Starting phenix.real_space_refine on Fri Feb 6 05:02:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9h84_51930/02_2026/9h84_51930.cif Found real_map, /net/cci-nas-00/data/ceres_data/9h84_51930/02_2026/9h84_51930.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9h84_51930/02_2026/9h84_51930.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9h84_51930/02_2026/9h84_51930.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9h84_51930/02_2026/9h84_51930.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9h84_51930/02_2026/9h84_51930.map" } resolution = 4.3 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 32 5.16 5 C 7233 2.51 5 N 1955 2.21 5 O 2266 1.98 5 H 11054 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22540 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 11178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 723, 11178 Classifications: {'peptide': 723} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 28, 'TRANS': 694} Chain: "B" Number of atoms: 5534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 5534 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 359} Chain: "C" Number of atoms: 964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 964 Classifications: {'peptide': 67} Modifications used: {'COO': 1, 'NH1NOTPRO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 59} Chain: "D" Number of atoms: 3461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 3461 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 205} Chain: "E" Number of atoms: 1403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 1403 Classifications: {'peptide': 91} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 85} Time building chain proxies: 3.95, per 1000 atoms: 0.18 Number of scatterers: 22540 At special positions: 0 Unit cell: (108.36, 142.76, 110.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 32 16.00 O 2266 8.00 N 1955 7.00 C 7233 6.00 H 11054 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 690 " - pdb=" SG CYS A 700 " 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 Time building additional restraints: 2.03 Conformation dependent library (CDL) restraints added in 755.6 milliseconds 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2686 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 17 sheets defined 23.4% alpha, 29.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'A' and resid 106 through 117 removed outlier: 3.510A pdb=" N LEU A 110 " --> pdb=" O LYS A 106 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLU A 115 " --> pdb=" O LYS A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 144 removed outlier: 4.280A pdb=" N ALA A 131 " --> pdb=" O ARG A 127 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ASP A 132 " --> pdb=" O THR A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 197 removed outlier: 3.796A pdb=" N LEU A 193 " --> pdb=" O THR A 189 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N HIS A 196 " --> pdb=" O GLU A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 234 removed outlier: 3.698A pdb=" N GLY A 221 " --> pdb=" O GLN A 217 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N GLU A 224 " --> pdb=" O ALA A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 289 removed outlier: 4.477A pdb=" N GLN A 286 " --> pdb=" O ALA A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 316 Processing helix chain 'A' and resid 361 through 367 removed outlier: 3.680A pdb=" N LEU A 365 " --> pdb=" O LYS A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 393 Processing helix chain 'A' and resid 422 through 423B Processing helix chain 'A' and resid 542 through 553 removed outlier: 4.202A pdb=" N TYR A 548 " --> pdb=" O ALA A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 622 through 624 No H-bonds generated for 'chain 'A' and resid 622 through 624' Processing helix chain 'A' and resid 647 through 651 Processing helix chain 'A' and resid 727 through 732 Processing helix chain 'C' and resid 38 through 43 removed outlier: 4.367A pdb=" N TYR C 41 " --> pdb=" O ASP C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 66 Processing helix chain 'D' and resid 31 through 46 Processing helix chain 'D' and resid 47 through 62 Processing helix chain 'D' and resid 67 through 81 Processing helix chain 'D' and resid 84 through 99 Processing helix chain 'D' and resid 104 through 119 Processing helix chain 'D' and resid 137 through 154 Processing helix chain 'D' and resid 159 through 189 Processing helix chain 'D' and resid 190 through 204 Processing helix chain 'D' and resid 208 through 225 Proline residue: D 216 - end of helix Processing helix chain 'D' and resid 227 through 240 removed outlier: 4.601A pdb=" N LYS D 233 " --> pdb=" O ALA D 229 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL D 234 " --> pdb=" O GLN D 230 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 44 Processing helix chain 'E' and resid 51 through 59 removed outlier: 4.215A pdb=" N TYR E 57 " --> pdb=" O GLN E 53 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 94 through 100 removed outlier: 4.220A pdb=" N ILE A 94 " --> pdb=" O VAL A 163 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LEU A 165 " --> pdb=" O ILE A 94 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N SER A 96 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N LEU A 167 " --> pdb=" O SER A 96 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N THR A 98 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N PHE A 169 " --> pdb=" O THR A 98 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N SER A 100 " --> pdb=" O PHE A 169 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 176 through 183 removed outlier: 7.982A pdb=" N VAL A 256 " --> pdb=" O GLN A 178 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N ILE A 180 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N VAL A 258 " --> pdb=" O ILE A 180 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ILE A 182 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ILE A 260 " --> pdb=" O ILE A 182 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 176 through 183 removed outlier: 7.982A pdb=" N VAL A 256 " --> pdb=" O GLN A 178 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N ILE A 180 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N VAL A 258 " --> pdb=" O ILE A 180 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ILE A 182 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ILE A 260 " --> pdb=" O ILE A 182 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 267 through 276 removed outlier: 4.325A pdb=" N LEU A 268 " --> pdb=" O VAL A 335 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N LEU A 337 " --> pdb=" O LEU A 268 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N GLY A 270 " --> pdb=" O LEU A 337 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N VAL A 339 " --> pdb=" O GLY A 270 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N GLU A 272 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N VAL A 341 " --> pdb=" O GLU A 272 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N SER A 274 " --> pdb=" O VAL A 341 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 348 through 355 removed outlier: 4.213A pdb=" N VAL A 349 " --> pdb=" O VAL A 412 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N VAL A 414 " --> pdb=" O VAL A 349 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N LYS A 351 " --> pdb=" O VAL A 414 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N TYR A 416 " --> pdb=" O LYS A 351 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ARG A 353 " --> pdb=" O TYR A 416 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N VAL A 418 " --> pdb=" O ARG A 353 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N GLU A 355 " --> pdb=" O VAL A 418 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N GLU A 420 " --> pdb=" O GLU A 355 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR A 397 " --> pdb=" O LYS A 419 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 426 through 430 removed outlier: 4.127A pdb=" N GLN A 446 " --> pdb=" O VAL A 456 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N VAL A 456 " --> pdb=" O GLN A 446 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ILE A 519 " --> pdb=" O ASN A 523 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ASN A 523 " --> pdb=" O ILE A 519 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N THR A 600 " --> pdb=" O TYR A 608 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N TYR A 608 " --> pdb=" O THR A 600 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N VAL A 628 " --> pdb=" O ILE A 719 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN A 789 " --> pdb=" O ALA A 770 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 673 through 674 Processing sheet with id=AA8, first strand: chain 'B' and resid 45 through 51 removed outlier: 5.704A pdb=" N THR B 46 " --> pdb=" O THR B 391 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N THR B 391 " --> pdb=" O THR B 46 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 66 through 68 removed outlier: 6.565A pdb=" N VAL B 81 " --> pdb=" O SER B 94 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N SER B 94 " --> pdb=" O VAL B 81 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ALA B 83 " --> pdb=" O ILE B 92 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 111 through 118 removed outlier: 6.082A pdb=" N GLY B 114 " --> pdb=" O GLY B 125 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N GLY B 125 " --> pdb=" O GLY B 114 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N GLN B 130 " --> pdb=" O SER B 126 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N ASN B 135 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N VAL B 141 " --> pdb=" O ASN B 135 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 156 through 158 removed outlier: 6.675A pdb=" N LEU B 171 " --> pdb=" O THR B 184 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N THR B 184 " --> pdb=" O LEU B 171 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ALA B 173 " --> pdb=" O LYS B 182 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 201 through 203 removed outlier: 6.734A pdb=" N VAL B 216 " --> pdb=" O GLN B 229 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N GLN B 229 " --> pdb=" O VAL B 216 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ALA B 218 " --> pdb=" O ILE B 227 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 252 through 254 removed outlier: 5.819A pdb=" N ASP B 271 " --> pdb=" O ILE B 277 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ILE B 277 " --> pdb=" O ASP B 271 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 288 through 291 removed outlier: 4.588A pdb=" N ASP B 288 " --> pdb=" O VAL B 299 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N VAL B 305 " --> pdb=" O THR B 318 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N THR B 318 " --> pdb=" O VAL B 305 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ALA B 307 " --> pdb=" O LEU B 316 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 331 through 333 removed outlier: 6.596A pdb=" N LEU B 346 " --> pdb=" O GLN B 359 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N GLN B 359 " --> pdb=" O LEU B 346 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N TRP B 348 " --> pdb=" O VAL B 357 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 32 through 35 removed outlier: 3.582A pdb=" N MET E 64 " --> pdb=" O PHE E 74 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 32 through 35 removed outlier: 7.162A pdb=" N GLN E 88 " --> pdb=" O PRO E 108 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N THR E 90 " --> pdb=" O ASN E 106 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ASN E 106 " --> pdb=" O THR E 90 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N THR E 92 " --> pdb=" O ILE E 104 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ILE E 104 " --> pdb=" O THR E 92 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N THR E 94 " --> pdb=" O THR E 102 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL E 100 " --> pdb=" O ASN E 96 " (cutoff:3.500A) 506 hydrogen bonds defined for protein. 1389 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.02 Time building geometry restraints manager: 2.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 11053 1.04 - 1.23: 519 1.23 - 1.43: 4586 1.43 - 1.63: 6577 1.63 - 1.83: 61 Bond restraints: 22796 Sorted by residual: bond pdb=" N CYS C 25 " pdb=" H1 CYS C 25 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.52e+01 bond pdb=" CG PRO B 36 " pdb=" CD PRO B 36 " ideal model delta sigma weight residual 1.503 1.374 0.129 3.40e-02 8.65e+02 1.45e+01 bond pdb=" N TRP B 93 " pdb=" CA TRP B 93 " ideal model delta sigma weight residual 1.457 1.501 -0.044 1.29e-02 6.01e+03 1.17e+01 bond pdb=" N ASP B 246 " pdb=" CA ASP B 246 " ideal model delta sigma weight residual 1.457 1.497 -0.040 1.29e-02 6.01e+03 9.64e+00 bond pdb=" N ILE B 92 " pdb=" CA ILE B 92 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.16e+00 ... (remaining 22791 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.84: 40590 3.84 - 7.68: 394 7.68 - 11.52: 15 11.52 - 15.36: 0 15.36 - 19.20: 2 Bond angle restraints: 41001 Sorted by residual: angle pdb=" CA PRO B 36 " pdb=" N PRO B 36 " pdb=" CD PRO B 36 " ideal model delta sigma weight residual 112.00 95.81 16.19 1.40e+00 5.10e-01 1.34e+02 angle pdb=" N LEU B 244 " pdb=" CA LEU B 244 " pdb=" C LEU B 244 " ideal model delta sigma weight residual 112.34 104.11 8.23 1.30e+00 5.92e-01 4.01e+01 angle pdb=" N PRO B 36 " pdb=" CD PRO B 36 " pdb=" CG PRO B 36 " ideal model delta sigma weight residual 103.20 95.35 7.85 1.50e+00 4.44e-01 2.74e+01 angle pdb=" N PRO D 28 " pdb=" CD PRO D 28 " pdb=" CG PRO D 28 " ideal model delta sigma weight residual 103.20 95.69 7.51 1.50e+00 4.44e-01 2.51e+01 angle pdb=" CA PRO D 28 " pdb=" N PRO D 28 " pdb=" CD PRO D 28 " ideal model delta sigma weight residual 112.00 105.13 6.87 1.40e+00 5.10e-01 2.41e+01 ... (remaining 40996 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 9670 18.00 - 36.01: 867 36.01 - 54.01: 229 54.01 - 72.01: 50 72.01 - 90.02: 16 Dihedral angle restraints: 10832 sinusoidal: 5828 harmonic: 5004 Sorted by residual: dihedral pdb=" CA VAL B 247 " pdb=" C VAL B 247 " pdb=" N ASP B 248 " pdb=" CA ASP B 248 " ideal model delta harmonic sigma weight residual 180.00 150.09 29.91 0 5.00e+00 4.00e-02 3.58e+01 dihedral pdb=" CA GLN B 130 " pdb=" C GLN B 130 " pdb=" N VAL B 131 " pdb=" CA VAL B 131 " ideal model delta harmonic sigma weight residual 180.00 150.28 29.72 0 5.00e+00 4.00e-02 3.53e+01 dihedral pdb=" CA ILE A 254 " pdb=" C ILE A 254 " pdb=" N TYR A 255 " pdb=" CA TYR A 255 " ideal model delta harmonic sigma weight residual 180.00 150.55 29.45 0 5.00e+00 4.00e-02 3.47e+01 ... (remaining 10829 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1308 0.057 - 0.114: 336 0.114 - 0.171: 77 0.171 - 0.228: 9 0.228 - 0.285: 4 Chirality restraints: 1734 Sorted by residual: chirality pdb=" CA ILE B 92 " pdb=" N ILE B 92 " pdb=" C ILE B 92 " pdb=" CB ILE B 92 " both_signs ideal model delta sigma weight residual False 2.43 2.72 -0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" CA SER B 245 " pdb=" N SER B 245 " pdb=" C SER B 245 " pdb=" CB SER B 245 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" CA ASN A 357 " pdb=" N ASN A 357 " pdb=" C ASN A 357 " pdb=" CB ASN A 357 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.47e+00 ... (remaining 1731 not shown) Planarity restraints: 3510 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 35 " -0.154 5.00e-02 4.00e+02 2.15e-01 7.39e+01 pdb=" N PRO B 36 " 0.370 5.00e-02 4.00e+02 pdb=" CA PRO B 36 " -0.129 5.00e-02 4.00e+02 pdb=" CD PRO B 36 " -0.087 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 287 " 0.052 2.00e-02 2.50e+03 4.47e-02 3.00e+01 pdb=" CG ASN B 287 " -0.058 2.00e-02 2.50e+03 pdb=" OD1 ASN B 287 " -0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN B 287 " -0.006 2.00e-02 2.50e+03 pdb="HD21 ASN B 287 " 0.063 2.00e-02 2.50e+03 pdb="HD22 ASN B 287 " -0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 107 " 0.021 2.00e-02 2.50e+03 3.02e-02 2.73e+01 pdb=" CG TYR D 107 " -0.010 2.00e-02 2.50e+03 pdb=" CD1 TYR D 107 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TYR D 107 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR D 107 " 0.025 2.00e-02 2.50e+03 pdb=" CE2 TYR D 107 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR D 107 " 0.018 2.00e-02 2.50e+03 pdb=" OH TYR D 107 " -0.050 2.00e-02 2.50e+03 pdb=" HD1 TYR D 107 " -0.055 2.00e-02 2.50e+03 pdb=" HD2 TYR D 107 " 0.004 2.00e-02 2.50e+03 pdb=" HE1 TYR D 107 " 0.059 2.00e-02 2.50e+03 pdb=" HE2 