Starting phenix.real_space_refine on Sat Feb 24 15:32:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sgl_25113/02_2024/7sgl_25113_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sgl_25113/02_2024/7sgl_25113.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sgl_25113/02_2024/7sgl_25113.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sgl_25113/02_2024/7sgl_25113.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sgl_25113/02_2024/7sgl_25113_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sgl_25113/02_2024/7sgl_25113_updated.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 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: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 74 5.49 5 Mg 3 5.21 5 S 264 5.16 5 C 28365 2.51 5 N 7583 2.21 5 O 8414 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 24": "NH1" <-> "NH2" Residue "A ARG 61": "NH1" <-> "NH2" Residue "A ARG 119": "NH1" <-> "NH2" Residue "A ARG 142": "NH1" <-> "NH2" Residue "A GLU 176": "OE1" <-> "OE2" Residue "A GLU 194": "OE1" <-> "OE2" Residue "A GLU 203": "OE1" <-> "OE2" Residue "A ARG 264": "NH1" <-> "NH2" Residue "A GLU 387": "OE1" <-> "OE2" Residue "A GLU 436": "OE1" <-> "OE2" Residue "A GLU 774": "OE1" <-> "OE2" Residue "A ARG 820": "NH1" <-> "NH2" Residue "A GLU 878": "OE1" <-> "OE2" Residue "A ARG 888": "NH1" <-> "NH2" Residue "A ARG 891": "NH1" <-> "NH2" Residue "A ARG 913": "NH1" <-> "NH2" Residue "A ARG 1087": "NH1" <-> "NH2" Residue "A ARG 1090": "NH1" <-> "NH2" Residue "A ARG 1151": "NH1" <-> "NH2" Residue "A ARG 1184": "NH1" <-> "NH2" Residue "A ARG 1245": "NH1" <-> "NH2" Residue "A GLU 1265": "OE1" <-> "OE2" Residue "A GLU 1273": "OE1" <-> "OE2" Residue "A GLU 1299": "OE1" <-> "OE2" Residue "A GLU 1343": "OE1" <-> "OE2" Residue "A ARG 1445": "NH1" <-> "NH2" Residue "A ARG 1460": "NH1" <-> "NH2" Residue "A GLU 1482": "OE1" <-> "OE2" Residue "A ARG 1606": "NH1" <-> "NH2" Residue "A ARG 1608": "NH1" <-> "NH2" Residue "A GLU 1715": "OE1" <-> "OE2" Residue "A ARG 1768": "NH1" <-> "NH2" Residue "A ARG 1811": "NH1" <-> "NH2" Residue "A ARG 1816": "NH1" <-> "NH2" Residue "A ARG 1837": "NH1" <-> "NH2" Residue "A ARG 1854": "NH1" <-> "NH2" Residue "A ASP 1878": "OD1" <-> "OD2" Residue "A ARG 1883": "NH1" <-> "NH2" Residue "A ARG 1938": "NH1" <-> "NH2" Residue "A ARG 2008": "NH1" <-> "NH2" Residue "A ARG 2012": "NH1" <-> "NH2" Residue "A GLU 2013": "OE1" <-> "OE2" Residue "A GLU 2038": "OE1" <-> "OE2" Residue "A ARG 2106": "NH1" <-> "NH2" Residue "A ARG 2120": "NH1" <-> "NH2" Residue "A ARG 2214": "NH1" <-> "NH2" Residue "A ARG 2232": "NH1" <-> "NH2" Residue "A ARG 2254": "NH1" <-> "NH2" Residue "A ARG 2311": "NH1" <-> "NH2" Residue "A ARG 2333": "NH1" <-> "NH2" Residue "A GLU 2357": "OE1" <-> "OE2" Residue "A ARG 2431": "NH1" <-> "NH2" Residue "A ARG 2522": "NH1" <-> "NH2" Residue "A GLU 2588": "OE1" <-> "OE2" Residue "A ARG 2776": "NH1" <-> "NH2" Residue "A GLU 2894": "OE1" <-> "OE2" Residue "A ARG 2899": "NH1" <-> "NH2" Residue "A ARG 2922": "NH1" <-> "NH2" Residue "A GLU 2946": "OE1" <-> "OE2" Residue "A GLU 3085": "OE1" <-> "OE2" Residue "A ARG 3098": "NH1" <-> "NH2" Residue "A GLU 3137": "OE1" <-> "OE2" Residue "A ARG 3167": "NH1" <-> "NH2" Residue "A ARG 3269": "NH1" <-> "NH2" Residue "A ARG 3282": "NH1" <-> "NH2" Residue "A ARG 3289": "NH1" <-> "NH2" Residue "A ARG 3324": "NH1" <-> "NH2" Residue "A ARG 3335": "NH1" <-> "NH2" Residue "A ARG 3357": "NH1" <-> "NH2" Residue "A ARG 3380": "NH1" <-> "NH2" Residue "A ARG 3425": "NH1" <-> "NH2" Residue "A GLU 3429": "OE1" <-> "OE2" Residue "A GLU 3520": "OE1" <-> "OE2" Residue "A ARG 3557": "NH1" <-> "NH2" Residue "A ARG 3653": "NH1" <-> "NH2" Residue "A GLU 3693": "OE1" <-> "OE2" Residue "A ARG 3696": "NH1" <-> "NH2" Residue "A ARG 3708": "NH1" <-> "NH2" Residue "A ARG 3737": "NH1" <-> "NH2" Residue "A ARG 3741": "NH1" <-> "NH2" Residue "A ARG 3746": "NH1" <-> "NH2" Residue "A ARG 3759": "NH1" <-> "NH2" Residue "A ARG 3763": "NH1" <-> "NH2" Residue "A ARG 3784": "NH1" <-> "NH2" Residue "A ARG 3789": "NH1" <-> "NH2" Residue "A ARG 3799": "NH1" <-> "NH2" Residue "A ARG 3833": "NH1" <-> "NH2" Residue "A ARG 3864": "NH1" <-> "NH2" Residue "A ARG 3962": "NH1" <-> "NH2" Residue "A PHE 4005": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 4008": "OE1" <-> "OE2" Residue "A GLU 4017": "OE1" <-> "OE2" Residue "A GLU 4030": "OE1" <-> "OE2" Residue "A ARG 4049": "NH1" <-> "NH2" Residue "A GLU 4063": "OE1" <-> "OE2" Residue "A ARG 4082": "NH1" <-> "NH2" Residue "A GLU 4101": "OE1" <-> "OE2" Residue "B ARG 35": "NH1" <-> "NH2" Residue "B ARG 252": "NH1" <-> "NH2" Residue "B ARG 254": "NH1" <-> "NH2" Residue "B ARG 258": "NH1" <-> "NH2" Residue "B ARG 290": "NH1" <-> "NH2" Residue "B ARG 301": "NH1" <-> "NH2" Residue "B ARG 325": "NH1" <-> "NH2" Residue "B GLU 330": "OE1" <-> "OE2" Residue "B GLU 336": "OE1" <-> "OE2" Residue "B ARG 363": "NH1" <-> "NH2" Residue "B ARG 399": "NH1" <-> "NH2" Residue "B ARG 404": "NH1" <-> "NH2" Residue "B ARG 444": "NH1" <-> "NH2" Residue "B ARG 470": "NH1" <-> "NH2" Residue "B ARG 517": "NH1" <-> "NH2" Residue "C GLU 28": "OE1" <-> "OE2" Residue "C GLU 128": "OE1" <-> "OE2" Residue "C ARG 232": "NH1" <-> "NH2" Residue "C GLU 287": "OE1" <-> "OE2" Residue "C ARG 315": "NH1" <-> "NH2" Residue "C PHE 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 448": "OE1" <-> "OE2" Residue "C ARG 486": "NH1" <-> "NH2" Residue "C ARG 489": "NH1" <-> "NH2" Residue "C ARG 497": "NH1" <-> "NH2" Residue "C GLU 621": "OE1" <-> "OE2" Residue "C GLU 676": "OE1" <-> "OE2" Residue "D ARG 43": "NH1" <-> "NH2" Residue "D ARG 49": "NH1" <-> "NH2" Residue "D ARG 81": "NH1" <-> "NH2" Residue "D GLU 86": "OE1" <-> "OE2" Residue "D GLU 104": "OE1" <-> "OE2" Residue "D ARG 138": "NH1" <-> "NH2" Residue "D ARG 146": "NH1" <-> "NH2" Residue "D GLU 148": "OE1" <-> "OE2" Residue "D ARG 155": "NH1" <-> "NH2" Residue "D GLU 180": "OE1" <-> "OE2" Residue "D ARG 249": "NH1" <-> "NH2" Residue "D ARG 257": "NH1" <-> "NH2" Residue "D ARG 277": "NH1" <-> "NH2" Residue "D TYR 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 324": "OE1" <-> "OE2" Residue "D ARG 402": "NH1" <-> "NH2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 44704 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 30853 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 3852, 30804 Classifications: {'peptide': 3852} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 168, 'TRANS': 3682} Chain breaks: 11 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'TPO:plan-1': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Conformer: "B" Number of residues, atoms: 3852, 30804 Classifications: {'peptide': 3852} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 168, 'TRANS': 3682} Chain breaks: 11 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'TPO:plan-1': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 bond proxies already assigned to first conformer: 31388 Chain: "B" Number of atoms: 4102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 4102 Classifications: {'peptide': 507} Link IDs: {'PTRANS': 28, 'TRANS': 478} Chain: "C" Number of atoms: 5099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 631, 5099 Classifications: {'peptide': 631} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 27, 'TRANS': 603} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 3311 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 406, 3299 Classifications: {'peptide': 406} Link IDs: {'PTRANS': 25, 'TRANS': 380} Conformer: "B" Number of residues, atoms: 406, 3299 Classifications: {'peptide': 406} Link IDs: {'PTRANS': 25, 'TRANS': 380} bond proxies already assigned to first conformer: 3370 Chain: "E" Number of atoms: 1104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 1104 Classifications: {'DNA': 54} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 53} Chain: "F" Number of atoms: 164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 164 Classifications: {'DNA': 8} Link IDs: {'rna3p': 7} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'IHP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 42128 SG CYS D 256 69.939 99.827 96.419 1.00 59.48 S ATOM 42270 SG CYS D 272 69.349 102.910 94.221 1.00 73.29 S Residues with excluded nonbonded symmetry interactions: 6 residue: pdb=" N ALYS A1000 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS A1000 " occ=0.50 residue: pdb=" N AGLN A2838 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN A2838 " occ=0.50 residue: pdb=" N AHIS A2865 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS A2865 " occ=0.50 residue: pdb=" N AHIS A3903 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS A3903 " occ=0.50 residue: pdb=" N APHE A4011 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE A4011 " occ=0.50 residue: pdb=" N ATYR D 391 " occ=0.50 ... (22 atoms not shown) pdb=" OH BTYR D 391 " occ=0.50 Time building chain proxies: 39.54, per 1000 atoms: 0.88 Number of scatterers: 44704 At special positions: 0 Unit cell: (144.109, 161.602, 248.234, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 264 16.00 P 74 15.00 Mg 3 11.99 O 8414 8.00 N 7583 7.00 C 28365 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: 18.98 Conformation dependent library (CDL) restraints added in 14.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D 803 " pdb="ZN ZN D 803 " - pdb=" ND1 HIS D 254 " pdb="ZN ZN D 803 " - pdb=" ND1 HIS D 228 " pdb="ZN ZN D 803 " - pdb=" SG CYS D 256 " pdb="ZN ZN D 803 " - pdb=" SG CYS D 272 " Number of angles added : 2 10734 Ramachandran restraints generated. 5367 Oldfield, 0 Emsley, 5367 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10346 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 260 helices and 16 sheets defined 55.4% alpha, 5.0% beta 29 base pairs and 50 stacking pairs defined. Time for finding SS restraints: 29.00 Creating SS restraints... Processing helix chain 'A' and resid 7 through 20 removed outlier: 3.861A pdb=" N LEU A 19 " --> pdb=" O LEU A 15 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N SER A 20 " --> pdb=" O GLN A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 44 removed outlier: 3.515A pdb=" N LEU A 44 " --> pdb=" O GLN A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 58 Processing helix chain 'A' and resid 65 through 72 Processing helix chain 'A' and resid 76 through 95 removed outlier: 3.532A pdb=" N ARG A 79 " --> pdb=" O ILE A 76 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N GLU A 80 " --> pdb=" O GLU A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 117 Processing helix chain 'A' and resid 121 through 123 No H-bonds generated for 'chain 'A' and resid 121 through 123' Processing helix chain 'A' and resid 125 through 137 removed outlier: 3.963A pdb=" N LEU A 131 " --> pdb=" O ALA A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 144 No H-bonds generated for 'chain 'A' and resid 142 through 144' Processing helix chain 'A' and resid 149 through 160 Processing helix chain 'A' and resid 168 through 184 removed outlier: 3.623A pdb=" N LYS A 173 " --> pdb=" O THR A 169 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLY A 182 " --> pdb=" O LEU A 178 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU A 183 " --> pdb=" O GLY A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 189 Processing helix chain 'A' and resid 193 through 208 removed outlier: 3.598A pdb=" N ARG A 198 " --> pdb=" O GLU A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 230 Processing helix chain 'A' and resid 242 through 256 removed outlier: 3.529A pdb=" N PHE A 249 " --> pdb=" O SER A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 277 Processing helix chain 'A' and resid 290 through 301 Processing helix chain 'A' and resid 307 through 329 Processing helix chain 'A' and resid 334 through 350 removed outlier: 4.819A pdb=" N GLN A 339 " --> pdb=" O LYS A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 373 Proline residue: A 372 - end of helix Processing helix chain 'A' and resid 378 through 396 removed outlier: 4.385A pdb=" N PHE A 383 " --> pdb=" O LYS A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 421 Proline residue: A 411 - end of helix Processing helix chain 'A' and resid 429 through 448 Proline residue: A 433 - end of helix removed outlier: 3.704A pdb=" N HIS A 437 " --> pdb=" O VAL A 434 " (cutoff:3.500A) Proline residue: A 447 - end of helix Processing helix chain 'A' and resid 451 through 468 removed outlier: 3.685A pdb=" N LEU A 455 " --> pdb=" O PRO A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 491 removed outlier: 4.381A pdb=" N CYS A 478 " --> pdb=" O VAL A 474 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE A 479 " --> pdb=" O LEU A 475 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER A 480 " --> pdb=" O ARG A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 526 No H-bonds generated for 'chain 'A' and resid 524 through 526' Processing helix chain 'A' and resid 528 through 535 Processing helix chain 'A' and resid 539 through 545 Processing helix chain 'A' and resid 558 through 576 removed outlier: 4.396A pdb=" N ASN A 561 " --> pdb=" O GLU A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 617 through 633 Processing helix chain 'A' and resid 636 through 639 Processing helix chain 'A' and resid 646 through 659 Processing helix chain 'A' and resid 664 through 679 Processing helix chain 'A' and resid 698 through 720 removed outlier: 4.545A pdb=" N LYS A 719 " --> pdb=" O ALA A 715 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N GLN A 720 " --> pdb=" O VAL A 716 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 735 Processing helix chain 'A' and resid 738 through 741 No H-bonds generated for 'chain 'A' and resid 738 through 741' Processing helix chain 'A' and resid 746 through 760 Proline residue: A 750 - end of helix removed outlier: 4.095A pdb=" N LEU A 760 " --> pdb=" O PHE A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 763 through 779 Processing helix chain 'A' and resid 782 through 800 Proline residue: A 787 - end of helix removed outlier: 4.773A pdb=" N LYS A 790 " --> pdb=" O GLN A 786 