Starting phenix.real_space_refine on Sat Sep 12 09:44:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6zqj_11366/09_2026/6zqj_11366.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zqj_11366/09_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_11366/09_2026/6zqj_11366.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zqj_11366/09_2026/6zqj_11366.map" model { file = "/net/cci-nas-00/data/ceres_data/6zqj_11366/09_2026/6zqj_11366.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zqj_11366/09_2026/6zqj_11366.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6zqj_11366/09_2026/6zqj_11366.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6zqj_11366/09_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/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 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 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 chiralities: 1 Time building chain proxies: 3.58, per 1000 atoms: 0.24 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: 1.05 Conformation dependent library (CDL) restraints added in 918.8 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: 0.51 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: 3.06 Time building geometry restraints manager: 1.49 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: 8418 17.94 - 35.88: 548 35.88 - 53.82: 111 53.82 - 71.76: 13 71.76 - 89.70: 15 Dihedral angle restraints: 9105 sinusoidal: 3546 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 9102 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: 0.02 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: 0.270 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: 0.000 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.650 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.040 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 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 : 12.303 89.703 5478 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/Z covalent geometry : bond 0.00209 / 0.11 (15432) covalent geometry : angle 0.55480 / 0.31 (20886) SS BOND : bond 0.00332 / 0.20 ( 27) SS BOND : angle 3.06333 / 1.89 ( 54) hydrogen bonds : bond 0.10017 / 7.23 ( 599) hydrogen bonds : angle 5.23965 / 3.66 ( 1740) link_NAG-ASN : bond 0.00298 / 0.14 ( 3) link_NAG-ASN : angle 1.09053 / 0.51 ( 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 : 0.416 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: 0.1230 time to fit residues: 134.0231 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 : 0.608 ------------------------------------------------------------------------------- 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... A 103 ASN A 236 HIS A 250 HIS A 448 GLN ** B 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.155990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.128465 restraints weight = 29304.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.131926 restraints weight = 18278.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.133309 restraints weight = 12194.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.133636 restraints weight = 10249.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.134122 restraints weight = 9621.649| |-----------------------------------------------------------------------------| r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.3677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 15462 Z= 0.178 Angle : 0.722 13.994 20949 Z= 0.378 Chirality : 0.047 0.262 2319 Planarity : 0.004 0.037 2661 Dihedral : 5.099 82.899 2103 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.43 % Allowed : 4.84 % Favored : 94.72 % 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: -0.23 (0.20), residues: 609 loop : -2.12 (0.18), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 2 TYR 0.025 0.002 TYR G 203 PHE 0.032 0.002 PHE C 157 TRP 0.022 0.001 TRP I 129 HIS 0.014 0.001 HIS A 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.18 (15432) covalent geometry : angle 0.69030 / 0.36 (20886) SS BOND : bond 0.00660 / 0.45 ( 27) SS BOND : angle 4.23169 / 2.73 ( 54) hydrogen bonds : bond 0.03983 / 2.67 ( 599) hydrogen bonds : angle 4.75358 / 3.31 ( 1740) link_NAG-ASN : bond 0.00244 / 0.13 ( 3) link_NAG-ASN : angle 1.19978 / 0.59 ( 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 : 0.597 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: 0.8596 (ttp) cc_final: 0.8362 (ttm) REVERT: A 76 THR cc_start: 0.8443 (m) cc_final: 0.8165 (m) REVERT: A 131 GLN cc_start: 0.7434 (mt0) cc_final: 0.6861 (mm-40) REVERT: A 133 GLU cc_start: 0.7601 (pm20) cc_final: 0.7372 (pm20) REVERT: A 147 GLN cc_start: 0.8380 (mt0) cc_final: 0.8172 (mt0) REVERT: A 156 THR cc_start: 0.8129 (p) cc_final: 0.7894 (t) REVERT: A 204 TYR cc_start: 0.8561 (t80) cc_final: 0.8351 (t80) REVERT: A 207 MET cc_start: 0.7950 (ttt) cc_final: 0.7733 (tmm) REVERT: A 294 LEU cc_start: 0.8858 (mt) cc_final: 0.8504 (mp) REVERT: A 415 THR cc_start: 0.8949 (m) cc_final: 0.8625 (p) REVERT: A 438 MET cc_start: 0.8872 (tpt) cc_final: 0.7070 (mpp) REVERT: B 5 LYS cc_start: 0.8921 (ptmt) cc_final: 0.8606 (pttt) REVERT: B 26 GLU cc_start: 0.8007 (tt0) cc_final: 0.7693 (tp30) REVERT: B 27 THR cc_start: 0.6926 (p) cc_final: 0.6506 (p) REVERT: B 63 GLU cc_start: 0.6433 (tt0) cc_final: 0.6035 (tm-30) REVERT: D 26 GLU cc_start: 0.8406 (mm-30) cc_final: 0.8197 (mm-30) REVERT: D 108 PHE cc_start: 0.6520 (m-10) cc_final: 0.6024 (m-10) REVERT: D 297 ASP cc_start: 0.7588 (p0) cc_final: 0.7329 (p0) REVERT: D 383 PHE cc_start: 0.8546 (m-80) cc_final: 0.8224 (m-10) REVERT: D 487 MET cc_start: 0.2311 (mpp) cc_final: 0.1971 (tmm) REVERT: E 44 MET cc_start: 0.5702 (tpp) cc_final: 0.5491 (tpp) REVERT: E 68 TRP cc_start: 0.7277 (p90) cc_final: 0.6970 (p90) REVERT: E 88 GLU cc_start: 0.7334 (mp0) cc_final: 0.7127 (mp0) REVERT: E 93 ARG cc_start: 0.7736 (mmp-170) cc_final: 0.7517 (mmp-170) REVERT: G 68 MET cc_start: 0.8559 (mtt) cc_final: 0.8250 (mtt) REVERT: G 140 LEU cc_start: 0.9203 (mt) cc_final: 0.8500 (mt) REVERT: G 151 MET cc_start: 0.5114 (tpt) cc_final: 0.4670 (tpp) REVERT: G 160 HIS cc_start: 0.7195 (m-70) cc_final: 0.6890 (m-70) REVERT: G 163 GLU cc_start: 0.7550 (pm20) cc_final: 0.7321 (pm20) REVERT: G 169 ASP cc_start: 0.7399 (p0) cc_final: 0.7197 (p0) REVERT: G 203 TYR cc_start: 0.8512 (m-80) cc_final: 0.8303 (m-80) REVERT: G 204 