRO D 524 " -0.074 5.00e-02 4.00e+02 pdb=" CD PRO D 524 " -0.071 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 793 " 0.021 2.00e-02 2.50e+03 4.22e-02 1.78e+01 pdb=" C ARG B 793 " -0.073 2.00e-02 2.50e+03 pdb=" O ARG B 793 " 0.028 2.00e-02 2.50e+03 pdb=" N PHE B 794 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA C 515 " -0.035 5.00e-02 4.00e+02 5.32e-02 4.52e+00 pdb=" N PRO C 516 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO C 516 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 516 " -0.029 5.00e-02 4.00e+02 ... (remaining 3407 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 615 2.71 - 3.26: 18351 3.26 - 3.81: 27105 3.81 - 4.35: 28257 4.35 - 4.90: 48936 Nonbonded interactions: 123264 Sorted by model distance: nonbonded pdb=" OG SER A 507 " pdb=" OE1 GLN A 509 " model vdw 2.167 3.040 nonbonded pdb=" OG SER D 551 " pdb=" OG1 THR D 624 " model vdw 2.204 3.040 nonbonded pdb=" OG1 THR D 519 " pdb=" OG1 THR D 630 " model vdw 2.212 3.040 nonbonded pdb=" OD1 ASP B 533 " pdb=" N GLU B 534 " model vdw 2.224 3.120 nonbonded pdb=" O GLY C 485 " pdb=" NH2 ARG C 523 " model vdw 2.230 3.120 ... (remaining 123259 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 25 through 439 or (resid 440 through 444 and (name N or na \ me CA or name C or name O or name CB )) or (resid 445 through 448 and (name N or \ name CA or name C or name O or name CB )) or resid 449 through 452 or (resid 45 \ 3 and (name N or name CA or name C or name O or name CB )) or resid 454 through \ 546 or (resid 547 through 566 and (name N or name CA or name C or name O or name \ CB )) or resid 567 through 614 or resid 628 through 731 or (resid 732 and (name \ N or name CA or name C or name O or name CB )) or resid 733 through 745 or (res \ id 746 and (name N or name CA or name C or name O or name CB )) or resid 747 thr \ ough 798)) selection = (chain 'C' and ((resid 25 through 394 and (name N or name CA or name C or name O \ or name CB )) or resid 395 through 397 or (resid 398 and (name N or name CA or \ name C or name O or name CB )) or resid 399 through 431 or (resid 432 through 43 \ 3 and (name N or name CA or name C or name O or name CB )) or resid 434 through \ 487 or (resid 488 through 489 and (name N or name CA or name C or name O or name \ CB )) or resid 490 or (resid 491 through 496 and (name N or name CA or name C o \ r name O or name CB )) or resid 497 through 510 or (resid 511 and (name N or nam \ e CA or name C or name O or name CB )) or resid 512 through 543 or (resid 544 th \ rough 566 and (name N or name CA or name C or name O or name CB )) or resid 567 \ through 693 or (resid 694 through 695 and (name N or name CA or name C or name O \ or name CB )) or resid 696 through 708 or (resid 709 and (name N or name CA or \ name C or name O or name CB )) or resid 710 through 787 or (resid 788 and (name \ N or name CA or name C or name O or name CB )) or resid 789 through 798)) } ncs_group { reference = (chain 'B' and (resid 38 through 529 or (resid 530 through 532 and (name N or na \ me CA or name C or name O or name CB )) or resid 533 through 541 or (resid 542 a \ nd (name N or name CA or name C or name O or name CB )) or resid 543 or (resid 5 \ 44 through 545 and (name N or name CA or name C or name O or name CB )) or resid \ 546 through 549 or (resid 550 and (name N or name CA or name C or name O or nam \ e CB )) or resid 551 through 579 or (resid 580 and (name N or name CA or name C \ or name O or name CB )) or resid 581 through 596 or (resid 597 and (name N or na \ me CA or name C or name O or name CB )) or resid 598 through 625 or (resid 626 a \ nd (name N or name CA or name C or name O or name CB )) or resid 627 through 660 \ or (resid 740 through 776 and (name N or name CA or name C or name O or name CB \ )) or resid 777 through 784 or (resid 785 and (name N or name CA or name C or n \ ame O or name CB )) or resid 786 through 829 or (resid 830 and (name N or name C \ A or name C or name O or name CB )) or resid 831 through 855 or (resid 856 throu \ gh 857 and (name N or name CA or name C or name O or name CB )) or resid 858 thr \ ough 892 or (resid 893 through 894 and (name N or name CA or name C or name O or \ name CB )) or resid 895 through 955)) selection = (chain 'D' and (resid 38 through 565 or (resid 566 and (name N or name CA or nam \ e C or name