Starting phenix.real_space_refine on Fri Sep 27 04:29:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vms_8712/09_2024/5vms_8712.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vms_8712/09_2024/5vms_8712.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vms_8712/09_2024/5vms_8712.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vms_8712/09_2024/5vms_8712.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vms_8712/09_2024/5vms_8712.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vms_8712/09_2024/5vms_8712.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 12 9.91 5 S 64 5.16 5 C 9708 2.51 5 N 2588 2.21 5 O 2544 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 14916 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2717 Classifications: {'peptide': 343} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 7, 'TRANS': 335} Chain breaks: 2 Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 43 Chain: "B" Number of atoms: 1009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1009 Classifications: {'peptide': 141} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 2, 'TRANS': 138} Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 79 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 10, 'ASN:plan1': 1, 'ASP:plan': 14} Unresolved non-hydrogen planarities: 89 Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Restraints were copied for chains: D, F, H, C, E, G Residues with excluded nonbonded symmetry interactions: 4 residue: pdb="CA CA B 202 " occ=0.83 residue: pdb="CA CA D 202 " occ=0.83 residue: pdb="CA CA F 202 " occ=0.83 residue: pdb="CA CA H 202 " occ=0.83 Time building chain proxies: 6.72, per 1000 atoms: 0.45 Number of scatterers: 14916 At special positions: 0 Unit cell: (107.9, 107.9, 123.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 12 19.99 S 64 16.00 O 2544 8.00 N 2588 7.00 C 9708 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.43 Conformation dependent library (CDL) restraints added in 2.0 seconds 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3600 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 0 sheets defined 82.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.29 Creating SS restraints... Processing helix chain 'A' and resid 95 through 105 Processing helix chain 'A' and resid 109 through 135 Processing helix chain 'A' and resid 136 through 138 No H-bonds generated for 'chain 'A' and resid 136 through 138' Processing helix chain 'A' and resid 139 through 168 removed outlier: 4.795A pdb=" N GLU A 144 " --> pdb=" O ASN A 140 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N THR A 145 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE A 151 " --> pdb=" O PHE A 147 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N VAL A 152 " --> pdb=" O TRP A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 171 No H-bonds generated for 'chain 'A' and resid 169 through 171' Processing helix chain 'A' and resid 175 through 186 removed outlier: 3.509A pdb=" N ARG A 180 " --> pdb=" O GLY A 176 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS A 186 " --> pdb=" O ARG A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 206 Processing helix chain 'A' and resid 218 through 228 removed outlier: 4.245A pdb=" N PHE A 222 " --> pdb=" O ARG A 218 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N MET A 228 " --> pdb=" O GLN A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 232 removed outlier: 3.532A pdb=" N ASP A 232 " --> pdb=" O LEU A 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 229 through 232' Processing helix chain 'A' and resid 235 through 248 removed outlier: 4.161A pdb=" N LEU A 240 " --> pdb=" O GLY A 236 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU A 241 " --> pdb=" O THR A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 274 removed outlier: 3.553A pdb=" N THR A 254 " --> pdb=" O GLN A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 302 Processing helix chain 'A' and resid 312 through 350 removed outlier: 4.131A pdb=" N VAL A 324 " --> pdb=" O SER A 320 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N PHE A 325 " --> pdb=" O CYS A 321 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA A 326 " --> pdb=" O PHE A 322 " (cutoff:3.500A) Proline residue: A 333 - end of helix Processing helix chain 'A' and resid 353 through 355 No H-bonds generated for 'chain 'A' and resid 353 through 355' Processing helix chain 'A' and resid 356 through 376 removed outlier: 4.582A pdb=" N ALA A 360 " --> pdb=" O ARG A 356 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLU A 375 " --> pdb=" O CYS A 371 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ASN A 376 " --> pdb=" O TYR A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 523 Processing helix chain 'A' and resid 526 through 556 Processing helix chain 'B' and resid 7 through 22 removed outlier: 4.180A pdb=" N LYS B 22 " --> pdb=" O SER B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 41 removed outlier: 3.536A pdb=" N LEU B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 57 removed outlier: 3.538A pdb=" N VAL B 56 " --> pdb=" O MET B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 75 Processing helix chain 'B' and resid 79 through 94 removed outlier: 3.651A pdb=" N GLU B 85 " --> pdb=" O ASP B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 113 Processing helix chain 'B' and resid 118 through 130 Processing helix chain 'B' and resid 138 through 146 Processing helix chain 'C' and resid 95 through 105 Processing helix chain 'C' and resid 109 through 135 Processing helix chain 'C' and resid 136 through 138 No H-bonds generated for 'chain 'C' and resid 136 through 138' Processing helix chain 'C' and resid 139 through 168 removed outlier: 4.795A pdb=" N GLU C 144 " --> pdb=" O ASN C 140 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N THR C 145 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE C 151 " --> pdb=" O PHE C 147 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N VAL C 152 " --> pdb=" O TRP C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 171 No H-bonds generated for 'chain 'C' and resid 169 through 171' Processing helix chain 'C' and resid 175 through 186 removed outlier: 3.509A pdb=" N ARG C 180 " --> pdb=" O GLY C 176 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS C 186 " --> pdb=" O ARG C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 206 Processing helix chain 'C' and resid 218 through 228 removed outlier: 4.245A pdb=" N PHE C 222 " --> pdb=" O ARG C 218 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N MET C 228 " --> pdb=" O GLN C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 232 removed outlier: 3.532A pdb=" N ASP C 232 " --> pdb=" O LEU C 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 229 through 232' Processing helix chain 'C' and resid 235 through 248 removed outlier: 4.161A pdb=" N LEU C 240 " --> pdb=" O GLY C 236 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU C 241 " --> pdb=" O THR C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 274 removed outlier: 3.553A pdb=" N THR C 254 " --> pdb=" O GLN C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 302 Processing helix chain 'C' and resid 312 through 350 removed outlier: 4.131A pdb=" N VAL C 324 " --> pdb=" O SER C 320 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N PHE C 325 " --> pdb=" O CYS C 321 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA C 326 " --> pdb=" O PHE C 322 " (cutoff:3.500A) Proline residue: C 333 - end of helix Processing helix chain 'C' and resid 353 through 355 No H-bonds generated for 'chain 'C' and resid 353 through 355' Processing helix chain 'C' and resid 356 through 376 removed outlier: 4.582A pdb=" N ALA C 360 " --> pdb=" O ARG C 356 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLU C 375 " --> pdb=" O CYS C 371 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ASN C 376 " --> pdb=" O TYR C 372 " (cutoff:3.500A) Processing helix chain 'C' and resid 498 through 523 Processing helix chain 'C' and resid 526 through 556 Processing helix chain 'D' and resid 7 through 22 removed outlier: 4.180A pdb=" N LYS D 22 " --> pdb=" O SER D 18 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 41 removed outlier: 3.536A pdb=" N LEU D 33 " --> pdb=" O THR D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 57 removed outlier: 3.538A pdb=" N VAL D 56 " --> pdb=" O MET D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 75 Processing helix chain 'D' and resid 79 through 94 removed outlier: 3.651A pdb=" N GLU D 85 " --> pdb=" O ASP D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 113 Processing helix chain 'D' and resid 118 through 130 Processing helix chain 'D' and resid 138 through 146 Processing helix chain 'E' and resid 95 through 105 Processing helix chain 'E' and resid 109 through 135 Processing helix chain 'E' and resid 136 through 138 No H-bonds generated for 'chain 'E' and resid 136 through 138' Processing helix chain 'E' and resid 139 through 168 removed outlier: 4.795A pdb=" N GLU E 144 " --> pdb=" O ASN E 140 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N THR E 145 " --> pdb=" O LEU E 141 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE E 151 " --> pdb=" O PHE E 147 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N VAL E 152 " --> pdb=" O TRP E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 169 through 171 No H-bonds generated for 'chain 'E' and resid 169 through 171' Processing helix chain 'E' and resid 175 through 186 removed outlier: 3.509A pdb=" N ARG E 180 " --> pdb=" O GLY E 176 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS E 186 " --> pdb=" O ARG E 182 " (cutoff:3.500A) Processing helix chain 'E' and resid 188 through 206 Processing helix chain 'E' and resid 218 through 228 removed outlier: 4.245A pdb=" N PHE E 222 " --> pdb=" O ARG E 218 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N MET E 228 " --> pdb=" O GLN E 224 " (cutoff:3.500A) Processing helix chain 'E' and resid 229 through 232 removed outlier: 3.532A pdb=" N ASP E 232 " --> pdb=" O LEU E 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 229 through 232' Processing helix chain 'E' and resid 235 through 248 removed outlier: 4.161A pdb=" N LEU E 240 " --> pdb=" O GLY E 236 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU E 241 " --> pdb=" O THR E 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 248 through 274 removed outlier: 3.553A pdb=" N THR E 254 " --> pdb=" O GLN E 250 " (cutoff:3.500A) Processing helix chain 'E' and resid 288 through 302 Processing helix chain 'E' and resid 312 through 350 removed outlier: 4.131A pdb=" N VAL E 324 " --> pdb=" O SER E 320 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N PHE E 325 " --> pdb=" O CYS E 321 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA E 326 " --> pdb=" O PHE E 322 " (cutoff:3.500A) Proline residue: E 333 - end of helix Processing helix chain 'E' and resid 353 through 355 No H-bonds generated for 'chain 'E' and resid 353 through 355' Processing helix chain 'E' and resid 356 through 376 removed outlier: 4.582A pdb=" N ALA E 360 " --> pdb=" O ARG E 356 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLU E 375 " --> pdb=" O CYS E 371 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ASN E 376 " --> pdb=" O TYR E 372 " (cutoff:3.500A) Processing helix chain 'E' and resid 498 through 523 Processing helix chain 'E' and resid 526 through 556 Processing helix chain 'F' and resid 7 through 22 removed outlier: 4.180A pdb=" N LYS F 22 " --> pdb=" O SER F 18 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 41 removed outlier: 3.536A pdb=" N LEU F 33 " --> pdb=" O THR F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 45 through 57 removed outlier: 3.538A pdb=" N VAL F 56 " --> pdb=" O MET F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 65 through 75 Processing helix chain 'F' and resid 79 through 94 removed outlier: 3.651A pdb=" N GLU F 85 " --> pdb=" O ASP F 81 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 113 Processing helix chain 'F' and resid 118 through 130 Processing helix chain 'F' and resid 138 through 146 Processing helix chain 'G' and resid 95 through 105 Processing helix chain 'G' and resid 109 through 135 Processing helix chain 'G' and resid 136 through 138 No H-bonds generated for 'chain 'G' and resid 136 through 138' Processing helix chain 'G' and resid 139 through 168 removed outlier: 4.795A pdb=" N GLU G 144 " --> pdb=" O ASN G 140 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N THR G 145 " --> pdb=" O LEU G 141 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE G 151 " --> pdb=" O PHE G 147 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N VAL G 152 " --> pdb=" O TRP G 148 " (cutoff:3.500A) Processing helix chain 'G' and resid 169 through 171 No H-bonds generated for 'chain 'G' and resid 169 through 171' Processing helix chain 'G' and resid 175 through 186 removed outlier: 3.509A pdb=" N ARG G 180 " --> pdb=" O GLY G 176 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS G 186 " --> pdb=" O ARG G 182 " (cutoff:3.500A) Processing helix chain 'G' and resid 188 through 206 Processing helix chain 'G' and resid 218 through 228 removed outlier: 4.245A pdb=" N PHE G 222 " --> pdb=" O ARG G 218 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N MET G 228 " --> pdb=" O GLN G 224 " (cutoff:3.500A) Processing helix chain 'G' and resid 229 through 232 removed outlier: 3.532A pdb=" N ASP G 232 " --> pdb=" O LEU G 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 229 through 232' Processing helix chain 'G' and resid 235 through 248 removed outlier: 4.161A pdb=" N LEU G 240 " --> pdb=" O GLY G 236 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU G 241 " --> pdb=" O THR G 237 " (cutoff:3.500A) Processing helix chain 'G' and resid 248 through 274 removed outlier: 3.553A pdb=" N THR G 254 " --> pdb=" O GLN G 250 " (cutoff:3.500A) Processing helix chain 'G' and resid 288 through 302 Processing helix chain 'G' and resid 312 through 350 removed outlier: 4.131A pdb=" N VAL G 324 " --> pdb=" O SER G 320 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N PHE G 325 " --> pdb=" O CYS G 321 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA G 326 " --> pdb=" O PHE G 322 " (cutoff:3.500A) Proline residue: G 333 - end of helix Processing helix chain 'G' and resid 353 through 355 No H-bonds generated for 'chain 'G' and resid 353 through 355' Processing helix chain 'G' and resid 356 through 376 removed outlier: 4.582A pdb=" N ALA G 360 " --> pdb=" O ARG G 356 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLU G 375 " --> pdb=" O CYS G 371 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ASN G 376 " --> pdb=" O TYR G 372 " (cutoff:3.500A) Processing helix chain 'G' and resid 498 through 523 Processing helix chain 'G' and resid 526 through 556 Processing helix chain 'H' and resid 7 through 22 removed outlier: 4.180A pdb=" N LYS H 22 " --> pdb=" O SER H 18 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 41 removed outlier: 3.536A pdb=" N LEU H 33 " --> pdb=" O THR H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 45 through 57 removed outlier: 3.538A pdb=" N VAL H 56 " --> pdb=" O MET H 52 " (cutoff:3.500A) Processing helix chain 'H' and resid 65 through 75 Processing helix chain 'H' and resid 79 through 94 removed outlier: 3.651A pdb=" N GLU H 85 " --> pdb=" O ASP H 81 " (cutoff:3.500A) Processing helix chain 'H' and resid 102 through 113 Processing helix chain 'H' and resid 118 through 130 Processing helix chain 'H' and resid 138 through 146 1112 hydrogen bonds defined for protein. 3336 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: 4.26 Time building geometry restraints manager: 4.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2476 1.33 - 1.45: 4192 1.45 - 1.57: 8440 1.57 - 1.69: 8 1.69 - 1.81: 112 Bond restraints: 15228 Sorted by residual: bond pdb=" C LEU E 332 " pdb=" O LEU E 332 " ideal model delta sigma weight residual 1.241 1.212 0.029 9.80e-03 1.04e+04 8.83e+00 bond pdb=" C LEU A 332 " pdb=" O LEU A 332 " ideal model delta sigma weight residual 1.241 1.212 0.029 9.80e-03 1.04e+04 8.83e+00 bond pdb=" C LEU C 332 " pdb=" O LEU C 332 " ideal model delta sigma weight residual 1.241 1.212 0.029 9.80e-03 1.04e+04 8.83e+00 bond pdb=" C LEU G 332 " pdb=" O LEU G 332 " ideal model delta sigma weight residual 1.241 1.212 0.029 9.80e-03 1.04e+04 8.83e+00 bond pdb=" C ILE C 264 " pdb=" O ILE C 264 " ideal model delta sigma weight residual 1.237 1.270 -0.033 1.13e-02 7.83e+03 8.52e+00 ... (remaining 15223 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.37: 13828 1.37 - 2.73: 5568 2.73 - 4.10: 1080 4.10 - 5.47: 124 5.47 - 6.83: 44 Bond angle restraints: 20644 Sorted by residual: angle pdb=" N ILE E 303 " pdb=" CA ILE E 303 " pdb=" C ILE E 303 " ideal model delta sigma weight residual 110.74 104.41 6.33 9.10e-01 1.21e+00 4.84e+01 angle pdb=" N ILE G 303 " pdb=" CA ILE G 303 " pdb=" C ILE G 303 " ideal model delta sigma weight residual 110.74 104.41 6.33 9.10e-01 1.21e+00 4.84e+01 angle pdb=" N ILE C 303 " pdb=" CA ILE C 303 " pdb=" C ILE C 303 " ideal model delta sigma weight residual 110.74 104.41 6.33 9.10e-01 1.21e+00 4.84e+01 angle pdb=" N ILE A 303 " pdb=" CA ILE A 303 " pdb=" C ILE A 303 " ideal model delta sigma weight residual 110.74 104.41 6.33 9.10e-01 1.21e+00 4.84e+01 angle pdb=" N ASP F 21 " pdb=" CA ASP F 21 " pdb=" C ASP F 21 " ideal model delta sigma weight residual 111.33 117.80 -6.47 1.21e+00 6.83e-01 2.86e+01 ... (remaining 20639 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.79: 7524 12.79 - 25.59: 1012 25.59 - 38.38: 228 38.38 - 51.17: 64 51.17 - 63.96: 20 Dihedral angle restraints: 8848 sinusoidal: 3260 harmonic: 5588 Sorted by residual: dihedral pdb=" CA SER C 323 " pdb=" C SER C 323 " pdb=" N VAL C 324 " pdb=" CA VAL C 324 " ideal model delta harmonic sigma weight residual -180.00 -155.83 -24.17 0 5.00e+00 4.00e-02 2.34e+01 dihedral pdb=" CA SER A 323 " pdb=" C SER A 323 " pdb=" N VAL A 324 " pdb=" CA VAL A 324 " ideal model delta harmonic sigma weight residual -180.00 -155.83 -24.17 0 5.00e+00 4.00e-02 2.34e+01 dihedral pdb=" CA SER G 323 " pdb=" C SER G 323 " pdb=" N VAL G 324 " pdb=" CA VAL G 324 " ideal model delta harmonic sigma weight residual -180.00 -155.83 -24.17 0 5.00e+00 4.00e-02 2.34e+01 ... (remaining 8845 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1764 0.071 - 0.143: 440 0.143 - 0.214: 128 0.214 - 0.285: 28 0.285 - 0.357: 8 Chirality restraints: 2368 Sorted by residual: chirality pdb=" CA LEU G 332 " pdb=" N LEU G 332 " pdb=" C LEU G 332 " pdb=" CB LEU G 332 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.18e+00 chirality pdb=" CA LEU A 332 " pdb=" N LEU A 332 " pdb=" C LEU A 332 " pdb=" CB LEU A 332 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.18e+00 chirality pdb=" CA LEU C 332 " pdb=" N LEU C 332 " pdb=" C LEU C 332 " pdb=" CB LEU C 332 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.18e+00 ... (remaining 2365 not shown) Planarity restraints: 2576 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 66 " 0.042 5.00e-02 4.00e+02 6.34e-02 6.44e+00 pdb=" N PRO B 67 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO B 67 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 67 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE H 66 " 0.042 5.00e-02 4.00e+02 6.34e-02 6.44e+00 pdb=" N PRO H 67 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO H 67 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO H 67 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE D 66 " -0.042 5.00e-02 4.00e+02 6.34e-02 6.44e+00 pdb=" N PRO D 67 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO D 67 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 67 " -0.035 5.00e-02 4.00e+02 ... (remaining 2573 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 560 2.77 - 3.30: 17496 3.30 - 3.83: 25306 3.83 - 4.37: 26534 4.37 - 4.90: 43930 Nonbonded interactions: 113826 Sorted by model distance: nonbonded pdb=" O THR F 63 " pdb="CA CA F 202 " model vdw 2.234 2.510 nonbonded pdb=" O THR H 63 " pdb="CA CA H 202 " model vdw 2.234 2.510 nonbonded pdb=" O THR B 63 " pdb="CA CA B 202 " model vdw 2.234 2.510 nonbonded pdb=" O THR D 63 " pdb="CA CA D 202 " model vdw 2.234 2.510 nonbonded pdb=" OE1 GLN E 549 " pdb=" CD1 LEU G 548 " model vdw 2.236 3.460 ... (remaining 113821 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' } 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=0.83 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.620 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 31.460 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 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 : 0.007 0.043 15228 Z= 0.488 Angle : 1.474 6.833 20644 Z= 1.155 Chirality : 0.074 0.357 2368 Planarity : 0.005 0.063 2576 Dihedral : 12.688 63.961 5248 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Cbeta Deviations : 0.67 % Peptide Plane: Cis-proline : 0.00 % 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: 2.06 (0.16), residues: 1904 helix: 2.39 (0.10), residues: 1472 sheet: None (None), residues: 0 loop : -2.54 (0.24), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 369 HIS 0.005 0.001 HIS E 116 PHE 0.019 0.002 PHE G 330 TYR 0.016 0.002 TYR G 534 ARG 0.003 0.001 ARG E 106 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 896 residues out of total 1660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 896 time to evaluate : 1.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 LEU cc_start: 0.8035 (tp) cc_final: 0.7812 (tt) REVERT: A 153 LEU cc_start: 0.9398 (tp) cc_final: 0.9176 (tp) REVERT: A 160 GLU cc_start: 0.9549 (tt0) cc_final: 0.9213 (tt0) REVERT: A 180 ARG cc_start: 0.8066 (mtt180) cc_final: 0.7701 (mmt-90) REVERT: A 291 ASP cc_start: 0.8333 (m-30) cc_final: 0.8074 (m-30) REVERT: A 308 LYS cc_start: 0.8849 (mttt) cc_final: 0.8597 (mttm) REVERT: A 358 ILE cc_start: 0.8879 (mt) cc_final: 0.8571 (mt) REVERT: A 499 HIS cc_start: 0.7998 (m-70) cc_final: 0.7671 (p90) REVERT: A 526 ASP cc_start: 0.8839 (t70) cc_final: 0.8448 (t70) REVERT: A 534 TYR cc_start: 0.8879 (t80) cc_final: 0.7769 (t80) REVERT: A 551 ARG cc_start: 0.8707 (tpp-160) cc_final: 0.8396 (tpt90) REVERT: B 37 MET cc_start: 0.9455 (mmm) cc_final: 0.9206 (mmm) REVERT: B 39 SER cc_start: 0.9561 (t) cc_final: 0.9307 (p) REVERT: B 45 THR cc_start: 0.8969 (m) cc_final: 0.8663 (t) REVERT: B 52 MET cc_start: 0.9423 (mtm) cc_final: 0.9002 (mtp) REVERT: B 80 THR cc_start: 0.8229 (p) cc_final: 0.8011 (p) REVERT: B 93 PHE cc_start: 0.8231 (m-80) cc_final: 0.7882 (m-80) REVERT: B 125 MET cc_start: 0.9466 (ttt) cc_final: 0.9245 (ttp) REVERT: B 142 PHE cc_start: 0.8570 (t80) cc_final: 0.8328 (t80) REVERT: C 141 LEU cc_start: 0.8035 (tp) cc_final: 0.7812 (tt) REVERT: C 153 LEU cc_start: 0.9400 (tp) cc_final: 0.9177 (tp) REVERT: C 160 GLU cc_start: 0.9549 (tt0) cc_final: 0.9214 (tt0) REVERT: C 180 ARG cc_start: 0.8068 (mtt180) cc_final: 0.7703 (mmt-90) REVERT: C 291 ASP cc_start: 0.8333 (m-30) cc_final: 0.8075 (m-30) REVERT: C 308 LYS cc_start: 0.8847 (mttt) cc_final: 0.8595 (mttm) REVERT: C 358 ILE cc_start: 0.8878 (mt) cc_final: 0.8570 (mt) REVERT: C 499 HIS cc_start: 0.7998 (m-70) cc_final: 0.7670 (p90) REVERT: C 526 ASP cc_start: 0.8837 (t70) cc_final: 0.8446 (t70) REVERT: C 534 TYR cc_start: 0.8878 (t80) cc_final: 0.7768 (t80) REVERT: C 550 ARG cc_start: 0.9169 (ttm110) cc_final: 0.8959 (mtp-110) REVERT: D 37 MET cc_start: 0.9454 (mmm) cc_final: 0.9206 (mmm) REVERT: D 39 SER cc_start: 0.9561 (t) cc_final: 0.9306 (p) REVERT: D 45 THR cc_start: 0.8971 (m) cc_final: 0.8665 (t) REVERT: D 52 MET cc_start: 0.9423 (mtm) cc_final: 0.9001 (mtp) REVERT: D 80 THR cc_start: 0.8229 (p) cc_final: 0.8012 (p) REVERT: D 93 PHE cc_start: 0.8230 (m-80) cc_final: 0.7880 (m-80) REVERT: D 125 MET cc_start: 0.9466 (ttt) cc_final: 0.9244 (ttp) REVERT: D 142 PHE cc_start: 0.8568 (t80) cc_final: 0.8328 (t80) REVERT: E 141 LEU cc_start: 0.8034 (tp) cc_final: 0.7811 (tt) REVERT: E 153 LEU cc_start: 0.9399 (tp) cc_final: 0.9177 (tp) REVERT: E 160 GLU cc_start: 0.9550 (tt0) cc_final: 0.9214 (tt0) REVERT: E 180 ARG cc_start: 0.8068 (mtt180) cc_final: 0.7703 (mmt-90) REVERT: E 291 ASP cc_start: 0.8333 (m-30) cc_final: 0.8075 (m-30) REVERT: E 308 LYS cc_start: 0.8848 (mttt) cc_final: 0.8595 (mttm) REVERT: E 358 ILE cc_start: 0.8877 (mt) cc_final: 0.8568 (mt) REVERT: E 499 HIS cc_start: 0.7999 (m-70) cc_final: 0.7671 (p90) REVERT: E 526 ASP cc_start: 0.8838 (t70) cc_final: 0.8446 (t70) REVERT: E 534 TYR cc_start: 0.8876 (t80) cc_final: 0.7768 (t80) REVERT: E 550 ARG cc_start: 0.9169 (ttm110) cc_final: 0.8960 (mtp-110) REVERT: F 37 MET cc_start: 0.9455 (mmm) cc_final: 0.9207 (mmm) REVERT: F 39 SER cc_start: 0.9560 (t) cc_final: 0.9306 (p) REVERT: F 45 THR cc_start: 0.8970 (m) cc_final: 0.8663 (t) REVERT: F 52 MET cc_start: 0.9423 (mtm) cc_final: 0.9001 (mtp) REVERT: F 80 THR cc_start: 0.8228 (p) cc_final: 0.8010 (p) REVERT: F 93 PHE cc_start: 0.8230 (m-80) cc_final: 0.7879 (m-80) REVERT: F 125 MET cc_start: 0.9466 (ttt) cc_final: 0.9244 (ttp) REVERT: F 142 PHE cc_start: 0.8569 (t80) cc_final: 0.8329 (t80) REVERT: G 141 LEU cc_start: 0.8034 (tp) cc_final: 0.7811 (tt) REVERT: G 153 LEU cc_start: 0.9398 (tp) cc_final: 0.9175 (tp) REVERT: G 160 GLU cc_start: 0.9550 (tt0) cc_final: 0.9213 (tt0) REVERT: G 180 ARG cc_start: 0.8067 (mtt180) cc_final: 0.7702 (mmt-90) REVERT: G 291 ASP cc_start: 0.8332 (m-30) cc_final: 0.8074 (m-30) REVERT: G 308 LYS cc_start: 0.8849 (mttt) cc_final: 0.8597 (mttm) REVERT: G 358 ILE cc_start: 0.8878 (mt) cc_final: 0.8570 (mt) REVERT: G 499 HIS cc_start: 0.8000 (m-70) cc_final: 0.7672 (p90) REVERT: G 526 ASP cc_start: 0.8838 (t70) cc_final: 0.8447 (t70) REVERT: G 534 TYR cc_start: 0.8877 (t80) cc_final: 0.7767 (t80) REVERT: H 37 MET cc_start: 0.9456 (mmm) cc_final: 0.9206 (mmm) REVERT: H 39 SER cc_start: 0.9561 (t) cc_final: 0.9306 (p) REVERT: H 45 THR cc_start: 0.8970 (m) cc_final: 0.8665 (t) REVERT: H 52 MET cc_start: 0.9424 (mtm) cc_final: 0.9003 (mtp) REVERT: H 80 THR cc_start: 0.8228 (p) cc_final: 0.8009 (p) REVERT: H 93 PHE cc_start: 0.8231 (m-80) cc_final: 0.7881 (m-80) REVERT: H 125 MET cc_start: 0.9466 (ttt) cc_final: 0.9245 (ttp) REVERT: H 142 PHE cc_start: 0.8569 (t80) cc_final: 0.8327 (t80) outliers start: 0 outliers final: 0 residues processed: 896 average time/residue: 0.2495 time to fit residues: 328.7924 Evaluate side-chains 692 residues out of total 1660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 692 time to evaluate : 1.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 3.9990 chunk 145 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 chunk 49 optimal weight: 5.9990 chunk 98 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 150 optimal weight: 0.6980 chunk 58 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 174 optimal weight: 0.9980 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 GLN ** A 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 112 ASN C 357 GLN ** C 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 112 ASN E 357 GLN ** E 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 112 ASN G 357 GLN ** G 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 112 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.2872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 15228 Z= 0.252 Angle : 0.607 5.999 20644 Z= 0.327 Chirality : 0.041 0.220 2368 Planarity : 0.004 0.040 2576 Dihedral : 3.983 23.151 2104 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 5.25 % Allowed : 17.89 % Favored : 76.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 4.05 (0.19), residues: 1904 helix: 3.73 (0.13), residues: 1484 sheet: None (None), residues: 0 loop : -1.63 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 369 HIS 0.006 0.001 HIS F 108 PHE 0.027 0.002 PHE D 17 TYR 0.025 0.002 TYR E 268 ARG 0.009 0.001 ARG F 75 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 758 residues out of total 1660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 682 time to evaluate : 1.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 TRP cc_start: 0.8166 (t60) cc_final: 0.7790 (t60) REVERT: A 180 ARG cc_start: 0.8279 (mtt180) cc_final: 0.7834 (mpt-90) REVERT: A 291 ASP cc_start: 0.8445 (m-30) cc_final: 0.8194 (m-30) REVERT: A 308 LYS cc_start: 0.8886 (mttt) cc_final: 0.8415 (mttm) REVERT: A 355 ASN cc_start: 0.8244 (p0) cc_final: 0.7856 (p0) REVERT: A 498 HIS cc_start: 0.8798 (OUTLIER) cc_final: 0.8563 (p-80) REVERT: A 499 HIS cc_start: 0.8351 (m-70) cc_final: 0.7990 (p-80) REVERT: A 522 ARG cc_start: 0.8869 (tpp80) cc_final: 0.8633 (mmm-85) REVERT: A 526 ASP cc_start: 0.9004 (t70) cc_final: 0.8335 (t70) REVERT: A 534 TYR cc_start: 0.9101 (t80) cc_final: 0.8855 (t80) REVERT: A 548 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8624 (tp) REVERT: A 551 ARG cc_start: 0.8613 (tpp-160) cc_final: 0.8167 (tpt170) REVERT: B 9 GLN cc_start: 0.8710 (mp10) cc_final: 0.8229 (pt0) REVERT: B 12 GLU cc_start: 0.9448 (tp30) cc_final: 0.9246 (mm-30) REVERT: B 39 SER cc_start: 0.9483 (t) cc_final: 0.9277 (p) REVERT: B 52 MET cc_start: 0.9259 (mtm) cc_final: 0.9017 (mtp) REVERT: B 77 MET cc_start: 0.8083 (mmm) cc_final: 0.7871 (mmm) REVERT: B 115 GLU cc_start: 0.8544 (mp0) cc_final: 0.8303 (mp0) REVERT: B 117 LEU cc_start: 0.9129 (OUTLIER) cc_final: 0.8550 (mt) REVERT: B 121 GLU cc_start: 0.9176 (mt-10) cc_final: 0.8520 (mm-30) REVERT: B 125 MET cc_start: 0.9596 (ttt) cc_final: 0.9375 (ttp) REVERT: B 127 ARG cc_start: 0.9274 (ttp-110) cc_final: 0.9048 (ttm110) REVERT: C 166 TRP cc_start: 0.8165 (t60) cc_final: 0.7790 (t60) REVERT: C 180 ARG cc_start: 0.8281 (mtt180) cc_final: 0.7835 (mpt-90) REVERT: C 291 ASP cc_start: 0.8445 (m-30) cc_final: 0.8193 (m-30) REVERT: C 308 LYS cc_start: 0.8886 (mttt) cc_final: 0.8416 (mttm) REVERT: C 355 ASN cc_start: 0.8243 (p0) cc_final: 0.7856 (p0) REVERT: C 498 HIS cc_start: 0.8799 (OUTLIER) cc_final: 0.8564 (p-80) REVERT: C 499 HIS cc_start: 0.8351 (m-70) cc_final: 0.7989 (p-80) REVERT: C 522 ARG cc_start: 0.8869 (tpp80) cc_final: 0.8632 (mmm-85) REVERT: C 526 ASP cc_start: 0.9003 (t70) cc_final: 0.8334 (t70) REVERT: C 534 TYR cc_start: 0.9102 (t80) cc_final: 0.8855 (t80) REVERT: D 9 GLN cc_start: 0.8708 (mp10) cc_final: 0.8228 (pt0) REVERT: D 12 GLU cc_start: 0.9449 (tp30) cc_final: 0.9245 (mm-30) REVERT: D 39 SER cc_start: 0.9483 (t) cc_final: 0.9277 (p) REVERT: D 52 MET cc_start: 0.9259 (mtm) cc_final: 0.9018 (mtp) REVERT: D 77 MET cc_start: 0.8087 (mmm) cc_final: 0.7875 (mmm) REVERT: D 115 GLU cc_start: 0.8544 (mp0) cc_final: 0.8304 (mp0) REVERT: D 117 LEU cc_start: 0.9131 (OUTLIER) cc_final: 0.8550 (mt) REVERT: D 121 GLU cc_start: 0.9175 (mt-10) cc_final: 0.8519 (mm-30) REVERT: D 125 MET cc_start: 0.9596 (ttt) cc_final: 0.9375 (ttp) REVERT: D 127 ARG cc_start: 0.9274 (ttp-110) cc_final: 0.9048 (ttm110) REVERT: E 166 TRP cc_start: 0.8166 (t60) cc_final: 0.7789 (t60) REVERT: E 180 ARG cc_start: 0.8280 (mtt180) cc_final: 0.7834 (mpt-90) REVERT: E 291 ASP cc_start: 0.8445 (m-30) cc_final: 0.8194 (m-30) REVERT: E 308 LYS cc_start: 0.8886 (mttt) cc_final: 0.8415 (mttm) REVERT: E 355 ASN cc_start: 0.8243 (p0) cc_final: 0.7855 (p0) REVERT: E 498 HIS cc_start: 0.8798 (OUTLIER) cc_final: 0.8563 (p-80) REVERT: E 499 HIS cc_start: 0.8351 (m-70) cc_final: 0.7990 (p-80) REVERT: E 522 ARG cc_start: 0.8869 (tpp80) cc_final: 0.8633 (mmm-85) REVERT: E 526 ASP cc_start: 0.9003 (t70) cc_final: 0.8337 (t70) REVERT: E 534 TYR cc_start: 0.9100 (t80) cc_final: 0.8856 (t80) REVERT: E 550 ARG cc_start: 0.9071 (ttm110) cc_final: 0.8848 (mtm110) REVERT: F 9 GLN cc_start: 0.8708 (mp10) cc_final: 0.8228 (pt0) REVERT: F 12 GLU cc_start: 0.9448 (tp30) cc_final: 0.9246 (mm-30) REVERT: F 39 SER cc_start: 0.9483 (t) cc_final: 0.9276 (p) REVERT: F 52 MET cc_start: 0.9259 (mtm) cc_final: 0.9018 (mtp) REVERT: F 77 MET cc_start: 0.8087 (mmm) cc_final: 0.7875 (mmm) REVERT: F 115 GLU cc_start: 0.8545 (mp0) cc_final: 0.8304 (mp0) REVERT: F 117 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8550 (mt) REVERT: F 121 GLU cc_start: 0.9176 (mt-10) cc_final: 0.8520 (mm-30) REVERT: F 125 MET cc_start: 0.9596 (ttt) cc_final: 0.9375 (ttp) REVERT: F 127 ARG cc_start: 0.9273 (ttp-110) cc_final: 0.9047 (ttm110) REVERT: G 166 TRP cc_start: 0.8166 (t60) cc_final: 0.7789 (t60) REVERT: G 180 ARG cc_start: 0.8277 (mtt180) cc_final: 0.7832 (mpt-90) REVERT: G 291 ASP cc_start: 0.8444 (m-30) cc_final: 0.8192 (m-30) REVERT: G 308 LYS cc_start: 0.8885 (mttt) cc_final: 0.8415 (mttm) REVERT: G 355 ASN cc_start: 0.8242 (p0) cc_final: 0.7856 (p0) REVERT: G 498 HIS cc_start: 0.8798 (OUTLIER) cc_final: 0.8563 (p-80) REVERT: G 499 HIS cc_start: 0.8351 (m-70) cc_final: 0.7989 (p-80) REVERT: G 522 ARG cc_start: 0.8869 (tpp80) cc_final: 0.8633 (mmm-85) REVERT: G 526 ASP cc_start: 0.9003 (t70) cc_final: 0.8334 (t70) REVERT: G 534 TYR cc_start: 0.9099 (t80) cc_final: 0.8856 (t80) REVERT: G 547 GLU cc_start: 0.8969 (tp30) cc_final: 0.8697 (tm-30) REVERT: G 548 LEU cc_start: 0.9182 (tp) cc_final: 0.8863 (tp) REVERT: G 549 GLN cc_start: 0.9248 (tp40) cc_final: 0.8915 (tp40) REVERT: H 9 GLN cc_start: 0.8709 (mp10) cc_final: 0.8228 (pt0) REVERT: H 12 GLU cc_start: 0.9449 (tp30) cc_final: 0.9246 (mm-30) REVERT: H 39 SER cc_start: 0.9483 (t) cc_final: 0.9277 (p) REVERT: H 52 MET cc_start: 0.9259 (mtm) cc_final: 0.9018 (mtp) REVERT: H 77 MET cc_start: 0.8084 (mmm) cc_final: 0.7873 (mmm) REVERT: H 115 GLU cc_start: 0.8544 (mp0) cc_final: 0.8303 (mp0) REVERT: H 117 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8550 (mt) REVERT: H 121 GLU cc_start: 0.9176 (mt-10) cc_final: 0.8519 (mm-30) REVERT: H 125 MET cc_start: 0.9596 (ttt) cc_final: 0.9376 (ttp) REVERT: H 127 ARG cc_start: 0.9274 (ttp-110) cc_final: 0.9048 (ttm110) outliers start: 76 outliers final: 52 residues processed: 714 average time/residue: 0.2379 time to fit residues: 254.5333 Evaluate side-chains 715 residues out of total 1660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 654 time to evaluate : 1.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 498 HIS Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 146 MET Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 498 HIS Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain C residue 530 VAL Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 146 MET Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain E residue 240 LEU Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain E residue 254 THR Chi-restraints excluded: chain E residue 345 VAL Chi-restraints excluded: chain E residue 498 HIS Chi-restraints excluded: chain E residue 513 VAL Chi-restraints excluded: chain E residue 530 VAL Chi-restraints excluded: chain E residue 543 VAL Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain F residue 146 MET Chi-restraints excluded: chain G residue 194 ILE Chi-restraints excluded: chain G residue 203 LEU Chi-restraints excluded: chain G residue 240 LEU Chi-restraints excluded: chain G residue 247 ILE Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain G residue 345 VAL Chi-restraints excluded: chain G residue 498 HIS Chi-restraints excluded: chain G residue 513 VAL Chi-restraints excluded: chain G residue 530 VAL Chi-restraints excluded: chain G residue 543 VAL Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 146 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 96 optimal weight: 6.9990 chunk 54 optimal weight: 1.9990 chunk 145 optimal weight: 4.9990 chunk 118 optimal weight: 3.9990 chunk 48 optimal weight: 6.9990 chunk 174 optimal weight: 0.9980 chunk 188 optimal weight: 0.9980 chunk 155 optimal weight: 10.0000 chunk 173 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 140 optimal weight: 0.6980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 366 GLN B 54 ASN B 112 ASN C 366 GLN D 54 ASN D 112 ASN E 366 GLN F 54 ASN F 112 ASN G 366 GLN H 54 ASN H 112 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.3355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15228 Z= 0.228 Angle : 0.574 6.621 20644 Z= 0.305 Chirality : 0.040 0.164 2368 Planarity : 0.004 0.045 2576 Dihedral : 3.930 23.982 2104 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 6.84 % Allowed : 19.82 % Favored : 73.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.97 (0.20), residues: 1904 helix: 3.62 (0.13), residues: 1484 sheet: None (None), residues: 0 loop : -1.41 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 295 HIS 0.006 0.001 HIS D 108 PHE 0.021 0.002 PHE E 260 TYR 0.013 0.002 TYR H 139 ARG 0.008 0.001 ARG H 91 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 767 residues out of total 1660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 668 time to evaluate : 2.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 LEU cc_start: 0.9060 (tp) cc_final: 0.8852 (tp) REVERT: A 166 TRP cc_start: 0.8221 (t60) cc_final: 0.7803 (t60) REVERT: A 180 ARG cc_start: 0.8284 (mtt180) cc_final: 0.7815 (mpt-90) REVERT: A 291 ASP cc_start: 0.8334 (m-30) cc_final: 0.8103 (m-30) REVERT: A 308 LYS cc_start: 0.8859 (mttt) cc_final: 0.8503 (mttm) REVERT: A 355 ASN cc_start: 0.8356 (p0) cc_final: 0.8051 (p0) REVERT: A 499 HIS cc_start: 0.8245 (m-70) cc_final: 0.7875 (p-80) REVERT: A 526 ASP cc_start: 0.8994 (t70) cc_final: 0.8315 (t70) REVERT: B 9 GLN cc_start: 0.8669 (mp10) cc_final: 0.8239 (pt0) REVERT: B 12 GLU cc_start: 0.9466 (tp30) cc_final: 0.9248 (mm-30) REVERT: B 39 SER cc_start: 0.9498 (t) cc_final: 0.9223 (p) REVERT: B 52 MET cc_start: 0.9277 (mtm) cc_final: 0.8975 (mtp) REVERT: B 54 ASN cc_start: 0.9139 (m-40) cc_final: 0.8837 (m110) REVERT: B 72 MET cc_start: 0.8997 (OUTLIER) cc_final: 0.8597 (mtp) REVERT: B 115 GLU cc_start: 0.8529 (mp0) cc_final: 0.8197 (mp0) REVERT: B 117 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8713 (mt) REVERT: B 119 ASP cc_start: 0.9153 (p0) cc_final: 0.8888 (p0) REVERT: B 120 GLU cc_start: 0.9206 (tp30) cc_final: 0.8890 (mm-30) REVERT: B 125 MET cc_start: 0.9622 (ttt) cc_final: 0.9372 (ttp) REVERT: B 127 ARG cc_start: 0.9280 (ttp-110) cc_final: 0.9058 (ttm110) REVERT: C 166 TRP cc_start: 0.8221 (t60) cc_final: 0.7808 (t60) REVERT: C 180 ARG cc_start: 0.8289 (mtt180) cc_final: 0.7819 (mpt-90) REVERT: C 291 ASP cc_start: 0.8330 (m-30) cc_final: 0.8097 (m-30) REVERT: C 308 LYS cc_start: 0.8853 (mttt) cc_final: 0.8498 (mttm) REVERT: C 355 ASN cc_start: 0.8355 (p0) cc_final: 0.8049 (p0) REVERT: C 499 HIS cc_start: 0.8244 (m-70) cc_final: 0.7874 (p-80) REVERT: C 526 ASP cc_start: 0.8992 (t70) cc_final: 0.8316 (t70) REVERT: C 533 GLN cc_start: 0.9158 (tm-30) cc_final: 0.8777 (tm-30) REVERT: D 9 GLN cc_start: 0.8668 (mp10) cc_final: 0.8239 (pt0) REVERT: D 12 GLU cc_start: 0.9467 (tp30) cc_final: 0.9249 (mm-30) REVERT: D 39 SER cc_start: 0.9499 (t) cc_final: 0.9223 (p) REVERT: D 52 MET cc_start: 0.9278 (mtm) cc_final: 0.8975 (mtp) REVERT: D 54 ASN cc_start: 0.9139 (m-40) cc_final: 0.8836 (m110) REVERT: D 72 MET cc_start: 0.8997 (OUTLIER) cc_final: 0.8596 (mtp) REVERT: D 115 GLU cc_start: 0.8527 (mp0) cc_final: 0.8196 (mp0) REVERT: D 117 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8713 (mt) REVERT: D 119 ASP cc_start: 0.9153 (p0) cc_final: 0.8892 (p0) REVERT: D 120 GLU cc_start: 0.9207 (tp30) cc_final: 0.8897 (mm-30) REVERT: D 125 MET cc_start: 0.9622 (ttt) cc_final: 0.9372 (ttp) REVERT: D 127 ARG cc_start: 0.9279 (ttp-110) cc_final: 0.9058 (ttm110) REVERT: E 104 LEU cc_start: 0.9060 (tp) cc_final: 0.8851 (tp) REVERT: E 166 TRP cc_start: 0.8222 (t60) cc_final: 0.7805 (t60) REVERT: E 180 ARG cc_start: 0.8286 (mtt180) cc_final: 0.7816 (mpt-90) REVERT: E 291 ASP cc_start: 0.8334 (m-30) cc_final: 0.8104 (m-30) REVERT: E 308 LYS cc_start: 0.8856 (mttt) cc_final: 0.8502 (mttm) REVERT: E 355 ASN cc_start: 0.8355 (p0) cc_final: 0.8049 (p0) REVERT: E 499 HIS cc_start: 0.8245 (m-70) cc_final: 0.7875 (p-80) REVERT: E 526 ASP cc_start: 0.8992 (t70) cc_final: 0.8315 (t70) REVERT: E 533 GLN cc_start: 0.9156 (tm-30) cc_final: 0.8776 (tm-30) REVERT: F 9 GLN cc_start: 0.8667 (mp10) cc_final: 0.8238 (pt0) REVERT: F 12 GLU cc_start: 0.9466 (tp30) cc_final: 0.9249 (mm-30) REVERT: F 39 SER cc_start: 0.9498 (t) cc_final: 0.9222 (p) REVERT: F 52 MET cc_start: 0.9276 (mtm) cc_final: 0.8975 (mtp) REVERT: F 54 ASN cc_start: 0.9134 (m-40) cc_final: 0.8834 (m110) REVERT: F 72 MET cc_start: 0.8996 (OUTLIER) cc_final: 0.8595 (mtp) REVERT: F 115 GLU cc_start: 0.8528 (mp0) cc_final: 0.8196 (mp0) REVERT: F 117 LEU cc_start: 0.9057 (OUTLIER) cc_final: 0.8710 (mt) REVERT: F 119 ASP cc_start: 0.9154 (p0) cc_final: 0.8889 (p0) REVERT: F 120 GLU cc_start: 0.9207 (tp30) cc_final: 0.8891 (mm-30) REVERT: F 125 MET cc_start: 0.9621 (ttt) cc_final: 0.9373 (ttp) REVERT: F 127 ARG cc_start: 0.9279 (ttp-110) cc_final: 0.9057 (ttm110) REVERT: G 166 TRP cc_start: 0.8221 (t60) cc_final: 0.7806 (t60) REVERT: G 180 ARG cc_start: 0.8289 (mtt180) cc_final: 0.7819 (mpt-90) REVERT: G 291 ASP cc_start: 0.8329 (m-30) cc_final: 0.8097 (m-30) REVERT: G 308 LYS cc_start: 0.8853 (mttt) cc_final: 0.8497 (mttm) REVERT: G 355 ASN cc_start: 0.8356 (p0) cc_final: 0.8050 (p0) REVERT: G 499 HIS cc_start: 0.8245 (m-70) cc_final: 0.7874 (p-80) REVERT: G 526 ASP cc_start: 0.8992 (t70) cc_final: 0.8315 (t70) REVERT: G 533 GLN cc_start: 0.9156 (tm-30) cc_final: 0.8776 (tm-30) REVERT: H 9 GLN cc_start: 0.8669 (mp10) cc_final: 0.8240 (pt0) REVERT: H 12 GLU cc_start: 0.9466 (tp30) cc_final: 0.9249 (mm-30) REVERT: H 39 SER cc_start: 0.9498 (t) cc_final: 0.9222 (p) REVERT: H 52 MET cc_start: 0.9277 (mtm) cc_final: 0.8976 (mtp) REVERT: H 54 ASN cc_start: 0.9135 (m-40) cc_final: 0.8835 (m110) REVERT: H 72 MET cc_start: 0.8997 (OUTLIER) cc_final: 0.8595 (mtp) REVERT: H 115 GLU cc_start: 0.8529 (mp0) cc_final: 0.8198 (mp0) REVERT: H 117 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8712 (mt) REVERT: H 119 ASP cc_start: 0.9153 (p0) cc_final: 0.8889 (p0) REVERT: H 120 GLU cc_start: 0.9207 (tp30) cc_final: 0.8890 (mm-30) REVERT: H 125 MET cc_start: 0.9622 (ttt) cc_final: 0.9373 (ttp) REVERT: H 127 ARG cc_start: 0.9279 (ttp-110) cc_final: 0.9058 (ttm110) outliers start: 99 outliers final: 67 residues processed: 700 average time/residue: 0.2305 time to fit residues: 244.2459 Evaluate side-chains 765 residues out of total 1660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 690 time to evaluate : 1.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 371 CYS Chi-restraints excluded: chain A residue 498 HIS Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 371 CYS Chi-restraints excluded: chain C residue 498 HIS Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 72 MET Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 240 LEU Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain E residue 254 THR Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 345 VAL Chi-restraints excluded: chain E residue 371 CYS Chi-restraints excluded: chain E residue 498 HIS Chi-restraints excluded: chain E residue 513 VAL Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain F residue 72 MET Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain G residue 194 ILE Chi-restraints excluded: chain G residue 240 LEU Chi-restraints excluded: chain G residue 247 ILE Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain G residue 261 LEU Chi-restraints excluded: chain G residue 345 VAL Chi-restraints excluded: chain G residue 371 CYS Chi-restraints excluded: chain G residue 498 HIS Chi-restraints excluded: chain G residue 513 VAL Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 72 MET Chi-restraints excluded: chain H residue 102 SER Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 118 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 172 optimal weight: 4.9990 chunk 131 optimal weight: 0.8980 chunk 90 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 175 optimal weight: 0.7980 chunk 185 optimal weight: 5.9990 chunk 91 optimal weight: 6.9990 chunk 166 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 112 ASN D 112 ASN F 112 ASN H 112 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.3780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 15228 Z= 0.245 Angle : 0.594 6.743 20644 Z= 0.309 Chirality : 0.040 0.226 2368 Planarity : 0.004 0.027 2576 Dihedral : 3.855 21.994 2104 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 6.70 % Allowed : 23.69 % Favored : 69.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.73 (0.20), residues: 1904 helix: 3.36 (0.13), residues: 1484 sheet: None (None), residues: 0 loop : -1.12 (0.33), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 369 HIS 0.005 0.001 HIS F 108 PHE 0.019 0.002 PHE G 260 TYR 0.018 0.002 TYR E 268 ARG 0.006 0.001 ARG C 522 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 751 residues out of total 1660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 654 time to evaluate : 1.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 LEU cc_start: 0.9040 (tp) cc_final: 0.8835 (tp) REVERT: A 166 TRP cc_start: 0.8150 (t60) cc_final: 0.7663 (t60) REVERT: A 180 ARG cc_start: 0.8095 (mtt180) cc_final: 0.7597 (mtt-85) REVERT: A 227 ARG cc_start: 0.9084 (OUTLIER) cc_final: 0.7770 (ttp80) REVERT: A 291 ASP cc_start: 0.8311 (m-30) cc_final: 0.8109 (m-30) REVERT: A 308 LYS cc_start: 0.8801 (mttt) cc_final: 0.8581 (mmtp) REVERT: A 355 ASN cc_start: 0.8416 (p0) cc_final: 0.8095 (p0) REVERT: A 499 HIS cc_start: 0.8120 (m-70) cc_final: 0.7761 (p-80) REVERT: A 526 ASP cc_start: 0.9028 (t70) cc_final: 0.8356 (t70) REVERT: A 533 GLN cc_start: 0.9141 (tm-30) cc_final: 0.8853 (tm-30) REVERT: A 534 TYR cc_start: 0.9290 (t80) cc_final: 0.8666 (t80) REVERT: B 9 GLN cc_start: 0.8779 (mp10) cc_final: 0.8359 (pt0) REVERT: B 12 GLU cc_start: 0.9478 (tp30) cc_final: 0.9232 (mm-30) REVERT: B 39 SER cc_start: 0.9378 (t) cc_final: 0.9128 (p) REVERT: B 46 GLU cc_start: 0.9017 (tp30) cc_final: 0.8754 (tp30) REVERT: B 52 MET cc_start: 0.9300 (mtm) cc_final: 0.9068 (mtp) REVERT: B 54 ASN cc_start: 0.9342 (m-40) cc_final: 0.8972 (m110) REVERT: B 72 MET cc_start: 0.9117 (OUTLIER) cc_final: 0.8684 (mtp) REVERT: B 115 GLU cc_start: 0.8722 (mp0) cc_final: 0.8336 (mp0) REVERT: B 117 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8473 (mt) REVERT: B 120 GLU cc_start: 0.9148 (tp30) cc_final: 0.8885 (mm-30) REVERT: B 121 GLU cc_start: 0.8994 (mt-10) cc_final: 0.8617 (mm-30) REVERT: B 125 MET cc_start: 0.9606 (ttt) cc_final: 0.9327 (ttt) REVERT: B 127 ARG cc_start: 0.9277 (ttp-110) cc_final: 0.8774 (mtm-85) REVERT: C 166 TRP cc_start: 0.8150 (t60) cc_final: 0.7670 (t60) REVERT: C 180 ARG cc_start: 0.8102 (mtt180) cc_final: 0.7602 (mtt-85) REVERT: C 227 ARG cc_start: 0.9085 (OUTLIER) cc_final: 0.7770 (ttp80) REVERT: C 291 ASP cc_start: 0.8305 (m-30) cc_final: 0.8101 (m-30) REVERT: C 308 LYS cc_start: 0.8786 (mttt) cc_final: 0.8566 (mmtp) REVERT: C 355 ASN cc_start: 0.8416 (p0) cc_final: 0.8095 (p0) REVERT: C 499 HIS cc_start: 0.8121 (m-70) cc_final: 0.7761 (p-80) REVERT: C 526 ASP cc_start: 0.9030 (t70) cc_final: 0.8360 (t70) REVERT: C 533 GLN cc_start: 0.9198 (tm-30) cc_final: 0.8792 (tm-30) REVERT: C 534 TYR cc_start: 0.9278 (t80) cc_final: 0.8700 (t80) REVERT: D 9 GLN cc_start: 0.8779 (mp10) cc_final: 0.8359 (pt0) REVERT: D 12 GLU cc_start: 0.9478 (tp30) cc_final: 0.9233 (mm-30) REVERT: D 39 SER cc_start: 0.9377 (t) cc_final: 0.9127 (p) REVERT: D 46 GLU cc_start: 0.9016 (tp30) cc_final: 0.8754 (tp30) REVERT: D 52 MET cc_start: 0.9301 (mtm) cc_final: 0.9070 (mtp) REVERT: D 54 ASN cc_start: 0.9344 (m-40) cc_final: 0.8975 (m110) REVERT: D 72 MET cc_start: 0.9117 (OUTLIER) cc_final: 0.8613 (mtm) REVERT: D 115 GLU cc_start: 0.8722 (mp0) cc_final: 0.8335 (mp0) REVERT: D 117 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8474 (mt) REVERT: D 120 GLU cc_start: 0.9148 (tp30) cc_final: 0.8885 (mm-30) REVERT: D 121 GLU cc_start: 0.8993 (mt-10) cc_final: 0.8617 (mm-30) REVERT: D 125 MET cc_start: 0.9605 (ttt) cc_final: 0.9326 (ttt) REVERT: D 127 ARG cc_start: 0.9277 (ttp-110) cc_final: 0.8774 (mtm-85) REVERT: E 104 LEU cc_start: 0.9039 (tp) cc_final: 0.8835 (tp) REVERT: E 166 TRP cc_start: 0.8150 (t60) cc_final: 0.7663 (t60) REVERT: E 180 ARG cc_start: 0.8097 (mtt180) cc_final: 0.7598 (mtt-85) REVERT: E 227 ARG cc_start: 0.9084 (OUTLIER) cc_final: 0.7769 (ttp80) REVERT: E 291 ASP cc_start: 0.8314 (m-30) cc_final: 0.8110 (m-30) REVERT: E 308 LYS cc_start: 0.8800 (mttt) cc_final: 0.8580 (mmtp) REVERT: E 355 ASN cc_start: 0.8417 (p0) cc_final: 0.8097 (p0) REVERT: E 499 HIS cc_start: 0.8122 (m-70) cc_final: 0.7761 (p-80) REVERT: E 526 ASP cc_start: 0.9030 (t70) cc_final: 0.8360 (t70) REVERT: E 533 GLN cc_start: 0.9197 (tm-30) cc_final: 0.8785 (tm-30) REVERT: E 534 TYR cc_start: 0.9276 (t80) cc_final: 0.8711 (t80) REVERT: F 9 GLN cc_start: 0.8780 (mp10) cc_final: 0.8360 (pt0) REVERT: F 12 GLU cc_start: 0.9478 (tp30) cc_final: 0.9232 (mm-30) REVERT: F 39 SER cc_start: 0.9376 (t) cc_final: 0.9125 (p) REVERT: F 46 GLU cc_start: 0.9015 (tp30) cc_final: 0.8753 (tp30) REVERT: F 52 MET cc_start: 0.9300 (mtm) cc_final: 0.9069 (mtp) REVERT: F 54 ASN cc_start: 0.9314 (m-40) cc_final: 0.8946 (m110) REVERT: F 72 MET cc_start: 0.9118 (OUTLIER) cc_final: 0.8685 (mtp) REVERT: F 115 GLU cc_start: 0.8717 (mp0) cc_final: 0.8304 (mp0) REVERT: F 117 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8470 (mt) REVERT: F 120 GLU cc_start: 0.9150 (tp30) cc_final: 0.8886 (mm-30) REVERT: F 121 GLU cc_start: 0.8993 (mt-10) cc_final: 0.8619 (mm-30) REVERT: F 125 MET cc_start: 0.9606 (ttt) cc_final: 0.9327 (ttt) REVERT: F 127 ARG cc_start: 0.9277 (ttp-110) cc_final: 0.8772 (mtm-85) REVERT: G 166 TRP cc_start: 0.8152 (t60) cc_final: 0.7670 (t60) REVERT: G 180 ARG cc_start: 0.8100 (mtt180) cc_final: 0.7600 (mtt-85) REVERT: G 227 ARG cc_start: 0.9083 (OUTLIER) cc_final: 0.7770 (ttp80) REVERT: G 291 ASP cc_start: 0.8303 (m-30) cc_final: 0.8099 (m-30) REVERT: G 308 LYS cc_start: 0.8787 (mttt) cc_final: 0.8566 (mmtp) REVERT: G 355 ASN cc_start: 0.8416 (p0) cc_final: 0.8094 (p0) REVERT: G 499 HIS cc_start: 0.8122 (m-70) cc_final: 0.7761 (p-80) REVERT: G 526 ASP cc_start: 0.9032 (t70) cc_final: 0.8361 (t70) REVERT: G 533 GLN cc_start: 0.9198 (tm-30) cc_final: 0.8786 (tm-30) REVERT: G 534 TYR cc_start: 0.9272 (t80) cc_final: 0.8694 (t80) REVERT: H 9 GLN cc_start: 0.8779 (mp10) cc_final: 0.8359 (pt0) REVERT: H 12 GLU cc_start: 0.9478 (tp30) cc_final: 0.9232 (mm-30) REVERT: H 39 SER cc_start: 0.9376 (t) cc_final: 0.9126 (p) REVERT: H 46 GLU cc_start: 0.9017 (tp30) cc_final: 0.8755 (tp30) REVERT: H 52 MET cc_start: 0.9301 (mtm) cc_final: 0.9069 (mtp) REVERT: H 54 ASN cc_start: 0.9314 (m-40) cc_final: 0.8946 (m110) REVERT: H 72 MET cc_start: 0.9117 (OUTLIER) cc_final: 0.8685 (mtp) REVERT: H 115 GLU cc_start: 0.8723 (mp0) cc_final: 0.8336 (mp0) REVERT: H 117 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8472 (mt) REVERT: H 120 GLU cc_start: 0.9150 (tp30) cc_final: 0.8886 (mm-30) REVERT: H 121 GLU cc_start: 0.8992 (mt-10) cc_final: 0.8618 (mm-30) REVERT: H 125 MET cc_start: 0.9605 (ttt) cc_final: 0.9326 (ttt) REVERT: H 127 ARG cc_start: 0.9276 (ttp-110) cc_final: 0.8774 (mtm-85) outliers start: 97 outliers final: 71 residues processed: 679 average time/residue: 0.2351 time to fit residues: 241.4589 Evaluate side-chains 724 residues out of total 1660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 641 time to evaluate : 1.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 TRP Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 227 ARG Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 371 CYS Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 547 GLU Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain C residue 110 TRP Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 227 ARG Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 371 CYS Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain C residue 530 VAL Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 72 MET Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain E residue 110 TRP Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 227 ARG Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain E residue 254 THR Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 371 CYS Chi-restraints excluded: chain E residue 513 VAL Chi-restraints excluded: chain E residue 530 VAL Chi-restraints excluded: chain E residue 543 VAL Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 72 MET Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain G residue 110 TRP Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 194 ILE Chi-restraints excluded: chain G residue 227 ARG Chi-restraints excluded: chain G residue 247 ILE Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain G residue 261 LEU Chi-restraints excluded: chain G residue 371 CYS Chi-restraints excluded: chain G residue 513 VAL Chi-restraints excluded: chain G residue 530 VAL Chi-restraints excluded: chain G residue 543 VAL Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 72 MET Chi-restraints excluded: chain H residue 102 SER Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 118 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 154 optimal weight: 6.9990 chunk 105 optimal weight: 5.9990 chunk 2 optimal weight: 4.9990 chunk 138 optimal weight: 0.6980 chunk 76 optimal weight: 4.9990 chunk 158 optimal weight: 0.6980 chunk 128 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 94 optimal weight: 0.0060 chunk 166 optimal weight: 1.9990 chunk 46 optimal weight: 0.0070 overall best weight: 0.4414 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 112 ASN D 112 ASN F 112 ASN H 112 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.3959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15228 Z= 0.172 Angle : 0.583 7.993 20644 Z= 0.293 Chirality : 0.039 0.150 2368 Planarity : 0.004 0.052 2576 Dihedral : 3.677 19.106 2104 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 4.70 % Allowed : 25.97 % Favored : 69.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.68 (0.20), residues: 1904 helix: 3.28 (0.13), residues: 1488 sheet: None (None), residues: 0 loop : -0.97 (0.34), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP E 369 HIS 0.005 0.001 HIS F 108 PHE 0.019 0.001 PHE E 260 TYR 0.018 0.002 TYR A 268 ARG 0.008 0.001 ARG H 91 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 734 residues out of total 1660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 666 time to evaluate : 1.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 LEU cc_start: 0.9054 (tp) cc_final: 0.8843 (tp) REVERT: A 166 TRP cc_start: 0.8141 (t60) cc_final: 0.7707 (t60) REVERT: A 180 ARG cc_start: 0.8035 (mtt180) cc_final: 0.7442 (mtt-85) REVERT: A 227 ARG cc_start: 0.9052 (OUTLIER) cc_final: 0.7919 (ttp80) REVERT: A 308 LYS cc_start: 0.8725 (mttt) cc_final: 0.8444 (mttm) REVERT: A 355 ASN cc_start: 0.8453 (p0) cc_final: 0.8094 (p0) REVERT: A 498 HIS cc_start: 0.8625 (m90) cc_final: 0.8400 (p-80) REVERT: A 499 HIS cc_start: 0.8047 (m-70) cc_final: 0.7822 (p-80) REVERT: A 526 ASP cc_start: 0.8964 (t70) cc_final: 0.8260 (t70) REVERT: A 534 TYR cc_start: 0.9157 (t80) cc_final: 0.8587 (t80) REVERT: B 12 GLU cc_start: 0.9482 (tp30) cc_final: 0.9229 (mm-30) REVERT: B 39 SER cc_start: 0.9344 (t) cc_final: 0.9074 (p) REVERT: B 46 GLU cc_start: 0.8956 (tp30) cc_final: 0.8694 (tp30) REVERT: B 52 MET cc_start: 0.9240 (mtm) cc_final: 0.8990 (mtp) REVERT: B 54 ASN cc_start: 0.9308 (m-40) cc_final: 0.8933 (m110) REVERT: B 115 GLU cc_start: 0.8770 (mp0) cc_final: 0.8305 (mp0) REVERT: B 117 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8434 (mt) REVERT: B 120 GLU cc_start: 0.9146 (tp30) cc_final: 0.8849 (mm-30) REVERT: B 121 GLU cc_start: 0.8901 (mt-10) cc_final: 0.8302 (mm-30) REVERT: B 124 GLU cc_start: 0.9052 (tp30) cc_final: 0.8772 (tp30) REVERT: B 125 MET cc_start: 0.9605 (ttt) cc_final: 0.9357 (ttp) REVERT: B 127 ARG cc_start: 0.9329 (ttp-110) cc_final: 0.9008 (ttm110) REVERT: C 166 TRP cc_start: 0.8141 (t60) cc_final: 0.7667 (t60) REVERT: C 180 ARG cc_start: 0.8037 (mtt180) cc_final: 0.7444 (mtt-85) REVERT: C 227 ARG cc_start: 0.9052 (OUTLIER) cc_final: 0.7792 (ttp80) REVERT: C 308 LYS cc_start: 0.8710 (mttt) cc_final: 0.8507 (mmtp) REVERT: C 355 ASN cc_start: 0.8449 (p0) cc_final: 0.8090 (p0) REVERT: C 498 HIS cc_start: 0.8625 (m90) cc_final: 0.8400 (p-80) REVERT: C 499 HIS cc_start: 0.8047 (m-70) cc_final: 0.7822 (p-80) REVERT: C 526 ASP cc_start: 0.8963 (t70) cc_final: 0.8259 (t70) REVERT: C 534 TYR cc_start: 0.9136 (t80) cc_final: 0.8578 (t80) REVERT: D 9 GLN cc_start: 0.8849 (mp10) cc_final: 0.8475 (pt0) REVERT: D 12 GLU cc_start: 0.9483 (tp30) cc_final: 0.9230 (mm-30) REVERT: D 39 SER cc_start: 0.9343 (t) cc_final: 0.9072 (p) REVERT: D 46 GLU cc_start: 0.8956 (tp30) cc_final: 0.8694 (tp30) REVERT: D 52 MET cc_start: 0.9240 (mtm) cc_final: 0.8990 (mtp) REVERT: D 54 ASN cc_start: 0.9308 (m-40) cc_final: 0.8934 (m110) REVERT: D 115 GLU cc_start: 0.8770 (mp0) cc_final: 0.8304 (mp0) REVERT: D 117 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8433 (mt) REVERT: D 120 GLU cc_start: 0.9146 (tp30) cc_final: 0.8849 (mm-30) REVERT: D 121 GLU cc_start: 0.8902 (mt-10) cc_final: 0.8304 (mm-30) REVERT: D 124 GLU cc_start: 0.9053 (tp30) cc_final: 0.8772 (tp30) REVERT: D 125 MET cc_start: 0.9604 (ttt) cc_final: 0.9358 (ttp) REVERT: D 127 ARG cc_start: 0.9330 (ttp-110) cc_final: 0.9007 (ttm110) REVERT: E 104 LEU cc_start: 0.9054 (tp) cc_final: 0.8844 (tp) REVERT: E 166 TRP cc_start: 0.8140 (t60) cc_final: 0.7706 (t60) REVERT: E 180 ARG cc_start: 0.8037 (mtt180) cc_final: 0.7444 (mtt-85) REVERT: E 227 ARG cc_start: 0.9051 (OUTLIER) cc_final: 0.7790 (ttp80) REVERT: E 308 LYS cc_start: 0.8726 (mttt) cc_final: 0.8443 (mttm) REVERT: E 355 ASN cc_start: 0.8450 (p0) cc_final: 0.8091 (p0) REVERT: E 498 HIS cc_start: 0.8625 (m90) cc_final: 0.8401 (p-80) REVERT: E 499 HIS cc_start: 0.8048 (m-70) cc_final: 0.7823 (p-80) REVERT: E 526 ASP cc_start: 0.8962 (t70) cc_final: 0.8261 (t70) REVERT: E 534 TYR cc_start: 0.9135 (t80) cc_final: 0.8596 (t80) REVERT: F 12 GLU cc_start: 0.9483 (tp30) cc_final: 0.9229 (mm-30) REVERT: F 39 SER cc_start: 0.9343 (t) cc_final: 0.9073 (p) REVERT: F 46 GLU cc_start: 0.8955 (tp30) cc_final: 0.8694 (tp30) REVERT: F 52 MET cc_start: 0.9240 (mtm) cc_final: 0.8989 (mtp) REVERT: F 54 ASN cc_start: 0.9279 (m-40) cc_final: 0.8889 (m110) REVERT: F 115 GLU cc_start: 0.8771 (mp0) cc_final: 0.8305 (mp0) REVERT: F 117 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8434 (mt) REVERT: F 120 GLU cc_start: 0.9146 (tp30) cc_final: 0.8850 (mm-30) REVERT: F 121 GLU cc_start: 0.8902 (mt-10) cc_final: 0.8304 (mm-30) REVERT: F 124 GLU cc_start: 0.9053 (tp30) cc_final: 0.8774 (tp30) REVERT: F 125 MET cc_start: 0.9605 (ttt) cc_final: 0.9358 (ttp) REVERT: F 127 ARG cc_start: 0.9329 (ttp-110) cc_final: 0.9008 (ttm110) REVERT: G 166 TRP cc_start: 0.8141 (t60) cc_final: 0.7666 (t60) REVERT: G 180 ARG cc_start: 0.8036 (mtt180) cc_final: 0.7444 (mtt-85) REVERT: G 227 ARG cc_start: 0.9050 (OUTLIER) cc_final: 0.7918 (ttp80) REVERT: G 308 LYS cc_start: 0.8709 (mttt) cc_final: 0.8507 (mmtp) REVERT: G 355 ASN cc_start: 0.8452 (p0) cc_final: 0.8092 (p0) REVERT: G 498 HIS cc_start: 0.8625 (m90) cc_final: 0.8400 (p-80) REVERT: G 499 HIS cc_start: 0.8049 (m-70) cc_final: 0.7823 (p-80) REVERT: G 526 ASP cc_start: 0.8964 (t70) cc_final: 0.8260 (t70) REVERT: G 534 TYR cc_start: 0.9141 (t80) cc_final: 0.8595 (t80) REVERT: H 12 GLU cc_start: 0.9482 (tp30) cc_final: 0.9230 (mm-30) REVERT: H 39 SER cc_start: 0.9344 (t) cc_final: 0.9074 (p) REVERT: H 46 GLU cc_start: 0.8955 (tp30) cc_final: 0.8694 (tp30) REVERT: H 52 MET cc_start: 0.9241 (mtm) cc_final: 0.8991 (mtp) REVERT: H 54 ASN cc_start: 0.9279 (m-40) cc_final: 0.8889 (m110) REVERT: H 115 GLU cc_start: 0.8769 (mp0) cc_final: 0.8304 (mp0) REVERT: H 117 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8432 (mt) REVERT: H 120 GLU cc_start: 0.9147 (tp30) cc_final: 0.8850 (mm-30) REVERT: H 121 GLU cc_start: 0.8901 (mt-10) cc_final: 0.8303 (mm-30) REVERT: H 124 GLU cc_start: 0.9052 (tp30) cc_final: 0.8773 (tp30) REVERT: H 125 MET cc_start: 0.9605 (ttt) cc_final: 0.9358 (ttp) REVERT: H 127 ARG cc_start: 0.9330 (ttp-110) cc_final: 0.9008 (ttm110) outliers start: 68 outliers final: 33 residues processed: 687 average time/residue: 0.2415 time to fit residues: 247.7556 Evaluate side-chains 687 residues out of total 1660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 646 time to evaluate : 1.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 TRP Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 227 ARG Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 547 GLU Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 146 MET Chi-restraints excluded: chain C residue 110 TRP Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 227 ARG Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 146 MET Chi-restraints excluded: chain E residue 110 TRP Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 227 ARG Chi-restraints excluded: chain E residue 513 VAL Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain F residue 146 MET Chi-restraints excluded: chain G residue 110 TRP Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain G residue 194 ILE Chi-restraints excluded: chain G residue 227 ARG Chi-restraints excluded: chain G residue 513 VAL Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 146 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 62 optimal weight: 0.9980 chunk 167 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 108 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 185 optimal weight: 0.0170 chunk 154 optimal weight: 3.9990 chunk 86 optimal weight: 0.3980 chunk 15 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 97 optimal weight: 0.7980 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 GLN B 112 ASN C 357 GLN D 112 ASN E 357 GLN F 112 ASN H 112 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.4131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15228 Z= 0.175 Angle : 0.570 10.271 20644 Z= 0.285 Chirality : 0.041 0.346 2368 Planarity : 0.003 0.033 2576 Dihedral : 3.544 17.767 2104 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 4.77 % Allowed : 26.59 % Favored : 68.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.49 (0.20), residues: 1904 helix: 3.13 (0.13), residues: 1488 sheet: None (None), residues: 0 loop : -0.99 (0.32), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP G 369 HIS 0.005 0.001 HIS F 108 PHE 0.018 0.001 PHE E 260 TYR 0.018 0.002 TYR A 268 ARG 0.006 0.001 ARG D 91 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 707 residues out of total 1660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 638 time to evaluate : 1.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 LEU cc_start: 0.8986 (tp) cc_final: 0.8760 (tp) REVERT: A 166 TRP cc_start: 0.8096 (t60) cc_final: 0.7610 (t60) REVERT: A 180 ARG cc_start: 0.8054 (mtt180) cc_final: 0.7452 (mtt-85) REVERT: A 227 ARG cc_start: 0.9013 (OUTLIER) cc_final: 0.7911 (ttp80) REVERT: A 229 LEU cc_start: 0.9544 (mt) cc_final: 0.9334 (mm) REVERT: A 308 LYS cc_start: 0.8721 (mttt) cc_final: 0.8449 (mttm) REVERT: A 355 ASN cc_start: 0.8466 (p0) cc_final: 0.8182 (p0) REVERT: A 498 HIS cc_start: 0.8637 (OUTLIER) cc_final: 0.8432 (p-80) REVERT: A 499 HIS cc_start: 0.8172 (m-70) cc_final: 0.7923 (p-80) REVERT: A 526 ASP cc_start: 0.8940 (t70) cc_final: 0.8168 (t70) REVERT: A 534 TYR cc_start: 0.9187 (t80) cc_final: 0.8818 (t80) REVERT: B 9 GLN cc_start: 0.8844 (mp10) cc_final: 0.8457 (pt0) REVERT: B 12 GLU cc_start: 0.9483 (tp30) cc_final: 0.9215 (mm-30) REVERT: B 39 SER cc_start: 0.9307 (t) cc_final: 0.9058 (p) REVERT: B 46 GLU cc_start: 0.8992 (tp30) cc_final: 0.8723 (tp30) REVERT: B 52 MET cc_start: 0.9137 (mtm) cc_final: 0.8826 (mtm) REVERT: B 54 ASN cc_start: 0.9285 (m-40) cc_final: 0.8918 (m110) REVERT: B 56 VAL cc_start: 0.8885 (t) cc_final: 0.8535 (p) REVERT: B 72 MET cc_start: 0.9331 (ptm) cc_final: 0.8724 (tmm) REVERT: B 75 ARG cc_start: 0.8239 (ttp-170) cc_final: 0.7795 (ptt90) REVERT: B 115 GLU cc_start: 0.8839 (mp0) cc_final: 0.8314 (mp0) REVERT: B 117 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8368 (mt) REVERT: B 121 GLU cc_start: 0.8778 (mt-10) cc_final: 0.8192 (mm-30) REVERT: B 125 MET cc_start: 0.9616 (ttt) cc_final: 0.9376 (ttp) REVERT: C 166 TRP cc_start: 0.8095 (t60) cc_final: 0.7615 (t60) REVERT: C 180 ARG cc_start: 0.8055 (mtt180) cc_final: 0.7453 (mtt-85) REVERT: C 227 ARG cc_start: 0.9014 (OUTLIER) cc_final: 0.7911 (ttp80) REVERT: C 229 LEU cc_start: 0.9545 (mt) cc_final: 0.9335 (mm) REVERT: C 308 LYS cc_start: 0.8703 (mttt) cc_final: 0.8438 (mttm) REVERT: C 355 ASN cc_start: 0.8467 (p0) cc_final: 0.8199 (p0) REVERT: C 498 HIS cc_start: 0.8638 (OUTLIER) cc_final: 0.8432 (p-80) REVERT: C 499 HIS cc_start: 0.8172 (m-70) cc_final: 0.7923 (p-80) REVERT: C 526 ASP cc_start: 0.8945 (t70) cc_final: 0.8168 (t70) REVERT: C 534 TYR cc_start: 0.9197 (t80) cc_final: 0.8913 (t80) REVERT: D 9 GLN cc_start: 0.8868 (mp10) cc_final: 0.8501 (pt0) REVERT: D 12 GLU cc_start: 0.9483 (tp30) cc_final: 0.9212 (mm-30) REVERT: D 39 SER cc_start: 0.9306 (t) cc_final: 0.9059 (p) REVERT: D 46 GLU cc_start: 0.8991 (tp30) cc_final: 0.8722 (tp30) REVERT: D 52 MET cc_start: 0.9136 (mtm) cc_final: 0.8825 (mtm) REVERT: D 54 ASN cc_start: 0.9285 (m-40) cc_final: 0.8917 (m110) REVERT: D 56 VAL cc_start: 0.8886 (t) cc_final: 0.8536 (p) REVERT: D 72 MET cc_start: 0.9329 (ptm) cc_final: 0.8722 (tmm) REVERT: D 75 ARG cc_start: 0.8240 (ttp-170) cc_final: 0.7795 (ptt90) REVERT: D 115 GLU cc_start: 0.8838 (mp0) cc_final: 0.8313 (mp0) REVERT: D 117 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8370 (mt) REVERT: D 121 GLU cc_start: 0.8777 (mt-10) cc_final: 0.8193 (mm-30) REVERT: D 125 MET cc_start: 0.9617 (ttt) cc_final: 0.9376 (ttp) REVERT: E 104 LEU cc_start: 0.8990 (tp) cc_final: 0.8763 (tp) REVERT: E 166 TRP cc_start: 0.8097 (t60) cc_final: 0.7612 (t60) REVERT: E 180 ARG cc_start: 0.8056 (mtt180) cc_final: 0.7454 (mtt-85) REVERT: E 227 ARG cc_start: 0.9013 (OUTLIER) cc_final: 0.7911 (ttp80) REVERT: E 229 LEU cc_start: 0.9545 (mt) cc_final: 0.9335 (mm) REVERT: E 308 LYS cc_start: 0.8722 (mttt) cc_final: 0.8449 (mttm) REVERT: E 355 ASN cc_start: 0.8467 (p0) cc_final: 0.8183 (p0) REVERT: E 498 HIS cc_start: 0.8636 (OUTLIER) cc_final: 0.8431 (p-80) REVERT: E 499 HIS cc_start: 0.8172 (m-70) cc_final: 0.7923 (p-80) REVERT: E 526 ASP cc_start: 0.8944 (t70) cc_final: 0.8167 (t70) REVERT: E 534 TYR cc_start: 0.9186 (t80) cc_final: 0.8874 (t80) REVERT: F 9 GLN cc_start: 0.8843 (mp10) cc_final: 0.8455 (pt0) REVERT: F 12 GLU cc_start: 0.9482 (tp30) cc_final: 0.9215 (mm-30) REVERT: F 39 SER cc_start: 0.9305 (t) cc_final: 0.9057 (p) REVERT: F 46 GLU cc_start: 0.8991 (tp30) cc_final: 0.8724 (tp30) REVERT: F 52 MET cc_start: 0.9142 (mtm) cc_final: 0.8824 (mtm) REVERT: F 54 ASN cc_start: 0.9257 (m-40) cc_final: 0.8874 (m110) REVERT: F 56 VAL cc_start: 0.8886 (t) cc_final: 0.8535 (p) REVERT: F 72 MET cc_start: 0.9331 (ptm) cc_final: 0.8723 (tmm) REVERT: F 75 ARG cc_start: 0.8240 (ttp-170) cc_final: 0.7795 (ptt90) REVERT: F 115 GLU cc_start: 0.8840 (mp0) cc_final: 0.8314 (mp0) REVERT: F 117 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8368 (mt) REVERT: F 121 GLU cc_start: 0.8778 (mt-10) cc_final: 0.8192 (mm-30) REVERT: F 125 MET cc_start: 0.9616 (ttt) cc_final: 0.9376 (ttp) REVERT: G 166 TRP cc_start: 0.8097 (t60) cc_final: 0.7616 (t60) REVERT: G 180 ARG cc_start: 0.8053 (mtt180) cc_final: 0.7451 (mtt-85) REVERT: G 227 ARG cc_start: 0.9013 (OUTLIER) cc_final: 0.7912 (ttp80) REVERT: G 229 LEU cc_start: 0.9544 (mt) cc_final: 0.9334 (mm) REVERT: G 308 LYS cc_start: 0.8702 (mttt) cc_final: 0.8436 (mttm) REVERT: G 355 ASN cc_start: 0.8467 (p0) cc_final: 0.8181 (p0) REVERT: G 498 HIS cc_start: 0.8636 (OUTLIER) cc_final: 0.8431 (p-80) REVERT: G 499 HIS cc_start: 0.8172 (m-70) cc_final: 0.7924 (p-80) REVERT: G 526 ASP cc_start: 0.8939 (t70) cc_final: 0.8163 (t70) REVERT: G 534 TYR cc_start: 0.9153 (t80) cc_final: 0.8884 (t80) REVERT: H 9 GLN cc_start: 0.8844 (mp10) cc_final: 0.8456 (pt0) REVERT: H 12 GLU cc_start: 0.9482 (tp30) cc_final: 0.9215 (mm-30) REVERT: H 39 SER cc_start: 0.9306 (t) cc_final: 0.9057 (p) REVERT: H 46 GLU cc_start: 0.8993 (tp30) cc_final: 0.8724 (tp30) REVERT: H 52 MET cc_start: 0.9144 (mtm) cc_final: 0.8828 (mtm) REVERT: H 54 ASN cc_start: 0.9258 (m-40) cc_final: 0.8876 (m110) REVERT: H 56 VAL cc_start: 0.8885 (t) cc_final: 0.8532 (p) REVERT: H 72 MET cc_start: 0.9331 (ptm) cc_final: 0.8723 (tmm) REVERT: H 75 ARG cc_start: 0.8239 (ttp-170) cc_final: 0.7794 (ptt90) REVERT: H 115 GLU cc_start: 0.8840 (mp0) cc_final: 0.8314 (mp0) REVERT: H 117 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8368 (mt) REVERT: H 121 GLU cc_start: 0.8779 (mt-10) cc_final: 0.8191 (mm-30) REVERT: H 125 MET cc_start: 0.9616 (ttt) cc_final: 0.9375 (ttp) outliers start: 69 outliers final: 46 residues processed: 661 average time/residue: 0.2438 time to fit residues: 239.5501 Evaluate side-chains 683 residues out of total 1660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 625 time to evaluate : 1.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 TRP Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 227 ARG Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 371 CYS Chi-restraints excluded: chain A residue 498 HIS Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 547 GLU Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 146 MET Chi-restraints excluded: chain C residue 110 TRP Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 227 ARG Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 371 CYS Chi-restraints excluded: chain C residue 498 HIS Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 146 MET Chi-restraints excluded: chain E residue 110 TRP Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 227 ARG Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 371 CYS Chi-restraints excluded: chain E residue 498 HIS Chi-restraints excluded: chain E residue 513 VAL Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain F residue 146 MET Chi-restraints excluded: chain G residue 110 TRP Chi-restraints excluded: chain G residue 193 LEU Chi-restraints excluded: chain G residue 227 ARG Chi-restraints excluded: chain G residue 261 LEU Chi-restraints excluded: chain G residue 371 CYS Chi-restraints excluded: chain G residue 498 HIS Chi-restraints excluded: chain G residue 513 VAL Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 102 SER Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 146 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 179 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 105 optimal weight: 5.9990 chunk 135 optimal weight: 4.9990 chunk 156 optimal weight: 0.9980 chunk 103 optimal weight: 5.9990 chunk 185 optimal weight: 3.9990 chunk 115 optimal weight: 0.9990 chunk 112 optimal weight: 0.9980 chunk 85 optimal weight: 3.9990 chunk 114 optimal weight: 0.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 112 ASN D 112 ASN F 112 ASN G 357 GLN H 112 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.4299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15228 Z= 0.209 Angle : 0.581 9.282 20644 Z= 0.293 Chirality : 0.039 0.232 2368 Planarity : 0.004 0.066 2576 Dihedral : 3.492 17.933 2104 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 4.77 % Allowed : 26.17 % Favored : 69.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.45 (0.20), residues: 1904 helix: 3.10 (0.13), residues: 1488 sheet: None (None), residues: 0 loop : -1.04 (0.32), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP E 369 HIS 0.004 0.001 HIS B 108 PHE 0.023 0.001 PHE E 341 TYR 0.020 0.002 TYR E 268 ARG 0.013 0.001 ARG B 91 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 697 residues out of total 1660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 628 time to evaluate : 1.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 LEU cc_start: 0.8990 (tp) cc_final: 0.8773 (tp) REVERT: A 166 TRP cc_start: 0.8112 (t60) cc_final: 0.7641 (t60) REVERT: A 180 ARG cc_start: 0.7868 (mtt180) cc_final: 0.7294 (mtt-85) REVERT: A 227 ARG cc_start: 0.8977 (OUTLIER) cc_final: 0.7818 (ttp80) REVERT: A 308 LYS cc_start: 0.8772 (mttt) cc_final: 0.8454 (mttm) REVERT: A 355 ASN cc_start: 0.8548 (p0) cc_final: 0.8285 (p0) REVERT: A 499 HIS cc_start: 0.8211 (m-70) cc_final: 0.7798 (p-80) REVERT: A 526 ASP cc_start: 0.8998 (t70) cc_final: 0.8321 (t70) REVERT: A 533 GLN cc_start: 0.9165 (tm-30) cc_final: 0.8938 (tm-30) REVERT: B 9 GLN cc_start: 0.8847 (mp10) cc_final: 0.8458 (pt0) REVERT: B 12 GLU cc_start: 0.9494 (tp30) cc_final: 0.9226 (mm-30) REVERT: B 39 SER cc_start: 0.9337 (t) cc_final: 0.9089 (p) REVERT: B 46 GLU cc_start: 0.9066 (tp30) cc_final: 0.8800 (tp30) REVERT: B 52 MET cc_start: 0.9147 (mtm) cc_final: 0.8784 (mtm) REVERT: B 54 ASN cc_start: 0.9281 (m-40) cc_final: 0.8895 (m110) REVERT: B 56 VAL cc_start: 0.8935 (t) cc_final: 0.8613 (p) REVERT: B 72 MET cc_start: 0.9399 (ptm) cc_final: 0.8807 (tmm) REVERT: B 115 GLU cc_start: 0.8888 (mp0) cc_final: 0.8371 (mp0) REVERT: B 117 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8305 (mt) REVERT: B 121 GLU cc_start: 0.8787 (mt-10) cc_final: 0.8049 (mm-30) REVERT: B 125 MET cc_start: 0.9633 (ttt) cc_final: 0.9376 (ttp) REVERT: C 166 TRP cc_start: 0.8113 (t60) cc_final: 0.7646 (t60) REVERT: C 180 ARG cc_start: 0.7870 (mtt180) cc_final: 0.7295 (mtt-85) REVERT: C 227 ARG cc_start: 0.8962 (OUTLIER) cc_final: 0.7776 (ttp80) REVERT: C 229 LEU cc_start: 0.9582 (mt) cc_final: 0.9381 (mm) REVERT: C 308 LYS cc_start: 0.8757 (mttt) cc_final: 0.8447 (mttm) REVERT: C 355 ASN cc_start: 0.8548 (p0) cc_final: 0.8284 (p0) REVERT: C 499 HIS cc_start: 0.8208 (m-70) cc_final: 0.7797 (p-80) REVERT: C 526 ASP cc_start: 0.9000 (t70) cc_final: 0.8321 (t70) REVERT: D 9 GLN cc_start: 0.8832 (mp10) cc_final: 0.8436 (pt0) REVERT: D 12 GLU cc_start: 0.9496 (tp30) cc_final: 0.9224 (mm-30) REVERT: D 39 SER cc_start: 0.9336 (t) cc_final: 0.9088 (p) REVERT: D 46 GLU cc_start: 0.9065 (tp30) cc_final: 0.8800 (tp30) REVERT: D 52 MET cc_start: 0.9146 (mtm) cc_final: 0.8783 (mtm) REVERT: D 54 ASN cc_start: 0.9281 (m-40) cc_final: 0.8896 (m110) REVERT: D 56 VAL cc_start: 0.8937 (t) cc_final: 0.8615 (p) REVERT: D 72 MET cc_start: 0.9398 (ptm) cc_final: 0.8807 (tmm) REVERT: D 115 GLU cc_start: 0.8890 (mp0) cc_final: 0.8372 (mp0) REVERT: D 117 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8307 (mt) REVERT: D 121 GLU cc_start: 0.8787 (mt-10) cc_final: 0.8048 (mm-30) REVERT: D 125 MET cc_start: 0.9634 (ttt) cc_final: 0.9375 (ttp) REVERT: E 104 LEU cc_start: 0.8991 (tp) cc_final: 0.8775 (tp) REVERT: E 166 TRP cc_start: 0.8110 (t60) cc_final: 0.7640 (t60) REVERT: E 180 ARG cc_start: 0.7870 (mtt180) cc_final: 0.7296 (mtt-85) REVERT: E 227 ARG cc_start: 0.8975 (OUTLIER) cc_final: 0.7816 (ttp80) REVERT: E 229 LEU cc_start: 0.9583 (mt) cc_final: 0.9382 (mm) REVERT: E 308 LYS cc_start: 0.8770 (mttt) cc_final: 0.8452 (mttm) REVERT: E 355 ASN cc_start: 0.8547 (p0) cc_final: 0.8284 (p0) REVERT: E 499 HIS cc_start: 0.8209 (m-70) cc_final: 0.7797 (p-80) REVERT: E 526 ASP cc_start: 0.9003 (t70) cc_final: 0.8325 (t70) REVERT: E 550 ARG cc_start: 0.8931 (OUTLIER) cc_final: 0.8699 (ttp80) REVERT: F 9 GLN cc_start: 0.8847 (mp10) cc_final: 0.8457 (pt0) REVERT: F 12 GLU cc_start: 0.9495 (tp30) cc_final: 0.9226 (mm-30) REVERT: F 39 SER cc_start: 0.9336 (t) cc_final: 0.9087 (p) REVERT: F 46 GLU cc_start: 0.9064 (tp30) cc_final: 0.8796 (tp30) REVERT: F 52 MET cc_start: 0.9148 (mtm) cc_final: 0.8838 (mtm) REVERT: F 54 ASN cc_start: 0.9249 (m-40) cc_final: 0.8850 (m110) REVERT: F 56 VAL cc_start: 0.8937 (t) cc_final: 0.8615 (p) REVERT: F 72 MET cc_start: 0.9397 (ptm) cc_final: 0.8806 (tmm) REVERT: F 115 GLU cc_start: 0.8892 (mp0) cc_final: 0.8373 (mp0) REVERT: F 117 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8308 (mt) REVERT: F 121 GLU cc_start: 0.8786 (mt-10) cc_final: 0.8047 (mm-30) REVERT: F 125 MET cc_start: 0.9634 (ttt) cc_final: 0.9376 (ttp) REVERT: G 166 TRP cc_start: 0.8112 (t60) cc_final: 0.7643 (t60) REVERT: G 180 ARG cc_start: 0.7869 (mtt180) cc_final: 0.7295 (mtt-85) REVERT: G 227 ARG cc_start: 0.8960 (OUTLIER) cc_final: 0.7774 (ttp80) REVERT: G 229 LEU cc_start: 0.9582 (mt) cc_final: 0.9381 (mm) REVERT: G 308 LYS cc_start: 0.8759 (mttt) cc_final: 0.8448 (mttm) REVERT: G 355 ASN cc_start: 0.8545 (p0) cc_final: 0.8286 (p0) REVERT: G 499 HIS cc_start: 0.8210 (m-70) cc_final: 0.7797 (p-80) REVERT: G 526 ASP cc_start: 0.9004 (t70) cc_final: 0.8322 (t70) REVERT: H 9 GLN cc_start: 0.8847 (mp10) cc_final: 0.8458 (pt0) REVERT: H 12 GLU cc_start: 0.9494 (tp30) cc_final: 0.9226 (mm-30) REVERT: H 39 SER cc_start: 0.9336 (t) cc_final: 0.9088 (p) REVERT: H 46 GLU cc_start: 0.9065 (tp30) cc_final: 0.8799 (tp30) REVERT: H 52 MET cc_start: 0.9145 (mtm) cc_final: 0.8782 (mtm) REVERT: H 54 ASN cc_start: 0.9248 (m-40) cc_final: 0.8849 (m110) REVERT: H 56 VAL cc_start: 0.8937 (t) cc_final: 0.8615 (p) REVERT: H 72 MET cc_start: 0.9399 (ptm) cc_final: 0.8807 (tmm) REVERT: H 115 GLU cc_start: 0.8891 (mp0) cc_final: 0.8375 (mp0) REVERT: H 117 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8304 (mt) REVERT: H 121 GLU cc_start: 0.8786 (mt-10) cc_final: 0.8047 (mm-30) REVERT: H 125 MET cc_start: 0.9633 (ttt) cc_final: 0.9376 (ttp) outliers start: 69 outliers final: 53 residues processed: 643 average time/residue: 0.2437 time to fit residues: 232.5516 Evaluate side-chains 681 residues out of total 1660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 619 time to evaluate : 1.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 TRP Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 227 ARG Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 371 CYS Chi-restraints excluded: chain A residue 498 HIS Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 547 GLU Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain C residue 110 TRP Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 227 ARG Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 371 CYS Chi-restraints excluded: chain C residue 498 HIS Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain E residue 110 TRP Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 227 ARG Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 371 CYS Chi-restraints excluded: chain E residue 498 HIS Chi-restraints excluded: chain E residue 513 VAL Chi-restraints excluded: chain E residue 550 ARG Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain G residue 110 TRP Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain G residue 135 ILE Chi-restraints excluded: chain G residue 227 ARG Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain G residue 255 THR Chi-restraints excluded: chain G residue 261 LEU Chi-restraints excluded: chain G residue 371 CYS Chi-restraints excluded: chain G residue 498 HIS Chi-restraints excluded: chain G residue 513 VAL Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 102 SER Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 118 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 73 optimal weight: 2.9990 chunk 110 optimal weight: 0.2980 chunk 55 optimal weight: 6.9990 chunk 36 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 117 optimal weight: 0.8980 chunk 126 optimal weight: 0.9990 chunk 91 optimal weight: 4.9990 chunk 17 optimal weight: 7.9990 chunk 145 optimal weight: 5.9990 chunk 168 optimal weight: 0.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.4497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15228 Z= 0.211 Angle : 0.581 9.882 20644 Z= 0.291 Chirality : 0.039 0.201 2368 Planarity : 0.004 0.056 2576 Dihedral : 3.452 18.028 2104 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 4.70 % Allowed : 27.90 % Favored : 67.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.41 (0.20), residues: 1904 helix: 3.03 (0.13), residues: 1508 sheet: None (None), residues: 0 loop : -1.06 (0.33), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP G 369 HIS 0.002 0.000 HIS A 230 PHE 0.018 0.002 PHE G 260 TYR 0.021 0.002 TYR E 268 ARG 0.011 0.001 ARG B 127 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 701 residues out of total 1660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 633 time to evaluate : 1.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 LEU cc_start: 0.8991 (tp) cc_final: 0.8739 (tp) REVERT: A 166 TRP cc_start: 0.8142 (t60) cc_final: 0.7667 (t60) REVERT: A 180 ARG cc_start: 0.7939 (mtt180) cc_final: 0.7335 (mmt-90) REVERT: A 227 ARG cc_start: 0.8957 (OUTLIER) cc_final: 0.7722 (ttp80) REVERT: A 308 LYS cc_start: 0.8794 (mttt) cc_final: 0.8468 (mttm) REVERT: A 355 ASN cc_start: 0.8555 (p0) cc_final: 0.8310 (p0) REVERT: A 499 HIS cc_start: 0.8225 (m-70) cc_final: 0.7835 (p-80) REVERT: A 526 ASP cc_start: 0.9033 (t70) cc_final: 0.8366 (t70) REVERT: A 534 TYR cc_start: 0.8977 (t80) cc_final: 0.7832 (t80) REVERT: B 9 GLN cc_start: 0.8895 (mp10) cc_final: 0.8486 (pt0) REVERT: B 12 GLU cc_start: 0.9503 (tp30) cc_final: 0.9211 (mm-30) REVERT: B 39 SER cc_start: 0.9304 (t) cc_final: 0.9073 (p) REVERT: B 46 GLU cc_start: 0.9046 (tp30) cc_final: 0.8771 (tp30) REVERT: B 52 MET cc_start: 0.9151 (mtm) cc_final: 0.8775 (mtm) REVERT: B 54 ASN cc_start: 0.9234 (m-40) cc_final: 0.8843 (m110) REVERT: B 56 VAL cc_start: 0.8966 (t) cc_final: 0.8658 (p) REVERT: B 72 MET cc_start: 0.9353 (ptm) cc_final: 0.8904 (tmm) REVERT: B 112 ASN cc_start: 0.8470 (m-40) cc_final: 0.7940 (m110) REVERT: B 115 GLU cc_start: 0.8922 (mp0) cc_final: 0.8353 (mp0) REVERT: B 117 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8456 (mt) REVERT: B 120 GLU cc_start: 0.9069 (mm-30) cc_final: 0.8815 (mm-30) REVERT: B 121 GLU cc_start: 0.8786 (mt-10) cc_final: 0.8371 (mm-30) REVERT: B 125 MET cc_start: 0.9635 (ttt) cc_final: 0.9386 (ttp) REVERT: B 127 ARG cc_start: 0.9345 (ttm110) cc_final: 0.9032 (ttp-110) REVERT: C 166 TRP cc_start: 0.8138 (t60) cc_final: 0.7665 (t60) REVERT: C 180 ARG cc_start: 0.7938 (mtt180) cc_final: 0.7333 (mmt-90) REVERT: C 308 LYS cc_start: 0.8779 (mttt) cc_final: 0.8452 (mttm) REVERT: C 355 ASN cc_start: 0.8550 (p0) cc_final: 0.8308 (p0) REVERT: C 499 HIS cc_start: 0.8223 (m-70) cc_final: 0.7834 (p-80) REVERT: C 526 ASP cc_start: 0.9032 (t70) cc_final: 0.8361 (t70) REVERT: C 534 TYR cc_start: 0.8867 (t80) cc_final: 0.8529 (t80) REVERT: C 547 GLU cc_start: 0.9026 (tp30) cc_final: 0.8825 (tm-30) REVERT: D 9 GLN cc_start: 0.8877 (mp10) cc_final: 0.8492 (pt0) REVERT: D 39 SER cc_start: 0.9304 (t) cc_final: 0.9077 (p) REVERT: D 46 GLU cc_start: 0.9046 (tp30) cc_final: 0.8772 (tp30) REVERT: D 52 MET cc_start: 0.9151 (mtm) cc_final: 0.8775 (mtm) REVERT: D 54 ASN cc_start: 0.9235 (m-40) cc_final: 0.8843 (m110) REVERT: D 56 VAL cc_start: 0.8968 (t) cc_final: 0.8659 (p) REVERT: D 72 MET cc_start: 0.9352 (ptm) cc_final: 0.8904 (tmm) REVERT: D 112 ASN cc_start: 0.8470 (m-40) cc_final: 0.7940 (m110) REVERT: D 115 GLU cc_start: 0.8894 (mp0) cc_final: 0.8256 (mp0) REVERT: D 117 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8455 (mt) REVERT: D 120 GLU cc_start: 0.9070 (mm-30) cc_final: 0.8817 (mm-30) REVERT: D 121 GLU cc_start: 0.8787 (mt-10) cc_final: 0.8373 (mm-30) REVERT: D 125 MET cc_start: 0.9636 (ttt) cc_final: 0.9386 (ttp) REVERT: D 127 ARG cc_start: 0.9344 (ttm110) cc_final: 0.9033 (ttp-110) REVERT: E 166 TRP cc_start: 0.8143 (t60) cc_final: 0.7670 (t60) REVERT: E 180 ARG cc_start: 0.7941 (mtt180) cc_final: 0.7336 (mmt-90) REVERT: E 308 LYS cc_start: 0.8793 (mttt) cc_final: 0.8468 (mttm) REVERT: E 355 ASN cc_start: 0.8553 (p0) cc_final: 0.8310 (p0) REVERT: E 499 HIS cc_start: 0.8223 (m-70) cc_final: 0.7834 (p-80) REVERT: E 526 ASP cc_start: 0.9032 (t70) cc_final: 0.8364 (t70) REVERT: E 534 TYR cc_start: 0.9066 (t80) cc_final: 0.8062 (t80) REVERT: E 550 ARG cc_start: 0.8925 (OUTLIER) cc_final: 0.8690 (ttp80) REVERT: F 9 GLN cc_start: 0.8894 (mp10) cc_final: 0.8486 (pt0) REVERT: F 12 GLU cc_start: 0.9502 (tp30) cc_final: 0.9210 (mm-30) REVERT: F 39 SER cc_start: 0.9303 (t) cc_final: 0.9077 (p) REVERT: F 46 GLU cc_start: 0.9048 (tp30) cc_final: 0.8773 (tp30) REVERT: F 52 MET cc_start: 0.9155 (mtm) cc_final: 0.8774 (mtm) REVERT: F 54 ASN cc_start: 0.9201 (m-40) cc_final: 0.8795 (m110) REVERT: F 56 VAL cc_start: 0.8967 (t) cc_final: 0.8659 (p) REVERT: F 72 MET cc_start: 0.9350 (ptm) cc_final: 0.8902 (tmm) REVERT: F 112 ASN cc_start: 0.8467 (m-40) cc_final: 0.7938 (m110) REVERT: F 115 GLU cc_start: 0.8928 (mp0) cc_final: 0.8360 (mp0) REVERT: F 117 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8457 (mt) REVERT: F 120 GLU cc_start: 0.9069 (mm-30) cc_final: 0.8816 (mm-30) REVERT: F 121 GLU cc_start: 0.8788 (mt-10) cc_final: 0.8372 (mm-30) REVERT: F 125 MET cc_start: 0.9635 (ttt) cc_final: 0.9387 (ttp) REVERT: F 127 ARG cc_start: 0.9343 (ttm110) cc_final: 0.9032 (ttp-110) REVERT: G 166 TRP cc_start: 0.8138 (t60) cc_final: 0.7664 (t60) REVERT: G 180 ARG cc_start: 0.7937 (mtt180) cc_final: 0.7332 (mmt-90) REVERT: G 308 LYS cc_start: 0.8780 (mttt) cc_final: 0.8453 (mttm) REVERT: G 355 ASN cc_start: 0.8550 (p0) cc_final: 0.8307 (p0) REVERT: G 499 HIS cc_start: 0.8224 (m-70) cc_final: 0.7835 (p-80) REVERT: G 526 ASP cc_start: 0.9033 (t70) cc_final: 0.8363 (t70) REVERT: G 534 TYR cc_start: 0.8980 (t80) cc_final: 0.7837 (t80) REVERT: H 9 GLN cc_start: 0.8894 (mp10) cc_final: 0.8486 (pt0) REVERT: H 12 GLU cc_start: 0.9502 (tp30) cc_final: 0.9210 (mm-30) REVERT: H 39 SER cc_start: 0.9304 (t) cc_final: 0.9072 (p) REVERT: H 46 GLU cc_start: 0.9045 (tp30) cc_final: 0.8770 (tp30) REVERT: H 52 MET cc_start: 0.9151 (mtm) cc_final: 0.8775 (mtm) REVERT: H 54 ASN cc_start: 0.9202 (m-40) cc_final: 0.8796 (m110) REVERT: H 56 VAL cc_start: 0.8968 (t) cc_final: 0.8660 (p) REVERT: H 72 MET cc_start: 0.9353 (ptm) cc_final: 0.8905 (tmm) REVERT: H 112 ASN cc_start: 0.8466 (m-40) cc_final: 0.7937 (m110) REVERT: H 115 GLU cc_start: 0.8894 (mp0) cc_final: 0.8257 (mp0) REVERT: H 117 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8455 (mt) REVERT: H 120 GLU cc_start: 0.9070 (mm-30) cc_final: 0.8816 (mm-30) REVERT: H 121 GLU cc_start: 0.8786 (mt-10) cc_final: 0.8371 (mm-30) REVERT: H 125 MET cc_start: 0.9635 (ttt) cc_final: 0.9386 (ttp) REVERT: H 127 ARG cc_start: 0.9345 (ttm110) cc_final: 0.9033 (ttp-110) outliers start: 68 outliers final: 48 residues processed: 654 average time/residue: 0.2260 time to fit residues: 223.3327 Evaluate side-chains 673 residues out of total 1660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 619 time to evaluate : 1.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 TRP Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 227 ARG Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 498 HIS Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 547 GLU Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain C residue 110 TRP Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 498 HIS Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain E residue 110 TRP Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 336 ILE Chi-restraints excluded: chain E residue 498 HIS Chi-restraints excluded: chain E residue 513 VAL Chi-restraints excluded: chain E residue 550 ARG Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain G residue 110 TRP Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain G residue 135 ILE Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain G residue 498 HIS Chi-restraints excluded: chain G residue 513 VAL Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 102 SER Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 118 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 177 optimal weight: 4.9990 chunk 161 optimal weight: 10.0000 chunk 172 optimal weight: 0.9990 chunk 103 optimal weight: 6.9990 chunk 75 optimal weight: 6.9990 chunk 135 optimal weight: 3.9990 chunk 52 optimal weight: 8.9990 chunk 155 optimal weight: 0.8980 chunk 163 optimal weight: 0.6980 chunk 171 optimal weight: 3.9990 chunk 113 optimal weight: 7.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.4547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 15228 Z= 0.341 Angle : 0.656 10.726 20644 Z= 0.340 Chirality : 0.040 0.173 2368 Planarity : 0.005 0.058 2576 Dihedral : 3.649 18.339 2104 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 4.90 % Allowed : 28.31 % Favored : 66.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.26 (0.20), residues: 1904 helix: 2.86 (0.13), residues: 1520 sheet: None (None), residues: 0 loop : -0.93 (0.34), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP E 369 HIS 0.003 0.001 HIS C 248 PHE 0.041 0.002 PHE E 341 TYR 0.029 0.002 TYR A 268 ARG 0.011 0.001 ARG B 127 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 690 residues out of total 1660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 619 time to evaluate : 1.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 ARG cc_start: 0.8072 (mtt180) cc_final: 0.7518 (mtt-85) REVERT: A 251 GLU cc_start: 0.9264 (tp30) cc_final: 0.8769 (mp0) REVERT: A 308 LYS cc_start: 0.8916 (mttt) cc_final: 0.8584 (mttm) REVERT: A 499 HIS cc_start: 0.8297 (m-70) cc_final: 0.7787 (p90) REVERT: A 526 ASP cc_start: 0.9119 (t70) cc_final: 0.8506 (t70) REVERT: A 534 TYR cc_start: 0.9000 (t80) cc_final: 0.8472 (t80) REVERT: B 39 SER cc_start: 0.9372 (t) cc_final: 0.9113 (p) REVERT: B 52 MET cc_start: 0.9247 (mtm) cc_final: 0.8744 (mtm) REVERT: B 54 ASN cc_start: 0.9270 (m-40) cc_final: 0.8888 (m110) REVERT: B 56 VAL cc_start: 0.8987 (t) cc_final: 0.8697 (p) REVERT: B 72 MET cc_start: 0.9472 (ptm) cc_final: 0.8936 (tmm) REVERT: B 115 GLU cc_start: 0.8915 (mp0) cc_final: 0.8293 (mp0) REVERT: B 117 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8791 (mt) REVERT: B 120 GLU cc_start: 0.9162 (mm-30) cc_final: 0.8882 (mm-30) REVERT: B 121 GLU cc_start: 0.8909 (mt-10) cc_final: 0.8333 (mm-30) REVERT: B 124 GLU cc_start: 0.9154 (tp30) cc_final: 0.8897 (tp30) REVERT: B 125 MET cc_start: 0.9632 (ttt) cc_final: 0.9289 (ttt) REVERT: B 127 ARG cc_start: 0.9422 (ttm110) cc_final: 0.9072 (ttp-110) REVERT: C 180 ARG cc_start: 0.8076 (mtt180) cc_final: 0.7522 (mtt-85) REVERT: C 229 LEU cc_start: 0.9326 (mm) cc_final: 0.9117 (mm) REVERT: C 308 LYS cc_start: 0.8910 (mttt) cc_final: 0.8571 (mttm) REVERT: C 499 HIS cc_start: 0.8296 (m-70) cc_final: 0.7786 (p90) REVERT: C 526 ASP cc_start: 0.9137 (t70) cc_final: 0.8480 (t70) REVERT: D 39 SER cc_start: 0.9373 (t) cc_final: 0.9114 (p) REVERT: D 52 MET cc_start: 0.9261 (mtm) cc_final: 0.8734 (mtm) REVERT: D 54 ASN cc_start: 0.9270 (m-40) cc_final: 0.8887 (m110) REVERT: D 56 VAL cc_start: 0.8990 (t) cc_final: 0.8699 (p) REVERT: D 72 MET cc_start: 0.9472 (ptm) cc_final: 0.8935 (tmm) REVERT: D 115 GLU cc_start: 0.8917 (mp0) cc_final: 0.8293 (mp0) REVERT: D 117 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8794 (mt) REVERT: D 120 GLU cc_start: 0.9163 (mm-30) cc_final: 0.8884 (mm-30) REVERT: D 121 GLU cc_start: 0.8909 (mt-10) cc_final: 0.8334 (mm-30) REVERT: D 124 GLU cc_start: 0.9154 (tp30) cc_final: 0.8896 (tp30) REVERT: D 125 MET cc_start: 0.9633 (ttt) cc_final: 0.9289 (ttt) REVERT: D 127 ARG cc_start: 0.9421 (ttm110) cc_final: 0.9072 (ttp-110) REVERT: E 180 ARG cc_start: 0.8077 (mtt180) cc_final: 0.7523 (mtt-85) REVERT: E 229 LEU cc_start: 0.9306 (mm) cc_final: 0.9092 (mm) REVERT: E 251 GLU cc_start: 0.9262 (tp30) cc_final: 0.8768 (mp0) REVERT: E 308 LYS cc_start: 0.8916 (mttt) cc_final: 0.8584 (mttm) REVERT: E 499 HIS cc_start: 0.8297 (m-70) cc_final: 0.7787 (p90) REVERT: E 526 ASP cc_start: 0.9107 (t70) cc_final: 0.8496 (t70) REVERT: F 39 SER cc_start: 0.9373 (t) cc_final: 0.9114 (p) REVERT: F 52 MET cc_start: 0.9249 (mtm) cc_final: 0.8742 (mtm) REVERT: F 54 ASN cc_start: 0.9269 (m-40) cc_final: 0.8889 (m110) REVERT: F 56 VAL cc_start: 0.8991 (t) cc_final: 0.8699 (p) REVERT: F 72 MET cc_start: 0.9471 (ptm) cc_final: 0.8935 (tmm) REVERT: F 115 GLU cc_start: 0.8917 (mp0) cc_final: 0.8324 (mp0) REVERT: F 117 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8804 (mt) REVERT: F 120 GLU cc_start: 0.9163 (mm-30) cc_final: 0.8884 (mm-30) REVERT: F 121 GLU cc_start: 0.8910 (mt-10) cc_final: 0.8336 (mm-30) REVERT: F 124 GLU cc_start: 0.9153 (tp30) cc_final: 0.8896 (tp30) REVERT: F 125 MET cc_start: 0.9632 (ttt) cc_final: 0.9290 (ttt) REVERT: F 127 ARG cc_start: 0.9414 (ttm110) cc_final: 0.9070 (ttp-110) REVERT: G 180 ARG cc_start: 0.8074 (mtt180) cc_final: 0.7520 (mtt-85) REVERT: G 229 LEU cc_start: 0.9327 (mm) cc_final: 0.9118 (mm) REVERT: G 308 LYS cc_start: 0.8911 (mttt) cc_final: 0.8570 (mttm) REVERT: G 499 HIS cc_start: 0.8297 (m-70) cc_final: 0.7786 (p90) REVERT: G 526 ASP cc_start: 0.9108 (t70) cc_final: 0.8498 (t70) REVERT: H 39 SER cc_start: 0.9372 (t) cc_final: 0.9113 (p) REVERT: H 52 MET cc_start: 0.9249 (mtm) cc_final: 0.8742 (mtm) REVERT: H 54 ASN cc_start: 0.9268 (m-40) cc_final: 0.8889 (m110) REVERT: H 56 VAL cc_start: 0.8990 (t) cc_final: 0.8699 (p) REVERT: H 72 MET cc_start: 0.9473 (ptm) cc_final: 0.8937 (tmm) REVERT: H 115 GLU cc_start: 0.8918 (mp0) cc_final: 0.8297 (mp0) REVERT: H 117 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8794 (mt) REVERT: H 120 GLU cc_start: 0.9163 (mm-30) cc_final: 0.8884 (mm-30) REVERT: H 121 GLU cc_start: 0.8906 (mt-10) cc_final: 0.8333 (mm-30) REVERT: H 124 GLU cc_start: 0.9154 (tp30) cc_final: 0.8896 (tp30) REVERT: H 125 MET cc_start: 0.9632 (ttt) cc_final: 0.9289 (ttt) REVERT: H 127 ARG cc_start: 0.9414 (ttm110) cc_final: 0.9069 (ttp-110) outliers start: 71 outliers final: 53 residues processed: 637 average time/residue: 0.2248 time to fit residues: 217.7330 Evaluate side-chains 651 residues out of total 1660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 594 time to evaluate : 1.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 TRP Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 371 CYS Chi-restraints excluded: chain A residue 498 HIS Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 547 GLU Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain C residue 110 TRP Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 371 CYS Chi-restraints excluded: chain C residue 498 HIS Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain C residue 530 VAL Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain E residue 110 TRP Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 254 THR Chi-restraints excluded: chain E residue 371 CYS Chi-restraints excluded: chain E residue 498 HIS Chi-restraints excluded: chain E residue 513 VAL Chi-restraints excluded: chain E residue 530 VAL Chi-restraints excluded: chain E residue 550 ARG Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain G residue 110 TRP Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain G residue 371 CYS Chi-restraints excluded: chain G residue 498 HIS Chi-restraints excluded: chain G residue 513 VAL Chi-restraints excluded: chain G residue 530 VAL Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 102 SER Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 118 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 182 optimal weight: 1.9990 chunk 111 optimal weight: 0.6980 chunk 86 optimal weight: 0.7980 chunk 126 optimal weight: 0.9980 chunk 191 optimal weight: 0.7980 chunk 176 optimal weight: 1.9990 chunk 152 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 117 optimal weight: 0.0770 chunk 93 optimal weight: 4.9990 chunk 120 optimal weight: 0.4980 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.4743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 15228 Z= 0.214 Angle : 0.663 11.787 20644 Z= 0.329 Chirality : 0.040 0.203 2368 Planarity : 0.004 0.046 2576 Dihedral : 3.587 18.165 2104 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.45 % Allowed : 32.73 % Favored : 63.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.25 (0.20), residues: 1904 helix: 2.87 (0.13), residues: 1508 sheet: None (None), residues: 0 loop : -0.88 (0.33), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP G 369 HIS 0.003 0.000 HIS A 230 PHE 0.035 0.002 PHE E 341 TYR 0.042 0.002 TYR G 161 ARG 0.011 0.001 ARG F 127 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 680 residues out of total 1660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 630 time to evaluate : 2.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 TRP cc_start: 0.8023 (t60) cc_final: 0.7500 (t60) REVERT: A 180 ARG cc_start: 0.8041 (mtt180) cc_final: 0.7450 (mmt-90) REVERT: A 251 GLU cc_start: 0.9300 (tp30) cc_final: 0.8960 (tp30) REVERT: A 308 LYS cc_start: 0.8830 (mttt) cc_final: 0.8488 (mttm) REVERT: A 498 HIS cc_start: 0.8793 (OUTLIER) cc_final: 0.8552 (p-80) REVERT: A 499 HIS cc_start: 0.8245 (m-70) cc_final: 0.7891 (p90) REVERT: A 509 MET cc_start: 0.9384 (mtp) cc_final: 0.9031 (ttm) REVERT: A 526 ASP cc_start: 0.9110 (t70) cc_final: 0.8419 (t70) REVERT: A 534 TYR cc_start: 0.9005 (t80) cc_final: 0.8401 (t80) REVERT: B 39 SER cc_start: 0.9332 (t) cc_final: 0.9061 (p) REVERT: B 52 MET cc_start: 0.9237 (mtm) cc_final: 0.9013 (mtm) REVERT: B 54 ASN cc_start: 0.9215 (m-40) cc_final: 0.8787 (m110) REVERT: B 56 VAL cc_start: 0.9026 (t) cc_final: 0.8804 (p) REVERT: B 72 MET cc_start: 0.9454 (ptm) cc_final: 0.8889 (tmm) REVERT: B 115 GLU cc_start: 0.8938 (mp0) cc_final: 0.8537 (mp0) REVERT: B 117 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8560 (mt) REVERT: B 120 GLU cc_start: 0.9134 (mm-30) cc_final: 0.8804 (mm-30) REVERT: B 121 GLU cc_start: 0.8801 (mt-10) cc_final: 0.8344 (mm-30) REVERT: B 124 GLU cc_start: 0.9136 (tp30) cc_final: 0.8903 (tp30) REVERT: B 127 ARG cc_start: 0.9388 (ttm110) cc_final: 0.9039 (ttp-110) REVERT: C 166 TRP cc_start: 0.8070 (t60) cc_final: 0.7548 (t60) REVERT: C 180 ARG cc_start: 0.8045 (mtt180) cc_final: 0.7452 (mmt-90) REVERT: C 308 LYS cc_start: 0.8820 (mttt) cc_final: 0.8491 (mttm) REVERT: C 498 HIS cc_start: 0.8797 (OUTLIER) cc_final: 0.8555 (p-80) REVERT: C 499 HIS cc_start: 0.8245 (m-70) cc_final: 0.7891 (p90) REVERT: C 509 MET cc_start: 0.9384 (mtp) cc_final: 0.9032 (ttm) REVERT: C 526 ASP cc_start: 0.9049 (t70) cc_final: 0.8315 (t70) REVERT: D 39 SER cc_start: 0.9333 (t) cc_final: 0.9062 (p) REVERT: D 52 MET cc_start: 0.9237 (mtm) cc_final: 0.9013 (mtm) REVERT: D 54 ASN cc_start: 0.9214 (m-40) cc_final: 0.8786 (m110) REVERT: D 56 VAL cc_start: 0.9028 (t) cc_final: 0.8805 (p) REVERT: D 72 MET cc_start: 0.9448 (ptm) cc_final: 0.8882 (tmm) REVERT: D 115 GLU cc_start: 0.8942 (mp0) cc_final: 0.8540 (mp0) REVERT: D 117 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8561 (mt) REVERT: D 120 GLU cc_start: 0.9134 (mm-30) cc_final: 0.8806 (mm-30) REVERT: D 121 GLU cc_start: 0.8801 (mt-10) cc_final: 0.8345 (mm-30) REVERT: D 124 GLU cc_start: 0.9135 (tp30) cc_final: 0.8902 (tp30) REVERT: D 127 ARG cc_start: 0.9388 (ttm110) cc_final: 0.9040 (ttp-110) REVERT: E 166 TRP cc_start: 0.8047 (t60) cc_final: 0.7531 (t60) REVERT: E 180 ARG cc_start: 0.8043 (mtt180) cc_final: 0.7451 (mmt-90) REVERT: E 251 GLU cc_start: 0.9300 (tp30) cc_final: 0.9008 (tp30) REVERT: E 308 LYS cc_start: 0.8832 (mttt) cc_final: 0.8489 (mttm) REVERT: E 498 HIS cc_start: 0.8794 (OUTLIER) cc_final: 0.8552 (p-80) REVERT: E 499 HIS cc_start: 0.8245 (m-70) cc_final: 0.7892 (p90) REVERT: E 509 MET cc_start: 0.9384 (mtp) cc_final: 0.9030 (ttm) REVERT: E 526 ASP cc_start: 0.9104 (t70) cc_final: 0.8412 (t70) REVERT: F 39 SER cc_start: 0.9332 (t) cc_final: 0.9061 (p) REVERT: F 52 MET cc_start: 0.9239 (mtm) cc_final: 0.9014 (mtm) REVERT: F 54 ASN cc_start: 0.9188 (m-40) cc_final: 0.8777 (m110) REVERT: F 56 VAL cc_start: 0.9027 (t) cc_final: 0.8807 (p) REVERT: F 72 MET cc_start: 0.9452 (ptm) cc_final: 0.8888 (tmm) REVERT: F 115 GLU cc_start: 0.8938 (mp0) cc_final: 0.8537 (mp0) REVERT: F 117 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8568 (mt) REVERT: F 120 GLU cc_start: 0.9135 (mm-30) cc_final: 0.8806 (mm-30) REVERT: F 121 GLU cc_start: 0.8802 (mt-10) cc_final: 0.8346 (mm-30) REVERT: F 124 GLU cc_start: 0.9136 (tp30) cc_final: 0.8902 (tp30) REVERT: F 127 ARG cc_start: 0.9388 (ttm110) cc_final: 0.9039 (ttp-110) REVERT: G 133 SER cc_start: 0.8622 (t) cc_final: 0.8321 (p) REVERT: G 166 TRP cc_start: 0.8072 (t60) cc_final: 0.7550 (t60) REVERT: G 180 ARG cc_start: 0.8045 (mtt180) cc_final: 0.7452 (mmt-90) REVERT: G 308 LYS cc_start: 0.8818 (mttt) cc_final: 0.8489 (mttm) REVERT: G 498 HIS cc_start: 0.8794 (OUTLIER) cc_final: 0.8552 (p-80) REVERT: G 499 HIS cc_start: 0.8246 (m-70) cc_final: 0.7891 (p90) REVERT: G 509 MET cc_start: 0.9383 (mtp) cc_final: 0.9029 (ttm) REVERT: G 526 ASP cc_start: 0.9103 (t70) cc_final: 0.8413 (t70) REVERT: H 39 SER cc_start: 0.9331 (t) cc_final: 0.9060 (p) REVERT: H 52 MET cc_start: 0.9237 (mtm) cc_final: 0.9015 (mtm) REVERT: H 54 ASN cc_start: 0.9189 (m-40) cc_final: 0.8778 (m110) REVERT: H 56 VAL cc_start: 0.9025 (t) cc_final: 0.8804 (p) REVERT: H 72 MET cc_start: 0.9453 (ptm) cc_final: 0.8890 (tmm) REVERT: H 115 GLU cc_start: 0.8938 (mp0) cc_final: 0.8539 (mp0) REVERT: H 117 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8560 (mt) REVERT: H 120 GLU cc_start: 0.9135 (mm-30) cc_final: 0.8806 (mm-30) REVERT: H 121 GLU cc_start: 0.8801 (mt-10) cc_final: 0.8343 (mm-30) REVERT: H 124 GLU cc_start: 0.9135 (tp30) cc_final: 0.8901 (tp30) REVERT: H 127 ARG cc_start: 0.9389 (ttm110) cc_final: 0.9040 (ttp-110) outliers start: 50 outliers final: 33 residues processed: 641 average time/residue: 0.2335 time to fit residues: 226.7960 Evaluate side-chains 647 residues out of total 1660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 606 time to evaluate : 1.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 498 HIS Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 547 GLU Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 498 HIS Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 498 HIS Chi-restraints excluded: chain E residue 513 VAL Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain G residue 193 LEU Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain G residue 498 HIS Chi-restraints excluded: chain G residue 513 VAL Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 102 SER Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 118 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 140 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 chunk 42 optimal weight: 0.5980 chunk 152 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 156 optimal weight: 0.1980 chunk 19 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 112 ASN D 112 ASN F 112 ASN H 112 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.093509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.076565 restraints weight = 38524.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.079289 restraints weight = 19764.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.081214 restraints weight = 12588.168| |-----------------------------------------------------------------------------| r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3080 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3080 r_free = 0.3080 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3080 r_free = 0.3080 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3080 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.4862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 15228 Z= 0.216 Angle : 0.665 11.611 20644 Z= 0.330 Chirality : 0.040 0.196 2368 Planarity : 0.004 0.045 2576 Dihedral : 3.498 18.336 2104 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.62 % Allowed : 34.53 % Favored : 62.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.22 (0.19), residues: 1904 helix: 2.83 (0.13), residues: 1500 sheet: None (None), residues: 0 loop : -0.71 (0.32), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP G 369 HIS 0.003 0.001 HIS G 230 PHE 0.017 0.001 PHE C 260 TYR 0.032 0.002 TYR G 161 ARG 0.010 0.001 ARG B 127 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4185.41 seconds wall clock time: 74 minutes 51.88 seconds (4491.88 seconds total)