Starting phenix.real_space_refine on Fri Feb 16 13:58:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t4q_25685/02_2024/7t4q_25685.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t4q_25685/02_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t4q_25685/02_2024/7t4q_25685.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t4q_25685/02_2024/7t4q_25685.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t4q_25685/02_2024/7t4q_25685.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t4q_25685/02_2024/7t4q_25685.pdb" } 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 Symmetric amino acids flipped None Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 8.14, per 1000 atoms: 0.53 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 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: 5.75 Conformation dependent library (CDL) restraints added in 2.8 seconds 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3656 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 28 sheets defined 29.0% alpha, 27.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.85 Creating SS restraints... Processing helix chain 'A' and resid 94 through 98 Processing helix chain 'A' and resid 99 through 107 removed outlier: 3.511A pdb=" N GLU A 103 " --> pdb=" O GLY A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 123 Processing helix chain 'A' and resid 263 through 266 Processing helix chain 'A' and resid 283 through 287 removed outlier: 4.364A pdb=" N ASN A 287 " --> pdb=" O LYS A 283 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 283 through 287' Processing helix chain 'A' and resid 289 through 294 Processing helix chain 'A' and resid 298 through 303 Processing helix chain 'A' and resid 308 through 316 Processing helix chain 'A' and resid 316 through 328 Processing helix chain 'A' and resid 334 through 353 Processing helix chain 'A' and resid 354 through 359 Processing helix chain 'A' and resid 362 through 385 Processing helix chain 'A' and resid 396 through 409 Processing helix chain 'A' and resid 415 through 429 removed outlier: 3.547A pdb=" N LEU A 419 " --> pdb=" O ASP A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 435 Processing helix chain 'A' and resid 436 through 454 removed outlier: 3.816A pdb=" N LEU A 440 " --> pdb=" O PRO A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 475 removed outlier: 4.056A pdb=" N HIS A 475 " --> pdb=" O GLY A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 495 removed outlier: 3.668A pdb=" N CYS A 495 " --> pdb=" O GLU A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 506 Processing helix chain 'A' and resid 514 through 519 Processing helix chain 'A' and resid 520 through 524 Processing helix chain 'A' and resid 531 through 537 Processing helix chain 'A' and resid 547 through 559 Processing helix chain 'A' and resid 671 through 680 Processing helix chain 'A' and resid 681 through 684 Processing helix chain 'B' and resid 46 through 56 Processing helix chain 'B' and resid 66 through 70 Processing helix chain 'B' and resid 85 through 87 No H-bonds generated for 'chain 'B' and resid 85 through 87' Processing helix chain 'B' and resid 95 through 99 Processing helix chain 'B' and resid 102 through 113 Processing helix chain 'B' and resid 117 through 128 Processing helix chain 'B' and resid 130 through 145 removed outlier: 3.916A pdb=" N TRP B 134 " --> pdb=" O THR B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 217 No H-bonds generated for 'chain 'B' and resid 215 through 217' Processing helix chain 'B' and resid 218 through 236 removed outlier: 3.656A pdb=" N PHE B 222 " --> pdb=" O GLY B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 253 removed outlier: 4.080A pdb=" N ARG B 244 " --> pdb=" O PRO B 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 82 removed outlier: 4.345A pdb=" N GLY C 75 " --> pdb=" O ALA C 71 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N MET C 80 " --> pdb=" O ILE C 76 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N HIS C 82 " --> pdb=" O THR C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 93 Processing helix chain 'C' and resid 94 through 97 Processing helix chain 'C' and resid 117 through 119 No H-bonds generated for 'chain 'C' and resid 117 through 119' Processing helix chain 'C' and resid 145 through 156 Processing helix chain 'D' and resid 53 through 57 removed outlier: 4.007A pdb=" N TYR D 56 " --> pdb=" O ALA D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 69 No H-bonds generated for 'chain 'D' and resid 67 through 69' Processing helix chain 'D' and resid 80 through 84 Processing helix chain 'D' and resid 104 through 118 removed outlier: 4.189A pdb=" N ASN D 118 " --> pdb=" O LEU D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 130 removed outlier: 3.697A pdb=" N GLN D 123 " --> pdb=" O GLN D 119 " (cutoff:3.500A) Proline residue: D 126 - end of helix Processing helix chain 'D' and resid 140 through 151 Processing helix chain 'E' and resid 21 through 26 removed outlier: 3.842A pdb=" N GLU E 26 " --> pdb=" O ARG E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 35 through 41 Processing helix chain 'E' and resid 45 through 69 Processing helix chain 'E' and resid 76 through 80 Processing helix chain 'E' and resid 81 through 95 Processing helix chain 'F' and resid 98 through 100 No H-bonds generated for 'chain 'F' and resid 98 through 100' Processing helix chain 'F' and resid 111 through 115 Processing helix chain 'G' and resid 104 through 108 Processing helix chain 'H' and resid 53 through 55 No H-bonds generated for 'chain 'H' and resid 53 through 55' Processing helix chain 'H' and resid 103 through 107 removed outlier: 3.712A pdb=" N PHE H 107 " --> pdb=" O PRO H 104 " (cutoff:3.500A) Processing helix chain 'I' and resid 51 