Starting phenix.real_space_refine on Fri Jun 13 22:32:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t4q_25685/06_2025/7t4q_25685.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t4q_25685/06_2025/7t4q_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_25685/06_2025/7t4q_25685.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t4q_25685/06_2025/7t4q_25685.map" model { file = "/net/cci-nas-00/data/ceres_data/7t4q_25685/06_2025/7t4q_25685.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t4q_25685/06_2025/7t4q_25685.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.025 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-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 9.12, per 1000 atoms: 0.59 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: 3.65 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 1.95 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: 5.63 Time building geometry restraints manager: 4.38 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: 2.120 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: 0.650 Check model and map are aligned: 0.120 Set scattering table: 0.140 Process input model: 36.560 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.800 ------------------------------------------------------------------------------- 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 : 5.12 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (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 TRP 0.020 0.003 TRP B 134 HIS 0.007 0.001 HIS E 35 PHE 0.029 0.002 PHE D 206 TYR 0.018 0.002 TYR C 44 ARG 0.020 0.002 ARG A 484 Details of bonding type rmsd link_NAG-ASN : bond 0.00271 ( 4) link_NAG-ASN : angle 2.43637 ( 12) hydrogen bonds : bond 0.16744 ( 652) hydrogen bonds : angle 7.59237 ( 1728) SS BOND : bond 0.00474 ( 18) SS BOND : angle 1.79628 ( 36) covalent geometry : bond 0.00330 (15833) covalent geometry : angle 0.61785 (21524) *********************** 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 : 1.854 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: 0.8150 (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: 1.3411 time to fit residues: 548.2001 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 : 1.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 161 optimal weight: 1.9990 chunk 144 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 149 optimal weight: 3.9990 chunk 57 optimal weight: 0.0030 chunk 91 optimal weight: 0.9990 chunk 111 optimal weight: 3.9990 chunk 173 optimal weight: 0.6980 overall best weight: 0.9396 ------------------------------------------------------------------------------- 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** 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 = 0.3591 r_free = 0.3591 target = 0.119171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.095951 restraints weight = 29464.386| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 2.23 r_work: 0.3099 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2987 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2987 r_free = 0.2987 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.97 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 = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2986 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 15855 Z= 0.165 Angle : 0.675 9.733 21572 Z= 0.350 Chirality : 0.046 0.185 2440 Planarity : 0.005 0.054 2748 Dihedral : 5.808 52.226 2272 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.29 % Allowed : 11.14 % Favored : 86.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.19), residues: 1912 helix: 0.44 (0.24), residues: 423 sheet: 0.21 (0.22), residues: 503 loop : 0.20 (0.20), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP J 70 HIS 0.008 0.001 HIS A 451 PHE 0.017 0.002 PHE D 206 TYR 0.019 0.002 TYR C 149 ARG 0.007 0.001 ARG A 117 Details of bonding type rmsd link_NAG-ASN : bond 0.00188 ( 4) link_NAG-ASN : angle 1.80252 ( 12) hydrogen bonds : bond 0.04374 ( 652) hydrogen bonds : angle 5.68345 ( 1728) SS BOND : bond 0.00550 ( 18) SS BOND : angle 2.04459 ( 36) covalent geometry : bond 0.00386 (15833) covalent geometry : angle 0.66876 (21524) *********************** 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 348 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 309 time to evaluate : 1.730 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 103 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.7826 (mp0) REVERT: A 529 ASP cc_start: 0.8127 (p0) cc_final: 0.7859 (p0) REVERT: A 564 GLU cc_start: 0.8492 (tm-30) cc_final: 0.8285 (tm-30) REVERT: C 157 LYS cc_start: 0.9171 (mptt) cc_final: 0.8749 (mmtm) REVERT: C 158 ARG cc_start: 0.7837 (OUTLIER) cc_final: 0.7351 (tpt-90) REVERT: D 75 GLN cc_start: 0.5524 (mp-120) cc_final: 0.5274 (mp10) REVERT: D 94 ARG cc_start: 0.8318 (OUTLIER) cc_final: 0.7153 (ptp90) REVERT: D 101 GLU cc_start: 0.8387 (mm-30) cc_final: 0.7761 (mp0) REVERT: E 84 GLU cc_start: 0.9016 (mt-10) cc_final: 0.8801 (mt-10) REVERT: E 121 GLU cc_start: 0.8884 (mt-10) cc_final: 0.8588 (mt-10) REVERT: F 51 SER cc_start: 0.8902 (t) cc_final: 0.8595 (t) REVERT: G 31 ARG cc_start: 0.7858 (OUTLIER) cc_final: 0.7595 (tpm-80) REVERT: K 27 MET cc_start: 0.9017 (mmm) cc_final: 0.8527 (mmt) REVERT: K 47 ARG cc_start: 0.8096 (mtt-85) cc_final: 0.7460 (mtp85) REVERT: K 109 TYR cc_start: 0.8417 (m-80) cc_final: 0.8167 (m-80) outliers start: 39 outliers final: 10 residues processed: 321 average time/residue: 1.2804 time to fit residues: 454.2345 Evaluate side-chains 287 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 273 time to evaluate : 1.782 ------------------------------------------------------------------------------- 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 41 VAL Chi-restraints excluded: chain G residue 92 SER Chi-restraints excluded: chain H residue 24 GLU 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 149 optimal weight: 0.7980 chunk 176 optimal weight: 0.7980 chunk 81 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 chunk 151 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 129 optimal weight: 2.9990 chunk 164 optimal weight: 3.9990 chunk 172 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 141 optimal weight: 0.2980 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 = 0.3572 r_free = 0.3572 target = 0.117461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.093967 restraints weight = 29653.017| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 2.27 r_work: 0.3070 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2951 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2951 r_free = 0.2951 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2951 r_free = 0.2951 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2951 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 15855 Z= 0.180 Angle : 0.641 9.401 21572 Z= 0.330 Chirality : 0.045 0.226 2440 Planarity : 0.005 0.058 2748 Dihedral : 5.528 51.442 2272 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.05 % Allowed : 13.48 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.19), residues: 1912 helix: 0.72 (0.25), residues: 430 sheet: 0.13 (0.22), residues: 520 loop : 0.30 (0.20), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP J 70 HIS 0.007 0.001 HIS C 156 PHE 0.021 0.002 PHE D 74 TYR 0.015 0.002 TYR D 61 ARG 0.006 0.001 ARG B 139 Details of bonding type rmsd link_NAG-ASN : bond 0.00199 ( 4) link_NAG-ASN : angle 2.79043 ( 12) hydrogen bonds : bond 0.04012 ( 652) hydrogen bonds : angle 5.39334 ( 1728) SS BOND : bond 0.00517 ( 18) SS BOND : angle 1.68819 ( 36) covalent geometry : bond 0.00425 (15833) covalent geometry : angle 0.63451 (21524) *********************** 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 341 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 289 time to evaluate : 2.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 380 MET cc_start: 0.9158 (mmm) cc_final: 0.8775 (mmm) REVERT: A 564 GLU cc_start: 0.8564 (tm-30) cc_final: 0.8331 (tm-30) REVERT: C 42 ARG cc_start: 0.7651 (mmp-170) cc_final: 0.7334 (mtp180) REVERT: C 62 GLU cc_start: 0.7584 (tt0) cc_final: 0.7214 (tm-30) REVERT: C 151 GLU cc_start: 0.8445 (tm-30) cc_final: 0.8162 (pp20) REVERT: C 157 LYS cc_start: 0.9142 (mptt) cc_final: 0.8746 (mmtm) REVERT: C 158 ARG cc_start: 0.7780 (OUTLIER) cc_final: 0.7296 (tpt-90) REVERT: D 75 GLN cc_start: 0.5621 (mp-120) cc_final: 0.5380 (mp-120) REVERT: D 94 ARG cc_start: 0.8342 (OUTLIER) cc_final: 0.7241 (ptp90) REVERT: D 134 ASP cc_start: 0.7504 (m-30) cc_final: 0.7204 (m-30) REVERT: D 142 GLU cc_start: 0.8633 (OUTLIER) cc_final: 0.8364 (pm20) REVERT: E 62 ASN cc_start: 0.8921 (m-40) cc_final: 0.8714 (m-40) REVERT: E 75 ASP cc_start: 0.8334 (OUTLIER) cc_final: 0.7884 (p0) REVERT: E 121 GLU cc_start: 0.8866 (mt-10) cc_final: 0.8569 (mt-10) REVERT: F 28 ARG cc_start: 0.8233 (ttp-170) cc_final: 0.7998 (ttp80) REVERT: F 51 SER cc_start: 0.8975 (t) cc_final: 0.8675 (t) REVERT: G 31 ARG cc_start: 0.7941 (OUTLIER) cc_final: 0.7634 (tpm-80) REVERT: K 27 MET cc_start: 0.9078 (mmm) cc_final: 0.8522 (mmt) REVERT: K 47 ARG cc_start: 0.8128 (mtt-85) cc_final: 0.7730 (mtp85) outliers start: 52 outliers final: 27 residues processed: 311 average time/residue: 1.3986 time to fit residues: 478.2419 Evaluate side-chains 302 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 270 time to evaluate : 2.556 ------------------------------------------------------------------------------- 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 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 75 ASP Chi-restraints excluded: chain E residue 123 SER Chi-restraints excluded: chain F residue 121 VAL Chi-restraints excluded: chain G residue 28 THR 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 24 GLU 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 J residue 112 GLU 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 48 optimal weight: 0.2980 chunk 115 optimal weight: 4.9990 chunk 103 optimal weight: 0.6980 chunk 163 optimal weight: 0.4980 chunk 66 optimal weight: 0.2980 chunk 185 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 158 optimal weight: 1.9990 chunk 57 optimal weight: 7.9990 chunk 146 optimal weight: 2.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 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 = 0.3597 r_free = 0.3597 target = 0.119210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.095937 restraints weight = 29655.206| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 2.27 r_work: 0.3101 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- 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 = 0.55 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 = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2988 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 15855 Z= 0.121 Angle : 0.597 8.804 21572 Z= 0.304 Chirality : 0.043 0.199 2440 Planarity : 0.004 0.058 2748 Dihedral : 5.244 52.345 2272 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 3.69 % Allowed : 14.60 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.19), residues: 1912 helix: 1.02 (0.25), residues: 430 sheet: 0.28 (0.22), residues: 526 loop : 0.37 (0.20), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 134 