Starting phenix.real_space_refine on Sat Jun 21 13:26:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/3jcl_6526/06_2025/3jcl_6526.cif Found real_map, /net/cci-nas-00/data/ceres_data/3jcl_6526/06_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_6526/06_2025/3jcl_6526.map" default_real_map = "/net/cci-nas-00/data/ceres_data/3jcl_6526/06_2025/3jcl_6526.map" model { file = "/net/cci-nas-00/data/ceres_data/3jcl_6526/06_2025/3jcl_6526.cif" } default_model = "/net/cci-nas-00/data/ceres_data/3jcl_6526/06_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-5710/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: 21.27, per 1000 atoms: 0.86 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=57, 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 Simple disulfide: pdb=" SG CYS C 21 " - pdb=" SG CYS C 158 " distance=2.02 Simple disulfide: pdb=" SG CYS B 21 " - pdb=" SG CYS B 158 " distance=2.02 Simple disulfide: pdb=" SG CYS C 153 " - pdb=" SG CYS C 187 " distance=2.04 Simple disulfide: pdb=" SG CYS B 153 " - pdb=" SG CYS B 187 " distance=2.04 Simple disulfide: pdb=" SG CYS C 165 " - pdb=" SG CYS C 246 " distance=2.13 Simple disulfide: pdb=" SG CYS B 165 " - pdb=" SG CYS B 246 " distance=2.13 Simple disulfide: pdb=" SG CYS C 284 " - pdb=" SG CYS C 294 " distance=2.03 Simple disulfide: pdb=" SG CYS B 284 " - pdb=" SG CYS B 294 " distance=2.03 Simple disulfide: pdb=" SG CYS C 329 " - pdb=" SG CYS C 354 " distance=2.02 Simple disulfide: pdb=" SG CYS B 329 " - pdb=" SG CYS B 354 " distance=2.02 Simple disulfide: pdb=" SG CYS C 372 " - pdb=" SG CYS C 425 " distance=2.72 Simple disulfide: pdb=" SG CYS B 372 " - pdb=" SG CYS B 425 " distance=2.72 Simple disulfide: pdb=" SG CYS C 384 " - pdb=" SG CYS C 564 " distance=2.03 Simple disulfide: pdb=" SG CYS B 384 " - pdb=" SG CYS B 564 " distance=2.03 Simple disulfide: pdb=" SG CYS C 471 " - pdb=" SG CYS C 479 " distance=2.02 Simple disulfide: pdb=" SG CYS B 471 " - pdb=" SG CYS B 479 " distance=2.02 Simple disulfide: pdb=" SG CYS C 481 " - pdb=" SG CYS C 528 " distance=2.03 Simple disulfide: pdb=" SG CYS B 481 " - pdb=" SG CYS B 528 " distance=2.03 Simple disulfide: pdb=" SG CYS C 490 " - pdb=" SG CYS C 517 " distance=2.02 Simple disulfide: pdb=" SG CYS B 490 " - pdb=" SG CYS B 517 " distance=2.02 Simple disulfide: pdb=" SG CYS C 507 " - pdb=" SG CYS C 526 " distance=2.07 Simple disulfide: pdb=" SG CYS B 507 " - pdb=" SG CYS B 526 " distance=2.07 Simple disulfide: pdb=" SG CYS C 541 " - pdb=" SG CYS C 547 " distance=2.04 Simple disulfide: pdb=" SG CYS B 541 " - pdb=" SG CYS B 547 " distance=2.04 Simple disulfide: pdb=" SG CYS C 580 " - pdb=" SG CYS C 633 " distance=2.08 Simple disulfide: pdb=" SG CYS B 580 " - pdb=" SG CYS B 633 " distance=2.08 Simple disulfide: pdb=" SG CYS C 658 " - pdb=" SG CYS C 682 " distance=2.03 Simple disulfide: pdb=" SG CYS B 658 " - pdb=" SG CYS B 682 " distance=2.03 Simple disulfide: pdb=" SG CYS C 697 " - pdb=" SG CYS C 706 " distance=2.03 Simple disulfide: pdb=" SG CYS B 697 " - pdb=" SG CYS B 706 " distance=2.03 Simple disulfide: pdb=" SG CYS C 775 " - pdb=" SG CYS C 797 " distance=2.11 Simple disulfide: pdb=" SG CYS B 775 " - pdb=" SG CYS B 797 " distance=2.11 Simple disulfide: pdb=" SG CYS C 780 " - pdb=" SG CYS C 786 " distance=2.04 Simple disulfide: pdb=" SG CYS B 780 " - pdb=" SG CYS B 786 " distance=2.04 Simple disulfide: pdb=" SG CYS C 894 " - pdb=" SG CYS C 905 " distance=2.03 Simple disulfide: pdb=" SG CYS B 894 " - pdb=" SG CYS B 905 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1093 " distance=2.05 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1093 " 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: 5.72 Conformation dependent library (CDL) restraints added in 2.9 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: 3.40 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: 11.55 Time building geometry restraints manager: 6.88 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: 14645 18.10 - 36.20: 373 36.20 - 54.30: 79 54.30 - 72.40: 59 72.40 - 90.50: 12 Dihedral angle restraints: 15168 sinusoidal: 5826 harmonic: 9342 Sorted by residual: dihedral pdb=" CB CYS C 329 " pdb=" SG CYS C 329 " pdb=" SG CYS C 354 " pdb=" CB CYS C 354 " ideal model delta sinusoidal sigma weight residual -86.00 -176.50 90.50 1 1.00e+01 1.00e-02 9.68e+01 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=" CB CYS B 329 " pdb=" SG CYS B 329 " pdb=" SG CYS B 354 " pdb=" CB CYS B 354 " ideal model delta sinusoidal sigma weight residual -86.00 -176.47 90.47 1 1.00e+01 1.00e-02 9.68e+01 ... (remaining 15165 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: 2.38 - 2.88: 10352 2.88 - 3.39: 23924 3.39 - 3.89: 43041 3.89 - 4.40: 51037 4.40 - 4.90: 79886 Nonbonded interactions: 208240 Sorted by model distance: nonbonded pdb=" O PHE B 371 " pdb=" SG CYS B 372 " model vdw 2.379 3.400 nonbonded pdb=" O PHE C 371 " pdb=" SG CYS C 372 " model vdw 2.380 3.400 nonbonded pdb=" O PHE A 371 " pdb=" SG CYS A 372 " model vdw 2.380 3.400 nonbonded pdb=" N TYR A 709 " pdb=" N SER A 710 " model vdw 2.393 2.560 nonbonded pdb=" N TYR C 709 " pdb=" N SER C 710 " model vdw 2.393 2.560 ... (remaining 208235 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: 0.15 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.860 Check model and map are aligned: 0.160 Set scattering table: 0.210 Process input model: 63.800 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.260 ------------------------------------------------------------------------------- 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 : 0.019 0.690 25431 Z= 1.027 Angle : 1.854 23.735 34683 Z= 1.249 Chirality : 0.094 0.476 3906 Planarity : 0.010 0.101 4512 Dihedral : 9.753 89.544 9021 Min Nonbonded Distance : 2.379 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 Details of bonding type rmsd hydrogen bonds : bond 0.15184 ( 1104) hydrogen bonds : angle 7.51686 ( 3051) SS BOND : bond 0.16166 ( 57) SS BOND : angle 5.04518 ( 114) covalent geometry : bond 0.01781 (25374) covalent geometry : angle 1.83423 (34569) *********************** 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 : 2.550 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: 0.3915 time to fit residues: 477.3247 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 : 2.464 ------------------------------------------------------------------------------- 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: 4.9990 chunk 241 optimal weight: 0.8980 chunk 133 optimal weight: 0.6980 chunk 82 optimal weight: 0.6980 chunk 162 optimal weight: 0.9980 chunk 128 optimal weight: 1.9990 chunk 249 optimal weight: 0.8980 chunk 96 optimal weight: 0.5980 chunk 151 optimal weight: 1.9990 chunk 185 optimal weight: 0.6980 chunk 288 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 192 ASN A 407 ASN A 415 ASN ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 441 HIS A 502 ASN A 506 HIS A 613 ASN A 696 ASN A 759 HIS ** A 789 GLN ** 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 506 HIS B 606 GLN B 613 ASN B 696 ASN B 759 HIS ** B 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 957 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1005 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 506 HIS C 696 ASN ** C 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1061 GLN ** C1086 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.192775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.183870 restraints weight = 39493.