Starting phenix.real_space_refine on Wed Mar 4 18:23:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t4q_25685/03_2026/7t4q_25685.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t4q_25685/03_2026/7t4q_25685.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7t4q_25685/03_2026/7t4q_25685.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t4q_25685/03_2026/7t4q_25685.map" model { file = "/net/cci-nas-00/data/ceres_data/7t4q_25685/03_2026/7t4q_25685.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t4q_25685/03_2026/7t4q_25685.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.025 sd= 0.591 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 74 5.16 5 C 9825 2.51 5 N 2658 2.21 5 O 2916 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15473 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 5018 Number of conformers: 1 Conformer: "" Number of residues, atoms: 623, 5018 Classifications: {'peptide': 623} Link IDs: {'PCIS': 2, 'PTRANS': 29, 'TRANS': 591} Chain breaks: 6 Chain: "B" Number of atoms: 1843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1843 Classifications: {'peptide': 233} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 213} Chain: "C" Number of atoms: 999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 999 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "D" Number of atoms: 1335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1335 Classifications: {'peptide': 164} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 153} Chain: "E" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 917 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 3, 'TRANS': 107} Chain: "F" Number of atoms: 962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 962 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 7, 'TRANS': 116} Chain: "G" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 828 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 6, 'TRANS': 105} Chain: "H" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 813 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 98} Chain: "I" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 960 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "J" Number of atoms: 924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 924 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "K" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 790 Classifications: {'peptide': 105} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 97} Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N GLU C 136 " occ=0.97 ... (7 atoms not shown) pdb=" OE2 GLU C 136 " occ=0.97 residue: pdb=" N ASP C 138 " occ=0.99 ... (6 atoms not shown) pdb=" OD2 ASP C 138 " occ=0.99 Time building chain proxies: 3.67, per 1000 atoms: 0.24 Number of scatterers: 15473 At special positions: 0 Unit cell: (176.83, 124.259, 169.662, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 74 16.00 O 2916 8.00 N 2658 7.00 C 9825 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 59 " - pdb=" SG CYS B 54 " distance=2.03 Simple disulfide: pdb=" SG CYS A 95 " - pdb=" SG CYS B 47 " distance=2.03 Simple disulfide: pdb=" SG CYS A 195 " - pdb=" SG CYS A 211 " distance=2.03 Simple disulfide: pdb=" SG CYS A 330 " - pdb=" SG CYS A 383 " distance=2.03 Simple disulfide: pdb=" SG CYS A 571 " - pdb=" SG CYS A 624 " distance=2.03 Simple disulfide: pdb=" SG CYS B 144 " - pdb=" SG CYS C 162 " distance=2.03 Simple disulfide: pdb=" SG CYS B 154 " - pdb=" SG CYS B 159 " distance=2.03 Simple disulfide: pdb=" SG CYS C 43 " - pdb=" SG CYS C 58 " distance=2.03 Simple disulfide: pdb=" SG CYS C 96 " - pdb=" SG CYS C 111 " distance=2.03 Simple disulfide: pdb=" SG CYS D 57 " - pdb=" SG CYS D 83 " distance=2.03 Simple disulfide: pdb=" SG CYS D 172 " - pdb=" SG CYS D 207 " distance=2.01 Simple disulfide: pdb=" SG CYS E 20 " - pdb=" SG CYS E 40 " distance=2.03 Simple disulfide: pdb=" SG CYS F 45 " - pdb=" SG CYS F 120 " distance=2.03 Simple disulfide: pdb=" SG CYS G 45 " - pdb=" SG CYS G 113 " distance=2.03 Simple disulfide: pdb=" SG CYS H 46 " - pdb=" SG CYS H 112 " distance=2.04 Simple disulfide: pdb=" SG CYS I 45 " - pdb=" SG CYS I 119 " distance=2.04 Simple disulfide: pdb=" SG CYS J 45 " - pdb=" SG CYS J 119 " distance=2.03 Simple disulfide: pdb=" SG CYS K 46 " - pdb=" SG CYS K 111 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 803 " - " ASN A 192 " " NAG B 301 " - " ASN B 74 " " NAG D 301 " - " ASN D 201 " " NAG E 201 " - " ASN E 81 " Time building additional restraints: 1.52 Conformation dependent library (CDL) restraints added in 609.5 milliseconds 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3656 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 28 sheets defined 29.0% alpha, 27.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'A' and resid 94 through 98 Processing helix chain 'A' and resid 99 through 107 removed outlier: 3.511A pdb=" N GLU A 103 " --> pdb=" O GLY A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 123 Processing helix chain 'A' and resid 263 through 266 Processing helix chain 'A' and resid 283 through 287 removed outlier: 4.364A pdb=" N ASN A 287 " --> pdb=" O LYS A 283 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 283 through 287' Processing helix chain 'A' and resid 289 through 294 Processing helix chain 'A' and resid 298 through 303 Processing helix chain 'A' and resid 308 through 316 Processing helix chain 'A' and resid 316 through 328 Processing helix chain 'A' and resid 334 through 353 Processing helix chain 'A' and resid 354 through 359 Processing helix chain 'A' and resid 362 through 385 Processing helix chain 'A' and resid 396 through 409 Processing helix chain 'A' and resid 415 through 429 removed outlier: 3.547A pdb=" N LEU A 419 " --> pdb=" O ASP A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 435 Processing helix chain 'A' and resid 436 through 454 removed outlier: 3.816A pdb=" N LEU A 440 " --> pdb=" O PRO A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 475 removed outlier: 4.056A pdb=" N HIS A 475 " --> pdb=" O GLY A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 495 removed outlier: 3.668A pdb=" N CYS A 495 " --> pdb=" O GLU A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 506 Processing helix chain 'A' and resid 514 through 519 Processing helix chain 'A' and resid 520 through 524 Processing helix chain 'A' and resid 531 through 537 Processing helix chain 'A' and resid 547 through 559 Processing helix chain 'A' and resid 671 through 680 Processing helix chain 'A' and resid 681 through 684 Processing helix chain 'B' and resid 46 through 56 Processing helix chain 'B' and resid 66 through 70 Processing helix chain 'B' and resid 85 through 87 No H-bonds generated for 'chain 'B' and resid 85 through 87' Processing helix chain 'B' and resid 95 through 99 Processing helix chain 'B' and resid 102 through 113 Processing helix chain 'B' and resid 117 through 128 Processing helix chain 'B' and resid 130 through 145 removed outlier: 3.916A pdb=" N TRP B 134 " --> pdb=" O THR B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 217 No H-bonds generated for 'chain 'B' and resid 215 through 217' Processing helix chain 'B' and resid 218 through 236 removed outlier: 3.656A pdb=" N PHE B 222 " --> pdb=" O GLY B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 253 removed outlier: 4.080A pdb=" N ARG B 244 " --> pdb=" O PRO B 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 82 removed outlier: 4.345A pdb=" N GLY C 75 " --> pdb=" O ALA C 71 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N MET C 80 " --> pdb=" O ILE C 76 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N HIS C 82 " --> pdb=" O THR C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 93 Processing helix chain 'C' and resid 94 through 97 Processing helix chain 'C' and resid 117 through 119 No H-bonds generated for 'chain 'C' and resid 117 through 119' Processing helix chain 'C' and resid 145 through 156 Processing helix chain 'D' and resid 53 through 57 removed outlier: 4.007A pdb=" N TYR D 56 " --> pdb=" O ALA D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 69 No H-bonds generated for 'chain 