TYR cc_start: 0.8683 (t80) cc_final: 0.8346 (t80) REVERT: G 250 HIS cc_start: 0.7733 (t70) cc_final: 0.7311 (t-170) REVERT: G 285 ILE cc_start: 0.8506 (mp) cc_final: 0.8143 (mt) REVERT: G 376 MET cc_start: 0.8717 (ttp) cc_final: 0.7981 (tmm) REVERT: G 383 PHE cc_start: 0.7449 (m-80) cc_final: 0.7199 (m-80) REVERT: G 439 PHE cc_start: 0.7572 (m-80) cc_final: 0.7067 (p90) REVERT: I 125 LYS cc_start: 0.9140 (mtpt) cc_final: 0.8778 (mtmt) REVERT: C 161 LEU cc_start: 0.8479 (mm) cc_final: 0.8265 (tp) outliers start: 7 outliers final: 3 residues processed: 532 average time/residue: 0.1203 time to fit residues: 95.9890 Evaluate side-chains 437 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 434 time to evaluate : 0.588 ------------------------------------------------------------------------------- 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: 0.7980 chunk 59 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 139 optimal weight: 4.9990 chunk 62 optimal weight: 6.9990 chunk 73 optimal weight: 6.9990 chunk 87 optimal weight: 0.9990 chunk 57 optimal weight: 0.7980 chunk 85 optimal weight: 3.9990 chunk 102 optimal weight: 6.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 89 GLN A 103 ASN A 236 HIS A 250 HIS B 83 HIS D 148 HIS D 289 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 = 0.3880 r_free = 0.3880 target = 0.156536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.128186 restraints weight = 29166.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.131182 restraints weight = 18297.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.133333 restraints weight = 13191.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.134643 restraints weight = 10468.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.135762 restraints weight = 8970.127| |-----------------------------------------------------------------------------| r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.4167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 15462 Z= 0.122 Angle : 0.649 15.824 20949 Z= 0.338 Chirality : 0.045 0.264 2319 Planarity : 0.003 0.035 2661 Dihedral : 4.980 82.826 2103 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.31 % Allowed : 3.91 % Favored : 95.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.85 (0.19), residues: 1947 helix: 1.52 (0.26), residues: 396 sheet: 0.01 (0.21), residues: 609 loop : -1.94 (0.18), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 247 TYR 0.018 0.001 TYR C 122 PHE 0.018 0.002 PHE A 445 TRP 0.018 0.001 TRP H 68 HIS 0.013 0.001 HIS G 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (15432) covalent geometry : angle 0.62118 / 0.33 (20886) SS BOND : bond 0.00635 / 0.42 ( 27) SS BOND : angle 3.76039 / 2.39 ( 54) hydrogen bonds : bond 0.03642 / 2.44 ( 599) hydrogen bonds : angle 4.47386 / 3.13 ( 1740) link_NAG-ASN : bond 0.00211 / 0.11 ( 3) link_NAG-ASN : angle 1.14254 / 0.59 ( 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 538 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 533 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: symmetry clash REVERT: A 53 MET cc_start: 0.7058 (ptp) cc_final: 0.6850 (ptm) REVERT: A 207 MET cc_start: 0.8268 (ttt) cc_final: 0.8061 (ttm) REVERT: A 294 LEU cc_start: 0.8863 (mt) cc_final: 0.8649 (mp) REVERT: A 415 THR cc_start: 0.8728 (m) cc_final: 0.8490 (p) REVERT: A 438 MET cc_start: 0.8778 (tpt) cc_final: 0.7010 (mpp) REVERT: A 489 PHE cc_start: 0.3148 (m-10) cc_final: 0.2868 (m-10) REVERT: B 5 LYS cc_start: 0.8772 (ptmt) cc_final: 0.8554 (pttt) REVERT: B 26 GLU cc_start: 0.7995 (tt0) cc_final: 0.7705 (tp30) REVERT: B 27 THR cc_start: 0.6963 (p) cc_final: 0.6309 (p) REVERT: B 63 GLU cc_start: 0.6629 (tt0) cc_final: 0.6315 (tm-30) REVERT: B 77 VAL cc_start: 0.8674 (p) cc_final: 0.8302 (m) REVERT: B 86 THR cc_start: 0.6754 (p) cc_final: 0.6520 (p) REVERT: D 53 MET cc_start: 0.7322 (ptp) cc_final: 0.7116 (ptp) REVERT: D 245 GLU cc_start: 0.8425 (tt0) cc_final: 0.8116 (tt0) REVERT: D 297 ASP cc_start: 0.7709 (p0) cc_final: 0.7266 (p0) REVERT: D 383 PHE cc_start: 0.8380 (m-80) cc_final: 0.8087 (m-10) REVERT: D 461 MET cc_start: 0.6330 (mpp) cc_final: 0.5729 (mmp) REVERT: D 476 MET cc_start: 0.7717 (tmm) cc_final: 0.7387 (tmm) REVERT: E 44 MET cc_start: 0.5484 (tpp) cc_final: 0.5236 (tpp) REVERT: G 68 MET cc_start: 0.8480 (mtt) cc_final: 0.8204 (mtp) REVERT: G 151 MET cc_start: 0.4693 (tpt) cc_final: 0.4059 (tpp) REVERT: G 160 HIS cc_start: 0.7305 (m-70) cc_final: 0.6987 (m-70) REVERT: G 207 MET cc_start: 0.8828 (tmm) cc_final: 0.7698 (tmm) REVERT: G 302 LYS cc_start: 0.8949 (tptp) cc_final: 0.8656 (tptp) REVERT: G 306 TYR cc_start: 0.7254 (m-10) cc_final: 0.6951 (m-10) REVERT: G 342 VAL cc_start: 0.9683 (p) cc_final: 0.9339 (p) REVERT: G 376 MET cc_start: 0.8613 (ttp) cc_final: 0.7966 (ttm) REVERT: G 383 PHE cc_start: 0.7367 (m-80) cc_final: 0.6982 (m-80) REVERT: G 439 PHE cc_start: 0.7577 (m-80) cc_final: 0.7129 (p90) REVERT: G 487 MET cc_start: 0.5733 (mtm) cc_final: 0.3820 (tmm) REVERT: I 125 LYS cc_start: 0.9147 (mtpt) cc_final: 0.8734 (mtmt) REVERT: C 161 LEU cc_start: 0.8474 (mm) cc_final: 0.8147 (tp) outliers start: 5 outliers final: 2 residues processed: 533 average time/residue: 0.1159 time to fit residues: 93.1458 Evaluate side-chains 436 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 434 time to evaluate : 0.584 ------------------------------------------------------------------------------- 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: 0.7980 chunk 44 optimal weight: 8.9990 chunk 170 optimal weight: 10.0000 chunk 119 optimal weight: 0.0870 chunk 191 optimal weight: 1.9990 chunk 139 optimal weight: 0.1980 chunk 34 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 178 optimal weight: 3.9990 chunk 155 optimal weight: 7.9990 chunk 169 optimal weight: 4.9990 overall best weight: 1.0162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 103 ASN A 236 HIS A 250 HIS D 448 GLN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.156216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.127828 restraints weight = 29537.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.130900 restraints weight = 18558.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.133028 restraints weight = 13344.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.134275 restraints weight = 10612.