Starting phenix.real_space_refine on Sun Jan 26 13:26:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/3jcl_6526/01_2025/3jcl_6526.cif Found real_map, /net/cci-nas-00/data/ceres_data/3jcl_6526/01_2025/3jcl_6526.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/3jcl_6526/01_2025/3jcl_6526.map" default_real_map = "/net/cci-nas-00/data/ceres_data/3jcl_6526/01_2025/3jcl_6526.map" model { file = "/net/cci-nas-00/data/ceres_data/3jcl_6526/01_2025/3jcl_6526.cif" } default_model = "/net/cci-nas-00/data/ceres_data/3jcl_6526/01_2025/3jcl_6526.cif" } resolution = 4.0 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= 0.006 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 144 5.16 5 C 15702 2.51 5 N 4218 2.21 5 O 4758 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 129 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 24822 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 8274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1067, 8274 Classifications: {'peptide': 1067} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 1022} Chain breaks: 1 Restraints were copied for chains: C, B Time building chain proxies: 20.97, per 1000 atoms: 0.84 Number of scatterers: 24822 At special positions: 0 Unit cell: (140.16, 137.24, 148.92, 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 144 16.00 O 4758 8.00 N 4218 7.00 C 15702 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=19, symmetry=0 Simple disulfide: pdb=" SG CYS A 21 " - pdb=" SG CYS A 158 " distance=2.02 Simple disulfide: pdb=" SG CYS A 153 " - pdb=" SG CYS A 187 " distance=2.04 Simple disulfide: pdb=" SG CYS A 165 " - pdb=" SG CYS A 246 " distance=2.13 Simple disulfide: pdb=" SG CYS A 284 " - pdb=" SG CYS A 294 " distance=2.03 Simple disulfide: pdb=" SG CYS A 329 " - pdb=" SG CYS A 354 " distance=2.02 Simple disulfide: pdb=" SG CYS A 372 " - pdb=" SG CYS A 425 " distance=2.72 Simple disulfide: pdb=" SG CYS A 384 " - pdb=" SG CYS A 564 " distance=2.03 Simple disulfide: pdb=" SG CYS A 471 " - pdb=" SG CYS A 479 " distance=2.02 Simple disulfide: pdb=" SG CYS A 481 " - pdb=" SG CYS A 528 " distance=2.03 Simple disulfide: pdb=" SG CYS A 490 " - pdb=" SG CYS A 517 " distance=2.02 Simple disulfide: pdb=" SG CYS A 507 " - pdb=" SG CYS A 526 " distance=2.07 Simple disulfide: pdb=" SG CYS A 541 " - pdb=" SG CYS A 547 " distance=2.04 Simple disulfide: pdb=" SG CYS A 580 " - pdb=" SG CYS A 633 " distance=2.07 Simple disulfide: pdb=" SG CYS A 658 " - pdb=" SG CYS A 682 " distance=2.04 Simple disulfide: pdb=" SG CYS A 697 " - pdb=" SG CYS A 706 " distance=2.03 Simple disulfide: pdb=" SG CYS A 775 " - pdb=" SG CYS A 797 " distance=2.11 Simple disulfide: pdb=" SG CYS A 780 " - pdb=" SG CYS A 786 " distance=2.04 Simple disulfide: pdb=" SG CYS A 894 " - pdb=" SG CYS A 905 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1093 " distance=2.05 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: 6.35 Conformation dependent library (CDL) restraints added in 3.1 seconds 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5976 Finding SS restraints... Secondary structure from input PDB file: 99 helices and 39 sheets defined 32.7% alpha, 23.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.17 Creating SS restraints... Processing helix chain 'A' and resid 43 through 47 Processing helix chain 'A' and resid 90 through 92 No H-bonds generated for 'chain 'A' and resid 90 through 92' Processing helix chain 'A' and resid 111 through 114 Processing helix chain 'A' and resid 250 through 254 Processing helix chain 'A' and resid 287 through 297 Processing helix chain 'A' and resid 330 through 336 removed outlier: 3.925A pdb=" N TRP A 334 " --> pdb=" O ASN A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 362 Processing helix chain 'A' and resid 376 through 381 Processing helix chain 'A' and resid 396 through 398 No H-bonds generated for 'chain 'A' and resid 396 through 398' Processing helix chain 'A' and resid 399 through 404 Processing helix chain 'A' and resid 466 through 471 Processing helix chain 'A' and resid 479 through 483 Processing helix chain 'A' and resid 520 through 524 Processing helix chain 'A' and resid 598 through 602 Processing helix chain 'A' and resid 657 through 664 Processing helix chain 'A' and resid 717 through 728 removed outlier: 3.724A pdb=" N THR A 721 " --> pdb=" O SER A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 734 through 751 removed outlier: 3.842A pdb=" N MET A 749 " --> pdb=" O GLY A 745 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 755 removed outlier: 4.079A pdb=" N PHE A 755 " --> pdb=" O PRO A 752 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 752 through 755' Processing helix chain 'A' and resid 774 through 780 Processing helix chain 'A' and resid 783 through 791 removed outlier: 3.777A pdb=" N GLN A 789 " --> pdb=" O ALA A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 793 through 824 removed outlier: 3.502A pdb=" N CYS A 797 " --> pdb=" O TYR A 793 " (cutoff:3.500A) Processing helix chain 'A' and resid 865 through 879 removed outlier: 4.370A pdb=" N PHE A 877 " --> pdb=" O GLU A 873 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LYS A 879 " --> pdb=" O LEU A 875 " (cutoff:3.500A) Processing helix chain 'A' and resid 883 through 894 Processing helix chain 'A' and resid 895 through 897 No H-bonds generated for 'chain 'A' and resid 895 through 897' Processing helix chain 'A' and resid 902 through 910 removed outlier: 4.672A pdb=" N SER A 908 " --> pdb=" O LEU A 904 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N PHE A 909 " --> pdb=" O CYS A 905 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASN A 910 " --> pdb=" O VAL A 906 " (cutoff:3.500A) Processing helix chain 'A' and resid 920 through 937 Processing helix chain 'A' and resid 938 through 945 Processing helix chain 'A' and resid 947 through 958 Processing helix chain 'A' and resid 968 through 988 removed outlier: 3.788A pdb=" N PHE A 988 " --> pdb=" O ILE A 984 " (cutoff:3.500A) Processing helix chain 'A' and resid 992 through 1016 removed outlier: 3.947A pdb=" N LEU A1016 " --> pdb=" O LEU A1012 " (cutoff:3.500A) Processing helix chain 'A' and resid 1017 through 1019 No H-bonds generated for 'chain 'A' and resid 1017 through 1019' Processing helix chain 'A' and resid 1026 through 1032 Processing helix chain 'A' and resid 1035 through 1083 Processing helix chain 'B' and resid 43 through 47 Processing helix chain 'B' and resid 90 through 92 No H-bonds generated for 'chain 'B' and resid 90 through 92' Processing helix chain 'B' and resid 111 through 114 Processing helix chain 'B' and resid 250 through 254 Processing helix chain 'B' and resid 287 through 297 Processing helix chain 'B' and resid 330 through 336 removed outlier: 3.925A pdb=" N TRP B 334 " --> pdb=" O ASN B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 362 Processing helix chain 'B' and resid 376 through 381 Processing helix chain 'B' and resid 396 through 398 No H-bonds generated for 'chain 'B' and resid 396 through 398' Processing helix chain 'B' and resid 399 through 404 Processing helix chain 'B' and resid 466 through 471 Processing helix chain 'B' and resid 479 through 483 Processing helix chain 'B' and resid 520 through 524 Processing helix chain 'B' and resid 598 through 602 Processing helix chain 'B' and resid 657 through 664 Processing helix chain 'B' and resid 717 through 728 removed outlier: 3.724A pdb=" N THR B 721 " --> pdb=" O SER B 717 " (cutoff:3.500A) Processing helix chain 'B' and resid 734 through 751 removed outlier: 3.842A pdb=" N MET B 749 " --> pdb=" O GLY B 745 " (cutoff:3.500A) Processing helix chain 'B' and resid 752 through 755 removed outlier: 4.079A pdb=" N PHE B 755 " --> pdb=" O PRO B 752 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 752 through 755' Processing helix chain 'B' and resid 774 through 780 Processing helix chain 'B' and resid 783 through 791 removed outlier: 3.776A pdb=" N GLN B 789 " --> pdb=" O ALA B 785 " (cutoff:3.500A) Processing helix chain 'B' and resid 793 through 824 removed outlier: 3.501A pdb=" N CYS B 797 " --> pdb=" O TYR B 793 " (cutoff:3.500A) Processing helix chain 'B' and resid 865 through 879 removed outlier: 4.369A pdb=" N PHE B 877 " --> pdb=" O GLU B 873 