TYR D 107 " 0.001 2.00e-02 2.50e+03 ... (remaining 3507 not shown) Histogram of nonbonded interaction distances: 1.16 - 1.85: 154 1.85 - 2.54: 19946 2.54 - 3.23: 70732 3.23 - 3.91: 88512 3.91 - 4.60: 139812 Nonbonded interactions: 319156 Sorted by model distance: nonbonded pdb=" HH TYR B 333 " pdb=" O GLY B 376 " model vdw 1.163 2.450 nonbonded pdb=" H GLY B 196 " pdb=" OD2 ASP B 212 " model vdw 1.381 2.450 nonbonded pdb=" OD1 ASP A 126 " pdb=" HG1 THR A 128 " model vdw 1.415 2.450 nonbonded pdb=" OD1 ASN A 102 " pdb=" HH TYR A 141 " model vdw 1.420 2.450 nonbonded pdb="HD21 ASN A 185 " pdb=" O PHE A 188 " model vdw 1.447 2.450 ... (remaining 319151 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 2.080 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: 0.150 Extract box with map and model: 0.350 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 21.510 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7110 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 : 0.005 0.129 11743 Z= 0.230 Angle : 1.015 19.201 15970 Z= 0.575 Chirality : 0.056 0.285 1734 Planarity : 0.010 0.215 2108 Dihedral : 14.593 90.019 4251 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.45 % Favored : 95.41 % Rotamer: Outliers : 0.16 % Allowed : 2.52 % Favored : 97.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.75 (0.20), residues: 1460 helix: -1.19 (0.24), residues: 301 sheet: -0.04 (0.24), residues: 381 loop : -1.75 (0.20), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.029 0.003 ARG A 421 TYR 0.036 0.007 TYR A 255 PHE 0.041 0.004 PHE A 238 TRP 0.030 0.005 TRP B 48 HIS 0.013 0.003 HIS A 677 Details of bonding type rmsd covalent geometry : bond 0.00463 (11742) covalent geometry : angle 1.01447 (15968) SS BOND : bond 0.00483 ( 1) SS BOND : angle 1.22957 ( 2) hydrogen bonds : bond 0.12750 ( 500) hydrogen bonds : angle 8.11626 ( 1389) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 241 time to evaluate : 0.658 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: 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 112 GLN cc_start: 0.8607 (mm-40) cc_final: 0.8064 (tp-100) REVERT: D 218 MET cc_start: 0.8787 (ttp) cc_final: 0.8541 (ttp) REVERT: E 31 ASP cc_start: 0.7851 (t70) cc_final: 0.7603 (t0) REVERT: E 63 LEU cc_start: 0.9138 (tp) cc_final: 0.8731 (tp) outliers start: 2 outliers final: 1 residues processed: 243 average time/residue: 0.2310 time to fit residues: 81.9261 Evaluate side-chains 180 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 179 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 4.9990 chunk 55 optimal weight: 7.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 ASN A 748 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.097750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.083517 restraints weight = 119139.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.086667 restraints weight = 54285.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.088697 restraints weight = 31106.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.089835 restraints weight = 20904.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.090764 restraints weight = 16172.178| |-----------------------------------------------------------------------------| r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11743 Z= 0.176 Angle : 0.726 7.744 15970 Z= 0.399 Chirality : 0.046 0.193 1734 Planarity : 0.006 0.112 2108 Dihedral : 8.556 74.487 1617 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.45 % Favored : 95.41 % Rotamer: Outliers : 0.24 % Allowed : 2.68 % Favored : 97.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.35 (0.21), residues: 1460 helix: 0.21 (0.28), residues: 308 sheet: -0.36 (0.25), residues: 383 loop : -1.66 (0.21), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 346 TYR 0.025 0.002 TYR A 255 PHE 0.020 0.002 PHE A 169 TRP 0.016 0.002 TRP A 376 HIS 0.004 0.001 HIS E 83 Details of bonding type rmsd covalent geometry : bond 0.00359 (11742) covalent geometry : angle 0.72640 (15968) SS BOND : bond 0.00523 ( 1) SS BOND : angle 1.18894 ( 2) hydrogen bonds : bond 0.04969 ( 500) hydrogen bonds : angle 7.06394 ( 1389) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 234 time to evaluate : 0.646 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: 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 112 GLN cc_start: 0.8836 (mm-40) cc_final: 0.8261 (mm-40) REVERT: A 176 GLU cc_start: 0.7610 (mm-30) cc_final: 0.6868 (mp0) REVERT: D 134 ASP cc_start: 0.8490 (p0) cc_final: 0.8175 (p0) REVERT: E 63 LEU cc_start: 0.9201 (tp) cc_final: 0.8919 (tp) outliers start: 3 outliers final: 1 residues processed: 237 average time/residue: 0.1979 time to fit residues: 72.4478 Evaluate side-chains 177 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 176 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 78 optimal weight: 3.9990 chunk 34 optimal weight: 9.9990 chunk 65 optimal weight: 6.9990 chunk 97 optimal weight: 9.9990 chunk 5 optimal weight: 6.9990 chunk 21 optimal weight: 3.9990 chunk 138 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 748 ASN ** C 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.095830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.081512 restraints weight = 119908.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.084537 restraints weight = 56602.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.086506 restraints weight = 33052.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.087574 restraints weight = 22544.