Starting phenix.real_space_refine on Sun Jul 5 01:35:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9i60_52644/07_2026/9i60_52644_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9i60_52644/07_2026/9i60_52644.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9i60_52644/07_2026/9i60_52644_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9i60_52644/07_2026/9i60_52644_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9i60_52644/07_2026/9i60_52644.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9i60_52644/07_2026/9i60_52644.map" } resolution = 3.31 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= 0.004 sd= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 8 5.49 5 S 48 5.16 5 C 7869 2.51 5 N 1831 2.21 5 O 2085 1.98 5 H 11527 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 23368 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 510, 7757 Classifications: {'peptide': 510} Link IDs: {'PTRANS': 13, 'TRANS': 496} Chain: "B" Number of atoms: 7595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 7595 Classifications: {'peptide': 501} Link IDs: {'PTRANS': 13, 'TRANS': 487} Chain: "C" Number of atoms: 7612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 502, 7612 Classifications: {'peptide': 502} Link IDs: {'PTRANS': 13, 'TRANS': 488} Chain: "A" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGT': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 102 Unusual residues: {'PGT': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 251 Unusual residues: {'CDL': 2, 'PGT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 4.38, per 1000 atoms: 0.19 Number of scatterers: 23368 At special positions: 0 Unit cell: (81.2773, 115.998, 111.263, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 48 16.00 P 8 15.00 O 2085 8.00 N 1831 7.00 C 7869 6.00 H 11527 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.35 Conformation dependent library (CDL) restraints added in 610.1 milliseconds 3014 Ramachandran restraints generated. 1507 Oldfield, 0 Emsley, 1507 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2690 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 0 sheets defined 82.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 59 through 80 Proline residue: A 65 - end of helix Processing helix chain 'A' and resid 80 through 119 removed outlier: 5.822A pdb=" N TRP A 101 " --> pdb=" O ASP A 97 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N ALA A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N THR A 108 " --> pdb=" O ILE A 104 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL A 111 " --> pdb=" O GLY A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 148 removed outlier: 3.519A pdb=" N ALA A 147 " --> pdb=" O SER A 143 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA A 148 " --> pdb=" O MET A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 169 removed outlier: 3.881A pdb=" N PHE A 156 " --> pdb=" O ILE A 152 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TYR A 157 " --> pdb=" O GLY A 153 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N THR A 159 " --> pdb=" O MET A 155 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N THR A 160 " --> pdb=" O PHE A 156 " (cutoff:3.500A) Proline residue: A 162 - end of helix Processing helix chain 'A' and resid 177 through 188 removed outlier: 3.654A pdb=" N HIS A 188 " --> pdb=" O THR A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 210 Processing helix chain 'A' and resid 216 through 221 removed outlier: 3.681A pdb=" N ALA A 220 " --> pdb=" O LEU A 216 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE A 221 " --> pdb=" O LEU A 217 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 216 through 221' Processing helix chain 'A' and resid 221 through 230 removed outlier: 6.584A pdb=" N GLU A 227 " --> pdb=" O PRO A 223 " (cutoff:3.500A) removed outlier: 9.032A pdb=" N LYS A 228 " --> pdb=" O LEU A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 268 removed outlier: 3.582A pdb=" N ASP A 239 " --> pdb=" O GLY A 235 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ILE A 240 " --> pdb=" O LYS A 236 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER A 266 " --> pdb=" O GLY A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 296 removed outlier: 3.526A pdb=" N SER A 296 " --> pdb=" O PHE A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 324 removed outlier: 3.526A pdb=" N GLN A 303 " --> pdb=" O GLY A 299 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N MET A 310 " --> pdb=" O SER A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 343 removed outlier: 3.762A pdb=" N LEU A 333 " --> pdb=" O ILE A 329 " (cutoff:3.500A) Proline residue: A 334 - end of helix Processing helix chain 'A' and resid 343 through 349 Processing helix chain 'A' and resid 360 through 366 removed outlier: 3.848A pdb=" N SER A 365 " --> pdb=" O GLU A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 389 Proline residue: A 379 - end of helix removed outlier: 4.060A pdb=" N ILE A 388 " --> pdb=" O PHE A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 426 Proline residue: A 405 - end of helix removed outlier: 4.263A pdb=" N THR A 419 " --> pdb=" O ILE A 415 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA A 420 " --> pdb=" O PHE A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 