Starting phenix.real_space_refine on Tue Dec 31 10:56:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t4q_25685/12_2024/7t4q_25685.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t4q_25685/12_2024/7t4q_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_25685/12_2024/7t4q_25685.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t4q_25685/12_2024/7t4q_25685.map" model { file = "/net/cci-nas-00/data/ceres_data/7t4q_25685/12_2024/7t4q_25685.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t4q_25685/12_2024/7t4q_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-5532/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: 8.75, per 1000 atoms: 0.57 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: 3.68 Conformation dependent library (CDL) restraints added in 1.7 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: 2.27 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: 6.64 Time building geometry restraints manager: 4.26 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: 1.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.600 Check model and map are aligned: 0.140 Set scattering table: 0.170 Process input model: 36.670 Find NCS groups from input model: 0.220 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: 0.010 Load rotamer database and sin/cos tables:13.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.090 ------------------------------------------------------------------------------- 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 15833 Z= 0.217 Angle : 0.618 7.468 21524 Z= 0.329 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 *********************** 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 : 1.842 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: 1.4195 time to fit residues: 577.8907 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 : 1.924 ------------------------------------------------------------------------------- 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: 1.9990 chunk 80 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.5980 chunk 77 optimal weight: 2.9990 chunk 149 optimal weight: 3.9990 chunk 57 optimal weight: 0.0030 chunk 91 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 173 optimal weight: 0.6980 overall best weight: 1.0594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 HIS A 271 GLN A 370 GLN ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 75 GLN D 123 GLN E 19 GLN F 109 ASN G 62 GLN J 29 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 15833 Z= 0.275 Angle : 0.680 9.905 21524 Z= 0.353 Chirality : 0.047 0.185 2440 Planarity : 0.005 0.054 2748 Dihedral : 5.801 52.304 2272 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.40 % Allowed : 11.20 % Favored : 86.40 % 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: 0.25 (0.19), residues: 1912 helix: 0.44 (0.24), residues: 424 sheet: 0.12 (0.22), residues: 514 loop : 0.23 (0.20), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP J 70 HIS 0.008 0.001 HIS A 451 PHE 0.018 0.002 PHE D 206 TYR 0.019 0.002 TYR C 149 ARG 0.008 0.001 ARG A 117 *********************** 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 350 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 309 time to evaluate : 1.709 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 103 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.7356 (mp0) REVERT: A 470 MET cc_start: 0.8834 (OUTLIER) cc_final: 0.8631 (mtm) REVERT: A 529 ASP cc_start: 0.7592 (p0) cc_final: 0.7348 (p0) REVERT: C 157 LYS cc_start: 0.8982 (mptt) cc_final: 0.8711 (mmtm) REVERT: C 158 ARG cc_start: 0.7651 (OUTLIER) cc_final: 0.7290 (tpt-90) REVERT: D 94 ARG cc_start: 0.8186 (OUTLIER) cc_final: 0.7076 (ptp90) REVERT: D 101 GLU cc_start: 0.7845 (mm-30) cc_final: 0.7469 (mp0) REVERT: E 121 GLU cc_start: 0.7982 (mt-10) cc_final: 0.7711 (mt-10) REVERT: F 51 SER cc_start: 0.8881 (t) cc_final: 0.8622 (t) REVERT: F 100 LYS cc_start: 0.8956 (OUTLIER) cc_final: 0.8728 (mtmt) REVERT: G 31 ARG cc_start: 0.7295 (OUTLIER) cc_final: 0.6954 (tpm-80) REVERT: I 114 THR cc_start: 0.9052 (m) cc_final: 0.8837 (m) REVERT: K 27 MET cc_start: 0.8635 (mmm) cc_final: 0.8207 (mmt) REVERT: K 109 TYR cc_start: 0.8107 (m-80) cc_final: 0.7815 (m-80) outliers start: 41 outliers final: 10 residues processed: 322 average time/residue: 1.3387 time to fit residues: 476.4585 Evaluate side-chains 292 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 276 time to evaluate : 1.