through 55 Processing helix chain 'I' and resid 110 through 114 Processing helix chain 'I' and resid 125 through 131 removed outlier: 3.582A pdb=" N TRP I 128 " --> pdb=" O TYR I 125 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE I 129 " --> pdb=" O LEU I 126 " (cutoff:3.500A) Processing helix chain 'J' and resid 51 through 55 removed outlier: 3.508A pdb=" N TYR J 55 " --> pdb=" O PHE J 52 " (cutoff:3.500A) Processing helix chain 'J' and resid 85 through 88 Processing helix chain 'J' and resid 110 through 114 Processing helix chain 'K' and resid 102 through 106 removed outlier: 3.744A pdb=" N VAL K 106 " --> pdb=" O PRO K 103 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 49 through 52 Processing sheet with id=AA2, first strand: chain 'A' and resid 89 through 92 removed outlier: 6.033A pdb=" N SER A 77 " --> pdb=" O PHE B 181 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N LEU B 183 " --> pdb=" O SER A 77 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N ASN A 79 " --> pdb=" O LEU B 183 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N VAL B 178 " --> pdb=" O ALA B 194 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ALA B 194 " --> pdb=" O VAL B 178 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N PHE B 189 " --> pdb=" O VAL B 210 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 125 through 126 removed outlier: 4.847A pdb=" N VAL A 281 " --> pdb=" O ALA A 126 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG A 270 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N VAL A 279 " --> pdb=" O ILE A 268 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N ILE A 268 " --> pdb=" O VAL A 279 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ARG A 136 " --> pdb=" O LEU A 269 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 125 through 126 removed outlier: 4.847A pdb=" N VAL A 281 " --> pdb=" O ALA A 126 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 194 through 197 Processing sheet with id=AA6, first strand: chain 'A' and resid 527 through 528 removed outlier: 3.831A pdb=" N PHE A 578 " --> pdb=" O ARG A 528 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 663 through 666 Processing sheet with id=AA8, first strand: chain 'B' and resid 82 through 83 removed outlier: 5.996A pdb=" N LEU B 82 " --> pdb=" O GLY B 170 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 150 through 155 removed outlier: 5.523A pdb=" N GLY B 161 " --> pdb=" O VAL D 100 " (cutoff:3.500A) removed outlier: 8.380A pdb=" N ARG D 102 " --> pdb=" O GLY B 161 " (cutoff:3.500A) removed outlier: 11.567A pdb=" N ASP B 163 " --> pdb=" O ARG D 102 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N LEU D 88 " --> pdb=" O ARG D 76 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N ARG D 76 " --> pdb=" O LEU D 88 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N LEU D 90 " --> pdb=" O PHE D 74 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N PHE D 74 " --> pdb=" O LEU D 90 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N TYR D 92 " --> pdb=" O SER D 72 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 45 through 50 removed outlier: 6.771A pdb=" N THR C 53 " --> pdb=" O CYS C 49 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 109 through 111 Processing sheet with id=AB3, first strand: chain 'C' and resid 130 through 132 removed outlier: 4.577A pdb=" N THR E 106 " --> pdb=" O ARG E 125 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 26 through 29 Processing sheet with id=AB5, first strand: chain 'F' and resid 33 through 35 removed outlier: 3.502A pdb=" N ALA F 74 " --> pdb=" O TRP F 61 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ARG F 63 " --> pdb=" O TRP F 72 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N TRP F 72 " --> pdb=" O ARG F 63 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 33 through 35 Processing sheet with id=AB7, first strand: chain 'G' and resid 32 through 35 removed outlier: 6.682A pdb=" N VAL G 33 " --> pdb=" O THR G 133 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N VAL G 58 " --> pdb=" O TYR G 74 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N TYR G 74 " --> pdb=" O VAL G 58 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N TRP G 60 " --> pdb=" O LEU G 72 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 32 through 35 removed outlier: 6.682A pdb=" N VAL G 33 " --> pdb=" O THR G 133 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 41 through 46 Processing sheet with id=AC1, first strand: chain 'H' and resid 27 through 30 Processing sheet with id=AC2, first strand: chain 'H' and resid 33 through 36 removed outlier: 6.342A pdb=" N LEU H 34 " --> pdb=" O GLU H 128 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N LEU H 57 " --> pdb=" O TYR H 73 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N TYR H 73 " --> pdb=" O LEU H 57 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N TRP H 59 " --> pdb=" O LEU H 71 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 26 through 30 Processing sheet with id=AC4, first strand: chain 'I' and resid 33 through 35 removed outlier: 6.739A pdb=" N MET I 57 " --> pdb=" O VAL I 73 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N VAL I 73 " --> pdb=" O MET I 57 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N TRP I 59 " --> pdb=" O VAL I 71 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 33 through 35 removed outlier: 3.726A pdb=" N TYR I 136 " --> pdb=" O LYS I 121 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'J' and resid 26 through 29 Processing sheet with id=AC7, first strand: chain 'J' and resid 33 through 35 removed outlier: 6.774A pdb=" N ILE J 57 " --> pdb=" O ILE J 73 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ILE J 73 " --> pdb=" O ILE J 57 