O or name CB )) or resid 567 through 642 or (resid 643 and (name N o \ r name CA or name C or name O or name CB )) or resid 644 through 659 or (resid 6 \ 60 through 741 and (name N or name CA or name C or name O or name CB )) or (resi \ d 742 through 769 and (name N or name CA or name C or name O or name CB )) or re \ sid 770 through 844 or (resid 845 and (name N or name CA or name C or name O or \ name CB )) or resid 846 through 955)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.310 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: 0.020 Extract box with map and model: 0.620 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 22.210 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6066 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 18142 Z= 0.136 Angle : 0.618 11.749 24913 Z= 0.351 Chirality : 0.045 0.256 3074 Planarity : 0.004 0.136 3410 Dihedral : 11.314 89.352 5119 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.55 % Allowed : 6.85 % Favored : 92.61 % Rotamer: Outliers : 0.21 % Allowed : 0.42 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % Twisted Proline : 0.75 % 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 aren not related in a simple way. whole: 0.07 (0.17), residues: 2935 helix: 2.05 (0.16), residues: 1128 sheet: -0.08 (0.28), residues: 398 loop : -1.68 (0.17), residues: 1409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 673 TYR 0.018 0.001 TYR B 831 PHE 0.028 0.002 PHE A 754 TRP 0.016 0.001 TRP B 613 HIS 0.003 0.001 HIS D 787 Details of bonding type rmsd covalent geometry : bond 0.00278 (18132) covalent geometry : angle 0.61737 (24893) SS BOND : bond 0.00228 ( 10) SS BOND : angle 1.15611 ( 20) hydrogen bonds : bond 0.15644 ( 913) hydrogen bonds : angle 5.98316 ( 2643) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5870 Ramachandran restraints generated. 2935 Oldfield, 0 Emsley, 2935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5870 Ramachandran restraints generated. 2935 Oldfield, 0 Emsley, 2935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 202 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 664 ILE cc_start: 0.7535 (mm) cc_final: 0.6994 (mm) REVERT: C 424 PHE cc_start: 0.7408 (m-80) cc_final: 0.7068 (m-80) outliers start: 2 outliers final: 2 residues processed: 204 average time/residue: 0.1027 time to fit residues: 35.9282 Evaluate side-chains 176 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 174 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 197 optimal weight: 0.0470 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 50.0000 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.0970 chunk 207 optimal weight: 30.0000 chunk 155 optimal weight: 0.0010 chunk 244 optimal weight: 50.0000 chunk 183 optimal weight: 50.0000 chunk 111 optimal weight: 30.0000 overall best weight: 1.0286 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4571 r_free = 0.4571 target = 0.178423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.156780 restraints weight = 55446.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.152278 restraints weight = 77110.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.149914 restraints weight = 74528.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.149832 restraints weight = 67912.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.149020 restraints weight = 53598.178| |-----------------------------------------------------------------------------| r_work (final): 0.4136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6183 moved from start: 0.0748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 18142 Z= 0.123 Angle : 0.548 9.239 24913 Z= 0.298 Chirality : 0.044 0.234 3074 Planarity : 0.004 0.137 3410 Dihedral : 4.179 36.019 3039 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.55 % Allowed : 6.24 % Favored : 93.22 % Rotamer: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % Twisted Proline : 0.75 % 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 aren not related in a simple way. whole: 0.07 (0.17), residues: 2935 helix: 2.11 (0.16), residues: 1160 sheet: -0.24 (0.27), residues: 390 loop : -1.77 (0.17), residues: 1385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 516 TYR 0.020 0.001 TYR B 579 PHE 0.048 0.002 PHE B 794 TRP 0.010 0.001 TRP C 498 HIS 0.003 0.001 HIS D 562 Details of bonding type rmsd covalent geometry : bond 0.00263 (18132) covalent geometry : angle 0.54782 (24893) SS BOND : bond 0.00251 ( 10) SS BOND : angle 0.77243 ( 20) hydrogen bonds : bond 0.03607 ( 913) hydrogen bonds : angle 4.43900 ( 2643) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5870 Ramachandran restraints generated. 