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LYS B 879 " --> pdb=" O LEU B 875 " (cutoff:3.500A) Processing helix chain 'B' and resid 883 through 894 Processing helix chain 'B' and resid 895 through 897 No H-bonds generated for 'chain 'B' and resid 895 through 897' Processing helix chain 'B' and resid 902 through 910 removed outlier: 4.672A pdb=" N SER B 908 " --> pdb=" O LEU B 904 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N PHE B 909 " --> pdb=" O CYS B 905 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASN B 910 " --> pdb=" O VAL B 906 " (cutoff:3.500A) Processing helix chain 'B' and resid 920 through 937 Processing helix chain 'B' and resid 938 through 945 Processing helix chain 'B' and resid 947 through 958 Processing helix chain 'B' and resid 968 through 988 removed outlier: 3.788A pdb=" N PHE B 988 " --> pdb=" O ILE B 984 " (cutoff:3.500A) Processing helix chain 'B' and resid 992 through 1016 removed outlier: 3.947A pdb=" N LEU B1016 " --> pdb=" O LEU B1012 " (cutoff:3.500A) Processing helix chain 'B' and resid 1017 through 1019 No H-bonds generated for 'chain 'B' and resid 1017 through 1019' Processing helix chain 'B' and resid 1026 through 1032 Processing helix chain 'B' and resid 1035 through 1083 Processing helix chain 'C' and resid 43 through 47 Processing helix chain 'C' and resid 90 through 92 No H-bonds generated for 'chain 'C' and resid 90 through 92' Processing helix chain 'C' and resid 111 through 114 Processing helix chain 'C' and resid 250 through 254 Processing helix chain 'C' and resid 287 through 297 Processing helix chain 'C' and resid 330 through 336 removed outlier: 3.925A pdb=" N TRP C 334 " --> pdb=" O ASN C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 362 Processing helix chain 'C' and resid 376 through 381 Processing helix chain 'C' and resid 396 through 398 No H-bonds generated for 'chain 'C' and resid 396 through 398' Processing helix chain 'C' and resid 399 through 404 Processing helix chain 'C' and resid 466 through 471 Processing helix chain 'C' and resid 479 through 483 Processing helix chain 'C' and resid 520 through 524 Processing helix chain 'C' and resid 598 through 602 Processing helix chain 'C' and resid 657 through 664 Processing helix chain 'C' and resid 717 through 728 removed outlier: 3.725A pdb=" N THR C 721 " --> pdb=" O SER C 717 " (cutoff:3.500A) Processing helix chain 'C' and resid 734 through 751 removed outlier: 3.842A pdb=" N MET C 749 " --> pdb=" O GLY C 745 " (cutoff:3.500A) Processing helix chain 'C' and resid 752 through 755 removed outlier: 4.079A pdb=" N PHE C 755 " --> pdb=" O PRO C 752 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 752 through 755' Processing helix chain 'C' and resid 774 through 780 Processing helix chain 'C' and resid 783 through 791 removed outlier: 3.777A pdb=" N GLN C 789 " --> pdb=" O ALA C 785 " (cutoff:3.500A) Processing helix chain 'C' and resid 793 through 824 removed outlier: 3.502A pdb=" N CYS C 797 " --> pdb=" O TYR C 793 " (cutoff:3.500A) Processing helix chain 'C' and resid 865 through 879 removed outlier: 4.369A pdb=" N PHE C 877 " --> pdb=" O GLU C 873 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LYS C 879 " --> pdb=" O LEU C 875 " (cutoff:3.500A) Processing helix chain 'C' and resid 883 through 894 Processing helix chain 'C' and resid 895 through 897 No H-bonds generated for 'chain 'C' and resid 895 through 897' Processing helix chain 'C' and resid 902 through 910 removed outlier: 4.671A pdb=" N SER C 908 " --> pdb=" O LEU C 904 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE C 909 " --> pdb=" O CYS C 905 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASN C 910 " --> pdb=" O VAL C 906 " (cutoff:3.500A) Processing helix chain 'C' and resid 920 through 937 Processing helix chain 'C' and resid 938 through 945 Processing helix chain 'C' and resid 947 through 958 Processing helix chain 'C' and resid 968 through 988 removed outlier: 3.788A pdb=" N PHE C 988 " --> pdb=" O ILE C 984 " (cutoff:3.500A) Processing helix chain 'C' and resid 992 through 1016 removed outlier: 3.947A pdb=" N LEU C1016 " --> pdb=" O LEU C1012 " (cutoff:3.500A) Processing helix chain 'C' and resid 1017 through 1019 No H-bonds generated for 'chain 'C' and resid 1017 through 1019' Processing helix chain 'C' and resid 1026 through 1032 Processing helix chain 'C' and resid 1035 through 1083 Processing sheet with id=A, first strand: chain 'A' and resid 26 through 28 removed outlier: 6.635A pdb=" N ASN A 26 " --> pdb=" O VAL A 87 " (cutoff:3.500A) No H-bonds generated for sheet with id=A Processing sheet with id=B, first strand: chain 'A' and resid 37 through 41 removed outlier: 5.060A pdb=" N PHE A 76 " --> pdb=" O SER A 38 " (cutoff:3.500A) removed outlier: 8.484A pdb=" N LYS A 75 " --> pdb=" O PRO A 262 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLY A 103 " --> pdb=" O LEU A 263 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N PHE A 213 " --> pdb=" O SER A 229 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N SER A 229 " --> pdb=" O PHE A 213 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ALA A 215 " --> pdb=" O LEU A 227 " (cutoff:3.500A) Processing sheet with id=C, first strand: chain 'A' and resid 61 through 70 removed outlier: 7.707A pdb=" N GLN A 267 " --> pdb=" O ASP A 283 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N ASP A 283 " --> pdb=" O GLN A 267 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N LEU A 269 " --> pdb=" O ALA A 281 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ALA A 281 " --> pdb=" O LEU A 269 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ASN A 271 " --> pdb=" O THR A 279 " (cutoff:3.500A) Processing sheet with id=D, first strand: chain 'A' and resid 82 through 83 removed outlier: 6.666A pdb=" N THR A 163 " --> pdb=" O ILE A 245 " (cutoff:3.500A) Processing sheet with id=E, first strand: chain 'A' and resid 98 through 99 removed outlier: 3.899A pdb=" N THR A 125 " --> pdb=" O LEU A 242 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N GLN A 154 " --> pdb=" O CYS A 187 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N CYS A 187 " --> pdb=" O GLN A 154 " (cutoff:3.500A) Processing sheet with id=F, first strand: chain 'A' and resid 304 through 307 removed outlier: 6.284A pdb=" N GLY A 304 " --> pdb=" O ALA A 641 " (cutoff:3.500A) Processing sheet with id=G, first strand: chain 'A' and resid 318 through 321 removed outlier: 4.188A pdb=" N THR A 627 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N ASN A 617 " --> pdb=" O ILE A 630 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N LEU A 609 " --> pdb=" O ASN A 617 " (cutoff:3.500A) Processing sheet with id=H, first strand: chain 'A' and resid 347 through 351 removed outlier: 7.138A pdb=" N THR A 430 " --> pdb=" O ALA A 367 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N ALA A 367 " --> pdb=" O THR A 430 " (cutoff:3.500A) Processing sheet with id=I, first strand: chain 'A' and resid 354 through 356 Processing sheet with id=J, first strand: chain 'A' and resid 442 through 455 removed outlier: 5.615A pdb=" N SER A 444 " --> pdb=" O VAL A 543 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N VAL A 543 " --> pdb=" O SER A 444 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG A 448 " --> pdb=" O ASP A 539 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N SER A 537 " --> pdb=" O TYR A 450 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N PHE A 452 " --> pdb=" O GLY A 535 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N GLY A 535 " --> pdb=" O PHE A 452 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ASP A 454 " --> pdb=" O PHE A 533 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N PHE A 533 " --> pdb=" O ASP A 454 " (cutoff:3.500A) Processing sheet with id=K, first strand: chain 'A' and resid 688 through 694 removed outlier: 6.294A pdb=" N LYS A 711 " --> pdb=" O THR A 690 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N GLU A 692 " --> pdb=" O LYS A 711 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N LEU A 699 " --> pdb=" O VAL A 707 " (cutoff:3.500A) Processing sheet with id=L, first strand: chain 'A' and resid 757 through 764 Processing sheet with id=M, first strand: chain 'A' and resid 770 through 773 removed outlier: 4.032A pdb=" N