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.088433 restraints weight = 17683.632| |-----------------------------------------------------------------------------| r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11743 Z= 0.217 Angle : 0.693 8.156 15970 Z= 0.382 Chirality : 0.045 0.198 1734 Planarity : 0.005 0.057 2108 Dihedral : 7.915 79.437 1617 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.16 % Favored : 93.77 % Rotamer: Outliers : 0.08 % Allowed : 1.46 % Favored : 98.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.21), residues: 1460 helix: 0.46 (0.29), residues: 311 sheet: -0.63 (0.25), residues: 396 loop : -1.78 (0.21), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 132 TYR 0.033 0.002 TYR E 37 PHE 0.021 0.002 PHE B 204 TRP 0.019 0.002 TRP A 810 HIS 0.004 0.001 HIS C 51 Details of bonding type rmsd covalent geometry : bond 0.00434 (11742) covalent geometry : angle 0.69334 (15968) SS BOND : bond 0.00291 ( 1) SS BOND : angle 0.86630 ( 2) hydrogen bonds : bond 0.04755 ( 500) hydrogen bonds : angle 6.96843 ( 1389) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 214 time to evaluate : 0.383 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: 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 112 GLN cc_start: 0.8818 (mm-40) cc_final: 0.8208 (mm-40) REVERT: A 176 GLU cc_start: 0.7617 (mm-30) cc_final: 0.6770 (mp0) REVERT: D 111 MET cc_start: 0.9098 (mmt) cc_final: 0.8893 (mmt) REVERT: E 31 ASP cc_start: 0.8712 (t70) cc_final: 0.8509 (t0) outliers start: 1 outliers final: 0 residues processed: 215 average time/residue: 0.1901 time to fit residues: 61.6165 Evaluate side-chains 169 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 137 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 3 optimal weight: 10.0000 chunk 97 optimal weight: 0.9980 chunk 59 optimal weight: 8.9990 chunk 23 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 chunk 60 optimal weight: 8.9990 chunk 115 optimal weight: 0.9980 chunk 80 optimal weight: 0.8980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 748 ASN ** C 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 36 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.096573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.082369 restraints weight = 119853.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.085445 restraints weight = 56132.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.087413 restraints weight = 32746.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.088658 restraints weight = 22305.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.089400 restraints weight = 17071.314| |-----------------------------------------------------------------------------| r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.3158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11743 Z= 0.160 Angle : 0.638 7.917 15970 Z= 0.349 Chirality : 0.044 0.198 1734 Planarity : 0.005 0.057 2108 Dihedral : 7.362 74.421 1617 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.82 % Favored : 94.11 % Rotamer: Outliers : 0.08 % Allowed : 2.44 % Favored : 97.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.22), residues: 1460 helix: 0.82 (0.29), residues: 310 sheet: -0.74 (0.25), residues: 413 loop : -1.68 (0.22), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 421 TYR 0.022 0.002 TYR B 263 PHE 0.020 0.002 PHE B 59 TRP 0.012 0.001 TRP A 376 HIS 0.003 0.001 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00323 (11742) covalent geometry : angle 0.63755 (15968) SS BOND : bond 0.00232 ( 1) SS BOND : angle 0.81423 ( 2) hydrogen bonds : bond 0.04296 ( 500) hydrogen bonds : angle 6.72426 ( 1389) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 212 time to evaluate : 0.370 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: 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 112 GLN cc_start: 0.8760 (mm-40) cc_final: 0.8123 (tp-100) REVERT: A 176 GLU cc_start: 0.7545 (mm-30) cc_final: 0.6778 (mp0) REVERT: A 222 ASP cc_start: 0.7071 (m-30) cc_final: 0.6844 (m-30) REVERT: B 259 PHE cc_start: 0.7862 (m-80) cc_final: 0.7629 (m-10) outliers start: 1 outliers final: 0 residues processed: 213 average time/residue: 0.1943 time to fit residues: 63.1939 Evaluate side-chains 176 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 109 optimal weight: 9.9990 chunk 72 optimal weight: 5.9990 chunk 78 optimal weight: 4.9990 chunk 137 optimal weight: 4.9990 chunk 36 optimal weight: 10.0000 chunk 3 optimal weight: 8.9990 chunk 79 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 chunk 123 optimal weight: 4.9990 chunk 23 optimal weight: 0.7980 chunk 119 optimal weight: 3.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 259 ASN A 748 ASN ** B 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.093166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.079199 restraints weight = 118571.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.082226 restraints weight = 54701.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.084146 restraints weight = 31295.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.085355 restraints weight = 21029.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.086181 restraints weight = 15909.707| |-----------------------------------------------------------------------------| r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.3575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 11743 Z= 0.295 Angle : 0.722 8.448 15970 Z= 0.401 Chirality : 0.045 0.191 1734 Planarity : 0.005 0.075 2108 Dihedral : 7.457 76.667 1617 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.74 % Favored : 92.19 % Rotamer: Outliers : 0.16 % Allowed : 1.79 % Favored : 98.