2935 Oldfield, 0 Emsley, 2935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5870 Ramachandran restraints generated. 2935 Oldfield, 0 Emsley, 2935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 202 time to evaluate : 0.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 501 MET cc_start: 0.8504 (tpp) cc_final: 0.7802 (mmt) REVERT: A 785 MET cc_start: 0.7616 (mmp) cc_final: 0.7416 (mmp) outliers start: 0 outliers final: 0 residues processed: 202 average time/residue: 0.1053 time to fit residues: 35.9448 Evaluate side-chains 172 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 217 optimal weight: 0.3980 chunk 2 optimal weight: 40.0000 chunk 116 optimal weight: 2.9990 chunk 214 optimal weight: 1.9990 chunk 8 optimal weight: 7.9990 chunk 258 optimal weight: 10.0000 chunk 115 optimal weight: 6.9990 chunk 124 optimal weight: 0.4980 chunk 169 optimal weight: 0.7980 chunk 250 optimal weight: 50.0000 chunk 62 optimal weight: 7.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 696 GLN C 770 GLN ** D 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4566 r_free = 0.4566 target = 0.177947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.154361 restraints weight = 56306.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.153220 restraints weight = 88333.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.148704 restraints weight = 67987.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.148681 restraints weight = 75016.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.148395 restraints weight = 60719.736| |-----------------------------------------------------------------------------| r_work (final): 0.4130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6207 moved from start: 0.1034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 18142 Z= 0.128 Angle : 0.539 10.649 24913 Z= 0.291 Chirality : 0.044 0.230 3074 Planarity : 0.004 0.137 3410 Dihedral : 4.096 36.069 3039 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.55 % Allowed : 6.37 % Favored : 93.08 % Rotamer: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % Twisted Proline : 1.49 % 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 aren not related in a simple way. whole: 0.20 (0.17), residues: 2935 helix: 2.22 (0.16), residues: 1166 sheet: -0.28 (0.26), residues: 410 loop : -1.69 (0.17), residues: 1359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 793 TYR 0.025 0.001 TYR B 579 PHE 0.020 0.002 PHE B 794 TRP 0.009 0.001 TRP C 498 HIS 0.004 0.001 HIS C 780 Details of bonding type rmsd covalent geometry : bond 0.00292 (18132) covalent geometry : angle 0.53836 (24893) SS BOND : bond 0.00345 ( 10) SS BOND : angle 0.83198 ( 20) hydrogen bonds : bond 0.03101 ( 913) hydrogen bonds : angle 3.99682 ( 2643) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5870 Ramachandran restraints generated. 2935 Oldfield, 0 Emsley, 2935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5870 Ramachandran restraints generated. 2935 Oldfield, 0 Emsley, 2935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 206 time to evaluate : 0.722 Fit side-chains revert: symmetry clash REVERT: A 501 MET cc_start: 0.8453 (tpp) cc_final: 0.7728 (mmt) REVERT: A 681 TYR cc_start: 0.7723 (p90) cc_final: 0.7467 (p90) REVERT: B 830 GLU cc_start: 0.7838 (pp20) cc_final: 0.7543 (pp20) REVERT: C 424 PHE cc_start: 0.7522 (m-80) cc_final: 0.7096 (m-10) outliers start: 0 outliers final: 0 residues processed: 206 average time/residue: 0.1055 time to fit residues: 36.5966 Evaluate side-chains 169 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 140 optimal weight: 0.7980 chunk 18 optimal weight: 4.9990 chunk 216 optimal weight: 0.5980 chunk 272 optimal weight: 0.8980 chunk 111 optimal weight: 8.9990 chunk 99 optimal weight: 40.0000 chunk 48 optimal weight: 2.9990 chunk 257 optimal weight: 50.0000 chunk 202 optimal weight: 5.9990 chunk 86 optimal weight: 9.9990 chunk 70 optimal weight: 3.