Starting phenix.real_space_refine on Thu Mar 21 05:28:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zh2_11211/03_2024/6zh2_11211.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zh2_11211/03_2024/6zh2_11211.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zh2_11211/03_2024/6zh2_11211.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zh2_11211/03_2024/6zh2_11211.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zh2_11211/03_2024/6zh2_11211.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zh2_11211/03_2024/6zh2_11211.pdb" } resolution = 3.92 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= 0.001 sd= 0.011 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 192 5.16 5 C 18814 2.51 5 N 4959 2.21 5 O 5348 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 9": "NH1" <-> "NH2" Residue "A ARG 61": "NH1" <-> "NH2" Residue "A ARG 70": "NH1" <-> "NH2" Residue "A ARG 79": "NH1" <-> "NH2" Residue "A ARG 82": "NH1" <-> "NH2" Residue "A ARG 142": "NH1" <-> "NH2" Residue "A GLU 183": "OE1" <-> "OE2" Residue "A ARG 257": "NH1" <-> "NH2" Residue "A ARG 264": "NH1" <-> "NH2" Residue "A GLU 295": "OE1" <-> "OE2" Residue "A GLU 307": "OE1" <-> "OE2" Residue "A GLU 332": "OE1" <-> "OE2" Residue "A ARG 476": "NH1" <-> "NH2" Residue "A GLU 567": "OE1" <-> "OE2" Residue "A GLU 577": "OE1" <-> "OE2" Residue "A GLU 632": "OE1" <-> "OE2" Residue "A GLU 699": "OE1" <-> "OE2" Residue "A GLU 713": "OE1" <-> "OE2" Residue "A GLU 724": "OE1" <-> "OE2" Residue "A GLU 742": "OE1" <-> "OE2" Residue "A GLU 774": "OE1" <-> "OE2" Residue "A ARG 888": "NH1" <-> "NH2" Residue "A ARG 891": "NH1" <-> "NH2" Residue "A ARG 913": "NH1" <-> "NH2" Residue "A ARG 1026": "NH1" <-> "NH2" Residue "A GLU 1088": "OE1" <-> "OE2" Residue "A ARG 1090": "NH1" <-> "NH2" Residue "A GLU 1109": "OE1" <-> "OE2" Residue "A ARG 1184": "NH1" <-> "NH2" Residue "A GLU 1189": "OE1" <-> "OE2" Residue "A ARG 1245": "NH1" <-> "NH2" Residue "A GLU 1273": "OE1" <-> "OE2" Residue "A PHE 1297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1321": "NH1" <-> "NH2" Residue "A GLU 1326": "OE1" <-> "OE2" Residue "A ARG 1445": "NH1" <-> "NH2" Residue "A ARG 1497": "NH1" <-> "NH2" Residue "A PHE 1553": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1608": "NH1" <-> "NH2" Residue "A GLU 1760": "OE1" <-> "OE2" Residue "A GLU 1769": "OE1" <-> "OE2" Residue "A GLU 1776": "OE1" <-> "OE2" Residue "A GLU 1803": "OE1" <-> "OE2" Residue "A ARG 1816": "NH1" <-> "NH2" Residue "A ARG 1837": "NH1" <-> "NH2" Residue "A ARG 1854": "NH1" <-> "NH2" Residue "A GLU 1910": "OE1" <-> "OE2" Residue "A ARG 1937": "NH1" <-> "NH2" Residue "A ARG 1938": "NH1" <-> "NH2" Residue "A ARG 2090": "NH1" <-> "NH2" Residue "A GLU 2092": "OE1" <-> "OE2" Residue "A ARG 2106": "NH1" <-> "NH2" Residue "A ARG 2120": "NH1" <-> "NH2" Residue "A ARG 2232": "NH1" <-> "NH2" Residue "A GLU 2243": "OE1" <-> "OE2" Residue "A ARG 2254": "NH1" <-> "NH2" Residue "A ARG 2311": "NH1" <-> "NH2" Residue "A ARG 2333": "NH1" <-> "NH2" Residue "A GLU 2343": "OE1" <-> "OE2" Residue "A GLU 2406": "OE1" <-> "OE2" Residue "A GLU 2430": "OE1" <-> "OE2" Residue "A ARG 2431": "NH1" <-> "NH2" Residue "A ARG 2596": "NH1" <-> "NH2" Residue "A ARG 2899": "NH1" <-> "NH2" Residue "A ARG 2922": "NH1" <-> "NH2" Residue "A GLU 2946": "OE1" <-> "OE2" Residue "A GLU 2985": "OE1" <-> "OE2" Residue "A GLU 3022": "OE1" <-> "OE2" Residue "A GLU 3079": "OE1" <-> "OE2" Residue "A GLU 3137": "OE1" <-> "OE2" Residue "A ARG 3282": "NH1" <-> "NH2" Residue "A ARG 3324": "NH1" <-> "NH2" Residue "A ARG 3335": "NH1" <-> "NH2" Residue "A GLU 3352": "OE1" <-> "OE2" Residue "A ARG 3357": "NH1" <-> "NH2" Residue "A ARG 3358": "NH1" <-> "NH2" Residue "A GLU 3361": "OE1" <-> "OE2" Residue "A ARG 3380": "NH1" <-> "NH2" Residue "A GLU 3387": "OE1" <-> "OE2" Residue "A ARG 3425": "NH1" <-> "NH2" Residue "A GLU 3582": "OE1" <-> "OE2" Residue "A ARG 3653": "NH1" <-> "NH2" Residue "A ARG 3696": "NH1" <-> "NH2" Residue "A ARG 3708": "NH1" <-> "NH2" Residue "A ARG 3725": "NH1" <-> "NH2" Residue "A ARG 3741": "NH1" <-> "NH2" Residue "A ARG 3746": "NH1" <-> "NH2" Residue "A ARG 3759": "NH1" <-> "NH2" Residue "A ARG 3799": "NH1" <-> "NH2" Residue "A GLU 3804": "OE1" <-> "OE2" Residue "A ARG 3833": "NH1" <-> "NH2" Residue "A GLU 3933": "OE1" <-> "OE2" Residue "A GLU 4017": "OE1" <-> "OE2" Residue "A GLU 4063": "OE1" <-> "OE2" Residue "A ARG 4082": "NH1" <-> "NH2" Residue "A ARG 4119": "NH1" <-> "NH2" Residue "A GLU 4125": "OE1" <-> "OE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 29313 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 29313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3704, 29313 Classifications: {'peptide': 3704} Incomplete info: {'truncation_to_alanine': 111} Link IDs: {'CIS': 2, 'PTRANS': 161, 'TRANS': 3540} Chain breaks: 19 Unresolved non-hydrogen bonds: 332 Unresolved non-hydrogen angles: 423 Unresolved non-hydrogen dihedrals: 253 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 8, 'UNK:plan-1': 28, 'TYR:plan': 2, 'ASN:plan1': 6, 'ASP:plan': 1, 'PHE:plan': 3, 'GLU:plan': 14, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 184 Time building chain proxies: 15.36, per 1000 atoms: 0.52 Number of scatterers: 29313 At special positions: 0 Unit cell: (120.62, 145.396, 183.212, 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 192 16.00 O 5348 8.00 N 4959 7.00 C 18814 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 12.01 Conformation dependent library (CDL) restraints added in 5.2 seconds 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7106 Finding SS restraints... Secondary structure from input PDB file: 218 helices and 6 sheets defined 71.4% alpha, 1.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.12 Creating SS restraints... Processing helix chain 'A' and resid 10 through 22 removed outlier: 4.351A pdb=" N ARG A 14 " --> pdb=" O CYS A 10 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N GLU A 17 " --> pdb=" O LEU A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 23 through 25 No H-bonds generated for 'chain 'A' and resid 23 through 25' Processing helix chain 'A' and resid 33 through 38 removed outlier: 4.055A pdb=" N GLY A 37 " --> pdb=" O GLN A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 45 removed outlier: 4.312A pdb=" N VAL A 43 " --> pdb=" O GLY A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 58 removed outlier: 3.585A pdb=" N THR A 55 " --> pdb=" O LEU A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 73 removed outlier: 4.445A pdb=" N ASP A 62 " --> pdb=" O VAL A 58 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLY A 64 " --> pdb=" O SER A 60 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU A 65 " --> pdb=" O ARG A 61 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LEU A 66 " --> pdb=" O ASP A 62 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N SER A 72 " --> pdb=" O PHE A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 97 removed outlier: 3.839A pdb=" N GLU A 80 " --> pdb=" O ILE A 76 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N ILE A 85 " --> pdb=" O CYS A 81 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LEU A 86 " --> pdb=" O ARG A 82 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS A 87 " --> pdb=" O GLU A 83 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLU A 94 " --> pdb=" O CYS A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 117 removed outlier: 3.667A pdb=" N LYS A 117 " --> pdb=" O SER A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 141 Processing helix chain 'A' and resid 147 through 151 Processing helix chain 'A' and resid 153 through 163 removed outlier: 3.504A pdb=" N TYR A 157 " --> pdb=" O PHE A 153 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA A 161 " --> pdb=" O TYR A 157 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU A 162 " --> pdb=" O GLY A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 172 No H-bonds generated for 'chain 'A' and resid 170 through 172' Processing helix chain 'A' and resid 173 through 178 removed outlier: 3.588A pdb=" N LEU A 177 " --> pdb=" O LYS A 173 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU A 178 " --> pdb=" O VAL A 174 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 173 through 178' Processing helix chain 'A' and resid 179 through 185 removed outlier: 4.040A pdb=" N GLU A 183 " --> pdb=" O GLY A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 207 removed outlier: 4.273A pdb=" N ALA A 199 " --> pdb=" O ASN A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 223 removed outlier: 4.229A pdb=" N CYS A 223 " --> pdb=" O VAL A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 231 removed outlier: 3.810A pdb=" N LEU A 227 " --> pdb=" O CYS A 223 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER A 228 " --> pdb=" O LEU A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 234 No H-bonds generated for 'chain 'A' and resid 232 through 234' Processing helix chain 'A' and resid 241 through 255 removed outlier: 3.548A pdb=" N SER A 245 " --> pdb=" O ASP A 241 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ALA A 255 " --> pdb=" O PHE A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 278 removed outlier: 3.659A pdb=" N LEU A 274 " --> pdb=" O ALA A 270 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N PHE A 275 " --> pdb=" O GLY A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 287 removed outlier: 3.653A pdb=" N LEU A 287 " --> pdb=" O THR A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 302 removed outlier: 4.537A pdb=" N GLU A 295 " --> pdb=" O VAL A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 328 Processing helix chain 'A' and resid 334 through 351 removed outlier: 3.685A pdb=" N ASN A 351 " --> pdb=" O GLY A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 376 removed outlier: 5.418A pdb=" N GLY A 371 " --> pdb=" O GLY A 367 " (cutoff:3.500A) Proline residue: A 372 - end of helix Processing helix chain 'A' and resid 380 through 397 removed outlier: 3.930A pdb=" N MET A 384 " --> pdb=" O ASP A 380 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N MET A 395 " --> pdb=" O ARG A 391 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE A 396 " --> pdb=" O CYS A 392 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU A 397 " --> pdb=" O LYS A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 408 No H-bonds generated for 'chain 'A' and resid 406 through 408' Processing helix chain 'A' and resid 409 through 424 removed outlier: 3.791A pdb=" N PHE A 413 " --> pdb=" O GLN A 409 