Starting phenix.real_space_refine on Fri Sep 19 09:27:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/3jcl_6526/09_2025/3jcl_6526.cif Found real_map, /net/cci-nas-00/data/ceres_data/3jcl_6526/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/3jcl_6526/09_2025/3jcl_6526.cif" } default_model = "/net/cci-nas-00/data/ceres_data/3jcl_6526/09_2025/3jcl_6526.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/3jcl_6526/09_2025/3jcl_6526.map" default_real_map = "/net/cci-nas-00/data/ceres_data/3jcl_6526/09_2025/3jcl_6526.map" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: B, C Time building chain proxies: 9.17, per 1000 atoms: 0.37 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 B 21 " - pdb=" SG CYS B 158 " distance=2.02 Simple disulfide: pdb=" SG CYS C 21 " - pdb=" SG CYS C 158 " distance=2.02 Simple disulfide: pdb=" SG CYS B 153 " - pdb=" SG CYS B 187 " distance=2.04 Simple disulfide: pdb=" SG CYS C 153 " - pdb=" SG CYS C 187 " distance=2.04 Simple disulfide: pdb=" SG CYS B 165 " - pdb=" SG CYS B 246 " distance=2.13 Simple disulfide: pdb=" SG CYS C 165 " - pdb=" SG CYS C 246 " distance=2.13 Simple disulfide: pdb=" SG CYS B 284 " - pdb=" SG CYS B 294 " distance=2.03 Simple disulfide: pdb=" SG CYS C 284 " - pdb=" SG CYS C 294 " distance=2.03 Simple disulfide: pdb=" SG CYS B 329 " - pdb=" SG CYS B 354 " distance=2.02 Simple disulfide: pdb=" SG CYS C 329 " - pdb=" SG CYS C 354 " distance=2.02 Simple disulfide: pdb=" SG CYS B 372 " - pdb=" SG CYS B 425 " distance=2.72 Simple disulfide: pdb=" SG CYS C 372 " - pdb=" SG CYS C 425 " distance=2.72 Simple disulfide: pdb=" SG CYS B 384 " - pdb=" SG CYS B 564 " distance=2.03 Simple disulfide: pdb=" SG CYS C 384 " - pdb=" SG CYS C 564 " distance=2.03 Simple disulfide: pdb=" SG CYS B 471 " - pdb=" SG CYS B 479 " distance=2.02 Simple disulfide: pdb=" SG CYS C 471 " - pdb=" SG CYS C 479 " distance=2.02 Simple disulfide: pdb=" SG CYS B 481 " - pdb=" SG CYS B 528 " distance=2.03 Simple disulfide: pdb=" SG CYS C 481 " - pdb=" SG CYS C 528 " distance=2.03 Simple disulfide: pdb=" SG CYS B 490 " - pdb=" SG CYS B 517 " distance=2.02 Simple disulfide: pdb=" SG CYS C 490 " - pdb=" SG CYS C 517 " distance=2.02 Simple disulfide: pdb=" SG CYS B 507 " - pdb=" SG CYS B 526 " distance=2.07 Simple disulfide: pdb=" SG CYS C 507 " - pdb=" SG CYS C 526 " distance=2.07 Simple disulfide: pdb=" SG CYS B 541 " - pdb=" SG CYS B 547 " distance=2.04 Simple disulfide: pdb=" SG CYS C 541 " - pdb=" SG CYS C 547 " distance=2.04 Simple disulfide: pdb=" SG CYS B 580 " - pdb=" SG CYS B 633 " distance=2.08 Simple disulfide: pdb=" SG CYS C 580 " - pdb=" SG CYS C 633 " distance=2.08 Simple disulfide: pdb=" SG CYS B 658 " - pdb=" SG CYS B 682 " distance=2.03 Simple disulfide: pdb=" SG CYS C 658 " - pdb=" SG CYS C 682 " distance=2.03 Simple disulfide: pdb=" SG CYS B 697 " - pdb=" SG CYS B 706 " distance=2.03 Simple disulfide: pdb=" SG CYS C 697 " - pdb=" SG CYS C 706 " distance=2.03 Simple disulfide: pdb=" SG CYS B 775 " - pdb=" SG CYS B 797 " distance=2.11 Simple disulfide: pdb=" SG CYS C 775 " - pdb=" SG CYS C 797 " distance=2.11 Simple disulfide: pdb=" SG CYS B 780 " - pdb=" SG CYS B 786 " distance=2.04 Simple disulfide: pdb=" SG CYS C 780 " - pdb=" SG CYS C 786 " distance=2.04 Simple disulfide: pdb=" SG CYS B 894 " - pdb=" SG CYS B 905 " distance=2.03 Simple disulfide: pdb=" SG CYS C 894 " - pdb=" SG CYS C 905 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1093 " distance=2.05 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1093 " 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: 2.09 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 1.2 microseconds 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: 1.15 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: 6.07 Time building geometry restraints manager: 2.73 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 1.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 27.510 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.280 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.72 (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 ARG 0.007 0.001 ARG A 397 TYR 0.042 0.009 TYR A 58 PHE 0.044 0.007 PHE C 123 TRP 0.031 0.007 TRP B 536 HIS 0.007 0.002 HIS A1098 Details of bonding type rmsd covalent geometry : bond 0.01781 (25374) covalent geometry : angle 1.83423 (34569) SS BOND : bond 0.16166 ( 57) SS BOND : angle 5.04518 ( 114) hydrogen bonds : bond 0.15184 ( 1104) hydrogen bonds : angle 7.51686 ( 3051) *********************** 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 : 0.715 Fit side-chains 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: 0.7811 (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: 0.4633 (t80) REVERT: B 361 LEU cc_start: 0.8735 (mt) cc_final: 0.8526 (tt) REVERT: B 436 VAL cc_start: 0.6579 (m) cc_final: 0.5573 (t) REVERT: B 446 TRP cc_start: 0.3453 (t-100) cc_final: 0.0732 (t-100) REVERT: B 447 ASN cc_start: 0.7123 (t0) cc_final: 0.6879 (t0) REVERT: B 485 ASP cc_start: 0.5412 (m-30) cc_final: 0.5165 (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: 0.9062 (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: 0.6430 (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: 0.0312 (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: 0.9027 (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: 0.8285 (mm) outliers start: 0 outliers final: 0 residues processed: 801 average time/residue: 0.1790 time to fit residues: 219.6706 Evaluate side-chains 395 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 395 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 0.5980 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 0.5980 chunk 298 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 168 ASN A 407 ASN A 415 ASN ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 441 HIS A 502 ASN A 613 ASN A 759 HIS ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 957 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1061 GLN ** A1086 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 168 ASN B 415 ASN B 441 HIS B 502 ASN B 606 GLN B 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 168 ASN C 415 ASN ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 441 HIS C 502 ASN ** C 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1061 GLN ** C1086 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.192073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.182740 restraints weight = 39610.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.181081 restraints weight = 59704.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.180566 restraints weight = 57857.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.179507 restraints weight = 49422.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.178218 restraints weight = 60862.704| |-----------------------------------------------------------------------------| r_work (final): 0.4101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6672 moved from start: 0.3273 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= 0.198 Angle : 0.794 9.802 34683 Z= 0.441 Chirality : 0.048 0.218 3906 Planarity : 0.006 0.064 4512 Dihedral : 6.269 36.793 3486 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 2.76 % Allowed : 7.12 % Favored : 90.