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N ASP A 791 " --> pdb=" O PRO A 787 " (cutoff:3.500A) Proline residue: A 794 - end of helix removed outlier: 3.845A pdb=" N ASP A 797 " --> pdb=" O LEU A 793 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N GLY A 798 " --> pdb=" O PRO A 794 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N TYR A 799 " --> pdb=" O CYS A 795 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LEU A 800 " --> pdb=" O LEU A 796 " (cutoff:3.500A) Processing helix chain 'A' and resid 815 through 821 removed outlier: 4.390A pdb=" N ARG A 820 " --> pdb=" O SER A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 861 Processing helix chain 'A' and resid 867 through 870 Processing helix chain 'A' and resid 873 through 883 removed outlier: 3.956A pdb=" N LYS A 881 " --> pdb=" O ASP A 877 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N SER A 882 " --> pdb=" O GLU A 878 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N TYR A 883 " --> pdb=" O MET A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 907 through 909 No H-bonds generated for 'chain 'A' and resid 907 through 909' Processing helix chain 'A' and resid 911 through 920 Processing helix chain 'A' and resid 924 through 946 Processing helix chain 'A' and resid 959 through 973 removed outlier: 4.166A 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 978 through 996 Proline residue: A 986 - end of helix removed outlier: 3.575A pdb=" N THR A 996 " --> pdb=" O ILE A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1016 Processing helix chain 'A' and resid 1024 through 1042 Processing helix chain 'A' and resid 1046 through 1051 removed outlier: 3.704A pdb=" N LYS A1051 " --> pdb=" O GLN A1047 " (cutoff:3.500A) Processing helix chain 'A' and resid 1054 through 1067 Processing helix chain 'A' and resid 1072 through 1091 removed outlier: 5.684A pdb=" N ARG A1087 " --> pdb=" O ASN A1083 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N GLU A1088 " --> pdb=" O ASN A1084 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N GLU A1091 " --> pdb=" O ARG A1087 " (cutoff:3.500A) Processing helix chain 'A' and resid 1093 through 1116 removed outlier: 5.882A pdb=" N PHE A1101 " --> pdb=" O GLU A1097 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N GLU A1102 " --> pdb=" O GLN A1098 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N HIS A1115 " --> pdb=" O LEU A1111 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N ALA A1116 " --> pdb=" O ALA A1112 " (cutoff:3.500A) Processing helix chain 'A' and resid 1123 through 1140 Processing helix chain 'A' and resid 1142 through 1145 No H-bonds generated for 'chain 'A' and resid 1142 through 1145' Processing helix chain 'A' and resid 1165 through 1174 Processing helix chain 'A' and resid 1181 through 1197 Proline residue: A1196 - end of helix Processing helix chain 'A' and resid 1204 through 1211 Processing helix chain 'A' and resid 1217 through 1224 Processing helix chain 'A' and resid 1231 through 1233 No H-bonds generated for 'chain 'A' and resid 1231 through 1233' Processing helix chain 'A' and resid 1241 through 1243 No H-bonds generated for 'chain 'A' and resid 1241 through 1243' Processing helix chain 'A' and resid 1250 through 1272 removed outlier: 3.687A pdb=" N TRP A1256 " --> pdb=" O ALA A1252 " (cutoff:3.500A) Processing helix chain 'A' and resid 1278 through 1282 removed outlier: 3.718A pdb=" N LEU A1282 " --> pdb=" O ALA A1278 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1278 through 1282' Processing helix chain 'A' and resid 1290 through 1300 Processing helix chain 'A' and resid 1306 through 1312 removed outlier: 4.253A pdb=" N CYS A1312 " --> pdb=" O ALA A1308 " (cutoff:3.500A) Processing helix chain 'A' and resid 1324 through 1351 removed outlier: 3.534A pdb=" N TYR A1330 " --> pdb=" O GLU A1326 " (cutoff:3.500A) Processing helix chain 'A' and resid 1358 through 1360 No H-bonds generated for 'chain 'A' and resid 1358 through 1360' Processing helix chain 'A' and resid 1367 through 1377 Processing helix chain 'A' and resid 1379 through 1381 No H-bonds generated for 'chain 'A' and resid 1379 through 1381' Processing helix chain 'A' and resid 1389 through 1392 No H-bonds generated for 'chain 'A' and resid 1389 through 1392' Processing helix chain 'A' and resid 1395 through 1406 Processing helix chain 'A' and resid 1410 through 1422 removed outlier: 4.158A pdb=" N ASP A1413 " --> pdb=" O PRO A1410 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE A1414 " --> pdb=" O TYR A1411 " (cutoff:3.500A) Processing helix chain 'A' and resid 1425 through 1431 Processing helix chain 'A' and resid 1442 through 1461 Processing helix chain 'A' and resid 1464 through 1467 No H-bonds generated for 'chain 'A' and resid 1464 through 1467' Processing helix chain 'A' and resid 1475 through 1489 Processing helix chain 'A' and resid 1505 through 1521 removed outlier: 3.539A pdb=" N GLN A1509 " --> pdb=" O LEU A1505 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER A1512 " --> pdb=" O LYS A1508 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU A1516 " --> pdb=" O SER A1512 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N PHE A1521 " --> pdb=" O LEU A1517 " (cutoff:3.500A) Processing helix chain 'A' and resid 1525 through 1532 Processing helix chain 'A' and resid 1555 through 1562 Processing helix chain 'A' and resid 1564 through 1571 removed outlier: 4.353A pdb=" N ASN A1568 " --> pdb=" O SER A1564 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N THR A1569 " --> pdb=" O GLU A1565 " (cutoff:3.500A) Processing helix chain 'A' and resid 1576 through 1584 removed outlier: 4.244A pdb=" N GLU A1581 " --> pdb=" O LEU A1577 " (cutoff:3.500A) Processing helix chain 'A' and resid 1592 through 1606 Processing helix chain 'A' and resid 1612 through 1623 Processing helix chain 'A' and resid 1626 through 1629 Processing helix chain 'A' and resid 1639 through 1655 removed outlier: 3.604A pdb=" N LEU A1653 " --> pdb=" O LEU A1649 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLN A1654 " --> pdb=" O ALA A1650 " (cutoff:3.500A) Processing helix chain 'A' and resid 1668 through 1679 removed outlier: 3.803A pdb=" N THR A1673 " --> pdb=" O PRO A1669 " (cutoff:3.500A) Processing helix chain 'A' and resid 1686 through 1698 removed outlier: 3.937A pdb=" N GLN A1691 " --> pdb=" O HIS A1687 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N LEU A1696 " --> pdb=" O ALA A1692 " (cutoff:3.500A) Proline residue: A1697 - end of helix Processing helix chain 'A' and resid 1705 through 1721 Processing helix chain 'A' and resid 1734 through 1753 Processing helix chain 'A' and resid 1759 through 1767 Processing helix chain 'A' and resid 1775 through 1788 Processing helix chain 'A' and resid 1791 through 1806 Processing helix chain 'A' and resid 1813 through 1829 removed outlier: 4.619A pdb=" N LEU A1825 " --> pdb=" O ASP A1821 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N THR A1826 " --> pdb=" O ARG A1822 " (cutoff:3.500A) Processing helix chain 'A' and resid 1836 through 1851 removed outlier: 5.052A pdb=" N VAL A1845 " --> pdb=" O SER A1841 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N ASP A1846 " --> pdb=" O THR A1842 " (cutoff:3.500A) Processing helix chain 'A' and resid 1862 through 1881 Processing helix chain 'A' and resid 1886 through 1890 Processing helix chain 'A' and resid 1894 through 1899 Processing helix chain 'A' and resid 1911 through 1923 Processing helix chain 'A' and resid 1934 through 1955 removed outlier: 4.248A pdb=" N VAL A1955 " --> pdb=" O VAL A1951 " (cutoff:3.500A) Processing helix chain 'A' and resid 1959 through 1966 Processing helix chain 'A' and resid 1999 through 2013 removed outlier: 4.172A pdb=" N TYR A2004 " --> pdb=" O ARG A2000 " (cutoff:3.500A) Processing helix chain 'A' and resid 2026 through 2028 No H-bonds generated for 'chain 'A' and resid 2026 through 2028' Processing helix chain 'A' and resid 2036 through 2044 removed outlier: 4.221A pdb=" N GLN A2042 " --> pdb=" O GLU A2038 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N PHE A2043 " --> pdb=" O GLU A2039 " (cutoff:3.500A) Processing helix chain 'A' and resid 2094 through 2106 removed outlier: 3.651A pdb=" N ARG A2106 " --> pdb=" O LYS A2102 " (cutoff:3.500A) Processing helix chain 'A' and resid 2124 through 2134 Processing helix chain 'A' and resid 2140 through 2152 Processing helix chain 'A' and resid 2154 through 2156 No H-bonds generated for 'chain 'A' and resid 2154 through 2156' Processing helix chain 'A' and resid 2158 through 2173 removed outlier: 5.364A pdb=" N LYS A2162 " --> pdb=" O PRO A2159 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LEU A2165 " --> pdb=" O LYS A2162 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER A2166 " --> pdb=" O HIS A2163 " (cutoff:3.500A) Proline residue: A2167 - end of helix removed outlier: 3.814A pdb=" N ALA A2173 " --> pdb=" O GLN A2170 " (cutoff:3.500A) Processing helix chain 'A' and resid 2184 through 2198 removed outlier: 4.791A pdb=" N GLY A2198 " --> pdb=" O LEU A2194 " (cutoff:3.500A) Processing helix chain 'A' and resid 2206 through 2221 Processing helix chain 'A' and resid 2228 through 2244 Processing helix chain 'A' and resid 2253 through 2260 Processing helix chain 'A' and resid 2269 through 2283 removed outlier: 4.105A pdb=" N GLY A2273 " --> pdb=" O ASP A2269 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASN A2283 " --> pdb=" O ILE A2279 " (cutoff:3.500A) Processing helix chain 'A' and resid 2296 through 2308 removed outlier: 3.777A pdb=" N ASN A2306 " --> pdb=" O ALA A2302 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N MET A2307 " --> pdb=" O LEU A2303 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N SER A2308 " --> pdb=" O VAL A2304 " (cutoff:3.500A) Processing helix chain 'A' and resid 2313 through 2332 removed outlier: 4.393A pdb=" N ALA A2318 " --> pdb=" O GLU A2314 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU A2332 " --> pdb=" O ARG A2328 " (cutoff:3.500A) Processing helix chain 'A' and resid 2338 through 2353 removed outlier: 3.884A pdb=" N HIS A2352 " --> pdb=" O GLN A2348 " (cutoff:3.500A) Processing helix chain 'A' and resid 2359 through 2368 Processing helix chain 'A' and resid 2372 through 2374 No H-bonds generated for 'chain 'A' and resid 2372 through 2374' Processing helix chain 'A' and resid 2379 through 2388 Proline residue: A2387 - end of helix Processing helix chain 'A' and resid 2392 through 2403 Processing helix chain 'A' and resid 2412 through 2417 Processing helix chain 'A' and resid 2420 through 2425 Processing helix chain 'A' and resid 2429 through 2445 Proline residue: A2444 - end of helix Processing helix chain 'A' and resid 2448 through 2463 Proline residue: A2457 - end of helix removed outlier: 4.712A pdb=" N GLU A2460 " --> pdb=" O ASN A2456 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N PHE A2461 " --> pdb=" O PRO A2457 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N VAL A2462 " --> pdb=" O VAL A2458 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N SER A2463 " --> pdb=" O VAL A2459 " (cutoff:3.500A) Processing helix chain 'A' and resid 2469 through 2483 Processing helix chain 'A' and resid 2495 through 2511 removed outlier: 3.757A pdb=" N LEU A2510 " --> pdb=" O LEU A2506 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N ILE A2511 " --> pdb=" O ILE A2507 " (cutoff:3.500A) Processing helix chain 'A' and resid 2515 through 2525 Processing helix chain 'A' and resid 2535 through 2545 removed outlier: 4.142A pdb=" N ASN A2543 " --> pdb=" O LEU A2539 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N SER A2544 " --> pdb=" O LEU A2540 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU A2545 " --> pdb=" O ALA A2541 " (cutoff:3.500A) Processing helix chain 'A' and resid 2554 through 2567 removed outlier: 4.336A pdb=" N MET A2565 " --> pdb=" O PHE A2561 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N THR A2566 " --> pdb=" O LEU A2562 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N SER A2567 " --> pdb=" O LEU A2563 " (cutoff:3.500A) Processing helix chain 'A' and resid 2581 through 2583 No H-bonds generated for 'chain 'A' and resid 2581 through 2583' Processing helix chain 'A' and resid 2594 through 2602 removed outlier: 3.541A pdb=" N ARG A2598 " --> pdb=" O ASP A2594 " (cutoff:3.500A) Processing helix chain 'A' and resid 2787 through 2798 Proline residue: A2793 - end of helix Processing helix chain 'A' and resid 2802 through 2822 removed outlier: 4.156A pdb=" N ASP A2821 " --> pdb=" O LEU A2817 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N LYS A2822 " --> pdb=" O LYS A2818 " (cutoff:3.500A) Processing helix chain 'A' and resid 2826 through 2845 Processing helix chain 'A' and resid 2852 through 2864 Processing helix chain 'A' and resid 2873 through 2883 Processing helix chain 'A' and resid 2886 through 2901 removed outlier: 3.893A pdb=" N LEU A2901 " --> pdb=" O LEU A2897 " (cutoff:3.500A) Processing helix chain 'A' and resid 2918 through 2933 removed outlier: 3.600A pdb=" N ILE A2933 " --> pdb=" O LEU A2929 " (cutoff:3.500A) Processing helix chain 'A' and resid 2936 through 2945 Processing helix chain 'A' and resid 2951 through 2961 Processing helix chain 'A' and resid 2965 through 2976 Processing helix chain 'A' and resid 2988 through 3004 Processing helix chain 'A' and resid 3008 through 3014 Processing helix chain 'A' and resid 3027 through 3031 Processing helix chain 'A' and resid 3034 through 3039 Processing helix chain 'A' and resid 3041 through 3053 Processing helix chain 'A' and resid 3060 through 3069 Processing helix chain 'A' and resid 3074 through 3081 removed outlier: 3.876A pdb=" N LEU A3080 " --> pdb=" O ALA A3076 " (cutoff:3.500A) Processing helix chain 'A' and resid 3083 through 3092 Processing helix chain 'A' and resid 3096 through 3114 Processing helix chain 'A' and resid 3122 through 3146 removed outlier: 4.422A pdb=" N SER A3131 " --> pdb=" O THR A3127 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N VAL A3132 " --> pdb=" O LYS A3128 