LYS A 770 " --> pdb=" O LEU A 915 " (cutoff:3.500A) Processing sheet with id=N, first strand: chain 'B' and resid 26 through 28 removed outlier: 6.635A pdb=" N ASN B 26 " --> pdb=" O VAL B 87 " (cutoff:3.500A) No H-bonds generated for sheet with id=N Processing sheet with id=O, first strand: chain 'B' and resid 37 through 41 removed outlier: 5.060A pdb=" N PHE B 76 " --> pdb=" O SER B 38 " (cutoff:3.500A) removed outlier: 8.484A pdb=" N LYS B 75 " --> pdb=" O PRO B 262 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLY B 103 " --> pdb=" O LEU B 263 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N PHE B 213 " --> pdb=" O SER B 229 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N SER B 229 " --> pdb=" O PHE B 213 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ALA B 215 " --> pdb=" O LEU B 227 " (cutoff:3.500A) Processing sheet with id=P, first strand: chain 'B' and resid 61 through 70 removed outlier: 7.707A pdb=" N GLN B 267 " --> pdb=" O ASP B 283 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N ASP B 283 " --> pdb=" O GLN B 267 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N LEU B 269 " --> pdb=" O ALA B 281 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ALA B 281 " --> pdb=" O LEU B 269 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ASN B 271 " --> pdb=" O THR B 279 " (cutoff:3.500A) Processing sheet with id=Q, first strand: chain 'B' and resid 82 through 83 removed outlier: 6.665A pdb=" N THR B 163 " --> pdb=" O ILE B 245 " (cutoff:3.500A) Processing sheet with id=R, first strand: chain 'B' and resid 98 through 99 removed outlier: 3.900A pdb=" N THR B 125 " --> pdb=" O LEU B 242 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N GLN B 154 " --> pdb=" O CYS B 187 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N CYS B 187 " --> pdb=" O GLN B 154 " (cutoff:3.500A) Processing sheet with id=S, first strand: chain 'B' and resid 304 through 307 removed outlier: 6.284A pdb=" N GLY B 304 " --> pdb=" O ALA B 641 " (cutoff:3.500A) Processing sheet with id=T, first strand: chain 'B' and resid 318 through 321 removed outlier: 4.188A pdb=" N THR B 627 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N ASN B 617 " --> pdb=" O ILE B 630 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N LEU B 609 " --> pdb=" O ASN B 617 " (cutoff:3.500A) Processing sheet with id=U, first strand: chain 'B' and resid 347 through 351 removed outlier: 7.138A pdb=" N THR B 430 " --> pdb=" O ALA B 367 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N ALA B 367 " --> pdb=" O THR B 430 " (cutoff:3.500A) Processing sheet with id=V, first strand: chain 'B' and resid 354 through 356 Processing sheet with id=W, first strand: chain 'B' and resid 442 through 455 removed outlier: 5.614A pdb=" N SER B 444 " --> pdb=" O VAL B 543 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N VAL B 543 " --> pdb=" O SER B 444 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG B 448 " --> pdb=" O ASP B 539 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N SER B 537 " --> pdb=" O TYR B 450 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N PHE B 452 " --> pdb=" O GLY B 535 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N GLY B 535 " --> pdb=" O PHE B 452 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ASP B 454 " --> pdb=" O PHE B 533 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N PHE B 533 " --> pdb=" O ASP B 454 " (cutoff:3.500A) Processing sheet with id=X, first strand: chain 'B' and resid 688 through 694 removed outlier: 6.296A pdb=" N LYS B 711 " --> pdb=" O THR B 690 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N GLU B 692 " --> pdb=" O LYS B 711 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N LEU B 699 " --> pdb=" O VAL B 707 " (cutoff:3.500A) Processing sheet with id=Y, first strand: chain 'B' and resid 757 through 764 Processing sheet with id=Z, first strand: chain 'B' and resid 770 through 773 removed outlier: 4.032A pdb=" N LYS B 770 " --> pdb=" O LEU B 915 " (cutoff:3.500A) Processing sheet with id=AA, first strand: chain 'C' and resid 26 through 28 removed outlier: 6.635A pdb=" N ASN C 26 " --> pdb=" O VAL C 87 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA Processing sheet with id=AB, first strand: chain 'C' and resid 37 through 41 removed outlier: 5.060A pdb=" N PHE C 76 " --> pdb=" O SER C 38 " (cutoff:3.500A) removed outlier: 8.483A pdb=" N LYS C 75 " --> pdb=" O PRO C 262 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLY C 103 " --> pdb=" O LEU C 263 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N PHE C 213 " --> pdb=" O SER C 229 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N SER C 229 " --> pdb=" O PHE C 213 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ALA C 215 " --> pdb=" O LEU C 227 " (cutoff:3.500A) Processing sheet with id=AC, first strand: chain 'C' and resid 61 through 70 removed outlier: 7.707A pdb=" N GLN C 267 " --> pdb=" O ASP C 283 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N ASP C 283 " --> pdb=" O GLN C 267 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N LEU C 269 " --> pdb=" O ALA C 281 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ALA C 281 " --> pdb=" O LEU C 269 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ASN C 271 " --> pdb=" O THR C 279 " (cutoff:3.500A) Processing sheet with id=AD, first strand: chain 'C' and resid 82 through 83 removed outlier: 6.666A pdb=" N THR C 163 " --> pdb=" O ILE C 245 " (cutoff:3.500A) Processing sheet with id=AE, first strand: chain 'C' and resid 98 through 99 removed outlier: 3.900A pdb=" N THR C 125 " --> pdb=" O LEU C 242 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N GLN C 154 " --> pdb=" O CYS C 187 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N CYS C 187 " --> pdb=" O GLN C 154 " (cutoff:3.500A) Processing sheet with id=AF, first strand: chain 'C' and resid 304 through 307 removed outlier: 6.284A pdb=" N GLY C 304 " --> pdb=" O ALA C 641 " (cutoff:3.500A) Processing sheet with id=AG, first strand: chain 'C' and resid 318 through 321 removed outlier: 4.188A pdb=" N THR C 627 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N ASN C 617 " --> pdb=" O ILE C 630 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N LEU C 609 " --> pdb=" O ASN C 617 " (cutoff:3.500A) Processing sheet with id=AH, first strand: chain 'C' and resid 347 through 351 removed outlier: 7.139A pdb=" N THR C 430 " --> pdb=" O ALA C 367 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N ALA C 367 " --> pdb=" O THR C 430 " (cutoff:3.500A) Processing sheet with id=AI, first strand: chain 'C' and resid 354 through 356 Processing sheet with id=AJ, first strand: chain 'C' and resid 442 through 455 removed outlier: 5.614A pdb=" N SER C 444 " --> pdb=" O VAL C 543 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N VAL C 543 " --> pdb=" O SER C 444 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG C 448 " --> pdb=" O ASP C 539 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N SER C 537 " --> pdb=" O TYR C 450 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N PHE C 452 " --> pdb=" O GLY C 535 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N GLY C 535 " --> pdb=" O PHE C 452 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ASP C 454 " --> pdb=" O PHE C 533 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N PHE C 533 " --> pdb=" O ASP C 454 " (cutoff:3.500A) Processing sheet with id=AK, first strand: chain 'C' and resid 688 through 694 removed outlier: 6.295A pdb=" N LYS C 711 " --> pdb=" O THR C 690 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N GLU C 692 " --> pdb=" O LYS C 711 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N LEU C 699 " --> pdb=" O VAL C 707 " (cutoff:3.500A) Processing sheet with id=AL, first strand: chain 'C' and resid 757 through 764 Processing sheet with id=AM, first strand: chain 'C' and resid 770 through 773 removed outlier: 4.032A pdb=" N LYS C 770 " --> pdb=" O LEU C 915 " (cutoff:3.500A) 1104 hydrogen bonds defined for protein. 3051 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: 13.13 Time building geometry restraints manager: 7.