'D' and resid 67 through 69' Processing helix chain 'D' and resid 80 through 84 Processing helix chain 'D' and resid 104 through 118 removed outlier: 4.189A pdb=" N ASN D 118 " --> pdb=" O LEU D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 130 removed outlier: 3.697A pdb=" N GLN D 123 " --> pdb=" O GLN D 119 " (cutoff:3.500A) Proline residue: D 126 - end of helix Processing helix chain 'D' and resid 140 through 151 Processing helix chain 'E' and resid 21 through 26 removed outlier: 3.842A pdb=" N GLU E 26 " --> pdb=" O ARG E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 35 through 41 Processing helix chain 'E' and resid 45 through 69 Processing helix chain 'E' and resid 76 through 80 Processing helix chain 'E' and resid 81 through 95 Processing helix chain 'F' and resid 98 through 100 No H-bonds generated for 'chain 'F' and resid 98 through 100' Processing helix chain 'F' and resid 111 through 115 Processing helix chain 'G' and resid 104 through 108 Processing helix chain 'H' and resid 53 through 55 No H-bonds generated for 'chain 'H' and resid 53 through 55' Processing helix chain 'H' and resid 103 through 107 removed outlier: 3.712A pdb=" N PHE H 107 " --> pdb=" O PRO H 104 " (cutoff:3.500A) Processing helix chain 'I' and resid 51 through 55 Processing helix chain 'I' and resid 110 through 114 Processing helix chain 'I' and resid 125 through 131 removed outlier: 3.582A pdb=" N TRP I 128 " --> pdb=" O TYR I 125 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE I 129 " --> pdb=" O LEU I 126 " (cutoff:3.500A) Processing helix chain 'J' and resid 51 through 55 removed outlier: 3.508A pdb=" N TYR J 55 " --> pdb=" O PHE J 52 " (cutoff:3.500A) Processing helix chain 'J' and resid 85 through 88 Processing helix chain 'J' and resid 110 through 114 Processing helix chain 'K' and resid 102 through 106 removed outlier: 3.744A pdb=" N VAL K 106 " --> pdb=" O PRO K 103 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 49 through 52 Processing sheet with id=AA2, first strand: chain 'A' and resid 89 through 92 removed outlier: 6.033A pdb=" N SER A 77 " --> pdb=" O PHE B 181 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N LEU B 183 " --> pdb=" O SER A 77 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N ASN A 79 " --> pdb=" O LEU B 183 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N VAL B 178 " --> pdb=" O ALA B 194 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ALA B 194 " --> pdb=" O VAL B 178 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N PHE B 189 " --> pdb=" O VAL B 210 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 125 through 126 removed outlier: 4.847A pdb=" N VAL A 281 " --> pdb=" O ALA A 126 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG A 270 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N VAL A 279 " --> pdb=" O ILE A 268 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N ILE A 268 " --> pdb=" O VAL A 279 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ARG A 136 " --> pdb=" O LEU A 269 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 125 through 126 removed outlier: 4.847A pdb=" N VAL A 281 " --> pdb=" O ALA A 126 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 194 through 197 Processing sheet with id=AA6, first strand: chain 'A' and resid 527 through 528 removed outlier: 3.831A pdb=" N PHE A 578 " --> pdb=" O ARG A 528 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 663 through 666 Processing sheet with id=AA8, first strand: chain 'B' and resid 82 through 83 removed outlier: 5.996A pdb=" N LEU B 82 " --> pdb=" O GLY B 170 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 150 through 155 removed outlier: 5.523A pdb=" N GLY B 161 " --> pdb=" O VAL D 100 " (cutoff:3.500A) removed outlier: 8.380A pdb=" N ARG D 102 " --> pdb=" O GLY B 161 " (cutoff:3.500A) removed outlier: 11.567A pdb=" N ASP B 163 " --> pdb=" O ARG D 102 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N LEU D 88 " --> pdb=" O ARG D 76 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N ARG D 76 " --> pdb=" O LEU D 88 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N LEU D 90 " --> pdb=" O PHE D 74 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N PHE D 74 " --> pdb=" O LEU D 90 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N TYR D 92 " --> pdb=" O SER D 72 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 45 through 50 removed outlier: 6.771A pdb=" N THR C 53 " --> pdb=" O CYS C 49 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 109 through 111 Processing sheet with id=AB3, first strand: chain 'C' and resid 130 through 132 removed outlier: 4.577A pdb=" N THR E 106 " --> pdb=" O ARG E 125 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 26 through 29 Processing sheet with id=AB5, first strand: chain 'F' and resid 33 through 35 removed outlier: 3.502A pdb=" N ALA F 74 " --> pdb=" O TRP F 61 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ARG F 63 " --> pdb=" O TRP F 72 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N TRP F 72 " --> pdb=" O ARG F 63 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 33 through 35 Processing sheet with id=AB7, first strand: chain 'G' and resid 32 through 35 removed outlier: 6.682A pdb=" N VAL G 33 " --> pdb=" O THR G 133 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N VAL G 58 " --> pdb=" O TYR G 74 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N TYR G 74 " --> pdb=" O VAL G 58 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N TRP G 60 " --> pdb=" O LEU G 72 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 32 through 35 removed outlier: 6.682A pdb=" N VAL G 33 " --> pdb=" O THR G 133 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 41 through 46 Processing sheet with id=AC1, first strand: chain 'H' and resid 27 through 30 Processing sheet with id=AC2, first strand: chain 'H' and resid 33 through 36 removed outlier: 6.342A pdb=" N LEU H 34 " --> pdb=" O GLU H 128 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N LEU H 57 " --> pdb=" O TYR H 73 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N TYR H 73 " --> pdb=" O LEU H 57 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N TRP H 59 " --> pdb=" O LEU H 71 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 26 through 30 Processing sheet with id=AC4, first strand: chain 'I' and resid 33 through 35 removed outlier: 6.739A pdb=" N MET I 57 " --> pdb=" O VAL I 73 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N VAL I 73 " --> pdb=" O MET I 57 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N TRP I 59 " --> pdb=" O VAL I 71 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 33 through 35 removed outlier: 3.726A pdb=" N TYR I 136 " --> pdb=" O LYS I 121 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'J' and resid 26 through 29 Processing sheet with id=AC7, first strand: chain 'J' and resid 33 through 35 removed outlier: 6.774A pdb=" N ILE J 57 " --> pdb=" O ILE J 73 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ILE J 73 " --> pdb=" O ILE J 57 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N TRP J 59 " --> pdb=" O MET J 71 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 33 through 35 removed outlier: 3.870A pdb=" N ASP J 135 " --> pdb=" O ARG J 121 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'K' and resid 27 through 30 removed outlier: 5.806A pdb=" N THR K 92 " --> pdb=" O ALA K 48 " (cutoff:3.500A) removed outlier: 10.223A pdb=" N GLN K 50 " --> pdb=" O SER K 90 " (cutoff:3.500A) removed outlier: 10.410A pdb=" N SER K 90 " --> pdb=" O GLN K 50 " (cutoff:3.500A) removed outlier: 11.599A pdb=" N ILE K 52 " --> pdb=" O SER K 88 " (cutoff:3.500A) removed outlier: 11.675A pdb=" N SER K 88 " --> pdb=" O ILE K 52 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'K' and resid 33 through 34 removed outlier: 6.535A pdb=" N TRP K 58 " --> pdb=" O LEU K 70 " (cutoff:3.500A) 676 hydrogen bonds defined for protein. 1728 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.86 Time building geometry restraints manager: 1.