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 509 GLN ** D 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4556 r_free = 0.4556 target = 0.177574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.151914 restraints weight = 55945.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.148498 restraints weight = 86851.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.146182 restraints weight = 72028.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.144531 restraints weight = 66224.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.145202 restraints weight = 58219.519| |-----------------------------------------------------------------------------| r_work (final): 0.4066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6332 moved from start: 0.1289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 18142 Z= 0.155 Angle : 0.558 10.237 24913 Z= 0.300 Chirality : 0.044 0.232 3074 Planarity : 0.004 0.138 3410 Dihedral : 4.169 36.686 3039 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.55 % Allowed : 7.09 % Favored : 92.37 % Rotamer: Outliers : 0.10 % Allowed : 5.93 % Favored : 93.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % Twisted Proline : 1.49 % 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 aren not related in a simple way. whole: 0.23 (0.17), residues: 2935 helix: 2.29 (0.16), residues: 1162 sheet: -0.30 (0.26), residues: 412 loop : -1.70 (0.17), residues: 1361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 793 TYR 0.030 0.002 TYR B 579 PHE 0.021 0.002 PHE A 484 TRP 0.010 0.001 TRP C 498 HIS 0.007 0.001 HIS C 780 Details of bonding type rmsd covalent geometry : bond 0.00361 (18132) covalent geometry : angle 0.55731 (24893) SS BOND : bond 0.00286 ( 10) SS BOND : angle 0.91121 ( 20) hydrogen bonds : bond 0.03061 ( 913) hydrogen bonds : angle 3.87593 ( 2643) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5870 Ramachandran restraints generated. 2935 Oldfield, 0 Emsley, 2935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5870 Ramachandran restraints generated. 2935 Oldfield, 0 Emsley, 2935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 202 time to evaluate : 0.680 Fit side-chains revert: symmetry clash REVERT: A 501 MET cc_start: 0.8491 (tpp) cc_final: 0.7844 (mmt) REVERT: A 664 ILE cc_start: 0.7609 (mm) cc_final: 0.7308 (mm) REVERT: A 681 TYR cc_start: 0.7818 (p90) cc_final: 0.7558 (p90) outliers start: 1 outliers final: 1 residues processed: 203 average time/residue: 0.1138 time to fit residues: 37.9593 Evaluate side-chains 169 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 168 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 244 optimal weight: 50.0000 chunk 125 optimal weight: 0.9990 chunk 216 optimal weight: 1.9990 chunk 196 optimal weight: 0.1980 chunk 39 optimal weight: 8.9990 chunk 31 optimal weight: 0.0170 chunk 162 optimal weight: 50.0000 chunk 179 optimal weight: 50.0000 chunk 219 optimal weight: 2.9990 chunk 120 optimal weight: 0.8980 chunk 23 optimal weight: 50.0000 overall best weight: 0.8222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4577 r_free = 0.4577 target = 0.179138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.156192 restraints weight = 55771.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.152909 restraints weight = 84702.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.149208 restraints weight = 73558.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.149317 restraints weight = 72528.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.148866 restraints weight = 57506.767| |-----------------------------------------------------------------------------| r_work (final): 0.4126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6193 moved from start: 0.1456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.069 18142 Z= 0.106 Angle : 0.525 9.121 24913 Z= 0.281 Chirality : 0.044 0.230 3074 Planarity : 0.004 0.139 3410 Dihedral : 3.971 35.575 3039 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.51 % Allowed : 5.83 % Favored : 93.66 % Rotamer: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % Twisted Proline : 1.49 % 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 aren not related in a simple way. whole: 0.35 (0.17), residues: 2935 helix: 2.39 (0.16), residues: 1165 sheet: -0.35 (0.26), residues: 422 loop : -1.62 (0.18), residues: 1348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 671 TYR 0.016 0.001 TYR B 579 PHE 0.026 0.001 PHE B 794 TRP 0.008 0.001 TRP D 608 HIS 0.004 0.001 HIS D 904 Details of bonding type rmsd covalent geometry : bond 0.00237 (18132) covalent geometry : angle 0.52506 (24893) SS BOND : bond 0.00383 ( 10) SS BOND : angle 0.87026 ( 20) hydrogen bonds : bond 0.02661 ( 913) hydrogen bonds : angle 3.68430 ( 2643) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5870 Ramachandran restraints generated. 