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N TYR A 423 " --> pdb=" O SER A 419 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LEU A 424 " --> pdb=" O VAL A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 445 Processing helix chain 'A' and resid 450 through 469 removed outlier: 4.122A pdb=" N LEU A 455 " --> pdb=" O PRO A 451 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N VAL A 456 " --> pdb=" O LYS A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 493 removed outlier: 4.494A pdb=" N ARG A 476 " --> pdb=" O GLY A 472 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N THR A 481 " --> pdb=" O ASN A 477 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LYS A 493 " --> pdb=" O ARG A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 526 Processing helix chain 'A' and resid 527 through 536 Processing helix chain 'A' and resid 539 through 544 removed outlier: 3.723A pdb=" N SER A 543 " --> pdb=" O GLN A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 579 Processing helix chain 'A' and resid 616 through 631 removed outlier: 3.751A pdb=" N PHE A 620 " --> pdb=" O LYS A 616 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASN A 625 " --> pdb=" O SER A 621 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 644 No H-bonds generated for 'chain 'A' and resid 642 through 644' Processing helix chain 'A' and resid 645 through 660 removed outlier: 3.531A pdb=" N LEU A 653 " --> pdb=" O PHE A 649 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ARG A 659 " --> pdb=" O LEU A 655 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU A 660 " --> pdb=" O GLN A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 680 removed outlier: 3.638A pdb=" N LYS A 668 " --> pdb=" O SER A 664 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU A 670 " --> pdb=" O PHE A 666 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N THR A 673 " --> pdb=" O LEU A 669 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS A 679 " --> pdb=" O ARG A 675 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE A 680 " --> pdb=" O ASN A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 718 Processing helix chain 'A' and resid 724 through 735 removed outlier: 3.702A pdb=" N SER A 728 " --> pdb=" O GLU A 724 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 742 Processing helix chain 'A' and resid 744 through 759 removed outlier: 4.093A pdb=" N TYR A 748 " --> pdb=" O ASP A 744 " (cutoff:3.500A) Proline residue: A 750 - end of helix Processing helix chain 'A' and resid 762 through 780 removed outlier: 3.505A pdb=" N ALA A 766 " --> pdb=" O TYR A 762 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE A 778 " --> pdb=" O GLU A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 781 through 786 Processing helix chain 'A' and resid 788 through 793 Processing helix chain 'A' and resid 794 through 800 removed outlier: 3.727A pdb=" N ASP A 797 " --> pdb=" O PRO A 794 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 862 Processing helix chain 'A' and resid 866 through 876 removed outlier: 4.101A pdb=" N VAL A 873 " --> pdb=" O LEU A 870 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N THR A 874 " --> pdb=" O LEU A 871 " (cutoff:3.500A) Processing helix chain 'A' and resid 906 through 909 removed outlier: 3.653A pdb=" N VAL A 909 " --> pdb=" O PHE A 906 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 906 through 909' Processing helix chain 'A' and resid 910 through 921 removed outlier: 3.978A pdb=" N GLU A 916 " --> pdb=" O PRO A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 925 through 946 removed outlier: 4.046A pdb=" N THR A 946 " --> pdb=" O LEU A 942 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 973 removed outlier: 4.015A pdb=" N ARG A 964 " --> pdb=" O GLN A 960 " (cutoff:3.500A) Proline residue: A 967 - end of helix Processing helix chain 'A' and resid 977 through 996 Proline residue: A 986 - end of helix Processing helix chain 'A' and resid 1002 through 1006 Processing helix chain 'A' and resid 1007 through 1015 removed outlier: 3.541A pdb=" N GLU A1011 " --> pdb=" O VAL A1007 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA A1012 " --> pdb=" O ALA A1008 " (cutoff:3.500A) Processing helix chain 'A' and resid 1023 through 1042 Processing helix chain 'A' and resid 1045 through 1052 removed outlier: 3.590A pdb=" N LYS A1051 " --> pdb=" O GLN A1047 " (cutoff:3.500A) Processing helix chain 'A' and resid 1055 through 1068 Processing helix chain 'A' and resid 1073 through 1083 Processing helix chain 'A' and resid 1092 through 1114 removed outlier: 6.252A pdb=" N PHE A1101 " --> pdb=" O GLU A1097 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N GLU A1102 " --> pdb=" O GLN A1098 " (cutoff:3.500A) Processing helix chain 'A' and resid 1115 through 1117 No H-bonds generated for 'chain 'A' and resid 1115 through 1117' Processing helix chain 'A' and resid 1122 through 1139 removed outlier: 3.595A pdb=" N ILE A1137 " --> pdb=" O HIS A1133 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU A1139 " --> pdb=" O CYS A1135 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1146 Processing helix chain 'A' and resid 1164 through 1175 Processing helix chain 'A' and resid 1182 through 1195 Processing helix chain 'A' and resid 1196 through 1198 No H-bonds generated for 'chain 'A' and resid 1196 through 1198' Processing helix chain 'A' and resid 1203 through 1215 Processing helix chain 'A' and resid 1216 through 1225 removed outlier: 4.117A pdb=" N LEU A1220 " --> pdb=" O GLY A1216 " (cutoff:3.500A) Processing helix chain 'A' and resid 1251 through 1273 removed outlier: 3.545A pdb=" N GLU A1273 " --> pdb=" O THR A1269 " (cutoff:3.500A) Processing helix chain 'A' and resid 1277 through 1281 Processing helix chain 'A' and resid 1288 through 1298 removed outlier: 4.427A pdb=" N LYS A1292 " --> pdb=" O SER A1288 " (cutoff:3.500A) Processing helix chain 'A' and resid 1299 through 1301 No H-bonds generated for 'chain 'A' and resid 1299 through 1301' Processing helix chain 'A' and resid 1317 through 1323 removed outlier: 4.132A pdb=" N ASN A1320 " --> pdb=" O ALA A1317 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N SER A1323 " --> pdb=" O ASN A1320 " (cutoff:3.500A) Processing helix chain 'A' and resid 1327 through 1351 Processing helix chain 'A' and resid 1356 through 1362 removed outlier: 3.794A pdb=" N ASP A1362 " --> pdb=" O LEU A1358 " (cutoff:3.500A) Processing helix chain 'A' and resid 1367 through 1378 removed outlier: 4.211A pdb=" N GLN A1374 " --> pdb=" O ARG A1370 " (cutoff:3.500A) Processing helix chain 'A' and resid 1390 through 1393 Processing helix chain 'A' and resid 1394 through 1409 removed outlier: 3.800A pdb=" N VAL A1398 " --> pdb=" O HIS A1394 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N MET A1408 " --> pdb=" O LYS A1404 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER A1409 " --> pdb=" O ALA A1405 " (cutoff:3.500A) Processing helix chain 'A' and resid 1411 through 1423 removed outlier: 3.711A pdb=" N LEU A1415 " --> pdb=" O TYR A1411 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU A1421 " --> pdb=" O THR A1417 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS A1422 " --> pdb=" O HIS A1418 " (cutoff:3.500A) Processing helix chain 'A' and resid 1424 through 1433 Processing helix chain 'A' and resid 1441 through 1462 removed outlier: 3.641A pdb=" N ARG A1445 " --> pdb=" O ALA A1441 " (cutoff:3.500A) Processing helix chain 'A' and resid 1463 through 1468 Processing helix chain 'A' and resid 1476 through 1484 removed outlier: 4.361A pdb=" N THR A1481 " --> pdb=" O HIS A1477 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU A1482 " --> pdb=" O SER A1478 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU A1484 " --> pdb=" O GLY A1480 " (cutoff:3.500A) Processing helix chain 'A' and resid 1506 through 1520 removed outlier: 3.749A pdb=" N LEU A1510 " --> pdb=" O SER A1506 " (cutoff:3.500A) Processing helix chain 'A' and resid 1524 through 1533 Processing helix chain 'A' and resid 1554 through 1563 Processing helix chain 'A' and resid 1563 through 1574 removed outlier: 3.692A pdb=" N THR A1569 " --> pdb=" O GLU A1565 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LYS A1573 " --> pdb=" O THR A1569 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASN A1574 " --> pdb=" O GLU A1570 " (cutoff:3.500A) Processing helix chain 'A' and resid 1574 through 1585 removed outlier: 3.721A pdb=" N LEU A1580 " --> pdb=" O ASP A1576 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N SER A1585 " --> pdb=" O GLU A1581 " (cutoff:3.500A) Processing helix chain 'A' and resid 1591 through 1607 Processing helix chain 'A' and resid 1611 through 1625 removed outlier: 4.059A pdb=" N GLY A1615 " --> pdb=" O GLN A1611 " (cutoff:3.500A) Processing helix chain 'A' and resid 1626 through 1633 removed outlier: 3.821A pdb=" N ASP A1630 " --> pdb=" O LYS A1627 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N SER A1631 " --> pdb=" O LYS A1628 " (cutoff:3.500A) Processing helix chain 'A' and resid 1638 through 1656 removed outlier: 3.535A pdb=" N ASP A1656 " --> pdb=" O ILE A1652 " (cutoff:3.500A) Processing helix chain 'A' and resid 1667 through 1681 removed outlier: 3.681A pdb=" N VAL A1671 " --> pdb=" O SER A1667 " (cutoff:3.500A) Processing helix chain 'A' and resid 1685 through 1694 Processing helix chain 'A' and resid 1695 through 1700 removed outlier: 3.539A pdb=" N PHE A1698 " --> pdb=" O LEU A1695 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N THR A1700 " --> pdb=" O PRO A1697 " (cutoff:3.500A) Processing helix chain 'A' and resid 1706 through 1722 removed outlier: 4.050A pdb=" N LEU A1710 " --> pdb=" O SER A1706 " (cutoff:3.500A) Processing helix chain 'A' and resid 1733 through 1754 Processing helix chain 'A' and resid 1755 through 1768 removed outlier: 3.690A pdb=" N LEU A1761 " --> pdb=" O MET A1757 " (cutoff:3.500A) Processing helix chain 'A' and resid 1774 through 1789 removed outlier: 3.908A pdb=" N ARG A1787 " --> pdb=" O ARG A1783 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG A1788 " --> pdb=" O ARG A1784 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLY A1789 " --> pdb=" O ILE A1785 " (cutoff:3.500A) Processing helix chain 'A' and resid 1790 through 1807 Processing helix chain 'A' and resid 1813 through 1823 Processing helix chain 'A' and resid 1823 through 1829 Processing helix chain 'A' and resid 1834 through 1853 removed outlier: 3.805A pdb=" N GLU A1838 " --> pdb=" O ASP A1834 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N