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N GLN A3133 " --> pdb=" O LEU A3129 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N ALA A3134 " --> pdb=" O GLN A3130 " (cutoff:3.500A) Processing helix chain 'A' and resid 3155 through 3164 Processing helix chain 'A' and resid 3176 through 3197 Processing helix chain 'A' and resid 3227 through 3248 Processing helix chain 'A' and resid 3252 through 3261 Processing helix chain 'A' and resid 3263 through 3267 removed outlier: 3.762A pdb=" N LYS A3267 " --> pdb=" O HIS A3263 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3263 through 3267' Processing helix chain 'A' and resid 3271 through 3287 Processing helix chain 'A' and resid 3293 through 3307 removed outlier: 3.674A pdb=" N VAL A3297 " --> pdb=" O CYS A3293 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU A3298 " --> pdb=" O SER A3294 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N LYS A3302 " --> pdb=" O LEU A3298 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N THR A3303 " --> pdb=" O THR A3299 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N VAL A3304 " --> pdb=" O VAL A3300 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N SER A3305 " --> pdb=" O LEU A3301 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N LEU A3306 " --> pdb=" O LYS A3302 " (cutoff:3.500A) Processing helix chain 'A' and resid 3313 through 3316 No H-bonds generated for 'chain 'A' and resid 3313 through 3316' Processing helix chain 'A' and resid 3320 through 3343 Processing helix chain 'A' and resid 3345 through 3348 removed outlier: 3.796A pdb=" N LEU A3348 " --> pdb=" O PRO A3345 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3345 through 3348' Processing helix chain 'A' and resid 3353 through 3363 Processing helix chain 'A' and resid 3370 through 3392 Processing helix chain 'A' and resid 3405 through 3429 removed outlier: 4.255A pdb=" N VAL A3409 " --> pdb=" O PRO A3405 " (cutoff:3.500A) Processing helix chain 'A' and resid 3438 through 3440 No H-bonds generated for 'chain 'A' and resid 3438 through 3440' Processing helix chain 'A' and resid 3442 through 3455 Processing helix chain 'A' and resid 3459 through 3474 removed outlier: 3.610A pdb=" N LYS A3464 " --> pdb=" O GLU A3460 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N PHE A3465 " --> pdb=" O ALA A3461 " (cutoff:3.500A) Proline residue: A3466 - end of helix removed outlier: 3.877A pdb=" N GLU A3473 " --> pdb=" O LEU A3469 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG A3474 " --> pdb=" O GLN A3470 " (cutoff:3.500A) Processing helix chain 'A' and resid 3476 through 3489 removed outlier: 6.004A pdb=" N SER A3481 " --> pdb=" O GLU A3477 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N LEU A3482 " --> pdb=" O GLU A3478 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N SER A3488 " --> pdb=" O THR A3484 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N SER A3489 " --> pdb=" O LYS A3485 " (cutoff:3.500A) Processing helix chain 'A' and resid 3492 through 3494 No H-bonds generated for 'chain 'A' and resid 3492 through 3494' Processing helix chain 'A' and resid 3496 through 3502 removed outlier: 5.269A pdb=" N SER A3500 " --> pdb=" O SER A3497 " (cutoff:3.500A) Processing helix chain 'A' and resid 3509 through 3524 removed outlier: 4.451A pdb=" N VAL A3512 " --> pdb=" O ASP A3509 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLN A3515 " --> pdb=" O VAL A3512 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N HIS A3516 " --> pdb=" O ALA A3513 " (cutoff:3.500A) Processing helix chain 'A' and resid 3526 through 3528 No H-bonds generated for 'chain 'A' and resid 3526 through 3528' Processing helix chain 'A' and resid 3530 through 3539 removed outlier: 3.893A pdb=" N GLU A3538 " --> pdb=" O ILE A3534 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N SER A3539 " --> pdb=" O ILE A3535 " (cutoff:3.500A) Processing helix chain 'A' and resid 3546 through 3562 removed outlier: 3.728A pdb=" N LYS A3550 " --> pdb=" O SER A3546 " (cutoff:3.500A) Processing helix chain 'A' and resid 3567 through 3578 removed outlier: 3.768A pdb=" N LEU A3578 " --> pdb=" O ALA A3574 " (cutoff:3.500A) Processing helix chain 'A' and resid 3581 through 3597 removed outlier: 3.655A pdb=" N LYS A3586 " --> pdb=" O GLU A3582 " (cutoff:3.500A) Processing helix chain 'A' and resid 3603 through 3617 removed outlier: 4.216A pdb=" N ALA A3616 " --> pdb=" O ARG A3612 " (cutoff:3.500A) Processing helix chain 'A' and resid 3627 through 3636 removed outlier: 3.658A pdb=" N PHE A3632 " --> pdb=" O PHE A3628 " (cutoff:3.500A) Processing helix chain 'A' and resid 3639 through 3642 No H-bonds generated for 'chain 'A' and resid 3639 through 3642' Processing helix chain 'A' and resid 3649 through 3652 No H-bonds generated for 'chain 'A' and resid 3649 through 3652' Processing helix chain 'A' and resid 3656 through 3671 removed outlier: 3.540A pdb=" N ASP A3661 " --> pdb=" O SER A3657 " (cutoff:3.500A) Processing helix chain 'A' and resid 3680 through 3682 No H-bonds generated for 'chain 'A' and resid 3680 through 3682' Processing helix chain 'A' and resid 3685 through 3688 No H-bonds generated for 'chain 'A' and resid 3685 through 3688' Processing helix chain 'A' and resid 3713 through 3715 No H-bonds generated for 'chain 'A' and resid 3713 through 3715' Processing helix chain 'A' and resid 3759 through 3777 removed outlier: 3.589A pdb=" N GLN A3777 " --> pdb=" O GLY A3773 " (cutoff:3.500A) Processing helix chain 'A' and resid 3779 through 3784 removed outlier: 3.992A pdb=" N ARG A3784 " --> pdb=" O ALA A3780 " (cutoff:3.500A) Processing helix chain 'A' and resid 3812 through 3819 Processing helix chain 'A' and resid 3822 through 3830 Processing helix chain 'A' and resid 3835 through 3847 removed outlier: 4.033A pdb=" N LYS A3840 " --> pdb=" O PRO A3836 " (cutoff:3.500A) Processing helix chain 'A' and resid 3852 through 3861 removed outlier: 3.849A pdb=" N TYR A3859 " --> pdb=" O MET A3856 " (cutoff:3.500A) Processing helix chain 'A' and resid 3864 through 3877 removed outlier: 3.639A pdb=" N SER A3876 " --> pdb=" O ARG A3872 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LYS A3877 " --> pdb=" O LYS A3873 " (cutoff:3.500A) Processing helix chain 'A' and resid 3882 through 3889 Processing helix chain 'A' and resid 3894 through 3918 Processing helix chain 'A' and resid 3925 through 3927 No H-bonds generated for 'chain 'A' and resid 3925 through 3927' Processing helix chain 'A' and resid 3948 through 3951 No H-bonds generated for 'chain 'A' and resid 3948 through 3951' Processing helix chain 'A' and resid 3965 through 3971 removed outlier: 3.754A pdb=" N MET A3971 " --> pdb=" O PHE A3967 " (cutoff:3.500A) Processing helix chain 'A' and resid 3979 through 3993 Processing helix chain 'A' and resid 3996 through 4006 Processing helix chain 'A' and resid 4013 through 4021 Processing helix chain 'A' and resid 4040 through 4052 removed outlier: 4.190A pdb=" N ILE A4044 " --> pdb=" O PRO A4040 " (cutoff:3.500A) Processing helix chain 'A' and resid 4056 through 4067 Processing helix chain 'A' and resid 4074 through 4082 Processing helix chain 'A' and resid 4100 through 4111 Processing helix chain 'A' and resid 4114 through 4119 removed outlier: 4.112A pdb=" N ARG A4119 " --> pdb=" O ASN A4115 " (cutoff:3.500A) Processing helix chain 'A' and resid 4122 through 4124 No H-bonds generated for 'chain 'A' and resid 4122 through 4124' Processing helix chain 'B' and resid 46 through 49 No H-bonds generated for 'chain 'B' and resid 46 through 49' Processing helix chain 'B' and resid 59 through 77 removed outlier: 3.975A pdb=" N ILE B 76 " --> pdb=" O ILE B 72 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER B 77 " --> pdb=" O SER B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 122 removed outlier: 4.242A pdb=" N PHE B 122 " --> pdb=" O GLU B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 134 removed outlier: 3.976A pdb=" N LYS B 129 " --> pdb=" O GLN B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 156 Processing helix chain 'B' and resid 181 through 196 Processing helix chain 'B' and resid 217 through 219 No H-bonds generated for 'chain 'B' and resid 217 through 219' Processing helix chain 'B' and resid 239 through 242 No H-bonds generated for 'chain 'B' and resid 239 through 242' Processing helix chain 'B' and resid 313 through 315 No H-bonds generated for 'chain 'B' and resid 313 through 315' Processing helix chain 'B' and resid 333 through 338 removed outlier: 3.813A pdb=" N LYS B 338 " --> pdb=" O THR B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 355 No H-bonds generated for 'chain 'B' and resid 353 through 355' Processing helix chain 'B' and resid 378 through 391 Processing helix chain 'B' and resid 456 through 469 removed outlier: 3.558A pdb=" N LEU B 469 " --> pdb=" O ILE B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 481 through 494 Processing helix chain 'B' and resid 511 through 518 removed outlier: 3.569A pdb=" N ASN B 515 " --> pdb=" O VAL B 511 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N LYS B 516 " --> pdb=" O GLU B 512 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ARG B 517 " --> pdb=" O ALA B 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 529 Processing helix chain 'C' and resid 19 through 21 No H-bonds generated for 'chain 'C' and resid 19 through 21' Processing helix chain 'C' and resid 30 through 47 Processing helix chain 'C' and resid 88 through 95 Processing helix chain 'C' and resid 107 through 121 Processing helix chain 'C' and resid 147 through 157 Processing helix chain 'C' and resid 199 through 216 removed outlier: 3.685A pdb=" N LEU C 215 " --> pdb=" O VAL C 211 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLU C 216 " --> pdb=" O MET C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 223 Processing helix chain 'C' and resid 229 through 231 No H-bonds generated for 'chain 'C' and resid 229 through 231' Processing helix chain 'C' and resid 286 through 288 No H-bonds generated for 'chain 'C' and resid 286 through 288' Processing helix chain 'C' and resid 325 through 330 Processing helix chain 'C' and resid 348 through 350 No H-bonds generated for 'chain 'C' and resid 348 through 350' Processing helix chain 'C' and resid 353 through 355 No H-bonds generated for 'chain 'C' and resid 353 through 355' Processing helix chain 'C' and resid 372 through 386 Processing helix chain 'C' and resid 427 through 429 No H-bonds generated for 'chain 'C' and resid 427 through 429' Processing helix chain 'C' and resid 448 through 460 Processing helix chain 'C' and resid 479 through 481 No H-bonds generated for 'chain 'C' and resid 479 through 481' Processing helix chain 'C' and resid 485 through 499 Processing helix chain 'C' and resid 510 through 515 Processing helix chain 'C' and resid 520 through 536 removed outlier: 4.966A pdb=" N ILE C 528 " --> pdb=" O THR C 524 " (cutoff:3.500A) Proline residue: C 529 - end of helix Processing helix chain 'C' and resid 550 through 553 No H-bonds generated for 'chain 'C' and resid 550 through 553' Processing helix chain 'C' and resid 609 through 625 removed outlier: 3.895A pdb=" N ASN C 614 " --> pdb=" O GLU C 610 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N GLN C 615 " --> pdb=" O GLU C 611 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ILE C 620 " --> pdb=" O LEU C 616 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU C 621 " --> pdb=" O ILE C 617 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLN C 622 " --> pdb=" O ASN C 618 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N PHE C 623 " --> pdb=" O HIS C 619 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASP C 625 " --> pdb=" O GLU C 621 " (cutoff:3.500A) Processing helix chain 'C' and resid 629 through 647 removed outlier: 3.942A pdb=" N ILE C 636 " --> pdb=" O PHE C 632 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ASP C 637 " --> pdb=" O MET C 633 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLU C 645 " --> pdb=" O ALA C 641 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N ALA C 646 " --> pdb=" O PHE C 642 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ILE C 647 " --> pdb=" O ARG C 643 " (cutoff:3.500A) Processing helix chain 'C' and resid 652 through 668 removed outlier: 4.106A pdb=" N ASN C 656 " --> pdb=" O GLU C 652 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N ASN C 657 " --> pdb=" O GLN C 653 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N PHE C 658 " --> pdb=" O ARG C 654 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ALA C 661 " --> pdb=" O ASN C 657 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLN C 663 " --> pdb=" O LEU C 659 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N VAL C 666 " --> pdb=" O LEU C 662 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLU C 667 " --> pdb=" O GLN C 663 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ILE C 668 " --> pdb=" O GLU C 664 " (cutoff:3.500A) Processing helix chain 'C' and resid 726 through 730 Processing helix chain 'D' and resid 23 through 25 No H-bonds generated for 'chain 'D' and resid 23 through 25' Processing helix chain 'D' and resid 36 through 38 No H-bonds generated for 'chain 'D' and resid 36 through 38' Processing helix chain 'D' and resid 45 through 53 removed outlier: 3.641A pdb=" N CYS D 53 " --> pdb=" O ARG D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 71 Processing helix chain 'D' and resid 73 through 78 removed outlier: 3.542A pdb=" N ARG D 76 " --> pdb=" O PRO D 73 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N PHE D 77 " --> pdb=" O LYS D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 146 No H-bonds generated for 'chain 'D' and resid 144 through 146' Processing helix chain 'D' and resid 179 through 194 Processing helix chain 'D' and resid 213 through 223 Processing helix chain 'D' and resid 233 through 235 No H-bonds generated for 'chain 'D' and resid 233 through 235' Processing helix chain 'D' and resid 239 through 244 removed outlier: 5.149A pdb=" N HIS D 244 " --> pdb=" O GLU D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 