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 470 MET 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 F residue 100 LYS 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 38 VAL 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 96 optimal weight: 0.6980 chunk 53 optimal weight: 3.9990 chunk 144 optimal weight: 0.7980 chunk 118 optimal weight: 0.6980 chunk 47 optimal weight: 5.9990 chunk 173 optimal weight: 0.9990 chunk 187 optimal weight: 3.9990 chunk 154 optimal weight: 4.9990 chunk 172 optimal weight: 0.6980 chunk 59 optimal weight: 2.9990 chunk 139 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 HIS ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 123 GLN E 62 ASN I 100 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 15833 Z= 0.220 Angle : 0.616 9.271 21524 Z= 0.317 Chirality : 0.044 0.172 2440 Planarity : 0.004 0.058 2748 Dihedral : 5.454 52.208 2272 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.99 % Allowed : 13.54 % 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: 0.49 (0.19), residues: 1912 helix: 0.77 (0.25), residues: 431 sheet: 0.14 (0.22), residues: 517 loop : 0.39 (0.20), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 70 HIS 0.007 0.001 HIS C 156 PHE 0.023 0.002 PHE D 74 TYR 0.015 0.002 TYR B 226 ARG 0.006 0.001 ARG B 139 *********************** 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 344 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 293 time to evaluate : 1.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 380 MET cc_start: 0.9023 (mmm) cc_final: 0.8595 (mmm) REVERT: A 470 MET cc_start: 0.8808 (OUTLIER) cc_final: 0.8366 (mtp) REVERT: C 151 GLU cc_start: 0.7916 (tm-30) cc_final: 0.7707 (pp20) REVERT: C 157 LYS cc_start: 0.8932 (mptt) cc_final: 0.8674 (mmtm) REVERT: C 158 ARG cc_start: 0.7563 (OUTLIER) cc_final: 0.7239 (tpt-90) REVERT: D 94 ARG cc_start: 0.8206 (OUTLIER) cc_final: 0.7196 (ptp90) REVERT: D 142 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7844 (pm20) REVERT: E 84 GLU cc_start: 0.8739 (mt-10) cc_final: 0.8520 (mt-10) REVERT: F 51 SER cc_start: 0.8946 (t) cc_final: 0.8696 (t) REVERT: F 100 LYS cc_start: 0.8991 (OUTLIER) cc_final: 0.8747 (mtmt) REVERT: G 31 ARG cc_start: 0.7357 (OUTLIER) cc_final: 0.7010 (tpm-80) REVERT: J 46 LYS cc_start: 0.8686 (OUTLIER) cc_final: 0.8486 (tptm) REVERT: K 27 MET cc_start: 0.8672 (mmm) cc_final: 0.8135 (mmt) REVERT: K 109 TYR cc_start: 0.8202 (m-80) cc_final: 0.7928 (m-80) outliers start: 51 outliers final: 24 residues processed: 313 average time/residue: 1.3546 time to fit residues: 467.6124 Evaluate side-chains 302 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 271 time to evaluate : 2.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 470 MET 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 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 30 SER Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain J residue 46 LYS 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 171 optimal weight: 0.4980 chunk 130 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 82 optimal weight: 0.9990 chunk 116 optimal weight: 0.9990 chunk 174 optimal weight: 0.5980 chunk 184 optimal weight: 0.8980 chunk 91 optimal weight: 0.7980 chunk 165 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 E 62 ASN I 100 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 15833 Z= 0.206 Angle : 0.596 8.944 21524 Z= 0.306 Chirality : 0.043 0.195 2440 Planarity : 0.004 0.058 2748 Dihedral : 5.268 52.095 2272 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 3.63 % Allowed : 14.83 % Favored : 81.54 % 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: 0.64 (0.19), residues: 1912 helix: 1.02 (0.25), residues: 430 sheet: 0.25 (0.22), residues: 527 loop : 0.41 (0.21), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP J 70 HIS 0.008 0.001 HIS C 156 PHE 0.012 0.001 PHE A 349 TYR 0.015 0.001 TYR B 226 ARG 0.010 0.001 ARG B 139 *********************** 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 353 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 291 time to evaluate : 1.