Starting phenix.real_space_refine on Sat Aug 23 02:15:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wcw_37450/08_2025/8wcw_37450.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wcw_37450/08_2025/8wcw_37450.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wcw_37450/08_2025/8wcw_37450.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wcw_37450/08_2025/8wcw_37450.map" model { file = "/net/cci-nas-00/data/ceres_data/8wcw_37450/08_2025/8wcw_37450.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wcw_37450/08_2025/8wcw_37450.cif" } resolution = 3.11 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= 0.066 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 33 5.16 5 C 5751 2.51 5 N 1600 2.21 5 O 1678 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 78 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9062 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 573, 4340 Classifications: {'peptide': 573} Link IDs: {'PTRANS': 19, 'TRANS': 553} Chain: "B" Number of atoms: 4722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 616, 4722 Classifications: {'peptide': 616} Link IDs: {'PTRANS': 19, 'TRANS': 596} Time building chain proxies: 2.44, per 1000 atoms: 0.27 Number of scatterers: 9062 At special positions: 0 Unit cell: (69.888, 97.344, 148.928, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 33 16.00 O 1678 8.00 N 1600 7.00 C 5751 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 0.87 Conformation dependent library (CDL) restraints added in 253.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2190 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 5 sheets defined 66.9% alpha, 4.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 1 through 7 Processing helix chain 'A' and resid 10 through 12 No H-bonds generated for 'chain 'A' and resid 10 through 12' Processing helix chain 'A' and resid 13 through 45 removed outlier: 3.711A pdb=" N LEU A 17 " --> pdb=" O TYR A 13 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE A 26 " --> pdb=" O VAL A 22 " (cutoff:3.500A) Proline residue: A 35 - end of helix Processing helix chain 'A' and resid 51 through 89 removed outlier: 4.765A pdb=" N GLY A 87 " --> pdb=" O ALA A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 99 removed outlier: 3.600A pdb=" N HIS A 97 " --> pdb=" O ALA A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 135 removed outlier: 4.104A pdb=" N ASP A 121 " --> pdb=" O ARG A 117 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N VAL A 122 " --> pdb=" O THR A 118 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLY A 123 " --> pdb=" O THR A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 154 Processing helix chain 'A' and resid 157 through 203 removed outlier: 4.077A pdb=" N LEU A 161 " --> pdb=" O LEU A 157 " (cutoff:3.500A) Proline residue: A 166 - end of helix Proline residue: A 181 - end of helix removed outlier: 3.671A pdb=" N GLY A 203 " --> pdb=" O ASP A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 212 removed outlier: 4.011A pdb=" N ARG A 212 " --> pdb=" O ALA A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 266 removed outlier: 3.561A pdb=" N VAL A 218 " --> pdb=" O PRO A 214 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ARG A 219 " --> pdb=" O LEU A 215 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N TRP A 237 " --> pdb=" O GLU A 233 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLN A 238 " --> pdb=" O ALA A 234 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N LEU A 240 " --> pdb=" O ARG A 236 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N LEU A 242 " --> pdb=" O GLN A 238 " (cutoff:3.500A) Proline residue: A 243 - end of helix removed outlier: 4.110A pdb=" N ALA A 266 " --> pdb=" O LEU A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 295 removed outlier: 3.741A pdb=" N LEU A 278 " --> pdb=" O LEU A 274 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ALA A 279 " --> pdb=" O ILE A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 314 removed outlier: 3.756A pdb=" N ALA A 301 " --> pdb=" O ILE A 297 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THR A 314 " --> pdb=" O GLU A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 