266 Processing helix chain 'D' and resid 294 through 296 No H-bonds generated for 'chain 'D' and resid 294 through 296' Processing helix chain 'D' and resid 322 through 332 Processing helix chain 'D' and resid 348 through 358 Proline residue: D 357 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 893 through 895 Processing sheet with id= B, first strand: chain 'A' and resid 2634 through 2636 Processing sheet with id= C, first strand: chain 'A' and resid 3793 through 3797 removed outlier: 6.735A pdb=" N LEU A3800 " --> pdb=" O MET A3796 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 3809 through 3811 Processing sheet with id= E, first strand: chain 'B' and resid 198 through 204 removed outlier: 8.505A pdb=" N PHE B 199 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LYS B 164 " --> pdb=" O PHE B 199 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N ASP B 201 " --> pdb=" O LYS B 164 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N ILE B 166 " --> pdb=" O ASP B 201 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N MET B 203 " --> pdb=" O ILE B 166 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N LEU B 168 " --> pdb=" O MET B 203 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N ARG B 35 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N LYS B 164 " --> pdb=" O ARG B 35 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N SER B 37 " --> pdb=" O LYS B 164 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N ILE B 166 " --> pdb=" O SER B 37 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ILE B 39 " --> pdb=" O ILE B 166 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N LEU B 168 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LEU B 41 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N THR B 170 " --> pdb=" O LEU B 41 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N ASP B 43 " --> pdb=" O THR B 170 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N LEU B 82 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N PHE B 40 " --> pdb=" O LEU B 82 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ALA B 84 " --> pdb=" O PHE B 40 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N VAL B 42 " --> pdb=" O ALA B 84 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N VAL B 86 " --> pdb=" O VAL B 42 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N PHE B 87 " --> pdb=" O VAL B 104 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N VAL B 104 " --> pdb=" O PHE B 87 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 257 through 262 removed outlier: 3.732A pdb=" N SER B 257 " --> pdb=" O ILE B 273 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE B 432 " --> pdb=" O VAL B 368 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA B 396 " --> pdb=" O LEU B 413 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N MET B 346 " --> pdb=" O ARG B 399 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 318 through 322 removed outlier: 3.574A pdb=" N ILE B 327 " --> pdb=" O GLN B 320 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 350 through 352 Processing sheet with id= I, first strand: chain 'B' and resid 419 through 421 removed outlier: 3.627A pdb=" N GLU B 419 " --> pdb=" O THR B 428 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N THR B 428 " --> pdb=" O GLU B 419 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ASP B 421 " --> pdb=" O GLN B 426 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N GLN B 426 " --> pdb=" O ASP B 421 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'C' and resid 224 through 226 removed outlier: 8.919A pdb=" N TYR C 225 " --> pdb=" O LEU C 161 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N PHE C 163 " --> pdb=" O TYR C 225 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N LYS C 7 " --> pdb=" O GLU C 128 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ARG C 130 " --> pdb=" O LYS C 7 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ALA C 9 " --> pdb=" O ARG C 130 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N ILE C 132 " --> pdb=" O ALA C 9 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N VAL C 11 " --> pdb=" O ILE C 132 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N ILE C 134 " --> pdb=" O VAL C 11 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N CYS C 13 " --> pdb=" O ILE C 134 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N GLU C 53 " --> pdb=" O VAL C 10 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N LEU C 12 " --> pdb=" O GLU C 53 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ALA C 55 " --> pdb=" O LEU C 12 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N MET C 14 " --> pdb=" O ALA C 55 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N VAL C 57 " --> pdb=" O MET C 14 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU C 58 " --> pdb=" O VAL C 79 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N VAL C 79 " --> pdb=" O LEU C 58 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 247 through 252 removed outlier: 6.630A pdb=" N VAL C 361 " --> pdb=" O SER C 266 " (cutoff:3.500A) removed outlier: 8.663A pdb=" N GLN C 360 " --> pdb=" O GLN C 423 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N GLN C 423 " --> pdb=" O GLN C 360 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N ALA C 366 " --> pdb=" O GLU C 417 " (cutoff:3.500A) removed outlier: 10.185A pdb=" N GLU C 417 " --> pdb=" O ALA C 366 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N CYS C 418 " --> pdb=" O HIS C 411 " (cutoff:3.500A) removed outlier: 8.613A pdb=" N MET C 389 " --> pdb=" O PRO C 410 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ARG C 394 " --> pdb=" O VAL C 342 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N VAL C 342 " --> pdb=" O ARG C 394 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N ALA C 396 " --> pdb=" O PHE C 340 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N PHE C 340 " --> pdb=" O ALA C 396 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 313 through 315 Processing sheet with id= M, first strand: chain 'C' and resid 464 through 467 removed outlier: 3.882A pdb=" N ASP C 467 " --> pdb=" O THR C 472 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N THR C 472 " --> pdb=" O ASP C 467 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 14 through 16 removed outlier: 6.537A pdb=" N ALA D 28 " --> pdb=" O SER D 15 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N CYS D 61 " --> pdb=" O ILE D 83 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 91 through 94 removed outlier: 3.525A pdb=" N GLY D 126 " --> pdb=" O GLY D 129 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLY D 129 " --> pdb=" O GLY D 126 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N SER D 161 " --> pdb=" O LEU D 132 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N THR D 134 " --> pdb=" O SER D 161 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N TYR D 163 " --> pdb=" O THR D 134 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 200 through 204 removed outlier: 6.087A pdb=" N HIS D 283 " --> pdb=" O VAL D 201 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N TRP D 203 " --> pdb=" O HIS D 283 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ILE D 285 " --> pdb=" O TRP D 203 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER D 311 " --> pdb=" O GLY D 308 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY D 308 " --> pdb=" O SER D 311 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N ARG D 313 " --> pdb=" O ARG D 306 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N ARG D 306 " --> pdb=" O ARG D 313 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N CYS D 315 " --> pdb=" O ILE D 304 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N ILE D 304 " --> pdb=" O CYS D 315 " (cutoff:3.500A) 1893 hydrogen bonds defined for protein. 5345 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 71 hydrogen bonds 142 hydrogen bond angles 0 basepair planarities 29 basepair parallelities 50 stacking parallelities Total time for adding SS restraints: 29.55 Time building geometry restraints manager: 20.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 7302 1.30 - 1.43: 11766 1.43 - 1.56: 26156 1.56 - 1.68: 135 1.68 - 1.81: 415 Bond restraints: 45774 Sorted by residual: bond pdb=" OG1 TPO A2645 " pdb=" P TPO A2645 " ideal model delta sigma weight residual 1.717 1.609 0.108 2.00e-02 2.50e+03 2.94e+01 bond pdb=" OG1 TPO A2609 " pdb=" P TPO A2609 " ideal model delta sigma weight residual 1.717 1.609 0.108 2.00e-02 2.50e+03 2.92e+01 bond pdb=" OG1 TPO A2638 " pdb=" P TPO A2638 " ideal model delta sigma weight residual 1.717 1.609 0.108 2.00e-02 2.50e+03 2.91e+01 bond pdb=" OG1 TPO A2647 " pdb=" P TPO A2647 " ideal model delta sigma weight residual 1.717 1.612 0.105 2.00e-02 2.50e+03 2.76e+01 bond pdb=" O1P TPO A2609 " pdb=" P TPO A2609 " ideal model delta sigma weight residual 1.525 1.611 -0.086 2.00e-02 2.50e+03 1.83e+01 ... (remaining 45769 not shown) Histogram of bond angle deviations from ideal: 96.40 - 103.96: 904 103.96 - 111.52: 20736 111.52 - 119.08: 16862 119.08 - 126.65: 22882 126.65 - 134.21: 759 Bond angle restraints: 62143 Sorted by residual: angle pdb=" N LEU A 435 " pdb=" CA LEU A 435 " pdb=" C LEU A 435 " ideal model delta sigma weight residual 111.07 120.87 -9.80 1.07e+00 8.73e-01 8.39e+01 angle pdb=" PB ATP A4201 " pdb=" O3B ATP A4201 " pdb=" PG ATP A4201 " ideal model delta sigma weight residual 139.87 131.95 7.92 1.00e+00 1.00e+00 6.27e+01 angle pdb=" N SER A1823 " pdb=" CA SER A1823 " pdb=" C SER A1823 " ideal model delta sigma weight residual 111.24 121.39 -10.15 1.29e+00 6.01e-01 6.19e+01 angle pdb=" C VAL A 434 " pdb=" CA VAL A 434 " pdb=" CB VAL A 434 " ideal model delta sigma weight residual 111.29 121.77 -10.48 1.64e+00 3.72e-01 4.08e+01 angle pdb=" C ARG A1822 " pdb=" CA ARG A1822 " pdb=" CB ARG A1822 " ideal model delta sigma weight residual 110.56 119.86 -9.30 1.83e+00 2.99e-01 2.59e+01 ... (remaining 62138 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.87: 26693 24.87 - 49.74: 869 49.74 - 74.61: 218 74.61 - 99.48: 61 99.48 - 124.36: 10 Dihedral angle restraints: 27851 sinusoidal: 11948 harmonic: 15903 Sorted by residual: dihedral pdb=" C VAL A 434 " pdb=" N VAL A 434 " pdb=" CA VAL A 434 " pdb=" CB VAL A 434 " ideal model delta harmonic sigma weight residual -122.00 -135.74 13.74 0 2.50e+00 1.60e-01 3.02e+01 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 -156.98 -23.02 0 5.00e+00 4.00e-02 2.12e+01 dihedral pdb=" O12 IHP B 701 " pdb=" C2 IHP B 701 " pdb=" C3 IHP B 701 " pdb=" O13 IHP B 701 " ideal model delta sinusoidal sigma weight residual 64.08 -60.28 124.36 1 3.00e+01 1.11e-03 1.67e+01 ... (remaining 27848 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.015: 6959 1.015 - 2.030: 0 2.030 - 3.044: 0 3.044 - 4.059: 0 4.059 - 5.074: 3 Chirality restraints: 6962 Sorted by residual: chirality pdb=" C4 IHP B 701 " pdb=" C3 IHP B 701 " pdb=" C5 IHP B 701 " pdb=" O14 IHP B 701 " both_signs ideal model delta sigma weight residual False 2.48 -2.59 5.07 2.00e-01 2.50e+01 6.44e+02 chirality pdb=" C2 IHP B 701 " pdb=" C1 IHP B 701 " pdb=" C3 IHP B 701 " pdb=" O12 IHP B 701 " both_signs ideal model delta sigma weight residual False -2.52 2.47 -4.98 2.00e-01 2.50e+01 6.21e+02 chirality pdb=" C1 IHP B 701 " pdb=" C2 IHP B 701 " pdb=" C6 IHP B 701 " pdb=" O11 IHP B 701 " both_signs ideal model delta sigma weight residual False 2.32 -2.57 4.89 2.00e-01 2.50e+01 5.97e+02 ... (remaining 6959 not shown) Planarity restraints: 7706 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA E 46 " 0.041 2.00e-02 2.50e+03 1.95e-02 1.04e+01 pdb=" N9 DA E 46 " -0.046 2.00e-02 2.50e+03 pdb=" C8 DA E 46 " -0.006 2.00e-02 2.50e+03 pdb=" N7 DA E 46 " 0.008 2.00e-02 2.50e+03 pdb=" C5 DA E 46 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DA E 46 " 0.009 2.00e-02 2.50e+03 pdb=" N6 DA E 46 " 0.006 2.00e-02 2.50e+03 pdb=" N1 DA E 46 " 0.000 2.00e-02 2.50e+03 pdb=" C2 DA E 46 " 0.002 2.00e-02 2.50e+03 pdb=" N3 DA E 46 " -0.008 2.00e-02 2.50e+03 pdb=" C4 DA E 46 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG E 13 " 0.006 2.00e-02 2.50e+03 1.55e-02 7.16e+00 pdb=" N9 DG E 13 " -0.021 2.00e-02 2.50e+03 pdb=" C8 DG E 13 " -0.000 2.00e-02 2.50e+03 pdb=" N7 DG E 13 " 0.001 2.00e-02 2.50e+03 pdb=" C5 DG E 13 " -0.006 2.00e-02 2.50e+03 pdb=" C6 DG E 13 " -0.003 2.00e-02 2.50e+03 pdb=" O6 DG E 13 " -0.004 2.00e-02 2.50e+03 pdb=" N1 DG E 13 " 0.007 2.00e-02 2.50e+03 pdb=" C2 DG E 13 " -0.001 2.00e-02 2.50e+03 pdb=" N2 DG E 13 " 0.001 2.00e-02 2.50e+03 pdb=" N3 DG E 13 " -0.023 2.00e-02 2.50e+03 pdb=" C4 DG E 13 " 0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA E 14 " 0.025 2.00e-02 2.50e+03 1.58e-02 6.85e+00 pdb=" N9 DA E 14 " -0.041 2.00e-02 2.50e+03 pdb=" C8 DA E 14 " 0.008 2.00e-02 2.50e+03 pdb=" N7 DA E 14 " 0.008 2.00e-02 2.50e+03 pdb=" C5 DA E 14 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DA E 14 " 0.007 2.00e-02 2.50e+03 pdb=" N6 DA E 14 " -0.006 2.00e-02 2.50e+03 pdb=" N1 DA E 14 " 0.011 2.00e-02 2.50e+03 pdb=" C2 DA E 14 " -0.004 2.00e-02 2.50e+03 pdb=" N3 DA E 14 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DA E 14 " -0.006 2.00e-02 2.50e+03 ... (remaining 7703 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 161 2.49 - 3.09: 32060 3.09 - 3.69: 67464 3.69 - 4.30: 101465 4.30 - 4.90: 164114 Nonbonded interactions: 365264 Sorted by model distance: nonbonded pdb=" OP1 DA E 25 " pdb="MG MG D 802 " model vdw 1.886 2.170 nonbonded pdb=" OD1 ASN A3927 " pdb="MG MG A4200 " model vdw 2.066 2.170 nonbonded pdb=" OD2 ASP A3941 " pdb="MG MG A4200 " model vdw 2.113 2.170 nonbonded pdb=" CD2 HIS D 38 " pdb="MG MG D 801 " model vdw 2.116 2.390 nonbonded pdb=" O ASN A2152 " pdb=" OD1 ASN A2152 " model vdw 2.173 3.040 ... (remaining 365259 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 6.780 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: 0.030 Extract box with map and model: 25.720 Check model and map are aligned: 0.820 Set scattering table: 0.460 Process input model: 169.830 Find NCS groups from input model: 1.190 Set up NCS constraints: 0.240 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:12.