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.29 (0.15), residues: 3189 helix: 1.13 (0.18), residues: 885 sheet: 0.49 (0.22), residues: 525 loop : -1.13 (0.14), residues: 1779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 338 TYR 0.033 0.002 TYR A 954 PHE 0.037 0.002 PHE B 500 TRP 0.019 0.003 TRP A 940 HIS 0.009 0.002 HIS C1098 Details of bonding type rmsd covalent geometry : bond 0.00434 (25374) covalent geometry : angle 0.78721 (34569) SS BOND : bond 0.00543 ( 57) SS BOND : angle 1.97391 ( 114) hydrogen bonds : bond 0.05846 ( 1104) hydrogen bonds : angle 6.11241 ( 3051) *********************** 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 508 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 432 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LEU cc_start: 0.6401 (tp) cc_final: 0.6142 (tp) REVERT: A 156 THR cc_start: 0.5998 (p) cc_final: 0.5758 (t) REVERT: A 203 TYR cc_start: 0.6426 (m-80) cc_final: 0.5898 (m-10) REVERT: A 294 CYS cc_start: 0.6793 (OUTLIER) cc_final: 0.6508 (m) REVERT: A 314 GLN cc_start: 0.6550 (mm110) cc_final: 0.6210 (mm110) REVERT: A 353 ASN cc_start: 0.7761 (m-40) cc_final: 0.7478 (p0) REVERT: A 824 GLN cc_start: 0.7798 (tm-30) cc_final: 0.7594 (tm-30) REVERT: A 954 TYR cc_start: 0.6330 (m-80) cc_final: 0.6105 (m-80) REVERT: A 1024 SER cc_start: 0.9176 (t) cc_final: 0.8923 (m) REVERT: B 191 ARG cc_start: 0.7423 (ttm170) cc_final: 0.7181 (ttm170) REVERT: B 299 MET cc_start: 0.7537 (mmp) cc_final: 0.7286 (mmt) REVERT: B 353 ASN cc_start: 0.7308 (m-40) cc_final: 0.6784 (p0) REVERT: B 423 THR cc_start: 0.9210 (m) cc_final: 0.8779 (p) REVERT: B 446 TRP cc_start: 0.2476 (t-100) cc_final: 0.0225 (t-100) REVERT: B 1024 SER cc_start: 0.9008 (t) cc_final: 0.8791 (m) REVERT: C 69 TYR cc_start: 0.8879 (m-80) cc_final: 0.8411 (m-80) REVERT: C 149 MET cc_start: 0.6173 (mmt) cc_final: 0.5806 (mmt) REVERT: C 203 TYR cc_start: 0.6001 (m-80) cc_final: 0.5373 (m-10) REVERT: C 287 SER cc_start: 0.8724 (p) cc_final: 0.8255 (m) REVERT: C 294 CYS cc_start: 0.6027 (OUTLIER) cc_final: 0.5622 (m) REVERT: C 299 MET cc_start: 0.7498 (mmp) cc_final: 0.7217 (mmm) REVERT: C 353 ASN cc_start: 0.7542 (m-40) cc_final: 0.7062 (p0) REVERT: C 1029 GLU cc_start: 0.7425 (tt0) cc_final: 0.6990 (tt0) REVERT: C 1076 ILE cc_start: 0.8643 (mt) cc_final: 0.8072 (mm) outliers start: 76 outliers final: 41 residues processed: 482 average time/residue: 0.1512 time to fit residues: 116.8354 Evaluate side-chains 370 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 327 time to evaluate : 0.897 ------------------------------------------------------------------------------- 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 867 ARG 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 867 ARG Chi-restraints excluded: chain B residue 929 THR Chi-restraints excluded: chain B residue 940 TRP Chi-restraints excluded: chain B residue 1064 ASP Chi-restraints excluded: chain B residue 1088 THR Chi-restraints excluded: chain B residue 1092 PHE Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain C residue 220 LYS Chi-restraints excluded: chain C residue 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 91 optimal weight: 6.9990 chunk 16 optimal weight: 8.9990 chunk 286 optimal weight: 3.9990 chunk 295 optimal weight: 0.0040 chunk 175 optimal weight: 0.5980 chunk 187 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 292 optimal weight: 0.8980 chunk 163 optimal weight: 1.9990 overall best weight: 1.0996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 GLN A 415 ASN A 506 HIS A 716 HIS ** A 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** A1018 ASN B 357 ASN B 415 ASN B 506 HIS B 696 ASN ** B 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 817 GLN B 957 ASN B 985 GLN B1018 ASN B1061 GLN ** B1086 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 415 ASN C 506 HIS C 696 ASN C 716 HIS ** 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: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.188488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.178754 restraints weight = 40167.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.177903 restraints weight = 62270.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.171333 restraints weight = 54354.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.168607 restraints weight = 63102.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.168398 restraints weight = 78657.589| |-----------------------------------------------------------------------------| r_work (final): 0.3983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6978 moved from start: 0.4162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 25431 Z= 0.194 Angle : 0.723 9.361 34683 Z= 0.393 Chirality : 0.047 0.268 3906 Planarity : 0.005 0.061 4512 Dihedral : 6.200 37.923 3486 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 2.98 % Allowed : 9.59 % Favored : 87.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.31 (0.15), residues: 3189 helix: 1.37 (0.18), residues: 888 sheet: 0.20 (0.21), residues: 540 loop : -1.21 (0.15), residues: 1761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 546 TYR 0.028 0.002 TYR A 954 PHE 0.026 0.002 PHE B 500 TRP 0.015 0.002 TRP B 91 HIS 0.008 0.002 HIS B1098 Details of bonding type rmsd covalent geometry : bond 0.00440 (25374) covalent geometry : angle 0.71644 (34569) SS BOND : bond 0.00563 ( 57) SS BOND : angle 1.81895 ( 114) hydrogen bonds : bond 0.05102 ( 1104) hydrogen bonds : angle 5.74195 ( 3051) *********************** 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 446 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 364 time to evaluate : 0.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 THR cc_start: 0.6407 (p) cc_final: 0.5863 (t) REVERT: A 404 GLN cc_start: 0.5857 (OUTLIER) cc_final: 0.4541 (tm130) REVERT: A 416 TYR cc_start: 0.8011 (t80) cc_final: 0.7649 (t80) REVERT: A 954 TYR cc_start: 0.6631 (m-80) cc_final: 0.6332 (m-80) REVERT: A 1018 ASN cc_start: 0.8750 (t0) cc_final: 0.8018 (t0) REVERT: A 1024 SER cc_start: 0.9284 (t) cc_final: 0.8867 (m) REVERT: B 41 THR cc_start: 0.7345 (OUTLIER) cc_final: 0.7144 (t) REVERT: B 92 PHE cc_start: 0.5648 (m-80) cc_final: 0.4306 (m-10) REVERT: B 149 MET cc_start: 0.5865 (mmt) cc_final: 0.5477 (mmt) REVERT: B 191 ARG cc_start: 0.7686 (ttm170) cc_final: 0.7370 (ttm-80) REVERT: B 299 MET cc_start: 0.7582 (mmp) cc_final: 0.7274 (mmt) REVERT: B 353 ASN cc_start: 0.7401 (m-40) cc_final: 0.7139 (p0) REVERT: B 416 TYR cc_start: 0.7927 (t80) cc_final: 0.7706 (t80) REVERT: B 423 THR cc_start: 0.9365 (m) cc_final: 0.9156 (p) REVERT: B 446 TRP cc_start: 0.3629 (t-100) cc_final: 0.1263 (t-100) REVERT: B 963 MET cc_start: 0.5912 (OUTLIER) cc_final: 0.3570 (pmm) REVERT: B 1024 SER cc_start: 0.9107 (t) cc_final: 0.8859 (m) REVERT: C 353 ASN cc_start: 0.7465 (m-40) cc_final: 0.7261 (p0) REVERT: C 423 THR cc_start: 0.9291 (m) cc_final: 0.8529 (p) REVERT: C 963 MET cc_start: 0.5936 (tpt) cc_final: 0.4408 (pmm) REVERT: C 1057 TYR cc_start: 0.8918 (t80) cc_final: 0.8630 (t80) REVERT: C 1076 ILE cc_start: 0.8485 (mt) cc_final: 0.8124 (mm) outliers start: 82 outliers final: 56 residues processed: 414 average time/residue: 0.1565 time to fit residues: 104.7933 Evaluate side-chains 355 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 296 time to evaluate : 0.860 ------------------------------------------------------------------------------- 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 766 THR Chi-restraints excluded: chain A residue 867 ARG Chi-restraints excluded: chain A residue 940 TRP Chi-restraints excluded: chain A residue 963 MET Chi-restraints excluded: chain A residue 1005 ASN Chi-restraints excluded: chain A residue 1064 ASP 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 318 VAL Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 671 ASN Chi-restraints excluded: chain B residue 818 VAL Chi-restraints excluded: chain B residue 867 ARG Chi-restraints excluded: chain B residue 929 THR Chi-restraints excluded: chain B residue 940 TRP Chi-restraints excluded: chain B residue 963 MET 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 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 230 VAL Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 485 ASP 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 1090 ILE Chi-restraints excluded: chain C residue 1103 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 56 optimal weight: 0.0980 chunk 149 optimal weight: 8.9990 chunk 272 optimal weight: 3.9990 chunk 24 optimal weight: 0.0670 chunk 266 optimal weight: 0.9990 chunk 305 optimal weight: 3.9990 chunk 146 optimal weight: 3.9990 chunk 21 optimal weight: 6.9990 chunk 261 optimal weight: 9.9990 chunk 205 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 overall best weight: 1.2324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 366 GLN ** A 783 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 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** 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 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 985 GLN ** C1086 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.186283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.176306 restraints weight = 40055.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 106)---------------| | r_work = 0.3921 r_free = 0.3921 target = 0.163465 restraints weight = 63918.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.161814 restraints weight = 65143.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.162266 restraints weight = 78879.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.162577 restraints weight = 62470.061| |-----------------------------------------------------------------------------| r_work (final): 0.3862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 moved from start: 0.4691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 25431 Z= 0.197 Angle : 0.705 8.797 34683 Z= 0.382 Chirality : 0.046 0.228 3906 Planarity : 0.005 0.061 4512 Dihedral : 6.166 37.489 3486 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 3.63 % Allowed : 10.60 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.38 (0.15), residues: 3189 helix: 1.42 (0.18), residues: 891 sheet: 0.04 (0.21), residues: 558 loop : -1.29 (0.15), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 546 TYR 0.020 0.002 TYR A 450 PHE 0.027 0.002 PHE C 948 TRP 0.014 0.002 TRP A 178 HIS 0.011 0.002 HIS C 716 Details of bonding type rmsd covalent geometry : bond 0.00449 (25374) covalent geometry : angle 0.69677 (34569) SS BOND : bond 0.00655 ( 57) SS BOND : angle 2.03304 ( 114) hydrogen bonds : bond 0.04907 ( 1104) hydrogen bonds : angle 5.68101 ( 3051) *********************** 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 427 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 327 time to evaluate : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 THR cc_start: 0.6810 (p) cc_final: 0.6145 (t) REVERT: A 294 CYS cc_start: 0.6701 (OUTLIER) cc_final: 0.6365 (m) REVERT: A 366 GLN cc_start: 0.7554 (OUTLIER) cc_final: 0.6877 (tp40) REVERT: A 404 GLN cc_start: 0.5414 (OUTLIER) cc_final: 0.4576 (tm-30) REVERT: A 416 TYR cc_start: 0.8071 (t80) cc_final: 0.7678 (t80) REVERT: A 749 MET cc_start: 0.5808 (mmt) cc_final: 0.5502 (mmm) REVERT: A 954 TYR cc_start: 0.7446 (m-80) cc_final: 0.6878 (m-80) REVERT: A 963 MET cc_start: 0.5429 (OUTLIER) cc_final: 0.2863 (pmm) REVERT: A 1024 SER cc_start: 0.9212 (t) cc_final: 0.8850 (m) REVERT: B 41 THR cc_start: 0.7461 (p) cc_final: 0.7224 (t) REVERT: B 92 PHE cc_start: 0.5644 (m-80) cc_final: 0.5342 (m-80) REVERT: B 191 ARG cc_start: 0.7561 (ttm170) cc_final: 0.7304 (ttm170) REVERT: B 416 TYR cc_start: 0.7950 (t80) cc_final: 0.7632 (t80) REVERT: B 423 THR cc_start: 0.9392 (m) cc_final: 0.9174 (p) REVERT: B 638 VAL cc_start: 0.8223 (OUTLIER) cc_final: 0.7880 (t) REVERT: B 904 LEU cc_start: 0.8250 (mm) cc_final: 0.7743 (mm) REVERT: B 957 ASN cc_start: 0.7874 (p0) cc_final: 0.6932 (m-40) REVERT: B 1024 SER cc_start: 0.9169 (t) cc_final: 0.8925 (m) REVERT: B 1067 LEU cc_start: 0.9104 (mt) cc_final: 0.8702 (tt) REVERT: C 92 PHE cc_start: 0.4721 (m-80) cc_final: 0.4311 (m-10) REVERT: C 294 CYS cc_start: 0.6102 (OUTLIER) cc_final: 0.5834 (m) REVERT: C 370 LEU cc_start: 0.8774 (tp) cc_final: 0.8480 (tt) REVERT: C 423 THR cc_start: 0.9404 (m) cc_final: 0.8638 (p) REVERT: C 963 MET cc_start: 0.6343 (tpt) cc_final: 0.4562 (pmm) REVERT: C 1018 ASN cc_start: 0.8803 (t0) cc_final: 0.8186 (t0) outliers start: 100 outliers final: 68 residues processed: 397 average time/residue: 0.1539 time to fit residues: 99.7373 Evaluate side-chains 368 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 294 time to evaluate : 0.872 ------------------------------------------------------------------------------- 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 163 THR Chi-restraints excluded: chain A residue 217 TYR Chi-restraints excluded: chain A residue 220 LYS Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 294 CYS Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 366 GLN Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 404 GLN Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 635 SER Chi-restraints excluded: chain A residue 676 PHE Chi-restraints excluded: chain A residue 747 TYR Chi-restraints excluded: chain A residue 867 ARG Chi-restraints excluded: chain A residue 963 MET Chi-restraints excluded: chain A residue 1005 ASN Chi-restraints excluded: chain A residue 1014 ASN Chi-restraints excluded: chain A residue 1046 LEU Chi-restraints excluded: chain A residue 1064 ASP Chi-restraints excluded: chain A residue 1067 LEU Chi-restraints excluded: chain A residue 1088 THR Chi-restraints excluded: chain A residue 1103 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 217 TYR Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 418 ILE 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 883 SER Chi-restraints excluded: chain B residue 929 THR Chi-restraints excluded: chain B residue 937 PHE Chi-restraints excluded: chain B residue 940 TRP Chi-restraints excluded: chain B residue 1064 ASP Chi-restraints excluded: chain B residue 1088 THR Chi-restraints excluded: chain B residue 1092 PHE Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain C residue 220 LYS Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 375 ILE Chi-restraints excluded: chain C residue 385 PHE Chi-restraints excluded: chain C residue 485 ASP 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 766 THR 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 1064 ASP 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 266 optimal weight: 7.9990 chunk 167 optimal weight: 0.8980 chunk 96 optimal weight: 0.9990 chunk 185 optimal weight: 0.6980 chunk 282 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 228 optimal weight: 9.9990 chunk 13 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 199 optimal weight: 3.9990 chunk 308 optimal weight: 0.8980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1080 ASN ** B1086 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1097 ASN C 415 ASN ** C 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** ** 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 = 0.4225 r_free = 0.4225 target = 0.187083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.175169 restraints weight = 39868.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.173115 restraints weight = 65771.