VAL A1845 " --> pdb=" O SER A1841 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N ASP A1846 " --> pdb=" O THR A1842 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N ASP A1849 " --> pdb=" O VAL A1845 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL A1850 " --> pdb=" O ASP A1846 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU A1851 " --> pdb=" O ALA A1847 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N SER A1853 " --> pdb=" O ASP A1849 " (cutoff:3.500A) Processing helix chain 'A' and resid 1862 through 1882 removed outlier: 4.014A pdb=" N GLN A1866 " --> pdb=" O THR A1862 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER A1882 " --> pdb=" O ASP A1878 " (cutoff:3.500A) Processing helix chain 'A' and resid 1885 through 1889 Processing helix chain 'A' and resid 1910 through 1923 removed outlier: 3.830A pdb=" N ASP A1921 " --> pdb=" O LYS A1917 " (cutoff:3.500A) Processing helix chain 'A' and resid 1934 through 1956 Processing helix chain 'A' and resid 1970 through 1975 removed outlier: 3.517A pdb=" N LEU A1975 " --> pdb=" O GLU A1972 " (cutoff:3.500A) Processing helix chain 'A' and resid 2093 through 2107 Processing helix chain 'A' and resid 2126 through 2135 Processing helix chain 'A' and resid 2139 through 2153 Processing helix chain 'A' and resid 2153 through 2158 removed outlier: 4.312A pdb=" N PHE A2157 " --> pdb=" O THR A2153 " (cutoff:3.500A) Processing helix chain 'A' and resid 2160 through 2172 removed outlier: 3.629A pdb=" N LEU A2165 " --> pdb=" O ALA A2161 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N SER A2166 " --> pdb=" O LYS A2162 " (cutoff:3.500A) Proline residue: A2167 - end of helix Processing helix chain 'A' and resid 2183 through 2195 Processing helix chain 'A' and resid 2205 through 2222 removed outlier: 4.204A pdb=" N GLU A2209 " --> pdb=" O VAL A2205 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ARG A2214 " --> pdb=" O VAL A2210 " (cutoff:3.500A) Processing helix chain 'A' and resid 2227 through 2246 Processing helix chain 'A' and resid 2247 through 2249 No H-bonds generated for 'chain 'A' and resid 2247 through 2249' Processing helix chain 'A' and resid 2253 through 2261 removed outlier: 3.568A pdb=" N PHE A2257 " --> pdb=" O TYR A2253 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLU A2258 " --> pdb=" O ARG A2254 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N LYS A2259 " --> pdb=" O LEU A2255 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N PHE A2260 " --> pdb=" O ILE A2256 " (cutoff:3.500A) Processing helix chain 'A' and resid 2268 through 2283 removed outlier: 3.767A pdb=" N GLY A2273 " --> pdb=" O ASP A2269 " (cutoff:3.500A) Processing helix chain 'A' and resid 2296 through 2306 Processing helix chain 'A' and resid 2307 through 2309 No H-bonds generated for 'chain 'A' and resid 2307 through 2309' Processing helix chain 'A' and resid 2313 through 2331 removed outlier: 3.724A pdb=" N ALA A2319 " --> pdb=" O VAL A2315 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N MET A2331 " --> pdb=" O LEU A2327 " (cutoff:3.500A) Processing helix chain 'A' and resid 2332 through 2334 No H-bonds generated for 'chain 'A' and resid 2332 through 2334' Processing helix chain 'A' and resid 2337 through 2356 removed outlier: 3.508A pdb=" N HIS A2352 " --> pdb=" O GLN A2348 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N MET A2356 " --> pdb=" O HIS A2352 " (cutoff:3.500A) Processing helix chain 'A' and resid 2357 through 2369 removed outlier: 3.585A pdb=" N ILE A2361 " --> pdb=" O GLU A2357 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N VAL A2362 " --> pdb=" O ASP A2358 " (cutoff:3.500A) Processing helix chain 'A' and resid 2371 through 2377 removed outlier: 3.775A pdb=" N LEU A2374 " --> pdb=" O PHE A2371 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP A2376 " --> pdb=" O PRO A2373 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ARG A2377 " --> pdb=" O LEU A2374 " (cutoff:3.500A) Processing helix chain 'A' and resid 2378 through 2386 Processing helix chain 'A' and resid 2387 through 2389 No H-bonds generated for 'chain 'A' and resid 2387 through 2389' Processing helix chain 'A' and resid 2391 through 2404 removed outlier: 3.981A pdb=" N THR A2395 " --> pdb=" O GLY A2391 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N CYS A2403 " --> pdb=" O GLU A2399 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ARG A2404 " --> pdb=" O VAL A2400 " (cutoff:3.500A) Processing helix chain 'A' and resid 2412 through 2418 removed outlier: 3.633A pdb=" N SER A2417 " --> pdb=" O PHE A2413 " (cutoff:3.500A) Processing helix chain 'A' and resid 2419 through 2426 removed outlier: 3.672A pdb=" N VAL A2423 " --> pdb=" O ASP A2419 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N MET A2424 " --> pdb=" O PHE A2420 " (cutoff:3.500A) Processing helix chain 'A' and resid 2428 through 2443 removed outlier: 3.537A pdb=" N LYS A2441 " --> pdb=" O ASP A2437 " (cutoff:3.500A) Processing helix chain 'A' and resid 2444 through 2446 No H-bonds generated for 'chain 'A' and resid 2444 through 2446' Processing helix chain 'A' and resid 2447 through 2459 removed outlier: 4.091A pdb=" N GLU A2453 " --> pdb=" O VAL A2449 " (cutoff:3.500A) Proline residue: A2457 - end of helix Processing helix chain 'A' and resid 2460 through 2462 No H-bonds generated for 'chain 'A' and resid 2460 through 2462' Processing helix chain 'A' and resid 2468 through 2484 removed outlier: 3.561A pdb=" N TRP A2479 " --> pdb=" O ASN A2475 " (cutoff:3.500A) Processing helix chain 'A' and resid 2494 through 2510 removed outlier: 3.717A pdb=" N LEU A2510 " --> pdb=" O LEU A2506 " (cutoff:3.500A) Processing helix chain 'A' and resid 2514 through 2526 Processing helix chain 'A' and resid 2535 through 2543 removed outlier: 4.152A pdb=" N ASN A2543 " --> pdb=" O LEU A2539 " (cutoff:3.500A) Processing helix chain 'A' and resid 2544 through 2546 No H-bonds generated for 'chain 'A' and resid 2544 through 2546' Processing helix chain 'A' and resid 2547 through 2551 removed outlier: 3.667A pdb=" N GLU A2551 " --> pdb=" O PRO A2548 " (cutoff:3.500A) Processing helix chain 'A' and resid 2556 through 2564 Processing helix chain 'A' and resid 2565 through 2569 Processing helix chain 'A' and resid 2786 through 2799 removed outlier: 3.730A pdb=" N LEU A2790 " --> pdb=" O LYS A2786 " (cutoff:3.500A) Proline residue: A2793 - end of helix Processing helix chain 'A' and resid 2801 through 2821 removed outlier: 3.577A pdb=" N SER A2811 " --> pdb=" O GLN A2807 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU A2819 " --> pdb=" O GLY A2815 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ASP A2821 " --> pdb=" O LEU A2817 " (cutoff:3.500A) Processing helix chain 'A' and resid 2825 through 2846 Processing helix chain 'A' and resid 2851 through 2865 removed outlier: 3.625A pdb=" N GLN A2864 " --> pdb=" O ASP A2860 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N HIS A2865 " --> pdb=" O ILE A2861 " (cutoff:3.500A) Processing helix chain 'A' and resid 2872 through 2884 Processing helix chain 'A' and resid 2885 through 2899 removed outlier: 3.931A pdb=" N GLY A2889 " --> pdb=" O GLN A2885 " (cutoff:3.500A) Processing helix chain 'A' and resid 2917 through 2934 removed outlier: 3.579A pdb=" N GLU A2925 " --> pdb=" O LEU A2921 " (cutoff:3.500A) Processing helix chain 'A' and resid 2935 through 2946 removed outlier: 3.685A pdb=" N LEU A2939 " --> pdb=" O GLU A2935 " (cutoff:3.500A) Processing helix chain 'A' and resid 2950 through 2962 removed outlier: 3.961A pdb=" N GLN A2954 " --> pdb=" O LYS A2950 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER A2955 " --> pdb=" O GLN A2951 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA A2956 " --> pdb=" O ILE A2952 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ARG A2962 " --> pdb=" O LEU A2958 " (cutoff:3.500A) Processing helix chain 'A' and resid 2964 through 2976 Processing helix chain 'A' and resid 2987 through 3005 Processing helix chain 'A' and resid 3007 through 3014 Processing helix chain 'A' and resid 3039 through 3054 removed outlier: 4.610A pdb=" N TYR A3043 " --> pdb=" O THR A3039 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N MET A3044 " --> pdb=" O TYR A3040 " (cutoff:3.500A) Processing helix chain 'A' and resid 3059 through 3070 removed outlier: 4.212A pdb=" N LYS A3067 " --> pdb=" O THR A3063 " (cutoff:3.500A) Processing helix chain 'A' and resid 3074 through 3082 removed outlier: 3.505A pdb=" N LEU A3078 " --> pdb=" O GLN A3074 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR A3082 " --> pdb=" O LEU A3078 " (cutoff:3.500A) Processing helix chain 'A' and resid 3082 through 3093 Processing helix chain 'A' and resid 3095 through 3117 removed outlier: 3.628A pdb=" N TYR A3101 " --> pdb=" O ASP A3097 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE A3117 " --> pdb=" O ASN A3113 " (cutoff:3.500A) Processing helix chain 'A' and resid 3121 through 3131 removed outlier: 4.000A pdb=" N SER A3131 " --> pdb=" O THR A3127 " (cutoff:3.500A) Processing helix chain 'A' and resid 3131 through 3147 removed outlier: 3.905A pdb=" N LEU A3135 " --> pdb=" O SER A3131 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LYS A3147 " --> pdb=" O SER A3143 " (cutoff:3.500A) Processing helix chain 'A' and resid 3153 through 3165 removed outlier: 4.217A pdb=" N LEU A3157 " --> pdb=" O SER A3153 " (cutoff:3.500A) Processing helix chain 'A' and resid 3175 through 3196 removed outlier: 3.627A pdb=" N TRP A3179 " --> pdb=" O PRO A3175 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASP A3181 " --> pdb=" O ASN A3177 " (cutoff:3.500A) Processing helix chain 'A' and resid 3229 through 3249 removed outlier: 3.512A pdb=" N ASP A3244 " --> pdb=" O MET A3240 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN A3249 " --> pdb=" O SER A3245 " (cutoff:3.500A) Processing helix chain 'A' and resid 3251 through 3263 Processing helix chain 'A' and resid 3264 through 3266 No H-bonds generated for 'chain 'A' and resid 3264 through 3266' Processing helix chain 'A' and resid 3270 through 3287 removed outlier: 3.627A pdb=" N VAL A3274 " --> pdb=" O ASP A3270 " (cutoff:3.500A) Processing helix chain 'A' and resid 3290 through 3307 removed outlier: 4.578A pdb=" N GLU A3295 " --> pdb=" O GLN A3291 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N GLN A3296 " --> pdb=" O GLY A3292 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N VAL A3297 " --> pdb=" O CYS A3293 " (cutoff:3.500A) Processing helix chain 'A' and resid 3322 through 3344 removed