Starting phenix.real_space_refine on Mon Sep 30 08:39:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jcl_6526/09_2024/3jcl_6526.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jcl_6526/09_2024/3jcl_6526.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jcl_6526/09_2024/3jcl_6526.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jcl_6526/09_2024/3jcl_6526.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jcl_6526/09_2024/3jcl_6526.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jcl_6526/09_2024/3jcl_6526.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 144 5.16 5 C 15702 2.51 5 N 4218 2.21 5 O 4758 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 129 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 24822 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 8274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1067, 8274 Classifications: {'peptide': 1067} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 1022} Chain breaks: 1 Restraints were copied for chains: C, B Time building chain proxies: 21.89, per 1000 atoms: 0.88 Number of scatterers: 24822 At special positions: 0 Unit cell: (140.16, 137.24, 148.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 144 16.00 O 4758 8.00 N 4218 7.00 C 15702 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=19, symmetry=0 Simple disulfide: pdb=" SG CYS A 21 " - pdb=" SG CYS A 158 " distance=2.02 Simple disulfide: pdb=" SG CYS A 153 " - pdb=" SG CYS A 187 " distance=2.04 Simple disulfide: pdb=" SG CYS A 165 " - pdb=" SG CYS A 246 " distance=2.13 Simple disulfide: pdb=" SG CYS A 284 " - pdb=" SG CYS A 294 " distance=2.03 Simple disulfide: pdb=" SG CYS A 329 " - pdb=" SG CYS A 354 " distance=2.02 Simple disulfide: pdb=" SG CYS A 372 " - pdb=" SG CYS A 425 " distance=2.72 Simple disulfide: pdb=" SG CYS A 384 " - pdb=" SG CYS A 564 " distance=2.03 Simple disulfide: pdb=" SG CYS A 471 " - pdb=" SG CYS A 479 " distance=2.02 Simple disulfide: pdb=" SG CYS A 481 " - pdb=" SG CYS A 528 " distance=2.03 Simple disulfide: pdb=" SG CYS A 490 " - pdb=" SG CYS A 517 " distance=2.02 Simple disulfide: pdb=" SG CYS A 507 " - pdb=" SG CYS A 526 " distance=2.07 Simple disulfide: pdb=" SG CYS A 541 " - pdb=" SG CYS A 547 " distance=2.04 Simple disulfide: pdb=" SG CYS A 580 " - pdb=" SG CYS A 633 " distance=2.07 Simple disulfide: pdb=" SG CYS A 658 " - pdb=" SG CYS A 682 " distance=2.04 Simple disulfide: pdb=" SG CYS A 697 " - pdb=" SG CYS A 706 " distance=2.03 Simple disulfide: pdb=" SG CYS A 775 " - pdb=" SG CYS A 797 " distance=2.11 Simple disulfide: pdb=" SG CYS A 780 " - pdb=" SG CYS A 786 " distance=2.04 Simple disulfide: pdb=" SG CYS A 894 " - pdb=" SG CYS A 905 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1093 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.06 Conformation dependent library (CDL) restraints added in 3.4 seconds 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5976 Finding SS restraints... Secondary structure from input PDB file: 99 helices and 39 sheets defined 32.7% alpha, 23.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.86 Creating SS restraints... Processing helix chain 'A' and resid 43 through 47 Processing helix chain 'A' and resid 90 through 92 No H-bonds generated for 'chain 'A' and resid 90 through 92' Processing helix chain 'A' and resid 111 through 114 Processing helix chain 'A' and resid 250 through 254 Processing helix chain 'A' and resid 287 through 297 Processing helix chain 'A' and resid 330 through 336 removed outlier: 3.925A pdb=" N TRP A 334 " --> pdb=" O ASN A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 362 Processing helix chain 'A' and resid 376 through 381 Processing helix chain 'A' and resid 396 through 398 No H-bonds generated for 'chain 'A' and resid 396 through 398' Processing helix chain 'A' and resid 399 through 404 Processing helix chain 'A' and resid 466 through 471 Processing helix chain 'A' and resid 479 through 483 Processing helix chain 'A' and resid 520 through 524 Processing helix chain 'A' and resid 598 through 602 Processing helix chain 'A' and resid 657 through 664 Processing helix chain 'A' and resid 717 through 728 removed outlier: 3.724A pdb=" N THR A 721 " --> pdb=" O SER A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 734 through 751 removed outlier: 3.842A pdb=" N MET A 749 " --> pdb=" O GLY A 745 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 755 removed outlier: 4.079A pdb=" N PHE A 755 " --> pdb=" O PRO A 752 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 752 through 755' Processing helix chain 'A' and resid 774 through 780 Processing helix chain 'A' and resid 783 through 791 removed outlier: 3.777A pdb=" N GLN A 789 " --> pdb=" O ALA A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 793 through 824 removed outlier: 3.502A pdb=" N CYS A 797 " --> pdb=" O TYR A 793 " (cutoff:3.500A) Processing helix chain 'A' and resid 865 through 879 removed outlier: 4.370A pdb=" N PHE A 877 " --> pdb=" O GLU A 873 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LYS A 879 " --> pdb=" O LEU A 875 " (cutoff:3.500A) Processing helix chain 'A' and resid 883 through 894 Processing helix chain 'A' and resid 895 through 897 No H-bonds generated for 'chain 'A' and resid 895 through 897' Processing helix chain 'A' and resid 902 through 910 removed outlier: 4.672A pdb=" N SER A 908 " --> pdb=" O LEU A 904 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N PHE A 909 " --> pdb=" O CYS A 905 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASN A 910 " --> pdb=" O VAL A 906 " (cutoff:3.500A) Processing helix chain 'A' and resid 920 through 937 Processing helix chain 'A' and resid 938 through 945 Processing helix chain 'A' and resid 947 through 958 Processing helix chain 'A' and resid 968 through 988 removed outlier: 3.788A pdb=" N PHE A 988 " --> pdb=" O ILE A 984 " (cutoff:3.500A) Processing helix chain 'A' and resid 992 through 1016 removed outlier: 3.947A pdb=" N LEU A1016 " --> pdb=" O LEU A1012 " (cutoff:3.500A) Processing helix chain 'A' and resid 1017 through 1019 No H-bonds generated for 'chain 'A' and resid 1017 through 1019' Processing helix chain 'A' and resid 1026 through 1032 Processing helix chain 'A' and resid 1035 through 1083 Processing helix chain 'B' and resid 43 through 47 Processing helix chain 'B' and resid 90 through 92 No H-bonds generated for 'chain 'B' and resid 90 through 92' Processing helix chain 'B' and resid 111 through 114 Processing helix chain 'B' and resid 250 through 254 Processing helix chain 'B' and resid 287 through 297 Processing helix chain 'B' and resid 330 through 336 removed outlier: 3.925A pdb=" N TRP B 334 " --> pdb=" O ASN B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 362 Processing helix chain 'B' and resid 376 through 381 Processing helix chain 'B' and resid 396 through 398 No H-bonds generated for 'chain 'B' and resid 396 through 398' Processing helix chain 'B' and resid 399 through 404 Processing helix chain 'B' and resid 466 through 471 Processing helix chain 'B' and resid 479 through 483 Processing helix chain 'B' and resid 520 through 524 Processing helix chain 'B' and resid 598 through 602 Processing helix chain 'B' and resid 657 through 664 Processing helix chain 'B' and resid 717 through 728 removed outlier: 3.724A pdb=" N THR B 721 " --> pdb=" O SER B 717 " (cutoff:3.500A) Processing helix chain 'B' and resid 734 through 751 removed outlier: 3.842A pdb=" N MET B 749 " --> pdb=" O GLY B 745 " (cutoff:3.500A) Processing helix chain 'B' and resid 752 through 755 removed outlier: 4.079A pdb=" N PHE B 755 " --> pdb=" O PRO B 752 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 752 through 755' Processing helix chain 'B' and resid 774 through 780 Processing helix chain 'B' and resid 783 through 791 removed outlier: 3.776A pdb=" N GLN B 789 " --> pdb=" O ALA B 785 " (cutoff:3.500A) Processing helix chain 'B' and resid 793 through 824 removed outlier: 3.501A pdb=" N CYS B 797 " --> pdb=" O TYR B 793 " (cutoff:3.500A) Processing helix chain 'B' and resid 865 through 879 removed outlier: 4.369A pdb=" N PHE B 877 " --> pdb=" O GLU B 873 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LYS B 879 " --> pdb=" O LEU B 875 " (cutoff:3.500A) Processing helix chain 'B' and resid 883 through 894 Processing helix chain 'B' and resid 895 through 897 No H-bonds generated for 'chain 'B' and resid 895 through 897' Processing helix chain 'B' and resid 902 through 910 removed outlier: 4.672A pdb=" N SER B 908 " --> pdb=" O LEU B 904 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N PHE B 909 " --> pdb=" O CYS B 905 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASN B 910 " --> pdb=" O VAL B 906 " (cutoff:3.500A) Processing helix chain 'B' and resid 920 through 937 Processing helix chain 'B' and resid 938 through 945 Processing helix chain 'B' and resid 947 through 958 Processing helix chain 'B' and resid 968 through 988 removed outlier: 3.788A pdb=" N PHE B 988 " --> pdb=" O ILE B 984 " (cutoff:3.500A) Processing helix chain 'B' and resid 992 through 1016 removed outlier: 3.947A pdb=" N LEU B1016 " --> pdb=" O LEU B1012 " (cutoff:3.500A) Processing helix chain 'B' and resid 1017 through 1019 No H-bonds generated for 'chain 'B' and resid 1017 through 1019' Processing helix chain 'B' and resid 1026 through 1032 Processing helix chain 'B' and resid 1035 through 1083 Processing helix chain 'C' and resid 43 through 47 Processing helix chain 'C' and resid 90 through 92 No H-bonds generated for 'chain 'C' and resid 90 through 92' Processing helix chain 'C' and resid 111 through 114 Processing helix chain 'C' and resid 250 through 254 Processing helix chain 'C' and resid 287 through 297 Processing helix chain 'C' and resid 330 through 336 removed outlier: 3.925A pdb=" N TRP C 334 " --> pdb=" O ASN C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 362 Processing helix chain 'C' and resid 376 through 381 Processing helix chain 'C' and resid 396 through 398 No H-bonds generated for 'chain 'C' and resid 396 through 398' Processing helix chain 'C' and resid 399 through 404 Processing helix chain 'C' and resid 466 through 471 Processing helix chain 'C' and resid 479 through 483 Processing helix chain 'C' and resid 520 through 524 Processing helix chain 'C' and resid 598 through 602 Processing helix chain 'C' and resid 657 through 664 Processing helix chain 'C' and resid 717 through 728 removed outlier: 3.725A pdb=" N THR C 721 " --> pdb=" O SER C 717 " (cutoff:3.500A) Processing helix chain 'C' and resid 734 through 751 removed outlier: 3.842A pdb=" N MET C 749 " --> pdb=" O GLY C 745 " (cutoff:3.500A) Processing helix chain 'C' and resid 752 through 755 removed outlier: 4.079A pdb=" N PHE C 755 " --> pdb=" O PRO C 752 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 752 through 755' Processing helix chain 'C' and resid 774 through 780 Processing helix chain 'C' and resid 783 through 791 removed outlier: 3.777A pdb=" N GLN C 789 " --> pdb=" O ALA C 785 " (cutoff:3.500A) Processing helix chain 'C' and resid 793 through 824 removed outlier: 3.502A pdb=" N CYS C 797 " --> pdb=" O TYR C 793 " (cutoff:3.500A) Processing helix chain 'C' and resid 865 through 879 removed outlier: 4.369A pdb=" N PHE C 877 " --> pdb=" O GLU C 873 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LYS C 879 " --> pdb=" O LEU C 875 " (cutoff:3.500A) Processing helix chain 'C' and resid 883 through 894 Processing helix chain 'C' and resid 895 through 897 No H-bonds generated for 'chain 'C' and resid 895 through 897' Processing helix chain 'C' and resid 902 through 910 removed outlier: 4.671A pdb=" N SER C 908 " --> pdb=" O LEU C 904 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE C 909 " --> pdb=" O CYS C 905 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASN C 910 " --> pdb=" O VAL C 906 " (cutoff:3.500A) Processing helix chain 'C' and resid 920 through 937 Processing helix chain 'C' and resid 938 through 945 Processing helix chain 'C' and resid 947 through 958 Processing helix chain 'C' and resid 968 through 988 removed outlier: 3.788A pdb=" N PHE C 988 " --> pdb=" O ILE C 984 " (cutoff:3.500A) Processing helix chain 'C' and resid 992 through 1016 removed outlier: 3.947A pdb=" N LEU C1016 " --> pdb=" O LEU C1012 " (cutoff:3.500A) Processing helix chain 'C' and resid 1017 through 1019 No H-bonds generated for 'chain 'C' and resid 1017 through 1019' Processing helix chain 'C' and resid 1026 through 1032 Processing helix chain 'C' and resid 1035 through 1083 Processing sheet with id=A, first strand: chain 'A' and resid 26 through 28 removed outlier: 6.635A pdb=" N ASN A 26 " --> pdb=" O VAL A 87 " (cutoff:3.500A) No H-bonds generated for sheet with id=A Processing sheet with id=B, first strand: chain 'A' and resid 37 through 41 removed outlier: 5.060A pdb=" N PHE A 76 " --> pdb=" O SER A 38 " (cutoff:3.500A) removed outlier: 8.484A pdb=" N LYS A 75 " --> pdb=" O PRO A 262 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLY A 103 " --> pdb=" O LEU A 263 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N PHE A 213 " --> pdb=" O SER A 229 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N SER A 229 " --> pdb=" O PHE A 213 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ALA A 215 " --> pdb=" O LEU A 227 " (cutoff:3.500A) Processing sheet with id=C, first strand: chain 'A' and resid 61 through 70 removed outlier: 7.707A pdb=" N GLN A 267 " --> pdb=" O ASP A 283 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N ASP A 283 " --> pdb=" O GLN A 267 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N LEU A 269 " --> pdb=" O ALA A 281 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ALA A 281 " --> pdb=" O LEU A 269 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ASN A 271 " --> pdb=" O THR A 279 " (cutoff:3.500A) Processing sheet with id=D, first strand: chain 'A' and resid 82 through 83 removed outlier: 6.666A pdb=" N THR A 163 " --> pdb=" O ILE A 245 " (cutoff:3.500A) Processing sheet with id=E, first strand: chain 'A' and resid 98 through 99 removed outlier: 3.899A pdb=" N THR A 125 " --> pdb=" O LEU A 242 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N GLN A 154 " --> pdb=" O CYS A 187 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N CYS A 187 " --> pdb=" O GLN A 154 " (cutoff:3.500A) Processing sheet with id=F, first strand: chain 'A' and resid 304 through 307 removed outlier: 6.284A pdb=" N GLY A 304 " --> pdb=" O ALA A 641 " (cutoff:3.500A) Processing sheet with id=G, first strand: chain 'A' and resid 318 through 321 removed outlier: 4.188A pdb=" N THR A 627 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N ASN A 617 " --> pdb=" O ILE A 630 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N LEU A 609 " --> pdb=" O ASN A 617 " (cutoff:3.500A) Processing sheet with id=H, first strand: chain 'A' and resid 347 through 351 removed outlier: 7.138A pdb=" N THR A 430 " --> pdb=" O ALA A 367 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N ALA A 367 " --> pdb=" O THR A 430 " (cutoff:3.500A) Processing sheet with id=I, first strand: chain 'A' and resid 354 through 356 Processing sheet with id=J, first strand: chain 'A' and resid 442 through 455 removed outlier: 5.615A pdb=" N SER A 444 " --> pdb=" O VAL A 543 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N VAL A 543 " --> pdb=" O SER A 444 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG A 448 " --> pdb=" O ASP A 539 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N SER A 537 " --> pdb=" O TYR A 450 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N PHE A 452 " --> pdb=" O GLY A 535 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N GLY A 535 " --> pdb=" O PHE A 452 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ASP A 454 " --> pdb=" O PHE A 533 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N PHE A 533 " --> pdb=" O ASP A 454 " (cutoff:3.500A) Processing sheet with id=K, first strand: chain 'A' and resid 688 through 694 removed outlier: 6.294A pdb=" N LYS A 711 " --> pdb=" O THR A 690 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N GLU A 692 " --> pdb=" O LYS A 711 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N LEU A 699 " --> pdb=" O VAL A 707 " (cutoff:3.500A) Processing sheet with id=L, first strand: chain 'A' and resid 757 through 764 Processing sheet with id=M, first strand: chain 'A' and resid 770 through 773 removed outlier: 4.032A pdb=" N LYS A 770 " --> pdb=" O LEU A 915 " (cutoff:3.500A) Processing sheet with id=N, first strand: chain 'B' and resid 26 through 28 removed outlier: 6.635A pdb=" N ASN B 26 " --> pdb=" O VAL B 87 " (cutoff:3.500A) No H-bonds generated for sheet with id=N Processing sheet with id=O, first strand: chain 'B' and resid 37 through 41 removed outlier: 5.060A pdb=" N PHE B 76 " --> pdb=" O SER B 38 " (cutoff:3.500A) removed outlier: 8.484A pdb=" N LYS B 75 " --> pdb=" O PRO B 262 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLY B 103 " --> pdb=" O LEU B 263 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N PHE B 213 " --> pdb=" O SER B 229 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N SER B 229 " --> pdb=" O PHE B 213 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ALA B 215 " --> pdb=" O LEU B 227 " (cutoff:3.500A) Processing sheet with id=P, first strand: chain 'B' and resid 61 through 70 removed outlier: 7.707A pdb=" N GLN B 267 " --> pdb=" O ASP B 283 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N ASP B 283 " --> pdb=" O GLN B 267 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N LEU B 269 " --> pdb=" O ALA B 281 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ALA B 281 " --> pdb=" O LEU B 269 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ASN B 271 " --> pdb=" O THR B 279 " (cutoff:3.500A) Processing sheet with id=Q, first strand: chain 'B' and resid 82 through 83 removed outlier: 6.665A pdb=" N THR B 163 " --> pdb=" O ILE B 245 " (cutoff:3.500A) Processing sheet with id=R, first strand: chain 'B' and resid 98 through 99 removed outlier: 3.900A pdb=" N THR B 125 " --> pdb=" O LEU B 242 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N GLN B 154 " --> pdb=" O CYS B 187 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N CYS B 187 " --> pdb=" O GLN B 154 " (cutoff:3.500A) Processing sheet with id=S, first strand: chain 'B' and resid 304 through 307 removed outlier: 6.284A pdb=" N GLY B 304 " --> pdb=" O ALA B 641 " (cutoff:3.500A) Processing sheet with id=T, first strand: chain 'B' and resid 318 through 321 removed outlier: 4.188A pdb=" N THR B 627 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N ASN B 617 " --> pdb=" O ILE B 630 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N LEU B 609 " --> pdb=" O ASN B 617 " (cutoff:3.500A) Processing sheet with id=U, first strand: chain 'B' and resid 347 through 351 removed outlier: 7.138A pdb=" N THR B 430 " --> pdb=" O ALA B 367 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N ALA B 367 " --> pdb=" O THR B 430 " (cutoff:3.500A) Processing sheet with id=V, first strand: chain 'B' and resid 354 through 356 Processing sheet with id=W, first strand: chain 'B' and resid 442 through 455 removed outlier: 5.614A pdb=" N SER B 444 " --> pdb=" O VAL B 543 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N VAL B 543 " --> pdb=" O SER B 444 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG B 448 " --> pdb=" O ASP B 539 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N SER B 537 " --> pdb=" O TYR B 450 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N PHE B 452 " --> pdb=" O GLY B 535 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N GLY B 535 " --> pdb=" O PHE B 452 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ASP B 454 " --> pdb=" O PHE B 533 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N PHE B 533 " --> pdb=" O ASP B 454 " (cutoff:3.500A) Processing sheet with id=X, first strand: chain 'B' and resid 688 through 694 removed outlier: 6.296A pdb=" N LYS B 711 " --> pdb=" O THR B 690 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N GLU B 692 " --> pdb=" O LYS B 711 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N LEU B 699 " --> pdb=" O VAL B 707 " (cutoff:3.500A) Processing sheet with id=Y, first strand: chain 'B' and resid 757 through 764 Processing sheet with id=Z, first strand: chain 'B' and resid 770 through 773 removed outlier: 4.032A pdb=" N LYS B 770 " --> pdb=" O LEU B 915 " (cutoff:3.500A) Processing sheet with id=AA, first strand: chain 'C' and resid 26 through 28 removed outlier: 6.635A pdb=" N ASN C 26 " --> pdb=" O VAL C 87 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA Processing sheet with id=AB, first strand: chain 'C' and resid 37 through 41 removed outlier: 5.060A pdb=" N PHE C 76 " --> pdb=" O SER C 38 " (cutoff:3.500A) removed outlier: 8.483A pdb=" N LYS C 75 " --> pdb=" O PRO C 262 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLY C 103 " --> pdb=" O LEU C 263 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N PHE C 213 " --> pdb=" O SER C 229 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N SER C 229 " --> pdb=" O PHE C 213 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ALA C 215 " --> pdb=" O LEU C 227 " (cutoff:3.500A) Processing sheet with id=AC, first strand: chain 'C' and resid 61 through 70 removed outlier: 7.707A pdb=" N GLN C 267 " --> pdb=" O ASP C 283 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N ASP C 283 " --> pdb=" O GLN C 267 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N LEU C 269 " --> pdb=" O ALA C 281 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ALA C 281 " --> pdb=" O LEU C 269 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ASN C 271 " --> pdb=" O THR C 279 " (cutoff:3.500A) Processing sheet with id=AD, first strand: chain 'C' and resid 82 through 83 removed outlier: 6.666A pdb=" N THR C 163 " --> pdb=" O ILE C 245 " (cutoff:3.500A) Processing sheet with id=AE, first strand: chain 'C' and resid 98 through 99 removed outlier: 3.900A pdb=" N THR C 125 " --> pdb=" O LEU C 242 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N GLN C 154 " --> pdb=" O CYS C 187 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N CYS C 187 " --> pdb=" O GLN C 154 " (cutoff:3.500A) Processing sheet with id=AF, first strand: chain 'C' and resid 304 through 307 removed outlier: 6.284A pdb=" N GLY C 304 " --> pdb=" O ALA C 641 " (cutoff:3.500A) Processing sheet with id=AG, first strand: chain 'C' and resid 318 through 321 removed outlier: 4.188A pdb=" N THR C 627 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N ASN C 617 " --> pdb=" O ILE C 630 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N LEU C 609 " --> pdb=" O ASN C 617 " (cutoff:3.500A) Processing sheet with id=AH, first strand: chain 'C' and resid 347 through 351 removed outlier: 7.139A pdb=" N THR C 430 " --> pdb=" O ALA C 367 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N ALA C 367 " --> pdb=" O THR C 430 " (cutoff:3.500A) Processing sheet with id=AI, first strand: chain 'C' and resid 354 through 356 Processing sheet with id=AJ, first strand: chain 'C' and resid 442 through 455 removed outlier: 5.614A pdb=" N SER C 444 " --> pdb=" O VAL C 543 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N VAL C 543 " --> pdb=" O SER C 444 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG C 448 " --> pdb=" O ASP C 539 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N SER C 537 " --> pdb=" O TYR C 450 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N PHE C 452 " --> pdb=" O GLY C 535 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N GLY C 535 " --> pdb=" O PHE C 452 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ASP C 454 " --> pdb=" O PHE C 533 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N PHE C 533 " --> pdb=" O ASP C 454 " (cutoff:3.500A) Processing sheet with id=AK, first strand: chain 'C' and resid 688 through 694 removed outlier: 6.295A pdb=" N LYS C 711 " --> pdb=" O THR C 690 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N GLU C 692 " --> pdb=" O LYS C 711 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N LEU C 699 " --> pdb=" O VAL C 707 " (cutoff:3.500A) Processing sheet with id=AL, first strand: chain 'C' and resid 757 through 764 Processing sheet with id=AM, first strand: chain 'C' and resid 770 through 773 removed outlier: 4.032A pdb=" N LYS C 770 " --> pdb=" O LEU C 915 " (cutoff:3.500A) 1104 hydrogen bonds defined for protein. 