446 Processing helix chain 'A' and resid 449 through 481 removed outlier: 4.154A pdb=" N MET A 453 " --> pdb=" O GLY A 449 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL A 475 " --> pdb=" O SER A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 509 removed outlier: 3.516A pdb=" N GLY A 496 " --> pdb=" O THR A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 527 Processing helix chain 'A' and resid 528 through 546 removed outlier: 3.989A pdb=" N VAL A 532 " --> pdb=" O PRO A 528 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N PHE A 538 " --> pdb=" O ILE A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 565 Processing helix chain 'B' and resid 59 through 80 Proline residue: B 65 - end of helix Processing helix chain 'B' and resid 80 through 119 removed outlier: 5.484A pdb=" N TRP B 101 " --> pdb=" O ASP B 97 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N ALA B 102 " --> pdb=" O ASN B 98 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N THR B 108 " --> pdb=" O ILE B 104 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N VAL B 111 " --> pdb=" O GLY B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 125 removed outlier: 3.618A pdb=" N THR B 124 " --> pdb=" O LYS B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 145 Processing helix chain 'B' and resid 159 through 168 removed outlier: 3.840A pdb=" N LEU B 163 " --> pdb=" O THR B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 188 removed outlier: 3.848A pdb=" N MET B 186 " --> pdb=" O MET B 182 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N HIS B 188 " --> pdb=" O THR B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 209 Processing helix chain 'B' and resid 217 through 220 Processing helix chain 'B' and resid 221 through 233 removed outlier: 7.003A pdb=" N GLU B 227 " --> pdb=" O PRO B 223 " (cutoff:3.500A) removed outlier: 8.841A pdb=" N LYS B 228 " --> pdb=" O LEU B 224 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLY B 229 " --> pdb=" O ILE B 225 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLU B 231 " --> pdb=" O GLU B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 268 removed outlier: 3.660A pdb=" N THR B 250 " --> pdb=" O THR B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 295 Processing helix chain 'B' and resid 300 through 323 removed outlier: 3.689A pdb=" N TYR B 304 " --> pdb=" O LYS B 300 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU B 305 " --> pdb=" O GLY B 301 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N MET B 310 " --> pdb=" O SER B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 331 Processing helix chain 'B' and resid 331 through 348 removed outlier: 3.713A pdb=" N GLY B 335 " --> pdb=" O ASN B 331 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N PHE B 345 " --> pdb=" O LEU B 341 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N GLN B 346 " --> pdb=" O SER B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 389 Proline residue: B 379 - end of helix removed outlier: 3.844A pdb=" N ARG B 387 " --> pdb=" O MET B 383 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ILE B 388 " --> pdb=" O PHE B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 426 Proline residue: B 405 - end of helix removed outlier: 4.190A pdb=" N THR B 419 " --> pdb=" O ILE B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 437 No H-bonds generated for 'chain 'B' and resid 435 through 437' Processing helix chain 'B' and resid 438 through 447 Processing helix chain 'B' and resid 450 through 480 removed outlier: 3.779A pdb=" N ILE B 455 " --> pdb=" O GLN B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 509 removed outlier: 3.560A pdb=" N LEU B 507 " --> pdb=" O GLY B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 546 removed outlier: 3.880A pdb=" N THR B 522 " --> pdb=" O LEU B 518 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N THR B 527 " --> pdb=" O ILE B 523 " (cutoff:3.500A) Proline residue: B 528 - end of helix removed outlier: 4.195A pdb=" N PHE B 531 " --> pdb=" O THR B 527 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL B 532 " --> pdb=" O PRO B 528 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE B 538 " --> pdb=" O ILE B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 550 through 556 removed outlier: 3.654A pdb=" N GLN B 556 " --> pdb=" O GLU B 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 80 Proline residue: C 65 - end of helix Processing helix chain 'C' and resid 80 through 120 removed outlier: 5.855A pdb=" N TRP C 101 " --> pdb=" O ASP C 97 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N ALA C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N THR C 108 " --> pdb=" O ILE C 104 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL C 109 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N VAL C 111 " --> pdb=" O GLY C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 125 removed outlier: 3.843A pdb=" N THR C 124 " --> pdb=" O LYS C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 147 Processing helix chain 'C' and resid 152 through 157 Processing helix chain 'C' and resid 159 through 168 removed outlier: 3.675A pdb=" N LEU C 163 " --> pdb=" O THR C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 190 removed outlier: 3.626A pdb=" N HIS C 188 " --> pdb=" O THR C 184 