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 5100 1.32 - 1.46: 8990 1.46 - 1.60: 11104 1.60 - 1.75: 27 1.75 - 1.89: 153 Bond restraints: 25374 Sorted by residual: bond pdb=" CB PHE A 270 " pdb=" CG PHE A 270 " ideal model delta sigma weight residual 1.502 1.365 0.137 2.30e-02 1.89e+03 3.56e+01 bond pdb=" CB PHE C 270 " pdb=" CG PHE C 270 " ideal model delta sigma weight residual 1.502 1.365 0.137 2.30e-02 1.89e+03 3.56e+01 bond pdb=" CB PHE B 270 " pdb=" CG PHE B 270 " ideal model delta sigma weight residual 1.502 1.366 0.136 2.30e-02 1.89e+03 3.49e+01 bond pdb=" CB LEU A 300 " pdb=" CG LEU A 300 " ideal model delta sigma weight residual 1.530 1.426 0.104 2.00e-02 2.50e+03 2.69e+01 bond pdb=" CB LEU B 300 " pdb=" CG LEU B 300 " ideal model delta sigma weight residual 1.530 1.427 0.103 2.00e-02 2.50e+03 2.67e+01 ... (remaining 25369 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.43: 32298 3.43 - 6.86: 2034 6.86 - 10.29: 210 10.29 - 13.73: 24 13.73 - 17.16: 3 Bond angle restraints: 34569 Sorted by residual: angle pdb=" N VAL A 946 " pdb=" CA VAL A 946 " pdb=" CB VAL A 946 " ideal model delta sigma weight residual 110.17 98.69 11.48 1.11e+00 8.12e-01 1.07e+02 angle pdb=" C ALA A 944 " pdb=" CA ALA A 944 " pdb=" CB ALA A 944 " ideal model delta sigma weight residual 110.79 93.63 17.16 1.66e+00 3.63e-01 1.07e+02 angle pdb=" N VAL C 946 " pdb=" CA VAL C 946 " pdb=" CB VAL C 946 " ideal model delta sigma weight residual 110.17 98.72 11.45 1.11e+00 8.12e-01 1.06e+02 angle pdb=" N VAL B 946 " pdb=" CA VAL B 946 " pdb=" CB VAL B 946 " ideal model delta sigma weight residual 110.17 98.72 11.45 1.11e+00 8.12e-01 1.06e+02 angle pdb=" C ALA C 944 " pdb=" CA ALA C 944 " pdb=" CB ALA C 944 " ideal model delta sigma weight residual 110.79 93.69 17.10 1.66e+00 3.63e-01 1.06e+02 ... (remaining 34564 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.10: 14597 18.10 - 36.19: 331 36.19 - 54.29: 58 54.29 - 72.39: 58 72.39 - 90.48: 10 Dihedral angle restraints: 15054 sinusoidal: 5712 harmonic: 9342 Sorted by residual: dihedral pdb=" CB CYS A 329 " pdb=" SG CYS A 329 " pdb=" SG CYS A 354 " pdb=" CB CYS A 354 " ideal model delta sinusoidal sigma weight residual -86.00 -176.48 90.48 1 1.00e+01 1.00e-02 9.68e+01 dihedral pdb=" C ALA A 944 " pdb=" N ALA A 944 " pdb=" CA ALA A 944 " pdb=" CB ALA A 944 " ideal model delta harmonic sigma weight residual -122.60 -103.48 -19.12 0 2.50e+00 1.60e-01 5.85e+01 dihedral pdb=" C ALA B 944 " pdb=" N ALA B 944 " pdb=" CA ALA B 944 " pdb=" CB ALA B 944 " ideal model delta harmonic sigma weight residual -122.60 -103.53 -19.07 0 2.50e+00 1.60e-01 5.82e+01 ... (remaining 15051 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 2752 0.095 - 0.191: 984 0.191 - 0.286: 149 0.286 - 0.381: 12 0.381 - 0.476: 9 Chirality restraints: 3906 Sorted by residual: chirality pdb=" CA TRP A 536 " pdb=" N TRP A 536 " pdb=" C TRP A 536 " pdb=" CB TRP A 536 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.68e+00 chirality pdb=" CA TRP B 536 " pdb=" N TRP B 536 " pdb=" C TRP B 536 " pdb=" CB TRP B 536 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.65e+00 chirality pdb=" CA TRP C 536 " pdb=" N TRP C 536 " pdb=" C TRP C 536 " pdb=" CB TRP C 536 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.61e+00 ... (remaining 3903 not shown) Planarity restraints: 4512 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE C 751 " 0.065 5.00e-02 4.00e+02 1.01e-01 1.64e+01 pdb=" N PRO C 752 " -0.175 5.00e-02 4.00e+02 pdb=" CA PRO C 752 " 0.057 5.00e-02 4.00e+02 pdb=" CD PRO C 752 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 751 " -0.065 5.00e-02 4.00e+02 1.01e-01 1.63e+01 pdb=" N PRO A 752 " 0.175 5.00e-02 4.00e+02 pdb=" CA PRO A 752 " -0.057 5.00e-02 4.00e+02 pdb=" CD PRO A 752 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 751 " -0.065 5.00e-02 4.00e+02 1.01e-01 1.63e+01 pdb=" N PRO B 752 " 0.175 5.00e-02 4.00e+02 pdb=" CA PRO B 752 " -0.057 5.00e-02 4.00e+02 pdb=" CD PRO B 752 " -0.053 5.00e-02 4.00e+02 ... (remaining 4509 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 228 2.60 - 3.17: 23220 3.17 - 3.75: 38183 3.75 - 4.32: 57463 4.32 - 4.90: 89260 Nonbonded interactions: 208354 Sorted by model distance: nonbonded pdb=" SG CYS B 490 " pdb=" SG CYS B 517 " model vdw 2.019 3.760 nonbonded pdb=" SG CYS C 490 " pdb=" SG CYS C 517 " model vdw 2.021 3.760 nonbonded pdb=" SG CYS C 21 " pdb=" SG CYS C 158 " model vdw 2.023 3.760 nonbonded pdb=" SG CYS C 329 " pdb=" SG CYS C 354 " model vdw 2.023 3.760 nonbonded pdb=" SG CYS B 21 " pdb=" SG CYS B 158 " model vdw 2.023 3.760 ... (remaining 208349 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: 0.18 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.910 Check model and map are aligned: 0.160 Set scattering table: 0.210 Process input model: 65.700 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 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 : 0.018 0.150 25374 Z= 1.161 Angle : 1.834 17.156 34569 Z= 1.244 Chirality : 0.094 0.476 3906 Planarity : 0.010 0.101 4512 Dihedral : 9.753 89.544 9021 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.56 % Allowed : 5.17 % Favored : 94.26 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.30 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.72 (0.14), residues: 3189 helix: 0.12 (0.17), residues: 843 sheet: 0.11 (0.21), residues: 567 loop : -0.95 (0.14), residues: 1779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.007 TRP B 536 HIS 0.007 0.002 HIS A1098 PHE 0.044 0.007 PHE C 123 TYR 0.042 0.009 TYR A 58 ARG 0.007 0.001 ARG A 397 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 801 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 801 time to evaluate : 2.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 384 CYS cc_start: 0.5014 (t) cc_final: 0.4740 (t) REVERT: A 416 TYR cc_start: 0.8273 (t80) cc_final: 0.7810 (t80) REVERT: A 447 ASN cc_start: 0.7086 (t0) cc_final: 0.6477 (t0) REVERT: A 633 CYS cc_start: 0.5191 (m) cc_final: 0.4826 (m) REVERT: A 928 THR cc_start: 0.9312 (p) cc_final: 0.9008 (t) REVERT: A 1018 ASN cc_start: 0.8806 (t0) cc_final: 0.8406 (t0) REVERT: A 1024 SER cc_start: 0.9360 (t) cc_final: 0.9092 (m) REVERT: B 220 LYS cc_start: 0.8360 (mttt) cc_final: 0.8094 (ttpp) REVERT: B 240 TYR cc_start: 0.4986 (t80) cc_final: 0.4634 (t80) REVERT: B 361 LEU cc_start: 0.8735 (mt) cc_final: 0.8527 (tt) REVERT: B 446 TRP cc_start: 0.3453 (t-100) cc_final: 0.0718 (t-100) REVERT: B 447 ASN cc_start: 0.7123 (t0) cc_final: 0.6884 (t0) REVERT: B 485 ASP cc_start: 0.5412 (m-30) cc_final: 0.5173 (m-30) REVERT: B 633 CYS cc_start: 0.4594 (m) cc_final: 0.4105 (m) REVERT: B 928 THR cc_start: 0.9112 (p) cc_final: 0.8771 (t) REVERT: B 971 LYS cc_start: 0.7659 (mttp) cc_final: 0.7456 (tppt) REVERT: B 1018 ASN cc_start: 0.8877 (t0) cc_final: 0.8157 (m-40) REVERT: B 1024 SER cc_start: 0.9295 (t) cc_final: 0.9061 (m) REVERT: C 99 GLN cc_start: 0.5904 (mm-40) cc_final: 0.5460 (mp10) REVERT: C 136 SER cc_start: 0.6653 (t) cc_final: 0.6431 (p) REVERT: C 162 TYR cc_start: 0.5141 (p90) cc_final: 0.4872 (p90) REVERT: C 287 SER cc_start: 0.8510 (p) cc_final: 0.8016 (m) REVERT: C 299 MET cc_start: 0.7622 (mmp) cc_final: 0.7319 (mmm) REVERT: C 361 LEU cc_start: 0.8659 (mt) cc_final: 0.8386 (tt) REVERT: C 423 THR cc_start: 0.8936 (m) cc_final: 0.8593 (p) REVERT: C 446 TRP cc_start: 0.3087 (t-100) cc_final: 0.0311 (t-100) REVERT: C 613 ASN cc_start: 0.7647 (m-40) cc_final: 0.7299 (m-40) REVERT: C 698 ASP cc_start: 0.7379 (t0) cc_final: 0.7032 (t0) REVERT: C 928 THR cc_start: 0.9264 (p) cc_final: 0.9026 (t) REVERT: C 1018 ASN cc_start: 0.9123 (t0) cc_final: 0.8313 (m-40) REVERT: C 1076 ILE cc_start: 0.8907 (mt) cc_final: 0.8587 (mm) REVERT: C 1099 ILE cc_start: 0.8530 (mm) cc_final: 0.8283 (mm) outliers start: 0 outliers final: 0 residues processed: 801 average time/residue: 0.3996 time to fit residues: 489.3555 Evaluate side-chains 394 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 394 time to evaluate : 2.