Starting phenix.real_space_refine on Mon Mar 11 07:42:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c9a_30310/03_2024/7c9a_30310_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c9a_30310/03_2024/7c9a_30310.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c9a_30310/03_2024/7c9a_30310.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c9a_30310/03_2024/7c9a_30310.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c9a_30310/03_2024/7c9a_30310_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c9a_30310/03_2024/7c9a_30310_updated.pdb" } resolution = 3.43 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 3 9.91 5 P 27 5.49 5 S 39 5.16 5 C 4674 2.51 5 N 1341 2.21 5 O 1506 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 43": "OE1" <-> "OE2" Residue "A GLU 59": "OE1" <-> "OE2" Residue "A GLU 118": "OE1" <-> "OE2" Residue "A GLU 322": "OE1" <-> "OE2" Residue "B GLU 43": "OE1" <-> "OE2" Residue "B GLU 59": "OE1" <-> "OE2" Residue "B GLU 118": "OE1" <-> "OE2" Residue "B GLU 322": "OE1" <-> "OE2" Residue "C GLU 43": "OE1" <-> "OE2" Residue "C GLU 59": "OE1" <-> "OE2" Residue "C GLU 118": "OE1" <-> "OE2" Residue "C GLU 322": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 7590 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2375 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 10, 'TRANS': 300} Chain breaks: 1 Chain: "B" Number of atoms: 2375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2375 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 10, 'TRANS': 300} Chain breaks: 1 Chain: "C" Number of atoms: 2375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2375 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 10, 'TRANS': 300} Chain breaks: 1 Chain: "D" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 180 Classifications: {'DNA': 9} Link IDs: {'rna3p': 8} Chain: "E" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 189 Classifications: {'DNA': 9} Link IDs: {'rna3p': 8} Chain: "A" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' CA': 2, 'ANP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' CA': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.51, per 1000 atoms: 0.59 Number of scatterers: 7590 At special positions: 0 Unit cell: (103.32, 84, 115.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 3 19.99 S 39 16.00 P 27 15.00 O 1506 8.00 N 1341 7.00 C 4674 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.73 Conformation dependent library (CDL) restraints added in 1.3 seconds 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1698 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 45 helices and 3 sheets defined 39.2% alpha, 10.3% beta 6 base pairs and 12 stacking pairs defined. Time for finding SS restraints: 3.14 Creating SS restraints... Processing helix chain 'A' and resid 25 through 30 removed outlier: 3.998A pdb=" N GLU A 29 " --> pdb=" O SER A 26 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLN A 30 " --> pdb=" O ARG A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 43 removed outlier: 3.528A pdb=" N GLU A 42 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU A 43 " --> pdb=" O LYS A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 53 removed outlier: 3.505A pdb=" N ALA A 53 " --> pdb=" O VAL A 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 49 through 53' Processing helix chain 'A' and resid 57 through 61 Processing helix chain 'A' and resid 68 through 76 removed outlier: 3.554A pdb=" N LEU A 75 " --> pdb=" O ALA A 71 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA A 76 " --> pdb=" O ASP A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 80 No H-bonds generated for 'chain 'A' and resid 78 through 80' Processing helix chain 'A' and resid 89 through 95 removed outlier: 3.740A pdb=" N GLN A 94 " --> pdb=" O THR A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 113 removed outlier: 3.598A pdb=" N LEU A 112 " --> pdb=" O GLU A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 145 removed outlier: 3.561A pdb=" N CYS A 137 " --> pdb=" O LYS A 133 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA A 141 " --> pdb=" O CYS A 137 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N VAL A 142 " --> pdb=" O HIS A 138 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N GLN A 145 " --> pdb=" O ALA A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 150 No H-bonds generated for 'chain 'A' and resid 148 through 150' Processing helix chain 'A' and resid 171 through 178 removed outlier: 3.579A pdb=" N ARG A 177 " --> pdb=" O ALA A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 187 Processing helix chain 'A' and resid 197 through 208 removed outlier: 4.078A pdb=" N LEU A 204 " --> pdb=" O GLN A 200 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N TYR A 205 " --> pdb=" O THR A 201 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLN A 206 " --> pdb=" O GLN A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 259 removed outlier: 3.521A pdb=" N MET A 243 " --> pdb=" O SER A 239 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N HIS A 244 " --> pdb=" O ALA A 240 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP A 257 " --> pdb=" O LEU A 253 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU A 258 " --> pdb=" O ARG A 254 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE A 259 " --> pdb=" O LEU A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 295 removed outlier: 3.717A pdb=" N ALA A 293 " --> pdb=" O GLY A 289 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N HIS A 294 " --> pdb=" O ASN A 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 30 removed outlier: 3.998A pdb=" N GLU B 29 " --> pdb=" O SER B 26 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLN B 30 " --> pdb=" O ARG B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 43 removed outlier: 3.528A pdb=" N GLU B 42 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU B 43 " --> pdb=" O LYS B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 53 removed outlier: 3.505A pdb=" N ALA B 53 " --> pdb=" O VAL B 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 49 through 53' Processing helix chain 'B' and resid 57 through 61 Processing helix chain 'B' and resid 68 through 76 removed outlier: 3.554A pdb=" N LEU B 75 " --> pdb=" O ALA B 71 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA B 76 " --> pdb=" O ASP B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 80 No H-bonds generated for 'chain 'B' and resid 78 through 80' Processing helix chain 'B' and resid 89 through 95 removed outlier: 3.740A pdb=" N GLN B 94 " --> pdb=" O THR B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 113 removed outlier: 3.599A pdb=" N LEU B 112 " --> pdb=" O GLU B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 145 removed outlier: 3.560A pdb=" N CYS B 137 " --> pdb=" O LYS B 133 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA B 141 " --> pdb=" O CYS B 137 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N VAL B 142 " --> pdb=" O HIS B 138 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N GLN B 145 " --> pdb=" O ALA B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 150 No H-bonds generated for 'chain 'B' and resid 148 through 150' Processing helix chain 'B' and resid 171 through 178 removed outlier: 3.579A pdb=" N ARG B 177 " --> pdb=" O ALA B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 187 Processing helix chain 'B' and resid 197 through 208 removed outlier: 4.078A pdb=" N LEU B 204 " --> pdb=" O GLN B 200 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N TYR B 205 " --> pdb=" O THR B 201 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLN B 206 " --> pdb=" O GLN B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 259 removed outlier: 3.521A pdb=" N MET B 243 " --> pdb=" O SER B 239 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N HIS B 244 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP B 257 " --> pdb=" O LEU B 253 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU B 258 " --> pdb=" O ARG B 254 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE B 259 " --> pdb=" O LEU B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 295 removed outlier: 3.718A pdb=" N ALA B 293 " --> pdb=" O GLY B 289 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N HIS B 294 " --> pdb=" O ASN B 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 30 removed outlier: 3.999A pdb=" N GLU C 29 " --> pdb=" O SER C 26 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLN C 30 " --> pdb=" O ARG C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 43 removed outlier: 3.527A pdb=" N GLU C 42 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU C 43 " --> pdb=" O LYS C 39 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 53 removed outlier: 3.505A pdb=" N ALA C 53 " --> pdb=" O VAL C 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 49 through 53' Processing helix chain 'C' and resid 57 through 61 Processing helix chain 'C' and resid 68 through 76 removed outlier: 3.554A pdb=" N LEU C 75 " --> pdb=" O ALA C 71 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA C 76 " --> pdb=" O ASP C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 80 No H-bonds generated for 'chain 'C' and resid 78 through 80' Processing helix chain 'C' and resid 89 through 95 removed outlier: 3.740A pdb=" N GLN C 94 " --> pdb=" O THR C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 113 removed outlier: 3.599A pdb=" N LEU C 112 " --> pdb=" O GLU C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 145 removed outlier: 3.561A pdb=" N CYS C 137 " --> pdb=" O LYS C 133 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA C 141 " --> pdb=" O CYS C 137 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N VAL C 142 " --> pdb=" O HIS C 138 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N GLN C 145 " --> pdb=" O ALA C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 150 No H-bonds generated for 'chain 'C' and resid 148 through 150' Processing helix chain 'C' and resid 171 through 178 removed outlier: 3.578A pdb=" N ARG C 177 " --> pdb=" O ALA C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 187 Processing helix chain 'C' and resid 197 through 208 removed outlier: 4.079A pdb=" N LEU C 204 " --> pdb=" O GLN C 200 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N TYR C 205 " --> pdb=" O THR C 201 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLN C 206 " --> pdb=" O GLN C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 259 removed outlier: 3.521A pdb=" N MET C 243 " --> pdb=" O SER C 239 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N HIS C 244 " --> pdb=" O ALA C 240 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASP C 257 " --> pdb=" O LEU C 253 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU C 258 " --> pdb=" O ARG C 254 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE C 259 " --> pdb=" O LEU C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 295 removed outlier: 3.718A pdb=" N ALA C 293 " --> pdb=" O GLY C 289 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N HIS C 294 " --> pdb=" O ASN C 290 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 324 through 326 removed outlier: 6.532A pdb=" N ARG A 299 " --> pdb=" O TYR A 315 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N VAL A 263 " --> pdb=" O THR A 123 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N MET A 125 " --> pdb=" O VAL A 263 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ILE A 265 " --> pdb=" O MET A 125 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LEU A 219 " --> pdb=" O VAL A 264 " (cutoff:3.500A) removed outlier: 8.229A pdb=" N THR A 266 " --> pdb=" O LEU A 219 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N VAL A 221 " --> pdb=" O THR A 266 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N MET A 158 " --> pdb=" O ILE A 220 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N ASP A 222 " --> pdb=" O MET A 158 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N ILE A 160 " --> pdb=" O ASP A 222 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 324 through 326 removed outlier: 6.531A pdb=" N ARG B 299 " --> pdb=" O TYR B 315 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N VAL B 263 " --> pdb=" O THR B 123 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N MET B 125 " --> pdb=" O VAL B 263 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ILE B 265 " --> pdb=" O MET B 125 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LEU B 219 " --> pdb=" O VAL B 264 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N THR B 266 " --> pdb=" O LEU B 219 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N VAL B 221 " --> pdb=" O THR B 266 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N MET B 158 " --> pdb=" O ILE B 220 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N ASP B 222 " --> pdb=" O MET B 158 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N ILE B 160 " --> pdb=" O ASP B 222 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 324 through 326 removed outlier: 6.532A pdb=" N ARG C 299 " --> pdb=" O TYR C 315 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N VAL C 263 " --> pdb=" O THR C 123 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N MET C 125 " --> pdb=" O VAL C 263 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ILE C 265 " --> pdb=" O MET C 125 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LEU C 219 " --> pdb=" O VAL C 264 " (cutoff:3.500A) removed outlier: 8.229A pdb=" N THR C 266 " --> pdb=" O LEU C 219 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N VAL C 221 " --> pdb=" O THR C 266 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N MET C 158 " --> pdb=" O ILE C 220 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N ASP C 222 " --> pdb=" O MET C 158 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N ILE C 160 " --> pdb=" O ASP C 222 " (cutoff:3.500A) 171 hydrogen bonds defined for protein. 495 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 12 hydrogen bonds 24 hydrogen bond angles 0 basepair planarities 6 basepair parallelities 12 stacking parallelities Total time for adding SS restraints: 1.86 Time building geometry restraints manager: 3.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2235 1.33 - 1.45: 1238 1.45 - 1.57: 4158 1.57 - 1.69: 47 1.69 - 1.81: 63 Bond restraints: 7741 Sorted by residual: bond pdb=" O3A ANP A 403 " pdb=" PB ANP A 403 " ideal model delta sigma weight residual 1.700 1.551 0.149 2.00e-02 2.50e+03 5.57e+01 bond pdb=" O3A ANP B 402 " pdb=" PB ANP B 402 " ideal model delta sigma weight residual 1.700 1.554 0.146 2.00e-02 2.50e+03 5.36e+01 bond pdb=" O3A ANP A 402 " pdb=" PB ANP A 402 " ideal model delta sigma weight residual 1.700 1.554 0.146 2.00e-02 2.50e+03 5.35e+01 bond pdb=" N3B ANP B 402 " pdb=" PG ANP B 402 " ideal model delta sigma weight residual 1.795 1.683 0.112 2.00e-02 2.50e+03 3.14e+01 bond pdb=" N3B ANP A 402 " pdb=" PG ANP A 402 " ideal model delta sigma weight residual 1.795 1.683 0.112 2.00e-02 2.50e+03 3.13e+01 ... (remaining 7736 not shown) Histogram of bond angle deviations from ideal: 100.24 - 106.75: 322 106.75 - 113.25: 4148 113.25 - 119.76: 2396 119.76 - 126.26: 3532 126.26 - 132.76: 139 Bond angle restraints: 10537 Sorted by residual: angle pdb=" PB ANP A 403 " pdb=" N3B ANP A 403 " pdb=" PG ANP A 403 " ideal model delta sigma weight residual 126.95 106.03 20.92 3.00e+00 1.11e-01 4.86e+01 angle pdb=" PB ANP A 402 " pdb=" N3B ANP A 402 " pdb=" PG ANP A 402 " ideal model delta sigma weight residual 126.95 108.92 18.03 3.00e+00 1.11e-01 3.61e+01 angle pdb=" PB ANP