3051 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.36 Time building geometry restraints manager: 8.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 5100 1.32 - 1.46: 8990 1.46 - 1.60: 11104 1.60 - 1.75: 27 1.75 - 1.89: 153 Bond restraints: 25374 Sorted by residual: bond pdb=" CB PHE A 270 " pdb=" CG PHE A 270 " ideal model delta sigma weight residual 1.502 1.365 0.137 2.30e-02 1.89e+03 3.56e+01 bond pdb=" CB PHE C 270 " pdb=" CG PHE C 270 " ideal model delta sigma weight residual 1.502 1.365 0.137 2.30e-02 1.89e+03 3.56e+01 bond pdb=" CB PHE B 270 " pdb=" CG PHE B 270 " ideal model delta sigma weight residual 1.502 1.366 0.136 2.30e-02 1.89e+03 3.49e+01 bond pdb=" CB LEU A 300 " pdb=" CG LEU A 300 " ideal model delta sigma weight residual 1.530 1.426 0.104 2.00e-02 2.50e+03 2.69e+01 bond pdb=" CB LEU B 300 " pdb=" CG LEU B 300 " ideal model delta sigma weight residual 1.530 1.427 0.103 2.00e-02 2.50e+03 2.67e+01 ... (remaining 25369 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.43: 32298 3.43 - 6.86: 2034 6.86 - 10.29: 210 10.29 - 13.73: 24 13.73 - 17.16: 3 Bond angle restraints: 34569 Sorted by residual: angle pdb=" N VAL A 946 " pdb=" CA VAL A 946 " pdb=" CB VAL A 946 " ideal model delta sigma weight residual 110.17 98.69 11.48 1.11e+00 8.12e-01 1.07e+02 angle pdb=" C ALA A 944 " pdb=" CA ALA A 944 " pdb=" CB ALA A 944 " ideal model delta sigma weight residual 110.79 93.63 17.16 1.66e+00 3.63e-01 1.07e+02 angle pdb=" N VAL C 946 " pdb=" CA VAL C 946 " pdb=" CB VAL C 946 " ideal model delta sigma weight residual 110.17 98.72 11.45 1.11e+00 8.12e-01 1.06e+02 angle pdb=" N VAL B 946 " pdb=" CA VAL B 946 " pdb=" CB VAL B 946 " ideal model delta sigma weight residual 110.17 98.72 11.45 1.11e+00 8.12e-01 1.06e+02 angle pdb=" C ALA C 944 " pdb=" CA ALA C 944 " pdb=" CB ALA C 944 " ideal model delta sigma weight residual 110.79 93.69 17.10 1.66e+00 3.63e-01 1.06e+02 ... (remaining 34564 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.10: 14597 18.10 - 36.19: 331 36.19 - 54.29: 58 54.29 - 72.39: 58 72.39 - 90.48: 10 Dihedral angle restraints: 15054 sinusoidal: 5712 harmonic: 9342 Sorted by residual: dihedral pdb=" CB CYS A 329 " pdb=" SG CYS A 329 " pdb=" SG CYS A 354 " pdb=" CB CYS A 354 " ideal model delta sinusoidal sigma weight residual -86.00 -176.48 90.48 1 1.00e+01 1.00e-02 9.68e+01 dihedral pdb=" C ALA A 944 " pdb=" N ALA A 944 " pdb=" CA ALA A 944 " pdb=" CB ALA A 944 " ideal model delta harmonic sigma weight residual -122.60 -103.48 -19.12 0 2.50e+00 1.60e-01 5.85e+01 dihedral pdb=" C ALA B 944 " pdb=" N ALA B 944 " pdb=" CA ALA B 944 " pdb=" CB ALA B 944 " ideal model delta harmonic sigma weight residual -122.60 -103.53 -19.07 0 2.50e+00 1.60e-01 5.82e+01 ... (remaining 15051 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 2752 0.095 - 0.191: 984 0.191 - 0.286: 149 0.286 - 0.381: 12 0.381 - 0.476: 9 Chirality restraints: 3906 Sorted by residual: chirality pdb=" CA TRP A 536 " pdb=" N TRP A 536 " pdb=" C TRP A 536 " pdb=" CB TRP A 536 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.68e+00 chirality pdb=" CA TRP B 536 " pdb=" N TRP B 536 " pdb=" C TRP B 536 " pdb=" CB TRP B 536 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.65e+00 chirality pdb=" CA TRP C 536 " pdb=" N TRP C 536 " pdb=" C TRP C 536 " pdb=" CB TRP C 536 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.61e+00 ... (remaining 3903 not shown) Planarity restraints: 4512 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE C 751 " 0.065 5.00e-02 4.00e+02 1.01e-01 1.64e+01 pdb=" N PRO C 752 " -0.175 5.00e-02 4.00e+02 pdb=" CA PRO C 752 " 0.057 5.00e-02 4.00e+02 pdb=" CD PRO C 752 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 751 " -0.065 5.00e-02 4.00e+02 1.01e-01 1.63e+01 pdb=" N PRO A 752 " 0.175 5.00e-02 4.00e+02 pdb=" CA PRO A 752 " -0.057 5.00e-02 4.00e+02 pdb=" CD PRO A 752 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 751 " -0.065 5.00e-02 4.00e+02 1.01e-01 1.63e+01 pdb=" N PRO B 752 " 0.175 5.00e-02 4.00e+02 pdb=" CA PRO B 752 " -0.057 5.00e-02 4.00e+02 pdb=" CD PRO B 752 " -0.053 5.00e-02 4.00e+02 ... (remaining 4509 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 228 2.60 - 3.17: 23220 3.17 - 3.75: 38183 3.75 - 4.32: 57463 4.32 - 4.90: 89260 Nonbonded interactions: 208354 Sorted by model distance: nonbonded pdb=" SG CYS B 490 " pdb=" SG CYS B 517 " model vdw 2.019 3.760 nonbonded pdb=" SG CYS C 490 " pdb=" SG CYS C 517 " model vdw 2.021 3.760 nonbonded pdb=" SG CYS C 21 " pdb=" SG CYS C 158 " model vdw 2.023 3.760 nonbonded pdb=" SG CYS C 329 " pdb=" SG CYS C 354 " model vdw 2.023 3.760 nonbonded pdb=" SG CYS B 21 " pdb=" SG CYS B 158 " model vdw 2.023 3.760 ... (remaining 208349 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 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: 1.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.980 Check model and map are aligned: 0.190 Set scattering table: 0.240 Process input model: 67.230 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.018 0.150 25374 Z= 1.161 Angle : 1.834 17.156 34569 Z= 1.244 Chirality : 0.094 0.476 3906 Planarity : 0.010 0.101 4512 Dihedral : 9.753 89.544 9021 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.56 % Allowed : 5.17 % Favored : 94.26 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.30 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.14), residues: 3189 helix: 0.12 (0.17), residues: 843 sheet: 0.11 (0.21), residues: 567 loop : -0.95 (0.14), residues: 1779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.007 TRP B 536 HIS 0.007 0.002 HIS A1098 PHE 0.044 0.007 PHE C 123 TYR 0.042 0.009 TYR A 58 ARG 0.007 0.001 ARG A 397 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 801 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 801 time to evaluate : 2.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 384 CYS cc_start: 0.5014 (t) cc_final: 0.4740 (t) REVERT: A 416 TYR cc_start: 0.8273 (t80) cc_final: 0.7810 (t80) REVERT: A 447 ASN cc_start: 0.7086 (t0) cc_final: 0.6477 (t0) REVERT: A 633 CYS cc_start: 0.5191 (m) cc_final: 0.4826 (m) REVERT: A 928 THR cc_start: 0.9312 (p) cc_final: 0.9008 (t) REVERT: A 1018 ASN cc_start: 0.8806 (t0) cc_final: 0.8406 (t0) REVERT: A 1024 SER cc_start: 0.9360 (t) cc_final: 0.9092 (m) REVERT: B 220 LYS cc_start: 0.8360 (mttt) cc_final: 0.8094 (ttpp) REVERT: B 240 TYR cc_start: 0.4986 (t80) cc_final: 0.4634 (t80) REVERT: B 361 LEU cc_start: 0.8735 (mt) cc_final: 0.8527 (tt) REVERT: B 446 TRP cc_start: 0.3453 (t-100) cc_final: 0.0718 (t-100) REVERT: B 447 ASN cc_start: 0.7123 (t0) cc_final: 0.6884 (t0) REVERT: B 485 ASP cc_start: 0.5412 (m-30) cc_final: 0.5173 (m-30) REVERT: B 633 CYS cc_start: 0.4594 (m) cc_final: 0.4105 (m) REVERT: B 928 THR cc_start: 0.9112 (p) cc_final: 0.8771 (t) REVERT: B 971 LYS cc_start: 0.7659 (mttp) cc_final: 0.7456 (tppt) REVERT: B 1018 ASN cc_start: 0.8877 (t0) cc_final: 0.8157 (m-40) REVERT: B 1024 SER cc_start: 0.9295 (t) cc_final: 0.9061 (m) REVERT: C 99 GLN cc_start: 0.5904 (mm-40) cc_final: 0.5460 (mp10) REVERT: C 136 SER cc_start: 0.6653 (t) cc_final: 0.6431 (p) REVERT: C 162 TYR cc_start: 0.5141 (p90) cc_final: 0.4872 (p90) REVERT: C 287 SER cc_start: 0.8510 (p) cc_final: 0.8016 (m) REVERT: C 299 MET cc_start: 0.7622 (mmp) cc_final: 0.7319 (mmm) REVERT: C 361 LEU cc_start: 0.8659 (mt) cc_final: 0.8386 (tt) REVERT: C 423 THR cc_start: 0.8936 (m) cc_final: 0.8593 (p) REVERT: C 446 TRP cc_start: 0.3087 (t-100) cc_final: 0.0311 (t-100) REVERT: C 613 ASN cc_start: 0.7647 (m-40) cc_final: 0.7299 (m-40) REVERT: C 698 ASP cc_start: 0.7379 (t0) cc_final: 0.7032 (t0) REVERT: C 928 THR cc_start: 0.9264 (p) cc_final: 0.9026 (t) REVERT: C 1018 ASN cc_start: 0.9123 (t0) cc_final: 0.8313 (m-40) REVERT: C 1076 ILE cc_start: 0.8907 (mt) cc_final: 0.8587 (mm) REVERT: C 1099 ILE cc_start: 0.8530 (mm) cc_final: 0.8283 (mm) outliers start: 0 outliers final: 0 residues processed: 801 average time/residue: 0.3732 time to fit residues: 453.7554 Evaluate side-chains 394 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 394 time to evaluate : 2.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 268 optimal weight: 3.9990 chunk 241 optimal weight: 0.8980 chunk 133 optimal weight: 0.9980 chunk 82 optimal weight: 0.6980 chunk 162 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 249 optimal weight: 0.7980 chunk 96 optimal weight: 0.5980 chunk 151 optimal weight: 2.9990 chunk 185 optimal weight: 0.6980 chunk 288 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 168 ASN A 407 ASN A 415 ASN ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 441 HIS A 502 ASN A 613 ASN A 759 HIS ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 957 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1061 GLN ** A1086 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 168 ASN B 415 ASN B 441 HIS B 502 ASN B 606 GLN B 613 ASN B 759 HIS ** B 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 957 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1011 ASN ** B1086 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 GLN C 168 ASN C 415 ASN ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 441 HIS C 502 ASN ** C 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 999 GLN C1061 GLN ** C1086 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.3308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 25374 Z= 0.273 Angle : 0.783 9.661 34569 Z= 0.435 Chirality : 0.048 0.209 3906 Planarity : 0.006 0.063 4512 Dihedral : 6.258 37.165 3486 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.58 % Favored : 94.39 % Rotamer: Outliers : 2.76 % Allowed : 7.26 % Favored : 89.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.15), residues: 3189 helix: 1.16 (0.18), residues: 885 sheet: 0.51 (0.22), residues: 528 loop : -1.02 (0.14), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 346 HIS 0.009 0.002 HIS C1098 PHE 0.038 0.002 PHE B 500 TYR 0.043 0.002 TYR A 954 ARG 0.006 0.001 ARG B 867 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 439 time to evaluate : 3.