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.80 (0.21), residues: 1460 helix: 0.38 (0.29), residues: 310 sheet: -0.93 (0.25), residues: 407 loop : -2.08 (0.22), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 223 TYR 0.029 0.002 TYR A 454 PHE 0.021 0.002 PHE A 494 TRP 0.014 0.002 TRP A 739 HIS 0.005 0.001 HIS C 51 Details of bonding type rmsd covalent geometry : bond 0.00593 (11742) covalent geometry : angle 0.72154 (15968) SS BOND : bond 0.00277 ( 1) SS BOND : angle 0.90635 ( 2) hydrogen bonds : bond 0.04754 ( 500) hydrogen bonds : angle 7.01601 ( 1389) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 200 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 112 GLN cc_start: 0.8846 (mm-40) cc_final: 0.8200 (tp-100) REVERT: A 222 ASP cc_start: 0.7303 (m-30) cc_final: 0.7065 (m-30) REVERT: B 259 PHE cc_start: 0.8119 (m-80) cc_final: 0.7828 (m-10) outliers start: 2 outliers final: 1 residues processed: 201 average time/residue: 0.1828 time to fit residues: 55.7387 Evaluate side-chains 163 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 162 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 56 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 chunk 108 optimal weight: 5.9990 chunk 140 optimal weight: 0.9990 chunk 110 optimal weight: 5.9990 chunk 100 optimal weight: 5.9990 chunk 102 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 ASN A 748 ASN ** C 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.093933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.079787 restraints weight = 119415.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.082789 restraints weight = 55193.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.084763 restraints weight = 32160.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.085928 restraints weight = 21770.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.086798 restraints weight = 16812.331| |-----------------------------------------------------------------------------| r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.3796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11743 Z= 0.198 Angle : 0.647 7.997 15970 Z= 0.356 Chirality : 0.045 0.198 1734 Planarity : 0.005 0.058 2108 Dihedral : 7.187 74.142 1617 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.33 % Favored : 92.60 % Rotamer: Outliers : 0.08 % Allowed : 1.22 % Favored : 98.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.66 (0.21), residues: 1460 helix: 0.70 (0.29), residues: 308 sheet: -0.92 (0.25), residues: 398 loop : -2.02 (0.22), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 77 TYR 0.024 0.002 TYR B 263 PHE 0.016 0.002 PHE A 494 TRP 0.013 0.001 TRP A 739 HIS 0.004 0.001 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00401 (11742) covalent geometry : angle 0.64736 (15968) SS BOND : bond 0.00280 ( 1) SS BOND : angle 0.94165 ( 2) hydrogen bonds : bond 0.04274 ( 500) hydrogen bonds : angle 6.76578 ( 1389) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 198 time to evaluate : 0.612 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: 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 112 GLN cc_start: 0.8848 (mm-40) cc_final: 0.8180 (tp-100) REVERT: A 259 ASN cc_start: 0.7843 (m-40) cc_final: 0.7532 (m-40) REVERT: A 307 ASP cc_start: 0.8316 (m-30) cc_final: 0.8103 (m-30) REVERT: A 578 TYR cc_start: 0.8350 (t80) cc_final: 0.8136 (t80) REVERT: B 261 LEU cc_start: 0.8581 (pp) cc_final: 0.8179 (pp) outliers start: 1 outliers final: 0 residues processed: 199 average time/residue: 0.1952 time to fit residues: 59.0938 Evaluate side-chains 167 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 110 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 102 optimal weight: 7.9990 chunk 44 optimal weight: 4.9990 chunk 67 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 chunk 17 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 748 ASN ** B 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.093591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.079469 restraints weight = 120356.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.082442 restraints weight = 55806.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.084380 restraints weight = 32547.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.085612 restraints weight = 22129.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.086428 restraints weight = 16886.969| |-----------------------------------------------------------------------------| r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.4027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11743 Z= 0.220 Angle : 0.654 9.529 15970 Z= 0.360 Chirality : 0.044 0.196 1734 Planarity : 0.005 0.058 2108 Dihedral : 7.085 72.578 1617 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.29 % Favored : 91.64 % Rotamer: Outliers : 0.08 % Allowed : 0.57 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.78 (0.21), residues: 1460 helix: 0.55 (0.29), residues: 303 sheet: -1.05 (0.25), residues: 403 loop : -2.01 (0.22), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 77 TYR 0.024 0.002 TYR A 504 PHE 0.021 0.002 PHE B 59 TRP 0.013 0.001 TRP A 739 HIS 0.003 0.001 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00444 (11742) covalent geometry : angle 0.65407 (15968) SS BOND : bond 0.00084 ( 1) SS BOND : angle 0.54255 ( 2) hydrogen bonds : bond 0.04279 ( 500) hydrogen bonds : angle 6.76400 ( 1389) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 200 time to evaluate : 0.651 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: 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 112 GLN cc_start: 0.8846 (mm-40) cc_final: 0.8215 (tp-100) REVERT: A 307 ASP cc_start: 0.8281 (m-30) cc_final: 0.8031 (m-30) REVERT: B 261 LEU cc_start: 0.8427 (pp) cc_final: 0.7901 (pp) outliers start: 1 outliers final: 0 residues processed: 201 average time/residue: 0.2022 time to fit residues: 61.3560 Evaluate side-chains 162 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 79 optimal weight: 4.9990 chunk 42 optimal weight: 6.9990 chunk 40 optimal weight: 1.9990 chunk 59 optimal weight: 10.0000 chunk 97 optimal weight: 5.9990 chunk 33 optimal weight: 7.9990 chunk 91 optimal weight: 7.9990 chunk 37 optimal weight: 8.9990 chunk 1 optimal weight: 5.9990 chunk 70 optimal weight: 9.9990 chunk 102 optimal weight: 6.