2935 Oldfield, 0 Emsley, 2935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5870 Ramachandran restraints generated. 2935 Oldfield, 0 Emsley, 2935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 205 time to evaluate : 0.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 681 TYR cc_start: 0.7751 (p90) cc_final: 0.7534 (p90) REVERT: C 424 PHE cc_start: 0.7548 (m-80) cc_final: 0.7265 (m-80) outliers start: 0 outliers final: 0 residues processed: 205 average time/residue: 0.1059 time to fit residues: 36.6977 Evaluate side-chains 177 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 65 optimal weight: 6.9990 chunk 148 optimal weight: 70.0000 chunk 241 optimal weight: 9.9990 chunk 271 optimal weight: 5.9990 chunk 125 optimal weight: 0.9990 chunk 278 optimal weight: 30.0000 chunk 99 optimal weight: 3.9990 chunk 74 optimal weight: 50.0000 chunk 225 optimal weight: 4.9990 chunk 157 optimal weight: 50.0000 chunk 12 optimal weight: 50.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 626 HIS C 471 ASN ** D 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.174058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.150698 restraints weight = 55188.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.147438 restraints weight = 86878.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.145116 restraints weight = 76354.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.145109 restraints weight = 74587.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.143858 restraints weight = 61161.666| |-----------------------------------------------------------------------------| r_work (final): 0.4052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6342 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.094 18142 Z= 0.336 Angle : 0.758 12.848 24913 Z= 0.403 Chirality : 0.049 0.389 3074 Planarity : 0.005 0.140 3410 Dihedral : 4.755 36.701 3039 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.58 % Allowed : 8.21 % Favored : 91.21 % Rotamer: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % Twisted Proline : 1.49 % 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 aren not related in a simple way. whole: 0.02 (0.16), residues: 2935 helix: 2.10 (0.16), residues: 1162 sheet: -0.35 (0.27), residues: 402 loop : -1.83 (0.17), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 793 TYR 0.045 0.003 TYR B 579 PHE 0.049 0.004 PHE A 484 TRP 0.018 0.002 TRP C 498 HIS 0.011 0.002 HIS C 780 Details of bonding type rmsd covalent geometry : bond 0.00798 (18132) covalent geometry : angle 0.75745 (24893) SS BOND : bond 0.00575 ( 10) SS BOND : angle 1.40378 ( 20) hydrogen bonds : bond 0.04088 ( 913) hydrogen bonds : angle 4.21250 ( 2643) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5870 Ramachandran restraints generated. 2935 Oldfield, 0 Emsley, 2935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5870 Ramachandran restraints generated. 2935 Oldfield, 0 Emsley, 2935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 0.685 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 501 MET cc_start: 0.8815 (tpp) cc_final: 0.8034 (mmt) REVERT: C 470 MET cc_start: 0.7485 (mmt) cc_final: 0.7137 (mmt) outliers start: 0 outliers final: 0 residues processed: 186 average time/residue: 0.0988 time to fit residues: 32.1123 Evaluate side-chains 162 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 149 optimal weight: 50.0000 chunk 105 optimal weight: 50.0000 chunk 2 optimal weight: 30.0000 chunk 136 optimal weight: 1.9990 chunk 130 optimal weight: 6.9990 chunk 72 optimal weight: 0.9980 chunk 29 optimal weight: 8.9990 chunk 14 optimal weight: 50.0000 chunk 60 optimal weight: 5.9990 chunk 269 optimal weight: 5.9990 chunk 34 optimal weight: 30.0000 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 592 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4513 r_free = 0.4513 target = 0.173511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.150342 restraints weight = 55670.