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 ARG cc_start: 0.6938 (ttp-110) cc_final: 0.6644 (mtm110) REVERT: A 380 MET cc_start: 0.9037 (mmm) cc_final: 0.8603 (mmm) REVERT: C 157 LYS cc_start: 0.8899 (mptt) cc_final: 0.8659 (mmtm) REVERT: C 158 ARG cc_start: 0.7648 (OUTLIER) cc_final: 0.7286 (tpt-90) REVERT: D 94 ARG cc_start: 0.8199 (OUTLIER) cc_final: 0.7206 (ptp90) REVERT: D 142 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7891 (pm20) REVERT: E 75 ASP cc_start: 0.7440 (OUTLIER) cc_final: 0.6994 (p0) REVERT: E 84 GLU cc_start: 0.8804 (mt-10) cc_final: 0.8524 (mt-10) REVERT: F 51 SER cc_start: 0.8936 (t) cc_final: 0.8693 (t) REVERT: F 102 GLN cc_start: 0.8062 (tt0) cc_final: 0.7706 (mt0) REVERT: G 31 ARG cc_start: 0.7371 (OUTLIER) cc_final: 0.7022 (tpm-80) REVERT: G 51 ASP cc_start: 0.8526 (OUTLIER) cc_final: 0.8159 (p0) REVERT: J 35 LYS cc_start: 0.8091 (OUTLIER) cc_final: 0.7881 (mtpp) REVERT: J 46 LYS cc_start: 0.8682 (OUTLIER) cc_final: 0.8477 (tptm) REVERT: K 27 MET cc_start: 0.8652 (mmm) cc_final: 0.8222 (mmt) outliers start: 62 outliers final: 25 residues processed: 317 average time/residue: 1.4588 time to fit residues: 517.0066 Evaluate side-chains 307 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 274 time to evaluate : 1.845 ------------------------------------------------------------------------------- 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 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 152 VAL 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 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 51 ASP Chi-restraints excluded: chain G residue 70 LYS Chi-restraints excluded: chain H residue 24 GLU Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain J residue 35 LYS Chi-restraints excluded: chain J residue 46 LYS 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 153 optimal weight: 6.9990 chunk 104 optimal weight: 0.8980 chunk 2 optimal weight: 0.0170 chunk 137 optimal weight: 4.9990 chunk 76 optimal weight: 0.9980 chunk 157 optimal weight: 0.9980 chunk 127 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 94 optimal weight: 1.9990 chunk 165 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 overall best weight: 0.7820 ------------------------------------------------------------------------------- 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** E 62 ASN I 100 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 15833 Z= 0.213 Angle : 0.595 9.025 21524 Z= 0.303 Chirality : 0.043 0.165 2440 Planarity : 0.004 0.056 2748 Dihedral : 5.093 52.092 2272 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.81 % Allowed : 15.94 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.67 (0.19), residues: 1912 helix: 1.09 (0.25), residues: 430 sheet: 0.33 (0.22), residues: 527 loop : 0.37 (0.20), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP J 70 HIS 0.008 0.001 HIS C 156 PHE 0.025 0.001 PHE D 74 TYR 0.016 0.001 TYR D 61 ARG 0.007 0.001 ARG B 139 *********************** 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 354 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 289 time to evaluate : 1.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 HIS cc_start: 0.7855 (OUTLIER) cc_final: 0.6972 (p-80) REVERT: A 380 MET cc_start: 0.8988 (mmm) cc_final: 0.8557 (mmm) REVERT: B 118 GLN cc_start: 0.8448 (tt0) cc_final: 0.7981 (tt0) REVERT: C 151 GLU cc_start: 0.7929 (tm-30) cc_final: 0.7717 (pp20) REVERT: C 157 LYS cc_start: 0.8806 (mptt) cc_final: 0.8553 (mmtm) REVERT: C 158 ARG cc_start: 0.7643 (OUTLIER) cc_final: 0.7317 (tpt-90) REVERT: C 163 ARG cc_start: 0.6608 (mmt90) cc_final: 0.6389 (mtt-85) REVERT: D 94 ARG cc_start: 0.8235 (OUTLIER) cc_final: 0.7319 (ptp90) REVERT: D 142 GLU cc_start: 0.8142 (pm20) cc_final: 0.7878 (pm20) REVERT: E 75 ASP cc_start: 0.7502 (OUTLIER) cc_final: 0.7070 (p0) REVERT: F 51 SER cc_start: 0.8943 (t) cc_final: 0.8693 (t) REVERT: F 102 GLN cc_start: 0.8128 (tt0) cc_final: 0.7752 (mt0) REVERT: G 51 ASP cc_start: 0.8547 (OUTLIER) cc_final: 0.8169 (p0) REVERT: J 46 LYS cc_start: 0.8677 (OUTLIER) cc_final: 0.8452 (tptm) REVERT: K 27 MET cc_start: 0.8662 (mmm) cc_final: 0.8243 (mmt) REVERT: K 109 TYR cc_start: 0.8032 (m-80) cc_final: 0.7825 (m-80) outliers start: 65 outliers final: 35 residues processed: 325 average time/residue: 1.2765 time to fit residues: 458.6484 Evaluate side-chains 310 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 269 time to evaluate : 1.764 ------------------------------------------------------------------------------- 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 281 VAL Chi-restraints