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5005 1.34 - 1.46: 3898 1.46 - 1.59: 6826 1.59 - 1.71: 0 1.71 - 1.83: 104 Bond restraints: 15833 Sorted by residual: bond pdb=" N ASN A 55 " pdb=" CA ASN A 55 " ideal model delta sigma weight residual 1.456 1.484 -0.028 1.31e-02 5.83e+03 4.45e+00 bond pdb=" N GLU A 54 " pdb=" CA GLU A 54 " ideal model delta sigma weight residual 1.457 1.483 -0.026 1.31e-02 5.83e+03 4.09e+00 bond pdb=" C1 NAG B 301 " pdb=" O5 NAG B 301 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 4.07e+00 bond pdb=" C1 NAG A 801 " pdb=" O5 NAG A 801 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.33e+00 bond pdb=" C1 NAG A 803 " pdb=" O5 NAG A 803 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.75e+00 ... (remaining 15828 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.49: 20821 1.49 - 2.99: 559 2.99 - 4.48: 124 4.48 - 5.97: 13 5.97 - 7.47: 7 Bond angle restraints: 21524 Sorted by residual: angle pdb=" CA ARG C 42 " pdb=" CB ARG C 42 " pdb=" CG ARG C 42 " ideal model delta sigma weight residual 114.10 121.57 -7.47 2.00e+00 2.50e-01 1.39e+01 angle pdb=" C GLU A 73 " pdb=" CA GLU A 73 " pdb=" CB GLU A 73 " ideal model delta sigma weight residual 109.62 115.88 -6.26 1.79e+00 3.12e-01 1.22e+01 angle pdb=" CA MET A 667 " pdb=" CB MET A 667 " pdb=" CG MET A 667 " ideal model delta sigma weight residual 114.10 120.88 -6.78 2.00e+00 2.50e-01 1.15e+01 angle pdb=" N ASN A 55 " pdb=" CA ASN A 55 " pdb=" C ASN A 55 " ideal model delta sigma weight residual 113.18 109.21 3.97 1.21e+00 6.83e-01 1.07e+01 angle pdb=" N PRO A 389 " pdb=" CD PRO A 389 " pdb=" CG PRO A 389 " ideal model delta sigma weight residual 103.20 98.61 4.59 1.50e+00 4.44e-01 9.35e+00 ... (remaining 21519 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 8883 17.93 - 35.85: 529 35.85 - 53.78: 100 53.78 - 71.71: 29 71.71 - 89.63: 21 Dihedral angle restraints: 9562 sinusoidal: 3880 harmonic: 5682 Sorted by residual: dihedral pdb=" CB CYS A 330 " pdb=" SG CYS A 330 " pdb=" SG CYS A 383 " pdb=" CB CYS A 383 " ideal model delta sinusoidal sigma weight residual -86.00 -175.63 89.63 1 1.00e+01 1.00e-02 9.54e+01 dihedral pdb=" CB CYS B 144 " pdb=" SG CYS B 144 " pdb=" SG CYS C 162 " pdb=" CB CYS C 162 " ideal model delta sinusoidal sigma weight residual 93.00 176.37 -83.37 1 1.00e+01 1.00e-02 8.49e+01 dihedral pdb=" CB CYS A 59 " pdb=" SG CYS A 59 " pdb=" SG CYS B 54 " pdb=" CB CYS B 54 " ideal model delta sinusoidal sigma weight residual -86.00 -140.12 54.12 1 1.00e+01 1.00e-02 3.97e+01 ... (remaining 9559 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 2085 0.058 - 0.116: 305 0.116 - 0.173: 48 0.173 - 0.231: 1 0.231 - 0.289: 1 Chirality restraints: 2440 Sorted by residual: chirality pdb=" C1 NAG B 301 " pdb=" ND2 ASN B 74 " pdb=" C2 NAG B 301 " pdb=" O5 NAG B 301 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.09e+00 chirality pdb=" CA GLU A 54 " pdb=" N GLU A 54 " pdb=" C GLU A 54 " pdb=" CB GLU A 54 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.19 2.00e-01 2.50e+01 9.47e-01 chirality pdb=" CA ILE K 71 " pdb=" N ILE K 71 " pdb=" C ILE K 71 " pdb=" CB ILE K 71 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.55e-01 ... (remaining 2437 not shown) Planarity restraints: 2752 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 544 " -0.050 5.00e-02 4.00e+02 7.52e-02 9.04e+00 pdb=" N PRO A 545 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO A 545 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 545 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 468 " -0.011 2.00e-02 2.50e+03 2.21e-02 4.89e+00 pdb=" C TYR A 468 " 0.038 2.00e-02 2.50e+03 pdb=" O TYR A 468 " -0.014 2.00e-02 2.50e+03 pdb=" N LEU A 469 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 270 " 0.171 9.50e-02 1.11e+02 7.69e-02 3.77e+00 pdb=" NE ARG A 270 " -0.012 2.00e-02 2.50e+03 pdb=" CZ ARG A 270 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG A 270 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 270 " 0.004 2.00e-02 2.50e+03 ... (remaining 2749 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 833 2.73 - 3.27: 16078 3.27 - 3.81: 25164 3.81 - 4.36: 32105 4.36 - 4.90: 54511 Nonbonded interactions: 128691 Sorted by model distance: nonbonded pdb=" NH1 ARG A 72 " pdb=" O GLU A 73 " model vdw 2.184 3.120 nonbonded pdb=" ND2 ASN C 97 " pdb=" O ARG E 32 " model vdw 2.243 3.120 nonbonded pdb=" ND1 HIS A 275 " pdb=" OH TYR A 306 " model vdw 2.244 3.120 nonbonded pdb=" NH2 ARG A 365 " pdb=" OD2 ASP A 368 " model vdw 2.259 3.120 nonbonded pdb=" N LEU I 123 " pdb=" OD2 ASP I 132 " model vdw 2.262 3.120 ... (remaining 128686 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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=0.97 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: 3.340 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: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 15.560 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 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:8.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 15855 Z= 0.144 Angle : 0.624 7.468 21572 Z= 0.331 Chirality : 0.044 0.289 2440 Planarity : 0.007 0.077 2748 Dihedral : 12.892 88.592 5852 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 0.00 % Allowed : 0.06 % Favored : 99.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.18), residues: 1912 helix: -0.89 (0.23), residues: 415 sheet: 0.13 (0.22), residues: 515 loop : -0.37 (0.19), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.002 ARG A 484 TYR 0.018 0.002 TYR C 44 PHE 0.029 0.002 PHE D 206 TRP 0.020 0.003 TRP B 134 HIS 0.007 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00330 (15833) covalent geometry : angle 0.61785 (21524) SS BOND : bond 0.00474 ( 18) SS BOND : angle 1.79628 ( 36) hydrogen bonds : bond 0.16744 ( 652) hydrogen bonds : angle 7.59237 ( 1728) link_NAG-ASN : bond 0.00271 ( 4) link_NAG-ASN : angle 2.43637 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 372 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 157 LYS cc_start: 0.8890 (mptt) cc_final: 0.8647 (mmtm) REVERT: F 51 SER cc_start: 0.8841 (t) cc_final: 0.8548 (t) REVERT: F 97 ASP cc_start: 0.8403 (t0) cc_final: 0.8093 (t0) REVERT: F 114 ASP cc_start: 0.8429 (m-30) cc_final: 0.8134 (m-30) REVERT: H 41 ARG cc_start: 0.8275 (ttt90) cc_final: 0.8072 (ttm170) REVERT: K 27 MET cc_start: 0.8630 (mmm) cc_final: 0.8151 (mmp) REVERT: K 47 ARG cc_start: 0.7487 (mtt-85) cc_final: 0.7178 (mtp85) outliers start: 0 outliers final: 0 residues processed: 372 average time/residue: 0.6430 time to fit residues: 261.6363 Evaluate side-chains 276 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 276 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 98 optimal weight: 0.1980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.0010 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 3.9990 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 HIS A 271 GLN A 370 GLN ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 75 GLN D 123 GLN F 109 ASN G 62 GLN J 29 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.120668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.097256 restraints weight = 29361.895| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 2.28 r_work: 0.3122 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3011 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3011 r_free = 0.3011 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.97 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3010 r_free = 0.3010 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3010 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 15855 Z= 0.139 Angle : 0.664 9.661 21572 Z= 0.344 Chirality : 0.046 0.181 2440 Planarity : 0.005 0.053 2748 Dihedral : 5.733 53.011 2272 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.17 % Allowed : 10.96 % Favored : 86.