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.171931 restraints weight = 68437.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.170301 restraints weight = 72754.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.170451 restraints weight = 65402.669| |-----------------------------------------------------------------------------| r_work (final): 0.4037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6892 moved from start: 0.5032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 25431 Z= 0.164 Angle : 0.670 9.255 34683 Z= 0.362 Chirality : 0.045 0.210 3906 Planarity : 0.005 0.083 4512 Dihedral : 6.027 36.828 3486 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 3.12 % Allowed : 11.91 % Favored : 84.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.27 (0.15), residues: 3189 helix: 1.59 (0.18), residues: 894 sheet: 0.04 (0.21), residues: 567 loop : -1.26 (0.15), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 546 TYR 0.025 0.002 TYR A 137 PHE 0.023 0.002 PHE B 642 TRP 0.016 0.002 TRP A 940 HIS 0.008 0.001 HIS C 716 Details of bonding type rmsd covalent geometry : bond 0.00372 (25374) covalent geometry : angle 0.66265 (34569) SS BOND : bond 0.00611 ( 57) SS BOND : angle 1.83091 ( 114) hydrogen bonds : bond 0.04633 ( 1104) hydrogen bonds : angle 5.54473 ( 3051) *********************** 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 418 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 332 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 TYR cc_start: 0.6873 (OUTLIER) cc_final: 0.6207 (t80) REVERT: A 294 CYS cc_start: 0.6325 (OUTLIER) cc_final: 0.5998 (m) REVERT: A 416 TYR cc_start: 0.7979 (t80) cc_final: 0.7690 (t80) REVERT: A 950 LEU cc_start: 0.6553 (tp) cc_final: 0.5930 (tp) REVERT: A 963 MET cc_start: 0.5398 (OUTLIER) cc_final: 0.3169 (pmm) REVERT: A 1018 ASN cc_start: 0.8697 (t0) cc_final: 0.8081 (t0) REVERT: A 1024 SER cc_start: 0.9217 (t) cc_final: 0.8624 (m) REVERT: B 92 PHE cc_start: 0.4462 (m-80) cc_final: 0.3920 (m-80) REVERT: B 366 GLN cc_start: 0.6622 (OUTLIER) cc_final: 0.6168 (tp40) REVERT: B 416 TYR cc_start: 0.7857 (t80) cc_final: 0.7632 (t80) REVERT: B 423 THR cc_start: 0.9374 (m) cc_final: 0.9171 (p) REVERT: B 638 VAL cc_start: 0.8129 (OUTLIER) cc_final: 0.7837 (t) REVERT: B 904 LEU cc_start: 0.8294 (mm) cc_final: 0.7700 (mm) REVERT: B 957 ASN cc_start: 0.7560 (p0) cc_final: 0.6704 (m-40) REVERT: B 1024 SER cc_start: 0.9218 (t) cc_final: 0.8902 (m) REVERT: C 104 ILE cc_start: 0.8453 (mt) cc_final: 0.8224 (tt) REVERT: C 294 CYS cc_start: 0.5943 (OUTLIER) cc_final: 0.5725 (m) REVERT: C 370 LEU cc_start: 0.8864 (tp) cc_final: 0.8519 (tt) REVERT: C 423 THR cc_start: 0.9377 (m) cc_final: 0.8696 (p) REVERT: C 503 VAL cc_start: 0.2860 (OUTLIER) cc_final: 0.2591 (t) REVERT: C 963 MET cc_start: 0.5533 (tpt) cc_final: 0.3889 (pmm) REVERT: C 1018 ASN cc_start: 0.8815 (t0) cc_final: 0.8003 (t0) REVERT: C 1076 ILE cc_start: 0.8454 (mt) cc_final: 0.8187 (mm) outliers start: 86 outliers final: 59 residues processed: 395 average time/residue: 0.1512 time to fit residues: 96.6097 Evaluate side-chains 356 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 290 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 137 TYR 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 330 ASN Chi-restraints excluded: chain A residue 344 LEU 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 716 HIS Chi-restraints excluded: chain A residue 747 TYR Chi-restraints excluded: chain A residue 867 ARG Chi-restraints excluded: chain A residue 963 MET Chi-restraints excluded: chain A residue 1005 ASN Chi-restraints excluded: chain A residue 1014 ASN Chi-restraints excluded: chain A residue 1046 LEU Chi-restraints excluded: chain A residue 1064 ASP Chi-restraints excluded: chain A residue 1067 LEU Chi-restraints excluded: chain A residue 1088 THR Chi-restraints excluded: chain A residue 1103 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 217 TYR Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 366 GLN 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 638 VAL Chi-restraints excluded: chain B residue 671 ASN Chi-restraints excluded: chain B residue 867 ARG Chi-restraints excluded: chain B residue 929 THR Chi-restraints excluded: chain B residue 937 PHE Chi-restraints excluded: chain B residue 940 TRP Chi-restraints excluded: chain B residue 1064 ASP Chi-restraints excluded: chain B residue 1088 THR Chi-restraints excluded: chain B residue 1092 PHE Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain C residue 220 LYS Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 375 ILE Chi-restraints excluded: chain C residue 503 VAL 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 929 THR Chi-restraints excluded: chain C residue 940 TRP Chi-restraints excluded: chain C residue 1046 LEU Chi-restraints excluded: chain C residue 1067 LEU Chi-restraints excluded: chain C residue 1088 THR Chi-restraints excluded: chain C residue 1090 ILE Chi-restraints excluded: chain C residue 1103 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 138 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 chunk 97 optimal weight: 0.6980 chunk 83 optimal weight: 0.8980 chunk 317 optimal weight: 0.8980 chunk 279 optimal weight: 1.9990 chunk 248 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 213 optimal weight: 0.0770 chunk 79 optimal weight: 0.7980 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 783 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 957 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1086 GLN ** 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** C1080 ASN ** C1086 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.187337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.180325 restraints weight = 39961.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.179105 restraints weight = 58601.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 81)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.170743 restraints weight = 48907.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.168625 restraints weight = 74028.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.168873 restraints weight = 75757.845| |-----------------------------------------------------------------------------| r_work (final): 0.3979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6983 moved from start: 0.5325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 25431 Z= 0.146 Angle : 0.641 9.115 34683 Z= 0.347 Chirality : 0.044 0.186 3906 Planarity : 0.005 0.054 4512 Dihedral : 5.854 35.346 3486 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 3.27 % Allowed : 12.93 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.24 (0.15), residues: 3189 helix: 1.64 (0.18), residues: 894 sheet: 0.03 (0.20), residues: 597 loop : -1.26 (0.15), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 546 TYR 0.026 0.002 TYR A 954 PHE 0.033 0.002 PHE C 948 TRP 0.025 0.002 TRP A 536 HIS 0.006 0.001 HIS B1098 Details of bonding type rmsd covalent geometry : bond 0.00332 (25374) covalent geometry : angle 0.63287 (34569) SS BOND : bond 0.00694 ( 57) SS BOND : angle 1.90512 ( 114) hydrogen bonds : bond 0.04497 ( 1104) hydrogen bonds : angle 5.43715 ( 3051) *********************** 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 419 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 329 time to evaluate : 0.899 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 92 PHE cc_start: 0.4648 (m-80) cc_final: 0.3784 (m-10) REVERT: A 137 TYR cc_start: 0.6661 (OUTLIER) cc_final: 