outlier: 3.805A pdb=" N LEU A3330 " --> pdb=" O GLN A3326 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU A3344 " --> pdb=" O ALA A3340 " (cutoff:3.500A) Processing helix chain 'A' and resid 3353 through 3364 removed outlier: 3.818A pdb=" N ARG A3357 " --> pdb=" O GLU A3353 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE A3359 " --> pdb=" O LYS A3355 " (cutoff:3.500A) Processing helix chain 'A' and resid 3369 through 3393 Processing helix chain 'A' and resid 3407 through 3430 removed outlier: 3.894A pdb=" N ASN A3430 " --> pdb=" O LYS A3426 " (cutoff:3.500A) Processing helix chain 'A' and resid 3441 through 3456 removed outlier: 4.020A pdb=" N LEU A3445 " --> pdb=" O ALA A3441 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU A3456 " --> pdb=" O LYS A3452 " (cutoff:3.500A) Processing helix chain 'A' and resid 3458 through 3463 Processing helix chain 'A' and resid 3464 through 3474 removed outlier: 3.933A pdb=" N LEU A3468 " --> pdb=" O LYS A3464 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU A3469 " --> pdb=" O PHE A3465 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ARG A3474 " --> pdb=" O GLN A3470 " (cutoff:3.500A) Processing helix chain 'A' and resid 3475 through 3479 removed outlier: 3.812A pdb=" N THR A3479 " --> pdb=" O PRO A3476 " (cutoff:3.500A) Processing helix chain 'A' and resid 3480 through 3485 Processing helix chain 'A' and resid 3495 through 3497 No H-bonds generated for 'chain 'A' and resid 3495 through 3497' Processing helix chain 'A' and resid 3498 through 3503 Processing helix chain 'A' and resid 3504 through 3506 No H-bonds generated for 'chain 'A' and resid 3504 through 3506' Processing helix chain 'A' and resid 3514 through 3525 Processing helix chain 'A' and resid 3529 through 3538 removed outlier: 3.560A pdb=" N GLU A3538 " --> pdb=" O ILE A3534 " (cutoff:3.500A) Processing helix chain 'A' and resid 3548 through 3562 removed outlier: 4.078A pdb=" N GLU A3553 " --> pdb=" O HIS A3549 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N PHE A3554 " --> pdb=" O LYS A3550 " (cutoff:3.500A) Processing helix chain 'A' and resid 3566 through 3576 Processing helix chain 'A' and resid 3577 through 3579 No H-bonds generated for 'chain 'A' and resid 3577 through 3579' Processing helix chain 'A' and resid 3580 through 3592 Processing helix chain 'A' and resid 3607 through 3617 removed outlier: 3.932A pdb=" N GLU A3611 " --> pdb=" O GLU A3607 " (cutoff:3.500A) Processing helix chain 'A' and resid 3626 through 3636 Processing helix chain 'A' and resid 3639 through 3644 Processing helix chain 'A' and resid 3658 through 3671 removed outlier: 4.267A pdb=" N MET A3665 " --> pdb=" O ASP A3661 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N LEU A3666 " --> pdb=" O ILE A3662 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN A3671 " --> pdb=" O LEU A3667 " (cutoff:3.500A) Processing helix chain 'A' and resid 3672 through 3674 No H-bonds generated for 'chain 'A' and resid 3672 through 3674' Processing helix chain 'A' and resid 3685 through 3690 removed outlier: 4.215A pdb=" N SER A3688 " --> pdb=" O PRO A3685 " (cutoff:3.500A) Processing helix chain 'A' and resid 3758 through 3778 Processing helix chain 'A' and resid 3779 through 3784 removed outlier: 3.761A pdb=" N ARG A3784 " --> pdb=" O ALA A3780 " (cutoff:3.500A) Processing helix chain 'A' and resid 3812 through 3820 removed outlier: 3.587A pdb=" N THR A3819 " --> pdb=" O LEU A3815 " (cutoff:3.500A) Processing helix chain 'A' and resid 3821 through 3830 Processing helix chain 'A' and resid 3834 through 3847 removed outlier: 4.697A pdb=" N LYS A3840 " --> pdb=" O PRO A3836 " (cutoff:3.500A) Processing helix chain 'A' and resid 3853 through 3862 removed outlier: 4.027A pdb=" N LEU A3857 " --> pdb=" O GLY A3853 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LYS A3860 " --> pdb=" O MET A3856 " (cutoff:3.500A) Processing helix chain 'A' and resid 3863 through 3878 removed outlier: 3.595A pdb=" N THR A3867 " --> pdb=" O ASN A3863 " (cutoff:3.500A) Processing helix chain 'A' and resid 3881 through 3891 removed outlier: 3.635A pdb=" N MET A3890 " --> pdb=" O ALA A3886 " (cutoff:3.500A) Processing helix chain 'A' and resid 3893 through 3919 removed outlier: 4.004A pdb=" N ALA A3899 " --> pdb=" O GLU A3895 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N TRP A3916 " --> pdb=" O CYS A3912 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ILE A3917 " --> pdb=" O ILE A3913 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU A3918 " --> pdb=" O SER A3914 " (cutoff:3.500A) Processing helix chain 'A' and resid 3924 through 3926 No H-bonds generated for 'chain 'A' and resid 3924 through 3926' Processing helix chain 'A' and resid 3947 through 3952 removed outlier: 3.723A pdb=" N PHE A3952 " --> pdb=" O SER A3948 " (cutoff:3.500A) Processing helix chain 'A' and resid 3964 through 3969 Processing helix chain 'A' and resid 3970 through 3972 No H-bonds generated for 'chain 'A' and resid 3970 through 3972' Processing helix chain 'A' and resid 3978 through 3994 removed outlier: 3.564A pdb=" N SER A3982 " --> pdb=" O GLY A3978 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ASP A3994 " --> pdb=" O ALA A3990 " (cutoff:3.500A) Processing helix chain 'A' and resid 3994 through 4007 removed outlier: 4.487A pdb=" N LEU A3998 " --> pdb=" O ASP A3994 " (cutoff:3.500A) Processing helix chain 'A' and resid 4012 through 4022 removed outlier: 3.712A pdb=" N LYS A4022 " --> pdb=" O GLN A4018 " (cutoff:3.500A) Processing helix chain 'A' and resid 4039 through 4050 removed outlier: 4.173A pdb=" N ALA A4047 " --> pdb=" O LYS A4043 " (cutoff:3.500A) Processing helix chain 'A' and resid 4055 through 4068 Processing helix chain 'A' and resid 4073 through 4083 Processing helix chain 'A' and resid 4099 through 4113 Processing helix chain 'A' and resid 4113 through 4119 Processing helix chain 'A' and resid 4120 through 4125 removed outlier: 6.065A pdb=" N GLY A4123 " --> pdb=" O THR A4120 " (cutoff:3.500A) Processing helix chain 'A' and resid 5009 through 5014 removed outlier: 4.317A pdb=" N UNK A5012 " --> pdb=" O UNK A5009 " (cutoff:3.500A) Processing helix chain 'A' and resid 6002 through 6016 removed outlier: 3.668A pdb=" N UNK A6008 " --> pdb=" O UNK A6004 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N UNK A6009 " --> pdb=" O UNK A6005 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 583 through 584 Processing sheet with id=AA2, first strand: chain 'A' and resid 894 through 895 Processing sheet with id=AA3, first strand: chain 'A' and resid 2586 through 2588 Processing sheet with id=AA4, first strand: chain 'A' and resid 3679 through 3680 removed outlier: 4.567A pdb=" N ASN A3679 " --> pdb=" O VAL A3726 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N VAL A3726 " --> pdb=" O ASN A3679 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ARG A3725 " --> pdb=" O ILE A3739 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ILE A3739 " --> pdb=" O ARG A3725 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N THR A3727 " --> pdb=" O ARG A3737 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N ILE A3739 " --> pdb=" O PHE A3722 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N PHE A3722 " --> pdb=" O ILE A3739 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N ARG A3741 " --> pdb=" O ALA A3720 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 3679 through 3680 removed outlier: 4.567A pdb=" N ASN A3679 " --> pdb=" O VAL A3726 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N VAL A3726 " --> pdb=" O ASN A3679 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ARG A3725 " --> pdb=" O ILE A3739 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ILE A3739 " --> pdb=" O ARG A3725 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N THR A3727 " --> pdb=" O ARG A3737 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS A3736 " --> pdb=" O VAL A3752 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILE A3740 " --> pdb=" O HIS A3748 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ARG A3746 " --> pdb=" O GLY A3742 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LEU A3800 " --> pdb=" O MET A3796 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 3809 through 3811 1575 hydrogen bonds defined for protein. 4602 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: 15.50 Time building geometry restraints manager: 12.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9210 1.34 - 1.46: 4050 1.46 - 1.58: 16356 1.58 - 1.70: 0 1.70 - 1.82: 299 Bond restraints: 29915 Sorted by residual: bond pdb=" N LEU A2531 " pdb=" CA LEU A2531 " ideal model delta sigma weight residual 1.457 1.436 0.021 1.41e-02 5.03e+03 2.17e+00 bond pdb=" C LEU A3073 " pdb=" N GLN A3074 " ideal model delta sigma weight residual 1.332 1.313 0.019 1.40e-02 5.10e+03 1.92e+00 bond pdb=" C PRO A3676 " pdb=" N PRO A3677 " ideal model delta sigma weight residual 1.334 1.364 -0.030 2.34e-02 1.83e+03 1.68e+00 bond pdb=" CB MET A1927 " pdb=" CG MET A1927 " ideal model delta sigma weight residual 1.520 1.554 -0.034 3.00e-02 1.11e+03 1.29e+00 bond pdb=" C PRO A2372 " pdb=" N PRO A2373 " ideal model delta sigma weight residual 1.334 1.360 -0.026 2.34e-02 1.83e+03 1.20e+00 ... (remaining 29910 not shown) Histogram of bond angle deviations from ideal: 97.04 - 104.45: 500 104.45 - 111.85: 14365 111.85 - 119.26: 10324 119.26 - 126.67: 14884 126.67 - 134.08: 395 Bond angle restraints: 40468 Sorted by residual: angle pdb=" N ILE A1306 " pdb=" CA ILE A1306 " pdb=" C ILE A1306 " ideal model delta sigma weight residual 113.71 108.14 5.57 9.50e-01 1.11e+00 3.44e+01 angle pdb=" CB MET A2576 " pdb=" CG MET A2576 " pdb=" SD MET A2576 " ideal model delta sigma weight residual 112.70 124.67 -11.97 3.00e+00 1.11e-01 1.59e+01 angle pdb=" N LYS A2388 " pdb=" CA LYS A2388 " pdb=" C LYS A2388 " ideal model delta sigma weight residual 114.56 109.85 4.71 1.27e+00 6.20e-01 1.38e+01 angle pdb=" N MET A1108 " pdb=" CA MET A1108 " pdb=" CB MET A1108 " ideal model delta sigma weight residual 110.22 115.82 -5.60 1.54e+00 4.22e-01 1.32e+01 angle pdb=" CA MET A1927 " pdb=" CB MET A1927 " pdb=" CG MET A1927 " ideal model delta sigma weight residual 114.10 121.07 -6.97 2.00e+00 2.50e-01 1.21e+01 ... (remaining 40463 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.33: 16201 17.33 - 34.66: 1671 34.66 - 52.00: 269 52.00 - 69.33: 70 69.33 - 86.66: 26 Dihedral angle restraints: 18237 sinusoidal: 7338 harmonic: 10899 Sorted by residual: dihedral pdb=" CA LYS A 722 " pdb=" C LYS A 722 " pdb=" N