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 217.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 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 : 0.006 0.117 45774 Z= 0.421 Angle : 0.594 12.809 62143 Z= 0.353 Chirality : 0.112 5.074 6962 Planarity : 0.003 0.039 7706 Dihedral : 13.502 124.356 17505 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.24 % Allowed : 4.34 % Favored : 94.42 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.11), residues: 5367 helix: -0.18 (0.09), residues: 3008 sheet: -1.75 (0.28), residues: 296 loop : -2.27 (0.12), residues: 2063 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 78 HIS 0.003 0.000 HIS D 33 PHE 0.020 0.001 PHE A1923 TYR 0.011 0.001 TYR A2316 ARG 0.002 0.000 ARG A1735 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10734 Ramachandran restraints generated. 5367 Oldfield, 0 Emsley, 5367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10734 Ramachandran restraints generated. 5367 Oldfield, 0 Emsley, 5367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 570 residues out of total 4826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 511 time to evaluate : 5.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.5178 (tpp) cc_final: 0.4977 (tmm) REVERT: A 408 TYR cc_start: 0.8300 (m-80) cc_final: 0.7847 (m-80) REVERT: A 1356 TRP cc_start: 0.7913 (p-90) cc_final: 0.7465 (p-90) REVERT: A 1362 ASP cc_start: 0.6882 (m-30) cc_final: 0.6538 (t0) REVERT: A 1592 MET cc_start: 0.8096 (tpt) cc_final: 0.7796 (tpt) REVERT: A 1625 HIS cc_start: 0.7743 (m90) cc_final: 0.7405 (m90) REVERT: A 1626 TRP cc_start: 0.7014 (m100) cc_final: 0.6548 (m100) REVERT: A 1668 PHE cc_start: 0.6937 (OUTLIER) cc_final: 0.5656 (t80) REVERT: A 1744 LYS cc_start: 0.8978 (ptpp) cc_final: 0.8435 (tppp) REVERT: A 1824 LEU cc_start: 0.8880 (tt) cc_final: 0.8590 (mp) REVERT: A 1829 TRP cc_start: 0.8595 (m100) cc_final: 0.8275 (m100) REVERT: A 1871 MET cc_start: 0.8096 (ptp) cc_final: 0.7715 (ptm) REVERT: A 1913 LYS cc_start: 0.8903 (tttt) cc_final: 0.8690 (tptt) REVERT: A 1927 MET cc_start: 0.7593 (mtp) cc_final: 0.7228 (mpm) REVERT: A 1933 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.7932 (mm) REVERT: A 1993 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.7276 (tm-30) REVERT: A 2094 MET cc_start: 0.8192 (tpt) cc_final: 0.7953 (tpt) REVERT: A 2097 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8737 (mt) REVERT: A 2437 ASP cc_start: 0.8222 (m-30) cc_final: 0.7953 (m-30) REVERT: A 3414 MET cc_start: 0.8515 (mmm) cc_final: 0.8167 (mmm) REVERT: A 3607 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.8125 (pt0) REVERT: A 3609 MET cc_start: 0.8278 (mmt) cc_final: 0.8023 (mmp) REVERT: C 730 ASP cc_start: 0.7622 (t70) cc_final: 0.7336 (m-30) outliers start: 59 outliers final: 15 residues processed: 565 average time/residue: 1.8547 time to fit residues: 1268.2500 Evaluate side-chains 279 residues out of total 4826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 259 time to evaluate : 5.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 ASN Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 1590 THR Chi-restraints excluded: chain A residue 1668 PHE Chi-restraints excluded: chain A residue 1671 VAL Chi-restraints excluded: chain A residue 1805 PHE Chi-restraints excluded: chain A residue 1933 LEU Chi-restraints excluded: chain A residue 1993 GLU Chi-restraints excluded: chain A residue 2097 LEU Chi-restraints excluded: chain A residue 2449 VAL Chi-restraints excluded: chain A residue 2899 ARG Chi-restraints excluded: chain A residue 3077 ILE Chi-restraints excluded: chain A residue 3544 ASP Chi-restraints excluded: chain A residue 3553 GLU Chi-restraints excluded: chain A residue 3607 GLU Chi-restraints excluded: chain A residue 4028 ILE Chi-restraints excluded: chain C residue 530 LEU Chi-restraints excluded: chain D residue 8 MET Chi-restraints excluded: chain D residue 19 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 543 random chunks: chunk 458 optimal weight: 6.9990 chunk 411 optimal weight: 4.9990 chunk 228 optimal weight: 0.9980 chunk 140 optimal weight: 20.0000 chunk 277 optimal weight: 7.9990 chunk 219 optimal weight: 0.7980 chunk 425 optimal weight: 5.9990 chunk 164 optimal weight: 9.9990 chunk 258 optimal weight: 0.2980 chunk 316 optimal weight: 4.9990 chunk 493 optimal weight: 20.0000 overall best weight: 2.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN A 281 GLN A 325 ASN A 377 ASN A 399 GLN A 409 GLN A 415 GLN A 442 GLN A 485 GLN A 562 HIS A 625 ASN A 857 GLN A 935 HIS A1004 GLN A1043 GLN A1222 ASN A1251 GLN A1287 GLN A1426 GLN A1442 GLN A1477 HIS ** A1725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1772 HIS A1779 GLN A1794 GLN A1941 HIS A1946 ASN A2213 ASN A2225 HIS A2493 ASN A2508 GLN A2784 GLN A2799 GLN A2834 GLN A3112 GLN A3139 GLN A3166 ASN A3278 GLN A3383 GLN A3515 GLN A3787 GLN A3818 ASN A3850 HIS A3944 HIS A3951 GLN A3966 GLN A3986 HIS A4000 ASN A4018 GLN A4110 GLN B 68 GLN B 320 GLN ** B 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 6 ASN ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 269 GLN C 423 GLN C 514 ASN ** C 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 23 ASN Total number of N/Q/H flips: 56 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 45774 Z= 0.291 Angle : 0.600 13.039 62143 Z= 0.303 Chirality : 0.042 0.368 6962 Planarity : 0.004 0.042 7706 Dihedral : 12.919 89.772 6634 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.21 % Allowed : 10.05 % Favored : 87.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.11), residues: 5367 helix: 0.65 (0.10), residues: 3031 sheet: -1.10 (0.29), residues: 269 loop : -1.71 (0.13), residues: 2067 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP D 267 HIS 0.009 0.001 HIS A2225 PHE 0.025 0.002 PHE A2260 TYR 0.020 0.001 TYR A1873 ARG 0.009 0.001 ARG A3833 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10734 Ramachandran restraints generated. 5367 Oldfield, 0 Emsley, 5367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10734 Ramachandran restraints generated. 5367 Oldfield, 0 Emsley, 5367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 4826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 273 time to evaluate : 5.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.5169 (tpp) cc_final: 0.4903 (tmm) REVERT: A 723 ASP cc_start: 0.7406 (OUTLIER) cc_final: 0.7090 (p0) REVERT: A 1356 TRP cc_start: 0.7961 (p-90) cc_final: 0.7552 (p-90) REVERT: A 1357 LYS cc_start: 0.8153 (pttm) cc_final: 0.7857 (tmmt) REVERT: A 1362 ASP cc_start: 0.7304 (m-30) cc_final: 0.7077 (t0) REVERT: A 1426 GLN cc_start: 0.8412 (OUTLIER) cc_final: 0.7746 (pm20) REVERT: A 1509 GLN cc_start: 0.8135 (tm-30) cc_final: 0.7810 (pm20) REVERT: A 1516 GLU cc_start: 0.8465 (tp30) cc_final: 0.8241 (mp0) REVERT: A 1592 MET cc_start: 0.8152 (tpt) cc_final: 0.7848 (tpt) REVERT: A 1668 PHE cc_start: 0.7010 (OUTLIER) cc_final: 0.5868 (t80) REVERT: A 1685 ASP cc_start: 0.6967 (OUTLIER) cc_final: 0.5689 (p0) REVERT: A 1744 LYS cc_start: 0.8918 (ptpp) cc_final: 0.8622 (tppp) REVERT: A 1829 TRP cc_start: 0.8604 (m100) cc_final: 0.8289 (m100) REVERT: A 1871 MET cc_start: 0.8331 (ptp) cc_final: 0.7916 (ptm) REVERT: A 1927 MET cc_start: 0.7671 (mtp) cc_final: 0.7212 (mpm) REVERT: A 1933 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.7907 (mm) REVERT: A 1993 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7737 (tm-30) REVERT: A 2094 MET cc_start: 0.8367 (tpt) cc_final: 0.8061 (tpt) REVERT: A 2154 GLU cc_start: 0.8742 (pp20) cc_final: 0.8135 (tm-30) REVERT: A 2437 ASP cc_start: 0.8271 (m-30) cc_final: 0.7951 (m-30) REVERT: A 2473 MET cc_start: 0.8780 (ttp) cc_final: 0.8455 (ttp) REVERT: A 2860 ASP cc_start: 0.7783 (OUTLIER) cc_final: 0.7561 (t0) REVERT: A 3769 GLN cc_start: 0.8175 (OUTLIER) cc_final: 0.7947 (mt0) REVERT: D 348 MET cc_start: 0.8044 (tpp) cc_final: 0.7772 (tpp) outliers start: 106 outliers final: 35 residues processed: 356 average time/residue: 1.6330 time to fit residues: 725.4811 Evaluate side-chains 272 residues out of total 4826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 229 time to evaluate : 5.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 LYS Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 289 ASN Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 723 ASP Chi-restraints excluded: chain A residue 1423 ILE Chi-restraints excluded: chain A residue 1426 GLN Chi-restraints excluded: chain A residue 1590 THR Chi-restraints excluded: chain A residue 1593 VAL Chi-restraints excluded: chain A residue 1668 PHE Chi-restraints excluded: chain A residue 1671 VAL Chi-restraints excluded: chain A residue 1685 ASP Chi-restraints excluded: chain A residue 1696 LEU Chi-restraints excluded: chain A residue 1805 PHE Chi-restraints excluded: chain A residue 1933 LEU Chi-restraints excluded: chain A residue 1993 GLU Chi-restraints excluded: chain A residue 2197 THR Chi-restraints excluded: chain A residue 2424 MET Chi-restraints excluded: chain A residue 2860 ASP Chi-restraints excluded: chain A residue 3479 THR Chi-restraints excluded: chain A residue 3530 VAL Chi-restraints excluded: chain A residue 3553 GLU Chi-restraints excluded: chain A residue 3694 PHE Chi-restraints excluded: chain A residue 3697 ASN Chi-restraints excluded: chain A residue 3769 GLN Chi-restraints excluded: chain A residue 3845 LYS Chi-restraints excluded: chain A residue 3850 HIS Chi-restraints excluded: chain A residue 3977 THR Chi-restraints excluded: chain A residue 4028 ILE Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain C residue 20 MET Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 346 CYS Chi-restraints excluded: chain D residue 8 MET Chi-restraints excluded: chain D residue 19 PHE Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain D residue 318 PHE Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 349 ASP Chi-restraints excluded: chain D residue 390 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 543 random chunks: chunk 274 optimal weight: 0.7980 chunk 153 optimal weight: 7.9990 chunk 410 optimal weight: 7.9990 chunk 335 optimal weight: 2.9990 chunk 136 optimal weight: 3.9990 chunk 493 optimal weight: 4.9990 chunk 533 optimal weight: 5.9990 chunk 439 optimal weight: 6.9990 chunk 489 optimal weight: 0.0020 chunk 168 optimal weight: 9.9990 chunk 396 optimal weight: 10.0000 overall best weight: 2.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2885 GLN A3643 HIS ** A3664 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3850 HIS ** B 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 174 ASN ** B 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 45774 Z= 0.295 Angle : 0.581 10.190 62143 Z= 0.293 Chirality : 0.041 0.385 6962 Planarity : 0.004 0.063 7706 Dihedral : 12.636 85.784 6616 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.05 % Allowed : 11.25 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.12), residues: 5367 helix: 0.90 (0.10), residues: 3021 sheet: -0.93 (0.30), residues: 266 loop : -1.49 (0.13), residues: 2080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP D 267 HIS 0.035 0.001 HIS A3850 PHE 0.025 0.002 PHE A2260 TYR 0.020 0.001 TYR A1873 ARG 0.007 0.001 ARG A3833 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10734 Ramachandran restraints generated. 5367 Oldfield, 0 Emsley, 5367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10734 Ramachandran restraints generated. 5367 Oldfield, 0 Emsley, 5367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 4826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 245 time to evaluate : 5.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.5181 (tpp) cc_final: 0.4838 (tmm) REVERT: A 899 ARG cc_start: 0.8275 (OUTLIER) cc_final: 0.7854 (ttp-170) REVERT: A 1197 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8556 (pp) REVERT: A 1356 TRP cc_start: 0.7890 (p-90) cc_final: 0.7497 (p-90) REVERT: A 1357 LYS cc_start: 0.8162 (pttm) cc_final: 0.7921 (tmmt) REVERT: A 1362 ASP cc_start: 0.7222 (m-30) cc_final: 0.6948 (t0) REVERT: A 1467 ILE cc_start: 0.8143 (mm) cc_final: 0.7894 (tp) REVERT: A 1509 GLN cc_start: 0.8150 (tm-30) cc_final: 0.7769 (pm20) REVERT: A 1592 MET cc_start: 0.8171 (tpt) cc_final: 0.7722 (tpt) REVERT: A 1668 PHE cc_start: 0.6932 (OUTLIER) cc_final: 0.5790 (t80) REVERT: A 1744 LYS cc_start: 0.9028 (ptpp) cc_final: 0.8697 (tppp) REVERT: A 1774 MET cc_start: 0.8444 (mmm) cc_final: 0.7763 (tpp) REVERT: A 1829 TRP cc_start: 0.8569 (m100) cc_final: 0.8353 (m100) REVERT: A 1874 TYR cc_start: 0.8299 (m-80) cc_final: 0.8096 (m-80) REVERT: A 1927 MET cc_start: 0.7700 (mtp) cc_final: 0.7221 (mpm) REVERT: A 1933 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.7907 (mm) REVERT: A 1993 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7497 (tm-30) REVERT: A 2094 MET cc_start: 0.8377 (tpt) cc_final: 0.8123 (tpt) REVERT: A 2437 ASP cc_start: 0.8276 (m-30) cc_final: 0.7973 (m-30) REVERT: A 2860 ASP cc_start: 0.7853 (OUTLIER) cc_final: 0.7621 (t0) REVERT: A 3502 MET cc_start: 0.8383 (OUTLIER) cc_final: 0.7628 (mtp) REVERT: A 3613 MET cc_start: 0.7876 (tmt) cc_final: 0.7434 (tmt) REVERT: A 3664 ASN cc_start: 0.7988 (OUTLIER) cc_final: 0.7651 (p0) REVERT: A 3769 GLN cc_start: 0.8179 (OUTLIER) cc_final: 0.7974 (mt0) REVERT: A 3796 MET cc_start: 0.8566 (OUTLIER) cc_final: 0.7782 (mtt) REVERT: D 1 MET cc_start: 0.7080 (tpp) cc_final: 0.6112 (mmt) REVERT: D 348 MET cc_start: 0.8060 (tpp) cc_final: 0.7859 (tpp) outliers start: 98 outliers final: 41 residues processed: 321 average time/residue: 1.5275 time to fit residues: 624.1332 Evaluate side-chains 275 residues out of total 4826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 224 time to evaluate : 5.