0.6391 (t80) REVERT: A 294 CYS cc_start: 0.6390 (OUTLIER) cc_final: 0.6049 (m) REVERT: A 416 TYR cc_start: 0.7911 (t80) cc_final: 0.7518 (t80) REVERT: A 574 GLU cc_start: 0.7276 (pp20) cc_final: 0.7004 (mp0) REVERT: A 971 LYS cc_start: 0.7818 (tppt) cc_final: 0.6776 (mtpt) REVERT: A 1018 ASN cc_start: 0.8591 (t0) cc_final: 0.7825 (t0) REVERT: A 1024 SER cc_start: 0.9073 (t) cc_final: 0.8492 (m) REVERT: A 1117 TYR cc_start: 0.7540 (OUTLIER) cc_final: 0.6434 (p90) REVERT: B 92 PHE cc_start: 0.5297 (m-80) cc_final: 0.4818 (m-10) REVERT: B 240 TYR cc_start: 0.4179 (OUTLIER) cc_final: 0.2537 (t80) REVERT: B 366 GLN cc_start: 0.6655 (OUTLIER) cc_final: 0.6278 (tp40) REVERT: B 574 GLU cc_start: 0.7301 (pp20) cc_final: 0.6928 (mp0) REVERT: B 612 VAL cc_start: 0.8424 (m) cc_final: 0.8192 (p) REVERT: B 638 VAL cc_start: 0.8060 (OUTLIER) cc_final: 0.7817 (t) REVERT: B 734 MET cc_start: 0.1660 (mmt) cc_final: 0.0142 (mmt) REVERT: B 1024 SER cc_start: 0.9225 (t) cc_final: 0.8899 (m) REVERT: C 164 ASP cc_start: 0.5747 (t0) cc_final: 0.5197 (t0) REVERT: C 294 CYS cc_start: 0.5789 (OUTLIER) cc_final: 0.5516 (m) REVERT: C 370 LEU cc_start: 0.8828 (tp) cc_final: 0.8502 (tt) REVERT: C 423 THR cc_start: 0.9420 (m) cc_final: 0.8729 (p) REVERT: C 503 VAL cc_start: 0.3038 (OUTLIER) cc_final: 0.2726 (t) REVERT: C 645 ASP cc_start: 0.6556 (p0) cc_final: 0.6273 (p0) REVERT: C 963 MET cc_start: 0.5423 (tpt) cc_final: 0.3635 (pmm) REVERT: C 1018 ASN cc_start: 0.8791 (t0) cc_final: 0.7993 (t0) REVERT: C 1076 ILE cc_start: 0.8709 (mt) cc_final: 0.8382 (mm) outliers start: 90 outliers final: 58 residues processed: 387 average time/residue: 0.1539 time to fit residues: 96.2633 Evaluate side-chains 366 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 300 time to evaluate : 0.608 ------------------------------------------------------------------------------- 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 137 TYR 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 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 1046 LEU Chi-restraints excluded: chain A residue 1067 LEU Chi-restraints excluded: chain A residue 1088 THR Chi-restraints excluded: chain A residue 1103 VAL Chi-restraints excluded: chain A residue 1117 TYR Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 217 TYR Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 240 TYR 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 405 LEU Chi-restraints excluded: chain B residue 437 THR 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 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 929 THR Chi-restraints excluded: chain B residue 937 PHE Chi-restraints excluded: chain B residue 940 TRP Chi-restraints excluded: chain B residue 1064 ASP Chi-restraints excluded: chain B residue 1088 THR Chi-restraints excluded: chain B residue 1092 PHE Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain C residue 220 LYS Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 375 ILE Chi-restraints excluded: chain C residue 503 VAL 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 1046 LEU Chi-restraints excluded: chain C residue 1088 THR Chi-restraints excluded: chain C residue 1092 PHE Chi-restraints excluded: chain C residue 1103 VAL 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 269 optimal weight: 1.9990 chunk 225 optimal weight: 5.9990 chunk 63 optimal weight: 0.7980 chunk 75 optimal weight: 0.6980 chunk 274 optimal weight: 0.7980 chunk 250 optimal weight: 0.4980 chunk 219 optimal weight: 0.6980 chunk 104 optimal weight: 7.9990 chunk 155 optimal weight: 10.0000 chunk 129 optimal weight: 0.2980 chunk 189 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 957 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1018 ASN B1086 GLN 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** 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 = 0.4232 r_free = 0.4232 target = 0.188041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.179845 restraints weight = 39924.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.169317 restraints weight = 67160.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.166528 restraints weight = 72773.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.166826 restraints weight = 92832.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.167449 restraints weight = 67556.785| |-----------------------------------------------------------------------------| r_work (final): 0.3937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7048 moved from start: 0.5549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 25431 Z= 0.140 Angle : 0.637 9.092 34683 Z= 0.344 Chirality : 0.044 0.199 3906 Planarity : 0.005 0.053 4512 Dihedral : 5.718 34.270 3486 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 3.38 % Allowed : 13.29 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.23 (0.15), residues: 3189 helix: 1.64 (0.18), residues: 894 sheet: 0.03 (0.20), residues: 597 loop : -1.25 (0.16), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 546 TYR 0.022 0.002 TYR A 450 PHE 0.026 0.002 PHE C 472 TRP 0.030 0.002 TRP B 536 HIS 0.006 0.001 HIS B1098 Details of bonding type rmsd covalent geometry : bond 0.00317 (25374) covalent geometry : angle 0.62931 (34569) SS BOND : bond 0.00552 ( 57) SS BOND : angle 1.78414 ( 114) hydrogen bonds : bond 0.04391 ( 1104) hydrogen bonds : angle 5.36083 ( 3051) *********************** 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 421 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 328 time to evaluate : 0.797 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: 0.4793 (m-80) cc_final: 0.4008 (m-10) REVERT: A 137 TYR cc_start: 0.7126 (OUTLIER) cc_final: 0.6541 (t80) REVERT: A 156 THR cc_start: 0.6527 (p) cc_final: 0.5988 (t) REVERT: A 294 CYS cc_start: 0.6311 (OUTLIER) cc_final: 0.5991 (m) REVERT: A 370 LEU cc_start: 0.8465 (tp) cc_final: 0.8115 (tt) REVERT: A 416 TYR cc_start: 0.7824 (t80) cc_final: 0.7407 (t80) REVERT: A 574 GLU cc_start: 0.7347 (pp20) cc_final: 0.7101 (mp0) REVERT: A 971 LYS cc_start: 0.7438 (tppt) cc_final: 0.6633 (mtpt) REVERT: A 1018 ASN cc_start: 0.8484 (t0) cc_final: 0.7809 (t0) REVERT: A 1024 SER cc_start: 0.9084 (t) cc_final: 0.8554 (m) REVERT: A 1117 TYR cc_start: 0.7521 (OUTLIER) cc_final: 0.6392 (p90) REVERT: B 92 PHE cc_start: 0.5416 (m-80) cc_final: 0.5190 (m-10) REVERT: B 231 TYR cc_start: 0.7017 (t80) cc_final: 0.6752 (t80) REVERT: B 240 TYR cc_start: 0.4595 (OUTLIER) cc_final: 0.2949 (t80) REVERT: B 366 GLN cc_start: 0.6631 (OUTLIER) cc_final: 0.6343 (tp40) REVERT: B 370 LEU cc_start: 0.8327 (tp) cc_final: 0.8019 (tt) REVERT: B 574 GLU cc_start: 0.7257 (pp20) cc_final: 0.6946 (mp0) REVERT: B 613 ASN cc_start: 0.6946 (t0) cc_final: 0.6225 (t0) REVERT: B 638 VAL cc_start: 0.8082 (OUTLIER) cc_final: 0.7829 (t) REVERT: B 734 MET cc_start: 0.1402 (mmt) cc_final: -0.0201 (mmt) REVERT: B 1018 ASN cc_start: 0.8249 (OUTLIER) cc_final: 0.7917 (m-40) REVERT: B 1024 SER cc_start: 0.9146 (t) cc_final: 0.8731 (m) REVERT: B 1117 TYR cc_start: 0.7101 (OUTLIER) cc_final: 0.6152 (p90) REVERT: C 164 ASP cc_start: 0.6012 (t0) cc_final: 0.5560 (t0) REVERT: C 294 CYS cc_start: 0.5668 (OUTLIER) cc_final: 0.5440 (m) REVERT: C 330 ASN cc_start: 0.6908 (p0) cc_final: 0.6589 (p0) REVERT: C 370 LEU cc_start: 0.8783 (tp) cc_final: 0.8496 (tt) REVERT: C 423 THR cc_start: 0.9419 (m) cc_final: 0.8728 (p) REVERT: C 734 MET cc_start: 0.1673 (mmt) cc_final: 0.1160 (mmt) REVERT: C 936 MET cc_start: 0.7168 (mtt) cc_final: 0.6896 (mmm) REVERT: C 948 PHE cc_start: 0.6177 (t80) cc_final: 0.5516 (t80) REVERT: C 