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TRP C 189 " --> pdb=" O THR C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 209 Processing helix chain 'C' and resid 216 through 221 removed outlier: 3.853A pdb=" N ALA C 220 " --> pdb=" O LEU C 216 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N PHE C 221 " --> pdb=" O LEU C 217 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 216 through 221' Processing helix chain 'C' and resid 221 through 231 removed outlier: 7.270A pdb=" N GLU C 227 " --> pdb=" O PRO C 223 " (cutoff:3.500A) removed outlier: 8.443A pdb=" N LYS C 228 " --> pdb=" O LEU C 224 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU C 231 " --> pdb=" O GLU C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 268 Processing helix chain 'C' and resid 277 through 295 Processing helix chain 'C' and resid 303 through 324 Processing helix chain 'C' and resid 327 through 344 Proline residue: C 334 - end of helix Processing helix chain 'C' and resid 362 through 367 Processing helix chain 'C' and resid 367 through 389 Proline residue: C 379 - end of helix removed outlier: 3.668A pdb=" N ARG C 387 " --> pdb=" O MET C 383 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ILE C 388 " --> pdb=" O PHE C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 393 through 427 Proline residue: C 405 - end of helix removed outlier: 4.121A pdb=" N THR C 419 " --> pdb=" O ILE C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 435 through 437 No H-bonds generated for 'chain 'C' and resid 435 through 437' Processing helix chain 'C' and resid 438 through 446 Processing helix chain 'C' and resid 449 through 480 removed outlier: 4.050A pdb=" N MET C 453 " --> pdb=" O GLY C 449 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE C 455 " --> pdb=" O GLN C 451 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 509 removed outlier: 3.934A pdb=" N LEU C 507 " --> pdb=" O GLY C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 514 through 546 removed outlier: 3.523A pdb=" N ILE C 523 " --> pdb=" O GLN C 519 " (cutoff:3.500A) Proline residue: C 528 - end of helix removed outlier: 4.411A pdb=" N PHE C 531 " --> pdb=" O THR C 527 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N VAL C 532 " --> pdb=" O PRO C 528 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N PHE C 538 " --> pdb=" O ILE C 534 " (cutoff:3.500A) Processing helix chain 'C' and resid 551 through 557 855 hydrogen bonds defined for protein. 2553 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: 5.20 Time building geometry restraints manager: 3.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 11524 1.03 - 1.23: 19 1.23 - 1.42: 5057 1.42 - 1.61: 6959 1.61 - 1.81: 101 Bond restraints: 23660 Sorted by residual: bond pdb=" OB5 CDL C 601 " pdb=" PB2 CDL C 601 " ideal model delta sigma weight residual 1.657 1.575 0.082 2.00e-02 2.50e+03 1.69e+01 bond pdb=" OB5 CDL C 603 " pdb=" PB2 CDL C 603 " ideal model delta sigma weight residual 1.657 1.580 0.077 2.00e-02 2.50e+03 1.49e+01 bond pdb=" OA5 CDL C 601 " pdb=" PA1 CDL C 601 " ideal model delta sigma weight residual 1.651 1.576 0.075 2.00e-02 2.50e+03 1.41e+01 bond pdb=" OA5 CDL C 603 " pdb=" PA1 CDL C 603 " ideal model delta sigma weight residual 1.651 1.583 0.068 2.00e-02 2.50e+03 1.15e+01 bond pdb=" OA2 CDL C 601 " pdb=" PA1 CDL C 601 " ideal model delta sigma weight residual 1.639 1.579 0.060 2.00e-02 2.50e+03 9.06e+00 ... (remaining 23655 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 41466 1.71 - 3.42: 872 3.42 - 5.13: 81 5.13 - 6.83: 18 6.83 - 8.54: 9 Bond angle restraints: 42446 Sorted by residual: angle pdb=" N VAL B 247 " pdb=" CA VAL B 247 " pdb=" C VAL B 247 " ideal model delta sigma weight residual 111.58 108.12 3.46 1.06e+00 8.90e-01 1.07e+01 angle pdb=" CA3 CDL C 601 " pdb=" CA4 CDL C 601 " pdb=" OA6 CDL C 601 " ideal model delta sigma weight residual 110.30 101.76 8.54 3.00e+00 1.11e-01 8.11e+00 angle pdb=" CA3 CDL C 603 " pdb=" CA4 CDL C 603 " pdb=" OA6 CDL C 603 " ideal model delta sigma weight residual 110.30 101.83 8.47 3.00e+00 1.11e-01 7.97e+00 angle pdb=" N ALA A 148 " pdb=" CA ALA A 148 " pdb=" CB ALA A 148 " ideal model delta sigma weight residual 113.65 109.73 3.92 1.47e+00 4.63e-01 7.12e+00 angle pdb=" CB2 CDL C 601 " pdb=" C1 CDL C 601 " pdb=" O1 CDL C 601 " ideal model delta sigma weight residual 111.29 103.36 7.93 3.00e+00 1.11e-01 6.99e+00 ... (remaining 42441 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 9894 17.97 - 35.94: 930 35.94 - 53.91: 323 53.91 - 71.88: 116 71.88 - 89.85: 7 Dihedral angle restraints: 11270 sinusoidal: 6012 harmonic: 5258 Sorted by residual: dihedral pdb=" CA PRO C 134 " pdb=" C PRO C 134 " pdb=" N GLU C 135 " pdb=" CA GLU C 135 " ideal model delta harmonic sigma weight residual -180.00 -161.41 -18.59 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CA ASP A 131 " pdb=" CB ASP A 131 " pdb=" CG ASP A 131 " pdb=" OD1 ASP A 131 " ideal model delta sinusoidal sigma weight residual -30.00 -88.21 58.21 1 2.00e+01 2.50e-03 1.14e+01 dihedral pdb=" CA ASP A 356 " pdb=" CB ASP A 356 " pdb=" CG ASP A 356 " pdb=" OD1 ASP A 356 " ideal model delta sinusoidal sigma weight residual -30.00 -87.27 57.27 1 2.00e+01 2.50e-03 1.10e+01 ... (remaining 11267 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 1769 0.077 - 0.154: 