B 402 " pdb=" N3B ANP B 402 " pdb=" PG ANP B 402 " ideal model delta sigma weight residual 126.95 108.92 18.03 3.00e+00 1.11e-01 3.61e+01 angle pdb=" CA GLU C 29 " pdb=" CB GLU C 29 " pdb=" CG GLU C 29 " ideal model delta sigma weight residual 114.10 122.93 -8.83 2.00e+00 2.50e-01 1.95e+01 angle pdb=" CA GLU B 29 " pdb=" CB GLU B 29 " pdb=" CG GLU B 29 " ideal model delta sigma weight residual 114.10 122.92 -8.82 2.00e+00 2.50e-01 1.94e+01 ... (remaining 10532 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.29: 4390 29.29 - 58.58: 253 58.58 - 87.87: 63 87.87 - 117.16: 1 117.16 - 146.45: 6 Dihedral angle restraints: 4713 sinusoidal: 2058 harmonic: 2655 Sorted by residual: dihedral pdb=" CA ASP C 222 " pdb=" C ASP C 222 " pdb=" N SER C 223 " pdb=" CA SER C 223 " ideal model delta harmonic sigma weight residual -180.00 -61.85 -118.15 0 5.00e+00 4.00e-02 5.58e+02 dihedral pdb=" CA ASP B 222 " pdb=" C ASP B 222 " pdb=" N SER B 223 " pdb=" CA SER B 223 " ideal model delta harmonic sigma weight residual -180.00 -61.86 -118.14 0 5.00e+00 4.00e-02 5.58e+02 dihedral pdb=" CA ASP A 222 " pdb=" C ASP A 222 " pdb=" N SER A 223 " pdb=" CA SER A 223 " ideal model delta harmonic sigma weight residual -180.00 -61.93 -118.07 0 5.00e+00 4.00e-02 5.58e+02 ... (remaining 4710 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 1010 0.063 - 0.126: 166 0.126 - 0.188: 18 0.188 - 0.251: 0 0.251 - 0.314: 3 Chirality restraints: 1197 Sorted by residual: chirality pdb=" C3' ANP B 402 " pdb=" C2' ANP B 402 " pdb=" C4' ANP B 402 " pdb=" O3' ANP B 402 " both_signs ideal model delta sigma weight residual False -2.36 -2.67 0.31 2.00e-01 2.50e+01 2.47e+00 chirality pdb=" C3' ANP A 402 " pdb=" C2' ANP A 402 " pdb=" C4' ANP A 402 " pdb=" O3' ANP A 402 " both_signs ideal model delta sigma weight residual False -2.36 -2.67 0.31 2.00e-01 2.50e+01 2.44e+00 chirality pdb=" C3' ANP A 403 " pdb=" C2' ANP A 403 " pdb=" C4' ANP A 403 " pdb=" O3' ANP A 403 " both_signs ideal model delta sigma weight residual False -2.36 -2.65 0.29 2.00e-01 2.50e+01 2.14e+00 ... (remaining 1194 not shown) Planarity restraints: 1293 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE B 166 " 0.017 2.00e-02 2.50e+03 3.48e-02 1.21e+01 pdb=" C PHE B 166 " -0.060 2.00e-02 2.50e+03 pdb=" O PHE B 166 " 0.023 2.00e-02 2.50e+03 pdb=" N ARG B 167 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE C 166 " 0.017 2.00e-02 2.50e+03 3.47e-02 1.21e+01 pdb=" C PHE C 166 " -0.060 2.00e-02 2.50e+03 pdb=" O PHE C 166 " 0.023 2.00e-02 2.50e+03 pdb=" N ARG C 167 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 166 " -0.017 2.00e-02 2.50e+03 3.47e-02 1.20e+01 pdb=" C PHE A 166 " 0.060 2.00e-02 2.50e+03 pdb=" O PHE A 166 " -0.023 2.00e-02 2.50e+03 pdb=" N ARG A 167 " -0.020 2.00e-02 2.50e+03 ... (remaining 1290 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.55: 44 2.55 - 3.14: 5178 3.14 - 3.73: 10620 3.73 - 4.31: 15885 4.31 - 4.90: 26323 Nonbonded interactions: 58050 Sorted by model distance: nonbonded pdb=" CE1 PHE A 129 " pdb=" O ALA B 293 " model vdw 1.965 3.340 nonbonded pdb=" CE1 PHE B 129 " pdb=" O ALA C 293 " model vdw 2.003 3.340 nonbonded pdb=" CD1 PHE A 129 " pdb=" O ALA B 293 " model vdw 2.063 3.340 nonbonded pdb="CA CA B 401 " pdb=" O2G ANP B 402 " model vdw 2.078 2.510 nonbonded pdb="CA CA A 401 " pdb=" O2G ANP A 402 " model vdw 2.079 2.510 ... (remaining 58045 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 22 through 336) selection = (chain 'B' and resid 22 through 336) selection = chain 'C' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 12.230 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 24.590 Find NCS groups from input model: 0.490 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: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.149 7741 Z= 0.413 Angle : 1.036 20.922 10537 Z= 0.565 Chirality : 0.048 0.314 1197 Planarity : 0.005 0.039 1293 Dihedral : 19.518 146.452 3015 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.34 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.96 (0.20), residues: 921 helix: -5.05 (0.06), residues: 387 sheet: 0.85 (0.48), residues: 120 loop : -2.66 (0.21), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 199 PHE 0.019 0.002 PHE B 129 TYR 0.013 0.002 TYR C 315 ARG 0.006 0.000 ARG A 306 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 235 time to evaluate : 0.883 Fit side-chains revert: symmetry clash REVERT: A 39 LYS cc_start: 0.8523 (mmtt) cc_final: 0.8107 (mmmt) REVERT: B 130 ARG cc_start: 0.7765 (ptt-90) cc_final: 0.7413 (ptp90) REVERT: B 156 LYS cc_start: 0.8757 (mttt) cc_final: 0.8307 (mtpt) REVERT: B 254 ARG cc_start: 0.8386 (ttp80) cc_final: 0.7977 (mtp-110) REVERT: B 285 LYS cc_start: 0.9038 (pttt) cc_final: 0.8745 (ptmm) REVERT: C 237 GLU cc_start: 0.8301 (mt-10) cc_final: 0.8069 (tt0) REVERT: C 285 LYS cc_start: 0.9110 (pttt) cc_final: 0.8877 (ptmm) outliers start: 0 outliers final: 0 residues processed: 235 average time/residue: 0.3262 time to fit residues: 91.6581 Evaluate side-chains 136 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 5.9990 chunk 70 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 GLN A 272 GLN B 34 ASN B 242 GLN C 242 