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.182907 restraints weight = 53025.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 74)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.176731 restraints weight = 53639.946| |-----------------------------------------------------------------------------| r_work (final): 0.4109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6706 moved from start: 0.3311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 25431 Z= 0.199 Angle : 0.794 9.817 34683 Z= 0.441 Chirality : 0.048 0.216 3906 Planarity : 0.006 0.063 4512 Dihedral : 6.230 36.822 3486 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 2.80 % Allowed : 6.94 % Favored : 90.27 % 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: -0.28 (0.15), residues: 3189 helix: 1.14 (0.18), residues: 885 sheet: 0.47 (0.22), residues: 525 loop : -1.12 (0.14), residues: 1779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP A 940 HIS 0.009 0.002 HIS C1098 PHE 0.037 0.002 PHE B 500 TYR 0.035 0.002 TYR A 954 ARG 0.006 0.001 ARG C1089 Details of bonding type rmsd hydrogen bonds : bond 0.05796 ( 1104) hydrogen bonds : angle 6.09199 ( 3051) SS BOND : bond 0.00620 ( 57) SS BOND : angle 1.94738 ( 114) covalent geometry : bond 0.00438 (25374) covalent geometry : angle 0.78711 (34569) *********************** 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 510 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 433 time to evaluate : 2.853 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 54 LEU cc_start: 0.6436 (tp) cc_final: 0.6161 (tp) REVERT: A 156 THR cc_start: 0.6214 (p) cc_final: 0.5952 (t) REVERT: A 203 TYR cc_start: 0.6424 (m-80) cc_final: 0.5950 (m-10) REVERT: A 294 CYS cc_start: 0.6674 (OUTLIER) cc_final: 0.6406 (m) REVERT: A 314 GLN cc_start: 0.6721 (mm110) cc_final: 0.6393 (mm110) REVERT: A 353 ASN cc_start: 0.7699 (m-40) cc_final: 0.7465 (p0) REVERT: A 954 TYR cc_start: 0.6323 (m-80) cc_final: 0.6062 (m-80) REVERT: A 1024 SER cc_start: 0.9168 (t) cc_final: 0.8889 (m) REVERT: B 41 THR cc_start: 0.7576 (p) cc_final: 0.7291 (t) REVERT: B 191 ARG cc_start: 0.7425 (ttm170) cc_final: 0.7205 (ttm170) REVERT: B 227 LEU cc_start: 0.6638 (tp) cc_final: 0.6426 (tp) REVERT: B 240 TYR cc_start: 0.4519 (t80) cc_final: 0.4276 (t80) REVERT: B 299 MET cc_start: 0.7485 (mmp) cc_final: 0.7174 (mmt) REVERT: B 353 ASN cc_start: 0.7246 (m-40) cc_final: 0.6769 (p0) REVERT: B 423 THR cc_start: 0.9218 (m) cc_final: 0.8769 (p) REVERT: B 446 TRP cc_start: 0.2491 (t-100) cc_final: 0.0281 (t-100) REVERT: B 1024 SER cc_start: 0.8974 (t) cc_final: 0.8726 (m) REVERT: C 69 TYR cc_start: 0.8853 (m-80) cc_final: 0.8548 (m-80) REVERT: C 99 GLN cc_start: 0.5308 (mm-40) cc_final: 0.5080 (mp10) REVERT: C 149 MET cc_start: 0.6223 (mmt) cc_final: 0.5835 (mmt) REVERT: C 203 TYR cc_start: 0.6004 (m-80) cc_final: 0.5399 (m-10) REVERT: C 287 SER cc_start: 0.8711 (p) cc_final: 0.8254 (m) REVERT: C 294 CYS cc_start: 0.5914 (OUTLIER) cc_final: 0.5511 (m) REVERT: C 299 MET cc_start: 0.7484 (mmp) cc_final: 0.7207 (mmm) REVERT: C 353 ASN cc_start: 0.7457 (m-40) cc_final: 0.7044 (p0) REVERT: C 1029 GLU cc_start: 0.7338 (tt0) cc_final: 0.6984 (tt0) REVERT: C 1076 ILE cc_start: 0.8653 (mt) cc_final: 0.8105 (mm) outliers start: 77 outliers final: 39 residues processed: 485 average time/residue: 0.3550 time to fit residues: 275.2241 Evaluate side-chains 370 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 329 time to evaluate : 2.492 ------------------------------------------------------------------------------- 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 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 1005 ASN Chi-restraints excluded: chain B residue 217 TYR Chi-restraints excluded: chain B residue 230 VAL 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 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 294 CYS Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 607 THR 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 308 optimal weight: 1.9990 chunk 284 optimal weight: 7.9990 chunk 280 optimal weight: 1.9990 chunk 313 optimal weight: 1.9990 chunk 175 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 290 optimal weight: 0.7980 chunk 72 optimal weight: 6.9990 chunk 209 optimal weight: 0.9980 chunk 214 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 716 HIS ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1018 ASN B 415 ASN ** B 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 817 GLN B 957 ASN B1018 ASN B1061 GLN ** B1086 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 415 ASN ** C 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1018 ASN 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 = 0.4250 r_free = 0.4250 target = 0.189750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.180059 restraints weight = 39596.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.178792 restraints weight = 58421.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.177947 restraints weight = 59556.606| |-----------------------------------------------------------------------------| r_work (final): 0.4122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6705 moved from start: 0.4102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 25431 Z= 0.183 Angle : 0.712 10.055 34683 Z= 0.388 Chirality : 0.046 0.238 3906 Planarity : 0.005 0.059 4512 Dihedral : 6.147 37.525 3486 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 2.83 % Allowed : 9.80 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.15), residues: 3189 helix: 1.45 (0.18), residues: 894 sheet: 0.23 (0.21), residues: 540 loop : -1.18 (0.15), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 346 HIS 0.007 0.002 HIS B1098 PHE 0.026 0.002 PHE B 500 TYR 0.029 0.002 TYR A 954 ARG 0.018 0.001 ARG B 546 Details of bonding type rmsd hydrogen bonds : bond 0.05084 ( 1104) hydrogen bonds : angle 5.72646 ( 3051) SS BOND : bond 0.00566 ( 57) SS BOND : angle 1.91886 ( 114) covalent geometry : bond 0.00414 (25374) covalent geometry : angle 0.70453 (34569) *********************** 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 441 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 363 time to evaluate : 2.