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.19), residues: 1912 helix: 0.53 (0.24), residues: 423 sheet: 0.21 (0.22), residues: 503 loop : 0.25 (0.20), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 72 TYR 0.018 0.002 TYR C 149 PHE 0.015 0.002 PHE A 349 TRP 0.011 0.001 TRP B 134 HIS 0.008 0.001 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00316 (15833) covalent geometry : angle 0.65882 (21524) SS BOND : bond 0.00418 ( 18) SS BOND : angle 1.87250 ( 36) hydrogen bonds : bond 0.04031 ( 652) hydrogen bonds : angle 5.62960 ( 1728) link_NAG-ASN : bond 0.00183 ( 4) link_NAG-ASN : angle 1.69969 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 314 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 103 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.7834 (mp0) REVERT: A 529 ASP cc_start: 0.8103 (p0) cc_final: 0.7819 (p0) REVERT: C 157 LYS cc_start: 0.9152 (mptt) cc_final: 0.8738 (mmtm) REVERT: C 158 ARG cc_start: 0.7824 (OUTLIER) cc_final: 0.7336 (tpt-90) REVERT: D 75 GLN cc_start: 0.5557 (mp-120) cc_final: 0.5302 (mp10) REVERT: D 90 LEU cc_start: 0.8592 (mp) cc_final: 0.8310 (mt) REVERT: D 94 ARG cc_start: 0.8313 (OUTLIER) cc_final: 0.7146 (ptp90) REVERT: D 101 GLU cc_start: 0.8378 (mm-30) cc_final: 0.7737 (mp0) REVERT: E 121 GLU cc_start: 0.8881 (mt-10) cc_final: 0.8644 (mt-10) REVERT: F 39 GLN cc_start: 0.8215 (mp10) cc_final: 0.8011 (mp10) REVERT: F 51 SER cc_start: 0.8889 (t) cc_final: 0.8589 (t) REVERT: G 31 ARG cc_start: 0.7864 (OUTLIER) cc_final: 0.7600 (tpm-80) REVERT: H 41 ARG cc_start: 0.8514 (ttt90) cc_final: 0.8241 (ttm110) REVERT: K 27 MET cc_start: 0.8992 (mmm) cc_final: 0.8595 (mmt) REVERT: K 47 ARG cc_start: 0.8090 (mtt-85) cc_final: 0.7545 (mtp85) outliers start: 37 outliers final: 8 residues processed: 325 average time/residue: 0.5980 time to fit residues: 214.3845 Evaluate side-chains 285 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 273 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain B residue 148 SER Chi-restraints excluded: chain C residue 136 GLU Chi-restraints excluded: chain C residue 158 ARG Chi-restraints excluded: chain D residue 94 ARG Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain E residue 75 ASP Chi-restraints excluded: chain E residue 123 SER Chi-restraints excluded: chain G residue 31 ARG Chi-restraints excluded: chain G residue 92 SER Chi-restraints excluded: chain K residue 65 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 150 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 146 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 148 optimal weight: 7.9990 chunk 162 optimal weight: 2.9990 chunk 177 optimal weight: 1.9990 chunk 2 optimal weight: 0.0040 chunk 40 optimal weight: 1.9990 chunk 141 optimal weight: 0.1980 chunk 101 optimal weight: 3.9990 overall best weight: 1.4398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 HIS ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 123 GLN E 62 ASN F 109 ASN I 100 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.116865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.093222 restraints weight = 29826.427| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 2.28 r_work: 0.3055 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2938 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2938 r_free = 0.2938 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2938 r_free = 0.2938 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2938 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 15855 Z= 0.208 Angle : 0.663 9.733 21572 Z= 0.340 Chirality : 0.046 0.211 2440 Planarity : 0.005 0.057 2748 Dihedral : 5.587 50.829 2272 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 3.28 % Allowed : 13.54 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.19), residues: 1912 helix: 0.72 (0.25), residues: 429 sheet: 0.11 (0.22), residues: 520 loop : 0.32 (0.20), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 117 TYR 0.017 0.002 TYR K 72 PHE 0.021 0.002 PHE D 74 TRP 0.013 0.002 TRP J 70 HIS 0.007 0.002 HIS C 156 Details of bonding type rmsd covalent geometry : bond 0.00494 (15833) covalent geometry : angle 0.65601 (21524) SS BOND : bond 0.00580 ( 18) SS BOND : angle 1.78761 ( 36) hydrogen bonds : bond 0.04151 ( 652) hydrogen bonds : angle 5.43272 ( 1728) link_NAG-ASN : bond 0.00287 ( 4) link_NAG-ASN : angle 2.87369 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 289 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 380 MET cc_start: 0.9162 (mmm) cc_final: 0.8780 (mmm) REVERT: C 42 ARG cc_start: 0.7652 (mmp-170) cc_final: 0.7310 (mtp-110) REVERT: C 151 GLU cc_start: 0.8457 (tm-30) cc_final: 0.8198 (pp20) REVERT: C 157 LYS cc_start: 0.9146 (mptt) cc_final: 0.8755 (mmtm) REVERT: C 158 ARG cc_start: 0.7895 (OUTLIER) cc_final: 0.7354 (tpt-90) REVERT: D 94 ARG cc_start: 0.8338 (OUTLIER) cc_final: 0.7275 (ptp90) REVERT: D 142 GLU cc_start: 0.8669 (OUTLIER) cc_final: 0.8398 (pm20) REVERT: E 62 ASN cc_start: 0.8916 (m-40) cc_final: 0.8711 (m-40) REVERT: E 75 ASP cc_start: 0.8374 (p0) cc_final: 0.7920 (p0) REVERT: E 84 GLU cc_start: 0.9041 (mt-10) cc_final: 0.8787 (mt-10) REVERT: F 28 ARG cc_start: 0.8247 (ttp-170) cc_final: 0.8002 (ttp80) REVERT: F 39 GLN cc_start: 0.8234 (mp10) cc_final: 0.7954 (mp10) REVERT: F 51 SER cc_start: 0.8988 (t) cc_final: 0.8688 (t) REVERT: G 31 ARG cc_start: 0.7929 (OUTLIER) cc_final: 0.7605 (tpm-80) REVERT: H 41 ARG cc_start: 0.8570 (ttt90) cc_final: 0.8331 (ttm170) REVERT: K 27 MET cc_start: 0.9087 (mmm) cc_final: 0.8493 (mmt) REVERT: K 47 ARG cc_start: 0.8078 (mtt-85) cc_final: 0.7668 (mtp85) REVERT: K 109 TYR cc_start: 0.8525 (m-80) cc_final: 0.8241 (m-80) outliers start: 56 outliers final: 25 residues processed: 317 average time/residue: 0.6216 time to fit residues: 216.3618 Evaluate side-chains 297 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 268 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain B residue 148 SER Chi-restraints excluded: chain C residue 69 LYS Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain C residue 136 GLU Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 158 ARG Chi-restraints excluded: chain D residue 94 ARG Chi-restraints excluded: chain D residue 118 ASN Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 142 GLU Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 123 SER Chi-restraints excluded: chain F residue 121 VAL Chi-restraints excluded: chain G residue 31 ARG Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 70 LYS Chi-restraints excluded: chain G residue 92 SER Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 72 ILE Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 65 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 25 optimal weight: 2.9990 chunk 115 optimal weight: 6.9990 chunk 177 optimal weight: 4.9990 chunk 154 optimal weight: 0.7980 chunk 62 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 79 optimal weight: 0.0270 chunk 140 optimal weight: 0.0770 chunk 26 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 overall best weight: 0.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 HIS ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 GLN D 123 GLN I 100 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.118175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.094770 restraints weight = 29874.838| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 2.28 r_work: 0.3083 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2968 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2968 r_free = 0.2968 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2968 r_free = 0.2968 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2968 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 15855 Z= 0.139 Angle : 0.604 9.060 21572 Z= 0.308 Chirality : 0.043 0.188 2440 Planarity : 0.004 0.058 2748 Dihedral : 5.294 51.830 2272 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.63 % Allowed : 14.71 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.19), residues: 1912 helix: 0.97 (0.25), residues: 430 sheet: 0.27 (0.22), residues: 524 loop : 0.32 (0.20), residues: 958 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 139 TYR 0.028 0.001 TYR K 72 PHE 0.013 0.001 PHE A 349 TRP 0.012 0.001 TRP J 70 HIS 0.009 0.001 HIS C 156 Details of bonding type rmsd covalent geometry : bond 0.00325 (15833) covalent geometry : angle 0.59849 (21524) SS BOND : bond 0.00450 ( 18) SS BOND : angle 1.46743 ( 36) hydrogen bonds : bond 0.03584 ( 652) hydrogen bonds : angle 5.15309 ( 