HIS 0.007 0.001 HIS C 156 PHE 0.012 0.001 PHE A 349 TYR 0.029 0.001 TYR K 72 ARG 0.009 0.000 ARG B 139 Details of bonding type rmsd link_NAG-ASN : bond 0.00864 ( 4) link_NAG-ASN : angle 2.86880 ( 12) hydrogen bonds : bond 0.03497 ( 652) hydrogen bonds : angle 5.09102 ( 1728) SS BOND : bond 0.00536 ( 18) SS BOND : angle 1.21584 ( 36) covalent geometry : bond 0.00278 (15833) covalent geometry : angle 0.59193 (21524) *********************** 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 362 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 299 time to evaluate : 2.510 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: 0.8793 (mmm) REVERT: A 564 GLU cc_start: 0.8551 (tm-30) cc_final: 0.8302 (tm-30) REVERT: C 42 ARG cc_start: 0.7577 (mmp-170) cc_final: 0.7261 (mtp-110) REVERT: C 62 GLU cc_start: 0.7549 (tt0) cc_final: 0.7192 (tm-30) REVERT: C 157 LYS cc_start: 0.9106 (mptt) cc_final: 0.8732 (mmtm) REVERT: C 158 ARG cc_start: 0.7903 (OUTLIER) cc_final: 0.7365 (tpt-90) REVERT: C 163 ARG cc_start: 0.6667 (mmt90) cc_final: 0.6250 (mmt90) REVERT: D 94 ARG cc_start: 0.8351 (OUTLIER) cc_final: 0.7315 (ptp90) REVERT: D 134 ASP cc_start: 0.7607 (m-30) cc_final: 0.7171 (m-30) REVERT: D 142 GLU cc_start: 0.8655 (OUTLIER) cc_final: 0.8375 (pm20) REVERT: E 62 ASN cc_start: 0.8907 (m-40) cc_final: 0.8687 (m-40) REVERT: E 75 ASP cc_start: 0.8269 (OUTLIER) cc_final: 0.7825 (p0) REVERT: E 84 GLU cc_start: 0.9001 (mt-10) cc_final: 0.8800 (mt-10) REVERT: E 121 GLU cc_start: 0.8826 (mt-10) cc_final: 0.8575 (mt-10) REVERT: F 28 ARG cc_start: 0.8199 (ttp-170) cc_final: 0.7941 (tmm-80) REVERT: F 51 SER cc_start: 0.8944 (t) cc_final: 0.8645 (t) REVERT: F 100 LYS cc_start: 0.8826 (OUTLIER) cc_final: 0.8448 (mtmt) REVERT: F 102 GLN cc_start: 0.8124 (tt0) cc_final: 0.7782 (mt0) REVERT: G 31 ARG cc_start: 0.7942 (OUTLIER) cc_final: 0.7637 (tpm-80) REVERT: J 35 LYS cc_start: 0.8291 (OUTLIER) cc_final: 0.8059 (mtpp) REVERT: J 46 LYS cc_start: 0.8874 (OUTLIER) cc_final: 0.8657 (tptm) REVERT: J 66 GLN cc_start: 0.8568 (OUTLIER) cc_final: 0.7988 (mp10) REVERT: K 27 MET cc_start: 0.9019 (mmm) cc_final: 0.8554 (mmt) REVERT: K 47 ARG cc_start: 0.8111 (mtt-85) cc_final: 0.7723 (mtp85) outliers start: 63 outliers final: 25 residues processed: 327 average time/residue: 1.2673 time to fit residues: 457.5951 Evaluate side-chains 307 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 273 time to evaluate : 1.920 ------------------------------------------------------------------------------- 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 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 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 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 70 LYS Chi-restraints excluded: chain G residue 92 SER Chi-restraints excluded: chain H residue 24 GLU Chi-restraints excluded: chain H residue 76 SER Chi-restraints excluded: chain J residue 35 LYS Chi-restraints excluded: chain J residue 46 LYS Chi-restraints excluded: chain J residue 66 GLN 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 8 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 chunk 173 optimal weight: 0.9980 chunk 133 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 88 optimal weight: 5.9990 chunk 51 optimal weight: 0.3980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 ASN ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 75 GLN G 120 ASN I 100 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.117247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.093746 restraints weight = 29967.398| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 2.28 r_work: 0.3064 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2948 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2948 r_free = 0.2948 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2948 r_free = 0.2948 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2948 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 15855 Z= 0.184 Angle : 0.628 9.253 21572 Z= 0.318 Chirality : 0.044 0.173 2440 Planarity : 0.004 0.058 2748 Dihedral : 5.245 51.329 2272 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 4.22 % Allowed : 15.47 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.19), residues: 1912 helix: 0.98 (0.25), residues: 437 sheet: 0.24 (0.22), residues: 531 loop : 0.28 (0.20), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 70 HIS 0.009 0.001 HIS C 156 PHE 0.023 0.002 PHE D 74 TYR 0.024 0.002 TYR K 72 ARG 0.007 0.001 ARG B 139 Details of bonding type rmsd link_NAG-ASN : bond 0.00554 ( 4) link_NAG-ASN : angle 2.29287 ( 12) hydrogen bonds : bond 0.03765 ( 652) hydrogen bonds : angle 5.11643 ( 1728) SS BOND : bond 0.00546 ( 18) SS BOND : angle 1.39169 ( 36) covalent geometry : bond 0.00436 (15833) covalent geometry : angle 0.62381 (21524) *********************** 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 352 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 280 time to evaluate : 1.