excluded: chain A residue 506 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 99 LEU Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 177 GLU Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 75 ASP Chi-restraints excluded: chain E residue 123 SER Chi-restraints excluded: chain F residue 121 VAL Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 51 ASP Chi-restraints excluded: chain G residue 70 LYS Chi-restraints excluded: chain G residue 92 SER 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 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 65 LYS Chi-restraints excluded: chain K residue 75 SER Chi-restraints excluded: chain K residue 92 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 62 optimal weight: 0.9990 chunk 166 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 45 optimal weight: 0.6980 chunk 184 optimal weight: 0.7980 chunk 153 optimal weight: 5.9990 chunk 85 optimal weight: 5.9990 chunk 15 optimal weight: 0.3980 chunk 61 optimal weight: 5.9990 chunk 97 optimal weight: 4.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 ASN G 120 ASN I 100 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 15833 Z= 0.243 Angle : 0.601 8.682 21524 Z= 0.306 Chirality : 0.043 0.190 2440 Planarity : 0.004 0.055 2748 Dihedral : 5.070 51.492 2272 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 4.10 % Allowed : 16.30 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.34 (0.22), residues: 528 loop : 0.24 (0.20), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP J 70 HIS 0.007 0.001 HIS C 156 PHE 0.014 0.001 PHE A 349 TYR 0.018 0.001 TYR K 72 ARG 0.007 0.001 ARG K 47 *********************** 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 344 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 274 time to evaluate : 1.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 HIS cc_start: 0.7815 (OUTLIER) cc_final: 0.6927 (p-80) REVERT: A 380 MET cc_start: 0.9025 (mmm) cc_final: 0.8596 (mmm) REVERT: B 118 GLN cc_start: 0.8499 (tt0) cc_final: 0.8064 (tt0) REVERT: C 151 GLU cc_start: 0.7936 (tm-30) cc_final: 0.7733 (pp20) REVERT: C 157 LYS cc_start: 0.8747 (mptt) cc_final: 0.8515 (mmtm) REVERT: C 158 ARG cc_start: 0.7765 (OUTLIER) cc_final: 0.7430 (tpt-90) REVERT: D 94 ARG cc_start: 0.8208 (OUTLIER) cc_final: 0.7532 (ptp90) REVERT: D 142 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7846 (pm20) REVERT: E 75 ASP cc_start: 0.7484 (p0) cc_final: 0.7035 (p0) REVERT: F 51 SER cc_start: 0.8930 (t) cc_final: 0.8684 (t) REVERT: F 52 LEU cc_start: 0.9156 (OUTLIER) cc_final: 0.8907 (mt) REVERT: F 102 GLN cc_start: 0.8158 (tt0) cc_final: 0.7764 (mt0) REVERT: J 35 LYS cc_start: 0.8145 (OUTLIER) cc_final: 0.7930 (mtpp) REVERT: J 46 LYS cc_start: 0.8672 (OUTLIER) cc_final: 0.8445 (tptm) outliers start: 70 outliers final: 38 residues processed: 313 average time/residue: 1.3349 time to fit residues: 459.9690 Evaluate side-chains 313 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 268 time to evaluate : 1.779 ------------------------------------------------------------------------------- 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 222 LEU Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 451 HIS Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 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 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 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 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 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 76 SER Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 35 LYS Chi-restraints excluded: chain J residue 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 178 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 105 optimal weight: 1.9990 chunk 134 optimal weight: 1.9990 chunk 104 optimal weight: 0.5980 chunk 155 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 184 optimal weight: 0.6980 chunk 115 optimal weight: 0.9990 chunk 112 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 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 ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 ASN I 100 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 15833 Z= 0.256 Angle : 0.633 13.576 21524 Z= 0.322 Chirality : 0.044 0.300 2440 Planarity : 0.004 0.055 2748 Dihedral : 5.031 51.361 2272 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.75 % Allowed : 17.29 % 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: 0.56 (0.19), residues: 1912 helix: 1.03 (0.25), residues: 435 sheet: 0.37 (0.23), residues: 522 loop : 0.20 (0.20), residues: 955 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 0.026 0.002 PHE D 74 TYR 0.018 0.002 TYR K 72 ARG 0.008 0.001 ARG K 47 *********************** 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 334 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 270 time to evaluate : 1.