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 THR cc_start: 0.5866 (p) cc_final: 0.5538 (t) REVERT: A 404 GLN cc_start: 0.5880 (OUTLIER) cc_final: 0.4518 (tm130) REVERT: A 416 TYR cc_start: 0.7853 (t80) cc_final: 0.7519 (t80) REVERT: A 1018 ASN cc_start: 0.8740 (t0) cc_final: 0.8067 (t0) REVERT: A 1024 SER cc_start: 0.9251 (t) cc_final: 0.8855 (m) REVERT: B 92 PHE cc_start: 0.5411 (m-80) cc_final: 0.4482 (m-10) REVERT: B 240 TYR cc_start: 0.4633 (t80) cc_final: 0.4360 (t80) REVERT: B 299 MET cc_start: 0.7301 (mmp) cc_final: 0.7073 (mmt) REVERT: B 353 ASN cc_start: 0.7386 (m-40) cc_final: 0.7115 (p0) REVERT: B 423 THR cc_start: 0.9350 (m) cc_final: 0.9097 (p) REVERT: B 446 TRP cc_start: 0.3288 (t-100) cc_final: 0.1129 (t-100) REVERT: B 613 ASN cc_start: 0.6651 (t0) cc_final: 0.5893 (t0) REVERT: C 99 GLN cc_start: 0.5533 (mm-40) cc_final: 0.5225 (mp10) REVERT: C 287 SER cc_start: 0.8796 (p) cc_final: 0.8499 (m) REVERT: C 376 ASP cc_start: 0.6238 (t70) cc_final: 0.5382 (t0) REVERT: C 416 TYR cc_start: 0.8218 (t80) cc_final: 0.8007 (t80) REVERT: C 963 MET cc_start: 0.5648 (tpt) cc_final: 0.4309 (pmm) REVERT: C 1076 ILE cc_start: 0.8473 (mt) cc_final: 0.8095 (mm) outliers start: 78 outliers final: 51 residues processed: 413 average time/residue: 0.3404 time to fit residues: 228.9613 Evaluate side-chains 344 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 292 time to evaluate : 2.792 ------------------------------------------------------------------------------- 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 404 GLN 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 635 SER Chi-restraints excluded: chain A residue 716 HIS Chi-restraints excluded: chain A residue 867 ARG Chi-restraints excluded: chain A residue 940 TRP Chi-restraints excluded: chain A residue 1005 ASN Chi-restraints excluded: chain A residue 1064 ASP 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 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 706 CYS 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 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 318 VAL Chi-restraints excluded: chain C residue 597 VAL 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 766 THR 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 1103 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 253 optimal weight: 6.9990 chunk 2 optimal weight: 4.9990 chunk 148 optimal weight: 0.7980 chunk 239 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 302 optimal weight: 5.9990 chunk 202 optimal weight: 1.9990 chunk 232 optimal weight: 0.7980 chunk 11 optimal weight: 6.9990 chunk 311 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 GLN ** A 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 783 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 985 GLN B 366 GLN ** 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** B 985 GLN B1080 ASN ** B1086 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 ASN C 415 ASN C 442 ASN ** C 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 716 HIS ** C 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 985 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.185259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.173676 restraints weight = 40467.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.171433 restraints weight = 60576.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.170879 restraints weight = 68580.173| |-----------------------------------------------------------------------------| r_work (final): 0.4042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6880 moved from start: 0.4704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.100 25431 Z= 0.228 Angle : 0.742 9.341 34683 Z= 0.400 Chirality : 0.047 0.220 3906 Planarity : 0.005 0.063 4512 Dihedral : 6.235 37.445 3486 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 3.56 % Allowed : 10.68 % Favored : 85.77 % 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: -0.47 (0.15), residues: 3189 helix: 1.28 (0.18), residues: 891 sheet: 0.03 (0.21), residues: 558 loop : -1.32 (0.15), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 178 HIS 0.018 0.002 HIS A 716 PHE 0.027 0.002 PHE C 948 TYR 0.038 0.002 TYR A 954 ARG 0.012 0.001 ARG A 546 Details of bonding type rmsd hydrogen bonds : bond 0.05083 ( 1104) hydrogen bonds : angle 5.73985 ( 3051) SS BOND : bond 0.00704 ( 57) SS BOND : angle 2.08233 ( 114) covalent geometry : bond 0.00523 (25374) covalent geometry : angle 0.73355 (34569) *********************** 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 432 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 334 time to evaluate : 2.471 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 54 LEU cc_start: 0.7025 (tp) cc_final: 0.6819 (tp) REVERT: A 104 ILE cc_start: 0.8224 (mt) cc_final: 0.8004 (tt) REVERT: A 156 THR cc_start: 0.6147 (p) cc_final: 0.5779 (t) REVERT: A 294 CYS cc_start: 0.6434 (OUTLIER) cc_final: 0.6077 (m) REVERT: A 416 TYR cc_start: 0.7926 (t80) cc_final: 0.7671 (t80) REVERT: A 1024 SER cc_start: 0.9172 (t) cc_final: 0.8791 (m) REVERT: B 92 PHE cc_start: 0.5601 (m-80) cc_final: 0.4641 (m-10) REVERT: B 416 TYR cc_start: 0.7883 (t80) cc_final: 0.7678 (t80) REVERT: B 423 THR cc_start: 0.9331 (m) cc_final: 0.9111 (p) REVERT: B 638 VAL cc_start: 0.8174 (OUTLIER) cc_final: 0.7809 (t) REVERT: B 899 GLU cc_start: 0.7352 (tp30) cc_final: 0.7117 (tp30) REVERT: B 904 LEU cc_start: 0.8232 (mm) cc_final: 0.7694 (mm) REVERT: B 957 ASN cc_start: 0.7298 (p0) cc_final: 0.6332 (m-40) REVERT: B 1067 LEU cc_start: 0.9069 (mt) cc_final: 0.8866 (mt) REVERT: C 99 GLN cc_start: 0.5749 (mm-40) cc_final: 0.5093 (mp10) REVERT: C 294 CYS cc_start: 0.5872 (OUTLIER) cc_final: 0.5584 (m) REVERT: C 370 LEU cc_start: 0.8814 (tp) cc_final: 0.8464 (tt) REVERT: C 423 THR cc_start: 0.9239 (m) cc_final: 0.8615 (p) REVERT: C 883 SER cc_start: 0.8739 (OUTLIER) cc_final: 0.8538 (t) outliers start: 98 outliers final: 66 residues processed: 407 average time/residue: 0.3489 time to fit residues: 233.4249 Evaluate side-chains 366 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 296 time to evaluate : 2.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 46 GLN Chi-restraints excluded: chain A residue 79 LEU 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 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 747 TYR Chi-restraints excluded: chain A residue 782 ASP 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 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 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 318 VAL Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 580 CYS Chi-restraints excluded: chain B residue 607 THR 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 701 MET Chi-restraints excluded: chain B residue 782 ASP Chi-restraints excluded: chain B residue 818 VAL 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 42 VAL 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 294 CYS Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 385 PHE Chi-restraints excluded: chain C residue 568 LEU 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 883 SER 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 1088 THR Chi-restraints excluded: chain C residue 1090 ILE 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: 5.9990 chunk 222 optimal weight: 6.9990 chunk 182 optimal weight: 0.0870 chunk 121 optimal weight: 0.0170 chunk 150 optimal weight: 10.0000 chunk 290 optimal weight: 0.5980 chunk 209 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 215 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 overall best weight: 0.5400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 366 GLN ** A 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 783 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 789 GLN ** 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 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 415 ASN ** C 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 957 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1018 ASN C1080 ASN ** C1086 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.188547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.176529 restraints weight = 40051.