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 ARG cc_start: 0.7435 (ttp-110) cc_final: 0.7138 (mtm110) REVERT: A 165 HIS cc_start: 0.8058 (OUTLIER) cc_final: 0.7141 (p-80) REVERT: A 564 GLU cc_start: 0.8607 (tm-30) cc_final: 0.8360 (tm-30) REVERT: B 118 GLN cc_start: 0.8862 (tt0) cc_final: 0.8474 (tt0) REVERT: C 42 ARG cc_start: 0.7610 (mmp-170) cc_final: 0.7245 (mtp-110) REVERT: C 62 GLU cc_start: 0.7617 (tt0) cc_final: 0.7254 (tm-30) REVERT: C 151 GLU cc_start: 0.8403 (tm-30) cc_final: 0.8120 (pp20) REVERT: C 157 LYS cc_start: 0.9063 (mptt) cc_final: 0.8645 (mmtm) REVERT: C 158 ARG cc_start: 0.7929 (OUTLIER) cc_final: 0.7407 (tpt-90) REVERT: C 163 ARG cc_start: 0.6796 (mmt90) cc_final: 0.6533 (mtt-85) REVERT: D 94 ARG cc_start: 0.8451 (OUTLIER) cc_final: 0.7480 (ptp90) REVERT: D 134 ASP cc_start: 0.7666 (OUTLIER) cc_final: 0.7250 (m-30) REVERT: D 142 GLU cc_start: 0.8692 (OUTLIER) cc_final: 0.8394 (pm20) REVERT: E 42 ARG cc_start: 0.8237 (mtm110) cc_final: 0.7817 (ptm160) REVERT: E 62 ASN cc_start: 0.8929 (m-40) cc_final: 0.8702 (m-40) REVERT: E 75 ASP cc_start: 0.8354 (p0) cc_final: 0.7900 (p0) REVERT: E 121 GLU cc_start: 0.8850 (mt-10) cc_final: 0.8619 (mt-10) REVERT: F 28 ARG cc_start: 0.8299 (ttp-170) cc_final: 0.8039 (tmm-80) REVERT: F 51 SER cc_start: 0.8933 (t) cc_final: 0.8633 (t) REVERT: F 100 LYS cc_start: 0.8782 (OUTLIER) cc_final: 0.8454 (mtmt) REVERT: F 102 GLN cc_start: 0.8126 (tt0) cc_final: 0.7721 (mt0) REVERT: G 31 ARG cc_start: 0.7927 (OUTLIER) cc_final: 0.7611 (tpm-80) REVERT: J 35 LYS cc_start: 0.8468 (OUTLIER) cc_final: 0.8204 (mtpp) REVERT: J 46 LYS cc_start: 0.8900 (OUTLIER) cc_final: 0.8695 (tptm) REVERT: K 27 MET cc_start: 0.9081 (mmm) cc_final: 0.8613 (mmt) REVERT: K 47 ARG cc_start: 0.8124 (mtt-85) cc_final: 0.7661 (mtp85) outliers start: 72 outliers final: 36 residues processed: 319 average time/residue: 1.3104 time to fit residues: 464.9587 Evaluate side-chains 312 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 267 time to evaluate : 1.918 ------------------------------------------------------------------------------- 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 165 HIS 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 69 LYS 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 134 ASP 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 123 SER Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain F residue 100 LYS Chi-restraints excluded: chain F residue 121 VAL Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain G residue 28 THR 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 H residue 24 GLU Chi-restraints excluded: chain H residue 76 SER Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain H residue 105 GLU Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 35 LYS Chi-restraints excluded: chain J residue 46 LYS Chi-restraints excluded: chain J residue 54 ASN 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 Chi-restraints excluded: chain K residue 75 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 36 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 81 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 144 optimal weight: 3.9990 chunk 152 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 80 optimal weight: 0.7980 chunk 182 optimal weight: 0.0020 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 GLN ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 GLN D 75 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 = 0.3590 r_free = 0.3590 target = 0.118614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.095238 restraints weight = 29802.756| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 2.28 r_work: 0.3094 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2977 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2977 r_free = 0.2977 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 = 0.2977 r_free = 0.2977 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2977 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.2653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15855 Z= 0.124 Angle : 0.598 8.534 21572 Z= 0.301 Chirality : 0.043 0.201 2440 Planarity : 0.004 0.056 2748 Dihedral : 5.032 52.263 2272 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 3.99 % Allowed : 16.59 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.19), residues: 1912 helix: 1.04 (0.25), residues: 436 sheet: 0.36 (0.22), residues: 536 loop : 0.23 (0.20), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 70 HIS 0.007 0.001 HIS C 156 PHE 0.012 0.001 PHE A 349 TYR 0.015 0.001 TYR B 226 ARG 0.007 0.000 ARG B 139 Details of bonding type rmsd link_NAG-ASN : bond 0.00227 ( 4) link_NAG-ASN : angle 2.01816 ( 12) hydrogen bonds : bond 0.03398 ( 652) hydrogen bonds : angle 4.97113 ( 1728) SS BOND : bond 0.00421 ( 18) SS BOND : angle 1.79633 ( 36) covalent geometry : bond 0.00291 (15833) covalent geometry : angle 0.59238 (21524) *********************** 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 346 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 278 time to evaluate : 1.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 GLN cc_start: 0.7825 (mm110) cc_final: 0.7376 (mp10) REVERT: A 165 HIS cc_start: 0.7981 (OUTLIER) cc_final: 0.7069 (p-80) REVERT: A 564 GLU cc_start: 0.8583 (tm-30) cc_final: 0.8315 (tm-30) REVERT: B 46 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7688 (pm20) REVERT: B 118 GLN cc_start: 0.8848 (OUTLIER) cc_final: 0.8468 (tt0) REVERT: C 62 GLU cc_start: 0.7641 (tt0) cc_final: 0.7410 (tm-30) REVERT: C 151 GLU cc_start: 0.8451 (tm-30) cc_final: 0.8176 (pp20) REVERT: C 157 LYS cc_start: 0.8981 (mptt) cc_final: 0.8579 (mmtm) REVERT: C 158 ARG cc_start: 0.7966 (OUTLIER) cc_final: 0.7446 (tpt-90) REVERT: D 94 ARG cc_start: 0.8460 (OUTLIER) cc_final: 0.7631 (ptp90) REVERT: D 95 GLU cc_start: 0.7813 (mt-10) cc_final: 0.7609 (mp0) REVERT: D 101 GLU cc_start: 0.8366 (mm-30) cc_final: 0.7816 (mp0) REVERT: D 134 ASP cc_start: 0.7571 (m-30) cc_final: 0.7095 (m-30) REVERT: D 142 GLU cc_start: 0.8641 (OUTLIER) cc_final: 0.8334 (pm20) REVERT: D 174 MET cc_start: 0.9107 (ttm) cc_final: 0.8834 (ttp) REVERT: E 62 ASN cc_start: 0.8907 (m-40) cc_final: 0.8693 (m-40) REVERT: E 75 ASP cc_start: 0.8275 (OUTLIER) cc_final: 0.7850 (p0) REVERT: E 