382 Processing helix chain 'A' and resid 403 through 410 Processing helix chain 'A' and resid 425 through 434 removed outlier: 4.469A pdb=" N GLY A 432 " --> pdb=" O ASN A 428 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ARG A 433 " --> pdb=" O LEU A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 447 Processing helix chain 'A' and resid 450 through 456 removed outlier: 3.664A pdb=" N VAL A 454 " --> pdb=" O ALA A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 489 removed outlier: 4.074A pdb=" N ARG A 488 " --> pdb=" O ARG A 484 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ARG A 489 " --> pdb=" O ALA A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 518 Processing helix chain 'A' and resid 552 through 559 Processing helix chain 'A' and resid 560 through 571 removed outlier: 4.502A pdb=" N ALA A 564 " --> pdb=" O CYS A 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 29 Processing helix chain 'B' and resid 31 through 51 removed outlier: 3.581A pdb=" N GLY B 49 " --> pdb=" O GLY B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 68 removed outlier: 3.746A pdb=" N GLY B 66 " --> pdb=" O LEU B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 88 Processing helix chain 'B' and resid 90 through 99 Processing helix chain 'B' and resid 109 through 158 removed outlier: 3.556A pdb=" N VAL B 113 " --> pdb=" O ASP B 109 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA B 148 " --> pdb=" O ARG B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 168 removed outlier: 3.754A pdb=" N PHE B 165 " --> pdb=" O PRO B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 213 removed outlier: 4.370A pdb=" N ASP B 180 " --> pdb=" O ARG B 176 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N VAL B 181 " --> pdb=" O VAL B 177 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASP B 182 " --> pdb=" O THR B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 223 Processing helix chain 'B' and resid 223 through 261 removed outlier: 3.670A pdb=" N SER B 227 " --> pdb=" O THR B 223 " (cutoff:3.500A) Proline residue: B 240 - end of helix removed outlier: 3.746A pdb=" N ALA B 244 " --> pdb=" O PRO B 240 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLN B 245 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 269 Processing helix chain 'B' and resid 272 through 324 removed outlier: 3.678A pdb=" N ALA B 276 " --> pdb=" O ARG B 272 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER B 289 " --> pdb=" O GLU B 285 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLY B 292 " --> pdb=" O GLN B 288 " (cutoff:3.500A) Proline residue: B 302 - end of helix removed outlier: 4.290A pdb=" N MET B 305 " --> pdb=" O SER B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 345 removed outlier: 3.576A pdb=" N ILE B 333 " --> pdb=" O THR B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 348 No H-bonds generated for 'chain 'B' and resid 346 through 348' Processing helix chain 'B' and resid 349 through 371 Processing helix chain 'B' and resid 431 through 438 Processing helix chain 'B' and resid 460 through 466 Processing helix chain 'B' and resid 480 through 487 Processing helix chain 'B' and resid 493 through 504 Processing helix chain 'B' and resid 506 through 513 Processing helix chain 'B' and resid 532 through 544 removed outlier: 3.606A pdb=" N ALA B 544 " --> pdb=" O ARG B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 573 Processing helix chain 'B' and resid 585 through 591 Processing helix chain 'B' and resid 610 through 615 Processing helix chain 'B' and resid 617 through 624 removed outlier: 3.743A pdb=" N GLU B 621 " --> pdb=" O GLY B 617 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 357 removed outlier: 5.188A pdb=" N VAL A 354 " --> pdb=" O ASP A 338 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ARG A 393 " --> pdb=" O GLY A 335 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 412 through 414 removed outlier: 3.647A pdb=" N SER A 527 " --> pdb=" O VAL A 366 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N GLY A 368 " --> pdb=" O SER A 527 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ALA A 365 " --> pdb=" O VAL A 540 