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.135433 restraints weight = 9142.318| |-----------------------------------------------------------------------------| r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.4524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 15462 Z= 0.119 Angle : 0.665 18.715 20949 Z= 0.345 Chirality : 0.046 0.274 2319 Planarity : 0.004 0.077 2661 Dihedral : 5.043 82.775 2103 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.31 % Allowed : 2.92 % Favored : 96.77 % 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: -0.62 (0.19), residues: 1947 helix: 1.75 (0.27), residues: 396 sheet: 0.20 (0.21), residues: 603 loop : -1.85 (0.18), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 2 TYR 0.017 0.001 TYR C 122 PHE 0.022 0.001 PHE C 157 TRP 0.020 0.001 TRP C 129 HIS 0.010 0.001 HIS A 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (15432) covalent geometry : angle 0.63320 / 0.33 (20886) SS BOND : bond 0.00656 / 0.43 ( 27) SS BOND : angle 4.02341 / 2.47 ( 54) hydrogen bonds : bond 0.03597 / 2.41 ( 599) hydrogen bonds : angle 4.31474 / 3.01 ( 1740) link_NAG-ASN : bond 0.00117 / 0.06 ( 3) link_NAG-ASN : angle 1.09324 / 0.56 ( 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 533 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 528 time to evaluate : 0.614 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: 0.8208 (m-40) cc_final: 0.7975 (m-40) REVERT: A 53 MET cc_start: 0.7065 (ptp) cc_final: 0.6779 (ptm) REVERT: A 77 GLN cc_start: 0.8089 (mm-40) cc_final: 0.7417 (mt0) REVERT: A 82 LEU cc_start: 0.9071 (tp) cc_final: 0.8602 (tp) REVERT: A 89 GLN cc_start: 0.8021 (mm-40) cc_final: 0.7744 (mm110) REVERT: A 192 GLU cc_start: 0.8848 (mm-30) cc_final: 0.8646 (mm-30) REVERT: A 207 MET cc_start: 0.8296 (ttt) cc_final: 0.7892 (ptm) REVERT: A 282 LYS cc_start: 0.8500 (ptpp) cc_final: 0.8295 (ptpp) REVERT: A 397 ILE cc_start: 0.9071 (pt) cc_final: 0.8556 (mp) REVERT: A 415 THR cc_start: 0.8721 (m) cc_final: 0.8498 (p) REVERT: A 438 MET cc_start: 0.8884 (tpt) cc_final: 0.7044 (mpp) REVERT: B 5 LYS cc_start: 0.8860 (ptmt) cc_final: 0.8655 (tttt) REVERT: B 9 THR cc_start: 0.9247 (t) cc_final: 0.9042 (t) REVERT: B 26 GLU cc_start: 0.7975 (tt0) cc_final: 0.7699 (tp30) REVERT: B 27 THR cc_start: 0.7190 (p) cc_final: 0.6612 (p) REVERT: B 63 GLU cc_start: 0.6743 (tt0) cc_final: 0.6521 (tm-30) REVERT: B 77 VAL cc_start: 0.8612 (p) cc_final: 0.8270 (p) REVERT: B 86 THR cc_start: 0.6490 (p) cc_final: 0.6266 (p) REVERT: D 108 PHE cc_start: 0.5885 (m-10) cc_final: 0.5405 (m-10) REVERT: D 245 GLU cc_start: 0.8445 (tt0) cc_final: 0.8223 (tt0) REVERT: D 297 ASP cc_start: 0.7749 (p0) cc_final: 0.7261 (p0) REVERT: D 349 ASP cc_start: 0.6777 (t0) cc_final: 0.6565 (t0) REVERT: D 383 PHE cc_start: 0.8323 (m-80) cc_final: 0.8027 (m-10) REVERT: D 461 MET cc_start: 0.6321 (mpp) cc_final: 0.5248 (mpp) REVERT: D 476 MET cc_start: 0.7665 (tmm) cc_final: 0.7339 (tmm) REVERT: E 44 MET cc_start: 0.5466 (tpp) cc_final: 0.5172 (tpp) REVERT: E 68 TRP cc_start: 0.7377 (p90) cc_final: 0.6689 (p90) REVERT: G 89 GLN cc_start: 0.8566 (mp10) cc_final: 0.8328 (pm20) REVERT: G 151 MET cc_start: 0.5026 (tpt) cc_final: 0.4137 (tpp) REVERT: G 207 MET cc_start: 0.9162 (tmm) cc_final: 0.8332 (tmm) REVERT: G 301 LEU cc_start: 0.9407 (tp) cc_final: 0.8917 (tt) REVERT: G 342 VAL cc_start: 0.9494 (p) cc_final: 0.9232 (p) REVERT: G 376 MET cc_start: 0.8436 (ttp) cc_final: 0.8133 (ttm) REVERT: G 439 PHE cc_start: 0.7571 (m-80) cc_final: 0.7190 (p90) REVERT: G 487 MET cc_start: 0.5673 (mtm) cc_final: 0.3844 (tmm) REVERT: H 88 GLU cc_start: 0.8774 (tp30) cc_final: 0.8365 (tp30) REVERT: I 127 GLU cc_start: 0.8559 (tp30) cc_final: 0.8190 (tp30) REVERT: C 161 LEU cc_start: 0.8524 (mm) cc_final: 0.8043 (tp) outliers start: 5 outliers final: 2 residues processed: 528 average time/residue: 0.1144 time to fit residues: 91.7470 Evaluate side-chains 426 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 424 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: 1.9990 chunk 171 optimal weight: 20.0000 chunk 74 optimal weight: 4.9990 chunk 52 optimal weight: 8.9990 chunk 184 optimal weight: 1.9990 chunk 130 optimal weight: 4.9990 chunk 95 optimal weight: 5.9990 chunk 131 optimal weight: 0.9980 chunk 25 optimal weight: 6.9990 chunk 53 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 77 GLN A 103 ASN A 236 HIS A 250 HIS ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 220 HIS D 289 HIS G 159 GLN G 250 HIS ** G 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.147810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.119907 restraints weight = 29995.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.122791 restraints weight = 19106.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.124779 restraints weight = 13909.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.126140 restraints weight = 11175.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.127032 restraints weight = 9615.007| |-----------------------------------------------------------------------------| r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.5292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 15462 Z= 0.216 Angle : 0.775 22.071 20949 Z= 0.404 Chirality : 0.048 0.302 2319 Planarity : 0.004 0.040 2661 Dihedral : 5.685 86.954 2103 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 0.19 % Allowed : 4.47 % Favored : 95.34 % 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: -0.80 (0.19), residues: 1947 helix: 1.52 (0.27), residues: 408 sheet: -0.01 (0.20), residues: 621 loop : -1.92 (0.19), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 421 TYR 0.021 0.002 TYR A 61 PHE 0.020 0.002 PHE C 157 TRP 0.023 0.002 TRP C 129 HIS 0.013 0.002 HIS A 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00488 / 0.22 (15432) covalent geometry : angle 0.74306 / 0.39 (20886) SS BOND : bond 0.00807 / 0.52 ( 27) SS BOND : angle 4.36949 / 2.69 ( 54) hydrogen bonds : bond 0.04399 / 2.92 ( 599) hydrogen bonds : angle 4.67890 / 3.27 ( 1740) link_NAG-ASN : bond 0.00209 / 0.10 ( 3) link_NAG-ASN : angle 0.96523 / 0.47 ( 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: 3 poor density : 488 time to evaluate : 0.570 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: 0.8335 (m-40) cc_final: 0.7950 (m-40) REVERT: A 82 LEU cc_start: 0.9026 (tp) cc_final: 0.8652 (tp) REVERT: A 85 MET cc_start: 0.7753 (mtp) cc_final: 0.7420 (mtp) REVERT: A 89 GLN cc_start: 0.8054 (mm-40) cc_final: 0.7795 (mm110) REVERT: A 131 GLN cc_start: 0.7844 (mt0) cc_final: 0.6922 (mm-40) REVERT: A 133 GLU cc_start: 0.7514 (pm20) cc_final: 0.6905 (tm-30) REVERT: A 167 ARG cc_start: 0.8312 (mtm110) cc_final: 0.8089 (mtm110) REVERT: A 190 GLU cc_start: 0.8157 (tp30) cc_final: 0.7816 (tp30) REVERT: A 192 GLU cc_start: 0.8911 (mm-30) cc_final: 0.8598 (mm-30) REVERT: A 282 LYS cc_start: 0.8573 (ptpp) cc_final: 0.8311 (ptpp) REVERT: A 304 MET cc_start: 0.8077 (ppp) cc_final: 0.7568 (ppp) REVERT: A 349 ASP cc_start: 0.7390 (t0) cc_final: 0.7190 (t0) REVERT: A 397 ILE cc_start: 0.9272 (pt) cc_final: 0.8920 (mp) REVERT: A 415 THR cc_start: 0.8837 (m) cc_final: 0.8621 (p) REVERT: A 438 MET cc_start: 0.8321 (tpt) cc_final: 0.6883 (mpp) REVERT: B 5 LYS cc_start: 0.8917 (ptmt) cc_final: 0.8623 (pttt) REVERT: B 27 THR cc_start: 0.7218 (p) cc_final: 0.6971 (p) REVERT: B 63 GLU cc_start: 0.7280 (tt0) cc_final: 0.6933 (tt0) REVERT: B 93 ARG cc_start: 0.7901 (ptp90) cc_final: 0.7600 (ptm160) REVERT: D 26 GLU cc_start: 0.8529 (mm-30) cc_final: 0.8254 (mm-30) REVERT: D 68 MET cc_start: 0.8841 (mtp) cc_final: 0.8440 (mtt) REVERT: D 108 PHE cc_start: 0.6209 (m-10) cc_final: 0.5759 (m-10) REVERT: D 202 LEU cc_start: 0.8220 (mt) cc_final: 0.8019 (mt) REVERT: D 245 GLU cc_start: 0.8250 (tt0) cc_final: 0.8043 (tt0) REVERT: D 297 ASP cc_start: 0.7697 (p0) cc_final: 0.7395 (p0) REVERT: D 349 ASP cc_start: 0.7186 (t0) cc_final: 0.6970 (t0) REVERT: D 461 MET cc_start: 0.6350 (mpp) cc_final: 0.6005 (mpp) REVERT: E 16 LYS cc_start: 0.7855 (tttt) cc_final: 0.7438 (tptt) REVERT: E 39 MET cc_start: 0.6667 (mmp) cc_final: 0.6391 (mmm) REVERT: E 49 MET cc_start: 0.8811 (ttt) cc_final: 0.8545 (tmm) REVERT: E 51 TYR cc_start: 0.8297 (p90) cc_final: 0.6632 (p90) REVERT: G 68 MET cc_start: 0.8548 (mtt) cc_final: 0.8301 (mtt) REVERT: G 151 MET cc_start: 0.5151 (tpt) cc_final: 0.4394 (tpp) REVERT: G 160 HIS cc_start: 0.7173 (m-70) cc_final: 0.6938 (m-70) REVERT: G 169 ASP cc_start: 0.7663 (p0) cc_final: 0.7424 (p0) REVERT: G 207 MET cc_start: 0.9107 (tmm) cc_final: 0.8295 (tmm) REVERT: G 236 HIS cc_start: 0.7772 (t-90) cc_final: 0.7567 (m90) REVERT: G 342 VAL cc_start: 0.9489 (p) cc_final: 0.9283 (p) REVERT: G 375 MET cc_start: 0.7919 (ppp) cc_final: 0.7616 (ppp) REVERT: G 376 MET cc_start: 0.8581 (ttp) cc_final: 0.8161 (ttm) REVERT: H 36 ILE cc_start: 0.7248 (mt) cc_final: 0.6836 (mt) REVERT: I 127 GLU cc_start: 0.8632 (tp30) cc_final: 0.8408 (tp30) REVERT: C 134 PRO cc_start: 0.7332 (Cg_endo) cc_final: 0.7113 (Cg_exo) REVERT: C 161 LEU cc_start: 0.8498 (mm) cc_final: 0.8224 (tp) outliers start: 3 outliers final: 1 residues processed: 488 average time/residue: 0.1101 time to fit residues: 81.8300 Evaluate side-chains 399 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 398 time to evaluate : 0.499 ------------------------------------------------------------------------------- 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: 3.9990 chunk 62 optimal weight: 2.9990 chunk 137 optimal weight: 10.0000 chunk 59 optimal weight: 0.0570 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 7.9990 chunk 88 optimal weight: 10.0000 chunk 50 optimal weight: 10.0000 chunk 61 optimal weight: 3.9990 chunk 95 optimal weight: 8.9990 chunk 133 optimal weight: 0.8980 overall best weight: 1.7904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 77 GLN A 236 HIS ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 83 HIS ** G 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 236 HIS G 479 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.149476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.123530 restraints weight = 29190.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.126889 restraints weight = 17868.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.127963 restraints weight = 11571.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.128319 restraints weight = 9902.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.128474 restraints weight = 9656.920| |-----------------------------------------------------------------------------| r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.5560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 15462 Z= 0.145 Angle : 0.724 18.849 20949 Z= 0.376 Chirality : 0.047 0.322 2319 Planarity : 0.004 0.035 2661 Dihedral : 5.474 83.381 2103 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % 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: -0.62 (0.19), residues: 1947 helix: 1.67 (0.27), residues: 411 sheet: 0.08 (0.21), residues: 621 loop : -1.80 (0.20), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 94 TYR 0.017 0.001 TYR C 122 PHE 0.022 0.002 PHE C 157 TRP 0.024 0.001 TRP C 129 HIS 0.008 0.001 HIS G 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 (15432) covalent geometry : angle 0.69097 / 0.36 (20886) SS BOND : bond 0.00853 / 0.53 ( 27) SS BOND : angle 4.26647 / 2.64 ( 54) hydrogen bonds : bond 0.03994 / 2.64 ( 599) hydrogen bonds : angle 4.46994 / 3.11 ( 1740) link_NAG-ASN : bond 0.00293 / 0.15 ( 3) link_NAG-ASN : angle 1.67447 / 0.86 ( 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 484 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 484 time to evaluate : 0.591 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: A 37 ASN cc_start: 0.8242 (m-40) cc_final: 0.7863 (m-40) REVERT: A 82 LEU cc_start: 0.9047 (tp) cc_final: 0.8530 (tp) REVERT: A 85 MET cc_start: 0.7752 (mtp) cc_final: 0.7379 (mtp) REVERT: A 89 GLN cc_start: 0.8022 (mm-40) cc_final: 0.7731 (mm110) REVERT: A 131 GLN cc_start: 0.7779 (mt0) cc_final: 0.7045 (mm-40) REVERT: A 133 GLU cc_start: 0.7701 (pm20) cc_final: 0.7226 (tm-30) REVERT: A 167 ARG cc_start: 0.8385 (mtm110) cc_final: 0.8180 (mtm110) REVERT: A 192 GLU cc_start: 0.8971 (mm-30) cc_final: 0.8635 (mm-30) REVERT: A 207 MET cc_start: 0.8359 (ttt) cc_final: 0.7974 (ptm) REVERT: A 282 LYS cc_start: 0.8661 (ptpp) cc_final: 0.8284 (ptpp) REVERT: A 304 MET cc_start: 0.8086 (ppp) cc_final: 0.7592 (ppp) REVERT: A 349 ASP cc_start: 0.7366 (t0) cc_final: 0.7156 (t0) REVERT: A 367 THR cc_start: 0.9049 (p) cc_final: 0.8725 (t) REVERT: A 397 ILE cc_start: 0.9231 (pt) cc_final: 0.8907 (mp) REVERT: A 415 THR cc_start: 0.8777 (m) cc_final: 0.8531 (p) REVERT: A 438 MET cc_start: 0.8313 (tpt) cc_final: 0.6868 (mpp) REVERT: B 26 GLU cc_start: 0.6217 (tp30) cc_final: 0.5734 (tp30) REVERT: B 63 GLU cc_start: 0.7591 (tt0) cc_final: 0.7353 (tt0) REVERT: B 86 THR cc_start: 0.7048 (p) cc_final: 0.6839 (p) REVERT: D 26 GLU cc_start: 0.8467 (mm-30) cc_final: 0.8178 (mm-30) REVERT: D 68 MET cc_start: 0.9016 (mtp) cc_final: 0.8589 (mtt) REVERT: D 73 ARG cc_start: 0.6986 (ttm170) cc_final: 0.6631 (ttm170) REVERT: D 96 TYR cc_start: 0.7882 (m-10) cc_final: 0.7675 (m-80) REVERT: D 108 PHE cc_start: 0.6359 (m-10) cc_final: 0.5802 (m-10) REVERT: D 178 GLU cc_start: 0.8209 (mt-10) cc_final: 0.7759 (mp0) REVERT: D 245 GLU cc_start: 0.8321 (tt0) cc_final: 0.8048 (tt0) REVERT: D 297 ASP cc_start: 0.7572 (p0) cc_final: 0.7155 (p0) REVERT: D 349 ASP cc_start: 0.7387 (t0) cc_final: 0.7187 (t0) REVERT: D 461 MET cc_start: 0.6350 (mpp) cc_final: 0.5940 (mpp) REVERT: E 16 LYS cc_start: 0.7895 (tttt) cc_final: 0.7521 (tptt) REVERT: E 39 MET cc_start: 0.6520 (mmp) cc_final: 0.6159 (mmm) REVERT: E 49 MET cc_start: 0.8708 (ttt) cc_final: 0.8485 (tmm) REVERT: E 51 TYR cc_start: 0.8150 (p90) cc_final: 0.6465 (p90) REVERT: E 63 GLU cc_start: 0.7204 (mp0) cc_final: 0.6955 (mp0) REVERT: E 88 GLU cc_start: 0.7470 (mp0) cc_final: 0.7074 (mp0) REVERT: G 151 MET cc_start: 0.5300 (tpt) cc_final: 0.4537 (tpp) REVERT: G 160 HIS cc_start: 0.7112 (m-70) cc_final: 0.6654 (m-70) REVERT: G 207 MET cc_start: 0.8916 (tmm) cc_final: 0.8220 (tmm) REVERT: G 342 VAL cc_start: 0.9554 (p) cc_final: 0.9349 (p) REVERT: G 375 MET cc_start: 0.7898 (ppp) cc_final: 0.7613 (ppp) REVERT: G 376 MET cc_start: 0.8558 (ttp) cc_final: 0.8129 (ttm) REVERT: H 12 MET cc_start: 0.6959 (ppp) cc_final: 0.6069 (mpp) REVERT: H 36 ILE cc_start: 0.7296 (mt) cc_final: 0.7050 (mt) REVERT: H 88 GLU cc_start: 0.8810 (tp30) cc_final: 0.8340 (tp30) REVERT: I 127 GLU cc_start: 0.8589 (tp30) cc_final: 0.8258 (tp30) REVERT: C 134 PRO cc_start: 0.7405 (Cg_endo) cc_final: 0.7132 (Cg_exo) REVERT: C 161 LEU cc_start: 0.8606 (mm) cc_final: 0.8303 (tp) outliers start: 0 outliers final: 0 residues processed: 484 average time/residue: 0.1147 time to fit residues: 84.2839 Evaluate side-chains 413 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 413 time to evaluate : 0.696 ------------------------------------------------------------------------------- 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: 4.9990 chunk 160 optimal weight: 5.9990 chunk 50 optimal weight: 9.9990 chunk 163 optimal weight: 6.9990 chunk 52 optimal weight: 6.9990 chunk 174 optimal weight: 10.0000 chunk 184 optimal weight: 0.0970 chunk 69 optimal weight: 5.9990 chunk 72 optimal weight: 0.9990 chunk 154 optimal weight: 1.9990 chunk 74 optimal weight: 7.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 77 GLN A 103 ASN A 164 ASN A 236 HIS ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 254 GLN D 400 HIS D 448 GLN ** G 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 236 HIS G 250 HIS ** G 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 128 ASN ** F 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.145632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.119968 restraints weight = 29090.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.122692 restraints weight = 19087.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.123825 restraints weight = 13086.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.124523 restraints weight = 10660.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.124721 restraints weight = 10044.798| |-----------------------------------------------------------------------------| r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.5972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 15462 Z= 0.202 Angle : 0.790 21.624 20949 Z= 0.409 Chirality : 0.048 0.338 2319 Planarity : 0.004 0.045 2661 Dihedral : 5.726 82.051 2103 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % 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: -0.72 (0.19), residues: 1947 helix: 1.58 (0.27), residues: 411 sheet: 0.00 (0.21), residues: 621 loop : -1.84 (0.20), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 33 TYR 0.019 0.002 TYR C 122 PHE 0.021 0.002 PHE A 445 TRP 0.028 0.002 TRP C 129 HIS 0.006 0.001 HIS G 211 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.20 (15432) covalent geometry : angle 0.75711 / 0.40 (20886) SS BOND : bond 0.00768 / 0.48 ( 27) SS BOND : angle 4.44605 / 2.76 ( 54) hydrogen bonds : bond 0.04447 / 2.94 ( 599) hydrogen bonds : angle 4.61359 / 3.21 ( 1740) link_NAG-ASN : bond 0.00443 / 0.22 ( 3) link_NAG-ASN : angle 1.66230 / 0.87 ( 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 477 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 477 time to evaluate : 0.608 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: 0.8291 (m-40) cc_final: 0.7918 (m-40) REVERT: A 82 LEU cc_start: 0.8860 (tp) cc_final: 0.8425 (tp) REVERT: A 85 MET cc_start: 0.7897 (mtp) cc_final: 0.7687 (mtp) REVERT: A 131 GLN cc_start: 0.7603 (mt0) cc_final: 0.6733 (mm-40) REVERT: A 133 GLU cc_start: 0.7487 (pm20) cc_final: 0.7279 (tm-30) REVERT: A 167 ARG cc_start: 0.8374 (mtm110) cc_final: 0.7975 (mtm110) REVERT: A 192 GLU cc_start: 0.8918 (mm-30) cc_final: 0.8579 (mm-30) REVERT: A 207 MET cc_start: 0.8427 (ttt) cc_final: 0.8105 (ptm) REVERT: A 282 LYS cc_start: 0.8670 (ptpp) cc_final: 0.8327 (ptpp) REVERT: A 349 ASP cc_start: 0.7313 (t0) cc_final: 0.7055 (t0) REVERT: A 397 ILE cc_start: 0.9270 (pt) cc_final: 0.8918 (mp) REVERT: A 415 THR cc_start: 0.8814 (m) cc_final: 0.8583 (p) REVERT: A 438 MET cc_start: 0.8407 (tpt) cc_final: 0.6913 (mpp) REVERT: B 26 GLU cc_start: 0.6591 (tp30) cc_final: 0.6253 (tp30) REVERT: B 27 THR cc_start: 0.6949 (p) cc_final: 0.6721 (p) REVERT: B 63 GLU cc_start: 0.7778 (tt0) cc_final: 0.6320 (tm-30) REVERT: B 64 ASP cc_start: 0.7242 (m-30) cc_final: 0.5932 (m-30) REVERT: D 26 GLU cc_start: 0.8169 (mm-30) cc_final: 0.7869 (mm-30) REVERT: D 96 TYR cc_start: 0.7869 (m-10) cc_final: 0.7647 (m-80) REVERT: D 108 PHE cc_start: 0.6773 (m-10) cc_final: 0.6186 (m-10) REVERT: D 201 ASP cc_start: 0.8502 (m-30) cc_final: 0.8133 (m-30) REVERT: D 245 GLU cc_start: 0.8294 (tt0) cc_final: 0.8030 (tt0) REVERT: D 297 ASP cc_start: 0.7793 (p0) cc_final: 0.7477 (p0) REVERT: D 396 LYS cc_start: 