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 87)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.166492 restraints weight = 64584.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.166359 restraints weight = 84462.766| |-----------------------------------------------------------------------------| r_work (final): 0.3964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7020 moved from start: 0.4987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 25431 Z= 0.144 Angle : 0.661 9.639 34683 Z= 0.356 Chirality : 0.044 0.209 3906 Planarity : 0.005 0.056 4512 Dihedral : 5.992 36.684 3486 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 3.09 % Allowed : 11.58 % Favored : 85.33 % 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: -0.34 (0.15), residues: 3189 helix: 1.47 (0.18), residues: 915 sheet: 0.05 (0.21), residues: 558 loop : -1.31 (0.15), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 334 HIS 0.006 0.001 HIS A 716 PHE 0.021 0.002 PHE C 948 TYR 0.036 0.002 TYR A 954 ARG 0.010 0.000 ARG A 546 Details of bonding type rmsd hydrogen bonds : bond 0.04608 ( 1104) hydrogen bonds : angle 5.53479 ( 3051) SS BOND : bond 0.00574 ( 57) SS BOND : angle 1.94749 ( 114) covalent geometry : bond 0.00322 (25374) covalent geometry : angle 0.65270 (34569) *********************** 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 419 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 334 time to evaluate : 2.488 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 54 LEU cc_start: 0.6968 (tp) cc_final: 0.6752 (tp) REVERT: A 104 ILE cc_start: 0.8236 (mt) cc_final: 0.8019 (tt) REVERT: A 164 ASP cc_start: 0.5316 (t0) cc_final: 0.4921 (t0) REVERT: A 191 ARG cc_start: 0.7855 (ttm170) cc_final: 0.7486 (ttm170) REVERT: A 294 CYS cc_start: 0.6305 (OUTLIER) cc_final: 0.5960 (m) REVERT: A 366 GLN cc_start: 0.7250 (OUTLIER) cc_final: 0.6707 (tp40) REVERT: A 971 LYS cc_start: 0.7611 (tppt) cc_final: 0.7110 (mttp) REVERT: A 1018 ASN cc_start: 0.8604 (t0) cc_final: 0.7879 (t0) REVERT: A 1024 SER cc_start: 0.9113 (t) cc_final: 0.8595 (m) REVERT: B 92 PHE cc_start: 0.5963 (m-80) cc_final: 0.5162 (m-80) REVERT: B 149 MET cc_start: 0.6051 (mmt) cc_final: 0.5755 (mtt) REVERT: B 164 ASP cc_start: 0.6033 (t0) cc_final: 0.5796 (t0) REVERT: B 366 GLN cc_start: 0.6543 (OUTLIER) cc_final: 0.6200 (mm-40) REVERT: B 416 TYR cc_start: 0.7910 (t80) cc_final: 0.7689 (t80) REVERT: B 423 THR cc_start: 0.9349 (m) cc_final: 0.9141 (p) REVERT: B 899 GLU cc_start: 0.7079 (tp30) cc_final: 0.6818 (tp30) REVERT: B 904 LEU cc_start: 0.8196 (mm) cc_final: 0.7623 (mm) REVERT: B 957 ASN cc_start: 0.7775 (p0) cc_final: 0.6873 (m-40) REVERT: C 99 GLN cc_start: 0.5788 (mm-40) cc_final: 0.5491 (mp10) REVERT: C 294 CYS cc_start: 0.6006 (OUTLIER) cc_final: 0.5747 (m) REVERT: C 370 LEU cc_start: 0.8776 (tp) cc_final: 0.8472 (tt) REVERT: C 423 THR cc_start: 0.9313 (m) cc_final: 0.8636 (p) REVERT: C 1018 ASN cc_start: 0.8664 (t0) cc_final: 0.8015 (t0) outliers start: 85 outliers final: 60 residues processed: 395 average time/residue: 0.3443 time to fit residues: 219.7123 Evaluate side-chains 350 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 286 time to evaluate : 2.615 ------------------------------------------------------------------------------- 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 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 627 THR Chi-restraints excluded: chain A residue 635 SER Chi-restraints excluded: chain A residue 747 TYR Chi-restraints excluded: chain A residue 867 ARG 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 41 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 98 ASN 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 318 VAL Chi-restraints excluded: chain B residue 366 GLN Chi-restraints excluded: chain B residue 375 ILE Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 671 ASN Chi-restraints excluded: chain B residue 701 MET Chi-restraints excluded: chain B residue 867 ARG 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 1092 PHE Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 42 VAL 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 294 CYS Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 479 CYS Chi-restraints excluded: chain C residue 568 LEU 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 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 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: 0.9980 chunk 71 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 242 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 chunk 294 optimal weight: 0.7980 chunk 316 optimal weight: 4.9990 chunk 112 optimal weight: 5.9990 chunk 223 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 chunk 221 optimal weight: 2.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 GLN ** A 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 591 GLN ** A 783 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1086 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.182890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.175767 restraints weight = 40068.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.174413 restraints weight = 61389.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.173137 restraints weight = 64214.376| |-----------------------------------------------------------------------------| r_work (final): 0.4065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6826 moved from start: 0.5420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.104 25431 Z= 0.228 Angle : 0.737 10.186 34683 Z= 0.395 Chirality : 0.047 0.205 3906 Planarity : 0.005 0.064 4512 Dihedral : 6.154 35.918 3486 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer: Outliers : 3.81 % Allowed : 12.20 % Favored : 83.99 % 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: -0.62 (0.15), residues: 3189 helix: 1.21 (0.18), residues: 903 sheet: -0.10 (0.20), residues: 597 loop : -1.48 (0.15), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 536 HIS 0.009 0.002 HIS B1098 PHE 0.032 0.002 PHE C 948 TYR 0.023 0.002 TYR A 450 ARG 0.008 0.001 ARG A 546 Details of bonding type rmsd hydrogen bonds : bond 0.05033 ( 1104) hydrogen bonds : angle 5.68397 ( 3051) SS BOND : bond 0.00771 ( 57) SS BOND : angle 2.02603 ( 114) covalent geometry : bond 0.00525 (25374) covalent geometry : angle 0.72851 (34569) *********************** 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 432 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 327 time to evaluate : 2.868 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: 0.4318 (m-80) cc_final: 0.3647 (m-10) REVERT: A 104 ILE cc_start: 0.8339 (mt) cc_final: 0.8111 (tt) REVERT: A 164 ASP cc_start: 0.4703 (t0) cc_final: 0.4459 (t0) REVERT: A 294 CYS cc_start: 0.6422 (OUTLIER) cc_final: 0.6129 (m) REVERT: A 574 GLU cc_start: 0.7356 (pp20) cc_final: 0.7076 (mp0) REVERT: A 971 LYS cc_start: 