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N TRP J 59 " --> pdb=" O MET J 71 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 33 through 35 removed outlier: 3.870A pdb=" N ASP J 135 " --> pdb=" O ARG J 121 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'K' and resid 27 through 30 removed outlier: 5.806A pdb=" N THR K 92 " --> pdb=" O ALA K 48 " (cutoff:3.500A) removed outlier: 10.223A pdb=" N GLN K 50 " --> pdb=" O SER K 90 " (cutoff:3.500A) removed outlier: 10.410A pdb=" N SER K 90 " --> pdb=" O GLN K 50 " (cutoff:3.500A) removed outlier: 11.599A pdb=" N ILE K 52 " --> pdb=" O SER K 88 " (cutoff:3.500A) removed outlier: 11.675A pdb=" N SER K 88 " --> pdb=" O ILE K 52 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'K' and resid 33 through 34 removed outlier: 6.535A pdb=" N TRP K 58 " --> pdb=" O LEU K 70 " (cutoff:3.500A) 676 hydrogen bonds defined for protein. 1728 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.72 Time building geometry restraints manager: 6.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5005 1.34 - 1.46: 3898 1.46 - 1.59: 6826 1.59 - 1.71: 0 1.71 - 1.83: 104 Bond restraints: 15833 Sorted by residual: bond pdb=" N ASN A 55 " pdb=" CA ASN A 55 " ideal model delta sigma weight residual 1.456 1.484 -0.028 1.31e-02 5.83e+03 4.45e+00 bond pdb=" N GLU A 54 " pdb=" CA GLU A 54 " ideal model delta sigma weight residual 1.457 1.483 -0.026 1.31e-02 5.83e+03 4.09e+00 bond pdb=" C1 NAG B 301 " pdb=" O5 NAG B 301 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 4.07e+00 bond pdb=" C1 NAG A 801 " pdb=" O5 NAG A 801 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.33e+00 bond pdb=" C1 NAG A 803 " pdb=" O5 NAG A 803 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.75e+00 ... (remaining 15828 not shown) Histogram of bond angle deviations from ideal: 98.61 - 105.70: 377 105.70 - 112.79: 8388 112.79 - 119.87: 5241 119.87 - 126.96: 7309 126.96 - 134.04: 209 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 2.520 nonbonded pdb=" ND2 ASN C 97 " pdb=" O ARG E 32 " model vdw 2.243 2.520 nonbonded pdb=" ND1 HIS A 275 " pdb=" OH TYR A 306 " model vdw 2.244 2.520 nonbonded pdb=" NH2 ARG A 365 " pdb=" OD2 ASP A 368 " model vdw 2.259 2.520 nonbonded pdb=" N LEU I 123 " pdb=" OD2 ASP I 132 " model vdw 2.262 2.520 ... (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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.97 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.750 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: 8.160 Check model and map are aligned: 0.260 Set scattering table: 0.160 Process input model: 42.640 Find NCS groups from input model: 0.500 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:14.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.170 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 372 time to evaluate : 1.834 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: 1.3158 time to fit residues: 538.2960 Evaluate side-chains 276 residues out of total 1706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 276 time to evaluate : 1.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 161 optimal weight: 1.9990 chunk 144 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.3980 chunk 77 optimal weight: 2.9990 chunk 149 optimal weight: 5.9990 chunk 57 optimal weight: 0.2980 chunk 91 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 173 optimal weight: 0.8980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 HIS A 271 GLN A 370 GLN ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 75 GLN D 123 GLN F 109 ASN ** G 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 62 GLN J 29 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.1519 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= 0.276 Angle : 0.665 9.804 21524 Z= 0.346 Chirality : 0.046 0.185 2440 Planarity : 0.005 0.053 2748 Dihedral : 5.852 52.343 2272 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.52 % Allowed : 10.61 % Favored : 86.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.22 (0.19), residues: 1912 helix: 0.44 (0.24), residues: 421 sheet: 0.19 (0.22), residues: 508 loop : 0.14 (0.20), residues: 983 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP J 70 HIS 0.008 0.001 HIS A 451 PHE 0.018 0.002 PHE D 206 TYR 0.016 0.002 TYR C 149 ARG 0.007 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 fitting. rotamer outliers: 43 poor density : 307 time to evaluate : 1.668 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 470 MET cc_start: 0.8826 (OUTLIER) cc_final: 0.8623 (mtm) REVERT: A 529 ASP cc_start: 0.7533 (p0) cc_final: 0.7298 (p0) REVERT: C 157 LYS cc_start: 0.8984 (mptt) cc_final: 0.8731 (mmtm) REVERT: D 94 ARG cc_start: 0.8150 (OUTLIER) cc_final: 0.7141 (ptp90) REVERT: D 101 GLU cc_start: 0.7883 (mm-30) cc_final: 0.7509 (mp0) REVERT: D 157 LYS cc_start: 0.8950 (OUTLIER) cc_final: 0.8489 (tmtm) REVERT: E 84 GLU cc_start: 0.8683 (mt-10) cc_final: 0.8479 (mt-10) REVERT: F 51 SER cc_start: 0.8902 (t) cc_final: 0.8634 (t) REVERT: F 100 LYS cc_start: 0.8952 (OUTLIER) cc_final: 0.8742 (mtmt) REVERT: G 31 ARG cc_start: 0.7287 (OUTLIER) cc_final: 0.6941 (tpm-80) REVERT: H 41 ARG cc_start: 0.8356 (ttt90) cc_final: 0.8094 (ttm170) REVERT: K 27 MET cc_start: 0.8642 (mmm) cc_final: 0.8179 (mmt) outliers start: 43 outliers final: 15 residues processed: 321 average time/residue: 1.2663 time to fit residues: 448.5815 Evaluate side-chains 293 residues out of total 1706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 273 time to evaluate : 1.