963 MET cc_start: 0.5520 (tpt) cc_final: 0.3723 (pmm) REVERT: C 1018 ASN cc_start: 0.8791 (t0) cc_final: 0.7901 (t0) REVERT: C 1076 ILE cc_start: 0.8639 (mt) cc_final: 0.8300 (mm) outliers start: 93 outliers final: 72 residues processed: 390 average time/residue: 0.1539 time to fit residues: 97.1013 Evaluate side-chains 373 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 292 time to evaluate : 0.947 ------------------------------------------------------------------------------- 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 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 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 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 230 VAL Chi-restraints excluded: chain B residue 240 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 405 LEU Chi-restraints excluded: chain B residue 437 THR 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 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 1018 ASN 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 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 294 CYS Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 375 ILE Chi-restraints excluded: chain C residue 385 PHE Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 472 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 677 ASP Chi-restraints excluded: chain C residue 940 TRP 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 73 optimal weight: 4.9990 chunk 68 optimal weight: 0.9980 chunk 279 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 178 optimal weight: 6.9990 chunk 239 optimal weight: 0.5980 chunk 104 optimal weight: 4.9990 chunk 148 optimal weight: 4.9990 chunk 275 optimal weight: 0.9980 chunk 113 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 442 ASN ** A 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 591 GLN ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 957 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 442 ASN ** B 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1015 GLN C 352 GLN ** 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 = 0.4182 r_free = 0.4182 target = 0.182868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.170938 restraints weight = 40572.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.166302 restraints weight = 74035.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.165036 restraints weight = 62641.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.163307 restraints weight = 71335.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.163923 restraints weight = 61222.064| |-----------------------------------------------------------------------------| r_work (final): 0.3928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7084 moved from start: 0.5851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 25431 Z= 0.221 Angle : 0.728 10.365 34683 Z= 0.388 Chirality : 0.047 0.199 3906 Planarity : 0.005 0.076 4512 Dihedral : 5.975 37.752 3486 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.09 % Favored : 91.91 % Rotamer: Outliers : 3.78 % Allowed : 13.87 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.52 (0.15), residues: 3189 helix: 1.32 (0.18), residues: 894 sheet: -0.12 (0.20), residues: 609 loop : -1.39 (0.15), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 724 TYR 0.028 0.002 TYR A 954 PHE 0.033 0.002 PHE C 550 TRP 0.030 0.003 TRP A 446 HIS 0.009 0.002 HIS B1098 Details of bonding type rmsd covalent geometry : bond 0.00510 (25374) covalent geometry : angle 0.72009 (34569) SS BOND : bond 0.00697 ( 57) SS BOND : angle 1.98124 ( 114) hydrogen bonds : bond 0.04938 ( 1104) hydrogen bonds : angle 5.56984 ( 3051) *********************** 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 405 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 301 time to evaluate : 0.737 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: 0.4690 (m-80) cc_final: 0.4366 (m-10) REVERT: A 137 TYR cc_start: 0.7238 (OUTLIER) cc_final: 0.6594 (t80) REVERT: A 144 TYR cc_start: 0.6499 (t80) cc_final: 0.6134 (t80) REVERT: A 156 THR cc_start: 0.6491 (p) cc_final: 0.5975 (t) REVERT: A 294 CYS cc_start: 0.6570 (OUTLIER) cc_final: 0.6232 (m) REVERT: A 971 LYS cc_start: 0.7799 (tppt) cc_final: 0.7280 (mttp) REVERT: A 1024 SER cc_start: 0.9186 (t) cc_final: 0.8611 (m) REVERT: A 1117 TYR cc_start: 0.7554 (OUTLIER) cc_final: 0.6522 (p90) REVERT: B 149 MET cc_start: 0.5305 (mtt) cc_final: 0.4995 (mtt) REVERT: B 240 TYR cc_start: 0.4634 (OUTLIER) cc_final: 0.3220 (t80) REVERT: B 338 ARG cc_start: 0.5541 (tpt90) cc_final: 0.5250 (tpt90) REVERT: B 366 GLN cc_start: 0.6397 (OUTLIER) cc_final: 0.6189 (mm110) REVERT: B 416 TYR cc_start: 0.7788 (t80) cc_final: 0.7586 (t80) REVERT: B 574 GLU cc_start: 0.7291 (pp20) cc_final: 0.6727 (mp0) REVERT: B 613 ASN cc_start: 0.7360 (t0) cc_final: 0.6970 (t0) REVERT: B 638 VAL cc_start: 0.8399 (OUTLIER) cc_final: 0.8106 (t) REVERT: B 734 MET cc_start: 0.1577 (mmt) cc_final: 0.0389 (mmt) REVERT: B 1018 ASN cc_start: 0.8347 (t0) cc_final: 0.7995 (m-40) REVERT: B 1024 SER cc_start: 0.9037 (t) cc_final: 0.8611 (m) REVERT: B 1117 TYR cc_start: 0.7241 (OUTLIER) cc_final: 0.6314 (p90) REVERT: C 137 TYR cc_start: 0.7029 (OUTLIER) cc_final: 0.5919 (t80) REVERT: C 164 ASP cc_start: 0.5717 (t0) cc_final: 0.5349 (t0) REVERT: C 294 CYS cc_start: 0.5994 (OUTLIER) cc_final: 0.5715 (m) REVERT: C 370 LEU cc_start: 0.8823 (tp) cc_final: 0.8535 (tt) REVERT: C 423 THR cc_start: 0.9426 (m) cc_final: 0.8775 (p) REVERT: C 734 MET cc_start: 0.2222 (mmt) cc_final: 0.1689 (mmt) REVERT: C 936 MET cc_start: 0.7532 (mtt) cc_final: 0.6814 (mtt) REVERT: C 948 PHE cc_start: 0.6212 (t80) cc_final: 0.5779 (t80) REVERT: C 963 MET cc_start: 0.4968 (tpt) cc_final: 0.3770 (pmm) REVERT: C 1076 ILE cc_start: 0.8684 (mt) cc_final: 0.8324 (mm) outliers start: 104 outliers final: 82 residues processed: 377 average time/residue: 0.1533 time to fit residues: 93.9123 Evaluate side-chains 369 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 278 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 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 235 ILE 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 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 607 THR Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 716 HIS 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 937 PHE Chi-restraints excluded: chain A residue 1005 ASN Chi-restraints excluded: chain A residue 1064 ASP Chi-restraints excluded: chain A residue 1067 LEU Chi-restraints excluded: chain A residue 1088 THR Chi-restraints excluded: chain A residue 1103 VAL Chi-restraints excluded: chain A residue 1117 TYR Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 217 TYR Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 240 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 385 PHE Chi-restraints excluded: chain B residue 437 THR 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 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 1064 ASP Chi-restraints excluded: chain B residue 1088 THR Chi-restraints excluded: chain B residue 1092 PHE 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 137 TYR Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain C residue 220 LYS Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 375 ILE Chi-restraints excluded: chain C residue 385 PHE Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 446 TRP 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 576 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 937 PHE 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 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 172 optimal weight: 0.9980 chunk 12 optimal weight: 6.9990 chunk 313 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 141 optimal weight: 4.9990 chunk 263 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 164 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 182 optimal weight: 0.9990 chunk 122 optimal weight: 6.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 502 ASN ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 957 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 979 ASN C 415 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 = 0.4194 r_free = 0.4194 target = 0.183991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.172247 restraints weight = 40579.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 77)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.164876 restraints weight = 73647.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.163792 restraints weight = 74330.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.163862 restraints weight = 68478.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.164048 restraints weight = 51864.173| |-----------------------------------------------------------------------------| r_work (final): 0.3926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 moved from start: 0.6054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 25431 Z= 0.185 Angle : 0.700 10.640 34683 Z= 0.374 Chirality : 0.046 0.186 3906 Planarity : 0.005 0.063 4512 Dihedral : 5.942 35.620 3486 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.75 % Favored : 92.19 % Rotamer: Outliers : 3.34 % Allowed : 15.00 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.51 (0.15), residues: 3189 helix: 1.40 (0.18), residues: 897 sheet: -0.20 (0.20), residues: 609 loop : -1.40 (0.15), residues: 1683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 724 TYR 0.023 0.002 TYR A 954 PHE 0.021 0.002 PHE B 371 TRP 0.036 0.002 TRP A 178 HIS 0.007 0.001 HIS B1098 Details of bonding type rmsd covalent geometry : bond 0.00428 (25374) covalent geometry : angle 0.69052 (34569) SS BOND : bond 0.00600 ( 57) SS BOND : angle 2.09375 ( 114) hydrogen bonds : bond 0.04716 ( 1104) hydrogen bonds : angle 5.51407 ( 3051) *********************** 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 399 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 307 time to evaluate : 0.841 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: 0.4834 (m-80) cc_final: 0.4318 (m-10) REVERT: A 137 TYR cc_start: 0.7274 (OUTLIER) cc_final: 0.6617 (t80) REVERT: A 156 THR cc_start: 0.6569 (p) cc_final: 0.6367 (t) REVERT: A 164 ASP cc_start: 0.5410 (t0) cc_final: 0.5165 (t0) REVERT: A 294 CYS cc_start: 0.6589 (OUTLIER) cc_final: 0.6275 (m) REVERT: A 971 LYS cc_start: 0.7747 (tppt) cc_final: 0.7007 (mtpt) REVERT: A 1018 ASN cc_start: 0.8769 (t0) cc_final: 0.7978 (t0) REVERT: A 1024 SER cc_start: 0.9191 (t) cc_final: 0.8628 (m) REVERT: A 1117 TYR cc_start: 0.7546 (OUTLIER) cc_final: 0.6428 (p90) REVERT: B 240 TYR cc_start: 0.4641 (OUTLIER) cc_final: 0.3157 (t80) REVERT: B 416 TYR cc_start: 0.7791 (t80) cc_final: 0.7587 (t80) REVERT: B 574 GLU cc_start: 0.7257 (pp20) cc_final: 0.6761 (mp0) REVERT: B 613 ASN cc_start: 0.7181 (t0) cc_final: 0.6825 (t0) REVERT: B 638 VAL cc_start: 0.8431 (OUTLIER) cc_final: 0.8139 (t) REVERT: B 734 MET cc_start: 0.1569 (mmt) cc_final: 0.1106 (mmt) REVERT: B 963 MET cc_start: 0.3349 (mmm) cc_final: 0.3122 (mmm) REVERT: B 1018 ASN cc_start: 0.8459 (t0) cc_final: 0.8032 (m-40) REVERT: B 1024 SER cc_start: 0.9084 (t) cc_final: 0.8614 (m) REVERT: C 137 TYR cc_start: 0.7122 (OUTLIER) cc_final: 0.5693 (t80) REVERT: C 164 ASP cc_start: 0.5681 (t0) cc_final: 0.5480 (t0) REVERT: C 294 CYS cc_start: 0.5986 (OUTLIER) cc_final: 0.5715 (m) REVERT: C 322 ARG cc_start: 0.6099 (ptm-80) cc_final: 0.5885 (ptm-80) REVERT: C 370 LEU cc_start: 0.8693 (tp) cc_final: 0.8374 (tt) REVERT: C 423 THR cc_start: 0.9433 (m) cc_final: 0.8800 (p) REVERT: C 734 MET cc_start: 0.1808 (mmt) cc_final: 0.1268 (mmt) REVERT: C 936 MET cc_start: 0.7452 (mtt) cc_final: 0.6718 (mtt) REVERT: C 948 PHE cc_start: 0.6221 (t80) cc_final: 0.5777 (t80) REVERT: C 963 MET cc_start: 0.4788 (tpt) cc_final: 0.3405 (pmm) REVERT: C 1018 ASN cc_start: 0.8943 (t0) cc_final: 0.8227 (t0) REVERT: C 1076 ILE cc_start: 0.8725 (mt) cc_final: 0.8320 (mm) outliers start: 92 outliers final: 77 residues processed: 364 average time/residue: 0.1504 time to fit residues: 89.6051 Evaluate side-chains 370 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 286 time to evaluate : 1.097 ------------------------------------------------------------------------------- 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 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 318 VAL 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 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 937 PHE Chi-restraints excluded: chain A residue 1005 ASN Chi-restraints excluded: chain A residue 1064 ASP Chi-restraints excluded: chain A residue 1067 LEU Chi-restraints excluded: chain A residue 1088 THR Chi-restraints excluded: chain A residue 1103 VAL Chi-restraints excluded: chain A residue 1117 TYR Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 217 TYR Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 240 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 385 PHE Chi-restraints excluded: chain B residue 437 THR 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 929 THR 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 B residue 1092 PHE Chi-restraints excluded: chain B residue 1103 VAL Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 137 TYR Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain C residue 220 LYS Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 375 ILE 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 576 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 894 CYS Chi-restraints excluded: chain C residue 929 THR Chi-restraints excluded: chain C residue 937 PHE Chi-restraints excluded: chain C residue 940 TRP 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 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 161 optimal weight: 3.9990 chunk 216 optimal weight: 0.9990 chunk 248 optimal weight: 0.9990 chunk 0 optimal weight: 9.9990 chunk 272 optimal weight: 3.9990 chunk 301 optimal weight: 0.6980 chunk 70 optimal weight: 7.9990 chunk 237 optimal weight: 0.7980 chunk 230 optimal weight: 0.8980 chunk 109 optimal weight: 0.6980 chunk 167 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 953 GLN A 957 ASN B 330 ASN B 407 ASN B 415 ASN ** B 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 979 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.184897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.173587 restraints weight = 40588.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 80)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.169870 restraints weight = 70264.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.168699 restraints weight = 74919.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.168476 restraints weight = 73265.