121 GLU cc_start: 0.8815 (mt-10) cc_final: 0.8552 (mt-10) REVERT: F 51 SER cc_start: 0.8895 (t) cc_final: 0.8599 (t) REVERT: F 52 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8849 (mt) REVERT: F 100 LYS cc_start: 0.8781 (OUTLIER) cc_final: 0.8458 (mtmt) REVERT: F 102 GLN cc_start: 0.8154 (tt0) cc_final: 0.7776 (mt0) REVERT: J 46 LYS cc_start: 0.8848 (OUTLIER) cc_final: 0.8639 (tptm) REVERT: K 27 MET cc_start: 0.9043 (mmm) cc_final: 0.8611 (mmt) REVERT: K 47 ARG cc_start: 0.8094 (mtt-85) cc_final: 0.7672 (mtp85) outliers start: 68 outliers final: 33 residues processed: 314 average time/residue: 1.2860 time to fit residues: 446.0642 Evaluate side-chains 310 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 267 time to evaluate : 1.735 ------------------------------------------------------------------------------- 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 165 HIS 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 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 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 C residue 158 ARG Chi-restraints excluded: chain D residue 94 ARG Chi-restraints excluded: chain D residue 99 LEU 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 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 28 THR 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 24 GLU 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 46 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 65 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 61 optimal weight: 7.9990 chunk 46 optimal weight: 0.7980 chunk 91 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 189 optimal weight: 3.9990 chunk 100 optimal weight: 10.0000 chunk 132 optimal weight: 0.0980 chunk 74 optimal weight: 3.9990 chunk 182 optimal weight: 0.2980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 118 GLN D 75 GLN I 100 ASN J 54 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.117671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.094267 restraints weight = 30143.206| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 2.29 r_work: 0.3075 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2958 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2958 r_free = 0.2958 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2958 r_free = 0.2958 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2958 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 15855 Z= 0.165 Angle : 0.649 13.975 21572 Z= 0.328 Chirality : 0.044 0.292 2440 Planarity : 0.004 0.055 2748 Dihedral : 5.062 51.744 2272 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 3.63 % Allowed : 17.41 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.19), residues: 1912 helix: 1.04 (0.25), residues: 434 sheet: 0.37 (0.22), residues: 531 loop : 0.18 (0.20), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 70 HIS 0.007 0.001 HIS C 156 PHE 0.022 0.002 PHE D 74 TYR 0.018 0.002 TYR G 74 ARG 0.009 0.001 ARG F 28 Details of bonding type rmsd link_NAG-ASN : bond 0.00280 ( 4) link_NAG-ASN : angle 2.05985 ( 12) hydrogen bonds : bond 0.03692 ( 652) hydrogen bonds : angle 5.02478 ( 1728) SS BOND : bond 0.00702 ( 18) SS BOND : angle 2.94976 ( 36) covalent geometry : bond 0.00392 (15833) covalent geometry : angle 0.63626 (21524) *********************** 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 330 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 268 time to evaluate : 1.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 HIS cc_start: 0.7995 (OUTLIER) cc_final: 0.7069 (p-80) REVERT: A 535 LEU cc_start: 0.9356 (OUTLIER) cc_final: 0.8845 (tt) REVERT: A 564 GLU cc_start: 0.8598 (tm-30) cc_final: 0.8325 (tm-30) REVERT: B 135 MET cc_start: 0.8751 (mmt) cc_final: 0.8467 (mtp) REVERT: B 158 LEU cc_start: 0.9201 (tt) cc_final: 0.8994 (tm) REVERT: C 42 ARG cc_start: 0.7651 (mmp-170) cc_final: 0.7256 (mtm-85) REVERT: C 62 GLU cc_start: 0.7668 (tt0) cc_final: 0.7428 (tm-30) REVERT: C 151 GLU cc_start: 0.8490 (tm-30) cc_final: 0.8214 (pp20) REVERT: C 157 LYS cc_start: 0.8924 (mptt) cc_final: 0.8556 (mmtm) REVERT: C 158 ARG cc_start: 0.7947 (OUTLIER) cc_final: 0.7424 (tpt-90) REVERT: D 94 ARG cc_start: 0.8471 (OUTLIER) cc_final: 0.7693 (ptp90) REVERT: D 95 GLU cc_start: 0.7800 (mt-10) cc_final: 0.7599 (mp0) REVERT: D 142 GLU cc_start: 0.8660 (OUTLIER) cc_final: 0.8354 (pm20) REVERT: D 174 MET cc_start: 0.9112 (ttm) cc_final: 0.8860 (ttp) REVERT: E 62 ASN cc_start: 0.8913 (m-40) cc_final: 0.8686 (m-40) REVERT: E 75 ASP cc_start: 0.8306 (p0) cc_final: 0.7875 (p0) REVERT: E 121 GLU cc_start: 0.8836 (mt-10) cc_final: 0.8602 (mt-10) REVERT: F 51 SER cc_start: 0.8912 (t) cc_final: 0.8615 (t) REVERT: F 52 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8868 (mt) REVERT: F 100 LYS cc_start: 0.8803 (OUTLIER) cc_final: 0.8466 (mtmt) REVERT: F 102 GLN cc_start: 0.8150 (tt0) cc_final: 0.7754 (mt0) REVERT: J 46 LYS cc_start: 0.8875 (OUTLIER) cc_final: 0.8654 (tptm) REVERT: K 27 MET cc_start: 0.9102 (mmm) cc_final: 0.8611 (mmt) outliers start: 62 outliers final: 40 residues processed: 302 average time/residue: 1.2885 time to fit residues: 428.2349 Evaluate side-chains 307 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 259 time to evaluate : 1.890 ------------------------------------------------------------------------------- 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 165 HIS 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 535 LEU Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain B residue 157 ASP 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 C residue 158 ARG 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 