1728) link_NAG-ASN : bond 0.00506 ( 4) link_NAG-ASN : angle 2.77266 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 292 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 380 MET cc_start: 0.9173 (mmm) cc_final: 0.8781 (mmm) REVERT: B 118 GLN cc_start: 0.8834 (OUTLIER) cc_final: 0.8437 (tt0) REVERT: B 148 SER cc_start: 0.8542 (OUTLIER) cc_final: 0.8266 (p) REVERT: C 42 ARG cc_start: 0.7601 (mmp-170) cc_final: 0.7240 (mtp180) REVERT: C 62 GLU cc_start: 0.7656 (tt0) cc_final: 0.7319 (tm-30) REVERT: C 157 LYS cc_start: 0.9076 (mptt) cc_final: 0.8665 (mmtm) REVERT: C 158 ARG cc_start: 0.7908 (OUTLIER) cc_final: 0.7396 (tpt-90) REVERT: D 94 ARG cc_start: 0.8379 (OUTLIER) cc_final: 0.7456 (ptp90) REVERT: D 142 GLU cc_start: 0.8647 (OUTLIER) cc_final: 0.8371 (pm20) REVERT: E 38 ASP cc_start: 0.8339 (m-30) cc_final: 0.7908 (m-30) REVERT: E 62 ASN cc_start: 0.8917 (m-40) cc_final: 0.8697 (m-40) REVERT: E 75 ASP cc_start: 0.8363 (OUTLIER) cc_final: 0.7918 (p0) REVERT: F 28 ARG cc_start: 0.8210 (ttp-170) cc_final: 0.7947 (tmm-80) REVERT: F 51 SER cc_start: 0.8945 (t) cc_final: 0.8646 (t) REVERT: F 100 LYS cc_start: 0.8828 (OUTLIER) cc_final: 0.8489 (mtmt) REVERT: F 102 GLN cc_start: 0.8077 (tt0) cc_final: 0.7733 (mt0) REVERT: G 31 ARG cc_start: 0.7936 (OUTLIER) cc_final: 0.7616 (tpm-80) REVERT: G 51 ASP cc_start: 0.8664 (OUTLIER) cc_final: 0.8318 (p0) REVERT: H 41 ARG cc_start: 0.8508 (ttt90) cc_final: 0.8272 (ttm170) REVERT: J 35 LYS cc_start: 0.8346 (OUTLIER) cc_final: 0.8116 (mtpp) REVERT: K 27 MET cc_start: 0.9026 (mmm) cc_final: 0.8534 (mmt) REVERT: K 47 ARG cc_start: 0.8123 (mtt-85) cc_final: 0.7701 (mtp85) REVERT: K 109 TYR cc_start: 0.8480 (m-80) cc_final: 0.8212 (m-80) outliers start: 62 outliers final: 25 residues processed: 320 average time/residue: 0.6026 time to fit residues: 211.6729 Evaluate side-chains 305 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 270 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain B residue 118 GLN Chi-restraints excluded: chain B residue 148 SER Chi-restraints excluded: chain C residue 69 LYS Chi-restraints excluded: chain C residue 92 LYS Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain C residue 136 GLU Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 158 ARG Chi-restraints excluded: chain D residue 94 ARG Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 142 GLU Chi-restraints excluded: chain D residue 154 LYS Chi-restraints excluded: chain D residue 177 GLU Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 75 ASP Chi-restraints excluded: chain E residue 123 SER Chi-restraints excluded: chain F residue 100 LYS Chi-restraints excluded: chain F residue 121 VAL Chi-restraints excluded: chain G residue 31 ARG Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 51 ASP Chi-restraints excluded: chain G residue 70 LYS Chi-restraints excluded: chain H residue 76 SER Chi-restraints excluded: chain J residue 35 LYS Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 65 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 76 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 140 optimal weight: 3.9990 chunk 159 optimal weight: 1.9990 chunk 160 optimal weight: 0.8980 chunk 173 optimal weight: 0.4980 chunk 0 optimal weight: 10.0000 chunk 52 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 chunk 105 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 ASN A 165 HIS A 451 HIS ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 100 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.118192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.094868 restraints weight = 29959.964| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 2.28 r_work: 0.3083 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2970 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2970 r_free = 0.2970 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2970 r_free = 0.2970 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2970 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 15855 Z= 0.138 Angle : 0.599 8.703 21572 Z= 0.304 Chirality : 0.043 0.169 2440 Planarity : 0.004 0.057 2748 Dihedral : 5.125 52.139 2272 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.52 % Allowed : 16.18 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.19), residues: 1912 helix: 1.02 (0.25), residues: 436 sheet: 0.31 (0.22), residues: 532 loop : 0.25 (0.20), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 139 TYR 0.025 0.001 TYR K 72 PHE 0.025 0.002 PHE D 74 TRP 0.011 0.001 TRP J 70 HIS 0.008 0.001 HIS C 156 Details of bonding type rmsd covalent geometry : bond 0.00325 (15833) covalent geometry : angle 0.59475 (21524) SS BOND : bond 0.00402 ( 18) SS BOND : angle 1.39318 ( 36) hydrogen bonds : bond 0.03461 ( 652) hydrogen bonds : angle 5.05163 ( 1728) link_NAG-ASN : bond 0.00357 ( 4) link_NAG-ASN : angle 2.27364 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 284 time to evaluate : 0.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 380 MET cc_start: 0.9178 (mmm) cc_final: 0.8790 (mmm) REVERT: C 42 ARG cc_start: 0.7594 (mmp-170) cc_final: 0.7250 (mtp180) REVERT: C 62 GLU cc_start: 0.7666 (tt0) cc_final: 0.7374 (tm-30) REVERT: C 151 GLU cc_start: 0.8466 (tm-30) cc_final: 0.8194 (pp20) REVERT: C 157 LYS cc_start: 0.8999 (mptt) cc_final: 0.8596 (mmtm) REVERT: C 158 ARG cc_start: 0.8011 (OUTLIER) cc_final: 0.7493 (tpt-90) REVERT: D 94 ARG cc_start: 0.8452 (OUTLIER) cc_final: 0.7485 (ptp90) REVERT: D 142 GLU cc_start: 0.8679 (OUTLIER) cc_final: 0.8393 (pm20) REVERT: E 62 ASN cc_start: 0.8924 (m-40) cc_final: 0.8699 (m-40) REVERT: E 75 ASP cc_start: 0.8320 (OUTLIER) cc_final: 0.7871 (p0) REVERT: F 51 SER cc_start: 0.8901 (t) cc_final: 0.8611 (t) REVERT: F 100 LYS cc_start: 0.8792 (OUTLIER) cc_final: 0.8455 (mtmt) REVERT: F 102 GLN cc_start: 0.8175 (tt0) cc_final: 0.7800 (mt0) REVERT: H 41 ARG cc_start: 0.8550 (ttt90) cc_final: 0.8290 (ttm170) REVERT: I 126 LEU cc_start: 0.8798 (mm) cc_final: 0.8580 (mp) REVERT: J 35 LYS cc_start: 0.8375 (OUTLIER) cc_final: 0.8128 (mtpp) REVERT: K 27 MET cc_start: 0.9045 (mmm) cc_final: 0.8623 (mmt) REVERT: K 47 ARG cc_start: 0.8093 (mtt-85) cc_final: 0.7671 (mtp85) outliers start: 60 outliers final: 32 residues processed: 317 average time/residue: 0.5985 time to fit residues: 209.1131 Evaluate side-chains 311 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 273 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 50 ARG Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain C residue 92 LYS Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain C residue 136 GLU Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 158 ARG Chi-restraints excluded: chain D residue 94 ARG Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 142 GLU Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 177 GLU Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 75 ASP Chi-restraints excluded: chain E residue 123 SER Chi-restraints excluded: chain F residue 100 LYS Chi-restraints excluded: chain F residue 121 VAL Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 70 LYS Chi-restraints excluded: chain G residue 92 SER Chi-restraints excluded: chain H residue 76 SER Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 35 LYS Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 56 LEU Chi-restraints excluded: chain K residue 65 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 56 optimal weight: 0.4980 chunk 100 optimal weight: 9.9990 chunk 133 optimal weight: 0.9980 chunk 61 optimal weight: 5.9990 chunk 122 optimal weight: 0.6980 chunk 187 optimal weight: 7.9990 chunk 168 optimal weight: 2.9990 chunk 180 optimal weight: 2.9990 chunk 108 optimal weight: 0.7980 chunk 190 optimal weight: 0.0030 chunk 54 optimal weight: 3.9990 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 HIS A 451 HIS B 118 GLN G 120 ASN I 100 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.119087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.095649 restraints weight = 29552.931| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 2.25 r_work: 0.3104 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2988 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2988 