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 470 MET Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 556 SER Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain B residue 148 SER Chi-restraints excluded: chain C residue 136 GLU Chi-restraints excluded: chain D residue 94 ARG Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 157 LYS 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 H residue 80 THR Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain K residue 24 ASP 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: 0.8980 chunk 53 optimal weight: 0.9990 chunk 144 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 chunk 173 optimal weight: 0.8980 chunk 187 optimal weight: 6.9990 chunk 154 optimal weight: 4.9990 chunk 172 optimal weight: 0.6980 chunk 59 optimal weight: 3.9990 chunk 139 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 GLN A 165 HIS ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 177 HIS D 123 GLN E 62 ASN F 109 ASN ** G 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 100 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 15833 Z= 0.263 Angle : 0.621 9.546 21524 Z= 0.320 Chirality : 0.045 0.231 2440 Planarity : 0.004 0.058 2748 Dihedral : 5.544 51.595 2272 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.93 % Allowed : 13.66 % Favored : 83.41 % 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: 0.38 (0.19), residues: 1912 helix: 0.77 (0.25), residues: 429 sheet: 0.13 (0.22), residues: 517 loop : 0.24 (0.20), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 70 HIS 0.009 0.001 HIS C 156 PHE 0.024 0.002 PHE D 74 TYR 0.015 0.002 TYR D 61 ARG 0.008 0.001 ARG A 117 *********************** 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 340 residues out of total 1706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 290 time to evaluate : 1.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 529 ASP cc_start: 0.7503 (p0) cc_final: 0.7289 (p0) REVERT: C 57 ARG cc_start: 0.8220 (ttp80) cc_final: 0.8019 (ttp80) REVERT: C 151 GLU cc_start: 0.7936 (tm-30) cc_final: 0.7719 (pp20) REVERT: C 157 LYS cc_start: 0.8946 (mptt) cc_final: 0.8705 (mmtm) REVERT: D 94 ARG cc_start: 0.8102 (OUTLIER) cc_final: 0.7143 (ptp90) REVERT: E 26 GLU cc_start: 0.8221 (mt-10) cc_final: 0.8021 (mt-10) REVERT: E 121 GLU cc_start: 0.7994 (mt-10) cc_final: 0.7728 (mt-10) REVERT: F 51 SER cc_start: 0.8991 (t) cc_final: 0.8733 (t) REVERT: F 100 LYS cc_start: 0.8976 (OUTLIER) cc_final: 0.8728 (mtmt) REVERT: G 31 ARG cc_start: 0.7329 (OUTLIER) cc_final: 0.6964 (tpm-80) REVERT: H 41 ARG cc_start: 0.8370 (ttt90) cc_final: 0.8136 (ttm170) REVERT: K 27 MET cc_start: 0.8688 (mmm) cc_final: 0.8114 (mmt) outliers start: 50 outliers final: 30 residues processed: 310 average time/residue: 1.2919 time to fit residues: 440.2407 Evaluate side-chains 308 residues out of total 1706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 275 time to evaluate : 1.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 556 SER 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 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 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 H residue 24 GLU Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 76 SER Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain H residue 105 GLU Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain K residue 24 ASP Chi-restraints excluded: chain K residue 38 VAL 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: 0.6980 chunk 130 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 82 optimal weight: 0.9990 chunk 116 optimal weight: 2.9990 chunk 174 optimal weight: 0.8980 chunk 184 optimal weight: 0.0870 chunk 91 optimal weight: 0.9980 chunk 165 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 HIS B 118 GLN D 123 GLN E 62 ASN ** G 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 100 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 15833 Z= 0.198 Angle : 0.583 9.229 21524 Z= 0.299 Chirality : 0.043 0.189 2440 Planarity : 0.004 0.057 2748 Dihedral : 5.310 52.102 2272 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.87 % Allowed : 14.24 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.19), residues: 1912 helix: 1.00 (0.25), residues: 435 sheet: 0.23 (0.22), residues: 528 loop : 0.24 (0.20), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 134 HIS 0.009 0.001 HIS C 156 PHE 0.013 0.001 PHE A 349 TYR 0.015 0.001 TYR B 226 ARG 0.009 0.000 ARG A 117 *********************** 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 366 residues out of total 1706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 300 time to evaluate : 2.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 157 LYS cc_start: 0.8925 (mptt) cc_final: 0.8702 (mmtm) REVERT: D 94 ARG cc_start: 0.8102 (OUTLIER) cc_final: 0.7150 (ptp90) REVERT: E 84 GLU cc_start: 0.8746 (mt-10) cc_final: 0.8539 (mt-10) REVERT: E 121 GLU cc_start: 0.7960 (mt-10) cc_final: 0.7695 (mt-10) REVERT: F 51 SER cc_start: 0.8964 (t) cc_final: 0.8714 (t) REVERT: F 100 LYS cc_start: 0.8990 (OUTLIER) cc_final: 0.8720 (mtmt) REVERT: F 102 GLN cc_start: 0.8011 (OUTLIER) cc_final: 0.7122 (tp-100) REVERT: G 31 ARG cc_start: 0.7339 (OUTLIER) cc_final: 0.6980 (tpm-80) REVERT: H 41 ARG cc_start: 0.8364 (ttt90) cc_final: 0.8124 (ttm170) REVERT: H 47 ARG cc_start: 0.7609 (ttm-80) cc_final: 0.7357 (mtt180) REVERT: I 39 ARG cc_start: 0.7689 (mmm-85) cc_final: 0.7459 (mmt90) REVERT: J 35 LYS cc_start: 0.8093 (OUTLIER) cc_final: 0.7887 (mtpp) REVERT: J 46 LYS cc_start: 0.8686 (OUTLIER) cc_final: 0.8479 (tptm) REVERT: K 27 MET cc_start: 0.8612 (mmm) cc_final: 0.8192 (mmt) outliers start: 66 outliers final: 28 residues processed: 324 average time/residue: 1.3759 time to fit residues: 491.7540 Evaluate side-chains 314 residues out of total 1706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 280 time to evaluate : 1.