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 HIS cc_start: 0.7833 (OUTLIER) cc_final: 0.6894 (p-80) REVERT: A 380 MET cc_start: 0.9026 (mmm) cc_final: 0.8601 (mmm) REVERT: B 118 GLN cc_start: 0.8490 (tt0) cc_final: 0.8075 (tt0) REVERT: C 157 LYS cc_start: 0.8693 (mptt) cc_final: 0.8487 (mmtm) REVERT: C 158 ARG cc_start: 0.7764 (OUTLIER) cc_final: 0.7426 (tpt-90) REVERT: D 94 ARG cc_start: 0.8313 (OUTLIER) cc_final: 0.7382 (ptp90) REVERT: E 75 ASP cc_start: 0.7447 (p0) cc_final: 0.7014 (p0) REVERT: F 51 SER cc_start: 0.8936 (t) cc_final: 0.8690 (t) REVERT: F 52 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8919 (mt) REVERT: F 102 GLN cc_start: 0.8139 (tt0) cc_final: 0.7718 (mt0) REVERT: J 35 LYS cc_start: 0.8135 (OUTLIER) cc_final: 0.7908 (mtpp) REVERT: J 46 LYS cc_start: 0.8672 (OUTLIER) cc_final: 0.8443 (tptm) outliers start: 64 outliers final: 42 residues processed: 305 average time/residue: 1.4446 time to fit residues: 493.2307 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 : 1.646 ------------------------------------------------------------------------------- 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 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 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 88 LEU Chi-restraints excluded: chain D residue 94 ARG Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 177 GLU Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 42 ARG Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 123 SER Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 99 SER 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 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 76 SER Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 35 LYS Chi-restraints excluded: chain J residue 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 113 optimal weight: 0.0980 chunk 73 optimal weight: 5.9990 chunk 109 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 35 optimal weight: 0.0970 chunk 117 optimal weight: 0.6980 chunk 125 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 144 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 70 GLN E 62 ASN J 54 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15833 Z= 0.218 Angle : 0.625 12.610 21524 Z= 0.316 Chirality : 0.043 0.269 2440 Planarity : 0.004 0.054 2748 Dihedral : 4.979 52.003 2272 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.52 % Allowed : 18.05 % 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: 0.52 (0.19), residues: 1912 helix: 0.96 (0.25), residues: 441 sheet: 0.43 (0.23), residues: 519 loop : 0.14 (0.20), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP J 70 HIS 0.007 0.001 HIS C 156 PHE 0.013 0.001 PHE A 349 TYR 0.018 0.001 TYR G 74 ARG 0.009 0.001 ARG F 28 *********************** 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 327 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 267 time to evaluate : 1.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 GLN cc_start: 0.7489 (mm110) cc_final: 0.7263 (mp10) REVERT: A 165 HIS cc_start: 0.7844 (OUTLIER) cc_final: 0.6891 (p-80) REVERT: B 118 GLN cc_start: 0.8523 (OUTLIER) cc_final: 0.8153 (tt0) REVERT: B 135 MET cc_start: 0.8215 (mmt) cc_final: 0.7979 (mtp) REVERT: C 157 LYS cc_start: 0.8666 (mptt) cc_final: 0.8427 (mmtm) REVERT: C 158 ARG cc_start: 0.7789 (OUTLIER) cc_final: 0.7466 (tpt-90) REVERT: D 94 ARG cc_start: 0.8187 (OUTLIER) cc_final: 0.7564 (ptp90) REVERT: D 174 MET cc_start: 0.8727 (ttm) cc_final: 0.8514 (ttp) REVERT: E 75 ASP cc_start: 0.7450 (OUTLIER) cc_final: 0.7014 (p0) REVERT: F 51 SER cc_start: 0.8923 (t) cc_final: 0.8680 (t) REVERT: F 52 LEU cc_start: 0.9162 (OUTLIER) cc_final: 0.8916 (mt) REVERT: F 102 GLN cc_start: 0.8167 (tt0) cc_final: 0.7754 (mt0) REVERT: J 35 LYS cc_start: 0.8072 (OUTLIER) cc_final: 0.7844 (mtpp) REVERT: J 46 LYS cc_start: 0.8688 (OUTLIER) cc_final: 0.8449 (tptm) outliers