0.8654 (ptpt) cc_final: 0.8410 (ptpp) REVERT: D 400 HIS cc_start: 0.7958 (t70) cc_final: 0.7737 (t-90) REVERT: D 461 MET cc_start: 0.6521 (mpp) cc_final: 0.6013 (mpp) REVERT: E 16 LYS cc_start: 0.8067 (tttt) cc_final: 0.7657 (tptt) REVERT: E 39 MET cc_start: 0.6598 (mmp) cc_final: 0.6120 (mmm) REVERT: E 63 GLU cc_start: 0.7340 (mp0) cc_final: 0.7132 (mp0) REVERT: G 151 MET cc_start: 0.6161 (tpt) cc_final: 0.5162 (tpp) REVERT: G 160 HIS cc_start: 0.7394 (m-70) cc_final: 0.7159 (m-70) REVERT: G 201 ASP cc_start: 0.7944 (t0) cc_final: 0.7689 (t0) REVERT: G 207 MET cc_start: 0.8939 (tmm) cc_final: 0.8253 (tmm) REVERT: G 342 VAL cc_start: 0.9556 (p) cc_final: 0.9355 (p) REVERT: G 375 MET cc_start: 0.8059 (ppp) cc_final: 0.7733 (ppp) REVERT: G 376 MET cc_start: 0.8613 (ttp) cc_final: 0.8056 (ttm) REVERT: H 36 ILE cc_start: 0.7308 (mt) cc_final: 0.7040 (mt) REVERT: H 37 GLN cc_start: 0.8333 (mm-40) cc_final: 0.7974 (mm-40) REVERT: H 88 GLU cc_start: 0.8863 (tp30) cc_final: 0.8460 (tp30) REVERT: I 128 ASN cc_start: 0.8962 (t0) cc_final: 0.8276 (t0) REVERT: C 134 PRO cc_start: 0.7408 (Cg_endo) cc_final: 0.7179 (Cg_exo) REVERT: C 161 LEU cc_start: 0.8596 (mm) cc_final: 0.8323 (tp) outliers start: 0 outliers final: 0 residues processed: 477 average time/residue: 0.1135 time to fit residues: 81.9136 Evaluate side-chains 400 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 400 time to evaluate : 0.581 ------------------------------------------------------------------------------- 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: 3.9990 chunk 68 optimal weight: 2.9990 chunk 174 optimal weight: 0.0970 chunk 188 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 112 optimal weight: 6.9990 chunk 61 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 HIS ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 289 HIS D 448 GLN ** G 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 324 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.146262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.121170 restraints weight = 29586.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.123253 restraints weight = 18473.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.124491 restraints weight = 13305.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.125329 restraints weight = 10841.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.125569 restraints weight = 10206.727| |-----------------------------------------------------------------------------| r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.6273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 15462 Z= 0.171 Angle : 0.789 23.500 20949 Z= 0.407 Chirality : 0.048 0.343 2319 Planarity : 0.004 0.037 2661 Dihedral : 5.693 82.486 2103 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % 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: -0.76 (0.19), residues: 1947 helix: 1.62 (0.27), residues: 411 sheet: -0.11 (0.20), residues: 627 loop : -1.84 (0.20), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 132 TYR 0.018 0.002 TYR A 306 PHE 0.022 0.002 PHE C 157 TRP 0.029 0.002 TRP C 129 HIS 0.006 0.001 HIS A 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.17 (15432) covalent geometry : angle 0.75611 / 0.39 (20886) SS BOND : bond 0.00901 / 0.56 ( 27) SS BOND : angle 4.47099 / 2.77 ( 54) hydrogen bonds : bond 0.04326 / 2.87 ( 599) hydrogen bonds : angle 4.54684 / 3.16 ( 1740) link_NAG-ASN : bond 0.00264 / 0.14 ( 3) link_NAG-ASN : angle 1.72701 / 0.86 ( 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 459 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 459 time to evaluate : 0.593 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: 0.8216 (m-40) cc_final: 0.7887 (m-40) REVERT: A 67 GLU cc_start: 0.8515 (mt-10) cc_final: 0.7784 (mp0) REVERT: A 82 LEU cc_start: 0.8862 (tp) cc_final: 0.8515 (tp) REVERT: A 131 GLN cc_start: 0.7661 (mt0) cc_final: 0.6765 (mm-40) REVERT: A 167 ARG cc_start: 0.8363 (mtm110) cc_final: 0.7953 (mtm110) REVERT: A 192 GLU cc_start: 0.8910 (mm-30) cc_final: 0.8577 (mm-30) REVERT: A 207 MET cc_start: 0.8550 (ttt) cc_final: 0.8251 (ptm) REVERT: A 282 LYS cc_start: 0.8891 (ptpp) cc_final: 0.8536 (ptpp) REVERT: A 397 ILE cc_start: 0.9259 (pt) cc_final: 0.8912 (mp) REVERT: A 438 MET cc_start: 0.8464 (tpt) cc_final: 0.7068 (mpp) REVERT: B 26 GLU cc_start: 0.6520 (tp30) cc_final: 0.6240 (tp30) REVERT: B 63 GLU cc_start: 0.7660 (tt0) cc_final: 0.6186 (tm-30) REVERT: B 64 ASP cc_start: 0.7245 (m-30) cc_final: 0.5916 (m-30) REVERT: D 26 GLU cc_start: 0.8101 (mm-30) cc_final: 0.7591 (mt-10) REVERT: D 73 ARG cc_start: 0.6767 (ttm170) cc_final: 0.6391 (ttm170) REVERT: D 96 TYR cc_start: 0.7655 (m-10) cc_final: 0.7439 (m-80) REVERT: D 108 PHE cc_start: 0.6708 (m-10) cc_final: 0.6096 (m-10) REVERT: D 178 GLU cc_start: 0.8198 (mt-10) cc_final: 0.7634 (mp0) REVERT: D 201 ASP cc_start: 0.8451 (m-30) cc_final: 0.8062 (m-30) REVERT: D 466 GLN cc_start: 0.6821 (mp10) cc_final: 0.6531 (mp10) REVERT: E 12 MET cc_start: 0.8626 (ppp) cc_final: 0.8082 (ppp) REVERT: E 16 LYS cc_start: 0.8103 (tttt) cc_final: 0.7760 (tttt) REVERT: G 27 HIS cc_start: 0.6260 (t-170) cc_final: 0.6051 (t-170) REVERT: G 151 MET cc_start: 0.6289 (tpt) cc_final: 0.5359 (tpp) REVERT: G 160 HIS cc_start: 0.7425 (m-70) cc_final: 0.7099 (m-70) REVERT: G 201 ASP cc_start: 0.7998 (t0) cc_final: 0.7668 (t0) REVERT: G 207 MET cc_start: 0.8874 (tmm) cc_final: 0.8180 (tmm) REVERT: G 375 MET cc_start: 0.8045 (ppp) cc_final: 0.7702 (ppp) REVERT: G 376 MET cc_start: 0.8503 (ttp) cc_final: 0.8045 (ttm) REVERT: H 36 ILE cc_start: 0.7350 (mt) cc_final: 0.7080 (mt) REVERT: H 37 GLN cc_start: 0.8390 (mm-40) cc_final: 0.7952 (mp10) REVERT: H 88 GLU cc_start: 0.8903 (tp30) cc_final: 0.8494 (tp30) REVERT: I 127 GLU cc_start: 0.8670 (tp30) cc_final: 0.8419 (tp30) REVERT: C 134 PRO cc_start: 0.7266 (Cg_endo) cc_final: 0.7027 (Cg_exo) REVERT: C 161 LEU cc_start: 0.8556 (mm) cc_final: 0.8287 (tp) outliers start: 0 outliers final: 0 residues processed: 459 average time/residue: 0.1183 time to fit residues: 81.7116 Evaluate side-chains 399 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 399 time to evaluate : 0.585 ------------------------------------------------------------------------------- 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: 10.0000 chunk 87 optimal weight: 6.9990 chunk 143 optimal weight: 6.9990 chunk 28 optimal weight: 10.0000 chunk 176 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 114 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 54 optimal weight: 9.9990 chunk 136 optimal weight: 1.9990 chunk 88 optimal weight: 10.0000 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 236 HIS ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 289 HIS D 400 HIS D 448 GLN ** G 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 227 HIS ** 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 = 0.3782 r_free = 0.3782 target = 0.148447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.123736 restraints weight = 29229.