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 LYS Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 289 ASN Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 899 ARG Chi-restraints excluded: chain A residue 1197 LEU Chi-restraints excluded: chain A residue 1593 VAL Chi-restraints excluded: chain A residue 1668 PHE Chi-restraints excluded: chain A residue 1671 VAL Chi-restraints excluded: chain A residue 1688 LEU Chi-restraints excluded: chain A residue 1696 LEU Chi-restraints excluded: chain A residue 1805 PHE Chi-restraints excluded: chain A residue 1867 ILE Chi-restraints excluded: chain A residue 1933 LEU Chi-restraints excluded: chain A residue 1993 GLU Chi-restraints excluded: chain A residue 2197 THR Chi-restraints excluded: chain A residue 2424 MET Chi-restraints excluded: chain A residue 2449 VAL Chi-restraints excluded: chain A residue 2860 ASP Chi-restraints excluded: chain A residue 3077 ILE Chi-restraints excluded: chain A residue 3479 THR Chi-restraints excluded: chain A residue 3480 LEU Chi-restraints excluded: chain A residue 3502 MET Chi-restraints excluded: chain A residue 3530 VAL Chi-restraints excluded: chain A residue 3553 GLU Chi-restraints excluded: chain A residue 3652 LEU Chi-restraints excluded: chain A residue 3662 ILE Chi-restraints excluded: chain A residue 3664 ASN Chi-restraints excluded: chain A residue 3694 PHE Chi-restraints excluded: chain A residue 3697 ASN Chi-restraints excluded: chain A residue 3769 GLN Chi-restraints excluded: chain A residue 3796 MET Chi-restraints excluded: chain A residue 3977 THR Chi-restraints excluded: chain A residue 4028 ILE Chi-restraints excluded: chain A residue 4122 GLU Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 455 THR Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain D residue 8 MET Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain D residue 318 PHE Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 349 ASP Chi-restraints excluded: chain D residue 390 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 543 random chunks: chunk 488 optimal weight: 9.9990 chunk 371 optimal weight: 2.9990 chunk 256 optimal weight: 0.7980 chunk 54 optimal weight: 8.9990 chunk 235 optimal weight: 3.9990 chunk 331 optimal weight: 0.9980 chunk 495 optimal weight: 7.9990 chunk 524 optimal weight: 4.9990 chunk 259 optimal weight: 2.9990 chunk 469 optimal weight: 20.0000 chunk 141 optimal weight: 7.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 192 ASN A 399 GLN A1426 GLN A1435 ASN ** A1725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3023 ASN ** A3664 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3850 HIS ** B 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 45774 Z= 0.275 Angle : 0.564 10.666 62143 Z= 0.284 Chirality : 0.041 0.357 6962 Planarity : 0.004 0.052 7706 Dihedral : 12.413 86.062 6613 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.28 % Allowed : 11.46 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.12), residues: 5367 helix: 1.03 (0.10), residues: 3026 sheet: -0.69 (0.30), residues: 264 loop : -1.35 (0.14), residues: 2077 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP D 267 HIS 0.010 0.001 HIS D 115 PHE 0.024 0.002 PHE A2260 TYR 0.027 0.001 TYR A1675 ARG 0.005 0.001 ARG A3833 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10734 Ramachandran restraints generated. 5367 Oldfield, 0 Emsley, 5367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10734 Ramachandran restraints generated. 5367 Oldfield, 0 Emsley, 5367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 4826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 230 time to evaluate : 5.436 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 1 MET cc_start: 0.5116 (tpp) cc_final: 0.4694 (tmm) REVERT: A 286 LEU cc_start: 0.7639 (OUTLIER) cc_final: 0.7338 (pp) REVERT: A 723 ASP cc_start: 0.7371 (OUTLIER) cc_final: 0.7143 (p0) REVERT: A 948 MET cc_start: 0.7295 (tpp) cc_final: 0.7078 (tpp) REVERT: A 1197 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8594 (pp) REVERT: A 1356 TRP cc_start: 0.7894 (p-90) cc_final: 0.7521 (p-90) REVERT: A 1467 ILE cc_start: 0.8038 (mm) cc_final: 0.7813 (tp) REVERT: A 1509 GLN cc_start: 0.8154 (tm-30) cc_final: 0.7791 (pm20) REVERT: A 1592 MET cc_start: 0.8213 (tpt) cc_final: 0.7794 (tpt) REVERT: A 1668 PHE cc_start: 0.6879 (OUTLIER) cc_final: 0.5777 (t80) REVERT: A 1744 LYS cc_start: 0.9034 (ptpp) cc_final: 0.8754 (tppp) REVERT: A 1774 MET cc_start: 0.8482 (mmm) cc_final: 0.7886 (tpp) REVERT: A 1829 TRP cc_start: 0.8625 (m100) cc_final: 0.8313 (m100) REVERT: A 1874 TYR cc_start: 0.8201 (m-80) cc_final: 0.7994 (m-80) REVERT: A 1927 MET cc_start: 0.7643 (mtp) cc_final: 0.7230 (mpm) REVERT: A 1933 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.7911 (mm) REVERT: A 1993 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7665 (tm-30) REVERT: A 2094 MET cc_start: 0.8385 (tpt) cc_final: 0.8112 (tpt) REVERT: A 2437 ASP cc_start: 0.8278 (m-30) cc_final: 0.7946 (m-30) REVERT: A 2800 ARG cc_start: 0.7979 (OUTLIER) cc_final: 0.7647 (mtp180) REVERT: A 2860 ASP cc_start: 0.7851 (OUTLIER) cc_final: 0.7612 (t0) REVERT: A 3613 MET cc_start: 0.7846 (tmt) cc_final: 0.7478 (tmt) REVERT: A 3769 GLN cc_start: 0.8165 (OUTLIER) cc_final: 0.7946 (mt0) REVERT: A 3796 MET cc_start: 0.8576 (OUTLIER) cc_final: 0.7833 (mtt) REVERT: D 8 MET cc_start: 0.8556 (OUTLIER) cc_final: 0.8351 (mtm) REVERT: D 348 MET cc_start: 0.8069 (tpp) cc_final: 0.7855 (tpp) outliers start: 109 outliers final: 39 residues processed: 318 average time/residue: 1.5694 time to fit residues: 631.5357 Evaluate side-chains 272 residues out of total 4826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 222 time to evaluate : 5.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 LYS Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 289 ASN Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 723 ASP Chi-restraints excluded: chain A residue 908 ASP Chi-restraints excluded: chain A residue 1197 LEU Chi-restraints excluded: chain A residue 1225 GLU Chi-restraints excluded: chain A residue 1593 VAL Chi-restraints excluded: chain A residue 1668 PHE Chi-restraints excluded: chain A residue 1671 VAL Chi-restraints excluded: chain A residue 1696 LEU Chi-restraints excluded: chain A residue 1747 LEU Chi-restraints excluded: chain A residue 1805 PHE Chi-restraints excluded: chain A residue 1867 ILE Chi-restraints excluded: chain A residue 1933 LEU Chi-restraints excluded: chain A residue 1993 GLU Chi-restraints excluded: chain A residue 2197 THR Chi-restraints excluded: chain A residue 2424 MET Chi-restraints excluded: chain A residue 2449 VAL Chi-restraints excluded: chain A residue 2631 VAL Chi-restraints excluded: chain A residue 2800 ARG Chi-restraints excluded: chain A residue 2860 ASP Chi-restraints excluded: chain A residue 2983 ASP Chi-restraints excluded: chain A residue 3157 LEU Chi-restraints excluded: chain A residue 3479 THR Chi-restraints excluded: chain A residue 3530 VAL Chi-restraints excluded: chain A residue 3553 GLU Chi-restraints excluded: chain A residue 3697 ASN Chi-restraints excluded: chain A residue 3769 GLN Chi-restraints excluded: chain A residue 3796 MET Chi-restraints excluded: chain A residue 3977 THR Chi-restraints excluded: chain A residue 4028 ILE Chi-restraints excluded: chain A residue 4122 GLU Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 455 THR Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 20 MET Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain D residue 8 MET Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 318 PHE Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 349 ASP Chi-restraints excluded: chain D residue 390 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 543 random chunks: chunk 437 optimal weight: 0.6980 chunk 297 optimal weight: 0.9990 chunk 7 optimal weight: 0.0980 chunk 390 optimal weight: 8.9990 chunk 216 optimal weight: 3.9990 chunk 447 optimal weight: 4.9990 chunk 362 optimal weight: 0.7980 chunk 0 optimal weight: 30.0000 chunk 268 optimal weight: 0.9990 chunk 471 optimal weight: 5.9990 chunk 132 optimal weight: 4.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 HIS A 192 ASN A 377 ASN ** A1898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2301 GLN A2305 ASN A2787 HIS A3384 HIS ** A3397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3664 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3850 HIS ** B 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 440 ASN D 92 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.2532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.080 45774 Z= 0.155 Angle : 0.519 10.589 62143 Z= 0.259 Chirality : 0.039 0.367 6962 Planarity : 0.004 0.047 7706 Dihedral : 12.126 86.426 6611 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.61 % Allowed : 12.55 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.12), residues: 5367 helix: 1.26 (0.10), residues: 3034 sheet: -0.55 (0.30), residues: 266 loop : -1.27 (0.14), residues: 2067 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP D 267 HIS 0.004 0.000 HIS A3850 PHE 0.027 0.001 PHE A1839 TYR 0.021 0.001 TYR A1675 ARG 0.005 0.000 ARG A3833 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10734 Ramachandran restraints generated. 5367 Oldfield, 0 Emsley, 5367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10734 Ramachandran restraints generated. 5367 Oldfield, 0 Emsley, 5367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 4826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 232 time to evaluate : 5.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.5118 (tpp) cc_final: 0.4688 (tmm) REVERT: A 286 LEU cc_start: 0.7565 (OUTLIER) cc_final: 0.7337 (pp) REVERT: A 899 ARG cc_start: 0.8224 (OUTLIER) cc_final: 0.7890 (ttp-170) REVERT: A 948 MET cc_start: 0.7249 (tpp) cc_final: 0.6980 (tpp) REVERT: A 1356 TRP cc_start: 0.7829 (p-90) cc_final: 0.7494 (p-90) REVERT: A 1467 ILE cc_start: 0.7974 (mm) cc_final: 0.7761 (tp) REVERT: A 1592 MET cc_start: 0.8161 (tpt) cc_final: 0.7892 (tpt) REVERT: A 1668 PHE cc_start: 0.6711 (OUTLIER) cc_final: 0.5548 (t80) REVERT: A 1744 LYS cc_start: 0.8964 (ptpp) cc_final: 0.8703 (tppp) REVERT: A 1774 MET cc_start: 0.8462 (mmm) cc_final: 0.7910 (tpp) REVERT: A 1829 TRP cc_start: 0.8601 (m100) cc_final: 0.8260 (m100) REVERT: A 1927 MET cc_start: 0.7539 (mtp) cc_final: 0.7196 (mpm) REVERT: A 1933 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.7923 (mm) REVERT: A 1993 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7311 (tm-30) REVERT: A 2094 MET cc_start: 0.8351 (tpt) cc_final: 0.8107 (tpt) REVERT: A 2289 ASP cc_start: 0.8025 (OUTLIER) cc_final: 0.7802 (t0) REVERT: A 2437 ASP cc_start: 0.8258 (m-30) cc_final: 0.7956 (m-30) REVERT: A 2605 MET cc_start: 0.8606 (mtt) cc_final: 0.8360 (mtt) REVERT: A 2800 ARG cc_start: 0.7955 (OUTLIER) cc_final: 0.7626 (mtp180) REVERT: A 2860 ASP cc_start: 0.7665 (t70) cc_final: 0.7439 (t0) REVERT: A 3414 MET cc_start: 0.8363 (mmm) cc_final: 0.7874 (mmm) REVERT: A 3613 MET cc_start: 0.7800 (tmt) cc_final: 0.7436 (tmt) REVERT: A 3664 ASN cc_start: 0.7953 (OUTLIER) cc_final: 0.7616 (p0) REVERT: A 3796 MET cc_start: 0.8503 (OUTLIER) cc_final: 0.7406 (mtt) REVERT: C 16 VAL cc_start: 0.4386 (OUTLIER) cc_final: 0.4185 (t) REVERT: D 1 MET cc_start: 0.7068 (tpp) cc_final: 0.6056 (tpp) outliers start: 77 outliers final: 31 residues processed: 292 average time/residue: 1.5842 time to fit residues: 584.6469 Evaluate side-chains 261 residues out of total 4826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 220 time to evaluate : 6.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 LYS Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 899 ARG Chi-restraints excluded: chain A residue 908 ASP Chi-restraints excluded: chain A residue 1590 THR Chi-restraints excluded: chain A residue 1593 VAL Chi-restraints excluded: chain A residue 1668 PHE Chi-restraints excluded: chain A residue 1671 VAL Chi-restraints excluded: chain A residue 1747 LEU Chi-restraints excluded: chain A residue 1798 LEU Chi-restraints excluded: chain A residue 1805 PHE Chi-restraints excluded: chain A residue 1867 ILE Chi-restraints excluded: chain A residue 1933 LEU Chi-restraints excluded: chain A residue 1993 GLU Chi-restraints excluded: chain A residue 2197 THR Chi-restraints excluded: chain A residue 2199 LEU Chi-restraints excluded: chain A residue 2289 ASP Chi-restraints excluded: chain A residue 2424 MET Chi-restraints excluded: chain A residue 2449 VAL Chi-restraints excluded: chain A residue 2800 ARG Chi-restraints excluded: chain A residue 3553 GLU Chi-restraints excluded: chain A residue 3664 ASN Chi-restraints excluded: chain A residue 3796 MET Chi-restraints excluded: chain A residue 3850 HIS Chi-restraints excluded: chain A residue 4028 ILE Chi-restraints excluded: chain A residue 4122 GLU Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 455 THR Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 20 MET Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 318 PHE Chi-restraints excluded: chain D residue 344 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 543 random chunks: chunk 176 optimal weight: 8.9990 chunk 472 optimal weight: 20.0000 chunk 103 optimal weight: 4.9990 chunk 308 optimal weight: 1.9990 chunk 129 optimal weight: 0.0870 chunk 525 optimal weight: 0.7980 chunk 436 optimal weight: 0.0870 chunk 243 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 chunk 173 optimal weight: 3.9990 chunk 275 optimal weight: 5.9990 overall best weight: 0.5336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 377 ASN A1725 GLN ** A1898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2301 GLN A2305 ASN ** A3397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3664 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3850 HIS B 359 HIS C 80 HIS ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.073 45774 Z= 0.148 Angle : 0.515 11.474 62143 Z= 0.255 Chirality : 0.038 0.357 6962 Planarity : 0.004 0.059 7706 Dihedral : 11.923 86.397 6608 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.70 % Allowed : 12.76 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.12), residues: 5367 helix: 1.39 (0.10), residues: 3030 sheet: -0.35 (0.30), residues: 271 loop : -1.20 (0.14), residues: 2066 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP D 267 HIS 0.027 0.001 HIS A3850 PHE 0.040 0.001 PHE A1839 TYR 0.015 0.001 TYR A 385 ARG 0.006 0.000 ARG B 230 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10734 Ramachandran restraints generated. 