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 268 optimal weight: 3.9990 chunk 241 optimal weight: 0.8980 chunk 133 optimal weight: 0.9980 chunk 82 optimal weight: 0.6980 chunk 162 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 249 optimal weight: 0.7980 chunk 96 optimal weight: 0.5980 chunk 151 optimal weight: 2.9990 chunk 185 optimal weight: 0.6980 chunk 288 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 168 ASN A 407 ASN A 415 ASN ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 441 HIS A 502 ASN A 613 ASN A 759 HIS ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 957 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1061 GLN ** A1086 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 168 ASN B 415 ASN B 441 HIS B 502 ASN B 606 GLN B 613 ASN B 759 HIS ** B 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 957 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1011 ASN ** B1086 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 GLN C 168 ASN C 415 ASN ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 441 HIS C 502 ASN ** C 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 999 GLN C1061 GLN ** C1086 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.192075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.179933 restraints weight = 39690.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.176573 restraints weight = 50210.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.176325 restraints weight = 61934.967| |-----------------------------------------------------------------------------| r_work (final): 0.4102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6732 moved from start: 0.3308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 25374 Z= 0.273 Angle : 0.783 9.661 34569 Z= 0.435 Chirality : 0.048 0.209 3906 Planarity : 0.006 0.063 4512 Dihedral : 6.258 37.165 3486 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.58 % Favored : 94.39 % Rotamer: Outliers : 2.76 % Allowed : 7.26 % Favored : 89.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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 (0.15), residues: 3189 helix: 1.16 (0.18), residues: 885 sheet: 0.51 (0.22), residues: 528 loop : -1.02 (0.14), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 346 HIS 0.009 0.002 HIS C1098 PHE 0.038 0.002 PHE B 500 TYR 0.043 0.002 TYR A 954 ARG 0.006 0.001 ARG B 867 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 439 time to evaluate : 2.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LEU cc_start: 0.6421 (tp) cc_final: 0.6145 (tp) REVERT: A 156 THR cc_start: 0.6159 (p) cc_final: 0.5911 (t) REVERT: A 203 TYR cc_start: 0.6422 (m-80) cc_final: 0.5912 (m-10) REVERT: A 294 CYS cc_start: 0.6562 (OUTLIER) cc_final: 0.6207 (m) REVERT: A 314 GLN cc_start: 0.6752 (mm110) cc_final: 0.6414 (mm110) REVERT: A 353 ASN cc_start: 0.7745 (m-40) cc_final: 0.7456 (p0) REVERT: A 954 TYR cc_start: 0.6269 (m-80) cc_final: 0.5944 (m-80) REVERT: A 957 ASN cc_start: 0.7151 (m110) cc_final: 0.6920 (p0) REVERT: A 1024 SER cc_start: 0.9189 (t) cc_final: 0.8920 (m) REVERT: B 240 TYR cc_start: 0.4484 (t80) cc_final: 0.4227 (t80) REVERT: B 299 MET cc_start: 0.7436 (mmp) cc_final: 0.7204 (mmt) REVERT: B 423 THR cc_start: 0.9160 (m) cc_final: 0.8756 (p) REVERT: B 446 TRP cc_start: 0.2529 (t-100) cc_final: 0.0278 (t-100) REVERT: B 797 CYS cc_start: 0.8577 (m) cc_final: 0.7625 (t) REVERT: B 1024 SER cc_start: 0.9047 (t) cc_final: 0.8838 (m) REVERT: C 69 TYR cc_start: 0.8791 (m-80) cc_final: 0.8431 (m-80) REVERT: C 99 GLN cc_start: 0.5228 (mm-40) cc_final: 0.5016 (mp10) REVERT: C 149 MET cc_start: 0.6219 (mmt) cc_final: 0.5853 (mmt) REVERT: C 287 SER cc_start: 0.8617 (p) cc_final: 0.8151 (m) REVERT: C 299 MET cc_start: 0.7409 (mmp) cc_final: 0.7127 (mmm) REVERT: C 353 ASN cc_start: 0.7262 (m-40) cc_final: 0.6741 (p0) REVERT: C 416 TYR cc_start: 0.8153 (t80) cc_final: 0.7929 (t80) REVERT: C 734 MET cc_start: 0.3391 (mmt) cc_final: 0.2310 (mmt) REVERT: C 1029 GLU cc_start: 0.7361 (tt0) cc_final: 0.7017 (tt0) REVERT: C 1076 ILE cc_start: 0.8723 (mt) cc_final: 0.8272 (mm) outliers start: 76 outliers final: 46 residues processed: 488 average time/residue: 0.3591 time to fit residues: 279.8821 Evaluate side-chains 384 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 337 time to evaluate : 2.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 217 TYR Chi-restraints excluded: chain A residue 220 LYS Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 284 CYS Chi-restraints excluded: chain A residue 294 CYS Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 632 SER Chi-restraints excluded: chain A residue 635 SER Chi-restraints excluded: chain A residue 716 HIS Chi-restraints excluded: chain A residue 867 ARG Chi-restraints excluded: chain A residue 1005 ASN Chi-restraints excluded: chain A residue 1067 LEU Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 217 TYR Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 284 CYS Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 671 ASN Chi-restraints excluded: chain B residue 867 ARG Chi-restraints excluded: chain B residue 929 THR Chi-restraints excluded: chain B residue 940 TRP Chi-restraints excluded: chain B residue 1064 ASP Chi-restraints excluded: chain B residue 1088 THR Chi-restraints excluded: chain B residue 1092 PHE Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain C residue 220 LYS Chi-restraints excluded: chain C residue 284 CYS Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 627 THR Chi-restraints excluded: chain C residue 635 SER Chi-restraints excluded: chain C residue 671 ASN Chi-restraints excluded: chain C residue 716 HIS Chi-restraints excluded: chain C residue 747 TYR Chi-restraints excluded: chain C residue 940 TRP Chi-restraints excluded: chain C residue 1046 LEU Chi-restraints excluded: chain C residue 1088 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 308 optimal weight: 0.9980 chunk 284 optimal weight: 7.9990 chunk 280 optimal weight: 3.9990 chunk 313 optimal weight: 1.9990 chunk 175 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 290 optimal weight: 0.8980 chunk 72 optimal weight: 7.9990 chunk 209 optimal weight: 2.9990 chunk 214 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 GLN A 415 ASN A 506 HIS A 716 HIS ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1018 ASN B 357 ASN B 415 ASN B 506 HIS ** B 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 817 GLN B 957 ASN B 985 GLN B1018 ASN B1061 GLN B1080 ASN ** B1086 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 ASN C 415 ASN ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 506 HIS C 716 HIS ** C 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 999 GLN C1018 ASN C1080 ASN ** C1086 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.186489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.173979 restraints weight = 40046.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.171177 restraints weight = 62475.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.170925 restraints weight = 73614.445| |-----------------------------------------------------------------------------| r_work (final): 0.4038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6871 moved from start: 0.4154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 25374 Z= 0.328 Angle : 0.743 9.138 34569 Z= 0.405 Chirality : 0.047 0.264 3906 Planarity : 0.005 0.063 4512 Dihedral : 6.203 37.660 3486 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 3.34 % Allowed : 9.84 % Favored : 86.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.35 (0.15), residues: 3189 helix: 1.23 (0.18), residues: 885 sheet: 0.26 (0.22), residues: 540 loop : -1.19 (0.15), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 178 HIS 0.009 0.002 HIS B1098 PHE 0.025 0.002 PHE B 500 TYR 0.025 0.002 TYR A 954 ARG 0.005 0.001 ARG A 383 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 368 time to evaluate : 2.