177 GLU Chi-restraints excluded: chain D residue 195 THR 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 52 LEU Chi-restraints excluded: chain F residue 100 LYS Chi-restraints excluded: chain F residue 121 VAL Chi-restraints excluded: chain G residue 28 THR 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 24 GLU 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 H residue 105 GLU Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 46 LYS 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 19 optimal weight: 0.5980 chunk 183 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 180 optimal weight: 0.5980 chunk 87 optimal weight: 4.9990 chunk 125 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 128 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 64 optimal weight: 0.0570 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 GLN B 177 HIS D 75 GLN I 100 ASN J 54 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.118486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.095218 restraints weight = 29929.603| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 2.28 r_work: 0.3088 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- 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 = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2970 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 15855 Z= 0.133 Angle : 0.639 12.785 21572 Z= 0.322 Chirality : 0.044 0.280 2440 Planarity : 0.004 0.054 2748 Dihedral : 4.991 52.098 2272 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 3.58 % Allowed : 18.00 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.19), residues: 1912 helix: 1.05 (0.25), residues: 434 sheet: 0.41 (0.23), residues: 531 loop : 0.18 (0.20), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP J 70 HIS 0.009 0.001 HIS C 156 PHE 0.024 0.001 PHE D 74 TYR 0.018 0.001 TYR G 74 ARG 0.007 0.001 ARG F 28 Details of bonding type rmsd link_NAG-ASN : bond 0.00255 ( 4) link_NAG-ASN : angle 1.97547 ( 12) hydrogen bonds : bond 0.03517 ( 652) hydrogen bonds : angle 4.96655 ( 1728) SS BOND : bond 0.00581 ( 18) SS BOND : angle 2.65089 ( 36) covalent geometry : bond 0.00313 (15833) covalent geometry : angle 0.62904 (21524) *********************** 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 329 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 268 time to evaluate : 1.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 HIS cc_start: 0.7996 (OUTLIER) cc_final: 0.7071 (p-80) REVERT: A 535 LEU cc_start: 0.9354 (OUTLIER) cc_final: 0.8835 (tt) REVERT: A 564 GLU cc_start: 0.8592 (tm-30) cc_final: 0.8315 (tm-30) REVERT: B 46 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.7713 (pm20) REVERT: C 42 ARG cc_start: 0.7695 (mmp-170) cc_final: 0.7346 (mtm-85) REVERT: C 151 GLU cc_start: 0.8531 (tm-30) cc_final: 0.8256 (pp20) REVERT: C 157 LYS cc_start: 0.8888 (mptt) cc_final: 0.8534 (mmtm) REVERT: C 158 ARG cc_start: 0.7997 (OUTLIER) cc_final: 0.7509 (tpt-90) REVERT: D 94 ARG cc_start: 0.8499 (OUTLIER) cc_final: 0.7728 (ptp90) REVERT: D 95 GLU cc_start: 0.7797 (mt-10) cc_final: 0.7589 (mp0) REVERT: D 142 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.8316 (pm20) REVERT: D 174 MET cc_start: 0.9109 (ttm) cc_final: 0.8881 (ttp) REVERT: E 62 ASN cc_start: 0.8903 (m-40) cc_final: 0.8683 (m-40) REVERT: E 75 ASP cc_start: 0.8290 (OUTLIER) cc_final: 0.7871 (p0) REVERT: E 121 GLU cc_start: 0.8830 (mt-10) cc_final: 0.8595 (mt-10) REVERT: F 51 SER cc_start: 0.8889 (t) cc_final: 0.8592 (t) REVERT: F 52 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8892 (mt) REVERT: F 100 LYS cc_start: 0.8768 (OUTLIER) cc_final: 0.8435 (mtmt) REVERT: F 102 GLN cc_start: 0.8123 (tt0) cc_final: 0.7730 (mt0) REVERT: J 46 LYS cc_start: 0.8868 (OUTLIER) cc_final: 0.8657 (tptm) REVERT: J 54 ASN cc_start: 0.8944 (OUTLIER) cc_final: 0.8431 (t0) REVERT: J 66 GLN cc_start: 0.8751 (OUTLIER) cc_final: 0.8122 (mp10) REVERT: K 27 MET cc_start: 0.9079 (mmm) cc_final: 0.8591 (mmt) outliers start: 61 outliers final: 37 residues processed: 301 average time/residue: 1.2917 time to fit residues: 428.5505 Evaluate side-chains 304 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 255 time to evaluate : 1.871 ------------------------------------------------------------------------------- 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 165 HIS Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 253 LEU 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 535 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 69 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 153 VAL Chi-restraints excluded: chain C residue 158 ARG 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 177 GLU Chi-restraints excluded: chain D residue 195 THR 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 28 THR 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 24 GLU 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 46 LYS Chi-restraints excluded: chain J residue 54 ASN Chi-restraints excluded: chain J residue 66 GLN 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 49 optimal weight: 0.7980 chunk 189 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 chunk 174 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 129 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 125 optimal weight: 0.9980 chunk 185 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 75 GLN E 73 ASN H 50 GLN I 100 ASN J 54 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.117918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.094616 restraints weight = 29874.265| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 2.28 r_work: 0.3079 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2965 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2965 r_free = 0.2965 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2965 r_free = 0.2965 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2965 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 15855 Z= 0.156 Angle : 0.663 13.250 21572 Z= 0.333 Chirality : 0.044 0.299 2440 Planarity : 0.004 0.054 2748 Dihedral : 5.021 51.701 2272 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.63 % Allowed : 18.35 % Favored : 78.