Starting phenix.real_space_refine on Wed Jan 22 05:38:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8usx_42522/01_2025/8usx_42522.cif Found real_map, /net/cci-nas-00/data/ceres_data/8usx_42522/01_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_42522/01_2025/8usx_42522.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8usx_42522/01_2025/8usx_42522.map" model { file = "/net/cci-nas-00/data/ceres_data/8usx_42522/01_2025/8usx_42522.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8usx_42522/01_2025/8usx_42522.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: {'GLN:plan1': 15, 'ASP:plan': 19, 'TYR:plan': 15, 'ASN:plan1': 26, 'TRP:plan': 10, 'HIS:plan': 14, 'PHE:plan': 14, 'GLU:plan': 28, 'ARG:plan': 27} 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, 'HIS:plan': 12, 'TYR:plan': 7, 'ASN:plan1': 23, 'TRP:plan': 9, 'ASP:plan': 19, 'PHE:plan': 24, 'GLU:plan': 25, 'ARG:plan': 19} 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: {'GLN:plan1': 16, 'ASP:plan': 19, 'TYR:plan': 15, 'ASN:plan1': 24, 'TRP:plan': 10, 'HIS:plan': 13, 'PHE:plan': 14, 'GLU:plan': 27, 'ARG:plan': 25} 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, 'HIS:plan': 13, 'TYR:plan': 8, 'ASN:plan1': 23, 'TRP:plan': 9, 'ASP:plan': 19, 'PHE:plan': 24, 'GLU:plan': 28, 'ARG:plan': 18} Unresolved non-hydrogen planarities: 762 Time building chain proxies: 12.56, per 1000 atoms: 0.70 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: 4.44 Conformation dependent library (CDL) restraints added in 3.3 seconds 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: 2.62 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: 7.80 Time building geometry restraints manager: 5.19 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: 3.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.700 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 45.880 Find NCS groups from input model: 1.270 Set up NCS constraints: 0.090 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: 0.010 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.060 ------------------------------------------------------------------------------- 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 18132 Z= 0.189 Angle : 0.617 11.749 24893 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.016 0.001 TRP B 613 HIS 0.003 0.001 HIS D 787 PHE 0.028 0.002 PHE A 754 TYR 0.018 0.001 TYR B 831 ARG 0.008 0.001 ARG C 673 *********************** 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 : 2.046 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: 0.2230 time to fit residues: 77.6556 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 : 1.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 249 optimal weight: 9.9990 chunk 223 optimal weight: 20.0000 chunk 124 optimal weight: 1.9990 chunk 76 optimal weight: 50.0000 chunk 150 optimal weight: 6.9990 chunk 119 optimal weight: 0.8980 chunk 231 optimal weight: 8.9990 chunk 89 optimal weight: 40.0000 chunk 140 optimal weight: 1.9990 chunk 172 optimal weight: 20.0000 chunk 267 optimal weight: 5.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 471 ASN C 696 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 = 0.4527 r_free = 0.4527 target = 0.175282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.152201 restraints weight = 55482.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.149161 restraints weight = 87085.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.146696 restraints weight = 74388.216| |-----------------------------------------------------------------------------| r_work (final): 0.4093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6250 moved from start: 0.1043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 18132 Z= 0.433 Angle : 0.678 11.550 24893 Z= 0.366 Chirality : 0.047 0.235 3074 Planarity : 0.005 0.136 3410 Dihedral : 4.688 37.176 3039 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.58 % Allowed : 8.07 % Favored : 91.35 % Rotamer: Outliers : 0.31 % Allowed : 8.11 % Favored : 91.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % Twisted Proline : 0.75 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.16), residues: 2935 helix: 1.82 (0.16), residues: 1171 sheet: -0.32 (0.27), residues: 403 loop : -1.92 (0.17), residues: 1361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 498 HIS 0.011 0.002 HIS C 780 PHE 0.056 0.003 PHE B 794 TYR 0.044 0.003 TYR B 579 ARG 0.006 0.001 ARG C 673 *********************** 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 187 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 184 time to evaluate : 2.189 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 501 MET cc_start: 0.8628 (tpp) cc_final: 0.8041 (mmt) outliers start: 3 outliers final: 3 residues processed: 187 average time/residue: 0.2245 time to fit residues: 72.2376 Evaluate side-chains 165 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 162 time to evaluate : 2.