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LEU cc_start: 0.6574 (tp) cc_final: 0.6323 (tp) REVERT: A 156 THR cc_start: 0.6697 (p) cc_final: 0.6294 (t) REVERT: A 203 TYR cc_start: 0.6382 (m-80) cc_final: 0.6156 (m-10) REVERT: A 294 CYS cc_start: 0.7429 (OUTLIER) cc_final: 0.7069 (m) REVERT: A 314 GLN cc_start: 0.6990 (mm110) cc_final: 0.6707 (mm110) REVERT: A 353 ASN cc_start: 0.8450 (m-40) cc_final: 0.7691 (p0) REVERT: A 416 TYR cc_start: 0.7985 (t80) cc_final: 0.7672 (t80) REVERT: A 751 ILE cc_start: 0.6034 (mm) cc_final: 0.5739 (pt) REVERT: A 898 GLN cc_start: 0.6568 (mm-40) cc_final: 0.6117 (mp10) REVERT: A 954 TYR cc_start: 0.7318 (m-80) cc_final: 0.6657 (m-80) REVERT: A 957 ASN cc_start: 0.7922 (m110) cc_final: 0.7420 (p0) REVERT: A 963 MET cc_start: 0.6034 (pmm) cc_final: 0.5765 (tpt) REVERT: B 240 TYR cc_start: 0.5321 (t80) cc_final: 0.4788 (t80) REVERT: B 299 MET cc_start: 0.7501 (mmp) cc_final: 0.7272 (mmt) REVERT: B 364 TYR cc_start: 0.5941 (m-10) cc_final: 0.5643 (m-10) REVERT: B 423 THR cc_start: 0.9217 (m) cc_final: 0.8800 (p) REVERT: B 446 TRP cc_start: 0.2945 (t-100) cc_final: 0.0353 (t-100) REVERT: B 797 CYS cc_start: 0.8807 (m) cc_final: 0.7870 (t) REVERT: B 963 MET cc_start: 0.5846 (pmm) cc_final: 0.5485 (tpt) REVERT: B 971 LYS cc_start: 0.7833 (mttp) cc_final: 0.7346 (tppt) REVERT: C 69 TYR cc_start: 0.8865 (m-80) cc_final: 0.8175 (m-80) REVERT: C 99 GLN cc_start: 0.5886 (mm-40) cc_final: 0.5306 (mp10) REVERT: C 149 MET cc_start: 0.7306 (mmt) cc_final: 0.6846 (mmt) REVERT: C 191 ARG cc_start: 0.6377 (ttm-80) cc_final: 0.5788 (tmm-80) REVERT: C 287 SER cc_start: 0.8701 (p) cc_final: 0.8326 (m) REVERT: C 299 MET cc_start: 0.7467 (mmp) cc_final: 0.7129 (mmm) REVERT: C 353 ASN cc_start: 0.8054 (m-40) cc_final: 0.7073 (p0) REVERT: C 416 TYR cc_start: 0.8445 (t80) cc_final: 0.8001 (t80) REVERT: C 734 MET cc_start: -0.0723 (mmt) cc_final: -0.1034 (mmt) REVERT: C 751 ILE cc_start: 0.5040 (mm) cc_final: 0.4830 (pt) REVERT: C 883 SER cc_start: 0.8416 (OUTLIER) cc_final: 0.7998 (p) REVERT: C 1029 GLU cc_start: 0.8234 (tt0) cc_final: 0.7889 (tt0) REVERT: C 1076 ILE cc_start: 0.8768 (mt) cc_final: 0.8300 (mm) REVERT: C 1092 PHE cc_start: 0.6147 (t80) cc_final: 0.5829 (t80) outliers start: 76 outliers final: 46 residues processed: 488 average time/residue: 0.3412 time to fit residues: 266.2969 Evaluate side-chains 387 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 339 time to evaluate : 2.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 217 TYR Chi-restraints excluded: chain A residue 220 LYS Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 284 CYS Chi-restraints excluded: chain A residue 294 CYS Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 632 SER Chi-restraints excluded: chain A residue 635 SER Chi-restraints excluded: chain A residue 716 HIS Chi-restraints excluded: chain A residue 867 ARG Chi-restraints excluded: chain A residue 1005 ASN Chi-restraints excluded: chain A residue 1067 LEU Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 217 TYR Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 284 CYS Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 671 ASN Chi-restraints excluded: chain B residue 867 ARG Chi-restraints excluded: chain B residue 929 THR Chi-restraints excluded: chain B residue 940 TRP Chi-restraints excluded: chain B residue 1064 ASP Chi-restraints excluded: chain B residue 1088 THR Chi-restraints excluded: chain B residue 1092 PHE Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain C residue 220 LYS Chi-restraints excluded: chain C residue 284 CYS Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 627 THR Chi-restraints excluded: chain C residue 635 SER Chi-restraints excluded: chain C residue 671 ASN Chi-restraints excluded: chain C residue 716 HIS Chi-restraints excluded: chain C residue 747 TYR Chi-restraints excluded: chain C residue 883 SER Chi-restraints excluded: chain C residue 940 TRP Chi-restraints excluded: chain C residue 1046 LEU Chi-restraints excluded: chain C residue 1088 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 160 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 240 optimal weight: 0.0970 chunk 196 optimal weight: 3.9990 chunk 79 optimal weight: 0.9990 chunk 289 optimal weight: 0.0000 chunk 312 optimal weight: 0.9990 chunk 257 optimal weight: 10.0000 chunk 286 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 232 optimal weight: 5.9990 overall best weight: 0.6186 ------------------------------------------------------------------------------- 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 696 ASN ** 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 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 817 GLN B 957 ASN B1018 ASN B1061 GLN B1080 ASN ** B1086 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 415 ASN ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 506 HIS ** C 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 999 GLN C1018 ASN C1080 ASN ** C1086 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.4047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 25374 Z= 0.213 Angle : 0.665 9.090 34569 Z= 0.367 Chirality : 0.045 0.258 3906 Planarity : 0.005 0.056 4512 Dihedral : 6.029 37.366 3486 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 2.72 % Allowed : 9.95 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.15), residues: 3189 helix: 1.37 (0.18), residues: 894 sheet: 0.34 (0.22), residues: 540 loop : -1.08 (0.15), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 178 HIS 0.006 0.001 HIS B1098 PHE 0.028 0.002 PHE B 500 TYR 0.028 0.002 TYR A 954 ARG 0.005 0.001 ARG A 383 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 376 time to evaluate : 2.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 THR cc_start: 0.6535 (p) cc_final: 0.5931 (t) REVERT: A 203 TYR cc_start: 0.6598 (m-80) cc_final: 0.6260 (m-10) REVERT: A 353 ASN cc_start: 0.8546 (m-40) cc_final: 0.7858 (p0) REVERT: A 404 GLN cc_start: 0.5376 (OUTLIER) cc_final: 0.4371 (tm130) REVERT: A 416 TYR cc_start: 0.7990 (t80) cc_final: 0.7696 (t80) REVERT: A 447 ASN cc_start: 0.7707 (t0) cc_final: 0.7498 (t0) REVERT: A 749 MET cc_start: 0.5564 (mmt) cc_final: 0.5292 (mmm) REVERT: A 751 ILE cc_start: 0.6105 (mm) cc_final: 0.5773 (tt) REVERT: A 950 LEU cc_start: 0.7310 (tp) cc_final: 0.7046 (tp) REVERT: A 954 TYR cc_start: 0.7396 (m-80) cc_final: 0.6700 (m-80) REVERT: A 1018 ASN cc_start: 0.8811 (t0) cc_final: 0.8049 (t0) REVERT: B 41 THR cc_start: 0.7571 (p) cc_final: 0.7286 (t) REVERT: B 92 PHE cc_start: 0.6396 (m-80) cc_final: 0.5417 (m-10) REVERT: B 191 ARG cc_start: 0.7696 (ttm170) cc_final: 0.7333 (ttm-80) REVERT: B 240 TYR cc_start: 0.5568 (t80) cc_final: 0.4734 (t80) REVERT: B 299 MET cc_start: 0.7532 (mmp) cc_final: 0.7287 (mmt) REVERT: B 364 TYR cc_start: 0.5933 (m-10) cc_final: 0.5695 (m-10) REVERT: B 416 TYR cc_start: 0.8175 (t80) cc_final: 0.7875 (t80) REVERT: B 446 TRP cc_start: 0.3619 (t-100) cc_final: 0.1235 (t-100) REVERT: B 613 ASN cc_start: 0.6807 (t0) cc_final: 0.6029 (t0) REVERT: B 797 CYS cc_start: 0.8911 (m) cc_final: 0.8114 (t) REVERT: B 883 SER cc_start: 0.8525 (OUTLIER) cc_final: 0.8321 (m) REVERT: B 957 ASN cc_start: 0.8285 (OUTLIER) cc_final: 0.8072 (p0) REVERT: B 963 MET cc_start: 0.5735 (pmm) cc_final: 0.5492 (tpt) REVERT: B 971 LYS cc_start: 0.7713 (mttp) cc_final: 0.7342 (tppt) REVERT: C 69 TYR cc_start: 0.8832 (m-80) cc_final: 0.7702 (m-80) REVERT: C 99 GLN cc_start: 0.5996 (mm-40) cc_final: 0.5519 (mp10) REVERT: C 149 MET cc_start: 0.6760 (mmt) cc_final: 0.6339 (mmt) REVERT: C 287 SER cc_start: 0.8787 (p) cc_final: 0.8511 (m) REVERT: C 299 MET cc_start: 0.7422 (mmp) cc_final: 0.7209 (mmm) REVERT: C 376 ASP cc_start: 0.7294 (t0) cc_final: 0.6783 (t0) REVERT: C 416 TYR cc_start: 0.8402 (t80) cc_final: 0.8018 (t80) REVERT: C 423 THR cc_start: 0.9327 (m) cc_final: 0.8625 (p) REVERT: C 517 CYS cc_start: 0.0286 (OUTLIER) cc_final: -0.1433 (p) REVERT: C 963 MET cc_start: 0.6284 (tpt) cc_final: 0.4715 (pmm) REVERT: C 1076 ILE cc_start: 0.8635 (mt) cc_final: 0.8213 (mm) REVERT: C 1092 PHE cc_start: 0.6310 (t80) cc_final: 0.6022 (t80) outliers start: 75 outliers final: 53 residues processed: 425 average time/residue: 0.3441 time to fit residues: 235.5737 Evaluate side-chains 363 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 306 time to evaluate : 2.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 TYR Chi-restraints excluded: chain A residue 220 LYS Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 404 GLN Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 635 SER Chi-restraints excluded: chain A residue 716 HIS Chi-restraints excluded: chain A residue 867 ARG Chi-restraints excluded: chain A residue 940 TRP Chi-restraints excluded: chain A residue 1005 ASN Chi-restraints excluded: chain A residue 1046 LEU Chi-restraints excluded: chain A residue 1064 ASP Chi-restraints excluded: chain A residue 1088 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 217 TYR Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 284 CYS Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 405 LEU 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 867 ARG Chi-restraints excluded: chain B residue 883 SER Chi-restraints excluded: chain B residue 894 CYS Chi-restraints excluded: chain B residue 929 THR Chi-restraints excluded: chain B residue 940 TRP Chi-restraints excluded: chain B residue 957 ASN Chi-restraints excluded: chain B residue 1064 ASP Chi-restraints excluded: chain B residue 1088 THR Chi-restraints excluded: chain B residue 1092 PHE Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain C residue 220 LYS Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 284 CYS Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 479 CYS Chi-restraints excluded: chain C residue 517 CYS Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 627 THR Chi-restraints excluded: chain C residue 671 ASN Chi-restraints excluded: chain C residue 716 HIS Chi-restraints excluded: chain C residue 766 THR Chi-restraints excluded: chain C residue 782 ASP Chi-restraints excluded: chain C residue 929 THR Chi-restraints excluded: chain C residue 940 TRP Chi-restraints excluded: chain C residue 1046 LEU Chi-restraints excluded: chain C residue 1088 THR Chi-restraints excluded: chain C residue 1103 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 285 optimal weight: 0.9980 chunk 217 optimal weight: 1.9990 chunk 150 optimal weight: 10.0000 chunk 32 optimal weight: 4.9990 chunk 138 optimal weight: 0.1980 chunk 194 optimal weight: 4.9990 chunk 290 optimal weight: 0.9980 chunk 307 optimal weight: 1.9990 chunk 151 optimal weight: 9.9990 chunk 275 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 366 GLN A 404 GLN ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 716 HIS ** A 783 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 985 GLN ** B 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 415 ASN ** B 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 ASN B 985 GLN ** B1086 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 ASN C 415 ASN C 442 ASN C 716 HIS ** C 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 ASN C1080 ASN ** C1086 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.4596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 25374 Z= 0.289 Angle : 0.689 10.593 34569 Z= 0.373 Chirality : 0.046 0.190 3906 Planarity : 0.005 0.060 4512 Dihedral : 6.057 37.047 3486 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 3.74 % Allowed : 10.06 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.15), residues: 3189 helix: 1.37 (0.18), residues: 897 sheet: 0.14 (0.21), residues: 561 loop : -1.25 (0.15), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 178 HIS 0.009 0.002 HIS B1098 PHE 0.027 0.002 PHE C 948 TYR 0.021 0.002 TYR A 450 ARG 0.006 0.001 ARG A 399 *********************** 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 450 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 347 time to evaluate : 2.498 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 