0.7753 (tppt) cc_final: 0.7413 (mttp) REVERT: A 1024 SER cc_start: 0.9145 (t) cc_final: 0.8604 (m) REVERT: A 1117 TYR cc_start: 0.7453 (OUTLIER) cc_final: 0.6461 (p90) REVERT: B 92 PHE cc_start: 0.4705 (m-80) cc_final: 0.4293 (m-80) REVERT: B 299 MET cc_start: 0.7928 (mmt) cc_final: 0.7467 (mmp) REVERT: B 366 GLN cc_start: 0.6405 (OUTLIER) cc_final: 0.6047 (mm110) REVERT: B 416 TYR cc_start: 0.8045 (t80) cc_final: 0.7772 (t80) REVERT: B 423 THR cc_start: 0.9305 (m) cc_final: 0.9102 (p) REVERT: B 446 TRP cc_start: 0.3640 (t-100) cc_final: 0.2607 (t-100) REVERT: B 613 ASN cc_start: 0.7173 (t0) cc_final: 0.6434 (t0) REVERT: B 638 VAL cc_start: 0.8393 (OUTLIER) cc_final: 0.8103 (t) REVERT: B 814 MET cc_start: 0.6788 (OUTLIER) cc_final: 0.6418 (mmt) REVERT: C 99 GLN cc_start: 0.5917 (mm-40) cc_final: 0.5589 (mp10) REVERT: C 104 ILE cc_start: 0.8482 (mt) cc_final: 0.8246 (tt) REVERT: C 164 ASP cc_start: 0.5179 (t0) cc_final: 0.4897 (t0) REVERT: C 370 LEU cc_start: 0.8869 (tp) cc_final: 0.8490 (tt) REVERT: C 423 THR cc_start: 0.9321 (m) cc_final: 0.8696 (p) REVERT: C 628 TYR cc_start: 0.8104 (m-80) cc_final: 0.7897 (m-80) REVERT: C 645 ASP cc_start: 0.6537 (p0) cc_final: 0.6242 (p0) REVERT: C 1076 ILE cc_start: 0.8767 (mt) cc_final: 0.8432 (mm) outliers start: 105 outliers final: 67 residues processed: 407 average time/residue: 0.3388 time to fit residues: 224.6896 Evaluate side-chains 362 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 290 time to evaluate : 2.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 79 LEU 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 344 LEU Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 747 TYR Chi-restraints excluded: chain A residue 867 ARG 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 217 TYR Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 366 GLN Chi-restraints excluded: chain B residue 375 ILE Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain B residue 597 VAL 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 701 MET Chi-restraints excluded: chain B residue 706 CYS 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 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 B residue 1092 PHE Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain C residue 220 LYS Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 385 PHE Chi-restraints excluded: chain C residue 479 CYS 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 635 SER Chi-restraints excluded: chain C residue 671 ASN Chi-restraints excluded: chain C residue 716 HIS 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 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: 3.9990 chunk 202 optimal weight: 0.7980 chunk 96 optimal weight: 0.9980 chunk 223 optimal weight: 10.0000 chunk 58 optimal weight: 3.9990 chunk 308 optimal weight: 0.9990 chunk 1 optimal weight: 5.9990 chunk 5 optimal weight: 0.6980 chunk 166 optimal weight: 0.8980 chunk 276 optimal weight: 0.9980 chunk 167 optimal weight: 3.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 442 ASN ** A 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 979 ASN B1018 ASN ** B1086 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 345 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.184710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.177906 restraints weight = 40023.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.176738 restraints weight = 61545.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.174048 restraints weight = 54328.910| |-----------------------------------------------------------------------------| r_work (final): 0.4070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6806 moved from start: 0.5602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 25431 Z= 0.163 Angle : 0.670 9.214 34683 Z= 0.361 Chirality : 0.045 0.210 3906 Planarity : 0.005 0.056 4512 Dihedral : 5.983 35.164 3486 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.12 % Favored : 92.85 % Rotamer: Outliers : 2.90 % Allowed : 13.91 % Favored : 83.19 % 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: -0.54 (0.15), residues: 3189 helix: 1.30 (0.18), residues: 912 sheet: -0.13 (0.20), residues: 594 loop : -1.43 (0.15), residues: 1683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 536 HIS 0.007 0.001 HIS C 716 PHE 0.025 0.002 PHE C 948 TYR 0.024 0.002 TYR A 954 ARG 0.007 0.000 ARG A 546 Details of bonding type rmsd hydrogen bonds : bond 0.04681 ( 1104) hydrogen bonds : angle 5.52572 ( 3051) SS BOND : bond 0.00668 ( 57) SS BOND : angle 1.92643 ( 114) covalent geometry : bond 0.00374 (25374) covalent geometry : angle 0.66175 (34569) *********************** REFINEMENT MACRO_CYCLE 7 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 404 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 324 time to evaluate : 2.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 PHE cc_start: 0.4221 (m-80) cc_final: 0.3934 (m-10) REVERT: A 164 ASP cc_start: 0.4869 (t0) cc_final: 0.4659 (t0) REVERT: A 294 CYS cc_start: 0.6457 (OUTLIER) cc_final: 0.6107 (m) REVERT: A 1018 ASN cc_start: 0.8724 (t0) cc_final: 0.8010 (t0) REVERT: A 1024 SER cc_start: 0.9097 (t) cc_final: 0.8545 (m) REVERT: A 1117 TYR cc_start: 0.7423 (OUTLIER) cc_final: 0.6397 (p90) REVERT: B 92 PHE cc_start: 0.5011 (m-80) cc_final: 0.4538 (m-80) REVERT: B 299 MET cc_start: 0.7864 (mmt) cc_final: 0.7569 (mmp) REVERT: B 366 GLN cc_start: 0.6296 (OUTLIER) cc_final: 0.6025 (mm110) REVERT: B 574 GLU cc_start: 0.7286 (pp20) cc_final: 0.6782 (mp0) REVERT: B 613 ASN cc_start: 0.7125 (t0) cc_final: 0.6376 (t0) REVERT: B 638 VAL cc_start: 0.8279 (OUTLIER) cc_final: 0.8034 (t) REVERT: B 734 MET cc_start: 0.2902 (mmt) cc_final: 0.2328 (mmt) REVERT: B 971 LYS cc_start: 0.7596 (tppt) cc_final: 0.6826 (mtpt) REVERT: B 1018 ASN cc_start: 0.8583 (t0) cc_final: 0.8290 (t0) REVERT: B 1067 LEU cc_start: 0.9063 (mt) cc_final: 0.8861 (tt) REVERT: B 1117 TYR cc_start: 0.7060 (OUTLIER) cc_final: 0.6158 (p90) REVERT: C 99 GLN cc_start: 0.5717 (mm-40) cc_final: 0.5507 (mp10) REVERT: C 104 ILE cc_start: 0.8390 (mt) cc_final: 0.8149 (tt) REVERT: C 164 ASP cc_start: 0.5091 (t0) cc_final: 0.4681 (t0) REVERT: C 370 LEU cc_start: 0.8785 (tp) cc_final: 0.8463 (tt) REVERT: C 423 THR cc_start: 0.9292 (m) cc_final: 0.8660 (p) REVERT: C 734 MET cc_start: 0.3423 (mmt) cc_final: 0.2807 (mmt) REVERT: C 936 MET cc_start: 0.7178 (mtt) cc_final: 0.6515 (mtt) REVERT: C 948 PHE cc_start: 0.6023 (t80) cc_final: 0.5629 (t80) REVERT: C 1018 ASN cc_start: 0.8727 (t0) cc_final: 0.7893 (t0) REVERT: C 1076 ILE cc_start: 0.8714 (mt) cc_final: 0.8379 (mm) outliers start: 80 outliers final: 65 residues processed: 373 average time/residue: 0.3277 time to fit residues: 199.8530 Evaluate side-chains 363 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 293 time to evaluate : 2.720 ------------------------------------------------------------------------------- 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 148 ILE 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 479 CYS Chi-restraints excluded: chain A residue 534 ILE Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 747 TYR Chi-restraints excluded: chain A residue 867 ARG Chi-restraints excluded: chain A residue 912 ILE Chi-restraints excluded: chain A residue 1005 ASN Chi-restraints excluded: chain A residue 1014 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 217 TYR Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 366 GLN Chi-restraints excluded: chain B residue 375 ILE Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 597 VAL 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 701 MET Chi-restraints excluded: chain B residue 867 ARG Chi-restraints excluded: chain B residue 904 LEU 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 1037 VAL 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 B residue 1117 TYR Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain C residue 220 LYS Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 385 PHE Chi-restraints excluded: chain C residue 479 CYS Chi-restraints excluded: chain C residue 534 ILE Chi-restraints excluded: chain C residue 568 LEU 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 866 ILE 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 1092 PHE Chi-restraints excluded: chain C residue 1103 VAL Chi-restraints excluded: chain C residue 1117 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 11 optimal weight: 10.0000 chunk 105 optimal weight: 0.6980 chunk 44 optimal weight: 9.9990 chunk 285 optimal weight: 3.9990 chunk 149 optimal weight: 6.9990 chunk 144 optimal weight: 0.6980 chunk 232 optimal weight: 5.9990 chunk 258 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 222 optimal weight: 3.9990 chunk 198 optimal weight: 0.9980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 314 GLN B 591 GLN ** B 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1086 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 345 ASN C 415 ASN ** C 538 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 556 ASN ** C 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.180698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.173806 restraints weight = 40139.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.172693 restraints weight = 58221.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.171051 restraints weight = 61358.081| |-----------------------------------------------------------------------------| r_work (final): 0.4037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6869 moved from start: 0.5982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 25431 Z= 0.238 Angle : 0.754 10.217 34683 Z= 0.402 Chirality : 0.048 0.196 3906 Planarity : 0.005 0.061 4512 Dihedral : 6.272 37.202 3486 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.40 % Favored : 91.53 % Rotamer: Outliers : 3.78 % Allowed : 13.91 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -0.80 (0.15), residues: 3189 helix: 1.06 (0.18), residues: 903 sheet: -0.28 (0.20), residues: 594 loop : -1.57 (0.15), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP A 940 HIS 0.010 0.002 HIS B1098 PHE 0.029 0.002 PHE A 676 TYR 0.029 0.002 TYR A 954 ARG 0.006 0.001 ARG A 546 Details of bonding type rmsd hydrogen bonds : bond 0.05152 ( 1104) hydrogen bonds : angle 5.74094 ( 3051) SS BOND : bond 0.00732 ( 57) SS BOND : angle 2.08516 ( 114) covalent geometry : bond 0.00548 (25374) covalent geometry : angle 0.74557 (34569) *********************** REFINEMENT MACRO_CYCLE 8 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 406 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 302 time to evaluate : 2.788 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 92 PHE cc_start: 0.4481 (m-80) cc_final: 0.4267 (m-10) REVERT: A 137 TYR cc_start: 0.7101 (OUTLIER) cc_final: 0.6666 (t80) REVERT: A 164 ASP cc_start: 0.4733 (t0) cc_final: 0.4485 (t0) REVERT: A 294 CYS cc_start: 0.6446 (OUTLIER) cc_final: 0.6203 (m) REVERT: A 628 TYR cc_start: 0.8181 (m-80) cc_final: 0.7750 (m-80) REVERT: A 971 LYS cc_start: 0.7876 (tppt) cc_final: 0.7198 (mtpt) REVERT: A 1024 SER cc_start: 0.9149 (t) cc_final: 0.8580 (m) REVERT: A 1117 TYR cc_start: 0.7419 (OUTLIER) cc_final: 0.6409 (p90) REVERT: B 92 PHE cc_start: 0.4923 (m-80) cc_final: 0.4511 (m-10) REVERT: B 137 TYR cc_start: 0.5919 (m-80) cc_final: 0.5328 (m-80) REVERT: B 366 GLN cc_start: 0.6293 (OUTLIER) cc_final: 0.6083 (mm110) REVERT: B 574 GLU cc_start: 0.7405 (pp20) cc_final: 0.6908 (mp0) REVERT: B 613 ASN cc_start: 0.7276 (t0) cc_final: 0.6857 (t0) REVERT: B 734 MET cc_start: 0.3187 (mmt) cc_final: 0.2582 (mmt) REVERT: B 971 LYS cc_start: 0.7597 (tppt) cc_final: 0.6842 (mtpt) REVERT: B 989 ASP cc_start: 0.6636 (m-30) cc_final: 0.6233 (m-30) REVERT: B 1018 ASN cc_start: 0.8751 (t0) cc_final: 0.8379 (t0) REVERT: B 1117 TYR cc_start: 0.7059 (OUTLIER) cc_final: 0.6135 (p90) REVERT: C 99 GLN cc_start: 0.5911 (mm-40) cc_final: 0.5699 (mp10) REVERT: C 164 ASP cc_start: 0.4985 (t0) cc_final: 0.4555 (t0) REVERT: C 370 LEU cc_start: 0.8677 (tp) cc_final: 0.8320 (tt) REVERT: C 423 THR cc_start: 0.9342 (m) cc_final: 0.8685 (p) REVERT: C 734 MET cc_start: 0.3449 (mmt) cc_final: 0.2822 (mmt) REVERT: C 936 MET cc_start: 0.7196 (mtt) cc_final: 0.6449 (mtt) REVERT: C 948 PHE cc_start: 0.6038 (t80) cc_final: 0.5602 (t80) REVERT: C 1076 ILE cc_start: 0.8734 (mt) cc_final: 0.8390 (mm) outliers start: 104 outliers final: 84 residues processed: 376 average time/residue: 0.3389 time to fit residues: 209.8121 Evaluate side-chains 362 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 273 time to evaluate : 2.829 ------------------------------------------------------------------------------- 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 79 LEU Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 137 TYR Chi-restraints excluded: chain A residue 139 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 235 ILE 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 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 627 THR Chi-restraints excluded: chain A residue 747 TYR Chi-restraints excluded: chain A residue 867 ARG Chi-restraints excluded: chain A residue 912 ILE 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 1087 THR 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 79 LEU 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 294 CYS Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 366 GLN Chi-restraints excluded: chain B residue 375 ILE Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain B residue 479 CYS Chi-restraints excluded: chain B residue 534 ILE Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 597 VAL 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 701 MET Chi-restraints excluded: chain B residue 706 CYS Chi-restraints excluded: chain B residue 818 VAL Chi-restraints excluded: chain B residue 867 ARG Chi-restraints excluded: chain B residue 912 ILE 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 1103 VAL Chi-restraints excluded: chain B residue 1117 TYR Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 42 VAL 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 241 VAL Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 385 PHE Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 534 ILE 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 585 LEU Chi-restraints excluded: chain C residue 607 THR 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 904 LEU 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 1092 PHE Chi-restraints excluded: chain C residue 1103 VAL Chi-restraints excluded: chain C residue 1117 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 80 optimal weight: 2.9990 chunk 16 optimal weight: 10.0000 chunk 254 optimal weight: 0.0570 chunk 189 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 214 optimal weight: 1.9990 chunk 143 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 253 optimal weight: 3.9990 chunk 195 optimal weight: 7.9990 chunk 54 optimal weight: 0.9980 overall best weight: 0.7300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 415 ASN ** A 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 442 ASN ** B 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 979 ASN ** B1086 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.184269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.174567 restraints weight = 40679.