ASP A 723 " pdb=" CA ASP A 723 " ideal model delta harmonic sigma weight residual 180.00 155.61 24.39 0 5.00e+00 4.00e-02 2.38e+01 dihedral pdb=" CA MET A 333 " pdb=" C MET A 333 " pdb=" N HIS A 334 " pdb=" CA HIS A 334 " ideal model delta harmonic sigma weight residual -180.00 -156.55 -23.45 0 5.00e+00 4.00e-02 2.20e+01 dihedral pdb=" CA ILE A2785 " pdb=" C ILE A2785 " pdb=" N LYS A2786 " pdb=" CA LYS A2786 " ideal model delta harmonic sigma weight residual 180.00 157.02 22.98 0 5.00e+00 4.00e-02 2.11e+01 ... (remaining 18234 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 3487 0.045 - 0.091: 938 0.091 - 0.136: 169 0.136 - 0.182: 14 0.182 - 0.227: 3 Chirality restraints: 4611 Sorted by residual: chirality pdb=" CA PHE A 197 " pdb=" N PHE A 197 " pdb=" C PHE A 197 " pdb=" CB PHE A 197 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CA GLU A3875 " pdb=" N GLU A3875 " pdb=" C GLU A3875 " pdb=" CB GLU A3875 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.98e-01 chirality pdb=" CA THR A2792 " pdb=" N THR A2792 " pdb=" C THR A2792 " pdb=" CB THR A2792 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.19 2.00e-01 2.50e+01 8.97e-01 ... (remaining 4608 not shown) Planarity restraints: 5143 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A3878 " 0.042 5.00e-02 4.00e+02 6.38e-02 6.52e+00 pdb=" N PRO A3879 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO A3879 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A3879 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PRO A2575 " 0.009 2.00e-02 2.50e+03 1.83e-02 3.35e+00 pdb=" C PRO A2575 " -0.032 2.00e-02 2.50e+03 pdb=" O PRO A2575 " 0.012 2.00e-02 2.50e+03 pdb=" N MET A2576 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A3386 " 0.009 2.00e-02 2.50e+03 1.71e-02 2.92e+00 pdb=" C SER A3386 " -0.030 2.00e-02 2.50e+03 pdb=" O SER A3386 " 0.011 2.00e-02 2.50e+03 pdb=" N GLU A3387 " 0.010 2.00e-02 2.50e+03 ... (remaining 5140 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 1211 2.72 - 3.26: 33974 3.26 - 3.81: 49525 3.81 - 4.35: 57868 4.35 - 4.90: 93110 Nonbonded interactions: 235688 Sorted by model distance: nonbonded pdb=" OG SER A2489 " pdb=" OE1 GLU A2490 " model vdw 2.169 2.440 nonbonded pdb=" OD1 ASP A3026 " pdb=" ND2 ASN A3028 " model vdw 2.214 2.520 nonbonded pdb=" O GLU A 41 " pdb=" OG SER A 45 " model vdw 2.222 2.440 nonbonded pdb=" O TRP A2595 " pdb=" NH1 ARG A2596 " model vdw 2.235 2.520 nonbonded pdb=" O LYS A4085 " pdb=" NE2 GLN A4092 " model vdw 2.236 2.520 ... (remaining 235683 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.110 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: 17.770 Check model and map are aligned: 0.430 Set scattering table: 0.270 Process input model: 85.070 Find NCS groups from input model: 0.930 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 110.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 29915 Z= 0.220 Angle : 0.663 11.966 40468 Z= 0.355 Chirality : 0.041 0.227 4611 Planarity : 0.004 0.064 5143 Dihedral : 14.538 86.659 11131 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 15.46 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.80 % Favored : 92.14 % Rotamer: Outliers : 0.06 % Allowed : 0.41 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % 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: -0.24 (0.15), residues: 3640 helix: 0.85 (0.11), residues: 2235 sheet: -1.39 (0.80), residues: 43 loop : -1.86 (0.18), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A2125 HIS 0.010 0.001 HIS A 935 PHE 0.018 0.001 PHE A 197 TYR 0.017 0.001 TYR A2160 ARG 0.007 0.000 ARG A3874 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 3288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 202 time to evaluate : 3.421 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 441 MET cc_start: 0.9328 (tmm) cc_final: 0.8992 (tmm) REVERT: A 476 ARG cc_start: 0.8898 (tmm160) cc_final: 0.8626 (tmm160) REVERT: A 478 CYS cc_start: 0.8017 (p) cc_final: 0.7663 (p) REVERT: A 1108 MET cc_start: 0.8809 (mpp) cc_final: 0.8435 (mpp) REVERT: A 1403 MET cc_start: 0.9447 (mpp) cc_final: 0.8943 (mpp) REVERT: A 1871 MET cc_start: 0.9349 (ttm) cc_final: 0.9137 (ptm) REVERT: A 2369 LYS cc_start: 0.7605 (mmpt) cc_final: 0.6312 (mmmm) REVERT: A 2399 GLU cc_start: 0.9341 (tt0) cc_final: 0.8716 (tm-30) REVERT: A 2576 MET cc_start: 0.9055 (pmm) cc_final: 0.8822 (pmm) REVERT: A 2894 GLU cc_start: 0.9223 (mm-30) cc_final: 0.8807 (mm-30) REVERT: A 3140 GLU cc_start: 0.8185 (tm-30) cc_final: 0.7938 (tm-30) REVERT: A 3665 MET cc_start: 0.9369 (ppp) cc_final: 0.9145 (ppp) REVERT: A 3898 LEU cc_start: 0.9355 (tp) cc_final: 0.9125 (tt) outliers start: 2 outliers final: 0 residues processed: 204 average time/residue: 0.4194 time to fit residues: 142.0467 Evaluate side-chains 162 residues out of total 3288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 162 time to evaluate : 3.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 312 optimal weight: 0.1980 chunk 280 optimal weight: 0.9990 chunk 155 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 chunk 189 optimal weight: 9.9990 chunk 149 optimal weight: 6.9990 chunk 290 optimal weight: 0.0470 chunk 112 optimal weight: 4.9990 chunk 176 optimal weight: 7.9990 chunk 215 optimal weight: 10.0000 chunk 336 optimal weight: 4.9990 overall best weight: 2.0484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1687 HIS ** A2283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4092 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.0843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 29915 Z= 0.194 Angle : 0.621 8.749 40468 Z= 0.315 Chirality : 0.040 0.214 4611 Planarity : 0.004 0.067 5143 Dihedral : 4.747 23.121 3968 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.31 % Favored : 92.66 % Rotamer: Outliers : 0.37 % Allowed : 7.62 % Favored : 92.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % 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: -0.08 (0.15), residues: 3640 helix: 0.98 (0.11), residues: 2296 sheet: -1.48 (0.69), residues: 53 loop : -1.90 (0.18), residues: 1291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A3031 HIS 0.009 0.001 HIS A 935 PHE 0.020 0.001 PHE A 78 TYR 0.013 0.001 TYR A2160 ARG 0.003 0.000 ARG A3874 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 3288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 179 time to evaluate : 3.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 476 ARG cc_start: 0.9008 (tmm160) cc_final: 0.8719 (tmm160) REVERT: A 1108 MET cc_start: 0.8795 (mpp) cc_final: 0.8524 (mpp) REVERT: A 1403 MET cc_start: 0.9447 (mpp) cc_final: 0.9091 (mpp) REVERT: A 1583 MET cc_start: 0.8988 (ttt) cc_final: 0.8674 (ttt) REVERT: A 1871 MET cc_start: 0.9365 (ttm) cc_final: 0.9130 (ptm) REVERT: A 2369 LYS cc_start: 0.7893 (mmpt) cc_final: 0.6814 (mmmm) REVERT: A 2399 GLU cc_start: 0.9332 (tt0) cc_final: 0.8689 (tm-30) REVERT: A 2576 MET cc_start: 0.9009 (pmm) cc_final: 0.8740 (pmm) REVERT: A 2894 GLU cc_start: 0.9183 (mm-30) cc_final: 0.8804 (mm-30) REVERT: A 3140 GLU cc_start: 0.8208 (tm-30) cc_final: 0.7979 (tm-30) REVERT: A 3609 MET cc_start: 0.8926 (pmm) cc_final: 0.8724 (pmm) REVERT: A 3898 LEU cc_start: 0.9365 (tp) cc_final: 0.9120 (tt) REVERT: A 4020 MET cc_start: 0.8969 (tpp) cc_final: 0.8748 (tpp) outliers start: 12 outliers final: 7 residues processed: 186 average time/residue: 0.4029 time to fit residues: 124.3467 Evaluate side-chains 165 residues out of total 3288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 158 time to evaluate : 3.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 TYR Chi-restraints excluded: chain A residue 156 PHE Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 1827 LEU Chi-restraints excluded: chain A residue 2478 MET Chi-restraints excluded: chain A residue 3174 ASP Chi-restraints excluded: chain A residue 3177 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 186 optimal weight: 20.0000 chunk 104 optimal weight: 20.0000 chunk 279 optimal weight: 2.9990 chunk 228 optimal weight: 0.9990 chunk 92 optimal weight: 0.9990 chunk 336 optimal weight: 8.9990 chunk 363 optimal weight: 0.7980 chunk 299 optimal weight: 6.9990 chunk 333 optimal weight: 0.0870 chunk 114 optimal weight: 5.9990 chunk 270 optimal weight: 3.9990 overall best weight: 1.1764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 ASN ** A 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1611 GLN A1687 HIS ** A1772 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4092 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.1180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 29915 Z= 0.157 Angle : 0.587 14.363 40468 Z= 0.292 Chirality : 0.039 0.192 4611 Planarity : 0.004 0.071 5143 Dihedral : 4.538 23.825 3968 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.51 % Favored : 93.46 % Rotamer: Outliers : 0.78 % Allowed : 10.18 % Favored : 89.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % 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: 0.12 (0.15), residues: 3640 helix: 1.16 (0.11), residues: 2280 sheet: -1.38 (0.70), residues: 53 loop : -1.84 (0.18), residues: 1307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A3031 HIS 0.007 0.001 HIS A 935 PHE 0.020 0.001 PHE A 78 TYR 0.012 0.001 TYR A1945 ARG 0.003 0.000 ARG A 142 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 3288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 177 time to evaluate : 3.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 476 ARG cc_start: 0.9006 (tmm160) cc_final: 0.8746 (tmm160) REVERT: A 1009 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8312 (tp) REVERT: A 1108 MET cc_start: 0.8811 (mpp) cc_final: 0.8493 (mpp) REVERT: A 1583 MET cc_start: 0.8984 (ttt) cc_final: 0.8578 (ttt) REVERT: A 1871 MET cc_start: 0.9344 (ttm) cc_final: 0.9101 (ptm) REVERT: A 2369 LYS cc_start: 0.8006 (mmpt) cc_final: 0.7000 (mmmm) REVERT: A 2399 GLU cc_start: 0.9321 (tt0) cc_final: 0.8664 (tm-30) REVERT: A 2894 GLU cc_start: 0.9136 (mm-30) cc_final: 0.8751 (mm-30) REVERT: A 3140 GLU cc_start: 0.8180 (tm-30) cc_final: 0.7952 (tm-30) REVERT: A 3665 MET cc_start: 0.9401 (ppp) cc_final: 0.9158 (ppp) REVERT: A 3898 LEU cc_start: 0.9344 (tp) cc_final: 0.9123 (tt) REVERT: A 4020 MET cc_start: 0.8928 (tpp) cc_final: 0.8545 (tpp) outliers start: 25 outliers final: 14 residues processed: 194 average time/residue: 0.4202 time to fit residues: 135.0628 Evaluate side-chains 178 residues out of total 3288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 163 time to evaluate : 3.