5367 Oldfield, 0 Emsley, 5367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10734 Ramachandran restraints generated. 5367 Oldfield, 0 Emsley, 5367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 4826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 228 time to evaluate : 5.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.5136 (tpp) cc_final: 0.4729 (tmm) REVERT: A 286 LEU cc_start: 0.7543 (OUTLIER) cc_final: 0.7310 (pp) REVERT: A 342 MET cc_start: 0.8595 (OUTLIER) cc_final: 0.8257 (mmm) REVERT: A 948 MET cc_start: 0.7254 (tpp) cc_final: 0.7027 (tpp) REVERT: A 1356 TRP cc_start: 0.7848 (p-90) cc_final: 0.7457 (p-90) REVERT: A 1509 GLN cc_start: 0.8081 (tm-30) cc_final: 0.7677 (pm20) REVERT: A 1592 MET cc_start: 0.8146 (tpt) cc_final: 0.7878 (tpt) REVERT: A 1668 PHE cc_start: 0.6682 (OUTLIER) cc_final: 0.5541 (t80) REVERT: A 1744 LYS cc_start: 0.8977 (ptpp) cc_final: 0.8729 (tppp) REVERT: A 1774 MET cc_start: 0.8428 (mmm) cc_final: 0.8189 (tpp) REVERT: A 1794 GLN cc_start: 0.7248 (OUTLIER) cc_final: 0.6835 (mp10) REVERT: A 1829 TRP cc_start: 0.8616 (m100) cc_final: 0.8304 (m100) REVERT: A 1927 MET cc_start: 0.7525 (mtp) cc_final: 0.7169 (mpm) REVERT: A 1933 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.7981 (mm) REVERT: A 1993 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7235 (tm-30) REVERT: A 2094 MET cc_start: 0.8383 (tpt) cc_final: 0.8140 (tpt) REVERT: A 2205 VAL cc_start: 0.8116 (t) cc_final: 0.7894 (t) REVERT: A 2289 ASP cc_start: 0.8032 (OUTLIER) cc_final: 0.7803 (t0) REVERT: A 2437 ASP cc_start: 0.8257 (m-30) cc_final: 0.7948 (m-30) REVERT: A 2800 ARG cc_start: 0.7952 (OUTLIER) cc_final: 0.7621 (mtp180) REVERT: A 2860 ASP cc_start: 0.7666 (t70) cc_final: 0.7430 (t0) REVERT: A 3414 MET cc_start: 0.8319 (mmm) cc_final: 0.7943 (mmm) REVERT: A 3613 MET cc_start: 0.7771 (tmt) cc_final: 0.7409 (tmt) REVERT: A 3664 ASN cc_start: 0.8007 (OUTLIER) cc_final: 0.7665 (p0) REVERT: A 3796 MET cc_start: 0.8460 (OUTLIER) cc_final: 0.7355 (mtt) REVERT: B 348 MET cc_start: 0.6548 (OUTLIER) cc_final: 0.5809 (mpt) REVERT: C 16 VAL cc_start: 0.4305 (OUTLIER) cc_final: 0.4099 (t) outliers start: 81 outliers final: 34 residues processed: 294 average time/residue: 1.5368 time to fit residues: 576.4056 Evaluate side-chains 266 residues out of total 4826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 220 time to evaluate : 5.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 LYS Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 342 MET Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 908 ASP Chi-restraints excluded: chain A residue 1225 GLU Chi-restraints excluded: chain A residue 1590 THR Chi-restraints excluded: chain A residue 1593 VAL Chi-restraints excluded: chain A residue 1668 PHE Chi-restraints excluded: chain A residue 1671 VAL Chi-restraints excluded: chain A residue 1696 LEU Chi-restraints excluded: chain A residue 1747 LEU Chi-restraints excluded: chain A residue 1794 GLN Chi-restraints excluded: chain A residue 1798 LEU Chi-restraints excluded: chain A residue 1867 ILE Chi-restraints excluded: chain A residue 1933 LEU Chi-restraints excluded: chain A residue 1993 GLU Chi-restraints excluded: chain A residue 2197 THR Chi-restraints excluded: chain A residue 2199 LEU Chi-restraints excluded: chain A residue 2289 ASP Chi-restraints excluded: chain A residue 2449 VAL Chi-restraints excluded: chain A residue 2800 ARG Chi-restraints excluded: chain A residue 2980 ASP Chi-restraints excluded: chain A residue 3480 LEU Chi-restraints excluded: chain A residue 3553 GLU Chi-restraints excluded: chain A residue 3657 SER Chi-restraints excluded: chain A residue 3664 ASN Chi-restraints excluded: chain A residue 3697 ASN Chi-restraints excluded: chain A residue 3796 MET Chi-restraints excluded: chain A residue 4028 ILE Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 455 THR Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 20 MET Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 344 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 543 random chunks: chunk 506 optimal weight: 3.9990 chunk 59 optimal weight: 0.0670 chunk 299 optimal weight: 7.9990 chunk 383 optimal weight: 2.9990 chunk 297 optimal weight: 0.9980 chunk 442 optimal weight: 20.0000 chunk 293 optimal weight: 4.9990 chunk 523 optimal weight: 1.9990 chunk 327 optimal weight: 3.9990 chunk 319 optimal weight: 0.6980 chunk 241 optimal weight: 1.9990 overall best weight: 1.1522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 377 ASN ** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2301 GLN A2305 ASN ** A3397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3664 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3850 HIS ** B 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.2717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 45774 Z= 0.176 Angle : 0.526 12.342 62143 Z= 0.260 Chirality : 0.039 0.349 6962 Planarity : 0.004 0.053 7706 Dihedral : 11.808 86.172 6606 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.59 % Allowed : 13.09 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.12), residues: 5367 helix: 1.42 (0.10), residues: 3043 sheet: -0.22 (0.31), residues: 269 loop : -1.14 (0.14), residues: 2055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP D 267 HIS 0.006 0.001 HIS D 115 PHE 0.032 0.001 PHE A1814 TYR 0.014 0.001 TYR A1107 ARG 0.007 0.000 ARG B 230 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10734 Ramachandran restraints generated. 5367 Oldfield, 0 Emsley, 5367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10734 Ramachandran restraints generated. 5367 Oldfield, 0 Emsley, 5367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 4826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 233 time to evaluate : 5.226 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 1 MET cc_start: 0.5091 (tpp) cc_final: 0.4584 (tmm) REVERT: A 286 LEU cc_start: 0.7502 (OUTLIER) cc_final: 0.7252 (pp) REVERT: A 342 MET cc_start: 0.8609 (OUTLIER) cc_final: 0.8275 (mmm) REVERT: A 948 MET cc_start: 0.7289 (tpp) cc_final: 0.7054 (tpp) REVERT: A 1356 TRP cc_start: 0.7892 (p-90) cc_final: 0.7488 (p-90) REVERT: A 1509 GLN cc_start: 0.8124 (tm-30) cc_final: 0.7727 (pm20) REVERT: A 1592 MET cc_start: 0.8151 (tpt) cc_final: 0.7860 (tpt) REVERT: A 1668 PHE cc_start: 0.6706 (OUTLIER) cc_final: 0.5610 (t80) REVERT: A 1744 LYS cc_start: 0.8972 (ptpp) cc_final: 0.8744 (tppp) REVERT: A 1774 MET cc_start: 0.8426 (mmm) cc_final: 0.8185 (tpp) REVERT: A 1794 GLN cc_start: 0.7235 (OUTLIER) cc_final: 0.6461 (mp-120) REVERT: A 1829 TRP cc_start: 0.8610 (m100) cc_final: 0.8290 (m100) REVERT: A 1927 MET cc_start: 0.7490 (mtp) cc_final: 0.7163 (mpm) REVERT: A 1933 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.7968 (mm) REVERT: A 1993 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7203 (tm-30) REVERT: A 2094 MET cc_start: 0.8373 (tpt) cc_final: 0.8134 (tpt) REVERT: A 2289 ASP cc_start: 0.8021 (OUTLIER) cc_final: 0.7782 (t0) REVERT: A 2437 ASP cc_start: 0.8279 (m-30) cc_final: 0.7971 (m-30) REVERT: A 2605 MET cc_start: 0.8643 (mtt) cc_final: 0.8374 (mtt) REVERT: A 2800 ARG cc_start: 0.8023 (OUTLIER) cc_final: 0.7668 (mtp180) REVERT: A 2860 ASP cc_start: 0.7762 (t70) cc_final: 0.7526 (t0) REVERT: A 3608 LYS cc_start: 0.8621 (tptt) cc_final: 0.8418 (tptp) REVERT: A 3613 MET cc_start: 0.7774 (tmt) cc_final: 0.7396 (tmt) REVERT: A 3664 ASN cc_start: 0.7985 (OUTLIER) cc_final: 0.7648 (p0) REVERT: A 3796 MET cc_start: 0.8511 (OUTLIER) cc_final: 0.7423 (mtt) outliers start: 76 outliers final: 40 residues processed: 294 average time/residue: 1.5300 time to fit residues: 569.4516 Evaluate side-chains 277 residues out of total 4826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 227 time to evaluate : 5.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 LYS Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 342 MET Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 908 ASP Chi-restraints excluded: chain A residue 1225 GLU Chi-restraints excluded: chain A residue 1448 LEU Chi-restraints excluded: chain A residue 1590 THR Chi-restraints excluded: chain A residue 1593 VAL Chi-restraints excluded: chain A residue 1633 TRP Chi-restraints excluded: chain A residue 1668 PHE Chi-restraints excluded: chain A residue 1671 VAL Chi-restraints excluded: chain A residue 1700 THR Chi-restraints excluded: chain A residue 1747 LEU Chi-restraints excluded: chain A residue 1794 GLN Chi-restraints excluded: chain A residue 1867 ILE Chi-restraints excluded: chain A residue 1933 LEU Chi-restraints excluded: chain A residue 1981 LEU Chi-restraints excluded: chain A residue 1993 GLU Chi-restraints excluded: chain A residue 2197 THR Chi-restraints excluded: chain A residue 2199 LEU Chi-restraints excluded: chain A residue 2289 ASP Chi-restraints excluded: chain A residue 2449 VAL Chi-restraints excluded: chain A residue 2800 ARG Chi-restraints excluded: chain A residue 2980 ASP Chi-restraints excluded: chain A residue 2983 ASP Chi-restraints excluded: chain A residue 3480 LEU Chi-restraints excluded: chain A residue 3553 GLU Chi-restraints excluded: chain A residue 3657 SER Chi-restraints excluded: chain A residue 3664 ASN Chi-restraints excluded: chain A residue 3697 ASN Chi-restraints excluded: chain A residue 3796 MET Chi-restraints excluded: chain A residue 4028 ILE Chi-restraints excluded: chain A residue 4122 GLU Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 455 THR Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain C residue 20 MET Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 318 PHE Chi-restraints excluded: chain D residue 344 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 543 random chunks: chunk 323 optimal weight: 4.9990 chunk 209 optimal weight: 4.9990 chunk 312 optimal weight: 8.9990 chunk 157 optimal weight: 8.9990 chunk 102 optimal weight: 0.9990 chunk 101 optimal weight: 0.8980 chunk 332 optimal weight: 0.9990 chunk 356 optimal weight: 0.9990 chunk 258 optimal weight: 0.0770 chunk 48 optimal weight: 1.9990 chunk 411 optimal weight: 9.9990 overall best weight: 0.7944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 377 ASN ** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2301 GLN A2305 ASN ** A3664 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3850 HIS ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 45774 Z= 0.156 Angle : 0.528 11.308 62143 Z= 0.259 Chirality : 0.039 0.344 6962 Planarity : 0.004 0.052 7706 Dihedral : 11.700 86.205 6606 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.53 % Allowed : 13.24 % Favored : 85.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.12), residues: 5367 helix: 1.48 (0.10), residues: 3034 sheet: -0.15 (0.31), residues: 269 loop : -1.08 (0.14), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP D 267 HIS 0.005 0.000 HIS A1418 PHE 0.021 0.001 PHE A2260 TYR 0.014 0.001 TYR A1873 ARG 0.007 0.000 ARG B 230 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10734 Ramachandran restraints generated. 5367 Oldfield, 0 Emsley, 5367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10734 Ramachandran restraints generated. 5367 Oldfield, 0 Emsley, 5367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 4826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 231 time to evaluate : 5.413 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 1 MET cc_start: 0.5035 (tpp) cc_final: 0.4533 (tmm) REVERT: A 286 LEU cc_start: 0.7494 (OUTLIER) cc_final: 0.7245 (pp) REVERT: A 342 MET cc_start: 0.8584 (OUTLIER) cc_final: 0.8241 (mmm) REVERT: A 948 MET cc_start: 0.7266 (tpp) cc_final: 0.7029 (tpp) REVERT: A 1356 TRP cc_start: 0.7886 (p-90) cc_final: 0.7484 (p-90) REVERT: A 1592 MET cc_start: 0.8142 (tpt) cc_final: 0.7853 (tpt) REVERT: A 1668 PHE cc_start: 0.6702 (OUTLIER) cc_final: 0.5577 (t80) REVERT: A 1688 LEU cc_start: 0.8621 (pp) cc_final: 0.7784 (tp) REVERT: A 1744 LYS cc_start: 0.8977 (ptpp) cc_final: 0.8740 (tppp) REVERT: A 1774 MET cc_start: 0.8423 (mmm) cc_final: 0.8190 (tpp) REVERT: A 1794 GLN cc_start: 0.7180 (OUTLIER) cc_final: 0.6755 (mp10) REVERT: A 1829 TRP cc_start: 0.8649 (m100) cc_final: 0.8285 (m100) REVERT: A 1927 MET cc_start: 0.7492 (mtp) cc_final: 0.7150 (mpm) REVERT: A 1933 LEU cc_start: 0.8297 (OUTLIER) cc_final: 0.7992 (mm) REVERT: A 1993 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7136 (tm-30) REVERT: A 2094 MET cc_start: 0.8370 (tpt) cc_final: 0.8133 (tpt) REVERT: A 2289 ASP cc_start: 0.8051 (OUTLIER) cc_final: 0.7794 (t0) REVERT: A 2357 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.7322 (pm20) REVERT: A 2437 ASP cc_start: 0.8286 (m-30) cc_final: 0.7974 (m-30) REVERT: A 2605 MET cc_start: 0.8631 (mtt) cc_final: 0.8365 (mtt) REVERT: A 2800 ARG cc_start: 0.8001 (OUTLIER) cc_final: 0.7632 (mtp180) REVERT: A 2860 ASP cc_start: 0.7703 (t70) cc_final: 0.7465 (t0) REVERT: A 3613 MET cc_start: 0.7748 (tmt) cc_final: 0.7383 (tmt) REVERT: A 3664 ASN cc_start: 0.7935 (OUTLIER) cc_final: 0.7573 (p0) REVERT: A 3796 MET cc_start: 0.8474 (OUTLIER) cc_final: 0.7379 (mtt) REVERT: B 232 HIS cc_start: 0.6878 (OUTLIER) cc_final: 0.5906 (m-70) outliers start: 73 outliers final: 41 residues processed: 292 average time/residue: 1.5159 time to fit residues: 562.0076 Evaluate side-chains 275 residues out of total 4826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 222 time to evaluate : 5.