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.168708 restraints weight = 59454.255| |-----------------------------------------------------------------------------| r_work (final): 0.4009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6931 moved from start: 0.6194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 25431 Z= 0.155 Angle : 0.680 11.883 34683 Z= 0.363 Chirality : 0.045 0.209 3906 Planarity : 0.005 0.063 4512 Dihedral : 5.831 34.835 3486 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.37 % Favored : 92.57 % Rotamer: Outliers : 3.20 % Allowed : 15.40 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.45 (0.15), residues: 3189 helix: 1.50 (0.18), residues: 900 sheet: -0.20 (0.20), residues: 609 loop : -1.38 (0.16), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 724 TYR 0.034 0.002 TYR A 954 PHE 0.024 0.002 PHE B 385 TRP 0.042 0.002 TRP C 178 HIS 0.006 0.001 HIS B1098 Details of bonding type rmsd covalent geometry : bond 0.00354 (25374) covalent geometry : angle 0.67143 (34569) SS BOND : bond 0.00530 ( 57) SS BOND : angle 1.97320 ( 114) hydrogen bonds : bond 0.04512 ( 1104) hydrogen bonds : angle 5.42360 ( 3051) ********************** 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 392 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 304 time to evaluate : 0.859 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: 0.4996 (m-80) cc_final: 0.4511 (m-10) REVERT: A 99 GLN cc_start: 0.6258 (mm-40) cc_final: 0.5913 (mp10) REVERT: A 137 TYR cc_start: 0.7043 (OUTLIER) cc_final: 0.6548 (t80) REVERT: A 156 THR cc_start: 0.6158 (p) cc_final: 0.5813 (t) REVERT: A 164 ASP cc_start: 0.4922 (t0) cc_final: 0.4677 (t0) REVERT: A 294 CYS cc_start: 0.6494 (OUTLIER) cc_final: 0.6069 (m) REVERT: A 370 LEU cc_start: 0.8310 (tp) cc_final: 0.8081 (tt) REVERT: A 628 TYR cc_start: 0.8057 (m-80) cc_final: 0.7695 (m-80) REVERT: A 724 ARG cc_start: 0.6828 (mmt-90) cc_final: 0.6541 (mmp80) REVERT: A 971 LYS cc_start: 0.7627 (tppt) cc_final: 0.6998 (mtpt) REVERT: A 1018 ASN cc_start: 0.8770 (t0) cc_final: 0.8026 (t0) REVERT: A 1024 SER cc_start: 0.9191 (t) cc_final: 0.8629 (m) REVERT: A 1117 TYR cc_start: 0.7178 (OUTLIER) cc_final: 0.6076 (p90) REVERT: B 240 TYR cc_start: 0.5079 (OUTLIER) cc_final: 0.3444 (t80) REVERT: B 574 GLU cc_start: 0.7198 (pp20) cc_final: 0.6741 (mp0) REVERT: B 613 ASN cc_start: 0.6711 (t0) cc_final: 0.6511 (t0) REVERT: B 638 VAL cc_start: 0.8301 (OUTLIER) cc_final: 0.8100 (t) REVERT: B 734 MET cc_start: 0.2483 (mmt) cc_final: 0.1995 (mmt) REVERT: B 971 LYS cc_start: 0.7612 (tppt) cc_final: 0.6676 (mtpt) REVERT: B 1018 ASN cc_start: 0.8246 (t0) cc_final: 0.7801 (m-40) REVERT: B 1024 SER cc_start: 0.9084 (t) cc_final: 0.8628 (m) REVERT: C 137 TYR cc_start: 0.6786 (OUTLIER) cc_final: 0.5321 (t80) REVERT: C 164 ASP cc_start: 0.5275 (t0) cc_final: 0.4911 (t0) REVERT: C 178 TRP cc_start: 0.3770 (p-90) cc_final: 0.2071 (p90) REVERT: C 294 CYS cc_start: 0.5887 (OUTLIER) cc_final: 0.5639 (m) REVERT: C 352 GLN cc_start: 0.7479 (mp10) cc_final: 0.7192 (mp10) REVERT: C 370 LEU cc_start: 0.8690 (tp) cc_final: 0.8334 (tt) REVERT: C 423 THR cc_start: 0.9433 (m) cc_final: 0.8753 (p) REVERT: C 724 ARG cc_start: 0.7062 (mmm160) cc_final: 0.6537 (mmp80) REVERT: C 734 MET cc_start: 0.2663 (mmt) cc_final: 0.2093 (mmt) REVERT: C 936 MET cc_start: 0.7352 (mtt) cc_final: 0.6667 (mtt) REVERT: C 948 PHE cc_start: 0.6101 (t80) cc_final: 0.5745 (t80) REVERT: C 963 MET cc_start: 0.4546 (tpt) cc_final: 0.3277 (pmm) REVERT: C 971 LYS cc_start: 0.7734 (tppt) cc_final: 0.7214 (mttt) REVERT: C 1018 ASN cc_start: 0.8897 (t0) cc_final: 0.8138 (t0) REVERT: C 1076 ILE cc_start: 0.8664 (mt) cc_final: 0.8289 (mm) outliers start: 88 outliers final: 74 residues processed: 361 average time/residue: 0.1447 time to fit residues: 84.5282 Evaluate side-chains 370 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 289 time to evaluate : 0.892 ------------------------------------------------------------------------------- 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 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 318 VAL 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 1088 THR Chi-restraints excluded: chain A residue 1103 VAL Chi-restraints excluded: chain A residue 1117 TYR Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 217 TYR Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 240 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 330 ASN Chi-restraints excluded: chain B residue 437 THR 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 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 972 MET 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 C residue 41 THR Chi-restraints excluded: chain C residue 137 TYR Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain C residue 220 LYS Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 375 ILE 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 576 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 929 THR Chi-restraints excluded: chain C residue 937 PHE Chi-restraints excluded: chain C residue 940 TRP 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 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 241 optimal weight: 0.8980 chunk 160 optimal weight: 3.9990 chunk 7 optimal weight: 9.9990 chunk 140 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 189 optimal weight: 3.9990 chunk 252 optimal weight: 5.9990 chunk 154 optimal weight: 9.9990 chunk 224 optimal weight: 5.9990 chunk 259 optimal weight: 4.9990 chunk 119 optimal weight: 8.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- 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 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 716 HIS ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 366 GLN B 415 ASN ** B 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 538 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 591 GLN ** B 783 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1091 ASN C 415 ASN ** C 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 538 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 556 ASN ** C 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 591 GLN 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.175972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.169625 restraints weight = 40907.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.168225 restraints weight = 69556.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.167291 restraints weight = 75569.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.157331 restraints weight = 69711.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.154807 restraints weight = 66024.312| |-----------------------------------------------------------------------------| r_work (final): 0.3765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.6545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.108 25431 Z= 0.404 Angle : 0.955 13.961 34683 Z= 0.507 Chirality : 0.055 0.218 3906 Planarity : 0.006 0.069 4512 Dihedral : 6.751 36.452 3486 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 15.14 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.66 % Favored : 90.28 % Rotamer: Outliers : 3.59 % Allowed : 15.07 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.76 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.41 (0.15), residues: 3189 helix: 0.42 (0.17), residues: 909 sheet: -0.67 (0.20), residues: 606 loop : -1.85 (0.15), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 338 TYR 0.035 0.003 TYR B 306 PHE 0.036 0.004 PHE A 676 TRP 0.058 0.004 TRP A 178 HIS 0.015 0.002 HIS B1098 Details of bonding type rmsd covalent geometry : bond 0.00932 (25374) covalent geometry : angle 0.94569 (34569) SS BOND : bond 0.00823 ( 57) SS BOND : angle 2.45716 ( 114) hydrogen bonds : bond 0.06089 ( 1104) hydrogen bonds : angle 6.17346 ( 3051) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3588.56 seconds wall clock time: 63 minutes 12.90 seconds (3792.90 seconds total)