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 103 TYR Chi-restraints excluded: chain A residue 156 PHE Chi-restraints excluded: chain A residue 197 PHE Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 858 MET Chi-restraints excluded: chain A residue 1009 LEU Chi-restraints excluded: chain A residue 1208 LEU Chi-restraints excluded: chain A residue 1827 LEU Chi-restraints excluded: chain A residue 2341 LEU Chi-restraints excluded: chain A residue 2478 MET Chi-restraints excluded: chain A residue 2895 GLU Chi-restraints excluded: chain A residue 3177 ASN Chi-restraints excluded: chain A residue 3256 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 332 optimal weight: 0.9990 chunk 253 optimal weight: 3.9990 chunk 174 optimal weight: 9.9990 chunk 37 optimal weight: 0.6980 chunk 160 optimal weight: 0.6980 chunk 226 optimal weight: 10.0000 chunk 337 optimal weight: 3.9990 chunk 357 optimal weight: 0.0570 chunk 176 optimal weight: 8.9990 chunk 320 optimal weight: 0.7980 chunk 96 optimal weight: 9.9990 overall best weight: 0.6500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1687 HIS A1721 HIS A1772 HIS A3339 ASN ** A4092 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 29915 Z= 0.143 Angle : 0.575 14.606 40468 Z= 0.284 Chirality : 0.039 0.193 4611 Planarity : 0.004 0.069 5143 Dihedral : 4.341 20.077 3968 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.82 % Favored : 94.15 % Rotamer: Outliers : 1.03 % Allowed : 12.05 % Favored : 86.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % 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: 0.20 (0.15), residues: 3640 helix: 1.21 (0.11), residues: 2300 sheet: -1.24 (0.69), residues: 53 loop : -1.84 (0.18), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A3031 HIS 0.006 0.001 HIS A 935 PHE 0.017 0.001 PHE A 78 TYR 0.012 0.001 TYR A2184 ARG 0.003 0.000 ARG A1854 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 3288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 183 time to evaluate : 3.438 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 96 MET cc_start: 0.6067 (tmm) cc_final: 0.5828 (tmt) REVERT: A 249 PHE cc_start: 0.9229 (OUTLIER) cc_final: 0.8979 (t80) REVERT: A 476 ARG cc_start: 0.9045 (tmm160) cc_final: 0.8792 (tmm160) REVERT: A 880 MET cc_start: 0.6045 (tpp) cc_final: 0.5514 (tpp) REVERT: A 883 TYR cc_start: 0.9031 (m-80) cc_final: 0.8770 (m-80) REVERT: A 1108 MET cc_start: 0.8799 (mpp) cc_final: 0.8507 (mpp) REVERT: A 1258 ASP cc_start: 0.8776 (t0) cc_final: 0.8515 (t0) REVERT: A 1871 MET cc_start: 0.9337 (ttm) cc_final: 0.9055 (ptm) REVERT: A 2369 LYS cc_start: 0.8121 (mmpt) cc_final: 0.7330 (mmmm) REVERT: A 2399 GLU cc_start: 0.9309 (tt0) cc_final: 0.8609 (tm-30) REVERT: A 2894 GLU cc_start: 0.9119 (mm-30) cc_final: 0.8752 (mm-30) REVERT: A 2933 ILE cc_start: 0.9510 (tt) cc_final: 0.9015 (tt) REVERT: A 3140 GLU cc_start: 0.8152 (tm-30) cc_final: 0.7866 (tm-30) REVERT: A 3898 LEU cc_start: 0.9328 (tp) cc_final: 0.9112 (tt) REVERT: A 3929 MET cc_start: 0.8918 (mmm) cc_final: 0.8717 (mtm) REVERT: A 3971 MET cc_start: 0.8537 (mmm) cc_final: 0.8018 (mtp) REVERT: A 4020 MET cc_start: 0.8901 (tpp) cc_final: 0.8486 (tpp) outliers start: 33 outliers final: 11 residues processed: 206 average time/residue: 0.4145 time to fit residues: 143.6774 Evaluate side-chains 177 residues out of total 3288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 165 time to evaluate : 3.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 TYR Chi-restraints excluded: chain A residue 197 PHE Chi-restraints excluded: chain A residue 249 PHE Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 1208 LEU Chi-restraints excluded: chain A residue 1724 MET Chi-restraints excluded: chain A residue 1827 LEU Chi-restraints excluded: chain A residue 2895 GLU Chi-restraints excluded: chain A residue 3783 GLN Chi-restraints excluded: chain A residue 3875 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 297 optimal weight: 10.0000 chunk 203 optimal weight: 1.9990 chunk 5 optimal weight: 8.9990 chunk 266 optimal weight: 20.0000 chunk 147 optimal weight: 5.9990 chunk 305 optimal weight: 0.7980 chunk 247 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 182 optimal weight: 6.9990 chunk 321 optimal weight: 0.9980 chunk 90 optimal weight: 0.0980 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1687 HIS ** A2859 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4092 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 29915 Z= 0.174 Angle : 0.572 11.504 40468 Z= 0.282 Chirality : 0.039 0.191 4611 Planarity : 0.004 0.069 5143 Dihedral : 4.295 21.059 3968 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.04 % Favored : 93.93 % Rotamer: Outliers : 1.22 % Allowed : 13.33 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % 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: 0.30 (0.15), residues: 3640 helix: 1.30 (0.11), residues: 2299 sheet: -1.12 (0.69), residues: 53 loop : -1.82 (0.18), residues: 1288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A3031 HIS 0.008 0.001 HIS A2787 PHE 0.016 0.001 PHE A 78 TYR 0.012 0.001 TYR A2184 ARG 0.002 0.000 ARG A 852 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 3288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 173 time to evaluate : 3.402 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 96 MET cc_start: 0.5848 (tmm) cc_final: 0.5595 (tmt) REVERT: A 208 MET cc_start: 0.8753 (tpp) cc_final: 0.8506 (tpp) REVERT: A 410 MET cc_start: 0.9149 (mmt) cc_final: 0.8814 (mmt) REVERT: A 476 ARG cc_start: 0.9037 (tmm160) cc_final: 0.8762 (tmm160) REVERT: A 883 TYR cc_start: 0.9048 (m-80) cc_final: 0.8845 (m-80) REVERT: A 1009 LEU cc_start: 0.8954 (pp) cc_final: 0.8436 (tp) REVERT: A 1108 MET cc_start: 0.8845 (OUTLIER) cc_final: 0.8529 (mpp) REVERT: A 1258 ASP cc_start: 0.8845 (t0) cc_final: 0.8543 (t0) REVERT: A 1342 MET cc_start: 0.9282 (mmm) cc_final: 0.9039 (mmm) REVERT: A 1762 MET cc_start: 0.9553 (mmm) cc_final: 0.9217 (mmt) REVERT: A 1871 MET cc_start: 0.9374 (ttm) cc_final: 0.9061 (ptm) REVERT: A 2281 MET cc_start: 0.8929 (mmp) cc_final: 0.8604 (tpp) REVERT: A 2369 LYS cc_start: 0.8233 (mmpt) cc_final: 0.7490 (mmmm) REVERT: A 2399 GLU cc_start: 0.9303 (tt0) cc_final: 0.8604 (tm-30) REVERT: A 2894 GLU cc_start: 0.9132 (mm-30) cc_final: 0.8790 (mm-30) REVERT: A 3140 GLU cc_start: 0.8195 (tm-30) cc_final: 0.7904 (tm-30) REVERT: A 3665 MET cc_start: 0.9440 (ppp) cc_final: 0.9217 (ppp) REVERT: A 3898 LEU cc_start: 0.9313 (tp) cc_final: 0.9100 (tt) REVERT: A 3971 MET cc_start: 0.8570 (mmm) cc_final: 0.8104 (mtp) REVERT: A 4020 MET cc_start: 0.8910 (tpp) cc_final: 0.8487 (tpp) outliers start: 39 outliers final: 23 residues processed: 199 average time/residue: 0.3972 time to fit residues: 132.4847 Evaluate side-chains 188 residues out of total 3288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 164 time to evaluate : 3.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 103 TYR Chi-restraints excluded: chain A residue 197 PHE Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 858 MET Chi-restraints excluded: chain A residue 996 THR Chi-restraints excluded: chain A residue 1108 MET Chi-restraints excluded: chain A residue 1123 THR Chi-restraints excluded: chain A residue 1208 LEU Chi-restraints excluded: chain A residue 1724 MET Chi-restraints excluded: chain A residue 1827 LEU Chi-restraints excluded: chain A residue 1955 VAL Chi-restraints excluded: chain A residue 2126 MET Chi-restraints excluded: chain A residue 2301 GLN Chi-restraints excluded: chain A residue 2478 MET Chi-restraints excluded: chain A residue 2895 GLU Chi-restraints excluded: chain A residue 3174 ASP Chi-restraints excluded: chain A residue 3390 GLN Chi-restraints excluded: chain A residue 3512 VAL Chi-restraints excluded: chain A residue 3783 GLN Chi-restraints excluded: chain A residue 3875 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 120 optimal weight: 7.9990 chunk 322 optimal weight: 8.9990 chunk 70 optimal weight: 2.9990 chunk 209 optimal weight: 2.9990 chunk 88 optimal weight: 5.9990 chunk 357 optimal weight: 7.9990 chunk 297 optimal weight: 10.0000 chunk 165 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 187 optimal weight: 4.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 947 GLN A1048 GLN ** A1367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1687 HIS ** A2152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2787 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2859 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3130 GLN ** A4092 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 29915 Z= 0.194 Angle : 0.583 11.940 40468 Z= 0.287 Chirality : 0.039 0.270 4611 Planarity : 0.004 0.068 5143 Dihedral : 4.278 22.781 3968 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.32 % Favored : 93.63 % Rotamer: Outliers : 1.56 % Allowed : 14.08 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % 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: 0.35 (0.15), residues: 3640 helix: 1.32 (0.11), residues: 2308 sheet: -1.09 (0.69), residues: 53 loop : -1.78 (0.18), residues: 1279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A3031 HIS 0.006 0.001 HIS A 935 PHE 0.016 0.001 PHE A 78 TYR 0.011 0.001 TYR A2184 ARG 0.003 0.000 ARG A1026 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 3288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 173 time to evaluate : 3.357 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 208 MET cc_start: 0.8769 (tpp) cc_final: 0.8549 (tpp) REVERT: A 410 MET cc_start: 0.9145 (mmt) cc_final: 0.8774 (mmt) REVERT: A 476 ARG cc_start: 0.9022 (tmm160) cc_final: 0.8728 (tmm160) REVERT: A 541 MET cc_start: 0.9215 (OUTLIER) cc_final: 0.8733 (tpp) REVERT: A 1009 LEU cc_start: 0.8931 (pp) cc_final: 0.8389 (tp) REVERT: A 1108 MET cc_start: 0.8835 (OUTLIER) cc_final: 0.8570 (mpp) REVERT: A 1197 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8909 (pp) REVERT: A 1258 ASP cc_start: 0.8880 (t0) cc_final: 0.8539 (t0) REVERT: A 1583 MET cc_start: 0.9027 (ttt) cc_final: 0.8494 (ttt) REVERT: A 1871 MET cc_start: 0.9387 (ttm) cc_final: 0.9027 (ptm) REVERT: A 1878 ASP cc_start: 0.8483 (t70) cc_final: 0.7774 (t0) REVERT: A 2281 MET cc_start: 0.8956 (mmp) cc_final: 0.8618 (tpp) REVERT: A 2369 LYS cc_start: 0.8357 (mmpt) cc_final: 0.7628 (mmmm) REVERT: A 2399 GLU cc_start: 0.9310 (tt0) cc_final: 0.8613 (tm-30) REVERT: A 2894 GLU cc_start: 0.9147 (mm-30) cc_final: 0.8784 (mm-30) REVERT: A 3140 GLU cc_start: 0.8213 (tm-30) cc_final: 0.7905 (tm-30) REVERT: A 3238 MET cc_start: 0.8883 (tpp) cc_final: 0.8653 (tpp) REVERT: A 3858 MET cc_start: 0.9390 (tmm) cc_final: 0.9175 (tmm) REVERT: A 3898 LEU cc_start: 0.9327 (tp) cc_final: 0.9104 (tt) REVERT: A 3971 MET cc_start: 0.8618 (mmm) cc_final: 0.8097 (mtp) REVERT: A 4020 MET cc_start: 0.8899 (tpp) cc_final: 0.8440 (tpp) REVERT: A 4108 MET cc_start: 0.9307 (mmm) cc_final: 0.9102 (mmt) outliers start: 50 outliers final: 28 residues processed: 212 average time/residue: 0.4035 time to fit residues: 143.9419 Evaluate side-chains 195 residues out of total 3288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 164 time to evaluate : 3.