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.125823 restraints weight = 18408.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.127117 restraints weight = 13100.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.127985 restraints weight = 10318.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.128193 restraints weight = 9332.165| |-----------------------------------------------------------------------------| r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.6310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 15462 Z= 0.130 Angle : 0.773 23.934 20949 Z= 0.395 Chirality : 0.047 0.340 2319 Planarity : 0.004 0.037 2661 Dihedral : 5.488 81.900 2103 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % 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: -0.62 (0.19), residues: 1947 helix: 1.85 (0.28), residues: 408 sheet: -0.04 (0.21), residues: 627 loop : -1.80 (0.19), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 94 TYR 0.020 0.001 TYR C 122 PHE 0.023 0.002 PHE C 157 TRP 0.032 0.001 TRP C 129 HIS 0.006 0.001 HIS A 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (15432) covalent geometry : angle 0.73954 / 0.38 (20886) SS BOND : bond 0.00906 / 0.56 ( 27) SS BOND : angle 4.42795 / 2.75 ( 54) hydrogen bonds : bond 0.04024 / 2.65 ( 599) hydrogen bonds : angle 4.41845 / 3.06 ( 1740) link_NAG-ASN : bond 0.00224 / 0.12 ( 3) link_NAG-ASN : angle 1.70944 / 0.83 ( 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 457 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 457 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ASN cc_start: 0.8170 (m-40) cc_final: 0.7856 (m-40) REVERT: A 67 GLU cc_start: 0.8528 (mt-10) cc_final: 0.7716 (mp0) REVERT: A 68 MET cc_start: 0.8794 (ttp) cc_final: 0.8535 (mtp) REVERT: A 82 LEU cc_start: 0.8924 (tp) cc_final: 0.7975 (tp) REVERT: A 167 ARG cc_start: 0.8448 (mtm110) cc_final: 0.8096 (mtm110) REVERT: A 192 GLU cc_start: 0.8884 (mm-30) cc_final: 0.8569 (mm-30) REVERT: A 207 MET cc_start: 0.8492 (ttt) cc_final: 0.8255 (ptm) REVERT: A 282 LYS cc_start: 0.8885 (ptpp) cc_final: 0.8549 (ptpp) REVERT: A 367 THR cc_start: 0.8830 (p) cc_final: 0.8570 (p) REVERT: A 397 ILE cc_start: 0.9220 (pt) cc_final: 0.8883 (mp) REVERT: A 438 MET cc_start: 0.8368 (tpt) cc_final: 0.7056 (mpp) REVERT: B 26 GLU cc_start: 0.6412 (tp30) cc_final: 0.6105 (tp30) REVERT: B 63 GLU cc_start: 0.7630 (tt0) cc_final: 0.6334 (tm-30) REVERT: B 64 ASP cc_start: 0.7279 (m-30) cc_final: 0.6400 (m-30) REVERT: B 68 TRP cc_start: 0.8283 (p90) cc_final: 0.7693 (p90) REVERT: D 96 TYR cc_start: 0.7910 (m-10) cc_final: 0.7468 (m-80) REVERT: D 108 PHE cc_start: 0.6708 (m-10) cc_final: 0.6147 (m-10) REVERT: D 178 GLU cc_start: 0.8092 (mt-10) cc_final: 0.7658 (mp0) REVERT: D 201 ASP cc_start: 0.8363 (m-30) cc_final: 0.8098 (m-30) REVERT: D 245 GLU cc_start: 0.8285 (tt0) cc_final: 0.8048 (tt0) REVERT: D 299 LEU cc_start: 0.8733 (tp) cc_final: 0.8521 (tp) REVERT: D 300 ARG cc_start: 0.6846 (ttt180) cc_final: 0.6637 (ttt180) REVERT: D 389 ILE cc_start: 0.9271 (mp) cc_final: 0.9012 (mm) REVERT: D 400 HIS cc_start: 0.7902 (t70) cc_final: 0.7693 (t-90) REVERT: E 16 LYS cc_start: 0.8130 (tttt) cc_final: 0.7719 (tttp) REVERT: E 39 MET cc_start: 0.6428 (mmp) cc_final: 0.6158 (mmm) REVERT: E 68 TRP cc_start: 0.7356 (p90) cc_final: 0.6567 (p90) REVERT: G 151 MET cc_start: 0.6220 (tpt) cc_final: 0.5389 (tpp) REVERT: G 160 HIS cc_start: 0.7371 (m-70) cc_final: 0.7046 (m-70) REVERT: G 201 ASP cc_start: 0.7928 (t0) cc_final: 0.7621 (t0) REVERT: G 207 MET cc_start: 0.8499 (tmm) cc_final: 0.7728 (tmm) REVERT: G 349 ASP cc_start: 0.8266 (t0) cc_final: 0.7777 (t70) REVERT: G 375 MET cc_start: 0.7989 (ppp) cc_final: 0.7768 (ppp) REVERT: G 376 MET cc_start: 0.8433 (ttp) cc_final: 0.7928 (ttm) REVERT: H 37 GLN cc_start: 0.8384 (mm-40) cc_final: 0.7981 (mp10) REVERT: H 88 GLU cc_start: 0.8878 (tp30) cc_final: 0.8416 (tp30) REVERT: F 132 ARG cc_start: 0.7504 (ttm-80) cc_final: 0.7103 (ttm110) REVERT: C 161 LEU cc_start: 0.8574 (mm) cc_final: 0.8258 (tp) outliers start: 0 outliers final: 0 residues processed: 457 average time/residue: 0.1079 time to fit residues: 75.0781 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 : 0.557 ------------------------------------------------------------------------------- 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: 10.0000 chunk 146 optimal weight: 0.8980 chunk 79 optimal weight: 10.0000 chunk 116 optimal weight: 3.9990 chunk 48 optimal weight: 0.0020 chunk 154 optimal weight: 6.9990 chunk 66 optimal weight: 0.9990 chunk 153 optimal weight: 10.0000 chunk 65 optimal weight: 0.8980 chunk 179 optimal weight: 3.9990 chunk 110 optimal weight: 5.9990 overall best weight: 1.3592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 236 HIS ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 289 HIS D 448 GLN G 27 HIS G 400 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 = 0.3770 r_free = 0.3770 target = 0.147559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.122112 restraints weight = 29668.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.124963 restraints weight = 19313.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.126340 restraints weight = 12766.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.126559 restraints weight = 10245.