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 50 ARG Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain B residue 148 SER 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 136 GLU Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain D residue 94 ARG Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain 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 102 GLN Chi-restraints excluded: chain F residue 121 VAL Chi-restraints excluded: chain G residue 31 ARG Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 70 LYS Chi-restraints excluded: chain G residue 92 SER Chi-restraints excluded: chain H residue 24 GLU Chi-restraints excluded: chain H residue 76 SER Chi-restraints excluded: chain H residue 125 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: 4.9990 chunk 104 optimal weight: 0.9990 chunk 2 optimal weight: 0.0070 chunk 137 optimal weight: 0.8980 chunk 76 optimal weight: 3.9990 chunk 157 optimal weight: 0.4980 chunk 127 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 94 optimal weight: 0.9990 chunk 165 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 overall best weight: 0.6802 ------------------------------------------------------------------------------- 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 ** G 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 100 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.2428 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= 0.193 Angle : 0.578 9.227 21524 Z= 0.292 Chirality : 0.042 0.178 2440 Planarity : 0.004 0.056 2748 Dihedral : 5.094 52.411 2272 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.93 % Allowed : 15.36 % Favored : 80.72 % 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: 0.59 (0.19), residues: 1912 helix: 1.11 (0.25), residues: 435 sheet: 0.23 (0.21), residues: 545 loop : 0.30 (0.21), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 60 HIS 0.008 0.001 HIS C 156 PHE 0.026 0.001 PHE D 74 TYR 0.016 0.001 TYR D 61 ARG 0.010 0.000 ARG K 47 *********************** 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 362 residues out of total 1706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 295 time to evaluate : 1.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 118 GLN cc_start: 0.8497 (OUTLIER) cc_final: 0.8028 (tt0) REVERT: B 148 SER cc_start: 0.8266 (OUTLIER) cc_final: 0.8049 (p) REVERT: C 151 GLU cc_start: 0.7985 (tm-30) cc_final: 0.7767 (pp20) REVERT: C 157 LYS cc_start: 0.8816 (mptt) cc_final: 0.8599 (mmtm) REVERT: C 163 ARG cc_start: 0.6535 (mmt90) cc_final: 0.6306 (mtt-85) REVERT: D 94 ARG cc_start: 0.8055 (OUTLIER) cc_final: 0.7130 (ptp90) REVERT: E 84 GLU cc_start: 0.8811 (mt-10) cc_final: 0.8525 (mt-10) REVERT: E 121 GLU cc_start: 0.7981 (mt-10) cc_final: 0.7704 (mt-10) REVERT: F 51 SER cc_start: 0.8929 (t) cc_final: 0.8682 (t) REVERT: F 102 GLN cc_start: 0.8062 (OUTLIER) cc_final: 0.7179 (tp-100) REVERT: G 31 ARG cc_start: 0.7347 (OUTLIER) cc_final: 0.7002 (tpm-80) REVERT: H 41 ARG cc_start: 0.8408 (ttt90) cc_final: 0.8173 (ttm170) REVERT: I 39 ARG cc_start: 0.7682 (mmm-85) cc_final: 0.7448 (mmt90) REVERT: J 46 LYS cc_start: 0.8685 (OUTLIER) cc_final: 0.8465 (tptm) REVERT: K 27 MET cc_start: 0.8644 (mmm) cc_final: 0.8305 (mmt) outliers start: 67 outliers final: 42 residues processed: 323 average time/residue: 1.2931 time to fit residues: 460.9791 Evaluate side-chains 322 residues out of total 1706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 274 time to evaluate : 2.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 50 ARG Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 556 SER Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain B residue 118 GLN Chi-restraints excluded: chain B residue 148 SER Chi-restraints excluded: chain B residue 157 ASP 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 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 154 LYS Chi-restraints excluded: chain D residue 177 GLU Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 42 ARG Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 75 ASP Chi-restraints excluded: chain E residue 123 SER Chi-restraints excluded: chain F residue 102 GLN Chi-restraints excluded: chain F residue 121 VAL Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain G residue 31 ARG Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 70 LYS Chi-restraints excluded: chain G residue 92 SER Chi-restraints excluded: chain H residue 24 GLU Chi-restraints excluded: chain H residue 76 SER Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain H residue 125 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 24 ASP 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 92 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 62 optimal weight: 0.0670 chunk 166 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 108 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 184 optimal weight: 3.9990 chunk 153 optimal weight: 0.6980 chunk 85 optimal weight: 6.9990 chunk 15 optimal weight: 0.0770 chunk 61 optimal weight: 5.9990 chunk 97 optimal weight: 5.9990 overall best weight: 0.5476 ------------------------------------------------------------------------------- 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** E 62 ASN ** G 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 100 ASN ** J 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 50 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 15833 Z= 0.180 Angle : 0.579 10.050 21524 Z= 0.291 Chirality : 0.042 0.219 2440 Planarity : 0.004 0.055 2748 Dihedral : 4.975 52.416 2272 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.75 % Allowed : 16.41 % Favored : 79.84 % 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: 0.63 (0.19), residues: 1912 helix: 1.20 (0.25), residues: 435 sheet: 0.28 (0.21), residues: 552 loop : 0.27 (0.21), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 106 HIS 0.008 0.001 HIS C 156 PHE 0.012 0.001 PHE A 349 TYR 0.017 0.001 TYR G 74 ARG 0.009 0.001 ARG F 28 *********************** 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 345 residues out of total 1706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 281 time to evaluate : 1.