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 103 TYR Chi-restraints excluded: chain A residue 197 PHE Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 541 MET Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 858 MET Chi-restraints excluded: chain A residue 905 ILE Chi-restraints excluded: chain A residue 996 THR Chi-restraints excluded: chain A residue 1108 MET Chi-restraints excluded: chain A residue 1123 THR Chi-restraints excluded: chain A residue 1197 LEU Chi-restraints excluded: chain A residue 1208 LEU Chi-restraints excluded: chain A residue 1724 MET Chi-restraints excluded: chain A residue 1827 LEU Chi-restraints excluded: chain A residue 1955 VAL Chi-restraints excluded: chain A residue 2126 MET Chi-restraints excluded: chain A residue 2266 ASN Chi-restraints excluded: chain A residue 2301 GLN Chi-restraints excluded: chain A residue 2478 MET Chi-restraints excluded: chain A residue 2895 GLU Chi-restraints excluded: chain A residue 3174 ASP Chi-restraints excluded: chain A residue 3177 ASN Chi-restraints excluded: chain A residue 3390 GLN Chi-restraints excluded: chain A residue 3512 VAL Chi-restraints excluded: chain A residue 3783 GLN Chi-restraints excluded: chain A residue 3875 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 345 optimal weight: 0.8980 chunk 40 optimal weight: 10.0000 chunk 203 optimal weight: 9.9990 chunk 261 optimal weight: 7.9990 chunk 202 optimal weight: 4.9990 chunk 301 optimal weight: 7.9990 chunk 199 optimal weight: 0.5980 chunk 356 optimal weight: 5.9990 chunk 223 optimal weight: 6.9990 chunk 217 optimal weight: 5.9990 chunk 164 optimal weight: 9.9990 overall best weight: 3.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1610 ASN A1687 HIS ** A2152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2859 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4092 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 29915 Z= 0.247 Angle : 0.617 15.346 40468 Z= 0.304 Chirality : 0.040 0.193 4611 Planarity : 0.004 0.058 5143 Dihedral : 4.336 22.640 3968 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.23 % Favored : 92.75 % Rotamer: Outliers : 1.59 % Allowed : 14.70 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % 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: 0.36 (0.15), residues: 3640 helix: 1.34 (0.11), residues: 2295 sheet: -1.14 (0.68), residues: 53 loop : -1.77 (0.18), residues: 1292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A3031 HIS 0.006 0.001 HIS A 935 PHE 0.015 0.001 PHE A 78 TYR 0.018 0.001 TYR A 883 ARG 0.003 0.000 ARG A1026 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 3288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 169 time to evaluate : 3.688 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 96 MET cc_start: 0.5311 (tmt) cc_final: 0.5099 (tmt) REVERT: A 476 ARG cc_start: 0.9014 (tmm160) cc_final: 0.8780 (tmm160) REVERT: A 541 MET cc_start: 0.9220 (tpp) cc_final: 0.8739 (tpp) REVERT: A 785 MET cc_start: 0.9067 (tpp) cc_final: 0.8440 (tmm) REVERT: A 1009 LEU cc_start: 0.8944 (pp) cc_final: 0.8404 (tp) REVERT: A 1108 MET cc_start: 0.8853 (OUTLIER) cc_final: 0.8574 (mpp) REVERT: A 1197 LEU cc_start: 0.9166 (OUTLIER) cc_final: 0.8927 (pp) REVERT: A 1258 ASP cc_start: 0.8921 (t0) cc_final: 0.8582 (t0) REVERT: A 1762 MET cc_start: 0.9451 (mmt) cc_final: 0.9249 (mmm) REVERT: A 1871 MET cc_start: 0.9423 (ttm) cc_final: 0.9052 (ptm) REVERT: A 1878 ASP cc_start: 0.8516 (t70) cc_final: 0.7819 (t70) REVERT: A 2281 MET cc_start: 0.8991 (mmp) cc_final: 0.8659 (tpp) REVERT: A 2369 LYS cc_start: 0.8488 (mmpt) cc_final: 0.7948 (mmmm) REVERT: A 2399 GLU cc_start: 0.9309 (tt0) cc_final: 0.8603 (tm-30) REVERT: A 2894 GLU cc_start: 0.9179 (mm-30) cc_final: 0.8828 (mm-30) REVERT: A 3140 GLU cc_start: 0.8250 (tm-30) cc_final: 0.7939 (tm-30) REVERT: A 3238 MET cc_start: 0.8893 (tpp) cc_final: 0.8658 (tpp) REVERT: A 3665 MET cc_start: 0.9458 (ppp) cc_final: 0.9243 (ppp) REVERT: A 3890 MET cc_start: 0.8703 (OUTLIER) cc_final: 0.8208 (ptp) REVERT: A 4020 MET cc_start: 0.8892 (tpp) cc_final: 0.8425 (tpp) outliers start: 51 outliers final: 36 residues processed: 208 average time/residue: 0.4124 time to fit residues: 145.6520 Evaluate side-chains 200 residues out of total 3288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 161 time to evaluate : 3.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 103 TYR Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 197 PHE Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 858 MET Chi-restraints excluded: chain A residue 905 ILE Chi-restraints excluded: chain A residue 958 MET Chi-restraints excluded: chain A residue 996 THR Chi-restraints excluded: chain A residue 1045 THR Chi-restraints excluded: chain A residue 1108 MET Chi-restraints excluded: chain A residue 1123 THR Chi-restraints excluded: chain A residue 1135 CYS Chi-restraints excluded: chain A residue 1197 LEU Chi-restraints excluded: chain A residue 1208 LEU Chi-restraints excluded: chain A residue 1610 ASN Chi-restraints excluded: chain A residue 1827 LEU Chi-restraints excluded: chain A residue 1955 VAL Chi-restraints excluded: chain A residue 2126 MET Chi-restraints excluded: chain A residue 2266 ASN Chi-restraints excluded: chain A residue 2301 GLN Chi-restraints excluded: chain A residue 2478 MET Chi-restraints excluded: chain A residue 2895 GLU Chi-restraints excluded: chain A residue 2933 ILE Chi-restraints excluded: chain A residue 3174 ASP Chi-restraints excluded: chain A residue 3177 ASN Chi-restraints excluded: chain A residue 3390 GLN Chi-restraints excluded: chain A residue 3512 VAL Chi-restraints excluded: chain A residue 3530 VAL Chi-restraints excluded: chain A residue 3729 MET Chi-restraints excluded: chain A residue 3783 GLN Chi-restraints excluded: chain A residue 3875 GLU Chi-restraints excluded: chain A residue 3890 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 220 optimal weight: 0.9990 chunk 142 optimal weight: 5.9990 chunk 212 optimal weight: 7.9990 chunk 107 optimal weight: 0.9980 chunk 70 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 chunk 226 optimal weight: 3.9990 chunk 242 optimal weight: 3.9990 chunk 176 optimal weight: 20.0000 chunk 33 optimal weight: 0.9980 chunk 280 optimal weight: 5.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1687 HIS ** A2152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2859 GLN ** A4092 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.064 29915 Z= 0.156 Angle : 0.608 14.593 40468 Z= 0.292 Chirality : 0.039 0.196 4611 Planarity : 0.004 0.057 5143 Dihedral : 4.246 23.895 3968 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.04 % Favored : 93.93 % Rotamer: Outliers : 1.22 % Allowed : 15.83 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % 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: 0.38 (0.15), residues: 3640 helix: 1.32 (0.11), residues: 2307 sheet: -0.95 (0.69), residues: 53 loop : -1.73 (0.18), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A3031 HIS 0.010 0.001 HIS A2787 PHE 0.014 0.001 PHE A1923 TYR 0.015 0.001 TYR A 883 ARG 0.004 0.000 ARG A1608 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 3288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 171 time to evaluate : 3.692 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 14 ARG cc_start: 0.8553 (ptt180) cc_final: 0.8307 (ptt-90) REVERT: A 476 ARG cc_start: 0.9027 (tmm160) cc_final: 0.8736 (tmm160) REVERT: A 541 MET cc_start: 0.9180 (tpp) cc_final: 0.8685 (tpp) REVERT: A 1009 LEU cc_start: 0.8852 (pp) cc_final: 0.8278 (tp) REVERT: A 1108 MET cc_start: 0.8774 (OUTLIER) cc_final: 0.8515 (mpp) REVERT: A 1197 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8879 (pp) REVERT: A 1258 ASP cc_start: 0.8889 (t0) cc_final: 0.8515 (t0) REVERT: A 1305 ASP cc_start: 0.8625 (m-30) cc_final: 0.7551 (p0) REVERT: A 1583 MET cc_start: 0.9051 (ttp) cc_final: 0.8415 (tmm) REVERT: A 1871 MET cc_start: 0.9385 (ttm) cc_final: 0.8996 (ptm) REVERT: A 2279 ILE cc_start: 0.9167 (OUTLIER) cc_final: 0.8957 (mm) REVERT: A 2281 MET cc_start: 0.8936 (mmp) cc_final: 0.8604 (tpp) REVERT: A 2307 MET cc_start: 0.8706 (mmm) cc_final: 0.8486 (mmt) REVERT: A 2369 LYS cc_start: 0.8449 (mmpt) cc_final: 0.8137 (mmmm) REVERT: A 2399 GLU cc_start: 0.9273 (tt0) cc_final: 0.8606 (tp30) REVERT: A 2894 GLU cc_start: 0.9123 (mm-30) cc_final: 0.8734 (mm-30) REVERT: A 3140 GLU cc_start: 0.8232 (tm-30) cc_final: 0.7912 (tm-30) REVERT: A 3665 MET cc_start: 0.9458 (ppp) cc_final: 0.9239 (ppp) REVERT: A 3898 LEU cc_start: 0.9306 (tp) cc_final: 0.9099 (tt) REVERT: A 3971 MET cc_start: 0.8591 (mmm) cc_final: 0.8034 (mtp) REVERT: A 4020 MET cc_start: 0.8870 (tpp) cc_final: 0.8395 (tpp) outliers start: 39 outliers final: 30 residues processed: 202 average time/residue: 0.4135 time to fit residues: 140.6250 Evaluate side-chains 196 residues out of total 3288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 163 time to evaluate : 3.