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.148424 restraints weight = 85824.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.147307 restraints weight = 61973.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.145353 restraints weight = 63990.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.144637 restraints weight = 61887.078| |-----------------------------------------------------------------------------| r_work (final): 0.4063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6290 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.080 18142 Z= 0.310 Angle : 0.726 11.288 24913 Z= 0.388 Chirality : 0.049 0.340 3074 Planarity : 0.005 0.140 3410 Dihedral : 4.967 36.719 3039 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.58 % Allowed : 8.01 % Favored : 91.41 % Rotamer: Outliers : 0.10 % Allowed : 3.64 % Favored : 96.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % Twisted Proline : 0.75 % Twisted General : 0.04 % 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 aren not related in a simple way. whole: -0.13 (0.16), residues: 2935 helix: 1.99 (0.16), residues: 1161 sheet: -0.43 (0.27), residues: 384 loop : -1.91 (0.17), residues: 1390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 638 TYR 0.035 0.003 TYR B 579 PHE 0.039 0.003 PHE A 484 TRP 0.016 0.002 TRP C 498 HIS 0.010 0.002 HIS C 780 Details of bonding type rmsd covalent geometry : bond 0.00731 (18132) covalent geometry : angle 0.72473 (24893) SS BOND : bond 0.00629 ( 10) SS BOND : angle 1.40973 ( 20) hydrogen bonds : bond 0.03910 ( 913) hydrogen bonds : angle 4.22786 ( 2643) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5870 Ramachandran restraints generated. 2935 Oldfield, 0 Emsley, 2935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5870 Ramachandran restraints generated. 2935 Oldfield, 0 Emsley, 2935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 188 time to evaluate : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 470 MET cc_start: 0.8801 (mpp) cc_final: 0.8546 (mpp) outliers start: 1 outliers final: 0 residues processed: 189 average time/residue: 0.1016 time to fit residues: 33.3074 Evaluate side-chains 161 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 268 optimal weight: 9.9990 chunk 253 optimal weight: 40.0000 chunk 135 optimal weight: 1.9990 chunk 120 optimal weight: 0.7980 chunk 193 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 41 optimal weight: 0.3980 chunk 110 optimal weight: 50.0000 chunk 189 optimal weight: 0.5980 chunk 15 optimal weight: 40.0000 chunk 94 optimal weight: 8.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 592 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4563 r_free = 0.4563 target = 0.177614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.154516 restraints weight = 55812.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.148900 restraints weight = 87916.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.146260 restraints weight = 83604.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.146363 restraints weight = 75073.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.145686 restraints weight = 58567.529| |-----------------------------------------------------------------------------| r_work (final): 0.4080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6300 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 18142 Z= 0.115 Angle : 0.570 11.373 24913 Z= 0.305 Chirality : 0.045 0.242 3074 Planarity : 0.005 0.142 3410 Dihedral : 4.322 34.000 3039 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.51 % Allowed : 6.17 % Favored : 93.32 % Rotamer: Outliers : 0.10 % Allowed : 0.94 % Favored : 98.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % Twisted Proline : 1.49 % 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 aren not related in a simple way. whole: 0.21 (0.17), residues: 2935 helix: 2.30 (0.16), residues: 1163 sheet: -0.43 (0.27), residues: 395 loop : -1.70 (0.17), residues: 1377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 516 TYR 0.017 0.001 TYR B 831 PHE 0.016 0.001 PHE C 679 TRP 0.016 0.001 TRP D 608 HIS 0.003 0.001 HIS C 404 Details of bonding type rmsd covalent geometry : bond 0.00258 (18132) covalent geometry : angle 0.56938 (24893) SS BOND : bond 0.00300 ( 10) SS BOND : angle 1.04234 ( 20) hydrogen bonds : bond 0.02748 ( 913) hydrogen bonds : angle 3.79863 ( 2643) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5870 Ramachandran restraints generated. 