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 THR cc_start: 0.6023 (p) cc_final: 0.5600 (t) REVERT: A 353 ASN cc_start: 0.7902 (m-40) cc_final: 0.7667 (p0) REVERT: A 366 GLN cc_start: 0.7141 (mt0) cc_final: 0.6763 (tp40) REVERT: A 404 GLN cc_start: 0.6019 (OUTLIER) cc_final: 0.4739 (tm130) REVERT: A 416 TYR cc_start: 0.7999 (t80) cc_final: 0.7589 (t80) REVERT: A 954 TYR cc_start: 0.6274 (m-80) cc_final: 0.5984 (m-80) REVERT: A 1018 ASN cc_start: 0.8929 (t0) cc_final: 0.8223 (t0) REVERT: A 1024 SER cc_start: 0.9247 (t) cc_final: 0.8846 (m) REVERT: B 41 THR cc_start: 0.7420 (p) cc_final: 0.7213 (t) REVERT: B 92 PHE cc_start: 0.5504 (m-80) cc_final: 0.4423 (m-10) REVERT: B 149 MET cc_start: 0.6045 (mmt) cc_final: 0.5486 (mmt) REVERT: B 423 THR cc_start: 0.9348 (m) cc_final: 0.9123 (p) REVERT: B 446 TRP cc_start: 0.3249 (t-100) cc_final: 0.0876 (t-100) REVERT: B 1024 SER cc_start: 0.9077 (t) cc_final: 0.8876 (m) REVERT: C 99 GLN cc_start: 0.5612 (mm-40) cc_final: 0.5302 (mp10) REVERT: C 299 MET cc_start: 0.7735 (mmp) cc_final: 0.7489 (mmm) REVERT: C 423 THR cc_start: 0.9274 (m) cc_final: 0.8547 (p) REVERT: C 963 MET cc_start: 0.5800 (tpt) cc_final: 0.4612 (pmm) REVERT: C 1018 ASN cc_start: 0.8713 (t0) cc_final: 0.8078 (t0) outliers start: 92 outliers final: 62 residues processed: 422 average time/residue: 0.3585 time to fit residues: 242.5340 Evaluate side-chains 367 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 304 time to evaluate : 2.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 TYR Chi-restraints excluded: chain A residue 220 LYS Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 404 GLN Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 635 SER Chi-restraints excluded: chain A residue 716 HIS Chi-restraints excluded: chain A residue 766 THR Chi-restraints excluded: chain A residue 867 ARG Chi-restraints excluded: chain A residue 914 VAL Chi-restraints excluded: chain A residue 940 TRP Chi-restraints excluded: chain A residue 963 MET Chi-restraints excluded: chain A residue 1005 ASN Chi-restraints excluded: chain A residue 1046 LEU Chi-restraints excluded: chain A residue 1064 ASP Chi-restraints excluded: chain A residue 1067 LEU Chi-restraints excluded: chain A residue 1088 THR Chi-restraints excluded: chain A residue 1103 VAL Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 217 TYR Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 284 CYS Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 671 ASN Chi-restraints excluded: chain B residue 818 VAL Chi-restraints excluded: chain B residue 867 ARG Chi-restraints excluded: chain B residue 894 CYS Chi-restraints excluded: chain B residue 929 THR Chi-restraints excluded: chain B residue 940 TRP Chi-restraints excluded: chain B residue 1064 ASP Chi-restraints excluded: chain B residue 1088 THR Chi-restraints excluded: chain B residue 1092 PHE Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain C residue 220 LYS Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 284 CYS Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 479 CYS Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 607 THR Chi-restraints excluded: chain C residue 627 THR Chi-restraints excluded: chain C residue 671 ASN Chi-restraints excluded: chain C residue 716 HIS Chi-restraints excluded: chain C residue 766 THR Chi-restraints excluded: chain C residue 782 ASP Chi-restraints excluded: chain C residue 883 SER Chi-restraints excluded: chain C residue 929 THR Chi-restraints excluded: chain C residue 940 TRP Chi-restraints excluded: chain C residue 1046 LEU Chi-restraints excluded: chain C residue 1088 THR Chi-restraints excluded: chain C residue 1090 ILE Chi-restraints excluded: chain C residue 1103 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 253 optimal weight: 0.9980 chunk 2 optimal weight: 0.0170 chunk 148 optimal weight: 0.9980 chunk 239 optimal weight: 0.8980 chunk 142 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 302 optimal weight: 4.9990 chunk 202 optimal weight: 0.9990 chunk 232 optimal weight: 5.9990 chunk 11 optimal weight: 9.9990 chunk 311 optimal weight: 0.9980 overall best weight: 0.7818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 783 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 415 ASN ** B 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 957 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1080 ASN ** B1086 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 415 ASN C 442 ASN ** C 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1080 ASN ** C1086 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.187465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.176511 restraints weight = 40455.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 70)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.168305 restraints weight = 67373.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.168265 restraints weight = 78784.361| |-----------------------------------------------------------------------------| r_work (final): 0.3979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6978 moved from start: 0.4595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 25374 Z= 0.230 Angle : 0.656 8.784 34569 Z= 0.357 Chirality : 0.044 0.193 3906 Planarity : 0.005 0.060 4512 Dihedral : 6.047 37.567 3486 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 3.41 % Allowed : 10.68 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.30 (0.15), residues: 3189 helix: 1.41 (0.18), residues: 900 sheet: 0.17 (0.21), residues: 552 loop : -1.24 (0.15), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 178 HIS 0.007 0.001 HIS B1098 PHE 0.025 0.002 PHE B 371 TYR 0.021 0.002 TYR A 954 ARG 0.017 0.001 ARG A 546 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 342 time to evaluate : 3.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 294 CYS cc_start: 0.6662 (OUTLIER) cc_final: 0.6295 (m) REVERT: A 353 ASN cc_start: 0.7952 (m-40) cc_final: 0.7630 (p0) REVERT: A 416 TYR cc_start: 0.8028 (t80) cc_final: 0.7668 (t80) REVERT: A 954 TYR cc_start: 0.6620 (m-80) cc_final: 0.6404 (m-80) REVERT: A 963 MET cc_start: 0.5001 (OUTLIER) cc_final: 0.2672 (pmm) REVERT: A 1018 ASN cc_start: 0.8800 (t0) cc_final: 0.8031 (t0) REVERT: A 1024 SER cc_start: 0.9268 (t) cc_final: 0.8884 (m) REVERT: B 92 PHE cc_start: 0.5560 (m-80) cc_final: 0.4351 (m-10) REVERT: B 353 ASN cc_start: 0.7159 (m-40) cc_final: 0.6823 (p0) REVERT: B 423 THR cc_start: 0.9371 (m) cc_final: 0.9137 (p) REVERT: B 517 CYS cc_start: 0.0487 (OUTLIER) cc_final: -0.0824 (p) REVERT: B 638 VAL cc_start: 0.8231 (OUTLIER) cc_final: 0.7855 (t) REVERT: B 892 ASN cc_start: 0.7272 (OUTLIER) cc_final: 0.6579 (t0) REVERT: B 899 GLU cc_start: 0.7238 (tp30) cc_final: 0.6652 (pm20) REVERT: B 957 ASN cc_start: 0.7595 (p0) cc_final: 0.6643 (m-40) REVERT: B 1024 SER cc_start: 0.9203 (t) cc_final: 0.8972 (m) REVERT: C 92 PHE cc_start: 0.4273 (m-80) cc_final: 0.4053 (m-10) REVERT: C 99 GLN cc_start: 0.5525 (mm-40) cc_final: 0.5235 (mp10) REVERT: C 299 MET cc_start: 0.7626 (mmp) cc_final: 0.7388 (mmm) REVERT: C 370 LEU cc_start: 0.8872 (tp) cc_final: 0.8629 (tt) REVERT: C 416 TYR cc_start: 0.7988 (t80) cc_final: 0.7776 (t80) REVERT: C 423 THR cc_start: 0.9431 (m) cc_final: 0.8708 (p) REVERT: C 517 CYS cc_start: -0.0034 (OUTLIER) cc_final: -0.2513 (p) REVERT: C 898 GLN cc_start: 0.6961 (OUTLIER) cc_final: 0.6724 (mp10) REVERT: C 963 MET cc_start: 0.5989 (tpt) cc_final: 0.4459 (pmm) REVERT: C 1018 ASN cc_start: 0.8755 (t0) cc_final: 0.8183 (t0) REVERT: C 1076 ILE cc_start: 0.8535 (mt) cc_final: 0.8277 (mm) outliers start: 94 outliers final: 64 residues processed: 409 average time/residue: 0.3410 time to fit residues: 226.0714 Evaluate side-chains 369 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 298 time to evaluate : 2.