149 MET cc_start: 0.4571 (OUTLIER) cc_final: 0.4232 (mtt) REVERT: A 156 THR cc_start: 0.6644 (p) cc_final: 0.6094 (t) REVERT: A 191 ARG cc_start: 0.7783 (ttm170) cc_final: 0.7446 (ttp-110) REVERT: A 294 CYS cc_start: 0.7320 (OUTLIER) cc_final: 0.7033 (m) REVERT: A 353 ASN cc_start: 0.8575 (m-40) cc_final: 0.7830 (p0) REVERT: A 416 TYR cc_start: 0.8203 (t80) cc_final: 0.7755 (t80) REVERT: A 749 MET cc_start: 0.5245 (mmt) cc_final: 0.5024 (mmm) REVERT: A 914 VAL cc_start: 0.9125 (OUTLIER) cc_final: 0.8675 (p) REVERT: A 950 LEU cc_start: 0.7446 (tp) cc_final: 0.7001 (tp) REVERT: A 954 TYR cc_start: 0.7536 (m-80) cc_final: 0.6815 (m-80) REVERT: A 963 MET cc_start: 0.5467 (tpt) cc_final: 0.3827 (pmm) REVERT: A 1018 ASN cc_start: 0.8926 (t0) cc_final: 0.8144 (t0) REVERT: B 41 THR cc_start: 0.7585 (p) cc_final: 0.7313 (t) REVERT: B 149 MET cc_start: 0.6336 (mmt) cc_final: 0.5610 (mmt) REVERT: B 191 ARG cc_start: 0.7745 (ttm170) cc_final: 0.7268 (ttm-80) REVERT: B 240 TYR cc_start: 0.5539 (t80) cc_final: 0.5079 (t80) REVERT: B 353 ASN cc_start: 0.7969 (m-40) cc_final: 0.7105 (p0) REVERT: B 416 TYR cc_start: 0.8219 (t80) cc_final: 0.7956 (t80) REVERT: B 517 CYS cc_start: 0.0286 (OUTLIER) cc_final: -0.0881 (p) REVERT: B 638 VAL cc_start: 0.8343 (OUTLIER) cc_final: 0.8034 (t) REVERT: B 899 GLU cc_start: 0.7319 (tp30) cc_final: 0.7083 (tp30) REVERT: B 971 LYS cc_start: 0.7915 (mttp) cc_final: 0.7427 (tppt) REVERT: C 99 GLN cc_start: 0.6043 (mm-40) cc_final: 0.5265 (mp10) REVERT: C 299 MET cc_start: 0.7591 (mmp) cc_final: 0.7327 (mmm) REVERT: C 353 ASN cc_start: 0.8144 (m-40) cc_final: 0.7800 (t0) REVERT: C 370 LEU cc_start: 0.8915 (tp) cc_final: 0.8654 (tt) REVERT: C 416 TYR cc_start: 0.8413 (t80) cc_final: 0.7997 (t80) REVERT: C 423 THR cc_start: 0.9436 (m) cc_final: 0.8809 (p) REVERT: C 898 GLN cc_start: 0.7262 (OUTLIER) cc_final: 0.7053 (mp10) REVERT: C 963 MET cc_start: 0.6467 (tpt) cc_final: 0.4699 (pmm) REVERT: C 1018 ASN cc_start: 0.8931 (t0) cc_final: 0.8210 (t0) REVERT: C 1076 ILE cc_start: 0.8644 (mt) cc_final: 0.8340 (mm) REVERT: C 1092 PHE cc_start: 0.6194 (t80) cc_final: 0.5676 (t80) outliers start: 103 outliers final: 67 residues processed: 420 average time/residue: 0.3486 time to fit residues: 234.4399 Evaluate side-chains 379 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 306 time to evaluate : 2.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 217 TYR Chi-restraints excluded: chain A residue 220 LYS Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 294 CYS Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 635 SER Chi-restraints excluded: chain A residue 716 HIS Chi-restraints excluded: chain A residue 867 ARG Chi-restraints excluded: chain A residue 914 VAL 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 148 ILE Chi-restraints excluded: chain B residue 217 TYR Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 284 CYS Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 375 ILE Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 517 CYS Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 638 VAL Chi-restraints excluded: chain B residue 671 ASN Chi-restraints excluded: chain B residue 818 VAL Chi-restraints excluded: chain B residue 867 ARG Chi-restraints excluded: chain B residue 894 CYS Chi-restraints excluded: chain B residue 929 THR Chi-restraints excluded: chain B residue 940 TRP Chi-restraints excluded: chain B residue 957 ASN Chi-restraints excluded: chain B residue 1064 ASP Chi-restraints excluded: chain B residue 1088 THR Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 136 SER Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain C residue 220 LYS Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 284 CYS Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 375 ILE Chi-restraints excluded: chain C residue 385 PHE Chi-restraints excluded: chain C residue 479 CYS Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 627 THR Chi-restraints excluded: chain C residue 633 CYS 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 782 ASP Chi-restraints excluded: chain C residue 898 GLN Chi-restraints excluded: chain C residue 929 THR Chi-restraints excluded: chain C residue 940 TRP Chi-restraints excluded: chain C residue 1046 LEU Chi-restraints excluded: chain C residue 1087 THR Chi-restraints excluded: chain C residue 1088 THR 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 255 optimal weight: 6.9990 chunk 174 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 chunk 228 optimal weight: 10.0000 chunk 126 optimal weight: 6.9990 chunk 262 optimal weight: 10.0000 chunk 212 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 156 optimal weight: 5.9990 chunk 275 optimal weight: 0.7980 chunk 77 optimal weight: 0.3980 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 591 GLN ** A 783 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 415 ASN ** B 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 ASN ** B1086 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1097 ASN C 415 ASN C 556 ASN ** C 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 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** C 985 GLN C1080 ASN ** C1086 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.5059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 25374 Z= 0.367 Angle : 0.732 9.589 34569 Z= 0.394 Chirality : 0.047 0.199 3906 Planarity : 0.005 0.064 4512 Dihedral : 6.142 37.010 3486 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.71 % Favored : 92.25 % Rotamer: Outliers : 4.18 % Allowed : 10.86 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.15), residues: 3189 helix: 0.95 (0.18), residues: 906 sheet: 0.06 (0.21), residues: 567 loop : -1.40 (0.15), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 940 HIS 0.010 0.002 HIS B1098 PHE 0.028 0.002 PHE B 371 TYR 0.027 0.002 TYR A 429 ARG 0.006 0.001 ARG A 546 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 326 time to evaluate : 2.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 ARG cc_start: 0.7700 (ttm170) cc_final: 0.7124 (ttm170) REVERT: A 294 CYS cc_start: 0.7293 (OUTLIER) cc_final: 0.6961 (m) REVERT: A 353 ASN cc_start: 0.8509 (m-40) cc_final: 0.7389 (p0) REVERT: A 416 TYR cc_start: 0.8213 (t80) cc_final: 0.7888 (t80) REVERT: A 950 LEU cc_start: 0.7316 (tp) cc_final: 0.6659 (tp) REVERT: A 954 TYR cc_start: 0.7881 (m-80) cc_final: 0.7149 (m-80) REVERT: A 963 MET cc_start: 0.5688 (tpt) cc_final: 0.3678 (pmm) REVERT: B 149 MET cc_start: 0.5791 (mmt) cc_final: 0.5576 (mmt) REVERT: B 191 ARG cc_start: 0.7436 (ttm170) cc_final: 0.7110 (ttm170) REVERT: B 240 TYR cc_start: 0.5483 (t80) cc_final: 0.5133 (t80) REVERT: B 353 ASN cc_start: 0.8129 (m-40) cc_final: 0.7198 (p0) REVERT: B 517 CYS cc_start: 0.0669 (OUTLIER) cc_final: -0.0711 (p) REVERT: B 613 ASN cc_start: 0.7186 (t0) cc_final: 0.6551 (t0) REVERT: B 638 VAL cc_start: 0.8514 (OUTLIER) cc_final: 0.8239 (t) REVERT: B 892 ASN cc_start: 0.8177 (OUTLIER) cc_final: 0.7445 (t0) REVERT: B 971 LYS cc_start: 0.7540 (mttp) cc_final: 0.7103 (tppt) REVERT: B 998 ILE cc_start: 0.9416 (mt) cc_final: 0.9149 (tt) REVERT: C 99 GLN cc_start: 0.6152 (mm-40) cc_final: 0.5389 (mp10) REVERT: C 299 MET cc_start: 0.7817 (mmp) cc_final: 0.7426 (mmm) REVERT: C 370 LEU cc_start: 0.8899 (tp) cc_final: 0.8580 (tt) REVERT: C 416 TYR cc_start: 0.8446 (t80) cc_final: 0.7978 (t80) REVERT: C 423 THR cc_start: 0.9469 (m) cc_final: 0.8868 (p) REVERT: C 517 CYS cc_start: -0.0141 (OUTLIER) cc_final: -0.1085 (p) REVERT: C 898 GLN cc_start: 0.7631 (OUTLIER) cc_final: 0.7235 (mp10) REVERT: C 963 MET cc_start: 0.6299 (tpt) cc_final: 0.4302 (pmm) REVERT: C 1018 ASN cc_start: 0.9130 (t0) cc_final: 0.8381 (t0) REVERT: C 1076 ILE cc_start: 0.8632 (mt) cc_final: 0.8322 (mm) REVERT: C 1091 ASN cc_start: 0.8165 (m-40) cc_final: 0.7939 (t0) outliers start: 115 outliers final: 79 residues processed: 413 average time/residue: 0.3344 time to fit residues: 222.2904 Evaluate side-chains 374 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 289 time to evaluate : 2.788 ------------------------------------------------------------------------------- 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 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 344 LEU Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 534 ILE 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 676 PHE Chi-restraints excluded: chain A residue 747 TYR Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain A residue 867 ARG Chi-restraints excluded: chain A residue 914 VAL Chi-restraints excluded: chain A residue 1005 ASN Chi-restraints excluded: chain A residue 1046 LEU Chi-restraints excluded: chain A residue 1064 ASP Chi-restraints excluded: chain A residue 1067 LEU Chi-restraints excluded: chain A residue 1088 THR Chi-restraints excluded: chain A residue 1090 ILE Chi-restraints excluded: chain A residue 1103 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 217 TYR Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 284 CYS Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 375 ILE Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 471 CYS Chi-restraints excluded: chain B residue 517 CYS Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 638 VAL Chi-restraints excluded: chain B residue 671 ASN 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 892 ASN Chi-restraints excluded: chain B residue 894 CYS Chi-restraints excluded: chain B residue 929 THR Chi-restraints excluded: chain B residue 940 TRP Chi-restraints excluded: chain B residue 1064 ASP Chi-restraints excluded: chain B residue 1088 THR Chi-restraints excluded: chain B residue 1090 ILE Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 136 SER Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain C residue 220 LYS Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 284 CYS Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 375 ILE Chi-restraints excluded: chain C residue 385 PHE Chi-restraints excluded: chain C residue 471 CYS Chi-restraints excluded: chain C residue 479 CYS Chi-restraints excluded: chain C residue 517 CYS Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 607 THR Chi-restraints excluded: chain C residue 627 THR Chi-restraints excluded: chain C residue 633 CYS Chi-restraints excluded: chain C residue 635 SER Chi-restraints excluded: chain C residue 671 ASN Chi-restraints excluded: chain C residue 766 THR Chi-restraints excluded: chain C residue 782 ASP Chi-restraints excluded: chain C residue 898 GLN Chi-restraints excluded: chain C residue 929 THR Chi-restraints excluded: chain C residue 940 TRP Chi-restraints excluded: chain C residue 1005 ASN Chi-restraints excluded: chain C residue 1013 LEU 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 1087 THR Chi-restraints excluded: chain C residue 1088 THR 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 103 optimal weight: 0.9980 chunk 276 optimal weight: 0.0270 chunk 60 optimal weight: 1.9990 chunk 180 optimal weight: 0.6980 chunk 75 optimal weight: 0.8980 chunk 307 optimal weight: 0.9980 chunk 255 optimal weight: 5.9990 chunk 142 optimal weight: 0.0670 chunk 25 optimal weight: 2.9990 chunk 101 optimal weight: 0.9980 chunk 161 optimal weight: 7.9990 overall best weight: 0.5376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 366 GLN ** A 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 696 ASN ** A 783 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 957 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 366 GLN B 415 ASN ** B 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 979 ASN B1018 ASN ** B1086 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 415 ASN ** C 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 957 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1080 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.5292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25374 Z= 0.193 Angle : 0.624 9.312 34569 Z= 0.337 Chirality : 0.043 0.182 3906 Planarity : 0.005 0.059 4512 Dihedral : 5.850 36.094 3486 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 3.05 % Allowed : 12.56 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.76 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.15), residues: 3189 helix: 1.36 (0.18), residues: 912 sheet: 0.11 (0.20), residues: 594 loop : -1.35 (0.15), residues: 1683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 536 HIS 0.006 0.001 HIS C 716 PHE 0.035 0.002 PHE C 948 TYR 0.024 0.002 TYR C 137 ARG 0.003 0.000 ARG A 399 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 348 time to evaluate : 2.