r_free = 0.2988 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2988 r_free = 0.2988 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.56 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2988 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 15855 Z= 0.122 Angle : 0.601 12.477 21572 Z= 0.304 Chirality : 0.043 0.283 2440 Planarity : 0.004 0.056 2748 Dihedral : 4.972 52.277 2272 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.75 % Allowed : 16.65 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.19), residues: 1912 helix: 1.08 (0.25), residues: 436 sheet: 0.37 (0.22), residues: 535 loop : 0.22 (0.20), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 28 TYR 0.022 0.001 TYR K 72 PHE 0.012 0.001 PHE A 349 TRP 0.010 0.001 TRP J 70 HIS 0.006 0.001 HIS C 156 Details of bonding type rmsd covalent geometry : bond 0.00284 (15833) covalent geometry : angle 0.59378 (21524) SS BOND : bond 0.00659 ( 18) SS BOND : angle 2.15420 ( 36) hydrogen bonds : bond 0.03351 ( 652) hydrogen bonds : angle 4.95518 ( 1728) link_NAG-ASN : bond 0.00241 ( 4) link_NAG-ASN : angle 2.00000 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 291 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 564 GLU cc_start: 0.8642 (OUTLIER) cc_final: 0.8169 (tm-30) REVERT: B 46 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7684 (pm20) REVERT: C 62 GLU cc_start: 0.7607 (tt0) cc_final: 0.7332 (tm-30) REVERT: C 151 GLU cc_start: 0.8408 (tm-30) cc_final: 0.8151 (pp20) REVERT: C 157 LYS cc_start: 0.8929 (mptt) cc_final: 0.8566 (mmtm) REVERT: C 158 ARG cc_start: 0.8040 (OUTLIER) cc_final: 0.7527 (tpt-90) REVERT: D 56 TYR cc_start: 0.8861 (m-10) cc_final: 0.8610 (m-80) REVERT: D 94 ARG cc_start: 0.8457 (OUTLIER) cc_final: 0.7616 (ptp90) REVERT: D 95 GLU cc_start: 0.7749 (mt-10) cc_final: 0.7545 (mp0) REVERT: D 101 GLU cc_start: 0.8436 (mm-30) cc_final: 0.7977 (mm-30) REVERT: D 142 GLU cc_start: 0.8651 (OUTLIER) cc_final: 0.8348 (pm20) REVERT: D 174 MET cc_start: 0.9094 (ttm) cc_final: 0.8820 (ttp) REVERT: E 62 ASN cc_start: 0.8913 (m-40) cc_final: 0.8703 (m-40) REVERT: E 75 ASP cc_start: 0.8189 (OUTLIER) cc_final: 0.7759 (p0) REVERT: E 121 GLU cc_start: 0.8827 (mt-10) cc_final: 0.8547 (mt-10) REVERT: F 51 SER cc_start: 0.8943 (t) cc_final: 0.8653 (t) REVERT: F 100 LYS cc_start: 0.8787 (OUTLIER) cc_final: 0.8409 (mtmt) REVERT: F 102 GLN cc_start: 0.8153 (tt0) cc_final: 0.7808 (mt0) REVERT: H 41 ARG cc_start: 0.8493 (ttt90) cc_final: 0.8237 (ttm170) REVERT: I 126 LEU cc_start: 0.8782 (mm) cc_final: 0.8575 (mp) REVERT: K 27 MET cc_start: 0.9030 (mmm) cc_final: 0.8576 (mmt) REVERT: K 47 ARG cc_start: 0.8144 (mtt-85) cc_final: 0.7744 (mtp85) outliers start: 64 outliers final: 31 residues processed: 324 average time/residue: 0.6247 time to fit residues: 222.4400 Evaluate side-chains 307 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 269 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 564 GLU Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 136 GLU Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 158 ARG Chi-restraints excluded: chain D residue 94 ARG Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 142 GLU Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 154 LYS Chi-restraints excluded: chain D residue 177 GLU Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 75 ASP Chi-restraints excluded: chain E residue 123 SER Chi-restraints excluded: chain F residue 100 LYS Chi-restraints excluded: chain F residue 121 VAL Chi-restraints excluded: chain G residue 36 SER Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 70 LYS Chi-restraints excluded: chain G residue 92 SER Chi-restraints excluded: chain H residue 76 SER Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 56 LEU Chi-restraints excluded: chain K residue 65 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 131 optimal weight: 0.9990 chunk 88 optimal weight: 0.9980 chunk 78 optimal weight: 6.9990 chunk 169 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 130 optimal weight: 0.3980 chunk 183 optimal weight: 3.9990 chunk 158 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 12 optimal weight: 0.0070 overall best weight: 0.8802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 GLN A 165 HIS A 451 HIS B 118 GLN B 177 HIS E 73 ASN I 100 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.118303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.095011 restraints weight = 29725.624| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 2.23 r_work: 0.3092 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2973 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2973 r_free = 0.2973 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.56 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2973 r_free = 0.2973 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.56 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2973 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 15855 Z= 0.148 Angle : 0.624 11.616 21572 Z= 0.314 Chirality : 0.044 0.269 2440 Planarity : 0.004 0.055 2748 Dihedral : 4.944 51.639 2272 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.69 % Allowed : 17.53 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.19), residues: 1912 helix: 1.08 (0.25), residues: 436 sheet: 0.44 (0.23), residues: 528 loop : 0.16 (0.20), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 50 TYR 0.022 0.001 TYR K 72 PHE 0.026 0.002 PHE D 74 TRP 0.010 0.001 TRP J 70 HIS 0.007 0.001 HIS C 156 Details of bonding type rmsd covalent geometry : bond 0.00350 (15833) covalent geometry : angle 0.61716 (21524) SS BOND : bond 0.00591 ( 18) SS BOND : angle 2.17526 ( 36) hydrogen bonds : bond 0.03425 ( 652) hydrogen bonds : angle 4.95289 ( 1728) link_NAG-ASN : bond 0.00263 ( 4) link_NAG-ASN : angle 1.90591 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 277 time to evaluate : 0.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 GLN cc_start: 0.7872 (mm110) cc_final: 0.7477 (mp10) REVERT: A 564 GLU cc_start: 0.8659 (OUTLIER) cc_final: 0.8139 (tm-30) REVERT: B 46 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7700 (pm20) REVERT: C 42 ARG cc_start: 0.7659 (mmp-170) cc_final: 0.7336 (mtm-85) REVERT: C 62 GLU cc_start: 0.7579 (tt0) cc_final: 0.7308 (tm-30) REVERT: C 151 GLU cc_start: 0.8467 (tm-30) cc_final: 0.8184 (pp20) REVERT: C 157 LYS cc_start: 0.8903 (mptt) cc_final: 0.8560 (mmtm) REVERT: C 158 ARG cc_start: 0.8118 (OUTLIER) cc_final: 0.7602 (tpt-90) REVERT: D 56 TYR cc_start: 0.8898 (m-10) cc_final: 0.8638 (m-80) REVERT: D 94 ARG cc_start: 0.8488 (OUTLIER) cc_final: 0.7545 (ptp90) REVERT: D 142 GLU cc_start: 0.8649 (OUTLIER) cc_final: 0.8322 (pm20) REVERT: D 174 MET cc_start: 0.9079 (ttm) cc_final: 0.8844 (ttp) REVERT: E 62 ASN cc_start: 0.8895 (m-40) cc_final: 0.8681 (m-40) REVERT: E 75 ASP cc_start: 0.8231 (OUTLIER) cc_final: 0.7800 (p0) REVERT: F 39 GLN cc_start: 0.7939 (mp10) cc_final: 0.7649 (mp10) REVERT: F 51 SER cc_start: 0.8940 (t) cc_final: 0.8651 (t) REVERT: F 52 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8884 (mt) REVERT: F 100 LYS cc_start: 0.8727 (OUTLIER) cc_final: 0.8408 (mtmt) REVERT: F 102 GLN cc_start: 0.8132 (tt0) cc_final: 0.7755 (mt0) REVERT: H 41 ARG cc_start: 0.8574 (ttt90) cc_final: 0.8315 (ttm170) REVERT: I 126 LEU cc_start: 0.8776 (mm) cc_final: 0.8557 (mp) REVERT: K 27 MET cc_start: 0.9094 (mmm) cc_final: 0.8580 (mmt) outliers start: 63 outliers final: 39 residues processed: 312 average time/residue: 0.5930 time to fit residues: 203.9578 Evaluate side-chains 309 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 262 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 564 GLU Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain C residue 92 LYS Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 136 GLU Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 158 ARG Chi-restraints excluded: chain D residue 94 ARG Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 142 GLU Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 177 GLU Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 42 ARG Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 