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 170 optimal weight: 40.0000 chunk 184 optimal weight: 30.0000 chunk 94 optimal weight: 10.0000 chunk 186 optimal weight: 2.9990 chunk 236 optimal weight: 50.0000 chunk 268 optimal weight: 8.9990 chunk 39 optimal weight: 4.9990 chunk 278 optimal weight: 0.0870 chunk 254 optimal weight: 10.0000 chunk 251 optimal weight: 50.0000 chunk 126 optimal weight: 4.9990 overall best weight: 4.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4510 r_free = 0.4510 target = 0.173616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.150110 restraints weight = 55280.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.146447 restraints weight = 89215.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.144787 restraints weight = 70643.032| |-----------------------------------------------------------------------------| r_work (final): 0.4059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6280 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.078 18132 Z= 0.511 Angle : 0.722 13.198 24893 Z= 0.388 Chirality : 0.048 0.241 3074 Planarity : 0.005 0.137 3410 Dihedral : 4.939 37.522 3039 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.58 % Allowed : 8.35 % Favored : 91.07 % Rotamer: Outliers : 0.10 % Allowed : 8.32 % Favored : 91.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % Twisted Proline : 0.75 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.16), residues: 2935 helix: 1.85 (0.16), residues: 1155 sheet: -0.42 (0.27), residues: 399 loop : -1.94 (0.17), residues: 1381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 498 HIS 0.010 0.002 HIS C 780 PHE 0.044 0.003 PHE B 649 TYR 0.037 0.003 TYR B 579 ARG 0.007 0.001 ARG D 793 *********************** 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 185 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 184 time to evaluate : 2.039 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 664 ILE cc_start: 0.7775 (mm) cc_final: 0.7478 (mm) outliers start: 1 outliers final: 0 residues processed: 185 average time/residue: 0.2149 time to fit residues: 69.3700 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 : 1.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 46 optimal weight: 0.3980 chunk 279 optimal weight: 6.9990 chunk 100 optimal weight: 0.0870 chunk 248 optimal weight: 0.9980 chunk 96 optimal weight: 50.0000 chunk 204 optimal weight: 30.0000 chunk 24 optimal weight: 50.0000 chunk 124 optimal weight: 2.9990 chunk 114 optimal weight: 0.9990 chunk 77 optimal weight: 6.9990 chunk 72 optimal weight: 6.9990 overall best weight: 1.0962 ------------------------------------------------------------------------------- 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 = 0.4560 r_free = 0.4560 target = 0.177394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.154345 restraints weight = 55565.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.150241 restraints weight = 88257.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.147498 restraints weight = 76017.613| |-----------------------------------------------------------------------------| r_work (final): 0.4110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6194 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 18132 Z= 0.181 Angle : 0.563 8.976 24893 Z= 0.302 Chirality : 0.044 0.240 3074 Planarity : 0.005 0.139 3410 Dihedral : 4.396 34.640 3039 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.51 % Allowed : 6.34 % Favored : 93.15 % Rotamer: Outliers : 0.10 % Allowed : 5.61 % Favored : 94.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % Twisted Proline : 1.49 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.17), residues: 2935 helix: 2.14 (0.16), residues: 1160 sheet: -0.46 (0.26), residues: 411 loop : -1.80 (0.17), residues: 1364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 792 HIS 0.008 0.001 HIS C 727 PHE 0.022 0.002 PHE B 794 TYR 0.015 0.001 TYR B 579 ARG 0.004 0.000 ARG D 660 *********************** 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 209 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 208 time to evaluate : 1.958 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 501 MET cc_start: 0.8288 (tpp) cc_final: 0.7898 (mmt) REVERT: A 664 ILE cc_start: 0.7804 (mm) cc_final: 0.7552 (mt) REVERT: C 424 PHE cc_start: 0.7546 (m-80) cc_final: 0.7302 (m-80) REVERT: D 547 MET cc_start: 0.6941 (tpt) cc_final: 0.6705 (tpp) REVERT: D 573 LYS cc_start: 0.7043 (tmtt) cc_final: 0.6371 (tptp) outliers start: 1 outliers final: 1 residues processed: 209 average time/residue: 0.2232 time to fit residues: 79.4311 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 : 2.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 240 optimal weight: 0.2980 chunk 195 optimal weight: 0.8980 chunk 69 optimal weight: 7.9990 chunk 194 optimal weight: 0.1980 chunk 271 optimal weight: 9.9990 chunk 184 optimal weight: 30.0000 chunk 146 optimal weight: 50.0000 chunk 239 optimal weight: 10.0000 chunk 15 optimal weight: 9.9990 chunk 173 optimal weight: 40.0000 chunk 185 optimal weight: 2.9990 overall best weight: 2.4784 ------------------------------------------------------------------------------- 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 = 0.4539 r_free = 0.4539 target = 0.175811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.152630 restraints weight = 55424.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.148374 restraints weight = 84752.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.146666 restraints weight = 71768.878| |-----------------------------------------------------------------------------| r_work (final): 0.4100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6228 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 18132 Z= 0.318 Angle : 0.616 9.946 24893 Z= 0.331 Chirality : 0.045 0.241 3074 Planarity : 0.005 0.140 3410 Dihedral : 4.481 34.230 3039 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.55 % Allowed : 7.67 % Favored : 91.79 % Rotamer: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % Twisted Proline : 0.75 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.17), residues: 2935 helix: 2.12 (0.16), residues: 1162 sheet: -0.45 (0.26), residues: 410 loop : -1.79 (0.17), residues: 1363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 498 HIS 0.005 0.001 HIS C 780 PHE 0.028 0.002 PHE B 649 TYR 0.026 0.002 TYR B 579 ARG 0.005 0.001 ARG D 660 *********************** 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 193 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 1.945 Fit side-chains revert: symmetry clash REVERT: A 664 ILE cc_start: 0.7838 (mm) cc_final: 0.7615 (mt) REVERT: C 470 MET cc_start: 0.7208 (mmt) cc_final: 0.6843 (mmt) REVERT: D 521 ILE cc_start: 0.8000 (tp) cc_final: 0.7793 (tp) REVERT: D 547 MET cc_start: 0.6937 (tpt) cc_final: 0.6691 (tpp) REVERT: D 573 LYS cc_start: 0.6776 (tmtt) cc_final: 0.6111 (tptp) outliers start: 0 outliers final: 0 residues processed: 193 average time/residue: 0.2314 time to fit residues: 77.1275 Evaluate side-chains 165 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 2.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 22 optimal weight: 50.0000 chunk 133 optimal weight: 1.9990 chunk 10 optimal weight: 50.0000 chunk 211 optimal weight: 0.0870 chunk 279 optimal weight: 0.0000 chunk 178 optimal weight: 50.0000 chunk 123 optimal weight: 2.9990 chunk 151 optimal weight: 50.0000 chunk 273 optimal weight: 2.9990 chunk 258 optimal weight: 50.0000 chunk 253 optimal weight: 50.0000 overall best weight: 1.6168 ------------------------------------------------------------------------------- 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 = 0.4551 r_free = 0.4551 target = 0.176104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.152190 restraints weight = 55576.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.149513 restraints weight = 87399.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.145845 restraints weight = 68928.622| |-----------------------------------------------------------------------------| r_work (final): 0.4101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6245 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 18132 Z= 0.221 Angle : 0.566 9.966 24893 Z= 0.303 Chirality : 0.044 0.242 3074 Planarity : 0.004 0.139 3410 Dihedral : 4.287 33.933 3039 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.51 % Allowed : 6.61 % Favored : 92.88 % Rotamer: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % Twisted Proline : 0.75 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.17), residues: 2935 helix: 2.26 (0.16), residues: 1163 sheet: -0.47 (0.26), residues: 412 loop : -1.73 (0.17), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 792 HIS 0.004 0.001 HIS B 814 PHE 0.026 0.002 PHE B 794 TYR 0.019 0.002 TYR B 579 ARG 0.010 0.001 ARG D 793 *********************** 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 196 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 1.912 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 501 MET cc_start: 0.8575 (tpp) cc_final: 0.7940 (mmt) REVERT: C 424 PHE cc_start: 0.7439 (m-80) cc_final: 0.7221 (m-10) REVERT: D 547 MET cc_start: 0.6947 (tpt) cc_final: 0.6732 (tpp) REVERT: D 573 LYS cc_start: 0.7041 (tmtt) cc_final: 0.6365 (tptt) outliers start: 0 outliers final: 0 residues processed: 196 average time/residue: 0.2199 time to fit residues: 74.9240 Evaluate side-chains 167 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 2.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 6 optimal weight: 8.9990 chunk 24 optimal weight: 50.0000 chunk 108 optimal weight: 9.9990 chunk 205 optimal weight: 20.0000 chunk 172 optimal weight: 9.9990 chunk 42 optimal weight: 0.2980 chunk 17 optimal weight: 30.0000 chunk 132 optimal weight: 4.9990 chunk 269 optimal weight: 0.0470 chunk 159 optimal weight: 50.0000 chunk 292 optimal weight: 3.9990 overall best weight: 3.6684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4514 r_free = 0.4514 target = 0.172607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.149324 restraints weight = 55195.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.147286 restraints weight = 85790.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.145428 restraints weight = 64661.939| |-----------------------------------------------------------------------------| r_work (final): 0.4095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6205 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 18132 Z= 0.442 Angle : 0.702 11.150 24893 Z= 0.376 Chirality : 0.047 0.243 3074 Planarity : 0.005 0.139 3410 Dihedral : 4.797 36.621 3039 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.58 % Allowed : 8.35 % Favored : 91.07 % Rotamer: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % Twisted Proline : 0.75 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.17), residues: 2935 helix: 2.06 (0.16), residues: 1157 sheet: -0.50 (0.27), residues: 395 loop : -1.82 (0.17), residues: 1383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP C 731 HIS 0.012 0.002 HIS C 780 PHE 0.048 0.003 PHE B 649 TYR 0.030 0.003 TYR B 579 ARG 0.006 0.001 ARG B 638 *********************** 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: 0 poor density : 189 time to evaluate : 2.024 Fit side-chains revert: symmetry clash REVERT: A 470 MET cc_start: 0.8793 (mpp) cc_final: 0.8531 (mpp) REVERT: A 501 MET cc_start: 0.8586 (tpp) cc_final: 0.7794 (mmt) REVERT: A 664 ILE cc_start: 0.7920 (mm) cc_final: 0.7712 (mt) REVERT: C 470 MET cc_start: 0.7307 (mmt) cc_final: 0.7083 (mmt) outliers start: 0 outliers final: 0 residues processed: 189 average time/residue: 0.2234 time to fit residues: 73.5193 Evaluate side-chains 160 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 2.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 161 optimal weight: 0.7980 chunk 267 optimal weight: 0.8980 chunk 234 optimal weight: 50.0000 chunk 184 optimal weight: 0.0050 chunk 224 optimal weight: 40.0000 chunk 178 optimal weight: 50.0000 chunk 114 optimal weight: 0.6980 chunk 163 optimal weight: 6.9990 chunk 195 optimal weight: 0.5980 chunk 109 optimal weight: 50.0000 chunk 280 optimal weight: 0.9990 overall best weight: 0.5994 ------------------------------------------------------------------------------- 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** ** C 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 727 HIS ** 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 = 0.4561 r_free = 0.4561 target = 0.176489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.154001 restraints weight = 55268.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.148806 restraints weight = 85537.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.146445 restraints weight = 78508.283| |-----------------------------------------------------------------------------| r_work (final): 0.4115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6186 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.064 18132 Z= 0.154 Angle : 0.563 10.926 24893 Z= 0.298 Chirality : 0.044 0.236 3074 Planarity : 0.004 0.141 3410 Dihedral : 4.265 33.593 3039 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.51 % Allowed : 6.00 % Favored : 93.49 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.17), residues: 2935 helix: 2.36 (0.16), residues: 1161 sheet: -0.57 (0.26), residues: 407 loop : -1.68 (0.17), residues: 1367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 608 HIS 0.005 0.001 HIS B 904 PHE 0.015 0.001 PHE C 754 TYR 0.019 0.001 TYR B 816 ARG 0.004 0.000 ARG D 793 *********************** 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 201 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 201 time to evaluate : 2.031 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 501 MET cc_start: 0.8323 (tpp) cc_final: 0.7702 (mmt) REVERT: C 426 VAL cc_start: 0.9163 (p) cc_final: 0.8960 (p) outliers start: 0 outliers final: 0 residues processed: 201 average time/residue: 0.2211 time to fit residues: 77.1854 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 : 2.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 193 optimal weight: 2.9990 chunk 0 optimal weight: 120.0000 chunk 150 optimal weight: 50.0000 chunk 258 optimal weight: 20.0000 chunk 22 optimal weight: 30.0000 chunk 16 optimal weight: 40.0000 chunk 136 optimal weight: 0.5980 chunk 2 optimal weight: 30.0000 chunk 235 optimal weight: 50.0000 chunk 233 optimal weight: 50.0000 chunk 252 optimal weight: 0.0020 overall best weight: 10.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 771 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 782 ASN ** C 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 562 HIS D 886 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.164478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.141752 restraints weight = 52195.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.138113 restraints weight = 78651.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.135758 restraints weight = 65127.311| |-----------------------------------------------------------------------------| r_work (final): 0.3983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6421 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.017 0.183 18132 Z= 1.182 Angle : 1.203 19.674 24893 Z= 0.637 Chirality : 0.063 0.428 3074 Planarity : 0.009 0.236 3410 Dihedral : 6.403 39.358 3039 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 17.47 Ramachandran Plot: Outliers : 0.85 % Allowed : 10.90 % Favored : 88.25 % Rotamer: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % Twisted Proline : 1.49 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.16), residues: 2935 helix: 1.16 (0.16), residues: 1138 sheet: -0.99 (0.26), residues: 387 loop : -2.13 (0.16), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.005 TRP C 731 HIS 0.028 0.004 HIS C 780 PHE 0.093 0.007 PHE B 649 TYR 0.050 0.006 TYR B 579 ARG 0.023 0.002 ARG B 638 *********************** 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 173 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 173 time to evaluate : 2.142 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 470 MET cc_start: 0.8896 (mpp) cc_final: 0.8600 (mpp) REVERT: A 681 TYR cc_start: 0.8221 (p90) cc_final: 0.7999 (p90) REVERT: C 470 MET cc_start: 0.7966 (mmt) cc_final: 0.7691 (mmt) outliers start: 0 outliers final: 0 residues processed: 173 average time/residue: 0.2173 time to fit residues: 66.3120 Evaluate side-chains 151 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 2.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 198 optimal weight: 0.8980 chunk 177 optimal weight: 4.9990 chunk 115 optimal weight: 0.7980 chunk 51 optimal weight: 0.9980 chunk 197 optimal weight: 1.9990 chunk 132 optimal weight: 0.8980 chunk 14 optimal weight: 50.0000 chunk 269 optimal weight: 1.9990 chunk 239 optimal weight: 50.0000 chunk 190 optimal weight: 10.0000 chunk 126 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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** ** C 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4542 r_free = 0.4542 target = 0.176012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.151845 restraints weight = 55059.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.147352 restraints weight = 84146.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.145416 restraints weight = 69737.691| |-----------------------------------------------------------------------------| r_work (final): 0.4079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6298 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 18132 Z= 0.215 Angle : 0.646 9.908 24893 Z= 0.344 Chirality : 0.046 0.231 3074 Planarity : 0.005 0.144 3410 Dihedral : 4.916 33.705 3039 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.48 % Allowed : 6.51 % Favored : 93.02 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % Twisted Proline : 0.75 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.16), residues: 2935 helix: 1.97 (0.16), residues: 1161 sheet: -0.66 (0.28), residues: 354 loop : -1.93 (0.17), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP B 608 HIS 0.004 0.001 HIS B 897 PHE 0.024 0.002 PHE B 899 TYR 0.022 0.002 TYR B 816 ARG 0.005 0.001 ARG C 794 ********************** 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 188 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 2.106 Fit side-chains REVERT: A 470 MET cc_start: 0.8755 (mpp) cc_final: 0.8485 (mpp) REVERT: A 501 MET cc_start: 0.8300 (tpp) cc_final: 0.7733 (mmt) REVERT: B 608 TRP cc_start: 0.7487 (t-100) cc_final: 0.7106 (t60) REVERT: B 816 TYR cc_start: 0.7728 (t80) cc_final: 0.7506 (t80) REVERT: C 426 VAL cc_start: 0.9226 (p) cc_final: 0.8970 (p) outliers start: 0 outliers final: 0 residues processed: 188 average time/residue: 0.2154 time to fit residues: 70.8509 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 : 1.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 277 optimal weight: 5.9990 chunk 58 optimal weight: 20.0000 chunk 71 optimal weight: 5.9990 chunk 5 optimal weight: 20.0000 chunk 263 optimal weight: 30.0000 chunk 76 optimal weight: 50.0000 chunk 28 optimal weight: 50.0000 chunk 183 optimal weight: 50.0000 chunk 190 optimal weight: 3.9990 chunk 195 optimal weight: 0.9980 chunk 25 optimal weight: 50.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4447 r_free = 0.4447 target = 0.165152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.141918 restraints weight = 53231.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.137841 restraints weight = 78653.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.135665 restraints weight = 77324.278| |-----------------------------------------------------------------------------| r_work (final): 0.3995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6395 moved from start: 0.3087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.122 18132 Z= 0.833 Angle : 0.960 17.228 24893 Z= 0.510 Chirality : 0.055 0.313 3074 Planarity : 0.008 0.166 3410 Dihedral : 5.826 37.672 3039 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.75 % Allowed : 10.19 % Favored : 89.06 % Rotamer: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % Twisted Proline : 0.75 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.16), residues: 2935 helix: 1.47 (0.16), residues: 1141 sheet: -0.85 (0.28), residues: 354 loop : -2.08 (0.16), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.004 TRP B 608 HIS 0.018 0.003 HIS C 780 PHE 0.069 0.005 PHE B 649 TYR 0.051 0.005 TYR B 873 ARG 0.012 0.001 ARG B 638 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4807.09 seconds wall clock time: 86 minutes 51.92 seconds (5211.92 seconds total)