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 748 ASN ** B 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 368 GLN ** C 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 89 GLN D 116 ASN ** E 36 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 = 0.3620 r_free = 0.3620 target = 0.089650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.075878 restraints weight = 122366.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.078692 restraints weight = 57256.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.080568 restraints weight = 33526.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.081763 restraints weight = 22911.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.082548 restraints weight = 17492.858| |-----------------------------------------------------------------------------| r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.4429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.063 11743 Z= 0.394 Angle : 0.801 9.606 15970 Z= 0.450 Chirality : 0.048 0.185 1734 Planarity : 0.006 0.064 2108 Dihedral : 7.697 76.541 1617 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 19.79 Ramachandran Plot: Outliers : 0.07 % Allowed : 11.03 % Favored : 88.90 % Rotamer: Outliers : 0.16 % Allowed : 0.97 % Favored : 98.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -2.57 (0.20), residues: 1460 helix: -0.30 (0.28), residues: 298 sheet: -1.34 (0.25), residues: 399 loop : -2.55 (0.20), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 77 TYR 0.023 0.003 TYR D 184 PHE 0.031 0.003 PHE B 59 TRP 0.019 0.002 TRP A 739 HIS 0.006 0.002 HIS B 347 Details of bonding type rmsd covalent geometry : bond 0.00789 (11742) covalent geometry : angle 0.80097 (15968) SS BOND : bond 0.00023 ( 1) SS BOND : angle 0.75642 ( 2) hydrogen bonds : bond 0.05066 ( 500) hydrogen bonds : angle 7.41108 ( 1389) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 189 time to evaluate : 0.611 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 259 ASN cc_start: 0.7605 (t0) cc_final: 0.7356 (m-40) REVERT: A 307 ASP cc_start: 0.8362 (m-30) cc_final: 0.8088 (m-30) REVERT: A 380 ASP cc_start: 0.8012 (p0) cc_final: 0.7288 (m-30) REVERT: B 32 MET cc_start: 0.7411 (pmm) cc_final: 0.7169 (pmm) REVERT: B 111 LEU cc_start: 0.8783 (tp) cc_final: 0.8500 (tp) REVERT: B 168 ASN cc_start: 0.8806 (t0) cc_final: 0.8472 (t0) REVERT: B 261 LEU cc_start: 0.8481 (pp) cc_final: 0.8109 (pp) REVERT: D 178 GLU cc_start: 0.8799 (mt-10) cc_final: 0.8574 (mt-10) REVERT: D 201 MET cc_start: 0.9229 (ttm) cc_final: 0.8855 (ttm) outliers start: 2 outliers final: 0 residues processed: 191 average time/residue: 0.1904 time to fit residues: 55.1917 Evaluate side-chains 157 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 87 optimal weight: 0.9990 chunk 88 optimal weight: 0.9990 chunk 114 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 35 optimal weight: 5.9990 chunk 64 optimal weight: 6.9990 chunk 136 optimal weight: 1.9990 chunk 142 optimal weight: 0.9980 chunk 131 optimal weight: 0.8980 chunk 118 optimal weight: 0.6980 chunk 103 optimal weight: 3.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 ASN A 748 ASN B 302 ASN ** B 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 36 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.093374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.079572 restraints weight = 119479.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.082563 restraints weight = 55488.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.084444 restraints weight = 32235.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.085735 restraints weight = 22169.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.086455 restraints weight = 16716.281| |-----------------------------------------------------------------------------| r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.4468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11743 Z= 0.145 Angle : 0.633 7.224 15970 Z= 0.347 Chirality : 0.045 0.206 1734 Planarity : 0.005 0.057 2108 Dihedral : 7.038 70.365 1617 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.47 % Favored : 92.47 % Rotamer: Outliers : 0.16 % Allowed : 1.14 % Favored : 98.