110 0.154 - 0.231: 0 0.231 - 0.307: 2 0.307 - 0.384: 2 Chirality restraints: 1883 Sorted by residual: chirality pdb=" CA4 CDL C 603 " pdb=" CA3 CDL C 603 " pdb=" CA6 CDL C 603 " pdb=" OA6 CDL C 603 " both_signs ideal model delta sigma weight residual False -2.53 -2.92 0.38 2.00e-01 2.50e+01 3.69e+00 chirality pdb=" CA4 CDL C 601 " pdb=" CA3 CDL C 601 " pdb=" CA6 CDL C 601 " pdb=" OA6 CDL C 601 " both_signs ideal model delta sigma weight residual False -2.53 -2.90 0.37 2.00e-01 2.50e+01 3.39e+00 chirality pdb=" CB4 CDL C 603 " pdb=" CB3 CDL C 603 " pdb=" CB6 CDL C 603 " pdb=" OB6 CDL C 603 " both_signs ideal model delta sigma weight residual False -2.61 -2.89 0.28 2.00e-01 2.50e+01 1.98e+00 ... (remaining 1880 not shown) Planarity restraints: 3457 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 464 " 0.031 2.00e-02 2.50e+03 2.27e-02 1.55e+01 pdb=" CG PHE A 464 " -0.062 2.00e-02 2.50e+03 pdb=" CD1 PHE A 464 " 0.029 2.00e-02 2.50e+03 pdb=" CD2 PHE A 464 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE A 464 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE A 464 " -0.009 2.00e-02 2.50e+03 pdb=" CZ PHE A 464 " -0.001 2.00e-02 2.50e+03 pdb=" HD1 PHE A 464 " -0.013 2.00e-02 2.50e+03 pdb=" HD2 PHE A 464 " 0.003 2.00e-02 2.50e+03 pdb=" HE1 PHE A 464 " 0.010 2.00e-02 2.50e+03 pdb=" HE2 PHE A 464 " 0.009 2.00e-02 2.50e+03 pdb=" HZ PHE A 464 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 414 " -0.010 2.00e-02 2.50e+03 2.06e-02 4.23e+00 pdb=" C SER B 414 " 0.036 2.00e-02 2.50e+03 pdb=" O SER B 414 " -0.013 2.00e-02 2.50e+03 pdb=" N ILE B 415 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 414 " -0.010 2.00e-02 2.50e+03 1.96e-02 3.83e+00 pdb=" C SER A 414 " 0.034 2.00e-02 2.50e+03 pdb=" O SER A 414 " -0.013 2.00e-02 2.50e+03 pdb=" N ILE A 415 " -0.011 2.00e-02 2.50e+03 ... (remaining 3454 not shown) Histogram of nonbonded interaction distances: 1.69 - 2.27: 3049 2.27 - 2.85: 52003 2.85 - 3.44: 63590 3.44 - 4.02: 85165 4.02 - 4.60: 132824 Nonbonded interactions: 336631 Sorted by model distance: nonbonded pdb=" O SER B 275 " pdb=" HG1 THR B 278 " model vdw 1.691 2.450 nonbonded pdb=" O LEU A 332 " pdb=" H SER A 336 " model vdw 1.698 2.450 nonbonded pdb="HH12 ARG B 210 " pdb=" OD2 ASP B 547 " model vdw 1.724 2.450 nonbonded pdb=" OD1 ASP A 82 " pdb=" H SER A 83 " model vdw 1.735 2.450 nonbonded pdb=" O ILE A 63 " pdb=" H LEU A 67 " model vdw 1.736 2.450 ... (remaining 336626 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 56 through 556) selection = (chain 'B' and resid 56 through 556) selection = (chain 'C' and resid 56 through 556) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.220 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: 0.160 Extract box with map and model: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 22.860 Find NCS groups from input model: 0.450 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:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 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 0.082 12133 Z= 0.231 Angle : 0.679 8.544 16455 Z= 0.356 Chirality : 0.042 0.384 1883 Planarity : 0.004 0.046 1986 Dihedral : 14.708 89.854 4226 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.21), residues: 1507 helix: 1.02 (0.15), residues: 1152 sheet: None (None), residues: 0 loop : -0.74 (0.33), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 350 TYR 0.010 0.001 TYR A 197 PHE 0.064 0.002 PHE A 464 TRP 0.019 0.001 TRP A 377 HIS 0.005 0.001 HIS A 445 Details of bonding type rmsd/Z covalent geometry : bond 0.00507 / 0.23 (12133) covalent geometry : angle 0.67853 / 0.36 (16455) hydrogen bonds : bond 0.13496 / 8.98 ( 855) hydrogen bonds : angle 6.46616 / 4.75 ( 2553) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3014 Ramachandran restraints generated. 1507 Oldfield, 0 Emsley, 1507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3014 Ramachandran restraints generated. 1507 Oldfield, 0 Emsley, 1507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.2679 time to fit residues: 25.9837 Evaluate side-chains 54 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 3.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.061785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.050455 restraints weight = 139676.179| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 3.12 r_work: 0.2797 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.0989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12133 Z= 0.173 Angle : 0.514 5.981 16455 Z= 0.292 Chirality : 0.036 0.128 1883 Planarity : 0.004 0.042 1986 Dihedral : 11.548 72.895 1928 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.51 % Allowed : 2.64 % Favored : 96.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.67 (0.22), residues: 1507 helix: 1.60 (0.15), residues: 1164 sheet: None (None), residues: 0 loop : -0.52 (0.35), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 387 TYR 0.006 0.001 TYR C 340 PHE 0.014 0.001 PHE C 146 TRP 0.013 0.001 TRP B 194 HIS 0.003 0.001 HIS C 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.17 (12133) covalent geometry : angle 0.51365 / 0.29 (16455) hydrogen bonds : bond 0.05055 / 3.37 ( 855) hydrogen bonds : angle 4.84893 / 3.57 ( 2553) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3014 Ramachandran restraints generated. 