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 217 TYR Chi-restraints excluded: chain A residue 220 LYS Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 294 CYS Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 635 SER Chi-restraints excluded: chain A residue 716 HIS Chi-restraints excluded: chain A residue 867 ARG Chi-restraints excluded: chain A residue 963 MET Chi-restraints excluded: chain A residue 1005 ASN Chi-restraints excluded: chain A residue 1014 ASN Chi-restraints excluded: chain A residue 1046 LEU Chi-restraints excluded: chain A residue 1064 ASP Chi-restraints excluded: chain A residue 1067 LEU Chi-restraints excluded: chain A residue 1088 THR Chi-restraints excluded: chain A residue 1103 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 217 TYR Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 284 CYS Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 471 CYS Chi-restraints excluded: chain B residue 517 CYS Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 638 VAL Chi-restraints excluded: chain B residue 671 ASN Chi-restraints excluded: chain B residue 867 ARG Chi-restraints excluded: chain B residue 892 ASN Chi-restraints excluded: chain B residue 894 CYS Chi-restraints excluded: chain B residue 929 THR Chi-restraints excluded: chain B residue 937 PHE Chi-restraints excluded: chain B residue 940 TRP Chi-restraints excluded: chain B residue 1064 ASP Chi-restraints excluded: chain B residue 1088 THR Chi-restraints excluded: chain B residue 1092 PHE Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain C residue 220 LYS Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 284 CYS Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 375 ILE Chi-restraints excluded: chain C residue 479 CYS Chi-restraints excluded: chain C residue 517 CYS Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 627 THR Chi-restraints excluded: chain C residue 633 CYS Chi-restraints excluded: chain C residue 671 ASN Chi-restraints excluded: chain C residue 716 HIS Chi-restraints excluded: chain C residue 766 THR Chi-restraints excluded: chain C residue 782 ASP Chi-restraints excluded: chain C residue 894 CYS Chi-restraints excluded: chain C residue 898 GLN Chi-restraints excluded: chain C residue 940 TRP Chi-restraints excluded: chain C residue 1046 LEU Chi-restraints excluded: chain C residue 1088 THR Chi-restraints excluded: chain C residue 1092 PHE Chi-restraints excluded: chain C residue 1103 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 289 optimal weight: 1.9990 chunk 238 optimal weight: 2.9990 chunk 222 optimal weight: 6.9990 chunk 182 optimal weight: 1.9990 chunk 121 optimal weight: 10.0000 chunk 150 optimal weight: 10.0000 chunk 290 optimal weight: 0.7980 chunk 209 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 215 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 366 GLN ** A 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 591 GLN A 716 HIS ** A 783 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 957 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 985 GLN ** B 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 415 ASN ** B 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1080 ASN ** B1086 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1097 ASN C 415 ASN C 556 ASN ** C 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 716 HIS ** C 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 957 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 985 GLN C1080 ASN ** C1086 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.183090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.171293 restraints weight = 40497.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.170077 restraints weight = 67802.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.169613 restraints weight = 61912.700| |-----------------------------------------------------------------------------| r_work (final): 0.4022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6903 moved from start: 0.5170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 25374 Z= 0.305 Angle : 0.700 10.049 34569 Z= 0.377 Chirality : 0.046 0.187 3906 Planarity : 0.005 0.063 4512 Dihedral : 6.068 36.929 3486 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer: Outliers : 4.25 % Allowed : 10.53 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.52 (0.15), residues: 3189 helix: 1.21 (0.18), residues: 888 sheet: 0.05 (0.21), residues: 567 loop : -1.36 (0.15), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 178 HIS 0.009 0.002 HIS B1098 PHE 0.026 0.002 PHE B 371 TYR 0.023 0.002 TYR A 306 ARG 0.009 0.001 ARG A 546 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 330 time to evaluate : 2.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 PHE cc_start: 0.4476 (m-80) cc_final: 0.3633 (m-10) REVERT: A 104 ILE cc_start: 0.8300 (mt) cc_final: 0.8025 (tt) REVERT: A 294 CYS cc_start: 0.6616 (OUTLIER) cc_final: 0.6334 (m) REVERT: A 353 ASN cc_start: 0.7851 (m-40) cc_final: 0.7172 (p0) REVERT: A 366 GLN cc_start: 0.7095 (OUTLIER) cc_final: 0.6774 (tp40) REVERT: A 416 TYR cc_start: 0.8027 (t80) cc_final: 0.7649 (t80) REVERT: A 950 LEU cc_start: 0.6523 (tp) cc_final: 0.5858 (tp) REVERT: A 971 LYS cc_start: 0.7993 (tppt) cc_final: 0.7591 (mttp) REVERT: A 1024 SER cc_start: 0.9183 (t) cc_final: 0.8661 (m) REVERT: B 92 PHE cc_start: 0.4711 (m-80) cc_final: 0.4478 (m-80) REVERT: B 423 THR cc_start: 0.9346 (m) cc_final: 0.9143 (p) REVERT: B 517 CYS cc_start: 0.0858 (OUTLIER) cc_final: -0.0488 (p) REVERT: B 613 ASN cc_start: 0.7046 (t0) cc_final: 0.6377 (t0) REVERT: B 892 ASN cc_start: 0.7325 (OUTLIER) cc_final: 0.6620 (t0) REVERT: B 1024 SER cc_start: 0.9139 (t) cc_final: 0.8881 (m) REVERT: C 99 GLN cc_start: 0.5934 (mm-40) cc_final: 0.5212 (mp10) REVERT: C 104 ILE cc_start: 0.8449 (mt) cc_final: 0.8233 (tt) REVERT: C 299 MET cc_start: 0.7769 (mmp) cc_final: 0.7411 (mmm) REVERT: C 370 LEU cc_start: 0.8885 (tp) cc_final: 0.8513 (tt) REVERT: C 416 TYR cc_start: 0.8056 (t80) cc_final: 0.7837 (t80) REVERT: C 423 THR cc_start: 0.9449 (m) cc_final: 0.8768 (p) REVERT: C 517 CYS cc_start: 0.0292 (OUTLIER) cc_final: -0.0691 (p) REVERT: C 645 ASP cc_start: 0.6635 (p0) cc_final: 0.6293 (p0) REVERT: C 898 GLN cc_start: 0.7286 (OUTLIER) cc_final: 0.7066 (mp10) REVERT: C 963 MET cc_start: 0.5555 (tpt) cc_final: 0.3904 (pmm) REVERT: C 1018 ASN cc_start: 0.8953 (t0) cc_final: 0.8305 (t0) outliers start: 117 outliers final: 84 residues processed: 420 average time/residue: 0.3469 time to fit residues: 236.4381 Evaluate side-chains 380 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 290 time to evaluate : 2.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 217 TYR Chi-restraints excluded: chain A residue 220 LYS Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 294 CYS Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 366 GLN Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 479 CYS Chi-restraints excluded: chain A residue 534 ILE Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 635 SER Chi-restraints excluded: chain A residue 676 PHE Chi-restraints excluded: chain A residue 716 HIS Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain A residue 867 ARG Chi-restraints excluded: chain A residue 963 MET Chi-restraints excluded: chain A residue 1005 ASN Chi-restraints excluded: chain A residue 1064 ASP Chi-restraints excluded: chain A residue 1067 LEU Chi-restraints excluded: chain A residue 1088 THR Chi-restraints excluded: chain A residue 1103 VAL Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 191 ARG Chi-restraints excluded: chain B residue 217 TYR Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 284 CYS Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 471 CYS Chi-restraints excluded: chain B residue 517 CYS Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 671 ASN Chi-restraints excluded: chain B residue 818 VAL Chi-restraints excluded: chain B residue 867 ARG Chi-restraints excluded: chain B residue 883 SER Chi-restraints excluded: chain B residue 892 ASN Chi-restraints excluded: chain B residue 894 CYS Chi-restraints excluded: chain B residue 929 THR Chi-restraints excluded: chain B residue 937 PHE Chi-restraints excluded: chain B residue 940 TRP Chi-restraints excluded: chain B residue 1064 ASP Chi-restraints excluded: chain B residue 1088 THR Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain C residue 220 LYS Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 284 CYS Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 375 ILE Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 471 CYS Chi-restraints excluded: chain C residue 479 CYS Chi-restraints excluded: chain C residue 517 CYS Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 575 VAL Chi-restraints excluded: chain C residue 607 THR Chi-restraints excluded: chain C residue 627 THR Chi-restraints excluded: chain C residue 633 CYS Chi-restraints excluded: chain C residue 635 SER Chi-restraints excluded: chain C residue 651 LEU Chi-restraints excluded: chain C residue 671 ASN Chi-restraints excluded: chain C residue 716 HIS Chi-restraints excluded: chain C residue 766 THR Chi-restraints excluded: chain C residue 782 ASP Chi-restraints excluded: chain C residue 894 CYS Chi-restraints excluded: chain C residue 898 GLN Chi-restraints excluded: chain C residue 929 THR Chi-restraints excluded: chain C residue 940 TRP Chi-restraints excluded: chain C residue 1005 ASN Chi-restraints excluded: chain C residue 1046 LEU Chi-restraints excluded: chain C residue 1064 ASP Chi-restraints excluded: chain C residue 1067 LEU Chi-restraints excluded: chain C residue 1088 THR Chi-restraints excluded: chain C residue 1090 ILE Chi-restraints excluded: chain C residue 1092 PHE Chi-restraints excluded: chain C residue 1103 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 82 optimal weight: 0.9990 chunk 71 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 242 optimal weight: 1.9990 chunk 79 optimal weight: 0.5980 chunk 294 optimal weight: 0.9990 chunk 316 optimal weight: 5.9990 chunk 112 optimal weight: 3.9990 chunk 223 optimal weight: 9.9990 chunk 95 optimal weight: 2.9990 chunk 221 optimal weight: 4.