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 103 TYR Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 197 PHE Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 858 MET Chi-restraints excluded: chain A residue 958 MET Chi-restraints excluded: chain A residue 996 THR Chi-restraints excluded: chain A residue 1045 THR Chi-restraints excluded: chain A residue 1108 MET Chi-restraints excluded: chain A residue 1123 THR Chi-restraints excluded: chain A residue 1135 CYS Chi-restraints excluded: chain A residue 1197 LEU Chi-restraints excluded: chain A residue 1208 LEU Chi-restraints excluded: chain A residue 1827 LEU Chi-restraints excluded: chain A residue 1955 VAL Chi-restraints excluded: chain A residue 2126 MET Chi-restraints excluded: chain A residue 2266 ASN Chi-restraints excluded: chain A residue 2279 ILE Chi-restraints excluded: chain A residue 2301 GLN Chi-restraints excluded: chain A residue 2478 MET Chi-restraints excluded: chain A residue 2895 GLU Chi-restraints excluded: chain A residue 3177 ASN Chi-restraints excluded: chain A residue 3390 GLN Chi-restraints excluded: chain A residue 3512 VAL Chi-restraints excluded: chain A residue 3783 GLN Chi-restraints excluded: chain A residue 3875 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 324 optimal weight: 0.6980 chunk 341 optimal weight: 4.9990 chunk 311 optimal weight: 0.8980 chunk 332 optimal weight: 0.8980 chunk 200 optimal weight: 10.0000 chunk 144 optimal weight: 7.9990 chunk 260 optimal weight: 0.0770 chunk 101 optimal weight: 3.9990 chunk 300 optimal weight: 4.9990 chunk 314 optimal weight: 0.0070 chunk 331 optimal weight: 0.8980 overall best weight: 0.5156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1367 HIS A1610 ASN A1687 HIS ** A2152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4092 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 29915 Z= 0.147 Angle : 0.605 13.787 40468 Z= 0.291 Chirality : 0.039 0.205 4611 Planarity : 0.004 0.081 5143 Dihedral : 4.154 24.419 3968 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.91 % Favored : 94.07 % Rotamer: Outliers : 1.28 % Allowed : 16.20 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % 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: 0.40 (0.15), residues: 3640 helix: 1.34 (0.11), residues: 2304 sheet: -1.24 (0.67), residues: 57 loop : -1.71 (0.18), residues: 1279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A3031 HIS 0.011 0.001 HIS A2787 PHE 0.016 0.001 PHE A 138 TYR 0.013 0.001 TYR A 883 ARG 0.022 0.000 ARG A 139 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 3288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 179 time to evaluate : 3.187 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 14 ARG cc_start: 0.8524 (ptt180) cc_final: 0.8288 (ptt-90) REVERT: A 96 MET cc_start: 0.5348 (tmt) cc_final: 0.5024 (tmt) REVERT: A 476 ARG cc_start: 0.9036 (tmm160) cc_final: 0.8756 (tmm160) REVERT: A 541 MET cc_start: 0.9166 (tpp) cc_final: 0.8660 (tpp) REVERT: A 1108 MET cc_start: 0.8735 (OUTLIER) cc_final: 0.8508 (mpp) REVERT: A 1197 LEU cc_start: 0.9095 (OUTLIER) cc_final: 0.8863 (pp) REVERT: A 1258 ASP cc_start: 0.8885 (t0) cc_final: 0.8540 (t0) REVERT: A 1305 ASP cc_start: 0.8556 (m-30) cc_final: 0.7603 (p0) REVERT: A 1583 MET cc_start: 0.8956 (ttp) cc_final: 0.8550 (ttp) REVERT: A 1762 MET cc_start: 0.9478 (mmm) cc_final: 0.9186 (mmm) REVERT: A 1871 MET cc_start: 0.9359 (ttm) cc_final: 0.8993 (ptm) REVERT: A 2281 MET cc_start: 0.8940 (mmp) cc_final: 0.8601 (tpp) REVERT: A 2307 MET cc_start: 0.8695 (mmm) cc_final: 0.8491 (mmt) REVERT: A 2399 GLU cc_start: 0.9266 (tt0) cc_final: 0.8622 (tp30) REVERT: A 2801 ASP cc_start: 0.8592 (t0) cc_final: 0.8074 (t0) REVERT: A 2894 GLU cc_start: 0.9104 (mm-30) cc_final: 0.8716 (mm-30) REVERT: A 3140 GLU cc_start: 0.8244 (tm-30) cc_final: 0.7898 (tm-30) REVERT: A 3238 MET cc_start: 0.8869 (tpp) cc_final: 0.8636 (tpp) REVERT: A 4020 MET cc_start: 0.8850 (tpp) cc_final: 0.8374 (tpp) outliers start: 41 outliers final: 32 residues processed: 209 average time/residue: 0.4053 time to fit residues: 143.8091 Evaluate side-chains 199 residues out of total 3288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 165 time to evaluate : 3.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 103 TYR Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 197 PHE Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 858 MET Chi-restraints excluded: chain A residue 958 MET Chi-restraints excluded: chain A residue 996 THR Chi-restraints excluded: chain A residue 1045 THR Chi-restraints excluded: chain A residue 1108 MET Chi-restraints excluded: chain A residue 1123 THR Chi-restraints excluded: chain A residue 1135 CYS Chi-restraints excluded: chain A residue 1197 LEU Chi-restraints excluded: chain A residue 1208 LEU Chi-restraints excluded: chain A residue 1610 ASN Chi-restraints excluded: chain A residue 1724 MET Chi-restraints excluded: chain A residue 1827 LEU Chi-restraints excluded: chain A residue 1955 VAL Chi-restraints excluded: chain A residue 2126 MET Chi-restraints excluded: chain A residue 2301 GLN Chi-restraints excluded: chain A residue 2478 MET Chi-restraints excluded: chain A residue 2895 GLU Chi-restraints excluded: chain A residue 3177 ASN Chi-restraints excluded: chain A residue 3390 GLN Chi-restraints excluded: chain A residue 3512 VAL Chi-restraints excluded: chain A residue 3729 MET Chi-restraints excluded: chain A residue 3783 GLN Chi-restraints excluded: chain A residue 3875 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 218 optimal weight: 8.9990 chunk 351 optimal weight: 5.9990 chunk 214 optimal weight: 6.9990 chunk 166 optimal weight: 5.9990 chunk 244 optimal weight: 0.8980 chunk 368 optimal weight: 20.0000 chunk 339 optimal weight: 10.0000 chunk 293 optimal weight: 3.9990 chunk 30 optimal weight: 10.0000 chunk 226 optimal weight: 0.9980 chunk 179 optimal weight: 5.9990 overall best weight: 3.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 484 HIS A1687 HIS ** A2152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 29915 Z= 0.243 Angle : 0.643 12.506 40468 Z= 0.310 Chirality : 0.040 0.220 4611 Planarity : 0.004 0.059 5143 Dihedral : 4.207 24.261 3968 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.40 % Favored : 93.57 % Rotamer: Outliers : 1.28 % Allowed : 16.36 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % 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: 0.42 (0.15), residues: 3640 helix: 1.34 (0.11), residues: 2330 sheet: -0.89 (0.67), residues: 53 loop : -1.74 (0.18), residues: 1257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A3031 HIS 0.010 0.001 HIS A2787 PHE 0.014 0.001 PHE A2145 TYR 0.013 0.001 TYR A2184 ARG 0.008 0.000 ARG A 139 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 3288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 162 time to evaluate : 3.419 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 96 MET cc_start: 0.5404 (tmt) cc_final: 0.5117 (tmt) REVERT: A 138 PHE cc_start: 0.9284 (m-80) cc_final: 0.8897 (m-80) REVERT: A 541 MET cc_start: 0.9193 (tpp) cc_final: 0.8696 (tpp) REVERT: A 785 MET cc_start: 0.9102 (tpp) cc_final: 0.8381 (tmm) REVERT: A 1108 MET cc_start: 0.8798 (OUTLIER) cc_final: 0.8538 (mpp) REVERT: A 1197 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8902 (pp) REVERT: A 1258 ASP cc_start: 0.8938 (t0) cc_final: 0.8605 (t0) REVERT: A 1305 ASP cc_start: 0.8674 (m-30) cc_final: 0.7661 (p0) REVERT: A 1583 MET cc_start: 0.9023 (ttp) cc_final: 0.8633 (ttp) REVERT: A 1871 MET cc_start: 0.9397 (ttm) cc_final: 0.9000 (ptm) REVERT: A 2279 ILE cc_start: 0.9154 (OUTLIER) cc_final: 0.8930 (mm) REVERT: A 2281 MET cc_start: 0.8998 (mmp) cc_final: 0.8665 (tpp) REVERT: A 2399 GLU cc_start: 0.9393 (tt0) cc_final: 0.8650 (tp30) REVERT: A 2801 ASP cc_start: 0.8626 (t0) cc_final: 0.8122 (t0) REVERT: A 2894 GLU cc_start: 0.9159 (mm-30) cc_final: 0.8827 (mm-30) REVERT: A 3140 GLU cc_start: 0.8286 (tm-30) cc_final: 0.7957 (tm-30) REVERT: A 3238 MET cc_start: 0.8861 (tpp) cc_final: 0.8641 (tpp) REVERT: A 4020 MET cc_start: 0.8865 (tpp) cc_final: 0.8399 (tpp) outliers start: 41 outliers final: 34 residues processed: 194 average time/residue: 0.3966 time to fit residues: 132.2886 Evaluate side-chains 197 residues out of total 3288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 160 time to evaluate : 3.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 103 TYR Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 197 PHE Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 858 MET Chi-restraints excluded: chain A residue 905 ILE Chi-restraints excluded: chain A residue 958 MET Chi-restraints excluded: chain A residue 996 THR Chi-restraints excluded: chain A residue 1045 THR Chi-restraints excluded: chain A residue 1108 MET Chi-restraints excluded: chain A residue 1123 THR Chi-restraints excluded: chain A residue 1135 CYS Chi-restraints excluded: chain A residue 1197 LEU Chi-restraints excluded: chain A residue 1208 LEU Chi-restraints excluded: chain A residue 1267 TYR Chi-restraints excluded: chain A residue 1724 MET Chi-restraints excluded: chain A residue 1827 LEU Chi-restraints excluded: chain A residue 1955 VAL Chi-restraints excluded: chain A residue 2126 MET Chi-restraints excluded: chain A residue 2279 ILE Chi-restraints excluded: chain A residue 2301 GLN Chi-restraints excluded: chain A residue 2478 MET Chi-restraints excluded: chain A residue 2895 GLU Chi-restraints excluded: chain A residue 3177 ASN Chi-restraints excluded: chain A residue 3390 GLN Chi-restraints excluded: chain A residue 3512 VAL Chi-restraints excluded: chain A residue 3530 VAL Chi-restraints excluded: chain A residue 3729 MET Chi-restraints excluded: chain A residue 3783 GLN Chi-restraints excluded: chain A residue 3875 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 233 optimal weight: 1.9990 chunk 312 optimal weight: 0.8980 chunk 89 optimal weight: 0.8980 chunk 270 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 81 optimal weight: 10.0000 chunk 293 optimal weight: 4.9990 chunk 123 optimal weight: 0.6980 chunk 301 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 54 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 442 GLN A1687 HIS ** A2152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4092 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.053677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.040340 restraints weight = 164654.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.041785 restraints weight = 92112.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.042739 restraints weight = 62426.036| |-----------------------------------------------------------------------------| r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 29915 Z= 0.151 Angle : 0.624 13.013 40468 Z= 0.296 Chirality : 0.040 0.213 4611 Planarity : 0.004 0.059 5143 Dihedral : 4.159 24.543 3968 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.07 % Favored : 93.90 % Rotamer: Outliers : 1.12 % Allowed : 16.80 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % 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: 0.39 (0.15), residues: 3640 helix: 1.32 (0.11), residues: 2326 sheet: -1.25 (0.66), residues: 59 loop : -1.74 (0.18), residues: 1255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A3031 HIS 0.009 0.001 HIS A2787 PHE 0.015 0.001 PHE A1923 TYR 0.017 0.001 TYR A2184 ARG 0.009 0.000 ARG A 139 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5868.21 seconds wall clock time: 107 minutes 36.86 seconds (6456.86 seconds total)