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.173687 restraints weight = 62619.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.172783 restraints weight = 59194.521| |-----------------------------------------------------------------------------| r_work (final): 0.4065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6832 moved from start: 0.6084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 25431 Z= 0.152 Angle : 0.677 13.670 34683 Z= 0.363 Chirality : 0.045 0.207 3906 Planarity : 0.005 0.060 4512 Dihedral : 5.984 35.696 3486 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.99 % Favored : 92.91 % Rotamer: Outliers : 2.90 % Allowed : 15.29 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.76 % Twisted General : 0.13 % 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: -0.61 (0.15), residues: 3189 helix: 1.27 (0.18), residues: 918 sheet: -0.27 (0.20), residues: 594 loop : -1.46 (0.15), residues: 1677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP C 178 HIS 0.006 0.001 HIS B1098 PHE 0.021 0.002 PHE A 371 TYR 0.035 0.002 TYR A 954 ARG 0.004 0.000 ARG A 546 Details of bonding type rmsd hydrogen bonds : bond 0.04638 ( 1104) hydrogen bonds : angle 5.53442 ( 3051) SS BOND : bond 0.00572 ( 57) SS BOND : angle 2.04735 ( 114) covalent geometry : bond 0.00343 (25374) covalent geometry : angle 0.66775 (34569) *********************** REFINEMENT MACRO_CYCLE 9 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 393 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 313 time to evaluate : 2.889 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 92 PHE cc_start: 0.4602 (m-80) cc_final: 0.4116 (m-10) REVERT: A 137 TYR cc_start: 0.7186 (OUTLIER) cc_final: 0.5957 (t80) REVERT: A 294 CYS cc_start: 0.6477 (OUTLIER) cc_final: 0.6177 (m) REVERT: A 370 LEU cc_start: 0.8257 (tp) cc_final: 0.7984 (tt) REVERT: A 628 TYR cc_start: 0.8131 (m-80) cc_final: 0.7813 (m-80) REVERT: A 971 LYS cc_start: 0.7737 (tppt) cc_final: 0.7059 (mtpt) REVERT: A 1018 ASN cc_start: 0.8643 (t0) cc_final: 0.7836 (t0) REVERT: A 1024 SER cc_start: 0.9051 (t) cc_final: 0.8491 (m) REVERT: A 1117 TYR cc_start: 0.7337 (OUTLIER) cc_final: 0.6229 (p90) REVERT: B 92 PHE cc_start: 0.5080 (m-80) cc_final: 0.4673 (m-10) REVERT: B 137 TYR cc_start: 0.6005 (m-80) cc_final: 0.5399 (m-80) REVERT: B 574 GLU cc_start: 0.7199 (pp20) cc_final: 0.6717 (mp0) REVERT: B 613 ASN cc_start: 0.7220 (t0) cc_final: 0.6800 (t0) REVERT: B 638 VAL cc_start: 0.8396 (OUTLIER) cc_final: 0.8132 (t) REVERT: B 734 MET cc_start: 0.2994 (mmt) cc_final: 0.2460 (mmt) REVERT: B 989 ASP cc_start: 0.6628 (m-30) cc_final: 0.6276 (m-30) REVERT: B 1018 ASN cc_start: 0.8637 (t0) cc_final: 0.8314 (t0) REVERT: C 164 ASP cc_start: 0.4935 (t0) cc_final: 0.4547 (t0) REVERT: C 178 TRP cc_start: 0.3650 (p-90) cc_final: 0.2023 (p90) REVERT: C 370 LEU cc_start: 0.8694 (tp) cc_final: 0.8343 (tt) REVERT: C 423 THR cc_start: 0.9320 (m) cc_final: 0.8681 (p) REVERT: C 734 MET cc_start: 0.2919 (mmt) cc_final: 0.2343 (mmt) REVERT: C 936 MET cc_start: 0.7132 (mtt) cc_final: 0.6523 (mtt) REVERT: C 948 PHE cc_start: 0.6095 (t80) cc_final: 0.5630 (t80) REVERT: C 971 LYS cc_start: 0.7535 (tppt) cc_final: 0.6749 (mttt) REVERT: C 1018 ASN cc_start: 0.8701 (t0) cc_final: 0.7920 (t0) REVERT: C 1076 ILE cc_start: 0.8703 (mt) cc_final: 0.8374 (mm) outliers start: 80 outliers final: 68 residues processed: 365 average time/residue: 0.3430 time to fit residues: 204.0185 Evaluate side-chains 355 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 283 time to evaluate : 2.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 137 TYR Chi-restraints excluded: chain A residue 139 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 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 479 CYS Chi-restraints excluded: chain A residue 534 ILE Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 747 TYR Chi-restraints excluded: chain A residue 867 ARG Chi-restraints excluded: chain A residue 912 ILE Chi-restraints excluded: chain A residue 1005 ASN Chi-restraints excluded: chain A residue 1014 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 241 VAL Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 375 ILE Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain B residue 479 CYS Chi-restraints excluded: chain B residue 534 ILE Chi-restraints excluded: chain B residue 585 LEU 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 701 MET Chi-restraints excluded: chain B residue 867 ARG Chi-restraints excluded: chain B residue 904 LEU Chi-restraints excluded: chain B residue 912 ILE Chi-restraints excluded: chain B residue 937 PHE Chi-restraints excluded: chain B residue 940 TRP Chi-restraints excluded: chain B residue 1037 VAL 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 42 VAL 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 241 VAL Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 385 PHE Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 534 ILE Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 627 THR Chi-restraints excluded: chain C residue 671 ASN Chi-restraints excluded: chain C residue 894 CYS 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 1088 THR Chi-restraints excluded: chain C residue 1092 PHE Chi-restraints excluded: chain C residue 1103 VAL Chi-restraints excluded: chain C residue 1117 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 216 optimal weight: 2.9990 chunk 87 optimal weight: 0.7980 chunk 90 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 170 optimal weight: 1.9990 chunk 305 optimal weight: 3.9990 chunk 7 optimal weight: 10.0000 chunk 18 optimal weight: 1.9990 chunk 147 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 572 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 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 415 ASN ** C 538 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 556 ASN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.180467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.173939 restraints weight = 40581.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.172344 restraints weight = 60003.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.163360 restraints weight = 79828.122| |-----------------------------------------------------------------------------| r_work (final): 0.3895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7123 moved from start: 0.6325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 25431 Z= 0.246 Angle : 0.772 12.618 34683 Z= 0.411 Chirality : 0.048 0.189 3906 Planarity : 0.005 0.063 4512 Dihedral : 6.236 36.238 3486 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.47 % Favored : 91.44 % Rotamer: Outliers : 3.01 % Allowed : 15.25 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.76 % Twisted General : 0.13 % 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: -0.87 (0.15), residues: 3189 helix: 1.04 (0.18), residues: 909 sheet: -0.41 (0.20), residues: 609 loop : -1.60 (0.15), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.003 TRP A 178 HIS 0.010 0.002 HIS A1098 PHE 0.029 0.002 PHE A 676 TYR 0.036 0.002 TYR C1057 ARG 0.006 0.001 ARG B 724 Details of bonding type rmsd hydrogen bonds : bond 0.05141 ( 1104) hydrogen bonds : angle 5.74432 ( 3051) SS BOND : bond 0.00714 ( 57) SS BOND : angle 2.17534 ( 114) covalent geometry : bond 0.00569 (25374) covalent geometry : angle 0.76351 (34569) ********************** REFINEMENT MACRO_CYCLE 10 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 368 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 285 time to evaluate : 2.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 PHE cc_start: 0.5438 (m-80) cc_final: 0.4912 (m-10) REVERT: A 137 TYR cc_start: 0.7684 (OUTLIER) cc_final: 0.6765 (t80) REVERT: A 191 ARG cc_start: 0.7909 (ptm160) cc_final: 0.7409 (ptm160) REVERT: A 294 CYS cc_start: 0.6429 (OUTLIER) cc_final: 0.6147 (m) REVERT: A 971 LYS cc_start: 0.8080 (tppt) cc_final: 0.7124 (mtpt) REVERT: A 1024 SER cc_start: 0.9152 (t) cc_final: 0.8615 (m) REVERT: A 1117 TYR cc_start: 0.7625 (OUTLIER) cc_final: 0.6427 (p90) REVERT: B 92 PHE cc_start: 0.5550 (m-80) cc_final: 0.5106 (m-10) REVERT: B 137 TYR cc_start: 0.6406 (m-80) cc_final: 0.5783 (m-80) REVERT: B 479 CYS cc_start: 0.2913 (OUTLIER) cc_final: 0.2473 (t) REVERT: B 574 GLU cc_start: 0.7461 (pp20) cc_final: 0.7202 (mp0) REVERT: B 613 ASN cc_start: 0.6759 (t0) cc_final: 0.6397 (t0) REVERT: B 638 VAL cc_start: 0.8598 (OUTLIER) cc_final: 0.8256 (t) REVERT: B 734 MET cc_start: 0.1956 (mmt) cc_final: 0.1435 (mmt) REVERT: B 971 LYS cc_start: 0.7717 (tppt) cc_final: 0.6630 (mtpp) REVERT: B 1018 ASN cc_start: 0.8766 (t0) cc_final: 0.8289 (t0) REVERT: C 164 ASP cc_start: 0.5728 (t0) cc_final: 0.5303 (t0) REVERT: C 370 LEU cc_start: 0.8514 (tp) cc_final: 0.8251 (tt) REVERT: C 423 THR cc_start: 0.9363 (m) cc_final: 0.8741 (p) REVERT: C 734 MET cc_start: 0.1746 (mmt) cc_final: 0.1208 (mmt) REVERT: C 936 MET cc_start: 0.7292 (mtt) cc_final: 0.6601 (mtt) REVERT: C 948 PHE cc_start: 0.6254 (t80) cc_final: 0.5779 (t80) REVERT: C 1076 ILE cc_start: 0.8553 (mt) cc_final: 0.8266 (mm) REVERT: C 1090 ILE cc_start: 0.6550 (tp) cc_final: 0.6295 (tp) outliers start: 83 outliers final: 74 residues processed: 344 average time/residue: 0.3453 time to fit residues: 193.8656 Evaluate side-chains 354 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 275 time to evaluate : 2.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 137 TYR Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 189 LEU 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 479 CYS Chi-restraints excluded: chain A residue 534 ILE Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 701 MET Chi-restraints excluded: chain A residue 747 TYR Chi-restraints excluded: chain A residue 867 ARG Chi-restraints excluded: chain A residue 912 ILE 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 42 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 294 CYS Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 375 ILE Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain B residue 479 CYS Chi-restraints excluded: chain B residue 534 ILE Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 597 VAL 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 701 MET Chi-restraints excluded: chain B residue 867 ARG Chi-restraints excluded: chain B residue 904 LEU Chi-restraints excluded: chain B residue 937 PHE Chi-restraints excluded: chain B residue 940 TRP Chi-restraints excluded: chain B residue 972 MET 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 42 VAL Chi-restraints excluded: chain C residue 136 SER 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 241 VAL Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 385 PHE Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 534 ILE Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 627 THR Chi-restraints excluded: chain C residue 671 ASN Chi-restraints excluded: chain C residue 894 CYS 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 1068 ILE Chi-restraints excluded: chain C residue 1088 THR Chi-restraints excluded: chain C residue 1092 PHE Chi-restraints excluded: chain C residue 1103 VAL Chi-restraints excluded: chain C residue 1117 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 267 optimal weight: 5.9990 chunk 268 optimal weight: 0.2980 chunk 154 optimal weight: 30.0000 chunk 302 optimal weight: 4.9990 chunk 138 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 235 optimal weight: 3.9990 chunk 149 optimal weight: 2.9990 chunk 184 optimal weight: 0.9980 chunk 55 optimal weight: 0.0470 overall best weight: 1.0280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 572 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 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 415 ASN ** C 538 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.183070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.171081 restraints weight = 40286.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.165410 restraints weight = 73483.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.165764 restraints weight = 62799.168| |-----------------------------------------------------------------------------| r_work (final): 0.3927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7086 moved from start: 0.6437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 25431 Z= 0.169 Angle : 0.696 11.273 34683 Z= 0.372 Chirality : 0.045 0.187 3906 Planarity : 0.005 0.061 4512 Dihedral : 6.050 35.636 3486 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.21 % Favored : 92.69 % Rotamer: Outliers : 3.16 % Allowed : 15.25 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 1.52 % Twisted General : 0.13 % 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 (0.15), residues: 3189 helix: 1.26 (0.18), residues: 912 sheet: -0.42 (0.20), residues: 612 loop : -1.54 (0.15), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.003 TRP A 178 HIS 0.006 0.001 HIS A1098 PHE 0.023 0.002 PHE A 619 TYR 0.035 0.002 TYR A 954 ARG 0.007 0.001 ARG C 322 Details of bonding type rmsd hydrogen bonds : bond 0.04732 ( 1104) hydrogen bonds : angle 5.57558 ( 3051) SS BOND : bond 0.00612 ( 57) SS BOND : angle 1.93398 ( 114) covalent geometry : bond 0.00387 (25374) covalent geometry : angle 0.68825 (34569) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7209.37 seconds wall clock time: 126 minutes 14.33 seconds (7574.33 seconds total)