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 442 ASN ** A 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 696 ASN A 716 HIS ** A 783 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 957 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 415 ASN ** B 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 979 ASN B1018 ASN ** B1086 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 353 ASN C 415 ASN C 426 GLN ** C 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 716 HIS ** C 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 957 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1080 ASN ** C1086 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.181854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.170798 restraints weight = 40329.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.169558 restraints weight = 68869.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.162187 restraints weight = 72852.366| |-----------------------------------------------------------------------------| r_work (final): 0.3914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7110 moved from start: 0.5445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 25374 Z= 0.317 Angle : 0.695 9.144 34569 Z= 0.375 Chirality : 0.046 0.199 3906 Planarity : 0.005 0.060 4512 Dihedral : 6.072 36.182 3486 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 4.07 % Allowed : 12.20 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 1.52 % Twisted General : 0.10 % 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: -0.65 (0.15), residues: 3189 helix: 1.13 (0.18), residues: 888 sheet: -0.02 (0.20), residues: 594 loop : -1.48 (0.15), residues: 1707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 536 HIS 0.009 0.002 HIS B1098 PHE 0.026 0.002 PHE B 371 TYR 0.031 0.002 TYR B 144 ARG 0.007 0.001 ARG C 546 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 309 time to evaluate : 2.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 PHE cc_start: 0.4694 (m-80) cc_final: 0.4259 (m-10) REVERT: A 104 ILE cc_start: 0.8475 (mt) cc_final: 0.8234 (tt) REVERT: A 137 TYR cc_start: 0.7284 (OUTLIER) cc_final: 0.5813 (t80) REVERT: A 294 CYS cc_start: 0.6504 (OUTLIER) cc_final: 0.6203 (m) REVERT: A 574 GLU cc_start: 0.7590 (pp20) cc_final: 0.7006 (mp0) REVERT: A 1024 SER cc_start: 0.9158 (t) cc_final: 0.8546 (m) REVERT: A 1117 TYR cc_start: 0.7677 (OUTLIER) cc_final: 0.6305 (p90) REVERT: B 92 PHE cc_start: 0.5692 (m-80) cc_final: 0.5128 (m-10) REVERT: B 423 THR cc_start: 0.9382 (m) cc_final: 0.9119 (p) REVERT: B 517 CYS cc_start: 0.0694 (OUTLIER) cc_final: -0.0813 (p) REVERT: B 613 ASN cc_start: 0.6995 (t0) cc_final: 0.6339 (t0) REVERT: B 734 MET cc_start: 0.1750 (mmt) cc_final: 0.0199 (mmt) REVERT: B 814 MET cc_start: 0.6845 (OUTLIER) cc_final: 0.6417 (mmt) REVERT: B 892 ASN cc_start: 0.7194 (OUTLIER) cc_final: 0.6580 (t0) REVERT: B 1018 ASN cc_start: 0.8633 (t0) cc_final: 0.8279 (t0) REVERT: B 1024 SER cc_start: 0.8997 (t) cc_final: 0.8512 (m) REVERT: C 48 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.7656 (mp) REVERT: C 99 GLN cc_start: 0.6104 (mm-40) cc_final: 0.5455 (mp10) REVERT: C 370 LEU cc_start: 0.8824 (tp) cc_final: 0.8568 (tt) REVERT: C 416 TYR cc_start: 0.8123 (t80) cc_final: 0.7861 (t80) REVERT: C 423 THR cc_start: 0.9481 (m) cc_final: 0.8750 (p) REVERT: C 517 CYS cc_start: 0.0049 (OUTLIER) cc_final: -0.0756 (p) REVERT: C 556 ASN cc_start: 0.9005 (OUTLIER) cc_final: 0.8404 (m-40) REVERT: C 645 ASP cc_start: 0.6914 (p0) cc_final: 0.6656 (p0) REVERT: C 898 GLN cc_start: 0.7329 (OUTLIER) cc_final: 0.7113 (mp10) REVERT: C 963 MET cc_start: 0.5648 (tpt) cc_final: 0.3772 (pmm) REVERT: C 1076 ILE cc_start: 0.8738 (mt) cc_final: 0.8370 (mm) outliers start: 112 outliers final: 82 residues processed: 388 average time/residue: 0.3298 time to fit residues: 213.2342 Evaluate side-chains 375 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 283 time to evaluate : 2.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 137 TYR Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 217 TYR Chi-restraints excluded: chain A residue 220 LYS Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 294 CYS Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 534 ILE Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 676 PHE Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain A residue 867 ARG Chi-restraints excluded: chain A residue 912 ILE Chi-restraints excluded: chain A residue 963 MET Chi-restraints excluded: chain A residue 1005 ASN Chi-restraints excluded: chain A residue 1064 ASP Chi-restraints excluded: chain A residue 1067 LEU Chi-restraints excluded: chain A residue 1088 THR Chi-restraints excluded: chain A residue 1103 VAL Chi-restraints excluded: chain A residue 1117 TYR Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 217 TYR Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 284 CYS Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 471 CYS Chi-restraints excluded: chain B residue 517 CYS Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 671 ASN Chi-restraints excluded: chain B residue 814 MET Chi-restraints excluded: chain B residue 818 VAL Chi-restraints excluded: chain B residue 867 ARG Chi-restraints excluded: chain B residue 883 SER Chi-restraints excluded: chain B residue 892 ASN Chi-restraints excluded: chain B residue 894 CYS Chi-restraints excluded: chain B residue 929 THR Chi-restraints excluded: chain B residue 937 PHE Chi-restraints excluded: chain B residue 940 TRP Chi-restraints excluded: chain B residue 1064 ASP Chi-restraints excluded: chain B residue 1088 THR Chi-restraints excluded: chain B residue 1090 ILE Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 137 TYR Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain C residue 220 LYS Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 284 CYS Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 375 ILE Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 471 CYS Chi-restraints excluded: chain C residue 479 CYS Chi-restraints excluded: chain C residue 517 CYS Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 607 THR Chi-restraints excluded: chain C residue 627 THR Chi-restraints excluded: chain C residue 633 CYS Chi-restraints excluded: chain C residue 635 SER Chi-restraints excluded: chain C residue 651 LEU Chi-restraints excluded: chain C residue 671 ASN Chi-restraints excluded: chain C residue 677 ASP Chi-restraints excluded: chain C residue 766 THR Chi-restraints excluded: chain C residue 782 ASP Chi-restraints excluded: chain C residue 894 CYS Chi-restraints excluded: chain C residue 898 GLN Chi-restraints excluded: chain C residue 929 THR Chi-restraints excluded: chain C residue 940 TRP Chi-restraints excluded: chain C residue 1005 ASN Chi-restraints excluded: chain C residue 1046 LEU Chi-restraints excluded: chain C residue 1064 ASP Chi-restraints excluded: chain C residue 1067 LEU Chi-restraints excluded: chain C residue 1088 THR Chi-restraints excluded: chain C residue 1090 ILE Chi-restraints excluded: chain C residue 1103 VAL Chi-restraints excluded: chain C residue 1117 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 41 optimal weight: 0.9980 chunk 202 optimal weight: 0.6980 chunk 96 optimal weight: 0.9990 chunk 223 optimal weight: 9.9990 chunk 58 optimal weight: 3.9990 chunk 308 optimal weight: 0.9980 chunk 1 optimal weight: 20.0000 chunk 5 optimal weight: 2.9990 chunk 166 optimal weight: 1.9990 chunk 276 optimal weight: 0.7980 chunk 167 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: