Starting phenix.real_space_refine on Wed Mar 4 17:10:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6zqj_11366/03_2026/6zqj_11366.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zqj_11366/03_2026/6zqj_11366.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6zqj_11366/03_2026/6zqj_11366.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zqj_11366/03_2026/6zqj_11366.map" model { file = "/net/cci-nas-00/data/ceres_data/6zqj_11366/03_2026/6zqj_11366.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zqj_11366/03_2026/6zqj_11366.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 129 5.16 5 C 9501 2.51 5 N 2625 2.21 5 O 2841 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 50 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15096 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 3835 Classifications: {'peptide': 504} Link IDs: {'PTRANS': 12, 'TRANS': 491} Chain: "B" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 790 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 6, 'TRANS': 94} Chain: "D" Number of atoms: 3835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 3835 Classifications: {'peptide': 504} Link IDs: {'PTRANS': 12, 'TRANS': 491} Chain: "E" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 790 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 6, 'TRANS': 94} Chain: "G" Number of atoms: 3835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 3835 Classifications: {'peptide': 504} Link IDs: {'PTRANS': 12, 'TRANS': 491} Chain: "H" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 790 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 6, 'TRANS': 94} Chain: "I" Number of atoms: 393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 393 Classifications: {'peptide': 50} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "F" Number of atoms: 393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 393 Classifications: {'peptide': 50} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "C" Number of atoms: 393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 393 Classifications: {'peptide': 50} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.82, per 1000 atoms: 0.25 Number of scatterers: 15096 At special positions: 0 Unit cell: (170.69, 179.14, 141.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 129 16.00 O 2841 8.00 N 2625 7.00 C 9501 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=27, symmetry=0 Simple disulfide: pdb=" SG CYS A 3 " - pdb=" SG CYS A 30 " distance=2.03 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 121 " distance=2.03 Simple disulfide: pdb=" SG CYS A 74 " - pdb=" SG CYS A 105 " distance=2.03 Simple disulfide: pdb=" SG CYS A 92 " - pdb=" SG CYS A 116 " distance=2.04 Simple disulfide: pdb=" SG CYS A 191 " - pdb=" SG CYS A 292 " distance=2.03 Simple disulfide: pdb=" SG CYS A 309 " - pdb=" SG CYS A 340 " distance=2.03 Simple disulfide: pdb=" SG CYS B 34 " - pdb=" SG CYS B 69 " distance=2.03 Simple disulfide: pdb=" SG CYS B 45 " - pdb=" SG CYS B 81 " distance=2.03 Simple disulfide: pdb=" SG CYS B 53 " - pdb=" SG CYS B 67 " distance=2.04 Simple disulfide: pdb=" SG CYS D 3 " - pdb=" SG CYS D 30 " distance=2.03 Simple disulfide: pdb=" SG CYS D 60 " - pdb=" SG CYS D 121 " distance=2.03 Simple disulfide: pdb=" SG CYS D 74 " - pdb=" SG CYS D 105 " distance=2.03 Simple disulfide: pdb=" SG CYS D 92 " - pdb=" SG CYS D 116 " distance=2.04 Simple disulfide: pdb=" SG CYS D 191 " - pdb=" SG CYS D 292 " distance=2.03 Simple disulfide: pdb=" SG CYS D 309 " - pdb=" SG CYS D 340 " distance=2.03 Simple disulfide: pdb=" SG CYS E 34 " - pdb=" SG CYS E 69 " distance=2.03 Simple disulfide: pdb=" SG CYS E 45 " - pdb=" SG CYS E 81 " distance=2.03 Simple disulfide: pdb=" SG CYS E 53 " - pdb=" SG CYS E 67 " distance=2.03 Simple disulfide: pdb=" SG CYS G 3 " - pdb=" SG CYS G 30 " distance=2.03 Simple disulfide: pdb=" SG CYS G 60 " - pdb=" SG CYS G 121 " distance=2.03 Simple disulfide: pdb=" SG CYS G 74 " - pdb=" SG CYS G 105 " distance=2.03 Simple disulfide: pdb=" SG CYS G 92 " - pdb=" SG CYS G 116 " distance=2.04 Simple disulfide: pdb=" SG CYS G 191 " - pdb=" SG CYS G 292 " distance=2.03 Simple disulfide: pdb=" SG CYS G 309 " - pdb=" SG CYS G 340 " distance=2.03 Simple disulfide: pdb=" SG CYS H 34 " - pdb=" SG CYS H 69 " distance=2.03 Simple disulfide: pdb=" SG CYS H 45 " - pdb=" SG CYS H 81 " distance=2.03 Simple disulfide: pdb=" SG CYS H 53 " - pdb=" SG CYS H 67 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG B 201 " - " ASN B 70 " " NAG E 201 " - " ASN E 70 " " NAG H 201 " - " ASN H 70 " Time building additional restraints: 1.36 Conformation dependent library (CDL) restraints added in 694.0 milliseconds 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3546 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 35 sheets defined 23.4% alpha, 30.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 82 through 86 removed outlier: 3.716A pdb=" N ALA A 86 " --> pdb=" O ASP A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 104 removed outlier: 3.544A pdb=" N GLY A 104 " --> pdb=" O TRP A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 133 No H-bonds generated for 'chain 'A' and resid 131 through 133' Processing helix chain 'A' and resid 216 through 220 removed outlier: 3.608A pdb=" N HIS A 220 " --> pdb=" O ARG A 216 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 216 through 220' Processing helix chain 'A' and resid 239 through 242 removed outlier: 3.971A pdb=" N ALA A 242 " --> pdb=" O ASN A 239 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 239 through 242' Processing helix chain 'A' and resid 262 through 270 Processing helix chain 'A' and resid 392 through 396 removed outlier: 3.594A pdb=" N THR A 395 " --> pdb=" O THR A 392 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LYS A 396 " --> pdb=" O GLY A 393 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 392 through 396' Processing helix chain 'A' and resid 406 through 425 Processing helix chain 'A' and resid 437 through 458 removed outlier: 5.782A pdb=" N SER A 452 " --> pdb=" O GLN A 448 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N ALA A 453 " --> pdb=" O VAL A 449 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA A 456 " --> pdb=" O SER A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 479 removed outlier: 3.540A pdb=" N LEU A 468 " --> pdb=" O PHE A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 502 removed outlier: 3.697A pdb=" N PHE A 489 " --> pdb=" O VAL A 485 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 86 removed outlier: 3.787A pdb=" N ALA D 86 " --> pdb=" O ASP D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 104 removed outlier: 3.516A pdb=" N GLY D 104 " --> pdb=" O TRP D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 133 No H-bonds generated for 'chain 'D' and resid 131 through 133' Processing helix chain 'D' and resid 216 through 220 removed outlier: 3.525A pdb=" N HIS D 220 " --> pdb=" O ARG D 216 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 216 through 220' Processing helix chain 'D' and resid 240 through 242 No H-bonds generated for 'chain 'D' and resid 240 through 242' Processing helix chain 'D' and resid 262 through 270 Processing helix chain 'D' and resid 392 through 396 removed outlier: 3.600A pdb=" N THR D 395 " --> pdb=" O THR D 392 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LYS D 396 " --> pdb=" O GLY D 393 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 392 through 396' Processing helix chain 'D' and resid 406 through 425 Processing helix chain 'D' and resid 437 through 458 removed outlier: 5.822A pdb=" N SER D 452 " --> pdb=" O GLN D 448 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N ALA D 453 " --> pdb=" O VAL D 449 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA D 456 " --> pdb=" O SER D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 464 through 479 removed outlier: 3.527A pdb=" N LEU D 468 " --> pdb=" O PHE D 464 " (cutoff:3.500A) Processing helix chain 'D' and resid 485 through 502 removed outlier: 3.699A pdb=" N PHE D 489 " --> pdb=" O VAL D 485 " (cutoff:3.500A) Processing helix chain 'G' and resid 82 through 86 removed outlier: 3.801A pdb=" N ALA G 86 " --> pdb=" O ASP G 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 100 through 104 removed outlier: 3.505A pdb=" N GLY G 104 " --> pdb=" O TRP G 101 " (cutoff:3.500A) Processing helix chain 'G' and resid 131 through 133 No H-bonds generated for 'chain 'G' and resid 131 through 133' Processing helix chain 'G' and resid 216 through 220 removed outlier: 3.666A pdb=" N HIS G 220 " --> pdb=" O ARG G 216 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 216 through 220' Processing helix chain 'G' and resid 240 through 242 No H-bonds generated for 'chain 'G' and resid 240 through 242' Processing helix chain 'G' and resid 262 through 270 Processing helix chain 'G' and resid 392 through 396 removed outlier: 3.598A pdb=" N THR G 395 " --> pdb=" O THR G 392 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LYS G 396 " --> pdb=" O GLY G 393 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 392 through 396' Processing helix chain 'G' and resid 406 through 425 Processing helix chain 'G' and resid 437 through 458 removed outlier: 5.801A pdb=" N SER G 452 " --> pdb=" O GLN G 448 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N ALA G 453 " --> pdb=" O VAL G 449 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA G 456 " --> pdb=" O SER G 452 " (cutoff:3.500A) Processing helix chain 'G' and resid 464 through 479 removed outlier: 3.571A pdb=" N LEU G 468 " --> pdb=" O PHE G 464 " (cutoff:3.500A) Processing helix chain 'G' and resid 485 through 502 removed outlier: 3.690A pdb=" N PHE G 489 " --> pdb=" O VAL G 485 " (cutoff:3.500A) Processing helix chain 'I' and resid 122 through 133 Processing helix chain 'I' and resid 133 through 146 removed outlier: 3.565A pdb=" N ALA I 137 " --> pdb=" O ASN I 133 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N THR I 146 " --> pdb=" O VAL I 142 " (cutoff:3.500A) Processing helix chain 'I' and resid 150 through 165 Processing helix chain 'F' and resid 122 through 133 Processing helix chain 'F' and resid 133 through 146 removed outlier: 3.991A pdb=" N THR F 146 " --> pdb=" O VAL F 142 " (cutoff:3.500A) Processing helix chain 'F' and resid 150 through 165 Processing helix chain 'C' and resid 122 through 133 Processing helix chain 'C' and resid 133 through 146 removed outlier: 3.986A pdb=" N THR C 146 " --> pdb=" O VAL C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 165 Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 13 removed outlier: 7.189A pdb=" N ARG A 138 " --> pdb=" O VAL A 46 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N THR A 48 " --> pdb=" O GLU A 136 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N GLU A 136 " --> pdb=" O THR A 48 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 12 through 13 removed outlier: 3.738A pdb=" N GLU A 277 " --> pdb=" O THR A 284 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 20 through 25 removed outlier: 3.942A pdb=" N LYS A 291 " --> pdb=" O GLU A 192 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 55 through 64 removed outlier: 6.170A pdb=" N VAL A 56 " --> pdb=" O LYS A 128 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N LYS A 128 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N SER A 58 " --> pdb=" O THR A 126 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N THR A 126 " --> pdb=" O SER A 58 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N CYS A 60 " --> pdb=" O LYS A 124 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N LYS A 124 " --> pdb=" O CYS A 60 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N GLU A 62 " --> pdb=" O VAL A 122 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N LEU A 274 " --> pdb=" O LEU A 213 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 69 through 73 Processing sheet with id=AA6, first strand: chain 'A' and resid 244 through 246 Processing sheet with id=AA7, first strand: chain 'A' and resid 307 through 308 removed outlier: 6.682A pdb=" N ALA A 307 " --> pdb=" O LYS A 341 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 312 through 315 removed outlier: 3.549A pdb=" N THR A 328 " --> pdb=" O SER A 320 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER A 320 " --> pdb=" O THR A 328 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 312 through 315 removed outlier: 3.957A pdb=" N ARG A 358 " --> pdb=" O ASP A 380 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 344 through 347 Processing sheet with id=AB2, first strand: chain 'B' and resid 2 through 5 removed outlier: 6.137A pdb=" N TYR B 10 " --> pdb=" O TRP B 75 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N VAL B 77 " --> pdb=" O TYR B 10 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N MET B 12 " --> pdb=" O VAL B 77 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N GLY B 79 " --> pdb=" O MET B 12 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 22 through 26 Processing sheet with id=AB4, first strand: chain 'D' and resid 9 through 13 removed outlier: 3.697A pdb=" N ASP D 10 " --> pdb=" O CYS D 30 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N THR D 32 " --> pdb=" O ASP D 10 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N PHE D 43 " --> pdb=" O SER D 142 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N SER D 142 " --> pdb=" O PHE D 43 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N LEU D 45 " --> pdb=" O LEU D 140 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N LEU D 140 " --> pdb=" O LEU D 45 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N THR D 47 " --> pdb=" O ARG D 138 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 9 through 13 removed outlier: 3.697A pdb=" N ASP D 10 " --> pdb=" O CYS D 30 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N THR D 32 " --> pdb=" O ASP D 10 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU D 277 " --> pdb=" O THR D 284 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 20 through 25 removed outlier: 3.942A pdb=" N LYS D 291 " --> pdb=" O GLU D 192 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 226 through 228 removed outlier: 7.065A pdb=" N GLY D 127 " --> pdb=" O VAL D 56 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N SER D 58 " --> pdb=" O LEU D 125 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU D 125 " --> pdb=" O SER D 58 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N CYS D 60 " --> pdb=" O LYS D 123 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N LYS D 123 " --> pdb=" O CYS D 60 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N GLU D 62 " --> pdb=" O CYS D 121 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N CYS D 121 " --> pdb=" O GLU D 62 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N LEU D 274 " --> pdb=" O LEU D 213 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 90 through 98 removed outlier: 6.675A pdb=" N MET D 68 " --> pdb=" O SER E 50 " (cutoff:3.500A) removed outlier: 8.645A pdb=" N GLU E 52 " --> pdb=" O MET D 68 " (cutoff:3.500A) removed outlier: 8.327A pdb=" N SER D 70 " --> pdb=" O GLU E 52 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N TYR E 10 " --> pdb=" O TRP E 75 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N VAL E 77 " --> pdb=" O TYR E 10 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N MET E 12 " --> pdb=" O VAL E 77 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N GLY E 79 " --> pdb=" O MET E 12 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 244 through 246 Processing sheet with id=AC1, first strand: chain 'D' and resid 307 through 308 removed outlier: 6.616A pdb=" N ALA D 307 " --> pdb=" O LYS D 341 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'D' and resid 312 through 315 removed outlier: 3.560A pdb=" N THR D 328 " --> pdb=" O SER D 320 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N SER D 320 " --> pdb=" O THR D 328 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 312 through 315 removed outlier: 3.952A pdb=" N ARG D 358 " --> pdb=" O ASP D 380 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 344 through 347 Processing sheet with id=AC5, first strand: chain 'E' and resid 23 through 26 Processing sheet with id=AC6, first strand: chain 'G' and resid 9 through 13 removed outlier: 3.742A pdb=" N ASP G 10 " --> pdb=" O CYS G 30 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N THR G 32 " --> pdb=" O ASP G 10 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N PHE G 43 " --> pdb=" O SER G 142 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N SER G 142 " --> pdb=" O PHE G 43 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N LEU G 45 " --> pdb=" O LEU G 140 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LEU G 140 " --> pdb=" O LEU G 45 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N THR G 47 " --> pdb=" O ARG G 138 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 9 through 13 removed outlier: 3.742A pdb=" N ASP G 10 " --> pdb=" O CYS G 30 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N THR G 32 " --> pdb=" O ASP G 10 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLU G 277 " --> pdb=" O THR G 284 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 20 through 25 removed outlier: 3.959A pdb=" N LYS G 291 " --> pdb=" O GLU G 192 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 226 through 228 removed outlier: 5.904A pdb=" N VAL G 56 " --> pdb=" O LYS G 128 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N LYS G 128 " --> pdb=" O VAL G 56 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N SER G 58 " --> pdb=" O THR G 126 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N THR G 126 " --> pdb=" O SER G 58 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N CYS G 60 " --> pdb=" O LYS G 124 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N LYS G 124 " --> pdb=" O CYS G 60 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N GLU G 62 " --> pdb=" O VAL G 122 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL G 122 " --> pdb=" O GLU G 62 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N LEU G 274 " --> pdb=" O LEU G 213 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 69 through 73 Processing sheet with id=AD2, first strand: chain 'G' and resid 244 through 246 Processing sheet with id=AD3, first strand: chain 'G' and resid 307 through 308 removed outlier: 6.692A pdb=" N ALA G 307 " --> pdb=" O LYS G 341 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'G' and resid 312 through 315 removed outlier: 3.593A pdb=" N THR G 328 " --> pdb=" O SER G 320 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER G 320 " --> pdb=" O THR G 328 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 312 through 315 removed outlier: 4.044A pdb=" N ARG G 358 " --> pdb=" O ASP G 380 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 344 through 347 Processing sheet with id=AD7, first strand: chain 'H' and resid 2 through 5 removed outlier: 6.451A pdb=" N TYR H 10 " --> pdb=" O TRP H 75 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N VAL H 77 " --> pdb=" O TYR H 10 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N MET H 12 " --> pdb=" O VAL H 77 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N GLY H 79 " --> pdb=" O MET H 12 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 22 through 26 629 hydrogen bonds defined for protein. 1740 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.74 Time building geometry restraints manager: 1.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 4937 1.35 - 1.46: 3726 1.46 - 1.58: 6565 1.58 - 1.70: 0 1.70 - 1.82: 204 Bond restraints: 15432 Sorted by residual: bond pdb=" C1 NAG B 201 " pdb=" O5 NAG B 201 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.07e+00 bond pdb=" C1 NAG E 201 " pdb=" O5 NAG E 201 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.97e+00 bond pdb=" C1 NAG H 201 " pdb=" O5 NAG H 201 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.96e+00 bond pdb=" C CYS G 74 " pdb=" N PRO G 75 " ideal model delta sigma weight residual 1.334 1.362 -0.028 2.34e-02 1.83e+03 1.44e+00 bond pdb=" C CYS D 74 " pdb=" N PRO D 75 " ideal model delta sigma weight residual 1.334 1.362 -0.028 2.34e-02 1.83e+03 1.44e+00 ... (remaining 15427 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 20622 2.04 - 4.07: 232 4.07 - 6.11: 25 6.11 - 8.15: 1 8.15 - 10.18: 6 Bond angle restraints: 20886 Sorted by residual: angle pdb=" CA CYS A 116 " pdb=" CB CYS A 116 " pdb=" SG CYS A 116 " ideal model delta sigma weight residual 114.40 124.58 -10.18 2.30e+00 1.89e-01 1.96e+01 angle pdb=" CA CYS D 116 " pdb=" CB CYS D 116 " pdb=" SG CYS D 116 " ideal model delta sigma weight residual 114.40 124.38 -9.98 2.30e+00 1.89e-01 1.88e+01 angle pdb=" CA CYS G 116 " pdb=" CB CYS G 116 " pdb=" SG CYS G 116 " ideal model delta sigma weight residual 114.40 124.33 -9.93 2.30e+00 1.89e-01 1.87e+01 angle pdb=" CA CYS D 92 " pdb=" CB CYS D 92 " pdb=" SG CYS D 92 " ideal model delta sigma weight residual 114.40 123.88 -9.48 2.30e+00 1.89e-01 1.70e+01 angle pdb=" CA CYS A 92 " pdb=" CB CYS A 92 " pdb=" SG CYS A 92 " ideal model delta sigma weight residual 114.40 123.72 -9.32 2.30e+00 1.89e-01 1.64e+01 ... (remaining 20881 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 8477 17.94 - 35.88: 552 35.88 - 53.82: 111 53.82 - 71.76: 13 71.76 - 89.70: 15 Dihedral angle restraints: 9168 sinusoidal: 3609 harmonic: 5559 Sorted by residual: dihedral pdb=" CB CYS A 74 " pdb=" SG CYS A 74 " pdb=" SG CYS A 105 " pdb=" CB CYS A 105 " ideal model delta sinusoidal sigma weight residual 93.00 178.72 -85.72 1 1.00e+01 1.00e-02 8.88e+01 dihedral pdb=" CB CYS D 74 " pdb=" SG CYS D 74 " pdb=" SG CYS D 105 " pdb=" CB CYS D 105 " ideal model delta sinusoidal sigma weight residual 93.00 175.19 -82.19 1 1.00e+01 1.00e-02 8.30e+01 dihedral pdb=" CB CYS G 74 " pdb=" SG CYS G 74 " pdb=" SG CYS G 105 " pdb=" CB CYS G 105 " ideal model delta sinusoidal sigma weight residual 93.00 173.98 -80.98 1 1.00e+01 1.00e-02 8.09e+01 ... (remaining 9165 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1662 0.039 - 0.077: 452 0.077 - 0.116: 163 0.116 - 0.155: 39 0.155 - 0.194: 3 Chirality restraints: 2319 Sorted by residual: chirality pdb=" CA CYS A 116 " pdb=" N CYS A 116 " pdb=" C CYS A 116 " pdb=" CB CYS A 116 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.37e-01 chirality pdb=" CA CYS D 116 " pdb=" N CYS D 116 " pdb=" C CYS D 116 " pdb=" CB CYS D 116 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.35e-01 chirality pdb=" CA CYS G 116 " pdb=" N CYS G 116 " pdb=" C CYS G 116 " pdb=" CB CYS G 116 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.12e-01 ... (remaining 2316 not shown) Planarity restraints: 2664 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY D 111 " 0.009 2.00e-02 2.50e+03 1.92e-02 3.67e+00 pdb=" C GLY D 111 " -0.033 2.00e-02 2.50e+03 pdb=" O GLY D 111 " 0.013 2.00e-02 2.50e+03 pdb=" N SER D 112 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY G 111 " 0.009 2.00e-02 2.50e+03 1.86e-02 3.47e+00 pdb=" C GLY G 111 " -0.032 2.00e-02 2.50e+03 pdb=" O GLY G 111 " 0.012 2.00e-02 2.50e+03 pdb=" N SER G 112 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR H 51 " -0.009 2.00e-02 2.50e+03 1.83e-02 3.36e+00 pdb=" C TYR H 51 " 0.032 2.00e-02 2.50e+03 pdb=" O TYR H 51 " -0.012 2.00e-02 2.50e+03 pdb=" N GLU H 52 " -0.011 2.00e-02 2.50e+03 ... (remaining 2661 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 4236 2.81 - 3.33: 13004 3.33 - 3.85: 22774 3.85 - 4.38: 24622 4.38 - 4.90: 44215 Nonbonded interactions: 108851 Sorted by model distance: nonbonded pdb=" OD1 ASP D 380 " pdb=" NH1 ARG D 403 " model vdw 2.286 3.120 nonbonded pdb=" OG SER G 348 " pdb=" NH2 ARG I 132 " model vdw 2.322 3.120 nonbonded pdb=" OD1 ASP G 380 " pdb=" NH1 ARG G 403 " model vdw 2.342 3.120 nonbonded pdb=" OD1 ASP A 380 " pdb=" NH1 ARG A 403 " model vdw 2.354 3.120 nonbonded pdb=" N ASN A 233 " pdb=" OD1 ASN A 233 " model vdw 2.370 3.120 ... (remaining 108846 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'I' } 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=1.00 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: 0.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.160 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 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 : 0.002 0.040 15462 Z= 0.106 Angle : 0.576 10.184 20949 Z= 0.322 Chirality : 0.042 0.194 2319 Planarity : 0.003 0.032 2661 Dihedral : 12.255 89.703 5541 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.93 % Favored : 96.97 % Rotamer: Outliers : 1.55 % Allowed : 4.03 % Favored : 94.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.13 (0.17), residues: 1947 helix: -0.01 (0.24), residues: 396 sheet: -0.54 (0.21), residues: 564 loop : -2.64 (0.15), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 247 TYR 0.009 0.001 TYR E 51 PHE 0.012 0.001 PHE A 445 TRP 0.010 0.001 TRP A 226 HIS 0.008 0.001 HIS B 83 Details of bonding type rmsd covalent geometry : bond 0.00209 (15432) covalent geometry : angle 0.55480 (20886) SS BOND : bond 0.00332 ( 27) SS BOND : angle 3.06333 ( 54) hydrogen bonds : bond 0.10017 ( 599) hydrogen bonds : angle 5.23965 ( 1740) link_NAG-ASN : bond 0.00298 ( 3) link_NAG-ASN : angle 1.09053 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 764 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 739 time to evaluate : 0.550 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: 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 23 ILE cc_start: 0.8763 (pt) cc_final: 0.8554 (mt) REVERT: A 36 ASN cc_start: 0.8292 (p0) cc_final: 0.7896 (p0) REVERT: A 118 LYS cc_start: 0.8792 (tttp) cc_final: 0.8161 (ttpt) REVERT: A 151 MET cc_start: 0.3263 (tpt) cc_final: 0.2899 (mmp) REVERT: A 207 MET cc_start: 0.7555 (ttt) cc_final: 0.7304 (tmm) REVERT: A 294 LEU cc_start: 0.8978 (mt) cc_final: 0.8344 (mp) REVERT: A 416 MET cc_start: 0.7953 (ttt) cc_final: 0.7011 (tpt) REVERT: A 489 PHE cc_start: 0.3431 (m-10) cc_final: 0.3035 (m-10) REVERT: B 12 MET cc_start: 0.8261 (mtm) cc_final: 0.8008 (mtp) REVERT: B 26 GLU cc_start: 0.8089 (tt0) cc_final: 0.7586 (tp30) REVERT: B 63 GLU cc_start: 0.6154 (tt0) cc_final: 0.5665 (tm-30) REVERT: B 93 ARG cc_start: 0.7308 (mtm-85) cc_final: 0.6645 (ptp90) REVERT: B 101 HIS cc_start: 0.5938 (OUTLIER) cc_final: 0.5179 (m-70) REVERT: D 118 LYS cc_start: 0.8352 (tttp) cc_final: 0.8145 (tttt) REVERT: D 253 LYS cc_start: 0.7519 (OUTLIER) cc_final: 0.7243 (pttp) REVERT: D 285 ILE cc_start: 0.8154 (mp) cc_final: 0.7697 (mp) REVERT: D 302 LYS cc_start: 0.7515 (tttt) cc_final: 0.7228 (tptt) REVERT: D 383 PHE cc_start: 0.8253 (m-80) cc_final: 0.7665 (m-10) REVERT: D 403 ARG cc_start: 0.8531 (ttt180) cc_final: 0.8050 (ptm160) REVERT: D 447 HIS cc_start: 0.8068 (t-90) cc_final: 0.7504 (t-90) REVERT: D 487 MET cc_start: 0.2812 (mpp) cc_final: 0.2581 (tmm) REVERT: D 495 MET cc_start: 0.6537 (ttm) cc_final: 0.6224 (mmm) REVERT: E 44 MET cc_start: 0.6487 (tpp) cc_final: 0.5743 (tpp) REVERT: E 101 HIS cc_start: 0.7632 (OUTLIER) cc_final: 0.5529 (m-70) REVERT: G 27 HIS cc_start: 0.5741 (t-90) cc_final: 0.5284 (t-90) REVERT: G 53 MET cc_start: 0.7557 (mtm) cc_final: 0.7303 (mtm) REVERT: G 71 ASP cc_start: 0.8438 (t0) cc_final: 0.7433 (t0) REVERT: G 87 ASP cc_start: 0.6750 (t0) cc_final: 0.5701 (t0) REVERT: G 90 PHE cc_start: 0.8620 (m-80) cc_final: 0.8150 (m-80) REVERT: G 131 GLN cc_start: 0.8603 (mm110) cc_final: 0.8357 (mt0) REVERT: G 140 LEU cc_start: 0.8785 (mt) cc_final: 0.8572 (mt) REVERT: G 151 MET cc_start: 0.4884 (tpt) cc_final: 0.4054 (tpp) REVERT: G 207 MET cc_start: 0.8681 (ttt) cc_final: 0.8076 (tmm) REVERT: G 248 GLU cc_start: 0.8076 (mt-10) cc_final: 0.7721 (pp20) REVERT: G 250 HIS cc_start: 0.6610 (t70) cc_final: 0.6226 (t-170) REVERT: G 294 LEU cc_start: 0.8230 (mt) cc_final: 0.7848 (mp) REVERT: G 302 LYS cc_start: 0.8546 (tttt) cc_final: 0.7956 (tptp) REVERT: G 313 PHE cc_start: 0.8367 (m-80) cc_final: 0.8165 (m-10) REVERT: G 341 LYS cc_start: 0.8801 (ttmt) cc_final: 0.8347 (mtmm) REVERT: G 376 MET cc_start: 0.8754 (ttp) cc_final: 0.8181 (tmm) REVERT: G 383 PHE cc_start: 0.7201 (m-80) cc_final: 0.6898 (m-80) REVERT: G 422 MET cc_start: 0.9304 (tpp) cc_final: 0.9010 (mmm) REVERT: G 435 VAL cc_start: 0.7062 (p) cc_final: 0.6861 (p) REVERT: G 439 PHE cc_start: 0.7315 (m-80) cc_final: 0.6777 (p90) REVERT: G 440 ASN cc_start: 0.7862 (t0) cc_final: 0.7553 (t0) REVERT: H 36 ILE cc_start: 0.7679 (mt) cc_final: 0.7431 (mt) REVERT: H 51 TYR cc_start: 0.8535 (p90) cc_final: 0.8233 (p90) REVERT: H 101 HIS cc_start: 0.6919 (OUTLIER) cc_final: 0.6194 (m-70) REVERT: I 125 LYS cc_start: 0.9071 (mtpt) cc_final: 0.8686 (mtmt) REVERT: I 128 ASN cc_start: 0.8098 (t0) cc_final: 0.7896 (t0) outliers start: 25 outliers final: 6 residues processed: 753 average time/residue: 0.1324 time to fit residues: 143.3760 Evaluate side-chains 483 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 473 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 0.0570 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 overall best weight: 2.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN A 236 HIS A 250 HIS A 448 GLN B 83 HIS B 101 HIS D 147 GLN D 148 HIS D 164 ASN D 400 HIS E 37 GLN E 83 HIS G 131 GLN G 254 GLN G 363 ASN G 400 HIS G 479 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.156093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.128746 restraints weight = 29089.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.132321 restraints weight = 17978.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.133570 restraints weight = 11977.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.133974 restraints weight = 10030.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.134354 restraints weight = 9375.999| |-----------------------------------------------------------------------------| r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.3693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 15462 Z= 0.181 Angle : 0.721 14.096 20949 Z= 0.377 Chirality : 0.047 0.263 2319 Planarity : 0.004 0.037 2661 Dihedral : 5.137 82.939 2166 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 0.43 % Allowed : 4.97 % Favored : 94.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.18), residues: 1947 helix: 1.12 (0.26), residues: 399 sheet: -0.22 (0.20), residues: 609 loop : -2.11 (0.18), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 2 TYR 0.026 0.002 TYR G 203 PHE 0.032 0.002 PHE C 157 TRP 0.022 0.001 TRP I 129 HIS 0.013 0.001 HIS A 235 Details of bonding type rmsd covalent geometry : bond 0.00408 (15432) covalent geometry : angle 0.68915 (20886) SS BOND : bond 0.00739 ( 27) SS BOND : angle 4.20809 ( 54) hydrogen bonds : bond 0.03983 ( 599) hydrogen bonds : angle 4.75805 ( 1740) link_NAG-ASN : bond 0.00368 ( 3) link_NAG-ASN : angle 1.04751 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 532 time to evaluate : 0.596 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 MET cc_start: 0.8627 (ttp) cc_final: 0.8394 (ttm) REVERT: A 76 THR cc_start: 0.8449 (m) cc_final: 0.8158 (m) REVERT: A 131 GLN cc_start: 0.7523 (mt0) cc_final: 0.6965 (mm-40) REVERT: A 133 GLU cc_start: 0.7595 (pm20) cc_final: 0.7372 (pm20) REVERT: A 147 GLN cc_start: 0.8387 (mt0) cc_final: 0.8182 (mt0) REVERT: A 204 TYR cc_start: 0.8573 (t80) cc_final: 0.8350 (t80) REVERT: A 207 MET cc_start: 0.7945 (ttt) cc_final: 0.7730 (tmm) REVERT: A 294 LEU cc_start: 0.8854 (mt) cc_final: 0.8511 (mp) REVERT: A 415 THR cc_start: 0.8955 (m) cc_final: 0.8627 (p) REVERT: A 438 MET cc_start: 0.8876 (tpt) cc_final: 0.7065 (mpp) REVERT: A 489 PHE cc_start: 0.3266 (m-10) cc_final: 0.3032 (m-10) REVERT: B 5 LYS cc_start: 0.8917 (ptmt) cc_final: 0.8605 (pttt) REVERT: B 26 GLU cc_start: 0.7999 (tt0) cc_final: 0.7693 (tp30) REVERT: B 27 THR cc_start: 0.7033 (p) cc_final: 0.6643 (p) REVERT: B 63 GLU cc_start: 0.6438 (tt0) cc_final: 0.6036 (tm-30) REVERT: D 26 GLU cc_start: 0.8394 (mm-30) cc_final: 0.8177 (mm-30) REVERT: D 108 PHE cc_start: 0.6481 (m-10) cc_final: 0.5991 (m-10) REVERT: D 297 ASP cc_start: 0.7589 (p0) cc_final: 0.7328 (p0) REVERT: D 383 PHE cc_start: 0.8547 (m-80) cc_final: 0.8221 (m-10) REVERT: D 487 MET cc_start: 0.2306 (mpp) cc_final: 0.1985 (tmm) REVERT: E 44 MET cc_start: 0.5714 (tpp) cc_final: 0.5507 (tpp) REVERT: E 68 TRP cc_start: 0.7289 (p90) cc_final: 0.6989 (p90) REVERT: E 88 GLU cc_start: 0.7329 (mp0) cc_final: 0.7122 (mp0) REVERT: E 93 ARG cc_start: 0.7742 (mmp-170) cc_final: 0.7516 (mmp-170) REVERT: G 44 GLU cc_start: 0.8345 (tt0) cc_final: 0.7217 (tt0) REVERT: G 68 MET cc_start: 0.8600 (mtt) cc_final: 0.8308 (mtt) REVERT: G 151 MET cc_start: 0.5128 (tpt) cc_final: 0.4569 (tpp) REVERT: G 160 HIS cc_start: 0.7184 (m-70) cc_final: 0.6826 (m-70) REVERT: G 169 ASP cc_start: 0.7408 (p0) cc_final: 0.7204 (p0) REVERT: G 203 TYR cc_start: 0.8506 (m-80) cc_final: 0.8289 (m-80) REVERT: G 204 TYR cc_start: 0.8542 (t80) cc_final: 0.8193 (t80) REVERT: G 250 HIS cc_start: 0.7727 (t70) cc_final: 0.7313 (t-170) REVERT: G 285 ILE cc_start: 0.8500 (mp) cc_final: 0.8150 (mt) REVERT: G 376 MET cc_start: 0.8719 (ttp) cc_final: 0.7991 (tmm) REVERT: G 383 PHE cc_start: 0.7453 (m-80) cc_final: 0.7203 (m-80) REVERT: G 439 PHE cc_start: 0.7466 (m-80) cc_final: 0.7093 (p90) REVERT: H 88 GLU cc_start: 0.8787 (tp30) cc_final: 0.8578 (tp30) REVERT: I 125 LYS cc_start: 0.9138 (mtpt) cc_final: 0.8779 (mtmt) REVERT: C 161 LEU cc_start: 0.8481 (mm) cc_final: 0.8259 (tp) outliers start: 7 outliers final: 3 residues processed: 532 average time/residue: 0.1181 time to fit residues: 94.3392 Evaluate side-chains 431 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 428 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 120 optimal weight: 6.9990 chunk 125 optimal weight: 0.5980 chunk 59 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 139 optimal weight: 6.9990 chunk 62 optimal weight: 6.9990 chunk 73 optimal weight: 3.9990 chunk 87 optimal weight: 0.5980 chunk 57 optimal weight: 2.9990 chunk 85 optimal weight: 7.9990 chunk 102 optimal weight: 7.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN A 103 ASN A 236 HIS A 250 HIS D 148 HIS D 289 HIS D 402 HIS D 448 GLN ** G 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 250 HIS ** G 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.154601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.126201 restraints weight = 29314.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.129218 restraints weight = 18464.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.131297 restraints weight = 13368.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.132741 restraints weight = 10638.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.133444 restraints weight = 9078.520| |-----------------------------------------------------------------------------| r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.4274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 15462 Z= 0.142 Angle : 0.663 15.859 20949 Z= 0.347 Chirality : 0.045 0.255 2319 Planarity : 0.004 0.035 2661 Dihedral : 5.080 83.771 2166 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.31 % Allowed : 4.35 % Favored : 95.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.19), residues: 1947 helix: 1.46 (0.26), residues: 399 sheet: -0.04 (0.21), residues: 609 loop : -1.93 (0.18), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 167 TYR 0.018 0.001 TYR C 122 PHE 0.017 0.002 PHE A 445 TRP 0.017 0.001 TRP H 68 HIS 0.012 0.001 HIS G 27 Details of bonding type rmsd covalent geometry : bond 0.00321 (15432) covalent geometry : angle 0.63663 (20886) SS BOND : bond 0.00480 ( 27) SS BOND : angle 3.70539 ( 54) hydrogen bonds : bond 0.03845 ( 599) hydrogen bonds : angle 4.56148 ( 1740) link_NAG-ASN : bond 0.00209 ( 3) link_NAG-ASN : angle 0.92430 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 527 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 522 time to evaluate : 0.550 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 ASN cc_start: 0.7948 (p0) cc_final: 0.7710 (p0) REVERT: A 82 LEU cc_start: 0.9155 (tp) cc_final: 0.8737 (tp) REVERT: A 85 MET cc_start: 0.7795 (mtm) cc_final: 0.7401 (mtp) REVERT: A 207 MET cc_start: 0.8281 (ttt) cc_final: 0.8025 (tmm) REVERT: A 294 LEU cc_start: 0.8905 (mt) cc_final: 0.8697 (mp) REVERT: A 415 THR cc_start: 0.8748 (m) cc_final: 0.8494 (p) REVERT: A 422 MET cc_start: 0.8447 (tpp) cc_final: 0.8089 (tpp) REVERT: A 438 MET cc_start: 0.8849 (tpt) cc_final: 0.6991 (mpp) REVERT: A 489 PHE cc_start: 0.3698 (m-10) cc_final: 0.3362 (m-10) REVERT: B 5 LYS cc_start: 0.8829 (ptmt) cc_final: 0.8569 (pttt) REVERT: B 27 THR cc_start: 0.6967 (p) cc_final: 0.6614 (p) REVERT: B 63 GLU cc_start: 0.6684 (tt0) cc_final: 0.6383 (tm-30) REVERT: B 77 VAL cc_start: 0.8679 (p) cc_final: 0.8365 (p) REVERT: B 86 THR cc_start: 0.6597 (p) cc_final: 0.6374 (p) REVERT: D 26 GLU cc_start: 0.8406 (mm-30) cc_final: 0.8198 (mm-30) REVERT: D 45 LEU cc_start: 0.8984 (tt) cc_final: 0.8282 (tp) REVERT: D 245 GLU cc_start: 0.8416 (tt0) cc_final: 0.8113 (tt0) REVERT: D 297 ASP cc_start: 0.7403 (p0) cc_final: 0.7040 (p0) REVERT: D 383 PHE cc_start: 0.8408 (m-80) cc_final: 0.8141 (m-10) REVERT: D 389 ILE cc_start: 0.9322 (mp) cc_final: 0.9025 (tp) REVERT: D 461 MET cc_start: 0.6402 (mpp) cc_final: 0.5154 (mpp) REVERT: D 476 MET cc_start: 0.7743 (tmm) cc_final: 0.7396 (tmm) REVERT: D 487 MET cc_start: 0.2285 (mpp) cc_final: 0.1911 (tmm) REVERT: E 44 MET cc_start: 0.5496 (tpp) cc_final: 0.5257 (tpp) REVERT: G 44 GLU cc_start: 0.8396 (tt0) cc_final: 0.8110 (tt0) REVERT: G 68 MET cc_start: 0.8510 (mtt) cc_final: 0.8217 (mtp) REVERT: G 151 MET cc_start: 0.4983 (tpt) cc_final: 0.4382 (tpp) REVERT: G 160 HIS cc_start: 0.7380 (m-70) cc_final: 0.7096 (m-70) REVERT: G 204 TYR cc_start: 0.8449 (t80) cc_final: 0.8159 (t80) REVERT: G 207 MET cc_start: 0.8861 (tmm) cc_final: 0.7724 (tmm) REVERT: G 306 TYR cc_start: 0.7331 (m-10) cc_final: 0.7052 (m-10) REVERT: G 439 PHE cc_start: 0.7603 (m-80) cc_final: 0.7149 (p90) REVERT: G 461 MET cc_start: 0.5771 (mpp) cc_final: 0.4491 (mmp) REVERT: G 487 MET cc_start: 0.5756 (mtm) cc_final: 0.3837 (tmm) REVERT: I 125 LYS cc_start: 0.9170 (mtpt) cc_final: 0.8752 (mtmt) REVERT: C 161 LEU cc_start: 0.8491 (mm) cc_final: 0.8172 (tp) outliers start: 5 outliers final: 2 residues processed: 522 average time/residue: 0.1197 time to fit residues: 93.7162 Evaluate side-chains 423 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 421 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 105 optimal weight: 7.9990 chunk 44 optimal weight: 5.9990 chunk 170 optimal weight: 9.9990 chunk 119 optimal weight: 5.9990 chunk 191 optimal weight: 4.9990 chunk 139 optimal weight: 8.9990 chunk 34 optimal weight: 0.0980 chunk 9 optimal weight: 6.9990 chunk 178 optimal weight: 0.1980 chunk 155 optimal weight: 10.0000 chunk 169 optimal weight: 6.9990 overall best weight: 3.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN A 164 ASN A 236 HIS ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 43 HIS G 159 GLN ** G 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.146724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.121178 restraints weight = 29496.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.124328 restraints weight = 17252.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.125504 restraints weight = 11430.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.126350 restraints weight = 9605.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.126497 restraints weight = 9142.720| |-----------------------------------------------------------------------------| r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.5251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 15462 Z= 0.241 Angle : 0.793 19.248 20949 Z= 0.414 Chirality : 0.049 0.284 2319 Planarity : 0.005 0.042 2661 Dihedral : 5.855 87.475 2166 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 0.37 % Allowed : 5.65 % Favored : 93.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.19), residues: 1947 helix: 1.27 (0.26), residues: 414 sheet: -0.14 (0.20), residues: 624 loop : -2.04 (0.19), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 2 TYR 0.022 0.002 TYR A 61 PHE 0.023 0.002 PHE C 157 TRP 0.023 0.002 TRP C 129 HIS 0.011 0.002 HIS A 27 Details of bonding type rmsd covalent geometry : bond 0.00551 (15432) covalent geometry : angle 0.76359 (20886) SS BOND : bond 0.00678 ( 27) SS BOND : angle 4.24433 ( 54) hydrogen bonds : bond 0.04571 ( 599) hydrogen bonds : angle 4.86821 ( 1740) link_NAG-ASN : bond 0.00153 ( 3) link_NAG-ASN : angle 1.00028 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 495 time to evaluate : 0.584 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: symmetry clash REVERT: A 36 ASN cc_start: 0.8230 (p0) cc_final: 0.7815 (p0) REVERT: A 37 ASN cc_start: 0.8583 (m-40) cc_final: 0.8158 (m-40) REVERT: A 65 ILE cc_start: 0.9275 (pt) cc_final: 0.9027 (pt) REVERT: A 82 LEU cc_start: 0.9290 (tp) cc_final: 0.8461 (tp) REVERT: A 85 MET cc_start: 0.7624 (mtm) cc_final: 0.7341 (mtp) REVERT: A 89 GLN cc_start: 0.8082 (mm-40) cc_final: 0.7840 (mm110) REVERT: A 131 GLN cc_start: 0.7776 (mt0) cc_final: 0.7111 (mm-40) REVERT: A 133 GLU cc_start: 0.7655 (pm20) cc_final: 0.7080 (tm-30) REVERT: A 282 LYS cc_start: 0.8588 (ptpp) cc_final: 0.8249 (ptpp) REVERT: A 304 MET cc_start: 0.8155 (ppp) cc_final: 0.7769 (ppp) REVERT: A 349 ASP cc_start: 0.7181 (t0) cc_final: 0.6914 (t0) REVERT: A 415 THR cc_start: 0.8836 (m) cc_final: 0.8614 (p) REVERT: A 438 MET cc_start: 0.8427 (tpt) cc_final: 0.6939 (mpp) REVERT: A 489 PHE cc_start: 0.3252 (m-10) cc_final: 0.3047 (m-10) REVERT: B 5 LYS cc_start: 0.9004 (ptmt) cc_final: 0.8627 (pttt) REVERT: B 26 GLU cc_start: 0.7250 (tp30) cc_final: 0.6800 (tp30) REVERT: B 63 GLU cc_start: 0.7007 (tt0) cc_final: 0.6703 (tt0) REVERT: B 86 THR cc_start: 0.7157 (p) cc_final: 0.6943 (p) REVERT: D 20 TRP cc_start: 0.8818 (m100) cc_final: 0.8519 (m100) REVERT: D 26 GLU cc_start: 0.8271 (mm-30) cc_final: 0.8041 (mm-30) REVERT: D 108 PHE cc_start: 0.6220 (m-10) cc_final: 0.5772 (m-10) REVERT: D 202 LEU cc_start: 0.8289 (mt) cc_final: 0.8070 (mt) REVERT: D 245 GLU cc_start: 0.8403 (tt0) cc_final: 0.8191 (tt0) REVERT: D 297 ASP cc_start: 0.7709 (p0) cc_final: 0.7447 (p0) REVERT: D 389 ILE cc_start: 0.9384 (mp) cc_final: 0.8895 (tp) REVERT: D 461 MET cc_start: 0.6584 (mpp) cc_final: 0.5442 (mpp) REVERT: D 487 MET cc_start: 0.4022 (mpp) cc_final: 0.3093 (tmm) REVERT: D 495 MET cc_start: 0.6822 (ttm) cc_final: 0.6297 (mmp) REVERT: G 44 GLU cc_start: 0.8532 (tt0) cc_final: 0.7614 (tt0) REVERT: G 68 MET cc_start: 0.8548 (mtt) cc_final: 0.8219 (mtp) REVERT: G 151 MET cc_start: 0.5357 (tpt) cc_final: 0.4525 (tpp) REVERT: G 160 HIS cc_start: 0.7592 (m-70) cc_final: 0.7207 (m90) REVERT: G 207 MET cc_start: 0.9150 (tmm) cc_final: 0.8257 (tmm) REVERT: H 36 ILE cc_start: 0.7776 (mt) cc_final: 0.7419 (mt) REVERT: H 39 MET cc_start: 0.6842 (ptp) cc_final: 0.6416 (ptp) REVERT: C 134 PRO cc_start: 0.7417 (Cg_endo) cc_final: 0.7167 (Cg_exo) REVERT: C 161 LEU cc_start: 0.8506 (mm) cc_final: 0.8277 (tp) outliers start: 6 outliers final: 2 residues processed: 496 average time/residue: 0.1211 time to fit residues: 89.8576 Evaluate side-chains 410 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 408 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 189 optimal weight: 0.9990 chunk 171 optimal weight: 10.0000 chunk 74 optimal weight: 0.8980 chunk 52 optimal weight: 20.0000 chunk 184 optimal weight: 2.9990 chunk 130 optimal weight: 6.9990 chunk 95 optimal weight: 1.9990 chunk 131 optimal weight: 5.9990 chunk 25 optimal weight: 0.8980 chunk 53 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 GLN A 236 HIS ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 448 GLN D 400 HIS D 448 GLN E 43 HIS E 83 HIS ** G 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 250 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.149463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.123302 restraints weight = 29319.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.126382 restraints weight = 17581.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.128529 restraints weight = 12286.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.129895 restraints weight = 9547.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.130926 restraints weight = 8085.438| |-----------------------------------------------------------------------------| r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.5415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 15462 Z= 0.140 Angle : 0.715 21.135 20949 Z= 0.371 Chirality : 0.047 0.311 2319 Planarity : 0.004 0.038 2661 Dihedral : 5.511 84.219 2166 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.12 % Allowed : 3.10 % Favored : 96.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.19), residues: 1947 helix: 1.52 (0.27), residues: 414 sheet: 0.00 (0.21), residues: 621 loop : -1.90 (0.19), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 421 TYR 0.018 0.001 TYR C 122 PHE 0.017 0.002 PHE A 445 TRP 0.020 0.001 TRP C 129 HIS 0.012 0.001 HIS A 27 Details of bonding type rmsd covalent geometry : bond 0.00314 (15432) covalent geometry : angle 0.68265 (20886) SS BOND : bond 0.00851 ( 27) SS BOND : angle 4.19361 ( 54) hydrogen bonds : bond 0.04002 ( 599) hydrogen bonds : angle 4.54703 ( 1740) link_NAG-ASN : bond 0.00224 ( 3) link_NAG-ASN : angle 1.26544 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 489 time to evaluate : 0.584 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 36 ASN cc_start: 0.8202 (p0) cc_final: 0.7725 (p0) REVERT: A 37 ASN cc_start: 0.8474 (m-40) cc_final: 0.8036 (m-40) REVERT: A 67 GLU cc_start: 0.8593 (mt-10) cc_final: 0.7887 (mp0) REVERT: A 82 LEU cc_start: 0.9210 (tp) cc_final: 0.8539 (tp) REVERT: A 89 GLN cc_start: 0.8006 (mm-40) cc_final: 0.7741 (mm110) REVERT: A 131 GLN cc_start: 0.7830 (mt0) cc_final: 0.7102 (mm-40) REVERT: A 133 GLU cc_start: 0.7738 (pm20) cc_final: 0.7268 (tm-30) REVERT: A 134 ASN cc_start: 0.7436 (m110) cc_final: 0.7036 (m110) REVERT: A 207 MET cc_start: 0.8392 (ttt) cc_final: 0.8016 (ptm) REVERT: A 282 LYS cc_start: 0.8542 (ptpp) cc_final: 0.8273 (ptpp) REVERT: A 306 TYR cc_start: 0.8335 (m-10) cc_final: 0.8018 (m-10) REVERT: A 367 THR cc_start: 0.9071 (p) cc_final: 0.8759 (t) REVERT: A 415 THR cc_start: 0.8758 (m) cc_final: 0.8530 (p) REVERT: A 438 MET cc_start: 0.8316 (tpt) cc_final: 0.6977 (mpp) REVERT: B 26 GLU cc_start: 0.6802 (tp30) cc_final: 0.6301 (tp30) REVERT: B 27 THR cc_start: 0.7059 (p) cc_final: 0.6770 (p) REVERT: D 57 ARG cc_start: 0.8375 (ttm170) cc_final: 0.8038 (ttm110) REVERT: D 108 PHE cc_start: 0.6109 (m-10) cc_final: 0.5664 (m-10) REVERT: D 201 ASP cc_start: 0.8552 (m-30) cc_final: 0.8342 (m-30) REVERT: D 297 ASP cc_start: 0.7562 (p0) cc_final: 0.7172 (p0) REVERT: D 299 LEU cc_start: 0.8664 (tp) cc_final: 0.8448 (tp) REVERT: D 349 ASP cc_start: 0.7064 (t0) cc_final: 0.6658 (t0) REVERT: D 389 ILE cc_start: 0.9322 (mp) cc_final: 0.8827 (tp) REVERT: D 461 MET cc_start: 0.6166 (mpp) cc_final: 0.5678 (mpp) REVERT: D 487 MET cc_start: 0.3791 (mpp) cc_final: 0.3035 (tmm) REVERT: D 495 MET cc_start: 0.6943 (ttm) cc_final: 0.5969 (mtt) REVERT: E 51 TYR cc_start: 0.8223 (p90) cc_final: 0.7878 (p90) REVERT: E 63 GLU cc_start: 0.7424 (tt0) cc_final: 0.7119 (mp0) REVERT: E 88 GLU cc_start: 0.7427 (mp0) cc_final: 0.7019 (mp0) REVERT: G 151 MET cc_start: 0.5752 (tpt) cc_final: 0.5006 (tpp) REVERT: G 160 HIS cc_start: 0.7331 (m-70) cc_final: 0.7075 (m90) REVERT: G 207 MET cc_start: 0.9161 (tmm) cc_final: 0.8258 (tmm) REVERT: G 349 ASP cc_start: 0.8042 (t0) cc_final: 0.7391 (p0) REVERT: H 88 GLU cc_start: 0.8812 (tp30) cc_final: 0.8546 (tp30) REVERT: I 128 ASN cc_start: 0.8910 (t0) cc_final: 0.8541 (t0) REVERT: C 134 PRO cc_start: 0.7450 (Cg_endo) cc_final: 0.7210 (Cg_exo) REVERT: C 161 LEU cc_start: 0.8459 (mm) cc_final: 0.8150 (tp) outliers start: 2 outliers final: 0 residues processed: 490 average time/residue: 0.1203 time to fit residues: 88.1134 Evaluate side-chains 407 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 407 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 125 optimal weight: 6.9990 chunk 62 optimal weight: 4.9990 chunk 137 optimal weight: 5.9990 chunk 59 optimal weight: 5.9990 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 0.6980 chunk 88 optimal weight: 9.9990 chunk 50 optimal weight: 10.0000 chunk 61 optimal weight: 5.9990 chunk 95 optimal weight: 7.9990 chunk 133 optimal weight: 1.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 GLN A 103 ASN A 236 HIS ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 448 GLN ** D 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 254 GLN D 289 HIS D 448 GLN E 43 HIS E 83 HIS ** G 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.143601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.117065 restraints weight = 29503.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.119978 restraints weight = 18167.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.121975 restraints weight = 12915.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.123183 restraints weight = 10187.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.124153 restraints weight = 8730.169| |-----------------------------------------------------------------------------| r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.6043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.091 15462 Z= 0.259 Angle : 0.822 23.053 20949 Z= 0.429 Chirality : 0.049 0.345 2319 Planarity : 0.005 0.042 2661 Dihedral : 6.009 82.313 2166 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 0.12 % Allowed : 3.23 % Favored : 96.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.19), residues: 1947 helix: 1.32 (0.26), residues: 414 sheet: -0.28 (0.20), residues: 654 loop : -2.00 (0.20), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 99 TYR 0.024 0.002 TYR G 203 PHE 0.027 0.002 PHE A 219 TRP 0.025 0.002 TRP C 129 HIS 0.014 0.002 HIS D 27 Details of bonding type rmsd covalent geometry : bond 0.00588 (15432) covalent geometry : angle 0.79124 (20886) SS BOND : bond 0.00887 ( 27) SS BOND : angle 4.39766 ( 54) hydrogen bonds : bond 0.04815 ( 599) hydrogen bonds : angle 4.88369 ( 1740) link_NAG-ASN : bond 0.00590 ( 3) link_NAG-ASN : angle 1.55515 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 472 time to evaluate : 0.636 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: symmetry clash REVERT: A 67 GLU cc_start: 0.8579 (mt-10) cc_final: 0.7999 (mp0) REVERT: A 82 LEU cc_start: 0.8956 (tp) cc_final: 0.8612 (tp) REVERT: A 85 MET cc_start: 0.8030 (mtp) cc_final: 0.7729 (mtp) REVERT: A 89 GLN cc_start: 0.8010 (mm-40) cc_final: 0.7747 (mm110) REVERT: A 98 ASP cc_start: 0.7492 (t70) cc_final: 0.7289 (t0) REVERT: A 131 GLN cc_start: 0.7626 (mt0) cc_final: 0.7273 (mm-40) REVERT: A 133 GLU cc_start: 0.7473 (pm20) cc_final: 0.7267 (tm-30) REVERT: A 134 ASN cc_start: 0.7960 (m110) cc_final: 0.7629 (m110) REVERT: A 282 LYS cc_start: 0.8580 (ptpp) cc_final: 0.8294 (ptpp) REVERT: A 302 LYS cc_start: 0.8858 (ttmm) cc_final: 0.8555 (ttmm) REVERT: A 304 MET cc_start: 0.8131 (ppp) cc_final: 0.7628 (ppp) REVERT: A 306 TYR cc_start: 0.8385 (m-10) cc_final: 0.8050 (m-10) REVERT: A 367 THR cc_start: 0.9041 (p) cc_final: 0.8639 (t) REVERT: A 415 THR cc_start: 0.8859 (m) cc_final: 0.8623 (p) REVERT: A 438 MET cc_start: 0.8213 (tpt) cc_final: 0.7162 (mpp) REVERT: A 489 PHE cc_start: 0.3163 (m-10) cc_final: 0.2791 (m-10) REVERT: A 495 MET cc_start: 0.6502 (mtp) cc_final: 0.5964 (mmp) REVERT: B 26 GLU cc_start: 0.6901 (tp30) cc_final: 0.6466 (tp30) REVERT: B 27 THR cc_start: 0.7125 (p) cc_final: 0.6854 (p) REVERT: D 26 GLU cc_start: 0.8169 (mm-30) cc_final: 0.7927 (mt-10) REVERT: D 73 ARG cc_start: 0.6878 (ttm170) cc_final: 0.6494 (ttm170) REVERT: D 108 PHE cc_start: 0.6544 (m-10) cc_final: 0.6012 (m-10) REVERT: D 201 ASP cc_start: 0.8591 (m-30) cc_final: 0.8211 (m-30) REVERT: D 245 GLU cc_start: 0.8281 (tt0) cc_final: 0.7998 (tt0) REVERT: D 297 ASP cc_start: 0.7789 (p0) cc_final: 0.7430 (p0) REVERT: D 487 MET cc_start: 0.3533 (mpp) cc_final: 0.2951 (tmm) REVERT: E 39 MET cc_start: 0.6821 (mmp) cc_final: 0.6257 (mmm) REVERT: G 151 MET cc_start: 0.6198 (tpt) cc_final: 0.5150 (tpp) REVERT: G 207 MET cc_start: 0.9131 (tmm) cc_final: 0.8262 (tmm) REVERT: G 301 LEU cc_start: 0.9107 (tp) cc_final: 0.8831 (tt) REVERT: G 341 LYS cc_start: 0.8664 (mtmm) cc_final: 0.8372 (mtmm) REVERT: G 403 ARG cc_start: 0.8169 (ttp-170) cc_final: 0.7941 (ttm170) REVERT: H 88 GLU cc_start: 0.8950 (tp30) cc_final: 0.8701 (tp30) REVERT: I 131 LEU cc_start: 0.9129 (mm) cc_final: 0.8882 (mm) REVERT: I 161 LEU cc_start: 0.6416 (mm) cc_final: 0.6026 (tp) REVERT: C 134 PRO cc_start: 0.7401 (Cg_endo) cc_final: 0.7141 (Cg_exo) REVERT: C 161 LEU cc_start: 0.8633 (mm) cc_final: 0.8372 (tp) outliers start: 2 outliers final: 0 residues processed: 473 average time/residue: 0.1155 time to fit residues: 81.7577 Evaluate side-chains 404 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 404 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 54 optimal weight: 9.9990 chunk 160 optimal weight: 3.9990 chunk 50 optimal weight: 9.9990 chunk 163 optimal weight: 6.9990 chunk 52 optimal weight: 10.0000 chunk 174 optimal weight: 2.9990 chunk 184 optimal weight: 2.9990 chunk 69 optimal weight: 10.0000 chunk 72 optimal weight: 6.9990 chunk 154 optimal weight: 2.9990 chunk 74 optimal weight: 0.5980 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 HIS ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 289 HIS D 400 HIS E 43 HIS G 144 HIS ** G 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 250 HIS ** G 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 128 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.144529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.118069 restraints weight = 29254.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.120986 restraints weight = 18065.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.123004 restraints weight = 12857.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.124383 restraints weight = 10185.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.125279 restraints weight = 8665.228| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.6266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 15462 Z= 0.193 Angle : 0.788 22.715 20949 Z= 0.408 Chirality : 0.048 0.338 2319 Planarity : 0.004 0.045 2661 Dihedral : 5.891 82.979 2166 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 0.12 % Allowed : 1.55 % Favored : 98.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.19), residues: 1947 helix: 1.52 (0.27), residues: 411 sheet: -0.19 (0.20), residues: 621 loop : -2.01 (0.19), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 2 TYR 0.017 0.002 TYR D 61 PHE 0.031 0.002 PHE C 157 TRP 0.031 0.002 TRP D 20 HIS 0.007 0.001 HIS G 27 Details of bonding type rmsd covalent geometry : bond 0.00442 (15432) covalent geometry : angle 0.75597 (20886) SS BOND : bond 0.00845 ( 27) SS BOND : angle 4.36505 ( 54) hydrogen bonds : bond 0.04443 ( 599) hydrogen bonds : angle 4.69448 ( 1740) link_NAG-ASN : bond 0.00372 ( 3) link_NAG-ASN : angle 1.80349 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 470 time to evaluate : 0.574 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 37 ASN cc_start: 0.8398 (m-40) cc_final: 0.7841 (m-40) REVERT: A 67 GLU cc_start: 0.8585 (mt-10) cc_final: 0.7964 (mp0) REVERT: A 82 LEU cc_start: 0.8850 (tp) cc_final: 0.8451 (tp) REVERT: A 126 THR cc_start: 0.8827 (p) cc_final: 0.8616 (p) REVERT: A 131 GLN cc_start: 0.7747 (mt0) cc_final: 0.7072 (mm-40) REVERT: A 134 ASN cc_start: 0.7944 (m110) cc_final: 0.7693 (m110) REVERT: A 206 THR cc_start: 0.9626 (m) cc_final: 0.9344 (p) REVERT: A 282 LYS cc_start: 0.8656 (ptpp) cc_final: 0.8316 (ptpp) REVERT: A 302 LYS cc_start: 0.8806 (ttmm) cc_final: 0.8461 (ttmm) REVERT: A 306 TYR cc_start: 0.8345 (m-10) cc_final: 0.7971 (m-10) REVERT: A 415 THR cc_start: 0.8820 (m) cc_final: 0.8590 (p) REVERT: A 438 MET cc_start: 0.8504 (tpt) cc_final: 0.7182 (mpp) REVERT: B 26 GLU cc_start: 0.6834 (tp30) cc_final: 0.6356 (tp30) REVERT: B 27 THR cc_start: 0.7079 (p) cc_final: 0.6798 (p) REVERT: D 73 ARG cc_start: 0.6974 (ttm170) cc_final: 0.6513 (ttm170) REVERT: D 108 PHE cc_start: 0.6678 (m-10) cc_final: 0.6202 (m-10) REVERT: D 195 SER cc_start: 0.8442 (p) cc_final: 0.8177 (p) REVERT: D 245 GLU cc_start: 0.8273 (tt0) cc_final: 0.8025 (tt0) REVERT: D 289 HIS cc_start: 0.8114 (p-80) cc_final: 0.7870 (p-80) REVERT: D 349 ASP cc_start: 0.7201 (t0) cc_final: 0.6959 (t0) REVERT: D 487 MET cc_start: 0.4268 (mpp) cc_final: 0.3284 (tmm) REVERT: E 16 LYS cc_start: 0.8334 (tttt) cc_final: 0.8069 (tttt) REVERT: E 39 MET cc_start: 0.6797 (mmp) cc_final: 0.6293 (mmm) REVERT: G 6 ILE cc_start: 0.9248 (mm) cc_final: 0.8987 (mm) REVERT: G 151 MET cc_start: 0.6208 (tpt) cc_final: 0.5388 (tpp) REVERT: G 160 HIS cc_start: 0.6845 (m90) cc_final: 0.6616 (m90) REVERT: G 207 MET cc_start: 0.9047 (tmm) cc_final: 0.8301 (tmm) REVERT: G 301 LEU cc_start: 0.9078 (tp) cc_final: 0.8793 (tt) REVERT: G 349 ASP cc_start: 0.8263 (t0) cc_final: 0.7645 (t70) REVERT: G 403 ARG cc_start: 0.8164 (ttp-170) cc_final: 0.7954 (ttm170) REVERT: H 37 GLN cc_start: 0.7424 (mm-40) cc_final: 0.7021 (mm-40) REVERT: H 88 GLU cc_start: 0.8836 (tp30) cc_final: 0.8574 (tp30) REVERT: I 161 LEU cc_start: 0.6707 (mm) cc_final: 0.6409 (tp) REVERT: C 134 PRO cc_start: 0.7343 (Cg_endo) cc_final: 0.7095 (Cg_exo) REVERT: C 147 LEU cc_start: 0.7888 (mt) cc_final: 0.7641 (mt) outliers start: 2 outliers final: 0 residues processed: 471 average time/residue: 0.1196 time to fit residues: 84.0013 Evaluate side-chains 403 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 403 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 14 optimal weight: 0.5980 chunk 68 optimal weight: 3.9990 chunk 174 optimal weight: 0.4980 chunk 188 optimal weight: 10.0000 chunk 12 optimal weight: 1.9990 chunk 112 optimal weight: 8.9990 chunk 61 optimal weight: 7.9990 chunk 34 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 HIS ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 448 GLN D 400 HIS E 43 HIS ** G 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 267 HIS ** G 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 133 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.146946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.120528 restraints weight = 29431.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.123480 restraints weight = 18276.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.125533 restraints weight = 12955.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.126942 restraints weight = 10207.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.127912 restraints weight = 8636.996| |-----------------------------------------------------------------------------| r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.6382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 15462 Z= 0.139 Angle : 0.775 21.635 20949 Z= 0.397 Chirality : 0.047 0.337 2319 Planarity : 0.004 0.055 2661 Dihedral : 5.647 82.192 2166 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 0.12 % Allowed : 0.99 % Favored : 98.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.19), residues: 1947 helix: 1.76 (0.28), residues: 411 sheet: -0.14 (0.20), residues: 621 loop : -1.94 (0.19), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 132 TYR 0.019 0.002 TYR C 122 PHE 0.024 0.002 PHE A 454 TRP 0.028 0.002 TRP C 129 HIS 0.005 0.001 HIS G 267 Details of bonding type rmsd covalent geometry : bond 0.00313 (15432) covalent geometry : angle 0.74234 (20886) SS BOND : bond 0.00864 ( 27) SS BOND : angle 4.38756 ( 54) hydrogen bonds : bond 0.04157 ( 599) hydrogen bonds : angle 4.50841 ( 1740) link_NAG-ASN : bond 0.00271 ( 3) link_NAG-ASN : angle 1.76350 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 466 time to evaluate : 0.555 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 37 ASN cc_start: 0.8098 (m-40) cc_final: 0.7754 (m-40) REVERT: A 67 GLU cc_start: 0.8536 (mt-10) cc_final: 0.7899 (mp0) REVERT: A 82 LEU cc_start: 0.8977 (tp) cc_final: 0.8059 (tp) REVERT: A 133 GLU cc_start: 0.8407 (tm-30) cc_final: 0.7919 (tm-30) REVERT: A 134 ASN cc_start: 0.7870 (m110) cc_final: 0.6657 (m110) REVERT: A 282 LYS cc_start: 0.8835 (ptpp) cc_final: 0.8543 (ptpp) REVERT: A 302 LYS cc_start: 0.8766 (ttmm) cc_final: 0.8538 (ttmm) REVERT: A 306 TYR cc_start: 0.8231 (m-10) cc_final: 0.7868 (m-10) REVERT: A 367 THR cc_start: 0.8920 (p) cc_final: 0.8717 (p) REVERT: A 415 THR cc_start: 0.8791 (m) cc_final: 0.8553 (p) REVERT: A 438 MET cc_start: 0.8333 (tpt) cc_final: 0.7089 (mpp) REVERT: A 489 PHE cc_start: 0.2737 (m-10) cc_final: 0.2001 (m-10) REVERT: B 26 GLU cc_start: 0.6701 (tp30) cc_final: 0.6266 (tp30) REVERT: B 27 THR cc_start: 0.7399 (p) cc_final: 0.7130 (p) REVERT: B 68 TRP cc_start: 0.8402 (p90) cc_final: 0.7670 (p90) REVERT: D 73 ARG cc_start: 0.6765 (ttm170) cc_final: 0.6415 (ttm170) REVERT: D 108 PHE cc_start: 0.6754 (m-10) cc_final: 0.6374 (m-10) REVERT: D 195 SER cc_start: 0.8407 (p) cc_final: 0.8095 (p) REVERT: D 201 ASP cc_start: 0.8432 (m-30) cc_final: 0.8094 (m-30) REVERT: D 245 GLU cc_start: 0.8288 (tt0) cc_final: 0.8048 (tt0) REVERT: D 289 HIS cc_start: 0.8001 (p-80) cc_final: 0.7691 (p-80) REVERT: D 349 ASP cc_start: 0.7081 (t0) cc_final: 0.6859 (t0) REVERT: D 400 HIS cc_start: 0.7929 (t70) cc_final: 0.7700 (t-90) REVERT: D 487 MET cc_start: 0.4744 (mpp) cc_final: 0.3818 (tmm) REVERT: E 4 THR cc_start: 0.6897 (t) cc_final: 0.6264 (t) REVERT: E 16 LYS cc_start: 0.8263 (tttt) cc_final: 0.7873 (tttp) REVERT: E 51 TYR cc_start: 0.8428 (p90) cc_final: 0.8058 (p90) REVERT: E 68 TRP cc_start: 0.7849 (p90) cc_final: 0.7511 (p90) REVERT: G 6 ILE cc_start: 0.9280 (mm) cc_final: 0.8949 (mm) REVERT: G 151 MET cc_start: 0.6084 (tpt) cc_final: 0.5357 (tpp) REVERT: G 167 ARG cc_start: 0.7944 (mtp-110) cc_final: 0.7734 (mtp-110) REVERT: G 201 ASP cc_start: 0.7871 (t0) cc_final: 0.7583 (t0) REVERT: G 204 TYR cc_start: 0.8438 (t80) cc_final: 0.8058 (t80) REVERT: G 207 MET cc_start: 0.8809 (tmm) cc_final: 0.7959 (tmm) REVERT: G 301 LEU cc_start: 0.9088 (tp) cc_final: 0.8795 (tt) REVERT: G 349 ASP cc_start: 0.8174 (t0) cc_final: 0.7661 (t70) REVERT: H 37 GLN cc_start: 0.7828 (mm-40) cc_final: 0.7434 (mm-40) REVERT: H 88 GLU cc_start: 0.8868 (tp30) cc_final: 0.8609 (tp30) REVERT: I 161 LEU cc_start: 0.6425 (mm) cc_final: 0.6032 (tp) REVERT: C 134 PRO cc_start: 0.7246 (Cg_endo) cc_final: 0.7014 (Cg_exo) REVERT: C 161 LEU cc_start: 0.8554 (tp) cc_final: 0.8327 (tp) outliers start: 2 outliers final: 0 residues processed: 468 average time/residue: 0.1195 time to fit residues: 83.3503 Evaluate side-chains 402 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 402 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 147 optimal weight: 9.9990 chunk 87 optimal weight: 10.0000 chunk 143 optimal weight: 0.0980 chunk 28 optimal weight: 10.0000 chunk 176 optimal weight: 6.9990 chunk 35 optimal weight: 0.9990 chunk 114 optimal weight: 5.9990 chunk 7 optimal weight: 0.1980 chunk 54 optimal weight: 3.9990 chunk 136 optimal weight: 5.9990 chunk 88 optimal weight: 9.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 HIS ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 43 HIS ** G 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.145018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.118545 restraints weight = 29452.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.121469 restraints weight = 18122.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.123476 restraints weight = 12904.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.124873 restraints weight = 10198.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.125855 restraints weight = 8630.244| |-----------------------------------------------------------------------------| r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.6550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 15462 Z= 0.173 Angle : 0.800 23.155 20949 Z= 0.412 Chirality : 0.048 0.343 2319 Planarity : 0.004 0.046 2661 Dihedral : 5.717 81.450 2166 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 0.06 % Allowed : 0.74 % Favored : 99.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.19), residues: 1947 helix: 1.71 (0.28), residues: 411 sheet: -0.27 (0.20), residues: 621 loop : -1.98 (0.19), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 132 TYR 0.019 0.002 TYR C 122 PHE 0.019 0.002 PHE A 445 TRP 0.031 0.002 TRP C 129 HIS 0.006 0.001 HIS G 211 Details of bonding type rmsd covalent geometry : bond 0.00395 (15432) covalent geometry : angle 0.76738 (20886) SS BOND : bond 0.00810 ( 27) SS BOND : angle 4.49432 ( 54) hydrogen bonds : bond 0.04393 ( 599) hydrogen bonds : angle 4.55656 ( 1740) link_NAG-ASN : bond 0.00279 ( 3) link_NAG-ASN : angle 1.66705 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 466 time to evaluate : 0.466 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: symmetry clash REVERT: A 37 ASN cc_start: 0.8166 (m-40) cc_final: 0.7828 (m-40) REVERT: A 67 GLU cc_start: 0.8410 (mt-10) cc_final: 0.7834 (mp0) REVERT: A 82 LEU cc_start: 0.9095 (tp) cc_final: 0.8571 (tp) REVERT: A 116 CYS cc_start: 0.5775 (p) cc_final: 0.5545 (p) REVERT: A 282 LYS cc_start: 0.8852 (ptpp) cc_final: 0.8564 (ptpp) REVERT: A 304 MET cc_start: 0.8278 (ppp) cc_final: 0.7852 (ppp) REVERT: A 306 TYR cc_start: 0.8218 (m-10) cc_final: 0.7906 (m-10) REVERT: A 349 ASP cc_start: 0.7605 (t0) cc_final: 0.7341 (t0) REVERT: A 367 THR cc_start: 0.8906 (p) cc_final: 0.8652 (p) REVERT: A 415 THR cc_start: 0.8809 (m) cc_final: 0.8595 (p) REVERT: A 438 MET cc_start: 0.8348 (tpt) cc_final: 0.6988 (mpp) REVERT: B 26 GLU cc_start: 0.6796 (tp30) cc_final: 0.6430 (tp30) REVERT: B 27 THR cc_start: 0.7388 (p) cc_final: 0.7142 (p) REVERT: B 68 TRP cc_start: 0.8350 (p90) cc_final: 0.7603 (p90) REVERT: B 93 ARG cc_start: 0.8515 (ptm160) cc_final: 0.8129 (ptp90) REVERT: D 53 MET cc_start: 0.7356 (ptp) cc_final: 0.7151 (ptp) REVERT: D 73 ARG cc_start: 0.6818 (ttm170) cc_final: 0.6312 (ttm170) REVERT: D 195 SER cc_start: 0.8609 (p) cc_final: 0.8256 (p) REVERT: D 245 GLU cc_start: 0.8292 (tt0) cc_final: 0.8064 (tt0) REVERT: D 289 HIS cc_start: 0.7891 (p-80) cc_final: 0.7534 (p-80) REVERT: D 349 ASP cc_start: 0.7235 (t0) cc_final: 0.6982 (t0) REVERT: D 487 MET cc_start: 0.4929 (mpp) cc_final: 0.3998 (tmm) REVERT: E 16 LYS cc_start: 0.8349 (tttt) cc_final: 0.8091 (tttp) REVERT: E 39 MET cc_start: 0.6657 (mmp) cc_final: 0.6296 (mmm) REVERT: E 68 TRP cc_start: 0.7892 (p90) cc_final: 0.7448 (p90) REVERT: G 6 ILE cc_start: 0.9258 (mm) cc_final: 0.9048 (mm) REVERT: G 68 MET cc_start: 0.8373 (mtt) cc_final: 0.7874 (mtp) REVERT: G 151 MET cc_start: 0.6264 (tpt) cc_final: 0.5503 (tpp) REVERT: G 201 ASP cc_start: 0.7778 (t0) cc_final: 0.7515 (t0) REVERT: G 207 MET cc_start: 0.8864 (tmm) cc_final: 0.8102 (tmm) REVERT: G 290 LEU cc_start: 0.8853 (tp) cc_final: 0.8627 (tp) REVERT: G 301 LEU cc_start: 0.9050 (tp) cc_final: 0.8756 (tt) REVERT: G 349 ASP cc_start: 0.8302 (t0) cc_final: 0.7810 (t70) REVERT: H 36 ILE cc_start: 0.7477 (mt) cc_final: 0.7160 (mt) REVERT: H 37 GLN cc_start: 0.7902 (mm-40) cc_final: 0.7461 (mm-40) REVERT: H 88 GLU cc_start: 0.8961 (tp30) cc_final: 0.8690 (tp30) REVERT: C 134 PRO cc_start: 0.7256 (Cg_endo) cc_final: 0.7044 (Cg_exo) outliers start: 1 outliers final: 0 residues processed: 467 average time/residue: 0.1147 time to fit residues: 79.8417 Evaluate side-chains 394 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 394 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 138 optimal weight: 6.9990 chunk 146 optimal weight: 2.9990 chunk 79 optimal weight: 10.0000 chunk 116 optimal weight: 0.9990 chunk 48 optimal weight: 5.9990 chunk 154 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 153 optimal weight: 8.9990 chunk 65 optimal weight: 0.9990 chunk 179 optimal weight: 6.9990 chunk 110 optimal weight: 10.0000 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 HIS ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 448 GLN D 400 HIS E 43 HIS ** G 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 250 HIS ** G 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.147261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.122382 restraints weight = 29507.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.125212 restraints weight = 18709.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.126552 restraints weight = 12554.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.127234 restraints weight = 10078.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.127542 restraints weight = 9520.314| |-----------------------------------------------------------------------------| r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.6621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 15462 Z= 0.140 Angle : 0.798 23.543 20949 Z= 0.410 Chirality : 0.048 0.333 2319 Planarity : 0.004 0.040 2661 Dihedral : 5.622 81.260 2166 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 0.06 % Allowed : 0.31 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.19), residues: 1947 helix: 1.74 (0.28), residues: 414 sheet: -0.24 (0.20), residues: 627 loop : -1.93 (0.19), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG I 132 TYR 0.012 0.001 TYR D 59 PHE 0.023 0.002 PHE A 454 TRP 0.033 0.002 TRP C 129 HIS 0.007 0.001 HIS G 27 Details of bonding type rmsd covalent geometry : bond 0.00315 (15432) covalent geometry : angle 0.76393 (20886) SS BOND : bond 0.00831 ( 27) SS BOND : angle 4.59280 ( 54) hydrogen bonds : bond 0.04177 ( 599) hydrogen bonds : angle 4.48677 ( 1740) link_NAG-ASN : bond 0.00274 ( 3) link_NAG-ASN : angle 1.68278 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 465 time to evaluate : 0.556 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: A 37 ASN cc_start: 0.8050 (m-40) cc_final: 0.7776 (m-40) REVERT: A 67 GLU cc_start: 0.8406 (mt-10) cc_final: 0.7851 (mp0) REVERT: A 82 LEU cc_start: 0.9066 (tp) cc_final: 0.8588 (tp) REVERT: A 116 CYS cc_start: 0.5802 (p) cc_final: 0.5558 (p) REVERT: A 282 LYS cc_start: 0.8879 (ptpp) cc_final: 0.8533 (ptpp) REVERT: A 306 TYR cc_start: 0.8151 (m-10) cc_final: 0.7917 (m-10) REVERT: A 349 ASP cc_start: 0.7581 (t0) cc_final: 0.7327 (t0) REVERT: A 367 THR cc_start: 0.8761 (p) cc_final: 0.8394 (p) REVERT: A 415 THR cc_start: 0.8792 (m) cc_final: 0.8541 (p) REVERT: A 438 MET cc_start: 0.8403 (tpt) cc_final: 0.7106 (mpp) REVERT: A 495 MET cc_start: 0.6221 (mtp) cc_final: 0.5742 (mmp) REVERT: B 27 THR cc_start: 0.7353 (p) cc_final: 0.7074 (p) REVERT: B 68 TRP cc_start: 0.8403 (p90) cc_final: 0.7613 (p90) REVERT: B 93 ARG cc_start: 0.8455 (ptm160) cc_final: 0.8094 (ptp90) REVERT: D 73 ARG cc_start: 0.6941 (ttm170) cc_final: 0.6454 (ttm170) REVERT: D 195 SER cc_start: 0.8621 (p) cc_final: 0.8271 (p) REVERT: D 201 ASP cc_start: 0.8534 (m-30) cc_final: 0.8234 (m-30) REVERT: D 245 GLU cc_start: 0.8294 (tt0) cc_final: 0.8058 (tt0) REVERT: D 289 HIS cc_start: 0.7887 (p-80) cc_final: 0.7570 (p-80) REVERT: D 349 ASP cc_start: 0.7163 (t0) cc_final: 0.6931 (t0) REVERT: D 487 MET cc_start: 0.5252 (mpp) cc_final: 0.4333 (tmm) REVERT: E 12 MET cc_start: 0.8257 (ppp) cc_final: 0.7899 (ppp) REVERT: E 16 LYS cc_start: 0.8322 (tttt) cc_final: 0.8097 (tttp) REVERT: E 39 MET cc_start: 0.6593 (mmp) cc_final: 0.6283 (mmm) REVERT: E 49 MET cc_start: 0.8614 (ttt) cc_final: 0.8282 (tpp) REVERT: E 51 TYR cc_start: 0.8425 (p90) cc_final: 0.7866 (p90) REVERT: E 68 TRP cc_start: 0.7895 (p90) cc_final: 0.7430 (p90) REVERT: G 46 VAL cc_start: 0.8604 (m) cc_final: 0.8001 (p) REVERT: G 67 GLU cc_start: 0.7998 (mt-10) cc_final: 0.7341 (tt0) REVERT: G 68 MET cc_start: 0.7929 (mtt) cc_final: 0.7383 (mtp) REVERT: G 140 LEU cc_start: 0.8867 (mp) cc_final: 0.8417 (pp) REVERT: G 151 MET cc_start: 0.6115 (tpt) cc_final: 0.5491 (tpp) REVERT: G 160 HIS cc_start: 0.7311 (m90) cc_final: 0.6956 (m90) REVERT: G 201 ASP cc_start: 0.7934 (t0) cc_final: 0.7543 (t0) REVERT: G 207 MET cc_start: 0.8461 (tmm) cc_final: 0.7611 (tmm) REVERT: G 290 LEU cc_start: 0.8883 (tp) cc_final: 0.8614 (tp) REVERT: G 301 LEU cc_start: 0.9069 (tp) cc_final: 0.8771 (tt) REVERT: G 349 ASP cc_start: 0.8150 (t0) cc_final: 0.7623 (t70) REVERT: G 438 MET cc_start: 0.7066 (mmm) cc_final: 0.6744 (mmp) REVERT: H 12 MET cc_start: 0.6999 (ppp) cc_final: 0.6251 (mpp) REVERT: H 37 GLN cc_start: 0.7944 (mm-40) cc_final: 0.7088 (mp10) REVERT: H 88 GLU cc_start: 0.8943 (tp30) cc_final: 0.8695 (tp30) REVERT: I 157 PHE cc_start: 0.8008 (m-80) cc_final: 0.7595 (m-10) REVERT: C 134 PRO cc_start: 0.7195 (Cg_endo) cc_final: 0.6994 (Cg_exo) outliers start: 1 outliers final: 0 residues processed: 466 average time/residue: 0.1068 time to fit residues: 74.7712 Evaluate side-chains 410 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 410 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 132 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 chunk 67 optimal weight: 8.9990 chunk 15 optimal weight: 10.0000 chunk 33 optimal weight: 6.9990 chunk 153 optimal weight: 4.9990 chunk 162 optimal weight: 6.9990 chunk 99 optimal weight: 4.9990 chunk 81 optimal weight: 0.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 GLN A 236 HIS ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 448 GLN ** D 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 400 HIS ** D 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 43 HIS ** G 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 289 HIS G 400 HIS ** G 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 43 HIS H 59 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.141952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.116516 restraints weight = 29377.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.119642 restraints weight = 17936.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.120666 restraints weight = 11829.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.121446 restraints weight = 10289.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.121595 restraints weight = 9650.816| |-----------------------------------------------------------------------------| r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.6984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.103 15462 Z= 0.266 Angle : 0.887 23.445 20949 Z= 0.462 Chirality : 0.051 0.340 2319 Planarity : 0.005 0.052 2661 Dihedral : 6.204 83.441 2166 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 0.06 % Allowed : 0.50 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.21 (0.19), residues: 1947 helix: 1.40 (0.27), residues: 411 sheet: -0.48 (0.20), residues: 624 loop : -2.13 (0.19), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 90 TYR 0.022 0.002 TYR C 122 PHE 0.026 0.003 PHE A 219 TRP 0.030 0.002 TRP H 68 HIS 0.007 0.002 HIS D 211 Details of bonding type rmsd covalent geometry : bond 0.00609 (15432) covalent geometry : angle 0.85495 (20886) SS BOND : bond 0.00835 ( 27) SS BOND : angle 4.70823 ( 54) hydrogen bonds : bond 0.04975 ( 599) hydrogen bonds : angle 4.93384 ( 1740) link_NAG-ASN : bond 0.00405 ( 3) link_NAG-ASN : angle 1.90084 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2808.59 seconds wall clock time: 49 minutes 26.17 seconds (2966.17 seconds total)