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 PHE cc_start: 0.6456 (m-80) cc_final: 0.6000 (m-10) REVERT: A 137 TYR cc_start: 0.7473 (OUTLIER) cc_final: 0.5837 (t80) REVERT: A 191 ARG cc_start: 0.7705 (ttm170) cc_final: 0.7252 (ttm170) REVERT: A 294 CYS cc_start: 0.7190 (OUTLIER) cc_final: 0.6868 (m) REVERT: A 353 ASN cc_start: 0.8107 (m-40) cc_final: 0.7892 (m-40) REVERT: A 366 GLN cc_start: 0.7591 (OUTLIER) cc_final: 0.6775 (tp40) REVERT: A 370 LEU cc_start: 0.8469 (tp) cc_final: 0.8165 (tt) REVERT: A 416 TYR cc_start: 0.8166 (t80) cc_final: 0.7912 (t80) REVERT: A 574 GLU cc_start: 0.7770 (pp20) cc_final: 0.7088 (mp0) REVERT: A 950 LEU cc_start: 0.7505 (tp) cc_final: 0.6847 (tp) REVERT: A 954 TYR cc_start: 0.7952 (m-80) cc_final: 0.7270 (m-80) REVERT: A 963 MET cc_start: 0.5531 (tpt) cc_final: 0.3443 (pmm) REVERT: A 1018 ASN cc_start: 0.8730 (t0) cc_final: 0.8061 (t0) REVERT: A 1117 TYR cc_start: 0.8066 (OUTLIER) cc_final: 0.7167 (p90) REVERT: B 191 ARG cc_start: 0.7267 (ttm170) cc_final: 0.6867 (ttm170) REVERT: B 240 TYR cc_start: 0.5443 (t80) cc_final: 0.5142 (t80) REVERT: B 366 GLN cc_start: 0.7957 (OUTLIER) cc_final: 0.7737 (mp10) REVERT: B 517 CYS cc_start: 0.0635 (OUTLIER) cc_final: -0.0804 (p) REVERT: B 734 MET cc_start: -0.2638 (mmt) cc_final: -0.3181 (mmt) REVERT: B 905 CYS cc_start: 0.9184 (t) cc_final: 0.8869 (t) REVERT: B 998 ILE cc_start: 0.9378 (mt) cc_final: 0.9084 (tt) REVERT: B 1014 ASN cc_start: 0.8992 (t0) cc_final: 0.8698 (t0) REVERT: B 1018 ASN cc_start: 0.8828 (t0) cc_final: 0.8361 (t0) REVERT: C 99 GLN cc_start: 0.6150 (mm-40) cc_final: 0.5467 (mp10) REVERT: C 137 TYR cc_start: 0.7706 (OUTLIER) cc_final: 0.6267 (t80) REVERT: C 299 MET cc_start: 0.7513 (mmp) cc_final: 0.7308 (mmm) REVERT: C 330 ASN cc_start: 0.6775 (p0) cc_final: 0.6568 (t0) REVERT: C 334 TRP cc_start: 0.7794 (t60) cc_final: 0.7494 (t60) REVERT: C 370 LEU cc_start: 0.8941 (tp) cc_final: 0.8638 (tt) REVERT: C 416 TYR cc_start: 0.8420 (t80) cc_final: 0.8015 (t80) REVERT: C 423 THR cc_start: 0.9432 (m) cc_final: 0.8857 (p) REVERT: C 517 CYS cc_start: -0.0007 (OUTLIER) cc_final: -0.0827 (p) REVERT: C 898 GLN cc_start: 0.7585 (OUTLIER) cc_final: 0.7135 (mp10) REVERT: C 905 CYS cc_start: 0.9149 (t) cc_final: 0.8785 (t) REVERT: C 936 MET cc_start: 0.7423 (mtt) cc_final: 0.7184 (mtt) REVERT: C 963 MET cc_start: 0.5938 (tpt) cc_final: 0.4033 (pmm) REVERT: C 1018 ASN cc_start: 0.8831 (t0) cc_final: 0.7932 (t0) REVERT: C 1076 ILE cc_start: 0.8649 (mt) cc_final: 0.8313 (mm) REVERT: C 1091 ASN cc_start: 0.8152 (m-40) cc_final: 0.7884 (t0) outliers start: 84 outliers final: 58 residues processed: 409 average time/residue: 0.3515 time to fit residues: 231.4513 Evaluate side-chains 371 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 304 time to evaluate : 2.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 366 GLN Chi-restraints excluded: chain A residue 568 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 747 TYR Chi-restraints excluded: chain A residue 867 ARG Chi-restraints excluded: chain A residue 1005 ASN Chi-restraints excluded: chain A residue 1014 ASN Chi-restraints excluded: chain A residue 1046 LEU Chi-restraints excluded: chain A residue 1064 ASP Chi-restraints excluded: chain A residue 1067 LEU Chi-restraints excluded: chain A residue 1117 TYR Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 98 ASN Chi-restraints excluded: chain B residue 217 TYR Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 284 CYS Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 366 GLN Chi-restraints excluded: chain B residue 375 ILE Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 471 CYS Chi-restraints excluded: chain B residue 517 CYS Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 671 ASN Chi-restraints excluded: chain B residue 867 ARG Chi-restraints excluded: chain B residue 894 CYS 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 C residue 41 THR Chi-restraints excluded: chain C residue 137 TYR Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain C residue 220 LYS Chi-restraints excluded: chain C residue 284 CYS Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 375 ILE Chi-restraints excluded: chain C residue 385 PHE Chi-restraints excluded: chain C residue 427 LEU Chi-restraints excluded: chain C residue 471 CYS Chi-restraints excluded: chain C residue 479 CYS Chi-restraints excluded: chain C residue 517 CYS Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 633 CYS 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 716 HIS Chi-restraints excluded: chain C residue 766 THR Chi-restraints excluded: chain C residue 866 ILE Chi-restraints excluded: chain C residue 898 GLN Chi-restraints excluded: chain C residue 940 TRP Chi-restraints excluded: chain C residue 1046 LEU Chi-restraints excluded: chain C residue 1088 THR Chi-restraints excluded: chain C residue 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 296 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 175 optimal weight: 2.9990 chunk 224 optimal weight: 6.9990 chunk 174 optimal weight: 1.9990 chunk 259 optimal weight: 7.9990 chunk 171 optimal weight: 1.9990 chunk 306 optimal weight: 4.9990 chunk 191 optimal weight: 1.9990 chunk 186 optimal weight: 2.9990 chunk 141 optimal weight: 5.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 502 ASN ** A 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 957 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 366 GLN B 415 ASN ** B 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 957 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1086 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 345 ASN C 415 ASN C 556 ASN ** C 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 957 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1080 ASN ** C1086 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1091 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.5727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 25374 Z= 0.467 Angle : 0.812 12.349 34569 Z= 0.435 Chirality : 0.050 0.320 3906 Planarity : 0.006 0.061 4512 Dihedral : 6.349 36.062 3486 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.47 % Favored : 91.53 % Rotamer: Outliers : 3.89 % Allowed : 12.75 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.76 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.15), residues: 3189 helix: 0.83 (0.18), residues: 900 sheet: -0.31 (0.20), residues: 603 loop : -1.64 (0.15), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP A 940 HIS 0.011 0.002 HIS B1098 PHE 0.039 0.003 PHE A 676 TYR 0.030 0.003 TYR B 306 ARG 0.009 0.001 ARG A 363 *********************** 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 fitting. rotamer outliers: 107 poor density : 314 time to evaluate : 2.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 GLN cc_start: 0.6766 (mm-40) cc_final: 0.6059 (mp10) REVERT: A 137 TYR cc_start: 0.8139 (OUTLIER) cc_final: 0.6975 (t80) REVERT: A 191 ARG cc_start: 0.7546 (ttm170) cc_final: 0.7041 (ttm170) REVERT: A 294 CYS cc_start: 0.7478 (OUTLIER) cc_final: 0.7136 (m) REVERT: A 320 TYR cc_start: 0.8581 (t80) cc_final: 0.8247 (t80) REVERT: A 574 GLU cc_start: 0.7971 (pp20) cc_final: 0.7167 (mp0) REVERT: A 877 PHE cc_start: 0.8388 (m-80) cc_final: 0.8170 (m-80) REVERT: A 950 LEU cc_start: 0.7654 (tp) cc_final: 0.6901 (tp) REVERT: A 954 TYR cc_start: 0.7872 (m-80) cc_final: 0.7272 (m-80) REVERT: A 963 MET cc_start: 0.5882 (tpt) cc_final: 0.3645 (pmm) REVERT: A 1117 TYR cc_start: 0.8170 (OUTLIER) cc_final: 0.7410 (p90) REVERT: B 149 MET cc_start: 0.6438 (mtt) cc_final: 0.6213 (mtt) REVERT: B 191 ARG cc_start: 0.7416 (ttm170) cc_final: 0.6847 (ttm170) REVERT: B 240 TYR cc_start: 0.5550 (t80) cc_final: 0.5256 (t80) REVERT: B 366 GLN cc_start: 0.7303 (OUTLIER) cc_final: 0.6731 (mm110) REVERT: B 517 CYS cc_start: 0.0103 (OUTLIER) cc_final: -0.1309 (p) REVERT: B 574 GLU cc_start: 0.8001 (pp20) cc_final: 0.7090 (mp0) REVERT: B 613 ASN cc_start: 0.7682 (t0) cc_final: 0.7321 (t0) REVERT: B 734 MET cc_start: -0.2580 (mmt) cc_final: -0.2994 (mmt) REVERT: B 892 ASN cc_start: 0.8216 (OUTLIER) cc_final: 0.7664 (t0) REVERT: B 998 ILE cc_start: 0.9464 (mt) cc_final: 0.9182 (tt) REVERT: B 1018 ASN cc_start: 0.8993 (t0) cc_final: 0.8436 (t0) REVERT: C 48 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.7680 (mp) REVERT: C 137 TYR cc_start: 0.7925 (OUTLIER) cc_final: 0.7057 (t80) REVERT: C 338 ARG cc_start: 0.5542 (ttt-90) cc_final: 0.4916 (ttp80) REVERT: C 370 LEU cc_start: 0.8949 (tp) cc_final: 0.8671 (tt) REVERT: C 423 THR cc_start: 0.9440 (m) cc_final: 0.8883 (p) REVERT: C 450 TYR cc_start: 0.7604 (p90) cc_final: 0.7329 (p90) REVERT: C 517 CYS cc_start: -0.0416 (OUTLIER) cc_final: -0.1688 (m) REVERT: C 898 GLN cc_start: 0.7979 (OUTLIER) cc_final: 0.7572 (mp10) REVERT: C 936 MET cc_start: 0.7592 (mtt) cc_final: 0.7250 (mtt) REVERT: C 1076 ILE cc_start: 0.8709 (mt) cc_final: 0.8385 (mm) REVERT: C 1091 ASN cc_start: 0.8080 (m110) cc_final: 0.7851 (t0) outliers start: 107 outliers final: 74 residues processed: 389 average time/residue: 0.3305 time to fit residues: 207.5510 Evaluate side-chains 363 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 279 time to evaluate : 2.573 ------------------------------------------------------------------------------- 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 217 TYR Chi-restraints excluded: chain A residue 220 LYS Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 294 CYS Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 391 ASP Chi-restraints excluded: chain A residue 426 GLN Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 485 ASP 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 694 LEU 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 1087 THR Chi-restraints excluded: chain A residue 1088 THR Chi-restraints excluded: chain A residue 1103 VAL Chi-restraints excluded: chain A residue 1117 TYR Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 217 TYR Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 284 CYS Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 366 GLN Chi-restraints excluded: chain B residue 375 ILE Chi-restraints excluded: chain B residue 471 CYS Chi-restraints excluded: chain B residue 517 CYS Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 671 ASN Chi-restraints excluded: chain B residue 867 ARG Chi-restraints excluded: chain B residue 892 ASN Chi-restraints excluded: chain B residue 912 ILE Chi-restraints excluded: chain B residue 929 THR Chi-restraints excluded: chain B residue 937 PHE Chi-restraints excluded: chain B residue 940 TRP Chi-restraints excluded: chain B residue 1064 ASP Chi-restraints excluded: chain B residue 1088 THR