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 7741 Z= 0.205 Angle : 0.574 7.693 10537 Z= 0.310 Chirality : 0.042 0.134 1197 Planarity : 0.004 0.031 1293 Dihedral : 17.338 152.275 1323 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.48 % Allowed : 15.52 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.67 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.85 (0.22), residues: 921 helix: -3.83 (0.14), residues: 393 sheet: 0.94 (0.50), residues: 123 loop : -2.22 (0.24), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 138 PHE 0.012 0.002 PHE A 126 TYR 0.009 0.001 TYR B 216 ARG 0.006 0.000 ARG C 130 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 171 time to evaluate : 0.891 Fit side-chains REVERT: A 29 GLU cc_start: 0.7409 (mp0) cc_final: 0.7080 (mm-30) REVERT: A 39 LYS cc_start: 0.8298 (mmtt) cc_final: 0.7867 (mmmt) REVERT: A 77 GLU cc_start: 0.7169 (mm-30) cc_final: 0.6934 (mm-30) REVERT: B 77 GLU cc_start: 0.7802 (mm-30) cc_final: 0.7471 (mm-30) REVERT: B 156 LYS cc_start: 0.8706 (mttt) cc_final: 0.8371 (mtpt) REVERT: B 254 ARG cc_start: 0.8400 (ttp80) cc_final: 0.7635 (ttp-110) REVERT: B 285 LYS cc_start: 0.9051 (pttt) cc_final: 0.8745 (ptmm) REVERT: C 110 ASP cc_start: 0.8618 (m-30) cc_final: 0.8376 (m-30) REVERT: C 130 ARG cc_start: 0.7461 (ptt-90) cc_final: 0.6238 (tpt170) REVERT: C 187 ASP cc_start: 0.8482 (t0) cc_final: 0.8237 (p0) REVERT: C 188 ASN cc_start: 0.8449 (m-40) cc_final: 0.8153 (m-40) REVERT: C 210 MET cc_start: 0.8154 (mtp) cc_final: 0.7722 (mtp) REVERT: C 254 ARG cc_start: 0.8244 (mtm110) cc_final: 0.7900 (ttp-110) REVERT: C 285 LYS cc_start: 0.9121 (pttt) cc_final: 0.8886 (pttp) outliers start: 11 outliers final: 5 residues processed: 175 average time/residue: 0.2864 time to fit residues: 61.4533 Evaluate side-chains 151 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 146 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain B residue 37 ASP Chi-restraints excluded: chain B residue 181 SER Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 231 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 46 optimal weight: 3.9990 chunk 26 optimal weight: 0.5980 chunk 70 optimal weight: 0.9990 chunk 57 optimal weight: 0.0980 chunk 23 optimal weight: 0.9990 chunk 84 optimal weight: 0.9980 chunk 91 optimal weight: 4.9990 chunk 75 optimal weight: 5.9990 chunk 83 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.3061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7741 Z= 0.152 Angle : 0.488 6.080 10537 Z= 0.265 Chirality : 0.040 0.121 1197 Planarity : 0.003 0.029 1293 Dihedral : 15.592 145.774 1323 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.62 % Allowed : 19.16 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.56 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.58 (0.24), residues: 921 helix: -2.55 (0.20), residues: 375 sheet: 0.86 (0.48), residues: 135 loop : -1.66 (0.26), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 138 PHE 0.010 0.001 PHE B 129 TYR 0.006 0.001 TYR B 315 ARG 0.006 0.000 ARG B 130 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 167 time to evaluate : 0.778 Fit side-chains REVERT: B 91 GLU cc_start: 0.8387 (tm-30) cc_final: 0.7740 (tm-30) REVERT: B 156 LYS cc_start: 0.8782 (mttt) cc_final: 0.8379 (mtmt) REVERT: B 254 ARG cc_start: 0.8423 (ttp80) cc_final: 0.7659 (ttp-110) REVERT: B 285 LYS cc_start: 0.9001 (pttt) cc_final: 0.8725 (ptmm) REVERT: C 39 LYS cc_start: 0.7875 (mmmt) cc_final: 0.7634 (mttp) REVERT: C 110 ASP cc_start: 0.8520 (m-30) cc_final: 0.8245 (m-30) REVERT: C 130 ARG cc_start: 0.7294 (ptt-90) cc_final: 0.6608 (tpt170) REVERT: C 187 ASP cc_start: 0.8518 (t0) cc_final: 0.8231 (p0) REVERT: C 188 ASN cc_start: 0.8493 (m-40) cc_final: 0.8158 (m-40) outliers start: 12 outliers final: 7 residues processed: 169 average time/residue: 0.2584 time to fit residues: 54.7865 Evaluate side-chains 168 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 161 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain B residue 34 ASN Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain C residue 163 GLU Chi-restraints excluded: chain C residue 216 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 83 optimal weight: 5.9990 chunk 63 optimal weight: 10.0000 chunk 43 optimal weight: 4.9990 chunk 9 optimal weight: 0.0370 chunk 40 optimal weight: 0.0040 chunk 56 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 89 optimal weight: 6.9990 chunk 44 optimal weight: 7.9990 chunk 80 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 overall best weight: 0.9874 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.3333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 7741 Z= 0.173 Angle : 0.476 5.771 10537 Z= 0.259 Chirality : 0.040 0.126 1197 Planarity : 0.003 0.030 1293 Dihedral : 15.200 147.154 1323 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 1.62 % Allowed : 19.84 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.26), residues: 921 helix: -1.38 (0.25), residues: 375 sheet: 0.96 (0.48), residues: 135 loop : -1.55 (0.27), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 138 PHE 0.009 0.001 PHE A 126 TYR 0.008 0.001 TYR B 315 ARG 0.006 0.000 ARG A 95 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 164 time