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.19), residues: 1912 helix: 0.98 (0.25), residues: 436 sheet: 0.41 (0.23), residues: 529 loop : 0.11 (0.21), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP J 70 HIS 0.009 0.001 HIS C 156 PHE 0.024 0.002 PHE D 74 TYR 0.018 0.001 TYR B 226 ARG 0.014 0.001 ARG A 117 Details of bonding type rmsd link_NAG-ASN : bond 0.00258 ( 4) link_NAG-ASN : angle 1.94914 ( 12) hydrogen bonds : bond 0.03665 ( 652) hydrogen bonds : angle 5.04057 ( 1728) SS BOND : bond 0.00619 ( 18) SS BOND : angle 3.24177 ( 36) covalent geometry : bond 0.00371 (15833) covalent geometry : angle 0.64860 (21524) *********************** 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 327 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 265 time to evaluate : 4.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 GLN cc_start: 0.7980 (mm110) cc_final: 0.7540 (mp10) REVERT: A 165 HIS cc_start: 0.8002 (OUTLIER) cc_final: 0.7058 (p-80) REVERT: A 535 LEU cc_start: 0.9361 (OUTLIER) cc_final: 0.8826 (tt) REVERT: A 564 GLU cc_start: 0.8600 (tm-30) cc_final: 0.8324 (tm-30) REVERT: B 46 GLU cc_start: 0.8318 (pm20) cc_final: 0.7821 (pm20) REVERT: B 118 GLN cc_start: 0.8882 (tt0) cc_final: 0.8468 (tt0) REVERT: B 135 MET cc_start: 0.8730 (mmt) cc_final: 0.8471 (mtp) REVERT: B 158 LEU cc_start: 0.9215 (tt) cc_final: 0.9006 (tm) REVERT: C 42 ARG cc_start: 0.7678 (mmp-170) cc_final: 0.7344 (mtm-85) REVERT: C 151 GLU cc_start: 0.8536 (tm-30) cc_final: 0.8263 (pp20) REVERT: C 157 LYS cc_start: 0.8869 (mptt) cc_final: 0.8509 (mmtm) REVERT: D 94 ARG cc_start: 0.8505 (OUTLIER) cc_final: 0.7756 (ptp90) REVERT: D 95 GLU cc_start: 0.7840 (mt-10) cc_final: 0.7612 (mp0) REVERT: D 142 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.8275 (pm20) REVERT: D 174 MET cc_start: 0.9122 (ttm) cc_final: 0.8894 (ttp) REVERT: E 62 ASN cc_start: 0.8904 (m-40) cc_final: 0.8686 (m-40) REVERT: E 75 ASP cc_start: 0.8314 (OUTLIER) cc_final: 0.7891 (p0) REVERT: E 121 GLU cc_start: 0.8830 (mt-10) cc_final: 0.8591 (mt-10) REVERT: F 51 SER cc_start: 0.8908 (t) cc_final: 0.8611 (t) REVERT: F 52 LEU cc_start: 0.9190 (OUTLIER) cc_final: 0.8908 (mt) REVERT: F 100 LYS cc_start: 0.8767 (OUTLIER) cc_final: 0.8432 (mtmt) REVERT: F 102 GLN cc_start: 0.8144 (tt0) cc_final: 0.7746 (mt0) REVERT: J 46 LYS cc_start: 0.8890 (OUTLIER) cc_final: 0.8661 (tptm) REVERT: J 54 ASN cc_start: 0.8892 (OUTLIER) cc_final: 0.8505 (t0) REVERT: J 110 ARG cc_start: 0.8319 (mpt-90) cc_final: 0.8042 (mpt-90) REVERT: K 27 MET cc_start: 0.9094 (mmm) cc_final: 0.8577 (mmt) outliers start: 62 outliers final: 41 residues processed: 297 average time/residue: 1.6587 time to fit residues: 550.9773 Evaluate side-chains 307 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 257 time to evaluate : 1.677 ------------------------------------------------------------------------------- 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 165 HIS Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 253 LEU 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 535 LEU Chi-restraints excluded: chain A residue 572 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 115 ASN 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 125 MET 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 20 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 52 LEU Chi-restraints excluded: chain F residue 100 LYS Chi-restraints excluded: chain F residue 121 VAL Chi-restraints excluded: chain G residue 28 THR 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 24 GLU 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 46 LYS 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 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 Chi-restraints excluded: chain K residue 108 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 80 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 182 optimal weight: 4.9990 chunk 61 optimal weight: 0.9990 chunk 64 optimal weight: 5.9990 chunk 183 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 157 optimal weight: 0.9990 chunk 165 optimal weight: 4.9990 chunk 126 optimal weight: 5.9990 chunk 45 optimal weight: 0.4980 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 315 ASN ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 75 GLN E 73 ASN H 50 GLN I 100 ASN J 54 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.117142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.093655 restraints weight = 30187.076| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 2.30 r_work: 0.3063 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2948 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2948 r_free = 0.2948 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2948 r_free = 0.2948 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2948 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 15855 Z= 0.186 Angle : 0.678 11.651 21572 Z= 0.340 Chirality : 0.045 0.243 2440 Planarity : 0.005 0.054 2748 Dihedral : 5.062 51.122 2272 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.34 % Allowed : 18.76 % Favored : 77.