1507 Oldfield, 0 Emsley, 1507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3014 Ramachandran restraints generated. 1507 Oldfield, 0 Emsley, 1507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 55 time to evaluate : 0.662 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: C 476 MET cc_start: 0.9332 (mtm) cc_final: 0.9111 (mtm) outliers start: 6 outliers final: 2 residues processed: 57 average time/residue: 0.2083 time to fit residues: 18.9742 Evaluate side-chains 55 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 53 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain B residue 377 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 52 optimal weight: 6.9990 chunk 37 optimal weight: 7.9990 chunk 115 optimal weight: 3.9990 chunk 128 optimal weight: 2.9990 chunk 135 optimal weight: 2.9990 chunk 23 optimal weight: 7.9990 chunk 149 optimal weight: 0.6980 chunk 69 optimal weight: 3.9990 chunk 147 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 80 optimal weight: 6.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 346 GLN B 176 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.060709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.049369 restraints weight = 140458.127| |-----------------------------------------------------------------------------| r_work (start): 0.2894 rms_B_bonded: 3.11 r_work: 0.2769 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 12133 Z= 0.181 Angle : 0.490 5.852 16455 Z= 0.277 Chirality : 0.036 0.132 1883 Planarity : 0.004 0.040 1986 Dihedral : 10.465 61.375 1928 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.34 % Allowed : 3.57 % Favored : 96.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.11 (0.22), residues: 1507 helix: 1.94 (0.15), residues: 1166 sheet: None (None), residues: 0 loop : -0.45 (0.35), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 213 TYR 0.006 0.001 TYR C 206 PHE 0.015 0.001 PHE A 464 TRP 0.013 0.001 TRP B 194 HIS 0.004 0.001 HIS C 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.18 (12133) covalent geometry : angle 0.48977 / 0.28 (16455) hydrogen bonds : bond 0.04706 / 3.15 ( 855) hydrogen bonds : angle 4.47614 / 3.32 ( 2553) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3014 Ramachandran restraints generated. 1507 Oldfield, 0 Emsley, 1507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3014 Ramachandran restraints generated. 1507 Oldfield, 0 Emsley, 1507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 52 time to evaluate : 0.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 310 MET cc_start: 0.8970 (tmm) cc_final: 0.8575 (tmm) REVERT: A 453 MET cc_start: 0.8868 (mmm) cc_final: 0.8634 (mmp) REVERT: C 476 MET cc_start: 0.9343 (mtm) cc_final: 0.9017 (mtm) outliers start: 4 outliers final: 3 residues processed: 55 average time/residue: 0.2043 time to fit residues: 17.9955 Evaluate side-chains 54 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 51 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain B residue 377 TRP Chi-restraints excluded: chain C residue 168 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 127 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 110 optimal weight: 8.9990 chunk 121 optimal weight: 4.9990 chunk 150 optimal weight: 7.9990 chunk 57 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 chunk 117 optimal weight: 4.9990 chunk 126 optimal weight: 4.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 445 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.058561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.046831 restraints weight = 143729.296| |-----------------------------------------------------------------------------| r_work (start): 0.2834 rms_B_bonded: 3.12 r_work: 0.2710 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 12133 Z= 0.281 Angle : 0.551 5.600 16455 Z= 0.317 Chirality : 0.038 0.123 1883 Planarity : 0.004 0.045 1986 Dihedral : 10.399 59.877 1928 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.26 % Allowed : 4.43 % Favored : 95.32 % 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: 2.09 (0.22), residues: 1507 helix: 1.94 (0.15), residues: 1168 sheet: None (None), residues: 0 loop : -0.54 (0.34), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 213 TYR 0.008 0.001 TYR A 157 PHE 0.014 0.001 PHE C 146 TRP 0.014 0.001 TRP C 194 HIS 0.005 0.001 HIS C 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00580 / 0.28 (12133) covalent geometry : angle 0.55129 / 0.32 (16455) hydrogen bonds : bond 0.04753 / 3.17 ( 855) hydrogen bonds : angle 4.52055 / 3.36 ( 2553) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3014 Ramachandran restraints generated. 1507 Oldfield, 0 Emsley, 1507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3014 Ramachandran restraints generated. 