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.126931 restraints weight = 9935.009| |-----------------------------------------------------------------------------| r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.6417 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= 0.136 Angle : 0.769 21.822 20949 Z= 0.394 Chirality : 0.047 0.336 2319 Planarity : 0.004 0.035 2661 Dihedral : 5.478 81.085 2103 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % 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: -0.59 (0.19), residues: 1947 helix: 1.89 (0.28), residues: 408 sheet: -0.03 (0.21), residues: 627 loop : -1.77 (0.19), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 132 TYR 0.015 0.001 TYR G 204 PHE 0.024 0.002 PHE C 157 TRP 0.033 0.001 TRP C 129 HIS 0.005 0.001 HIS G 211 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 (15432) covalent geometry : angle 0.73482 / 0.38 (20886) SS BOND : bond 0.00856 / 0.52 ( 27) SS BOND : angle 4.46520 / 2.76 ( 54) hydrogen bonds : bond 0.04088 / 2.68 ( 599) hydrogen bonds : angle 4.40740 / 3.05 ( 1740) link_NAG-ASN : bond 0.00235 / 0.12 ( 3) link_NAG-ASN : angle 1.53238 / 0.76 ( 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 449 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 448 time to evaluate : 0.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ASN cc_start: 0.8205 (m-40) cc_final: 0.7980 (m-40) REVERT: A 67 GLU cc_start: 0.8357 (mt-10) cc_final: 0.7615 (mp0) REVERT: A 82 LEU cc_start: 0.9085 (tp) cc_final: 0.8505 (tp) REVERT: A 116 CYS cc_start: 0.5980 (p) cc_final: 0.5618 (p) REVERT: A 167 ARG cc_start: 0.8463 (mtm110) cc_final: 0.8236 (mtm110) REVERT: A 192 GLU cc_start: 0.8908 (mm-30) cc_final: 0.8565 (mm-30) REVERT: A 207 MET cc_start: 0.8468 (ttt) cc_final: 0.8258 (ptm) REVERT: A 282 LYS cc_start: 0.8888 (ptpp) cc_final: 0.8552 (ptpp) REVERT: A 349 ASP cc_start: 0.7498 (t0) cc_final: 0.7282 (t0) REVERT: A 367 THR cc_start: 0.8808 (p) cc_final: 0.8501 (p) REVERT: A 397 ILE cc_start: 0.9154 (pt) cc_final: 0.8896 (mp) REVERT: A 438 MET cc_start: 0.7975 (tpt) cc_final: 0.6959 (mpp) REVERT: B 26 GLU cc_start: 0.6317 (tp30) cc_final: 0.6113 (tp30) REVERT: B 27 THR cc_start: 0.7464 (p) cc_final: 0.7132 (p) REVERT: B 63 GLU cc_start: 0.7668 (tt0) cc_final: 0.6365 (tm-30) REVERT: B 64 ASP cc_start: 0.7278 (m-30) cc_final: 0.6411 (m-30) REVERT: B 68 TRP cc_start: 0.8291 (p90) cc_final: 0.7611 (p90) REVERT: D 68 MET cc_start: 0.8733 (mtp) cc_final: 0.8431 (mtt) REVERT: D 96 TYR cc_start: 0.7894 (m-10) cc_final: 0.7294 (m-80) REVERT: D 108 PHE cc_start: 0.6868 (m-10) cc_final: 0.6494 (m-10) REVERT: D 178 GLU cc_start: 0.8060 (mt-10) cc_final: 0.7636 (mp0) REVERT: D 201 ASP cc_start: 0.8407 (m-30) cc_final: 0.8113 (m-30) REVERT: D 203 TYR cc_start: 0.8287 (m-80) cc_final: 0.8051 (m-80) REVERT: D 221 ASP cc_start: 0.5758 (t0) cc_final: 0.5442 (t0) REVERT: D 245 GLU cc_start: 0.8268 (tt0) cc_final: 0.8059 (tt0) REVERT: D 349 ASP cc_start: 0.6793 (t0) cc_final: 0.6578 (t0) REVERT: E 16 LYS cc_start: 0.8212 (tttt) cc_final: 0.7772 (tttp) REVERT: E 39 MET cc_start: 0.6549 (mmp) cc_final: 0.6283 (mmm) REVERT: G 31 VAL cc_start: 0.9406 (p) cc_final: 0.9112 (m) REVERT: G 151 MET cc_start: 0.6222 (tpt) cc_final: 0.5455 (tpp) REVERT: G 160 HIS cc_start: 0.7406 (m-70) cc_final: 0.7077 (m-70) REVERT: G 201 ASP cc_start: 0.7998 (t0) cc_final: 0.7757 (t0) REVERT: G 207 MET cc_start: 0.8785 (tmm) cc_final: 0.8138 (tmm) REVERT: G 349 ASP cc_start: 0.8226 (t0) cc_final: 0.7777 (p0) REVERT: G 375 MET cc_start: 0.7982 (ppp) cc_final: 0.7756 (ppp) REVERT: G 376 MET cc_start: 0.8500 (ttp) cc_final: 0.7997 (ttm) REVERT: G 380 ASP cc_start: 0.8004 (t0) cc_final: 0.7402 (p0) REVERT: G 438 MET cc_start: 0.7111 (mmm) cc_final: 0.6766 (mmp) REVERT: H 36 ILE cc_start: 0.7887 (mt) cc_final: 0.7676 (mt) REVERT: H 37 GLN cc_start: 0.8472 (mm-40) cc_final: 0.8027 (mp10) REVERT: H 88 GLU cc_start: 0.8856 (tp30) cc_final: 0.8395 (tp30) REVERT: F 132 ARG cc_start: 0.7488 (ttm-80) cc_final: 0.7082 (ttm110) REVERT: C 161 LEU cc_start: 0.8593 (mm) cc_final: 0.8293 (tp) outliers start: 1 outliers final: 0 residues processed: 449 average time/residue: 0.1111 time to fit residues: 75.1620 Evaluate side-chains 396 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 396 time to evaluate : 0.465 ------------------------------------------------------------------------------- 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: 1.9990 chunk 5 optimal weight: 2.9990 chunk 49 optimal weight: 9.9990 chunk 98 optimal weight: 4.9990 chunk 67 optimal weight: 7.9990 chunk 15 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 153 optimal weight: 10.0000 chunk 162 optimal weight: 6.9990 chunk 99 optimal weight: 8.9990 chunk 81 optimal weight: 4.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 77 GLN ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 131 GLN A 236 HIS ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 289 HIS D 400 HIS D 448 GLN G 289 HIS ** G 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.144579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.119162 restraints weight = 29352.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.121421 restraints weight = 19761.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.122740 restraints weight = 13581.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.124121 restraints weight = 11055.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.124375 restraints weight = 10048.634| |-----------------------------------------------------------------------------| r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.6655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 15462 Z= 0.196 Angle : 0.824 24.745 20949 Z= 0.423 Chirality : 0.048 0.329 2319 Planarity : 0.004 0.035 2661 Dihedral : 5.743 81.225 2103 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % 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: -0.77 (0.19), residues: 1947 helix: 1.69 (0.27), residues: 411 sheet: -0.14 (0.21), residues: 621 loop : -1.86 (0.19), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 94 TYR 0.021 0.002 TYR C 122 PHE 0.023 0.002 PHE C 157 TRP 0.032 0.002 TRP C 129 HIS 0.011 0.002 HIS A 447 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.20 (15432) covalent geometry : angle 0.79145 / 0.41 (20886) SS BOND : bond 0.00841 / 0.52 ( 27) SS BOND : angle 4.56375 / 2.80 ( 54) hydrogen bonds : bond 0.04447 / 2.95 ( 599) hydrogen bonds : angle 4.64048 / 3.21 ( 1740) link_NAG-ASN : bond 0.00288 / 0.15 ( 3) link_NAG-ASN : angle 1.62862 / 0.82 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2769.22 seconds wall clock time: 48 minutes 42.14 seconds (2922.14 seconds total)