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.94 (0.21), residues: 1460 helix: 0.41 (0.29), residues: 309 sheet: -1.22 (0.24), residues: 413 loop : -2.10 (0.22), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 77 TYR 0.021 0.002 TYR A 585 PHE 0.017 0.002 PHE B 59 TRP 0.013 0.001 TRP A 739 HIS 0.005 0.001 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00299 (11742) covalent geometry : angle 0.63313 (15968) SS BOND : bond 0.00101 ( 1) SS BOND : angle 0.81735 ( 2) hydrogen bonds : bond 0.04122 ( 500) hydrogen bonds : angle 6.72200 ( 1389) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 200 time to evaluate : 0.579 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: 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 307 ASP cc_start: 0.8216 (m-30) cc_final: 0.7979 (m-30) REVERT: A 605 ASP cc_start: 0.7419 (m-30) cc_final: 0.6823 (t70) REVERT: B 32 MET cc_start: 0.7311 (pmm) cc_final: 0.7030 (pmm) REVERT: B 261 LEU cc_start: 0.8412 (pp) cc_final: 0.8048 (pp) REVERT: D 146 ASP cc_start: 0.8345 (m-30) cc_final: 0.8107 (m-30) REVERT: E 28 TYR cc_start: 0.8245 (t80) cc_final: 0.7310 (t80) outliers start: 2 outliers final: 1 residues processed: 201 average time/residue: 0.1932 time to fit residues: 60.0528 Evaluate side-chains 162 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 161 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 104 optimal weight: 6.9990 chunk 54 optimal weight: 5.9990 chunk 88 optimal weight: 6.9990 chunk 111 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 44 optimal weight: 6.9990 chunk 97 optimal weight: 0.0060 chunk 108 optimal weight: 8.9990 chunk 96 optimal weight: 4.9990 chunk 89 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 overall best weight: 2.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 563 ASN A 748 ASN B 168 ASN B 302 ASN ** B 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 54 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.092711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.078908 restraints weight = 120353.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.081839 restraints weight = 55992.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.083775 restraints weight = 32699.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.084985 restraints weight = 22259.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.085720 restraints weight = 16926.257| |-----------------------------------------------------------------------------| r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.4597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11743 Z= 0.191 Angle : 0.639 7.814 15970 Z= 0.351 Chirality : 0.044 0.201 1734 Planarity : 0.005 0.107 2108 Dihedral : 6.923 67.672 1617 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.29 % Favored : 91.64 % Rotamer: Outliers : 0.08 % Allowed : 0.41 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.89 (0.21), residues: 1460 helix: 0.60 (0.29), residues: 302 sheet: -1.24 (0.24), residues: 408 loop : -2.08 (0.22), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 421 TYR 0.020 0.002 TYR B 263 PHE 0.015 0.002 PHE A 494 TRP 0.018 0.002 TRP A 376 HIS 0.004 0.001 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00390 (11742) covalent geometry : angle 0.63931 (15968) SS BOND : bond 0.00072 ( 1) SS BOND : angle 0.47558 ( 2) hydrogen bonds : bond 0.04198 ( 500) hydrogen bonds : angle 6.67580 ( 1389) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 192 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: 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 307 ASP cc_start: 0.8264 (m-30) cc_final: 0.8025 (m-30) REVERT: A 371 GLN cc_start: 0.8572 (tm-30) cc_final: 0.7935 (tm-30) REVERT: B 32 MET cc_start: 0.7353 (pmm) cc_final: 0.7026 (pmm) REVERT: B 261 LEU cc_start: 0.8552 (pp) cc_final: 0.8152 (pp) REVERT: D 201 MET cc_start: 0.9077 (ttm) cc_final: 0.8648 (ttm) outliers start: 1 outliers final: 0 residues processed: 193 average time/residue: 0.1867 time to fit residues: 55.3966 Evaluate side-chains 162 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 14 optimal weight: 4.9990 chunk 112 optimal weight: 0.0570 chunk 141 optimal weight: 0.6980 chunk 130 optimal weight: 0.9980 chunk 135 optimal weight: 0.6980 chunk 95 optimal weight: 2.9990 chunk 5 optimal weight: 7.9990 chunk 49 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 overall best weight: 1.0900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 748 ASN ** B 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 54 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.094056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.080179 restraints weight = 118562.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.083145 restraints weight = 54508.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.085101 restraints weight = 31840.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.086244 restraints weight = 21699.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.087078 restraints weight = 16707.108| |-----------------------------------------------------------------------------| r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.4684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 11743 Z= 0.134 Angle : 0.606 7.374 15970 Z= 0.330 Chirality : 0.044 0.205 1734 Planarity : 0.005 0.052 2108 Dihedral : 6.628 64.122 1617 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.19 % Favored : 92.74 % Rotamer: Outliers : 0.08 % Allowed : 0.24 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.68 (0.22), residues: 1460 helix: 0.72 (0.29), residues: 308 sheet: -1.14 (0.24), residues: 411 loop : -1.92 (0.23), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 77 TYR 0.028 0.002 TYR A 585 PHE 0.022 0.002 PHE A 169 TRP 0.010 0.001 TRP A 739 HIS 0.004 0.001 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00277 (11742) covalent geometry : angle 0.60626 (15968) SS BOND : bond 0.00083 ( 1) SS BOND : angle 0.61247 ( 2) hydrogen bonds : bond 0.03981 ( 500) hydrogen bonds : angle 6.41992 ( 1389) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3412.67 seconds wall clock time: 59 minutes 5.78 seconds (3545.78 seconds total)