1507 Oldfield, 0 Emsley, 1507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 51 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 310 MET cc_start: 0.9097 (tmm) cc_final: 0.8702 (tmm) REVERT: A 453 MET cc_start: 0.9066 (mmm) cc_final: 0.8615 (mmm) REVERT: B 144 MET cc_start: 0.9152 (mtm) cc_final: 0.8903 (mtt) REVERT: C 476 MET cc_start: 0.9360 (mtm) cc_final: 0.9009 (mtm) outliers start: 3 outliers final: 3 residues processed: 54 average time/residue: 0.2039 time to fit residues: 17.6368 Evaluate side-chains 54 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 51 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain B residue 377 TRP Chi-restraints excluded: chain C residue 168 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 85 optimal weight: 4.9990 chunk 95 optimal weight: 7.9990 chunk 100 optimal weight: 9.9990 chunk 124 optimal weight: 7.9990 chunk 121 optimal weight: 7.9990 chunk 19 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 88 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 517 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.059293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.047782 restraints weight = 142160.254| |-----------------------------------------------------------------------------| r_work (start): 0.2861 rms_B_bonded: 3.15 r_work: 0.2735 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 12133 Z= 0.182 Angle : 0.477 5.606 16455 Z= 0.271 Chirality : 0.036 0.124 1883 Planarity : 0.003 0.041 1986 Dihedral : 10.048 58.283 1928 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.26 % Allowed : 5.11 % Favored : 94.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.36 (0.22), residues: 1507 helix: 2.13 (0.15), residues: 1171 sheet: None (None), residues: 0 loop : -0.47 (0.34), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 392 TYR 0.006 0.001 TYR C 206 PHE 0.012 0.001 PHE C 146 TRP 0.013 0.001 TRP B 194 HIS 0.004 0.001 HIS C 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.18 (12133) covalent geometry : angle 0.47699 / 0.27 (16455) hydrogen bonds : bond 0.04446 / 2.96 ( 855) hydrogen bonds : angle 4.30318 / 3.20 ( 2553) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3014 Ramachandran restraints generated. 1507 Oldfield, 0 Emsley, 1507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3014 Ramachandran restraints generated. 1507 Oldfield, 0 Emsley, 1507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 51 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 310 MET cc_start: 0.9070 (tmm) cc_final: 0.8666 (tmm) REVERT: A 453 MET cc_start: 0.9006 (mmm) cc_final: 0.8598 (mmm) REVERT: B 144 MET cc_start: 0.9062 (mtm) cc_final: 0.8631 (mtt) REVERT: C 476 MET cc_start: 0.9348 (mtm) cc_final: 0.8961 (mtm) outliers start: 3 outliers final: 2 residues processed: 54 average time/residue: 0.2047 time to fit residues: 17.7358 Evaluate side-chains 53 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 51 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain B residue 377 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 88 optimal weight: 5.9990 chunk 44 optimal weight: 7.9990 chunk 28 optimal weight: 4.9990 chunk 102 optimal weight: 7.9990 chunk 136 optimal weight: 0.6980 chunk 48 optimal weight: 5.9990 chunk 105 optimal weight: 3.9990 chunk 45 optimal weight: 0.6980 chunk 60 optimal weight: 3.9990 chunk 119 optimal weight: 4.9990 chunk 56 optimal weight: 0.6980 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.059841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.048295 restraints weight = 142040.403| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 3.17 r_work: 0.2748 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12133 Z= 0.142 Angle : 0.450 5.589 16455 Z= 0.254 Chirality : 0.035 0.126 1883 Planarity : 0.003 0.039 1986 Dihedral : 9.654 59.785 1928 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.17 % Allowed : 5.45 % Favored : 94.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.61 (0.22), residues: 1507 helix: 2.33 (0.15), residues: 1170 sheet: None (None), residues: 0 loop : -0.42 (0.35), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 392 TYR 0.005 0.001 TYR A 197 PHE 0.010 0.001 PHE B 441 TRP 0.013 0.001 TRP B 194 HIS 0.003 0.001 HIS C 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.14 (12133) covalent geometry : angle 0.44995 / 0.25 (16455) hydrogen bonds : bond 0.04139 / 2.75 ( 855) hydrogen bonds : angle 4.13640 / 3.07 ( 2553) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3014 Ramachandran restraints generated. 1507 Oldfield, 0 Emsley, 1507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3014 Ramachandran restraints generated. 1507 Oldfield, 0 Emsley, 1507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 51 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 310 MET cc_start: 0.9077 (tmm) cc_final: 0.8690 (tmm) REVERT: A 353 MET cc_start: 0.8963 (tpp) cc_final: 0.8634 (tpp) REVERT: A 453 MET cc_start: 0.9034 (mmm) cc_final: 0.8602 (mmm) REVERT: B 144 MET cc_start: 0.9059 (mtm) cc_final: 0.8440 (mtt) REVERT: C 476 MET cc_start: 0.9338 (mtm) cc_final: 0.8926 (mtm) outliers start: 2 outliers final: 2 residues processed: 53 average time/residue: 0.1989 time to fit residues: 16.8584 Evaluate side-chains 53 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 51 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain B residue 377 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 35 optimal weight: 4.9990 chunk 137 optimal weight: 4.9990 chunk 48 optimal weight: 6.9990 chunk 75 optimal weight: 9.9990 chunk 2 optimal weight: 0.9990 chunk 50 optimal weight: 10.0000 chunk 149 optimal weight: 3.9990 chunk 108 optimal weight: 0.2980 chunk 148 optimal weight: 0.9980 chunk 124 optimal weight: 7.9990 chunk 144 optimal weight: 10.0000 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.059774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.048200 restraints weight = 141557.675| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 3.18 r_work: 0.2749 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12133 Z= 0.154 Angle : 0.451 5.542 16455 Z= 0.255 Chirality : 0.035 0.124 1883 Planarity : 0.003 0.039 1986 Dihedral : 9.325 59.896 1928 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.34 % Allowed : 5.53 % Favored : 94.