75 ASP Chi-restraints excluded: chain E residue 123 SER Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 100 LYS Chi-restraints excluded: chain F residue 121 VAL Chi-restraints excluded: chain G residue 36 SER Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 70 LYS Chi-restraints excluded: chain G residue 92 SER Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 76 SER Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 112 GLU Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 56 LEU Chi-restraints excluded: chain K residue 65 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 57 optimal weight: 0.2980 chunk 37 optimal weight: 0.9980 chunk 98 optimal weight: 0.0570 chunk 77 optimal weight: 0.7980 chunk 64 optimal weight: 6.9990 chunk 4 optimal weight: 7.9990 chunk 188 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 121 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 HIS A 451 HIS B 118 GLN E 73 ASN F 53 ASN I 100 ASN J 54 ASN K 50 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.119347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.096099 restraints weight = 29888.594| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 2.25 r_work: 0.3112 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2993 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2993 r_free = 0.2993 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.56 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2993 r_free = 0.2993 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2993 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.2895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15855 Z= 0.121 Angle : 0.617 15.370 21572 Z= 0.310 Chirality : 0.043 0.283 2440 Planarity : 0.004 0.054 2748 Dihedral : 4.853 52.447 2272 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.99 % Allowed : 18.76 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.19), residues: 1912 helix: 1.11 (0.25), residues: 436 sheet: 0.54 (0.22), residues: 537 loop : 0.15 (0.21), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG J 124 TYR 0.021 0.001 TYR K 72 PHE 0.012 0.001 PHE A 349 TRP 0.010 0.001 TRP D 106 HIS 0.006 0.001 HIS C 156 Details of bonding type rmsd covalent geometry : bond 0.00282 (15833) covalent geometry : angle 0.60898 (21524) SS BOND : bond 0.00540 ( 18) SS BOND : angle 2.32918 ( 36) hydrogen bonds : bond 0.03249 ( 652) hydrogen bonds : angle 4.86709 ( 1728) link_NAG-ASN : bond 0.00266 ( 4) link_NAG-ASN : angle 1.92297 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 283 time to evaluate : 0.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 564 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.8149 (tm-30) REVERT: B 46 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7693 (pm20) REVERT: B 65 TYR cc_start: 0.7507 (m-80) cc_final: 0.7298 (m-80) REVERT: B 118 GLN cc_start: 0.8871 (OUTLIER) cc_final: 0.8473 (tt0) REVERT: B 135 MET cc_start: 0.8798 (mmt) cc_final: 0.8547 (mtp) REVERT: C 42 ARG cc_start: 0.7661 (mmp-170) cc_final: 0.7385 (mtm-85) REVERT: C 62 GLU cc_start: 0.7437 (tt0) cc_final: 0.7189 (tm-30) REVERT: C 151 GLU cc_start: 0.8468 (tm-30) cc_final: 0.8201 (pp20) REVERT: C 157 LYS cc_start: 0.8877 (mptt) cc_final: 0.8536 (mmtm) REVERT: D 56 TYR cc_start: 0.8928 (m-10) cc_final: 0.8706 (m-80) REVERT: D 94 ARG cc_start: 0.8504 (OUTLIER) cc_final: 0.7694 (ptp90) REVERT: D 99 LEU cc_start: 0.9058 (tt) cc_final: 0.8498 (OUTLIER) REVERT: D 101 GLU cc_start: 0.8517 (mm-30) cc_final: 0.8017 (mp0) REVERT: D 142 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.8280 (pm20) REVERT: D 174 MET cc_start: 0.9063 (ttm) cc_final: 0.8799 (ttp) REVERT: E 75 ASP cc_start: 0.8208 (OUTLIER) cc_final: 0.7287 (p0) REVERT: E 121 GLU cc_start: 0.8818 (mt-10) cc_final: 0.8514 (mt-10) REVERT: F 39 GLN cc_start: 0.7953 (mp10) cc_final: 0.7606 (mp10) REVERT: F 51 SER cc_start: 0.8907 (t) cc_final: 0.8620 (t) REVERT: F 52 LEU cc_start: 0.9164 (OUTLIER) cc_final: 0.8895 (mt) REVERT: F 100 LYS cc_start: 0.8721 (OUTLIER) cc_final: 0.8401 (mtmt) REVERT: F 102 GLN cc_start: 0.8104 (tt0) cc_final: 0.7735 (mt0) REVERT: H 41 ARG cc_start: 0.8548 (ttt90) cc_final: 0.8296 (ttm170) REVERT: I 126 LEU cc_start: 0.8724 (mm) cc_final: 0.8507 (mp) REVERT: K 27 MET cc_start: 0.9081 (mmm) cc_final: 0.8571 (mmt) outliers start: 51 outliers final: 32 residues processed: 308 average time/residue: 0.6310 time to fit residues: 213.7406 Evaluate side-chains 306 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 267 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 564 GLU Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 118 GLN Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain D residue 94 ARG Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 142 GLU Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain E residue 42 ARG Chi-restraints excluded: chain E residue 75 ASP Chi-restraints excluded: chain E residue 123 SER Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 100 LYS Chi-restraints excluded: chain F residue 121 VAL Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 70 LYS Chi-restraints excluded: chain G residue 92 SER Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 76 SER Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 112 GLU Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 56 LEU Chi-restraints excluded: chain K residue 65 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 43 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 124 optimal weight: 7.9990 chunk 181 optimal weight: 0.9990 chunk 129 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 HIS A 315 ASN ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 GLN E 62 ASN F 53 ASN G 29 GLN I 100 ASN J 54 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.116850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.093404 restraints weight = 29747.885| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 2.23 r_work: 0.3057 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2944 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2944 r_free = 0.2944 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2944 r_free = 0.2944 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.56 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2944 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 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 : 0.005 0.097 15855 Z= 0.215 Angle : 0.698 14.703 21572 Z= 0.352 Chirality : 0.046 0.283 2440 Planarity : 0.005 0.052 2748 Dihedral : 5.126 50.485 2272 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.11 % Allowed : 19.11 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.19), residues: 1912 helix: 0.98 (0.25), residues: 435 sheet: 0.44 (0.23), residues: 527 loop : 0.04 (0.20), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 117 TYR 0.022 0.002 TYR K 72 PHE 0.025 0.002 PHE D 74 TRP 0.012 0.001 TRP J 70 HIS 0.013 0.001 HIS C 156 Details of bonding type rmsd covalent geometry : bond 0.00515 (15833) covalent geometry : angle 0.68444 (21524) SS BOND : bond 0.00800 ( 18) SS BOND : angle 3.28449 ( 36) hydrogen bonds : bond 0.03827 ( 652) hydrogen bonds : angle 5.11487 ( 1728) link_NAG-ASN : bond 0.00300 ( 4) link_NAG-ASN : angle 1.99409 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 272 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 GLN cc_start: 0.7989 (mm110) cc_final: 0.7648 (mp10) REVERT: A 564 GLU cc_start: 0.8717 (OUTLIER) cc_final: 0.8160 (tm-30) REVERT: B 46 GLU cc_start: 0.8418 (pm20) cc_final: 0.7925 (pm20) REVERT: C 42 ARG cc_start: 0.7794 (mmp-170) cc_final: 0.7425 (mtm-85) REVERT: C 62 GLU cc_start: 0.7495 (tt0) cc_final: 0.7267 (tm-30) REVERT: C 72 GLU cc_start: 0.8512 (mp0) cc_final: 0.7967 (mp0) REVERT: C 151 GLU cc_start: 0.8481 (tm-30) cc_final: 0.8212 (pp20) REVERT: C 157 LYS cc_start: 0.8904 (mptt) cc_final: 0.8534 (mmtm) REVERT: D 56 TYR cc_start: 0.8963 (m-10) cc_final: 0.8721 (m-80) REVERT: D 94 ARG cc_start: 0.8553 (OUTLIER) cc_final: 0.7472 (ptp90) REVERT: D 142 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.8253 (pm20) REVERT: D 174 MET cc_start: 0.9114 (ttm) cc_final: 0.8863 (ttp) REVERT: F 51 