start: 60 outliers final: 42 residues processed: 299 average time/residue: 1.3278 time to fit residues: 438.1836 Evaluate side-chains 305 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 255 time to evaluate : 1.797 ------------------------------------------------------------------------------- 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 222 LEU 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 660 THR Chi-restraints excluded: chain B residue 118 GLN 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 92 LYS Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 136 GLU Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 158 ARG Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 94 ARG Chi-restraints excluded: chain D residue 121 ILE 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 75 ASP Chi-restraints excluded: chain E residue 123 SER Chi-restraints excluded: chain F residue 52 LEU 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 G residue 92 SER 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 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 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 167 optimal weight: 0.0870 chunk 176 optimal weight: 0.9980 chunk 160 optimal weight: 0.8980 chunk 171 optimal weight: 0.9990 chunk 103 optimal weight: 0.0020 chunk 74 optimal weight: 3.9990 chunk 134 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 155 optimal weight: 1.9990 chunk 162 optimal weight: 0.6980 chunk 170 optimal weight: 4.9990 overall best weight: 0.5366 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 118 GLN B 177 HIS E 62 ASN E 73 ASN I 100 ASN J 54 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.2919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 15833 Z= 0.203 Angle : 0.641 12.906 21524 Z= 0.323 Chirality : 0.044 0.315 2440 Planarity : 0.004 0.053 2748 Dihedral : 4.924 52.432 2272 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 3.52 % Allowed : 18.41 % Favored : 78.08 % 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: 0.53 (0.19), residues: 1912 helix: 0.97 (0.25), residues: 441 sheet: 0.45 (0.23), residues: 519 loop : 0.12 (0.21), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP J 70 HIS 0.006 0.001 HIS C 156 PHE 0.028 0.001 PHE D 74 TYR 0.018 0.001 TYR G 74 ARG 0.014 0.001 ARG A 117 *********************** 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 326 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 266 time to evaluate : 1.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 HIS cc_start: 0.7838 (OUTLIER) cc_final: 0.6880 (p-80) REVERT: A 448 LEU cc_start: 0.8692 (mm) cc_final: 0.8482 (tm) REVERT: B 135 MET cc_start: 0.8183 (mmt) cc_final: 0.7938 (mtp) REVERT: C 158 ARG cc_start: 0.7767 (OUTLIER) cc_final: 0.7466 (tpt-90) REVERT: D 94 ARG cc_start: 0.8335 (OUTLIER) cc_final: 0.7334 (ptp90) REVERT: D 174 MET cc_start: 0.8739 (ttm) cc_final: 0.8521 (ttp) REVERT: E 75 ASP cc_start: 0.7402 (OUTLIER) cc_final: 0.6532 (p0) REVERT: F 51 SER cc_start: 0.8906 (t) cc_final: 0.8663 (t) REVERT: F 52 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8936 (mt) REVERT: F 102 GLN cc_start: 0.8117 (OUTLIER) cc_final: 0.7723 (mt0) REVERT: J 35 LYS cc_start: 0.7985 (OUTLIER) cc_final: 0.7763 (mtpp) REVERT: J 46 LYS cc_start: 0.8676 (OUTLIER) cc_final: 0.8451 (tptm) REVERT: J 54 ASN cc_start: 0.8392 (OUTLIER) cc_final: 0.7882 (t0) outliers start: 60 outliers final: 39 residues processed: 298 average time/residue: 1.3039 time to fit residues: 429.5634 Evaluate side-chains 310 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 262 time to evaluate : 1.819 ------------------------------------------------------------------------------- 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 222 LEU 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 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 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 75 ASP Chi-restraints excluded: chain E residue 123 SER Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain F residue 102 GLN 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 G residue 92 SER 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 112 optimal weight: 0.7980 chunk 181 optimal weight: 3.9990 chunk 110 optimal weight: 0.6980 chunk 86 optimal weight: 2.9990 chunk 126 optimal weight: 3.9990 chunk 190 optimal weight: 0.5980 chunk 175 optimal weight: 