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 LYS Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 342 MET Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 908 ASP Chi-restraints excluded: chain A residue 1225 GLU Chi-restraints excluded: chain A residue 1448 LEU Chi-restraints excluded: chain A residue 1590 THR Chi-restraints excluded: chain A residue 1593 VAL Chi-restraints excluded: chain A residue 1633 TRP Chi-restraints excluded: chain A residue 1668 PHE Chi-restraints excluded: chain A residue 1671 VAL Chi-restraints excluded: chain A residue 1747 LEU Chi-restraints excluded: chain A residue 1794 GLN Chi-restraints excluded: chain A residue 1867 ILE Chi-restraints excluded: chain A residue 1933 LEU Chi-restraints excluded: chain A residue 1993 GLU Chi-restraints excluded: chain A residue 2100 LEU Chi-restraints excluded: chain A residue 2197 THR Chi-restraints excluded: chain A residue 2199 LEU Chi-restraints excluded: chain A residue 2205 VAL Chi-restraints excluded: chain A residue 2289 ASP Chi-restraints excluded: chain A residue 2357 GLU Chi-restraints excluded: chain A residue 2449 VAL Chi-restraints excluded: chain A residue 2800 ARG Chi-restraints excluded: chain A residue 2980 ASP Chi-restraints excluded: chain A residue 2983 ASP Chi-restraints excluded: chain A residue 3480 LEU Chi-restraints excluded: chain A residue 3553 GLU Chi-restraints excluded: chain A residue 3657 SER Chi-restraints excluded: chain A residue 3664 ASN Chi-restraints excluded: chain A residue 3697 ASN Chi-restraints excluded: chain A residue 3796 MET Chi-restraints excluded: chain A residue 3850 HIS Chi-restraints excluded: chain A residue 4028 ILE Chi-restraints excluded: chain A residue 4122 GLU Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 232 HIS Chi-restraints excluded: chain B residue 455 THR Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain C residue 20 MET Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain D residue 19 PHE Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 344 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 543 random chunks: chunk 476 optimal weight: 5.9990 chunk 501 optimal weight: 4.9990 chunk 457 optimal weight: 4.9990 chunk 487 optimal weight: 10.0000 chunk 293 optimal weight: 0.5980 chunk 212 optimal weight: 2.9990 chunk 382 optimal weight: 2.9990 chunk 149 optimal weight: 7.9990 chunk 440 optimal weight: 40.0000 chunk 461 optimal weight: 3.9990 chunk 486 optimal weight: 0.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 377 ASN ** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1890 HIS ** A1898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2301 GLN A2305 ASN ** A3664 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3850 HIS ** B 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 320 GLN ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 45774 Z= 0.268 Angle : 0.569 12.053 62143 Z= 0.283 Chirality : 0.041 0.333 6962 Planarity : 0.004 0.051 7706 Dihedral : 11.801 85.664 6606 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.53 % Allowed : 13.36 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.12), residues: 5367 helix: 1.40 (0.10), residues: 3034 sheet: -0.19 (0.31), residues: 264 loop : -1.09 (0.14), residues: 2069 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.001 TRP D 267 HIS 0.015 0.001 HIS A3850 PHE 0.023 0.001 PHE A2260 TYR 0.023 0.001 TYR A1873 ARG 0.007 0.000 ARG B 230 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10734 Ramachandran restraints generated. 5367 Oldfield, 0 Emsley, 5367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10734 Ramachandran restraints generated. 5367 Oldfield, 0 Emsley, 5367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 4826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 225 time to evaluate : 5.388 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 1 MET cc_start: 0.5061 (tpp) cc_final: 0.4537 (tmm) REVERT: A 286 LEU cc_start: 0.7504 (OUTLIER) cc_final: 0.7251 (pp) REVERT: A 342 MET cc_start: 0.8576 (OUTLIER) cc_final: 0.8258 (mmm) REVERT: A 408 TYR cc_start: 0.8306 (m-80) cc_final: 0.8103 (m-80) REVERT: A 1356 TRP cc_start: 0.7901 (p-90) cc_final: 0.7552 (p-90) REVERT: A 1592 MET cc_start: 0.8209 (tpt) cc_final: 0.7943 (tpt) REVERT: A 1668 PHE cc_start: 0.6817 (OUTLIER) cc_final: 0.5729 (t80) REVERT: A 1744 LYS cc_start: 0.8971 (ptpp) cc_final: 0.8758 (tppp) REVERT: A 1774 MET cc_start: 0.8443 (mmm) cc_final: 0.8213 (tpp) REVERT: A 1829 TRP cc_start: 0.8586 (m100) cc_final: 0.8285 (m100) REVERT: A 1927 MET cc_start: 0.7497 (mtp) cc_final: 0.7164 (mpm) REVERT: A 1933 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.7981 (mm) REVERT: A 1993 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7260 (tm-30) REVERT: A 2094 MET cc_start: 0.8377 (tpt) cc_final: 0.8111 (tpt) REVERT: A 2289 ASP cc_start: 0.8033 (OUTLIER) cc_final: 0.7767 (t0) REVERT: A 2437 ASP cc_start: 0.8301 (m-30) cc_final: 0.7968 (m-30) REVERT: A 2605 MET cc_start: 0.8662 (mtt) cc_final: 0.8387 (mtt) REVERT: A 2800 ARG cc_start: 0.8041 (OUTLIER) cc_final: 0.7685 (mtp180) REVERT: A 2860 ASP cc_start: 0.7843 (t70) cc_final: 0.7624 (t0) REVERT: A 3613 MET cc_start: 0.7750 (tmt) cc_final: 0.7524 (tmt) REVERT: A 3664 ASN cc_start: 0.7953 (OUTLIER) cc_final: 0.7587 (p0) REVERT: A 3796 MET cc_start: 0.8550 (OUTLIER) cc_final: 0.7796 (mtt) REVERT: B 71 TYR cc_start: 0.7696 (OUTLIER) cc_final: 0.6942 (t80) REVERT: C 427 MET cc_start: 0.6704 (OUTLIER) cc_final: 0.5347 (ppp) outliers start: 73 outliers final: 37 residues processed: 287 average time/residue: 1.5920 time to fit residues: 576.9507 Evaluate side-chains 266 residues out of total 4826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 218 time to evaluate : 5.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 LYS Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 342 MET Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 908 ASP Chi-restraints excluded: chain A residue 1225 GLU Chi-restraints excluded: chain A residue 1448 LEU Chi-restraints excluded: chain A residue 1590 THR Chi-restraints excluded: chain A residue 1593 VAL Chi-restraints excluded: chain A residue 1668 PHE Chi-restraints excluded: chain A residue 1671 VAL Chi-restraints excluded: chain A residue 1747 LEU Chi-restraints excluded: chain A residue 1794 GLN Chi-restraints excluded: chain A residue 1867 ILE Chi-restraints excluded: chain A residue 1933 LEU Chi-restraints excluded: chain A residue 1993 GLU Chi-restraints excluded: chain A residue 2100 LEU Chi-restraints excluded: chain A residue 2197 THR Chi-restraints excluded: chain A residue 2205 VAL Chi-restraints excluded: chain A residue 2289 ASP Chi-restraints excluded: chain A residue 2449 VAL Chi-restraints excluded: chain A residue 2800 ARG Chi-restraints excluded: chain A residue 2983 ASP Chi-restraints excluded: chain A residue 3480 LEU Chi-restraints excluded: chain A residue 3530 VAL Chi-restraints excluded: chain A residue 3553 GLU Chi-restraints excluded: chain A residue 3664 ASN Chi-restraints excluded: chain A residue 3796 MET Chi-restraints excluded: chain A residue 3977 THR Chi-restraints excluded: chain A residue 4028 ILE Chi-restraints excluded: chain A residue 4122 GLU Chi-restraints excluded: chain B residue 71 TYR Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 455 THR Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain C residue 20 MET Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 427 MET Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 344 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 543 random chunks: chunk 320 optimal weight: 0.8980 chunk 515 optimal weight: 3.9990 chunk 314 optimal weight: 4.9990 chunk 244 optimal weight: 0.5980 chunk 358 optimal weight: 2.9990 chunk 540 optimal weight: 8.9990 chunk 497 optimal weight: 0.0170 chunk 430 optimal weight: 0.6980 chunk 44 optimal weight: 0.5980 chunk 332 optimal weight: 0.0670 chunk 264 optimal weight: 0.9980 overall best weight: 0.3956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 377 ASN A 399 GLN A1890 HIS A2301 GLN A2305 ASN ** A3397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3664 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 320 GLN ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 496 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.2904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 45774 Z= 0.141 Angle : 0.538 18.241 62143 Z= 0.263 Chirality : 0.039 0.331 6962 Planarity : 0.003 0.052 7706 Dihedral : 11.616 85.886 6606 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.20 % Allowed : 13.82 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.12), residues: 5367 helix: 1.53 (0.10), residues: 3032 sheet: -0.31 (0.30), residues: 283 loop : -1.02 (0.14), residues: 2052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.001 TRP D 267 HIS 0.004 0.000 HIS A1418 PHE 0.020 0.001 PHE A2260 TYR 0.026 0.001 TYR A1873 ARG 0.007 0.000 ARG B 230 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10734 Ramachandran restraints generated. 5367 Oldfield, 0 Emsley, 5367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10734 Ramachandran restraints generated. 5367 Oldfield, 0 Emsley, 5367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 4826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 224 time to evaluate : 5.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.5041 (tpp) cc_final: 0.4515 (tmm) REVERT: A 286 LEU cc_start: 0.7478 (OUTLIER) cc_final: 0.7222 (pp) REVERT: A 342 MET cc_start: 0.8575 (OUTLIER) cc_final: 0.8230 (mmm) REVERT: A 1356 TRP cc_start: 0.7856 (p-90) cc_final: 0.7519 (p-90) REVERT: A 1592 MET cc_start: 0.8145 (tpt) cc_final: 0.7868 (tpt) REVERT: A 1668 PHE cc_start: 0.6704 (OUTLIER) cc_final: 0.5572 (t80) REVERT: A 1688 LEU cc_start: 0.8583 (pp) cc_final: 0.8316 (tp) REVERT: A 1794 GLN cc_start: 0.7103 (OUTLIER) cc_final: 0.6290 (mp-120) REVERT: A 1829 TRP cc_start: 0.8656 (m100) cc_final: 0.8346 (m100) REVERT: A 1927 MET cc_start: 0.7465 (mtp) cc_final: 0.7133 (mpm) REVERT: A 1933 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.7966 (mm) REVERT: A 1993 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7276 (tm-30) REVERT: A 2094 MET cc_start: 0.8371 (tpt) cc_final: 0.8143 (tpt) REVERT: A 2289 ASP cc_start: 0.8029 (OUTLIER) cc_final: 0.7789 (t0) REVERT: A 2437 ASP cc_start: 0.8276 (m-30) cc_final: 0.7952 (m-30) REVERT: A 2605 MET cc_start: 0.8633 (mtt) cc_final: 0.8371 (mtt) REVERT: A 2800 ARG cc_start: 0.7972 (OUTLIER) cc_final: 0.7635 (mtp180) REVERT: A 2860 ASP cc_start: 0.7680 (t70) cc_final: 0.7450 (t0) REVERT: A 3613 MET cc_start: 0.7612 (tmt) cc_final: 0.7256 (tmt) REVERT: A 3664 ASN cc_start: 0.7973 (OUTLIER) cc_final: 0.7603 (p0) REVERT: A 3796 MET cc_start: 0.8479 (OUTLIER) cc_final: 0.7383 (mtt) outliers start: 57 outliers final: 32 residues processed: 272 average time/residue: 1.6116 time to fit residues: 552.4856 Evaluate side-chains 260 residues out of total 4826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 218 time to evaluate : 5.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 LYS Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 342 MET Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 908 ASP Chi-restraints excluded: chain A residue 1225 GLU Chi-restraints excluded: chain A residue 1448 LEU Chi-restraints excluded: chain A residue 1590 THR Chi-restraints excluded: chain A residue 1668 PHE Chi-restraints excluded: chain A residue 1671 VAL Chi-restraints excluded: chain A residue 1794 GLN Chi-restraints excluded: chain A residue 1867 ILE Chi-restraints excluded: chain A residue 1933 LEU Chi-restraints excluded: chain A residue 1993 GLU Chi-restraints excluded: chain A residue 2100 LEU Chi-restraints excluded: chain A residue 2197 THR Chi-restraints excluded: chain A residue 2205 VAL Chi-restraints excluded: chain A residue 2289 ASP Chi-restraints excluded: chain A residue 2449 VAL Chi-restraints excluded: chain A residue 2800 ARG Chi-restraints excluded: chain A residue 2983 ASP Chi-restraints excluded: chain A residue 3530 VAL Chi-restraints excluded: chain A residue 3553 GLU Chi-restraints excluded: chain A residue 3664 ASN Chi-restraints excluded: chain A residue 3697 ASN Chi-restraints excluded: chain A residue 3796 MET Chi-restraints excluded: chain A residue 4028 ILE Chi-restraints excluded: chain A residue 4122 GLU Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 455 THR Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain C residue 20 MET Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 344 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 543 random chunks: chunk 342 optimal weight: 0.7980 chunk 458 optimal weight: 30.0000 chunk 131 optimal weight: 0.5980 chunk 397 optimal weight: 6.9990 chunk 63 optimal weight: 0.7980 chunk 119 optimal weight: 0.7980 chunk 431 optimal weight: 0.0010 chunk 180 optimal weight: 0.9990 chunk 443 optimal weight: 3.9990 chunk 54 optimal weight: 0.6980 chunk 79 optimal weight: 1.9990 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 377 ASN A1725 GLN A2301 GLN A2305 ASN ** A3397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3664 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4032 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 496 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 622 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.101043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.068358 restraints weight = 261362.556| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 4.71 r_work: 0.2943 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2948 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2948 r_free = 0.2948 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2948 r_free = 0.2948 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2948 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 45774 Z= 0.148 Angle : 0.539 17.108 62143 Z= 0.265 Chirality : 0.038 0.326 6962 Planarity : 0.003 0.052 7706 Dihedral : 11.534 85.399 6606 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.12 % Allowed : 14.04 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.12), residues: 5367 helix: 1.56 (0.10), residues: 3035 sheet: -0.21 (0.30), residues: 281 loop : -1.01 (0.14), residues: 2051 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.001 TRP D 267 HIS 0.004 0.000 HIS A1418 PHE 0.020 0.001 PHE A2260 TYR 0.022 0.001 TYR A1945 ARG 0.007 0.000 ARG B 230 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13981.16 seconds wall clock time: 253 minutes 59.89 seconds (15239.89 seconds total)