SER cc_start: 0.8930 (t) cc_final: 0.8629 (t) REVERT: F 52 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8864 (mt) REVERT: F 100 LYS cc_start: 0.8751 (OUTLIER) cc_final: 0.8430 (mtmt) REVERT: F 102 GLN cc_start: 0.8164 (tt0) cc_final: 0.7733 (mt0) REVERT: H 41 ARG cc_start: 0.8561 (ttt90) cc_final: 0.8350 (ttm170) REVERT: I 126 LEU cc_start: 0.8804 (mm) cc_final: 0.8582 (mp) REVERT: J 54 ASN cc_start: 0.8938 (OUTLIER) cc_final: 0.8390 (t0) outliers start: 53 outliers final: 35 residues processed: 303 average time/residue: 0.6285 time to fit residues: 209.6939 Evaluate side-chains 302 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 261 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 451 HIS Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 564 GLU Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 136 GLU Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain D residue 94 ARG Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 142 GLU Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 42 ARG Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 123 SER Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 100 LYS Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 121 VAL Chi-restraints excluded: chain G residue 36 SER Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 70 LYS Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 76 SER Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 54 ASN Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 56 LEU Chi-restraints excluded: chain K residue 65 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 173 optimal weight: 0.1980 chunk 73 optimal weight: 3.9990 chunk 109 optimal weight: 0.9980 chunk 159 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 17 optimal weight: 0.0980 chunk 126 optimal weight: 4.9990 chunk 171 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 37 optimal weight: 0.3980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 HIS A 451 HIS ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 ASN F 53 ASN G 29 GLN I 100 ASN J 54 ASN K 50 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.118809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.095645 restraints weight = 29925.388| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 2.25 r_work: 0.3103 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2985 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2985 r_free = 0.2985 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.56 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2985 r_free = 0.2985 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.56 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2985 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.3009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 15855 Z= 0.122 Angle : 0.649 13.916 21572 Z= 0.324 Chirality : 0.043 0.266 2440 Planarity : 0.004 0.052 2748 Dihedral : 4.942 52.066 2272 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.64 % Allowed : 19.87 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.19), residues: 1912 helix: 1.07 (0.25), residues: 436 sheet: 0.51 (0.22), residues: 538 loop : 0.05 (0.21), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 117 TYR 0.021 0.001 TYR K 72 PHE 0.011 0.001 PHE A 349 TRP 0.010 0.001 TRP D 106 HIS 0.005 0.001 HIS A 693 Details of bonding type rmsd covalent geometry : bond 0.00285 (15833) covalent geometry : angle 0.63687 (21524) SS BOND : bond 0.00574 ( 18) SS BOND : angle 2.64750 ( 36) hydrogen bonds : bond 0.03344 ( 652) hydrogen bonds : angle 4.94078 ( 1728) link_NAG-ASN : bond 0.00272 ( 4) link_NAG-ASN : angle 2.84509 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 270 time to evaluate : 0.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 472 SER cc_start: 0.8494 (t) cc_final: 0.8084 (m) REVERT: A 564 GLU cc_start: 0.8701 (pt0) cc_final: 0.8161 (tm-30) REVERT: B 46 GLU cc_start: 0.8345 (pm20) cc_final: 0.7822 (pm20) REVERT: B 135 MET cc_start: 0.8763 (mmt) cc_final: 0.8524 (mtp) REVERT: C 62 GLU cc_start: 0.7408 (tt0) cc_final: 0.7139 (tm-30) REVERT: C 92 LYS cc_start: 0.8827 (ttmm) cc_final: 0.8573 (mttm) REVERT: C 151 GLU cc_start: 0.8450 (tm-30) cc_final: 0.8170 (pp20) REVERT: C 157 LYS cc_start: 0.8878 (mptt) cc_final: 0.8521 (mmtm) REVERT: D 94 ARG cc_start: 0.8438 (OUTLIER) cc_final: 0.7509 (ptp90) REVERT: D 101 GLU cc_start: 0.8426 (mm-30) cc_final: 0.8056 (mm-30) REVERT: D 142 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.8234 (pm20) REVERT: D 174 MET cc_start: 0.9076 (ttm) cc_final: 0.8860 (ttp) REVERT: E 73 ASN cc_start: 0.8973 (t0) cc_final: 0.8652 (t0) REVERT: F 51 SER cc_start: 0.8843 (t) cc_final: 0.8556 (t) REVERT: F 52 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8836 (mt) REVERT: F 100 LYS cc_start: 0.8729 (OUTLIER) cc_final: 0.8398 (mtmt) REVERT: F 102 GLN cc_start: 0.8125 (tt0) cc_final: 0.7750 (mt0) REVERT: H 41 ARG cc_start: 0.8537 (ttt90) cc_final: 0.8328 (ttm170) REVERT: I 126 LEU cc_start: 0.8721 (mm) cc_final: 0.8499 (mp) REVERT: J 54 ASN cc_start: 0.8853 (OUTLIER) cc_final: 0.8304 (t0) outliers start: 45 outliers final: 35 residues processed: 293 average time/residue: 0.6278 time to fit residues: 202.3071 Evaluate side-chains 305 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 265 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain C residue 69 LYS Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 94 ARG Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 142 GLU Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 42 ARG Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 123 SER Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain F residue 100 LYS Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 121 VAL Chi-restraints excluded: chain G residue 36 SER Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 70 LYS Chi-restraints excluded: chain H residue 76 SER Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 54 ASN Chi-restraints excluded: chain J residue 112 GLU Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 56 LEU Chi-restraints excluded: chain K residue 65 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 173 optimal weight: 0.3980 chunk 172 optimal weight: 0.6980 chunk 132 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 41 optimal weight: 0.5980 chunk 86 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 chunk 112 optimal weight: 0.7980 chunk 144 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 HIS A 451 HIS B 118 GLN E 62 ASN E 95 GLN F 53 ASN I 100 ASN I 105 GLN J 54 ASN K 50 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.118708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.095736 restraints weight = 29591.087| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 2.22 r_work: 0.3104 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2986 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2986 r_free = 0.2986 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.56 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2986 r_free = 0.2986 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2986 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 15855 Z= 0.135 Angle : 0.653 13.862 21572 Z= 0.326 Chirality : 0.044 0.250 2440 Planarity : 0.004 0.054 2748 Dihedral : 4.909 52.049 2272 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.64 % Allowed : 20.11 % Favored : 77.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.19), residues: 1912 helix: 1.07 (0.25), residues: 436 sheet: 0.50 (0.22), residues: 538 loop : 0.07 (0.21), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C 142 TYR 0.022 0.001 TYR K 72 PHE 0.028 0.001 PHE D 74 TRP 0.010 0.001 TRP J 70 HIS 0.005 0.001 HIS A 693 Details of bonding type rmsd covalent geometry : bond 0.00319 (15833) covalent geometry : angle 0.64165 (21524) SS BOND : bond 0.00576 ( 18) SS BOND : angle 2.69267 ( 36) hydrogen bonds : bond 0.03369 ( 652) hydrogen bonds : angle 4.90430 ( 1728) link_NAG-ASN : bond 0.00227 ( 4) link_NAG-ASN : angle 2.42536 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7531.69 seconds wall clock time: 128 minutes 26.36 seconds (7706.36 seconds total)