Chi-restraints excluded: chain B residue 1090 ILE Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 137 TYR Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain C residue 220 LYS Chi-restraints excluded: chain C residue 284 CYS Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 375 ILE Chi-restraints excluded: chain C residue 427 LEU Chi-restraints excluded: chain C residue 471 CYS Chi-restraints excluded: chain C residue 479 CYS Chi-restraints excluded: chain C residue 517 CYS Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 575 VAL Chi-restraints excluded: chain C residue 627 THR Chi-restraints excluded: chain C residue 633 CYS Chi-restraints excluded: chain C residue 635 SER Chi-restraints excluded: chain C residue 671 ASN Chi-restraints excluded: chain C residue 677 ASP Chi-restraints excluded: chain C residue 766 THR Chi-restraints excluded: chain C residue 898 GLN 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 189 optimal weight: 0.9980 chunk 122 optimal weight: 6.9990 chunk 183 optimal weight: 0.7980 chunk 92 optimal weight: 7.9990 chunk 60 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 194 optimal weight: 3.9990 chunk 208 optimal weight: 0.6980 chunk 151 optimal weight: 6.9990 chunk 28 optimal weight: 3.9990 chunk 240 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 GLN ** A 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 957 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 366 GLN B 415 ASN ** B 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 ASN B 979 ASN ** B1086 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.5887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 25374 Z= 0.221 Angle : 0.656 9.443 34569 Z= 0.353 Chirality : 0.045 0.210 3906 Planarity : 0.005 0.062 4512 Dihedral : 6.006 35.085 3486 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.77 % Favored : 93.20 % Rotamer: Outliers : 3.16 % Allowed : 14.45 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 1.52 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.15), residues: 3189 helix: 1.24 (0.18), residues: 909 sheet: -0.30 (0.20), residues: 600 loop : -1.54 (0.15), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 334 HIS 0.006 0.001 HIS C1098 PHE 0.029 0.002 PHE C 550 TYR 0.022 0.002 TYR C 240 ARG 0.004 0.001 ARG A 399 *********************** 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 fitting. rotamer outliers: 87 poor density : 318 time to evaluate : 2.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 GLN cc_start: 0.6570 (mm-40) cc_final: 0.6087 (mp10) REVERT: A 137 TYR cc_start: 0.7865 (OUTLIER) cc_final: 0.7083 (t80) REVERT: A 191 ARG cc_start: 0.7503 (ttm170) cc_final: 0.7009 (ttm170) REVERT: A 294 CYS cc_start: 0.7432 (OUTLIER) cc_final: 0.7037 (m) REVERT: A 313 VAL cc_start: 0.8570 (t) cc_final: 0.8368 (p) REVERT: A 574 GLU cc_start: 0.7956 (pp20) cc_final: 0.7169 (mp0) REVERT: A 889 GLU cc_start: 0.5999 (tp30) cc_final: 0.5717 (tp30) REVERT: A 950 LEU cc_start: 0.7578 (tp) cc_final: 0.6728 (tp) REVERT: A 954 TYR cc_start: 0.7939 (m-80) cc_final: 0.7201 (m-80) REVERT: A 963 MET cc_start: 0.5678 (tpt) cc_final: 0.3437 (pmm) REVERT: A 1018 ASN cc_start: 0.8810 (t0) cc_final: 0.8127 (t0) REVERT: A 1117 TYR cc_start: 0.8089 (OUTLIER) cc_final: 0.7207 (p90) REVERT: B 191 ARG cc_start: 0.7438 (ttm170) cc_final: 0.6890 (ttm170) REVERT: B 240 TYR cc_start: 0.5547 (t80) cc_final: 0.5230 (t80) REVERT: B 366 GLN cc_start: 0.7518 (OUTLIER) cc_final: 0.6666 (mm110) REVERT: B 517 CYS cc_start: 0.0132 (OUTLIER) cc_final: -0.1279 (p) REVERT: B 613 ASN cc_start: 0.7403 (t0) cc_final: 0.7051 (t0) REVERT: B 957 ASN cc_start: 0.8431 (OUTLIER) cc_final: 0.7774 (m-40) REVERT: B 1018 ASN cc_start: 0.8792 (t0) cc_final: 0.8317 (t0) REVERT: B 1117 TYR cc_start: 0.7751 (OUTLIER) cc_final: 0.7176 (p90) REVERT: C 48 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.7693 (mp) REVERT: C 99 GLN cc_start: 0.6294 (mm-40) cc_final: 0.5790 (mp10) REVERT: C 137 TYR cc_start: 0.7895 (OUTLIER) cc_final: 0.6894 (t80) REVERT: C 156 THR cc_start: 0.7369 (p) cc_final: 0.6932 (t) REVERT: C 191 ARG cc_start: 0.6958 (ptm160) cc_final: 0.6568 (ptm160) REVERT: C 322 ARG cc_start: 0.6872 (ptm-80) cc_final: 0.6419 (ptm-80) REVERT: C 334 TRP cc_start: 0.7814 (t60) cc_final: 0.7485 (t60) REVERT: C 338 ARG cc_start: 0.5487 (ttt-90) cc_final: 0.4884 (ttp80) REVERT: C 370 LEU cc_start: 0.8767 (tp) cc_final: 0.8411 (tt) REVERT: C 423 THR cc_start: 0.9434 (m) cc_final: 0.8826 (p) REVERT: C 517 CYS cc_start: -0.0037 (OUTLIER) cc_final: -0.0821 (p) REVERT: C 734 MET cc_start: -0.2706 (mmt) cc_final: -0.2910 (mmt) REVERT: C 898 GLN cc_start: 0.7902 (OUTLIER) cc_final: 0.7501 (mp10) REVERT: C 936 MET cc_start: 0.7485 (mtt) cc_final: 0.7241 (mtt) REVERT: C 950 LEU cc_start: 0.7908 (tp) cc_final: 0.7532 (tp) REVERT: C 1018 ASN cc_start: 0.9005 (t0) cc_final: 0.8122 (t0) REVERT: C 1091 ASN cc_start: 0.8018 (m110) cc_final: 0.7795 (t0) outliers start: 87 outliers final: 66 residues processed: 375 average time/residue: 0.3373 time to fit residues: 202.8037 Evaluate side-chains 379 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 302 time to evaluate : 2.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 120 THR 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 385 PHE Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 479 CYS Chi-restraints excluded: chain A residue 534 ILE Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 747 TYR Chi-restraints excluded: chain A residue 867 ARG Chi-restraints excluded: chain A residue 912 ILE Chi-restraints excluded: chain A residue 937 PHE 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 1117 TYR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 98 ASN Chi-restraints excluded: chain B residue 217 TYR Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 284 CYS Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 366 GLN Chi-restraints excluded: chain B residue 375 ILE Chi-restraints excluded: chain B residue 391 ASP Chi-restraints excluded: chain B residue 471 CYS Chi-restraints excluded: chain B residue 517 CYS 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 671 ASN Chi-restraints excluded: chain B residue 867 ARG Chi-restraints excluded: chain B residue 912 ILE Chi-restraints excluded: chain B residue 937 PHE Chi-restraints excluded: chain B residue 940 TRP Chi-restraints excluded: chain B residue 957 ASN Chi-restraints excluded: chain B residue 972 MET Chi-restraints excluded: chain B residue 1064 ASP Chi-restraints excluded: chain B residue 1117 TYR Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 137 TYR Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain C residue 220 LYS Chi-restraints excluded: chain C residue 284 CYS Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 375 ILE Chi-restraints excluded: chain C residue 385 PHE Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 471 CYS Chi-restraints excluded: chain C residue 479 CYS Chi-restraints excluded: chain C residue 517 CYS Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 607 THR Chi-restraints excluded: chain C residue 627 THR Chi-restraints excluded: chain C residue 633 CYS Chi-restraints excluded: chain C residue 671 ASN Chi-restraints excluded: chain C residue 677 ASP Chi-restraints excluded: chain C residue 766 THR Chi-restraints excluded: chain C residue 898 GLN 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 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 278 optimal weight: 0.9980 chunk 293 optimal weight: 5.9990 chunk 267 optimal weight: 0.9980 chunk 285 optimal weight: 2.9990 chunk 171 optimal weight: 4.9990 chunk 124 optimal weight: 5.9990 chunk 224 optimal weight: 7.9990 chunk 87 optimal weight: 0.8980 chunk 258 optimal weight: 4.9990 chunk 270 optimal weight: 0.9990 chunk 284 optimal weight: 3.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 GLN ** A 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 957 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 366 GLN B 415 ASN ** B 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 957 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1086 GLN ** 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.6081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 25374 Z= 0.301 Angle : 0.703 12.144 34569 Z= 0.375 Chirality : 0.046 0.192 3906 Planarity : 0.005 0.063 4512 Dihedral : 6.046 34.630 3486 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.40 % Favored : 91.53 % Rotamer: Outliers : 3.41 % Allowed : 14.67 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 1.52 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.15), residues: 3189 helix: 1.18 (0.18), residues: 912 sheet: -0.39 (0.20), residues: 603 loop : -1.58 (0.15), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP A 334 HIS 0.009 0.002 HIS B1098 PHE 0.029 0.002 PHE B 371 TYR 0.023 0.002 TYR A 450 ARG 0.008 0.001 ARG B 955 *********************** 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 400 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 306 time to evaluate : 2.643 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 99 GLN cc_start: 0.6633 (mm-40) cc_final: 0.6213 (mp10) REVERT: A 137 TYR cc_start: 0.8037 (OUTLIER) cc_final: 0.6944 (t80) REVERT: A 156 THR cc_start: 0.6952 (p) cc_final: 0.6630 (t) REVERT: A 191 ARG cc_start: 0.7465 (ttm170) cc_final: 0.6992 (ttm170) REVERT: A 294 CYS cc_start: 0.7418 (OUTLIER) cc_final: 0.7039 (m) REVERT: A 574 GLU cc_start: 0.7678 (pp20) cc_final: 0.7009 (mp0) REVERT: A 724 ARG cc_start: 0.7336 (mmt-90) cc_final: 0.6886 (mmp80) REVERT: A 889 GLU cc_start: 0.6007 (tp30) cc_final: 0.5704 (tp30) REVERT: A 950 LEU cc_start: 0.7609 (tp) cc_final: 0.6721 (tp) REVERT: A 954 TYR cc_start: 0.7882 (m-80) cc_final: 0.7486 (m-80) REVERT: A 963 MET cc_start: 0.5767 (tpt) cc_final: 0.3441 (pmm) REVERT: A 1018 ASN cc_start: 0.8979 (t0) cc_final: 0.8224 (t0) REVERT: A 1117 TYR cc_start: 0.8109 (OUTLIER) cc_final: 0.7218 (p90) REVERT: B 92 PHE cc_start: 0.6610 (m-80) cc_final: 0.5489 (m-10) REVERT: B 191 ARG cc_start: 0.7363 (ttm170) cc_final: 0.6815 (ttm170) REVERT: B 240 TYR cc_start: 0.5462 (t80) cc_final: 0.4685 (t80) REVERT: B 416 TYR cc_start: 0.8332 (t80) cc_final: 0.8103 (t80) REVERT: B 517 CYS cc_start: 0.0146 (OUTLIER) cc_final: -0.1299 (p) REVERT: B 613 ASN cc_start: 0.7531 (t0) cc_final: 0.7185 (t0) REVERT: B 998 ILE cc_start: 0.9394 (mt) cc_final: 0.9142 (tt) REVERT: B 1018 ASN cc_start: 0.8845 (t0) cc_final: 0.8412 (t0) REVERT: B 1117 TYR cc_start: 0.7803 (OUTLIER) cc_final: 0.7144 (p90) REVERT: C 48 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.7673 (mp) REVERT: C 99 GLN cc_start: 0.6447 (mm-40) cc_final: 0.5924 (mp10) REVERT: C 137 TYR cc_start: 0.8009 (OUTLIER) cc_final: 0.6937 (t80) REVERT: C 156 THR cc_start: 0.7185 (p) cc_final: 0.6763 (t) REVERT: C 338 ARG cc_start: 0.5525 (ttt-90) cc_final: 0.4947 (ttp80) REVERT: C 370 LEU cc_start: 0.8762 (tp) cc_final: 0.8391 (tt) REVERT: C 423 THR cc_start: 0.9434 (m) cc_final: 0.8805 (p) REVERT: C 517 CYS cc_start: -0.0514 (OUTLIER) cc_final: -0.1353 (p) REVERT: C 898 GLN cc_start: 0.8064 (OUTLIER) cc_final: 0.7602 (mp10) REVERT: C 936 MET cc_start: 0.7539 (mtt) cc_final: 0.7244 (mtt) REVERT: C 950 LEU cc_start: 0.7697 (tp) cc_final: 0.7203 (tp) REVERT: C 1076 ILE cc_start: 0.8987 (mt) cc_final: 0.8540 (mm) REVERT: C 1091 ASN cc_start: 0.8179 (m110) cc_final: 0.7843 (t0) outliers start: 94 outliers final: 76 residues processed: 368 average time/residue: 0.3357 time to fit residues: 200.2842 Evaluate side-chains 376 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 291 time to evaluate : 2.