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 151 GLU cc_start: 0.7974 (tm-30) cc_final: 0.7762 (pp20) REVERT: C 163 ARG cc_start: 0.6487 (mmt90) cc_final: 0.6242 (mtt-85) REVERT: D 94 ARG cc_start: 0.8034 (OUTLIER) cc_final: 0.7073 (ptp90) REVERT: D 99 LEU cc_start: 0.8990 (tt) cc_final: 0.8381 (OUTLIER) REVERT: D 174 MET cc_start: 0.8749 (ttm) cc_final: 0.8546 (ttp) REVERT: E 121 GLU cc_start: 0.7935 (mt-10) cc_final: 0.7639 (mt-10) REVERT: F 51 SER cc_start: 0.8913 (t) cc_final: 0.8663 (t) REVERT: F 100 LYS cc_start: 0.8899 (OUTLIER) cc_final: 0.8559 (mtmt) REVERT: H 41 ARG cc_start: 0.8406 (ttt90) cc_final: 0.8199 (ttm170) REVERT: H 47 ARG cc_start: 0.7566 (ttm-80) cc_final: 0.7321 (mtt180) REVERT: I 39 ARG cc_start: 0.7736 (mmm-85) cc_final: 0.7494 (mmt90) REVERT: J 46 LYS cc_start: 0.8676 (OUTLIER) cc_final: 0.8444 (tptm) REVERT: K 27 MET cc_start: 0.8633 (mmm) cc_final: 0.8296 (mmt) outliers start: 64 outliers final: 33 residues processed: 314 average time/residue: 1.2340 time to fit residues: 428.4449 Evaluate side-chains 308 residues out of total 1706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 273 time to evaluate : 2.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain C residue 69 LYS Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain D residue 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 E residue 42 ARG Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 75 ASP Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain F residue 100 LYS Chi-restraints excluded: chain F residue 121 VAL Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 41 VAL 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 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 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: 1.9990 chunk 105 optimal weight: 5.9990 chunk 134 optimal weight: 1.9990 chunk 104 optimal weight: 0.6980 chunk 155 optimal weight: 4.9990 chunk 103 optimal weight: 0.9980 chunk 184 optimal weight: 0.9980 chunk 115 optimal weight: 3.9990 chunk 112 optimal weight: 0.2980 chunk 84 optimal weight: 3.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 ** G 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 120 ASN I 100 ASN ** J 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 15833 Z= 0.241 Angle : 0.597 8.470 21524 Z= 0.302 Chirality : 0.044 0.276 2440 Planarity : 0.004 0.053 2748 Dihedral : 5.039 51.450 2272 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 4.04 % Allowed : 16.82 % Favored : 79.13 % 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: 0.61 (0.19), residues: 1912 helix: 1.14 (0.25), residues: 435 sheet: 0.33 (0.22), residues: 545 loop : 0.24 (0.21), residues: 932 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 0.029 0.002 PHE D 74 TYR 0.017 0.002 TYR D 61 ARG 0.010 0.001 ARG A 50 *********************** 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 351 residues out of total 1706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 282 time to evaluate : 2.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 135 MET cc_start: 0.8175 (mmt) cc_final: 0.7943 (mtp) REVERT: C 151 GLU cc_start: 0.7972 (tm-30) cc_final: 0.7764 (pp20) REVERT: C 158 ARG cc_start: 0.7389 (tmm-80) cc_final: 0.7153 (tpt-90) REVERT: D 94 ARG cc_start: 0.8068 (OUTLIER) cc_final: 0.7093 (ptp90) REVERT: E 75 ASP cc_start: 0.7514 (p0) cc_final: 0.7052 (p0) REVERT: E 121 GLU cc_start: 0.7995 (mt-10) cc_final: 0.7708 (mt-10) REVERT: F 51 SER cc_start: 0.8912 (t) cc_final: 0.8667 (t) REVERT: F 100 LYS cc_start: 0.8903 (OUTLIER) cc_final: 0.8574 (mtmt) REVERT: H 41 ARG cc_start: 0.8395 (ttt90) cc_final: 0.8185 (ttm170) REVERT: J 46 LYS cc_start: 0.8698 (OUTLIER) cc_final: 0.8483 (tptm) REVERT: K 126 LYS cc_start: 0.8454 (mtpp) cc_final: 0.8167 (ttmm) outliers start: 69 outliers final: 48 residues processed: 316 average time/residue: 1.3149 time to fit residues: 458.7404 Evaluate side-chains 321 residues out of total 1706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 270 time to evaluate : 1.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 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 556 SER Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 660 THR 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 136 GLU Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain D residue 60 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 154 LYS 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 100 LYS Chi-restraints excluded: chain F residue 102 GLN 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 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 46 LYS Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain K residue 24 ASP Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 56 LEU Chi-restraints excluded: chain K residue 65 LYS Chi-restraints excluded: chain K residue 75 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 113 optimal weight: 0.7980 chunk 73 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 125 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 144 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 ASN A 165 HIS A 315 ASN ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 ASN ** G 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 100 ASN ** J 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 15833 Z= 0.368 Angle : 0.667 8.659 21524 Z= 0.338 Chirality : 0.046 0.179 2440 Planarity : 0.005 0.051 2748 Dihedral : 5.314 50.078 2272 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 4.51 % Allowed : 16.76 % Favored : 78.72 % 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: 0.38 (0.19), residues: 1912 helix: 0.95 (0.25), residues: 435 sheet: 0.21 (0.22), residues: 547 loop : 0.08 (0.21), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP J 70 HIS 0.009 0.001 HIS C 156 PHE 0.018 0.002 PHE A 349 TYR 0.020 0.002 TYR K 72 ARG 0.012 0.001 ARG A 117 *********************** 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 350 residues out of total 1706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 273 time to evaluate : 1.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 46 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7485 (pm20) REVERT: B 118 GLN cc_start: 0.8586 (tt0) cc_final: 0.8130 (tt0) REVERT: C 72 GLU cc_start: 0.8040 (mp0) cc_final: 0.7718 (mp0) REVERT: D 94 ARG cc_start: 0.8086 (OUTLIER) cc_final: 0.7053 (ptp90) REVERT: D 174 MET cc_start: 0.9231 (ttp) cc_final: 0.8957 (ttm) REVERT: E 75 ASP cc_start: 0.7553 (OUTLIER) cc_final: 0.7076 (p0) REVERT: F 51 SER cc_start: 0.8985 (t) cc_final: 0.8725 (t) REVERT: F 100 LYS cc_start: 0.8909 (OUTLIER) cc_final: 0.8586 (mtmt) REVERT: H 41 ARG cc_start: 0.8409 (ttt90) cc_final: 0.8180 (ttm170) REVERT: K 126 LYS cc_start: 0.8499 (mtpp) cc_final: 0.8209 (ttmm) outliers start: 77 outliers final: 49 residues processed: 312 average time/residue: 1.3518 time to fit residues: 467.2705 Evaluate side-chains 321 residues out of total 1706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 268 time to evaluate : 1.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 253 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 556 SER Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 64 LYS 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 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 154 LYS Chi-restraints excluded: chain D residue 177 GLU Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 42 ARG Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 75 ASP Chi-restraints excluded: chain E residue 123 SER Chi-restraints excluded: chain F residue 100 LYS Chi-restraints excluded: chain F residue 113 VAL 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 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 H residue 105 GLU Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain J residue 125 ILE Chi-restraints excluded: chain K residue 24 ASP Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 56 LEU Chi-restraints excluded: chain K residue 65 LYS Chi-restraints excluded: chain K residue 75 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 167 optimal weight: 0.7980 chunk 176 optimal weight: 0.0570 chunk 160 optimal weight: 2.9990 chunk 171 optimal weight: 0.5980 chunk 103 optimal weight: 1.9990 chunk 74 optimal weight: 0.4980 chunk 134 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 155 optimal weight: 1.9990 chunk 162 optimal weight: 1.9990 chunk 170 optimal weight: 2.9990 overall best weight: 0.7900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 HIS ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 ASN ** G 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 100 ASN ** J 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 50 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15833 Z= 0.215 Angle : 0.611 9.306 21524 Z= 0.305 Chirality : 0.043 0.172 2440 Planarity : 0.004 0.051 2748 Dihedral : 5.076 51.961 2272 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.63 % Allowed : 18.41 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.19), residues: 1912 helix: 1.12 (0.25), residues: 429 sheet: 0.26 (0.22), residues: 548 loop : 0.06 (0.21), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 106 HIS 0.007 0.001 HIS C 156 PHE 0.028 0.001 PHE D 74 TYR 0.023 0.001 TYR K 72 ARG 0.015 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 337 residues out of total 1706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 275 time to evaluate : 2.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 118 GLN cc_start: 0.8506 (tt0) cc_final: 0.8043 (tt0) REVERT: C 137 TYR cc_start: 0.7834 (m-80) cc_final: 0.7595 (m-80) REVERT: D 94 ARG cc_start: 0.8076 (OUTLIER) cc_final: 0.7044 (ptp90) REVERT: D 174 MET cc_start: 0.9231 (ttp) cc_final: 0.8904 (ttm) REVERT: E 75 ASP cc_start: 0.7516 (OUTLIER) cc_final: 0.7045 (p0) REVERT: F 51 SER cc_start: 0.8945 (t) cc_final: 0.8689 (t) REVERT: F 100 LYS cc_start: 0.8893 (OUTLIER) cc_final: 0.8567 (mtmt) REVERT: H 41 ARG cc_start: 0.8417 (ttt90) cc_final: 0.8166 (ttm170) REVERT: J 46 LYS cc_start: 0.8670 (OUTLIER) cc_final: 0.8426 (tptm) REVERT: K 126 LYS cc_start: 0.8466 (mtpp) cc_final: 0.8163 (ttmm) outliers start: 62 outliers final: 38 residues processed: 309 average time/residue: 1.2752 time to fit residues: 436.6917 Evaluate side-chains 307 residues out of total 1706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 265 time to evaluate : 1.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR 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 556 SER Chi-restraints excluded: chain A residue 592 THR 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 136 GLU Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain D residue 94 ARG Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 125 MET Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 177 GLU Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 42 ARG Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 75 ASP Chi-restraints excluded: chain E residue 123 SER Chi-restraints excluded: chain F residue 100 LYS Chi-restraints excluded: chain F residue 121 VAL Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 36 SER Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 70 LYS Chi-restraints excluded: chain H residue 24 GLU Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 76 