0.9980 chunk 151 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 117 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 ASN E 95 GLN I 100 ASN J 54 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 15833 Z= 0.254 Angle : 0.648 11.737 21524 Z= 0.327 Chirality : 0.044 0.248 2440 Planarity : 0.004 0.053 2748 Dihedral : 4.958 51.733 2272 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.11 % Allowed : 19.28 % Favored : 77.61 % 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: 1.00 (0.25), residues: 436 sheet: 0.45 (0.23), residues: 517 loop : 0.07 (0.20), residues: 959 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 70 HIS 0.004 0.001 HIS A 693 PHE 0.014 0.002 PHE A 349 TYR 0.018 0.001 TYR G 74 ARG 0.015 0.001 ARG A 117 ********************** 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 321 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 268 time to evaluate : 1.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 HIS cc_start: 0.7856 (OUTLIER) cc_final: 0.6893 (p-80) REVERT: B 135 MET cc_start: 0.8182 (mmt) cc_final: 0.7945 (mtp) REVERT: C 158 ARG cc_start: 0.7772 (OUTLIER) cc_final: 0.7465 (tpt-90) REVERT: D 94 ARG cc_start: 0.8132 (OUTLIER) cc_final: 0.7494 (ptp90) REVERT: D 174 MET cc_start: 0.8762 (ttm) cc_final: 0.8543 (ttp) REVERT: E 73 ASN cc_start: 0.8242 (t0) cc_final: 0.7850 (t0) REVERT: F 51 SER cc_start: 0.8929 (t) cc_final: 0.8688 (t) REVERT: F 52 LEU cc_start: 0.9172 (OUTLIER) cc_final: 0.8912 (mt) REVERT: F 102 GLN cc_start: 0.8122 (OUTLIER) cc_final: 0.7697 (mt0) REVERT: J 35 LYS cc_start: 0.8122 (OUTLIER) cc_final: 0.7866 (mtpp) REVERT: J 46 LYS cc_start: 0.8699 (OUTLIER) cc_final: 0.8462 (tptm) REVERT: J 54 ASN cc_start: 0.8438 (OUTLIER) cc_final: 0.7972 (t0) outliers start: 53 outliers final: 38 residues processed: 297 average time/residue: 1.3888 time to fit residues: 455.7661 Evaluate side-chains 307 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 261 time to evaluate : 2.012 ------------------------------------------------------------------------------- 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 596 LEU Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain C residue 69 LYS Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain C residue 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 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 102 GLN 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 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 76 SER Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 35 LYS Chi-restraints excluded: chain J residue 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 120 optimal weight: 1.9990 chunk 161 optimal weight: 0.0770 chunk 46 optimal weight: 0.7980 chunk 139 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 151 optimal weight: 1.9990 chunk 63 optimal weight: 5.9990 chunk 155 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 overall best weight: 0.9540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 315 ASN ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 ASN E 95 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 = 0.3579 r_free = 0.3579 target = 0.118249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.095299 restraints weight = 29827.575| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 2.22 r_work: 0.3088 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2973 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2973 r_free = 0.2973 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.97 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2973 r_free = 0.2973 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2973 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 15833 Z= 0.245 Angle : 0.656 10.968 21524 Z= 0.331 Chirality : 0.044 0.236 2440 Planarity : 0.004 0.054 2748 Dihedral : 4.953 51.668 2272 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.11 % Allowed : 19.58 % Favored : 77.32 % 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: 0.48 (0.19), residues: 1912 helix: 0.99 (0.25), residues: 436 sheet: 0.45 (0.23), residues: 517 loop : 0.05 (0.20), residues: 959 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 0.028 0.002 PHE D 74 TYR 0.021 0.002 TYR J 55 ARG 0.015 0.001 ARG A 117 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7256.41 seconds wall clock time: 130 minutes 49.83 seconds (7849.83 seconds total)