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 137 TYR Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 217 TYR Chi-restraints excluded: chain A residue 220 LYS Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 294 CYS Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 479 CYS Chi-restraints excluded: chain A residue 534 ILE Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 747 TYR Chi-restraints excluded: chain A residue 867 ARG Chi-restraints excluded: chain A residue 912 ILE Chi-restraints excluded: chain A residue 1005 ASN Chi-restraints excluded: chain A residue 1064 ASP Chi-restraints excluded: chain A residue 1066 THR 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 98 ASN Chi-restraints excluded: chain B residue 217 TYR Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 284 CYS Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 375 ILE Chi-restraints excluded: chain B residue 391 ASP Chi-restraints excluded: chain B residue 471 CYS Chi-restraints excluded: chain B residue 517 CYS 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 671 ASN Chi-restraints excluded: chain B residue 818 VAL Chi-restraints excluded: chain B residue 867 ARG Chi-restraints excluded: chain B residue 912 ILE Chi-restraints excluded: chain B residue 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 1103 VAL Chi-restraints excluded: chain B residue 1117 TYR Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 137 TYR Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain C residue 220 LYS Chi-restraints excluded: chain C residue 284 CYS Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 375 ILE Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 471 CYS Chi-restraints excluded: chain C residue 479 CYS Chi-restraints excluded: chain C residue 517 CYS Chi-restraints excluded: chain C residue 568 LEU 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 633 CYS Chi-restraints excluded: chain C residue 671 ASN Chi-restraints excluded: chain C residue 677 ASP Chi-restraints excluded: chain C residue 716 HIS Chi-restraints excluded: chain C residue 766 THR Chi-restraints excluded: chain C residue 898 GLN Chi-restraints excluded: chain C residue 929 THR Chi-restraints excluded: chain C residue 940 TRP Chi-restraints excluded: chain C residue 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 187 optimal weight: 1.9990 chunk 302 optimal weight: 5.9990 chunk 184 optimal weight: 0.7980 chunk 143 optimal weight: 0.8980 chunk 209 optimal weight: 0.9980 chunk 316 optimal weight: 5.9990 chunk 291 optimal weight: 0.5980 chunk 252 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 194 optimal weight: 0.9990 chunk 154 optimal weight: 30.0000 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 ASN A 415 ASN ** A 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 923 GLN ** A 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 957 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 415 ASN B 442 ASN ** B 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 957 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1086 GLN ** 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** C1005 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.6216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25374 Z= 0.221 Angle : 0.651 10.291 34569 Z= 0.349 Chirality : 0.044 0.194 3906 Planarity : 0.005 0.062 4512 Dihedral : 5.872 33.944 3486 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.77 % Favored : 93.16 % Rotamer: Outliers : 3.09 % Allowed : 15.18 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.76 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.15), residues: 3189 helix: 1.33 (0.18), residues: 918 sheet: -0.38 (0.19), residues: 621 loop : -1.52 (0.16), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.003 TRP B 446 HIS 0.006 0.001 HIS C1098 PHE 0.029 0.002 PHE B 371 TYR 0.023 0.002 TYR A 450 ARG 0.005 0.000 ARG C 546 ********************** 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 401 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 316 time to evaluate : 2.683 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 99 GLN cc_start: 0.6452 (mm-40) cc_final: 0.6207 (mp10) REVERT: A 137 TYR cc_start: 0.7972 (OUTLIER) cc_final: 0.6966 (t80) REVERT: A 144 TYR cc_start: 0.6164 (t80) cc_final: 0.5874 (t80) REVERT: A 156 THR cc_start: 0.6918 (p) cc_final: 0.6632 (t) REVERT: A 294 CYS cc_start: 0.7385 (OUTLIER) cc_final: 0.7004 (m) REVERT: A 370 LEU cc_start: 0.8246 (tp) cc_final: 0.8029 (tt) REVERT: A 574 GLU cc_start: 0.7633 (pp20) cc_final: 0.7022 (mp0) REVERT: A 889 GLU cc_start: 0.6004 (tp30) cc_final: 0.5719 (tp30) REVERT: A 950 LEU cc_start: 0.7558 (tp) cc_final: 0.7335 (tp) REVERT: A 963 MET cc_start: 0.5813 (tpt) cc_final: 0.3875 (pmm) REVERT: A 971 LYS cc_start: 0.7624 (tppt) cc_final: 0.6585 (mttt) REVERT: A 1018 ASN cc_start: 0.8729 (t0) cc_final: 0.7901 (t0) REVERT: A 1117 TYR cc_start: 0.8044 (OUTLIER) cc_final: 0.7046 (p90) REVERT: B 92 PHE cc_start: 0.6688 (m-80) cc_final: 0.5564 (m-10) REVERT: B 240 TYR cc_start: 0.5467 (t80) cc_final: 0.4726 (t80) REVERT: B 334 TRP cc_start: 0.7610 (t60) cc_final: 0.7206 (t60) REVERT: B 416 TYR cc_start: 0.8323 (t80) cc_final: 0.8041 (t80) REVERT: B 517 CYS cc_start: 0.0168 (OUTLIER) cc_final: -0.1300 (p) REVERT: B 613 ASN cc_start: 0.7535 (t0) cc_final: 0.7196 (t0) REVERT: B 664 ASN cc_start: 0.7792 (m-40) cc_final: 0.7535 (t0) REVERT: B 998 ILE cc_start: 0.9366 (mt) cc_final: 0.9141 (tt) REVERT: B 1018 ASN cc_start: 0.8786 (t0) cc_final: 0.8316 (t0) REVERT: B 1117 TYR cc_start: 0.7803 (OUTLIER) cc_final: 0.7239 (p90) REVERT: C 48 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.7630 (mp) REVERT: C 99 GLN cc_start: 0.6474 (mm-40) cc_final: 0.6136 (mp10) REVERT: C 137 TYR cc_start: 0.8003 (OUTLIER) cc_final: 0.6989 (t80) REVERT: C 156 THR cc_start: 0.7443 (p) cc_final: 0.7012 (t) REVERT: C 178 TRP cc_start: 0.5271 (p-90) cc_final: 0.2936 (p90) REVERT: C 191 ARG cc_start: 0.7144 (ptm160) cc_final: 0.6570 (ptm160) REVERT: C 334 TRP cc_start: 0.7798 (t60) cc_final: 0.7365 (t60) REVERT: C 338 ARG cc_start: 0.5559 (ttt-90) cc_final: 0.4937 (ttp80) REVERT: C 370 LEU cc_start: 0.8642 (tp) cc_final: 0.8358 (tt) REVERT: C 423 THR cc_start: 0.9428 (m) cc_final: 0.8796 (p) REVERT: C 517 CYS cc_start: -0.0270 (OUTLIER) cc_final: -0.1087 (p) REVERT: C 898 GLN cc_start: 0.7904 (OUTLIER) cc_final: 0.7130 (mp10) REVERT: C 936 MET cc_start: 0.7459 (mtt) cc_final: 0.7256 (mtt) REVERT: C 950 LEU cc_start: 0.7732 (tp) cc_final: 0.7315 (tp) REVERT: C 971 LYS cc_start: 0.8155 (tppt) cc_final: 0.7013 (mtpt) REVERT: C 1018 ASN cc_start: 0.9019 (t0) cc_final: 0.8110 (t0) REVERT: C 1076 ILE cc_start: 0.8932 (mt) cc_final: 0.8487 (mm) REVERT: C 1091 ASN cc_start: 0.8143 (m110) cc_final: 0.7834 (t0) outliers start: 85 outliers final: 74 residues processed: 369 average time/residue: 0.3331 time to fit residues: 200.0732 Evaluate side-chains 380 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 297 time to evaluate : 2.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 137 TYR Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 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 437 THR Chi-restraints excluded: chain A residue 479 CYS Chi-restraints excluded: chain A residue 534 ILE Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 747 TYR Chi-restraints excluded: chain A residue 867 ARG Chi-restraints excluded: chain A residue 904 LEU 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 98 ASN Chi-restraints excluded: chain B residue 217 TYR Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 284 CYS Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 330 ASN Chi-restraints excluded: chain B residue 375 ILE Chi-restraints excluded: chain B residue 391 ASP Chi-restraints excluded: chain B residue 471 CYS Chi-restraints excluded: chain B residue 517 CYS Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 671 ASN Chi-restraints excluded: chain B residue 912 ILE Chi-restraints excluded: chain B residue 937 PHE Chi-restraints excluded: chain B residue 940 TRP Chi-restraints excluded: chain B residue 972 MET Chi-restraints excluded: chain B residue 1064 ASP Chi-restraints excluded: chain B residue 1088 THR Chi-restraints excluded: chain B residue 1103 VAL Chi-restraints excluded: chain B residue 1117 TYR Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 137 TYR Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain C residue 220 LYS Chi-restraints excluded: chain C residue 284 CYS Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 375 ILE Chi-restraints excluded: chain C residue 385 PHE Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 471 CYS Chi-restraints excluded: chain C residue 479 CYS Chi-restraints excluded: chain C residue 517 CYS Chi-restraints excluded: chain C residue 568 LEU 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 633 CYS Chi-restraints excluded: chain C residue 671 ASN Chi-restraints excluded: chain C residue 677 ASP Chi-restraints excluded: chain C residue 716 HIS Chi-restraints excluded: chain C residue 898 GLN Chi-restraints excluded: chain C residue 904 LEU Chi-restraints excluded: chain C residue 929 THR Chi-restraints excluded: chain C residue 940 TRP Chi-restraints excluded: chain C residue 1005 ASN Chi-restraints excluded: chain C residue 1046 LEU Chi-restraints excluded: chain C residue 1064 ASP Chi-restraints excluded: chain C residue 1067 LEU Chi-restraints excluded: chain C residue 1088 THR Chi-restraints excluded: chain C residue 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 200 optimal weight: 2.9990 chunk 268 optimal weight: 0.0000 chunk 77 optimal weight: 1.9990 chunk 232 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 70 optimal weight: 7.9990 chunk 252 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 chunk 259 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 46 optimal weight: 0.8980 overall best weight: 0.8786 ------------------------------------------------------------------------------- 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 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 957 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 ASN ** B1086 GLN ** 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** C1005 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.182992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.172670 restraints weight = 40293.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 91)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.160133 restraints weight = 71707.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.159026 restraints weight = 66251.671| |-----------------------------------------------------------------------------| r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.6249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.192 25374 Z= 0.358 Angle : 0.799 59.197 34569 Z= 0.459 Chirality : 0.048 1.088 3906 Planarity : 0.005 0.088 4512 Dihedral : 5.877 33.881 3486 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.93 % Favored : 93.01 % Rotamer: Outliers : 3.30 % Allowed : 15.61 % Favored : 81.08 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.76 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.15), residues: 3189 helix: 1.33 (0.18), residues: 915 sheet: -0.38 (0.19), residues: 621 loop : -1.53 (0.16), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.199 0.006 TRP A 446 HIS 0.006 0.001 HIS C1098 PHE 0.062 0.002 PHE A 948 TYR 0.021 0.002 TYR A 450 ARG 0.018 0.000 ARG A 191 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5117.49 seconds wall clock time: 92 minutes 37.43 seconds (5557.43 seconds total)