2935 Oldfield, 0 Emsley, 2935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5870 Ramachandran restraints generated. 2935 Oldfield, 0 Emsley, 2935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 196 time to evaluate : 0.677 Fit side-chains revert: symmetry clash REVERT: A 470 MET cc_start: 0.8704 (mpp) cc_final: 0.8493 (mpp) REVERT: A 501 MET cc_start: 0.8569 (mmt) cc_final: 0.8364 (tpp) outliers start: 1 outliers final: 0 residues processed: 197 average time/residue: 0.0985 time to fit residues: 33.7881 Evaluate side-chains 168 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 85 optimal weight: 0.9990 chunk 237 optimal weight: 50.0000 chunk 194 optimal weight: 3.9990 chunk 144 optimal weight: 6.9990 chunk 100 optimal weight: 0.0670 chunk 284 optimal weight: 3.9990 chunk 74 optimal weight: 30.0000 chunk 226 optimal weight: 7.9990 chunk 280 optimal weight: 2.9990 chunk 34 optimal weight: 40.0000 chunk 188 optimal weight: 2.9990 overall best weight: 2.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 592 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4540 r_free = 0.4540 target = 0.175624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.151898 restraints weight = 55240.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.145102 restraints weight = 87139.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.142782 restraints weight = 82267.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.142970 restraints weight = 76269.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.142266 restraints weight = 62319.960| |-----------------------------------------------------------------------------| r_work (final): 0.4027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6408 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 18142 Z= 0.181 Angle : 0.612 11.066 24913 Z= 0.327 Chirality : 0.046 0.245 3074 Planarity : 0.005 0.141 3410 Dihedral : 4.412 33.316 3039 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.55 % Allowed : 7.50 % Favored : 91.96 % Rotamer: Outliers : 0.10 % Allowed : 0.83 % Favored : 99.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % Twisted Proline : 1.49 % 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 aren not related in a simple way. whole: 0.20 (0.17), residues: 2935 helix: 2.31 (0.16), residues: 1161 sheet: -0.42 (0.27), residues: 395 loop : -1.72 (0.17), residues: 1379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 793 TYR 0.027 0.002 TYR B 579 PHE 0.020 0.002 PHE C 533 TRP 0.043 0.002 TRP C 731 HIS 0.006 0.001 HIS D 523 Details of bonding type rmsd covalent geometry : bond 0.00429 (18132) covalent geometry : angle 0.61106 (24893) SS BOND : bond 0.00372 ( 10) SS BOND : angle 1.03913 ( 20) hydrogen bonds : bond 0.03174 ( 913) hydrogen bonds : angle 3.83686 ( 2643) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5870 Ramachandran restraints generated. 2935 Oldfield, 0 Emsley, 2935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5870 Ramachandran restraints generated. 2935 Oldfield, 0 Emsley, 2935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 187 time to evaluate : 0.722 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 470 MET cc_start: 0.8743 (mpp) cc_final: 0.8471 (mpp) outliers start: 1 outliers final: 0 residues processed: 188 average time/residue: 0.1010 time to fit residues: 33.0886 Evaluate side-chains 162 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 36 optimal weight: 30.0000 chunk 91 optimal weight: 50.0000 chunk 122 optimal weight: 2.9990 chunk 99 optimal weight: 50.0000 chunk 286 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 60 optimal weight: 6.9990 chunk 7 optimal weight: 8.9990 chunk 42 optimal weight: 2.9990 chunk 287 optimal weight: 0.9980 chunk 94 optimal weight: 6.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 592 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4530 r_free = 0.4530 target = 0.174960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.151002 restraints weight = 54841.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.146206 restraints weight = 86067.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.143970 restraints weight = 75650.