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.73 (0.22), residues: 1507 helix: 2.39 (0.15), residues: 1171 sheet: None (None), residues: 0 loop : -0.33 (0.35), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 213 TYR 0.005 0.001 TYR C 206 PHE 0.012 0.001 PHE C 146 TRP 0.012 0.001 TRP B 194 HIS 0.003 0.000 HIS C 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.15 (12133) covalent geometry : angle 0.45078 / 0.25 (16455) hydrogen bonds : bond 0.04083 / 2.72 ( 855) hydrogen bonds : angle 4.09185 / 3.04 ( 2553) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3014 Ramachandran restraints generated. 1507 Oldfield, 0 Emsley, 1507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3014 Ramachandran restraints generated. 1507 Oldfield, 0 Emsley, 1507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 52 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 310 MET cc_start: 0.9093 (tmm) cc_final: 0.8709 (tmm) REVERT: A 353 MET cc_start: 0.8951 (tpp) cc_final: 0.8602 (tpp) REVERT: A 453 MET cc_start: 0.9023 (mmm) cc_final: 0.8582 (mmm) REVERT: B 144 MET cc_start: 0.9042 (mtm) cc_final: 0.8418 (mtt) REVERT: C 476 MET cc_start: 0.9345 (mtm) cc_final: 0.8930 (mtm) outliers start: 4 outliers final: 3 residues processed: 56 average time/residue: 0.2093 time to fit residues: 18.7862 Evaluate side-chains 54 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 51 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain B residue 377 TRP Chi-restraints excluded: chain C residue 168 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 46 optimal weight: 3.9990 chunk 103 optimal weight: 7.9990 chunk 122 optimal weight: 5.9990 chunk 146 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 65 optimal weight: 4.9990 chunk 125 optimal weight: 9.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 343 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.059355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.047806 restraints weight = 142248.978| |-----------------------------------------------------------------------------| r_work (start): 0.2865 rms_B_bonded: 3.18 r_work: 0.2739 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 12133 Z= 0.176 Angle : 0.466 5.563 16455 Z= 0.263 Chirality : 0.035 0.125 1883 Planarity : 0.003 0.039 1986 Dihedral : 9.230 57.332 1928 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.26 % Allowed : 5.79 % Favored : 93.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.77 (0.22), residues: 1507 helix: 2.43 (0.15), residues: 1171 sheet: None (None), residues: 0 loop : -0.34 (0.35), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 213 TYR 0.006 0.001 TYR C 206 PHE 0.011 0.001 PHE C 146 TRP 0.012 0.001 TRP B 194 HIS 0.003 0.001 HIS C 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.18 (12133) covalent geometry : angle 0.46572 / 0.26 (16455) hydrogen bonds : bond 0.04103 / 2.74 ( 855) hydrogen bonds : angle 4.09798 / 3.04 ( 2553) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3014 Ramachandran restraints generated. 1507 Oldfield, 0 Emsley, 1507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3014 Ramachandran restraints generated. 1507 Oldfield, 0 Emsley, 1507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 51 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 310 MET cc_start: 0.9103 (tmm) cc_final: 0.8723 (tmm) REVERT: A 353 MET cc_start: 0.8956 (tpp) cc_final: 0.8607 (tpp) REVERT: A 453 MET cc_start: 0.9024 (mmm) cc_final: 0.8582 (mmm) REVERT: B 144 MET cc_start: 0.9048 (mtm) cc_final: 0.8435 (mtt) REVERT: C 476 MET cc_start: 0.9338 (mtm) cc_final: 0.8925 (mtm) outliers start: 3 outliers final: 3 residues processed: 54 average time/residue: 0.2125 time to fit residues: 18.3336 Evaluate side-chains 54 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 51 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain B residue 377 TRP Chi-restraints excluded: chain C residue 168 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 112 optimal weight: 5.9990 chunk 69 optimal weight: 3.9990 chunk 135 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 133 optimal weight: 0.9980 chunk 52 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 121 optimal weight: 5.9990 chunk 49 optimal weight: 6.9990 chunk 130 optimal weight: 5.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.058523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.047020 restraints weight = 143544.044| |-----------------------------------------------------------------------------| r_work (start): 0.2841 rms_B_bonded: 3.14 r_work: 0.2713 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 12133 Z= 0.240 Angle : 0.511 5.606 16455 Z= 0.291 Chirality : 0.036 0.119 1883 Planarity : 0.003 0.040 1986 Dihedral : 9.409 57.975 1928 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 0.26 % Allowed : 5.96 % Favored : 93.