SER Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 46 LYS Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain J residue 125 ILE 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: 0.9990 chunk 110 optimal weight: 3.9990 chunk 86 optimal weight: 5.9990 chunk 126 optimal weight: 3.9990 chunk 190 optimal weight: 0.6980 chunk 175 optimal weight: 0.7980 chunk 151 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 117 optimal weight: 2.9990 chunk 92 optimal weight: 0.3980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 HIS ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 GLN E 62 ASN ** G 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 100 ASN ** J 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 50 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 15833 Z= 0.215 Angle : 0.636 11.468 21524 Z= 0.319 Chirality : 0.044 0.283 2440 Planarity : 0.004 0.051 2748 Dihedral : 5.021 52.054 2272 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.99 % Allowed : 18.82 % Favored : 78.19 % 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: 0.45 (0.19), residues: 1912 helix: 1.14 (0.25), residues: 429 sheet: 0.31 (0.22), residues: 547 loop : 0.02 (0.21), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP J 70 HIS 0.014 0.001 HIS C 156 PHE 0.015 0.001 PHE B 174 TYR 0.026 0.001 TYR K 72 ARG 0.016 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 326 residues out of total 1706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 275 time to evaluate : 1.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 118 GLN cc_start: 0.8521 (OUTLIER) cc_final: 0.8117 (tt0) REVERT: C 151 GLU cc_start: 0.7932 (tm-30) cc_final: 0.7687 (pp20) REVERT: C 163 ARG cc_start: 0.6117 (ttm-80) cc_final: 0.5628 (ttm-80) REVERT: D 94 ARG cc_start: 0.8061 (OUTLIER) cc_final: 0.6983 (ptp90) REVERT: D 99 LEU cc_start: 0.8975 (tt) cc_final: 0.8738 (tp) REVERT: D 101 GLU cc_start: 0.7726 (mm-30) cc_final: 0.7495 (mp0) REVERT: D 174 MET cc_start: 0.9228 (ttp) cc_final: 0.8925 (ttm) REVERT: E 75 ASP cc_start: 0.7434 (OUTLIER) cc_final: 0.6953 (p0) REVERT: F 51 SER cc_start: 0.8915 (t) cc_final: 0.8663 (t) REVERT: F 100 LYS cc_start: 0.8868 (OUTLIER) cc_final: 0.8564 (mtmt) REVERT: H 41 ARG cc_start: 0.8415 (ttt90) cc_final: 0.8163 (ttm170) REVERT: H 47 ARG cc_start: 0.7562 (ttm-80) cc_final: 0.7194 (mpt180) REVERT: J 46 LYS cc_start: 0.8669 (OUTLIER) cc_final: 0.8422 (tptm) REVERT: K 126 LYS cc_start: 0.8451 (mtpp) cc_final: 0.8148 (ttmm) outliers start: 51 outliers final: 38 residues processed: 302 average time/residue: 1.3645 time to fit residues: 455.7144 Evaluate side-chains 309 residues out of total 1706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 266 time to evaluate : 1.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR 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 451 HIS Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain B residue 64 LYS Chi-restraints excluded: chain B residue 118 GLN Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain C residue 69 LYS Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain D residue 94 ARG Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 125 MET Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 177 GLU Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 42 ARG Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 75 ASP Chi-restraints excluded: chain E residue 123 SER Chi-restraints excluded: chain F residue 100 LYS Chi-restraints excluded: chain F residue 121 VAL Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 36 SER Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 70 LYS Chi-restraints excluded: chain H residue 24 GLU Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 76 SER Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 46 LYS Chi-restraints excluded: chain J residue 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 120 optimal weight: 2.9990 chunk 161 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 139 optimal weight: 4.9990 chunk 22 optimal weight: 0.6980 chunk 42 optimal weight: 0.3980 chunk 151 optimal weight: 0.8980 chunk 63 optimal weight: 0.0870 chunk 155 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 HIS ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 ASN ** G 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 100 ASN ** J 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 50 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.118298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.095029 restraints weight = 29734.237| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 2.26 r_work: 0.3085 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2969 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2969 r_free = 0.2969 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 = 0.2969 r_free = 0.2969 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2969 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 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 0.177 15833 Z= 0.275 Angle : 0.971 61.579 21524 Z= 0.514 Chirality : 0.051 1.114 2440 Planarity : 0.005 0.059 2748 Dihedral : 5.082 52.065 2272 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.72 % Favored : 97.23 % Rotamer: Outliers : 2.99 % Allowed : 18.76 % Favored : 78.25 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 8.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 0.45 (0.19), residues: 1912 helix: 1.13 (0.25), residues: 429 sheet: 0.30 (0.22), residues: 547 loop : 0.03 (0.21), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP J 70 HIS 0.012 0.001 HIS C 156 PHE 0.014 0.001 PHE B 174 TYR 0.025 0.001 TYR K 72 ARG 0.024 0.001 ARG A 117 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7208.96 seconds wall clock time: 128 minutes 34.28 seconds (7714.28 seconds total)