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.143310 restraints weight = 70238.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.142656 restraints weight = 63534.211| |-----------------------------------------------------------------------------| r_work (final): 0.4028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6413 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 18142 Z= 0.227 Angle : 0.655 10.722 24913 Z= 0.350 Chirality : 0.047 0.298 3074 Planarity : 0.005 0.141 3410 Dihedral : 4.625 33.825 3039 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.55 % Allowed : 7.50 % Favored : 91.96 % Rotamer: Outliers : 0.10 % Allowed : 0.73 % Favored : 99.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % Twisted Proline : 0.75 % 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 aren not related in a simple way. whole: 0.11 (0.17), residues: 2935 helix: 2.27 (0.16), residues: 1160 sheet: -0.53 (0.27), residues: 401 loop : -1.77 (0.17), residues: 1374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 793 TYR 0.031 0.002 TYR B 579 PHE 0.038 0.003 PHE B 899 TRP 0.024 0.002 TRP C 731 HIS 0.009 0.001 HIS C 780 Details of bonding type rmsd covalent geometry : bond 0.00542 (18132) covalent geometry : angle 0.65385 (24893) SS BOND : bond 0.00499 ( 10) SS BOND : angle 1.53841 ( 20) hydrogen bonds : bond 0.03407 ( 913) hydrogen bonds : angle 3.95848 ( 2643) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5870 Ramachandran restraints generated. 2935 Oldfield, 0 Emsley, 2935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5870 Ramachandran restraints generated. 2935 Oldfield, 0 Emsley, 2935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 184 time to evaluate : 0.726 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 470 MET cc_start: 0.8753 (mpp) cc_final: 0.8518 (mpp) outliers start: 1 outliers final: 0 residues processed: 185 average time/residue: 0.0961 time to fit residues: 31.1125 Evaluate side-chains 159 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 274 optimal weight: 10.0000 chunk 81 optimal weight: 40.0000 chunk 42 optimal weight: 9.9990 chunk 278 optimal weight: 20.0000 chunk 175 optimal weight: 8.9990 chunk 271 optimal weight: 1.9990 chunk 187 optimal weight: 6.9990 chunk 259 optimal weight: 50.0000 chunk 63 optimal weight: 0.9980 chunk 168 optimal weight: 50.0000 chunk 243 optimal weight: 20.0000 overall best weight: 5.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 592 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.167202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.142615 restraints weight = 53976.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.137452 restraints weight = 90845.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.135532 restraints weight = 80326.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.134600 restraints weight = 78095.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.133786 restraints weight = 66097.076| |-----------------------------------------------------------------------------| r_work (final): 0.3965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6496 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.102 18142 Z= 0.410 Angle : 0.855 13.337 24913 Z= 0.456 Chirality : 0.052 0.355 3074 Planarity : 0.006 0.143 3410 Dihedral : 5.416 35.003 3039 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.58 % Allowed : 8.96 % Favored : 90.46 % Rotamer: Outliers : 0.10 % Allowed : 0.52 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % Twisted Proline : 0.75 % Twisted General : 0.04 % 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 aren not related in a simple way. whole: -0.31 (0.16), residues: 2935 helix: 1.85 (0.16), residues: 1162 sheet: -0.63 (0.27), residues: 377 loop : -1.98 (0.17), residues: 1396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 638 TYR 0.042 0.004 TYR B 579 PHE 0.052 0.004 PHE B 842 TRP 0.034 0.003 TRP C 731 HIS 0.014 0.002 HIS C 780 Details of bonding type rmsd covalent geometry : bond 0.00975 (18132) covalent geometry : angle 0.85317 (24893) SS BOND : bond 0.00687 ( 10) SS BOND : angle 1.93114 ( 20) hydrogen bonds : bond 0.04476 ( 913) hydrogen bonds : angle 4.46330 ( 2643) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2870.01 seconds wall clock time: 50 minutes 5.22 seconds (3005.22 seconds total)