to evaluate : 0.834 Fit side-chains REVERT: A 39 LYS cc_start: 0.8357 (mmtp) cc_final: 0.7832 (mmmt) REVERT: A 176 GLU cc_start: 0.8106 (tt0) cc_final: 0.7870 (mt-10) REVERT: B 91 GLU cc_start: 0.8376 (tm-30) cc_final: 0.7744 (tm-30) REVERT: B 156 LYS cc_start: 0.8843 (mttt) cc_final: 0.8409 (mtmt) REVERT: B 285 LYS cc_start: 0.9061 (pttt) cc_final: 0.8771 (ptmm) REVERT: C 94 GLN cc_start: 0.8749 (mm-40) cc_final: 0.8438 (tp40) REVERT: C 110 ASP cc_start: 0.8517 (m-30) cc_final: 0.8246 (m-30) REVERT: C 130 ARG cc_start: 0.7297 (ptt-90) cc_final: 0.6797 (tpt170) REVERT: C 187 ASP cc_start: 0.8538 (t0) cc_final: 0.8209 (p0) REVERT: C 188 ASN cc_start: 0.8584 (m-40) cc_final: 0.8138 (m-40) REVERT: C 254 ARG cc_start: 0.8349 (mtm110) cc_final: 0.8022 (ttp-110) outliers start: 12 outliers final: 9 residues processed: 169 average time/residue: 0.2489 time to fit residues: 53.2080 Evaluate side-chains 163 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 154 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 PHE Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain B residue 31 CYS Chi-restraints excluded: chain B residue 34 ASN Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain C residue 216 TYR Chi-restraints excluded: chain C residue 231 ASP Chi-restraints excluded: chain C residue 330 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 74 optimal weight: 5.9990 chunk 51 optimal weight: 0.5980 chunk 1 optimal weight: 8.9990 chunk 66 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 76 optimal weight: 0.4980 chunk 62 optimal weight: 7.9990 chunk 0 optimal weight: 6.9990 chunk 45 optimal weight: 5.9990 chunk 80 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 290 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.3531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 7741 Z= 0.144 Angle : 0.452 5.418 10537 Z= 0.245 Chirality : 0.039 0.124 1197 Planarity : 0.003 0.036 1293 Dihedral : 14.947 147.284 1323 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.43 % Allowed : 19.84 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.27), residues: 921 helix: -0.64 (0.26), residues: 390 sheet: 1.10 (0.49), residues: 135 loop : -1.61 (0.27), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 138 PHE 0.008 0.001 PHE A 126 TYR 0.006 0.001 TYR A 216 ARG 0.006 0.000 ARG A 95 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 164 time to evaluate : 0.826 Fit side-chains REVERT: A 39 LYS cc_start: 0.8351 (mmtp) cc_final: 0.7836 (mmmt) REVERT: B 91 GLU cc_start: 0.8345 (tm-30) cc_final: 0.7706 (tm-30) REVERT: B 156 LYS cc_start: 0.8812 (mttt) cc_final: 0.8401 (mtmt) REVERT: B 285 LYS cc_start: 0.9039 (pttt) cc_final: 0.8759 (ptmm) REVERT: C 37 ASP cc_start: 0.7092 (m-30) cc_final: 0.6710 (m-30) REVERT: C 94 GLN cc_start: 0.8746 (mm-40) cc_final: 0.8475 (tp40) REVERT: C 110 ASP cc_start: 0.8467 (m-30) cc_final: 0.8175 (m-30) REVERT: C 187 ASP cc_start: 0.8573 (t0) cc_final: 0.8190 (p0) REVERT: C 188 ASN cc_start: 0.8494 (m-40) cc_final: 0.8082 (m-40) outliers start: 18 outliers final: 13 residues processed: 171 average time/residue: 0.2469 time to fit residues: 53.5562 Evaluate side-chains 161 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 148 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 129 PHE Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 326 MET Chi-restraints excluded: chain B residue 34 ASN Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 181 SER Chi-restraints excluded: chain C residue 163 GLU Chi-restraints excluded: chain C residue 216 TYR Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 330 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 30 optimal weight: 0.7980 chunk 80 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 chunk 52 optimal weight: 6.9990 chunk 22 optimal weight: 1.9990 chunk 89 optimal weight: 5.9990 chunk 74 optimal weight: 0.4980 chunk 41 optimal weight: 0.2980 chunk 7 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 47 optimal weight: 7.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.3657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7741 Z= 0.164 Angle : 0.467 5.516 10537 Z= 0.251 Chirality : 0.039 0.126 1197 Planarity : 0.003 0.026 1293 Dihedral : 14.911 146.102 1323 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 3.51 % Allowed : 19.16 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.27), residues: 921 helix: -0.17 (0.27), residues: 390 sheet: 1.17 (0.49), residues: 135 loop : -1.45 (0.27), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 138 PHE 0.009 0.001 PHE A 126 TYR 0.006 0.001 TYR B 315 ARG 0.006 0.000 ARG C 130 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 157 time to evaluate : 0.829 Fit side-chains REVERT: A 39 LYS cc_start: 0.8410 (mmtp) cc_final: 0.7900 (mmmt) REVERT: B 91 GLU cc_start: 0.8353 (tm-30) cc_final: 0.7693 (tm-30) REVERT: B 156 LYS cc_start: 0.8835 (mttt) cc_final: 0.8419 (mtmt) REVERT: B 285 LYS cc_start: 0.9051 (pttt) cc_final: 0.8762 (ptmm) REVERT: C 91 GLU cc_start: 0.8064 (tm-30) cc_final: 0.7673 (tm-30) REVERT: C 110 ASP cc_start: 0.8359 (m-30) cc_final: 0.8138 (m-30) REVERT: C 187 ASP cc_start: 0.8567 (t0) cc_final: 0.8173 (p0) REVERT: C 188 ASN cc_start: 0.8523 (m-40) cc_final: 0.8086 (m-40) outliers start: 26 outliers final: 22 residues processed: 170 average time/residue: 0.2123 time to fit residues: 47.4447 Evaluate side-chains 168 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 146 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 129 PHE Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain B residue 31 CYS Chi-restraints excluded: chain B residue 34 ASN Chi-restraints excluded: chain B residue 37 ASP Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 129 PHE Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 181 SER Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain C residue 163 GLU Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 216 TYR Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 330 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 86 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 65 optimal weight: 0.5980 chunk 50 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 chunk 56 optimal weight: 0.0170 chunk 54 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 overall best weight: 0.7018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.3807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 7741 Z= 0.142 Angle : 0.448 5.310 10537 Z= 0.240 Chirality : 0.039 0.123 1197 Planarity : 0.002 0.026 1293 Dihedral : 14.768 145.701 1323 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.43 % Allowed : 21.05 % Favored : 76.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.28), residues: 921 helix: -0.01 (0.27), residues: 405 sheet: 1.21 (0.49), residues: 135 loop : -1.32 (0.29), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 138 PHE 0.008 0.001 PHE A 126 TYR 0.008 0.001 TYR A 216 ARG 0.006 0.000 ARG A 95 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 152 time to evaluate : 0.816 Fit side-chains REVERT: A 39 LYS cc_start: 0.8457 (mmtp) cc_final: 0.7934 (mmmt) REVERT: B 91 GLU cc_start: 0.8349 (tm-30) cc_final: 0.7696 (tm-30) REVERT: B 156 LYS cc_start: 0.8828 (mttt) cc_final: 0.8422 (mtmt) REVERT: B 285 LYS cc_start: 0.9020 (pttt) cc_final: 0.8745 (ptmm) REVERT: C 91 GLU cc_start: 0.8032 (tm-30) cc_final: 0.7652 (tm-30) REVERT: C 110 ASP cc_start: 0.8376 (m-30) cc_final: 0.8153 (m-30) REVERT: C 187 ASP cc_start: 0.8565 (t0) cc_final: 0.8176 (p0) REVERT: C 188 ASN cc_start: 0.8499 (m-40) cc_final: 0.8057 (m-40) outliers start: 18 outliers final: 14 residues processed: 160 average time/residue: 0.2303 time to fit residues: 47.3618 Evaluate side-chains 159 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 145 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 129 PHE Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 129 PHE Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 216 TYR Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 330 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 35 optimal weight: 5.9990 chunk 53 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 56 optimal weight: 0.7980 chunk 61 optimal weight: 0.0870 chunk 44 optimal weight: 7.9990 chunk 8 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.3904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7741 Z= 0.143 Angle : 0.454 5.386 10537 Z= 0.241 Chirality : 0.039 0.125 1197 Planarity : 0.003 0.029 1293 Dihedral : 14.699 144.382 1323 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.83 % Allowed : 21.46 % Favored : 75.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.28), residues: 921 helix: 0.14 (0.27), residues: 408 sheet: 1.28 (0.49), residues: 135 loop : -1.20 (0.29), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 138 PHE 0.008 0.001 PHE B 126 TYR 0.007 0.001 TYR A 216 ARG 0.007 0.000 ARG A 95 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 150 time to evaluate : 0.869 Fit side-chains REVERT: A 39 LYS cc_start: 0.8408 (mmtp) cc_final: 0.7901 (mmmt) REVERT: A 205 TYR cc_start: 0.8348 (m-10) cc_final: 0.8009 (m-10) REVERT: B 91 GLU cc_start: 0.8347 (tm-30) cc_final: 0.7697 (tm-30) REVERT: B 156 LYS cc_start: 0.8832 (mttt) cc_final: 0.8425 (mtmt) REVERT: B 285 LYS cc_start: 0.9018 (pttt) cc_final: 0.8733 (ptmm) REVERT: C 91 GLU cc_start: 0.8038 (tm-30) cc_final: 0.7668 (tm-30) REVERT: C 110 ASP cc_start: 0.8323 (m-30) cc_final: 0.8112 (m-30) REVERT: C 187 ASP cc_start: 0.8567 (t0) cc_final: 0.8176 (p0) REVERT: C 188 ASN cc_start: 0.8506 (m-40) cc_final: 0.8065 (m-40) outliers start: 21 outliers final: 16 residues processed: 162 average time/residue: 0.2551 time to fit residues: 53.6967 Evaluate side-chains 160 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 144 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 129 PHE Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 129 PHE Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 181 SER Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 216 TYR Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 330 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 7.9990 chunk 83 optimal weight: 7.9990 chunk 85 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 65 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 79 optimal weight: 0.7980 chunk 54 optimal weight: 0.5980 chunk 88 