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.63 (0.22), residues: 1507 helix: 2.34 (0.15), residues: 1171 sheet: None (None), residues: 0 loop : -0.43 (0.35), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 213 TYR 0.008 0.001 TYR C 206 PHE 0.014 0.001 PHE C 146 TRP 0.014 0.001 TRP C 194 HIS 0.004 0.001 HIS C 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00502 / 0.24 (12133) covalent geometry : angle 0.51087 / 0.29 (16455) hydrogen bonds : bond 0.04336 / 2.89 ( 855) hydrogen bonds : angle 4.23123 / 3.14 ( 2553) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3014 Ramachandran restraints generated. 1507 Oldfield, 0 Emsley, 1507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3014 Ramachandran restraints generated. 1507 Oldfield, 0 Emsley, 1507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 51 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 310 MET cc_start: 0.9116 (tmm) cc_final: 0.8746 (tmm) REVERT: A 353 MET cc_start: 0.8969 (tpp) cc_final: 0.8587 (tpp) REVERT: A 453 MET cc_start: 0.9066 (mmm) cc_final: 0.8586 (mmm) REVERT: B 144 MET cc_start: 0.9037 (mtm) cc_final: 0.8390 (mtt) outliers start: 3 outliers final: 3 residues processed: 54 average time/residue: 0.2022 time to fit residues: 17.4644 Evaluate side-chains 54 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 51 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain B residue 377 TRP Chi-restraints excluded: chain C residue 168 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 119 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 132 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 108 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 71 optimal weight: 7.9990 chunk 87 optimal weight: 0.8980 chunk 63 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.059662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.048070 restraints weight = 141451.631| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 3.07 r_work: 0.2765 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12133 Z= 0.128 Angle : 0.444 5.808 16455 Z= 0.249 Chirality : 0.035 0.126 1883 Planarity : 0.003 0.038 1986 Dihedral : 9.084 55.800 1928 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.26 % Allowed : 5.96 % Favored : 93.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.81 (0.22), residues: 1507 helix: 2.47 (0.15), residues: 1171 sheet: None (None), residues: 0 loop : -0.37 (0.35), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 392 TYR 0.005 0.001 TYR A 197 PHE 0.010 0.001 PHE C 146 TRP 0.013 0.001 TRP A 377 HIS 0.003 0.001 HIS C 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.13 (12133) covalent geometry : angle 0.44429 / 0.25 (16455) hydrogen bonds : bond 0.04061 / 2.70 ( 855) hydrogen bonds : angle 4.03442 / 3.00 ( 2553) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3014 Ramachandran restraints generated. 1507 Oldfield, 0 Emsley, 1507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3014 Ramachandran restraints generated. 1507 Oldfield, 0 Emsley, 1507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 52 time to evaluate : 0.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 310 MET cc_start: 0.9083 (tmm) cc_final: 0.8703 (tmm) REVERT: A 353 MET cc_start: 0.8919 (tpp) cc_final: 0.8549 (tpp) REVERT: A 453 MET cc_start: 0.9039 (mmm) cc_final: 0.8542 (mmm) REVERT: B 144 MET cc_start: 0.9028 (mtm) cc_final: 0.8380 (mtt) REVERT: C 476 MET cc_start: 0.9382 (mtm) cc_final: 0.8973 (mtm) outliers start: 3 outliers final: 3 residues processed: 55 average time/residue: 0.2174 time to fit residues: 19.1104 Evaluate side-chains 54 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 51 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain B residue 377 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 146 optimal weight: 6.9990 chunk 48 optimal weight: 0.7980 chunk 34 optimal weight: 0.0370 chunk 79 optimal weight: 1.9990 chunk 143 optimal weight: 10.0000 chunk 60 optimal weight: 7.9990 chunk 135 optimal weight: 3.9990 chunk 94 optimal weight: 8.9990 chunk 132 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 110 optimal weight: 2.9990 overall best weight: 1.9664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.059712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.048129 restraints weight = 141071.986| |-----------------------------------------------------------------------------| r_work (start): 0.2898 rms_B_bonded: 3.07 r_work: 0.2767 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12133 Z= 0.141 Angle : 0.443 5.554 16455 Z= 0.249 Chirality : 0.035 0.125 1883 Planarity : 0.003 0.038 1986 Dihedral : 8.823 57.597 1928 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.34 % Allowed : 5.87 % Favored : 93.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.92 (0.22), residues: 1507 helix: 2.54 (0.15), residues: 1171 sheet: None (None), residues: 0 loop : -0.33 (0.35), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 213 TYR 0.005 0.001 TYR C 206 PHE 0.013 0.001 PHE C 146 TRP 0.012 0.001 TRP B 194 HIS 0.002 0.000 HIS C 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.14 (12133) covalent geometry : angle 0.44261 / 0.25 (16455) hydrogen bonds : bond 0.03935 / 2.62 ( 855) hydrogen bonds : angle 3.99304 / 2.96 ( 2553) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3981.09 seconds wall clock time: 68 minutes 35.13 seconds (4115.13 seconds total)