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.19), residues: 1912 helix: 0.95 (0.25), residues: 435 sheet: 0.38 (0.23), residues: 529 loop : 0.08 (0.21), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 70 HIS 0.009 0.001 HIS C 156 PHE 0.022 0.002 PHE D 74 TYR 0.018 0.002 TYR G 74 ARG 0.017 0.001 ARG A 117 Details of bonding type rmsd link_NAG-ASN : bond 0.00222 ( 4) link_NAG-ASN : angle 2.87017 ( 12) hydrogen bonds : bond 0.03769 ( 652) hydrogen bonds : angle 5.08719 ( 1728) SS BOND : bond 0.00708 ( 18) SS BOND : angle 2.73939 ( 36) covalent geometry : bond 0.00441 (15833) covalent geometry : angle 0.66630 (21524) ********************** 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: 57 poor density : 258 time to evaluate : 1.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 GLN cc_start: 0.8014 (mm110) cc_final: 0.7694 (mp10) REVERT: A 165 HIS cc_start: 0.8021 (OUTLIER) cc_final: 0.7036 (p-80) REVERT: A 535 LEU cc_start: 0.9369 (OUTLIER) cc_final: 0.8833 (tt) REVERT: A 564 GLU cc_start: 0.8622 (tm-30) cc_final: 0.8341 (tm-30) REVERT: B 46 GLU cc_start: 0.8356 (pm20) cc_final: 0.7831 (pm20) REVERT: B 118 GLN cc_start: 0.8861 (tt0) cc_final: 0.8470 (tt0) REVERT: B 158 LEU cc_start: 0.9210 (tt) cc_final: 0.9000 (tm) REVERT: C 42 ARG cc_start: 0.7679 (mmp-170) cc_final: 0.7351 (mtm-85) REVERT: C 72 GLU cc_start: 0.8554 (mp0) cc_final: 0.8009 (mp0) REVERT: C 151 GLU cc_start: 0.8541 (tm-30) cc_final: 0.8303 (pp20) REVERT: C 154 LYS cc_start: 0.8339 (tttt) cc_final: 0.8118 (ttmt) REVERT: C 157 LYS cc_start: 0.8862 (mptt) cc_final: 0.8453 (mmtm) REVERT: D 75 GLN cc_start: 0.5292 (OUTLIER) cc_final: 0.4435 (mp10) REVERT: D 94 ARG cc_start: 0.8534 (OUTLIER) cc_final: 0.7704 (ptp90) REVERT: D 95 GLU cc_start: 0.7892 (mt-10) cc_final: 0.7650 (mp0) REVERT: D 142 GLU cc_start: 0.8633 (OUTLIER) cc_final: 0.8290 (pm20) REVERT: D 174 MET cc_start: 0.9137 (ttm) cc_final: 0.8902 (ttp) REVERT: E 62 ASN cc_start: 0.8913 (m-40) cc_final: 0.8694 (m-40) REVERT: E 75 ASP cc_start: 0.8338 (p0) cc_final: 0.7904 (p0) REVERT: F 51 SER cc_start: 0.8927 (t) cc_final: 0.8629 (t) REVERT: F 52 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8875 (mt) REVERT: F 100 LYS cc_start: 0.8770 (OUTLIER) cc_final: 0.8437 (mtmt) REVERT: F 102 GLN cc_start: 0.8145 (tt0) cc_final: 0.7704 (mt0) REVERT: J 46 LYS cc_start: 0.8899 (OUTLIER) cc_final: 0.8672 (tptm) REVERT: J 54 ASN cc_start: 0.8930 (OUTLIER) cc_final: 0.8530 (t0) REVERT: K 27 MET cc_start: 0.9113 (mmm) cc_final: 0.8580 (mmt) outliers start: 57 outliers final: 41 residues processed: 287 average time/residue: 1.3547 time to fit residues: 428.5356 Evaluate side-chains 307 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 257 time to evaluate : 1.871 ------------------------------------------------------------------------------- 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 165 HIS Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 253 LEU 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 535 LEU Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain B residue 157 ASP 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 75 GLN 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 125 MET 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 20 CYS 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 28 THR 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 24 GLU 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 46 LYS 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 Chi-restraints excluded: chain K residue 108 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 5 optimal weight: 0.7980 chunk 131 optimal weight: 0.7980 chunk 164 optimal weight: 0.5980 chunk 37 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 142 optimal weight: 6.9990 chunk 180 optimal weight: 0.9980 chunk 113 optimal weight: 0.0570 chunk 184 optimal weight: 2.9990 chunk 146 optimal weight: 2.9990 chunk 125 optimal weight: 1.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 GLN D 75 GLN E 73 ASN H 50 GLN J 54 ASN K 50 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.118216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.094889 restraints weight = 29710.058| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 2.29 r_work: 0.3084 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- 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 = 0.52 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 = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2968 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.2970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15855 Z= 0.131 Angle : 0.650 11.773 21572 Z= 0.326 Chirality : 0.043 0.221 2440 Planarity : 0.004 0.053 2748 Dihedral : 5.002 51.804 2272 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.22 % Allowed : 18.82 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.19), residues: 1912 helix: 1.07 (0.25), residues: 429 sheet: 0.42 (0.23), residues: 527 loop : 0.07 (0.21), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 106 HIS 0.006 0.001 HIS C 156 PHE 0.013 0.001 PHE A 349 TYR 0.018 0.001 TYR G 74 ARG 0.016 0.001 ARG A 117 Details of bonding type rmsd link_NAG-ASN : bond 0.00245 ( 4) link_NAG-ASN : angle 2.52285 ( 12) hydrogen bonds : bond 0.03569 ( 652) hydrogen bonds : angle 5.00978 ( 1728) SS BOND : bond 0.00592 ( 18) SS BOND : angle 2.54604 ( 36) covalent geometry : bond 0.00305 (15833) covalent geometry : angle 0.63958 (21524) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17628.13 seconds wall clock time: 308 minutes 48.64 seconds (18528.64 seconds total)