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.3924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 7741 Z= 0.150 Angle : 0.468 5.999 10537 Z= 0.246 Chirality : 0.039 0.125 1197 Planarity : 0.003 0.049 1293 Dihedral : 14.708 143.675 1323 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.29 % Allowed : 21.86 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.28), residues: 921 helix: 0.26 (0.27), residues: 408 sheet: 1.30 (0.49), residues: 135 loop : -1.15 (0.29), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 138 PHE 0.008 0.001 PHE B 126 TYR 0.007 0.001 TYR A 216 ARG 0.011 0.000 ARG A 27 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 148 time to evaluate : 0.860 Fit side-chains REVERT: A 39 LYS cc_start: 0.8444 (mmtp) cc_final: 0.7913 (mmmt) REVERT: A 205 TYR cc_start: 0.8374 (m-10) cc_final: 0.8023 (m-10) REVERT: B 91 GLU cc_start: 0.8331 (tm-30) cc_final: 0.7703 (tm-30) REVERT: B 156 LYS cc_start: 0.8816 (mttt) cc_final: 0.8410 (mtmt) REVERT: B 285 LYS cc_start: 0.8985 (pttt) cc_final: 0.8700 (ptmm) REVERT: C 91 GLU cc_start: 0.8009 (tm-30) cc_final: 0.7662 (tm-30) REVERT: C 110 ASP cc_start: 0.8307 (m-30) cc_final: 0.8095 (m-30) REVERT: C 187 ASP cc_start: 0.8567 (t0) cc_final: 0.8176 (p0) REVERT: C 188 ASN cc_start: 0.8530 (m-40) cc_final: 0.8088 (m-40) outliers start: 17 outliers final: 16 residues processed: 159 average time/residue: 0.2233 time to fit residues: 46.2465 Evaluate side-chains 162 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 146 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 129 PHE Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 129 PHE Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 181 SER Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 216 TYR Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 330 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 53 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 73 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 56 optimal weight: 0.0980 chunk 45 optimal weight: 5.9990 chunk 58 optimal weight: 0.7980 chunk 78 optimal weight: 7.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.4002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 7741 Z= 0.148 Angle : 0.466 5.609 10537 Z= 0.245 Chirality : 0.039 0.126 1197 Planarity : 0.003 0.047 1293 Dihedral : 14.639 143.123 1323 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.02 % Allowed : 21.73 % Favored : 76.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.28), residues: 921 helix: 0.34 (0.27), residues: 408 sheet: 1.30 (0.49), residues: 135 loop : -1.08 (0.30), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 138 PHE 0.008 0.001 PHE B 126 TYR 0.007 0.001 TYR A 216 ARG 0.011 0.000 ARG A 27 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 148 time to evaluate : 0.871 Fit side-chains REVERT: A 205 TYR cc_start: 0.8368 (m-10) cc_final: 0.8032 (m-10) REVERT: B 91 GLU cc_start: 0.8325 (tm-30) cc_final: 0.7701 (tm-30) REVERT: B 156 LYS cc_start: 0.8808 (mttt) cc_final: 0.8402 (mtmt) REVERT: B 285 LYS cc_start: 0.8982 (pttt) cc_final: 0.8693 (ptmm) REVERT: C 91 GLU cc_start: 0.7999 (tm-30) cc_final: 0.7648 (tm-30) REVERT: C 110 ASP cc_start: 0.8288 (m-30) cc_final: 0.8072 (m-30) REVERT: C 187 ASP cc_start: 0.8574 (t0) cc_final: 0.8172 (p0) REVERT: C 188 ASN cc_start: 0.8559 (m-40) cc_final: 0.8101 (m-40) outliers start: 15 outliers final: 13 residues processed: 158 average time/residue: 0.2271 time to fit residues: 46.6273 Evaluate side-chains 157 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 144 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 129 PHE Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 129 PHE Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 181 SER Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain C residue 216 TYR Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 330 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 22 optimal weight: 3.9990 chunk 68 optimal weight: 0.0470 chunk 10 optimal weight: 0.9980 chunk 20 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 75 optimal weight: 7.9990 chunk 9 optimal weight: 0.0040 chunk 13 optimal weight: 7.9990 chunk 64 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 overall best weight: 0.7692 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.127941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.101624 restraints weight = 10667.349| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 2.28 r_work: 0.2945 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.4023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 7741 Z= 0.148 Angle : 0.464 5.622 10537 Z= 0.244 Chirality : 0.039 0.127 1197 Planarity : 0.003 0.036 1293 Dihedral : 14.602 142.609 1323 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.16 % Allowed : 21.59 % Favored : 76.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.28), residues: 921 helix: 0.29 (0.27), residues: 414 sheet: 1.31 (0.49), residues: 135 loop : -1.12 (0.30), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 138 PHE 0.008 0.001 PHE A 126 TYR 0.007 0.001 TYR A 216 ARG 0.009 0.000 ARG A 27 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2070.61 seconds wall clock time: 37 minutes 52.53 seconds (2272.53 seconds total)