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N ILE A 542 " --> pdb=" O ALA A 365 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N VAL A 367 " --> pdb=" O ILE A 542 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 423 through 424 removed outlier: 3.577A pdb=" N GLY A 423 " --> pdb=" O VAL A 465 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 391 through 397 removed outlier: 3.834A pdb=" N VAL B 396 " --> pdb=" O SER B 445 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N SER B 445 " --> pdb=" O VAL B 396 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N VAL B 453 " --> pdb=" O ILE B 450 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 469 through 470 removed outlier: 6.765A pdb=" N VAL B 470 " --> pdb=" O ASP B 552 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N LEU B 549 " --> pdb=" O PHE B 580 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N ILE B 582 " --> pdb=" O LEU B 549 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N LEU B 551 " --> pdb=" O ILE B 582 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 571 hydrogen bonds defined for protein. 1704 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: 1.45 Time building geometry restraints manager: 1.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3056 1.34 - 1.46: 1312 1.46 - 1.57: 4787 1.57 - 1.69: 0 1.69 - 1.81: 61 Bond restraints: 9216 Sorted by residual: bond pdb=" C SER B 301 " pdb=" N PRO B 302 " ideal model delta sigma weight residual 1.332 1.371 -0.039 8.20e-03 1.49e+04 2.22e+01 bond pdb=" C LEU B 29 " pdb=" N PRO B 30 " ideal model delta sigma weight residual 1.333 1.363 -0.030 1.44e-02 4.82e+03 4.29e+00 bond pdb=" CB THR A 36 " pdb=" CG2 THR A 36 " ideal model delta sigma weight residual 1.521 1.473 0.048 3.30e-02 9.18e+02 2.15e+00 bond pdb=" CA SER B 301 " pdb=" C SER B 301 " ideal model delta sigma weight residual 1.521 1.534 -0.012 1.11e-02 8.12e+03 1.25e+00 bond pdb=" C GLU B 415 " pdb=" N PRO B 416 " ideal model delta sigma weight residual 1.334 1.359 -0.025 2.34e-02 1.83e+03 1.17e+00 ... (remaining 9211 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.28: 12339 2.28 - 4.56: 176 4.56 - 6.84: 29 6.84 - 9.12: 1 9.12 - 11.41: 1 Bond angle restraints: 12546 Sorted by residual: angle pdb=" N GLY B 107 " pdb=" CA GLY B 107 " pdb=" C GLY B 107 " ideal model delta sigma weight residual 113.18 124.59 -11.41 2.37e+00 1.78e-01 2.32e+01 angle pdb=" C GLY B 107 " pdb=" N VAL B 108 " pdb=" CA VAL B 108 " ideal model delta sigma weight residual 121.97 115.25 6.72 1.80e+00 3.09e-01 1.39e+01 angle pdb=" N ALA A 47 " pdb=" CA ALA A 47 " pdb=" C ALA A 47 " ideal model delta sigma weight residual 114.75 110.91 3.84 1.26e+00 6.30e-01 9.28e+00 angle pdb=" N PHE A 499 " pdb=" CA PHE A 499 " pdb=" C PHE A 499 " ideal model delta sigma weight residual 114.75 110.92 3.83 1.26e+00 6.30e-01 9.22e+00 angle pdb=" N VAL A 163 " pdb=" CA VAL A 163 " pdb=" C VAL A 163 " ideal model delta sigma weight residual 113.42 109.97 3.45 1.17e+00 7.31e-01 8.70e+00 ... (remaining 12541 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 4918 17.81 - 35.62: 456 35.62 - 53.43: 96 53.43 - 71.24: 12 71.24 - 89.06: 5 Dihedral angle restraints: 5487 sinusoidal: 2086 harmonic: 3401 Sorted by residual: dihedral pdb=" CA VAL A 46 " pdb=" C VAL A 46 " pdb=" N ALA A 47 " pdb=" CA ALA A 47 " ideal model delta harmonic sigma weight residual 180.00 151.07 28.93 0 5.00e+00 4.00e-02 3.35e+01 dihedral pdb=" CA SER B 600 " pdb=" C SER B 600 " pdb=" N GLY B 601 " pdb=" CA GLY B 601 " ideal model delta harmonic sigma weight residual -180.00 -157.57 -22.43 0 5.00e+00 4.00e-02 2.01e+01 dihedral pdb=" CA ASP A 496 " pdb=" C ASP A 496 " pdb=" N ASP A 497 " pdb=" CA ASP A 497 " ideal model delta harmonic sigma weight residual 180.00 157.66 22.34 0 5.00e+00 4.00e-02 2.00e+01 ... (remaining 5484 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 851 0.033 - 0.066: 469 0.066 - 0.098: 138 0.098 - 0.131: 44 0.131 - 0.164: 9 Chirality restraints: 1511 Sorted by residual: chirality pdb=" CA GLU B 376 " pdb=" N GLU B 376 " pdb=" C GLU B 376 " pdb=" CB GLU B 376 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.72e-01 chirality pdb=" CA PRO B 53 " pdb=" N PRO B 53 " pdb=" C PRO B 53 " pdb=" CB PRO B 53 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.23e-01 chirality pdb=" CA SER B 301 " pdb=" N SER B 301 " pdb=" C SER B 301 " pdb=" CB SER B 301 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.48e-01 ... (remaining 1508 not shown) Planarity restraints: 1613 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG B 602 " 0.013 2.00e-02 2.50e+03 2.62e-02 6.86e+00 pdb=" C ARG B 602 " -0.045 2.00e-02 2.50e+03 pdb=" O ARG B 602 " 0.017 2.00e-02 2.50e+03 pdb=" N ILE B 603 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 103 " -0.010 2.00e-02 2.50e+03 2.09e-02 4.35e+00 pdb=" C ALA A 103 " 0.036 2.00e-02 2.50e+03 pdb=" O ALA A 103 " -0.014 2.00e-02 2.50e+03 pdb=" N GLU A 104 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER B 213 " 0.034 5.00e-02 4.00e+02 5.19e-02 4.31e+00 pdb=" N PRO B 214 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO B 214 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 214 " 0.029 5.00e-02 4.00e+02 ... (remaining 1610 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1529 2.76 - 3.29: 9332 3.29 - 3.83: 14667 3.83 - 4.36: 16809 4.36 - 4.90: 29898 Nonbonded interactions: 72235 Sorted by model distance: nonbonded pdb=" OG1 THR A 340 " pdb=" OG1 THR A 388 " model vdw 2.219 3.040 nonbonded pdb=" O HIS A 97 " pdb=" OG1 THR A 100 " model vdw 2.256 3.040 nonbonded pdb=" O ARG B 168 " pdb=" NH1 ARG B 170 " model vdw 2.282 3.120 nonbonded pdb=" NH2 ARG B 489 " pdb=" OE1 GLU B 496 " model vdw 2.284 3.120 nonbonded pdb=" O PRO B 416 " pdb=" OG1 THR B 578 " model vdw 2.289 3.040 ... (remaining 72230 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.650 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 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 : 0.006 0.048 9216 Z= 0.261 Angle : 0.726 11.406 12546 Z= 0.419 Chirality : 0.044 0.164 1511 Planarity : 0.004 0.052 1613 Dihedral : 14.371 89.055 3297 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.04 % Favored : 89.96 % Rotamer: Outliers : 0.21 % Allowed : 8.28 % Favored : 91.51 % 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 aren not related in a simple way. whole: -3.12 (0.21), residues: 1185 helix: -0.96 (0.17), residues: 772 sheet: -3.72 (0.73), residues: 27 loop : -4.23 (0.22), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 27 TYR 0.019 0.002 TYR A 431 PHE 0.016 0.002 PHE A 341 TRP 0.008 0.001 TRP A 442 HIS 0.004 0.001 HIS A 152 Details of bonding type rmsd covalent geometry : bond 0.00607 ( 9216) covalent geometry : angle 0.72642 (12546) hydrogen bonds : bond 0.12511 ( 571) hydrogen bonds : angle 5.88077 ( 1704) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 102 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 MET cc_start: 0.8331 (mmp) cc_final: 0.7891 (mmp) REVERT: A 195 ARG cc_start: 0.7474 (ttp80) cc_final: 0.7194 (ttp-110) REVERT: A 337 HIS cc_start: 0.7519 (m-70) cc_final: 0.7242 (m170) REVERT: B 139 ASN cc_start: 0.8244 (t0) cc_final: 0.7964 (t0) REVERT: B 509 PHE cc_start: 0.7632 (t80) cc_final: 0.7066 (t80) REVERT: B 594 LEU cc_start: 0.8337 (tp) cc_final: 0.7862 (tp) outliers start: 2 outliers final: 0 residues processed: 104 average time/residue: 0.1463 time to fit residues: 19.5539 Evaluate side-chains 84 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 10.0000 chunk 49 optimal weight: 0.0270 chunk 97 optimal weight: 0.4980 chunk 113 optimal weight: 5.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 117 optimal weight: 10.0000 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN A 187 GLN A 225 GLN A 416 GLN A 428 ASN A 471 ASN A 528 GLN B 245 GLN B 344 ASN B 484 ASN B 609 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.136557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.096923 restraints weight = 12578.191| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 2.66 r_work: 0.3069 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.1225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9216 Z= 0.136 Angle : 0.600 10.303 12546 Z= 0.317 Chirality : 0.041 0.138 1511 Planarity : 0.004 0.053 1613 Dihedral : 4.818 30.222 1303 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.37 % Favored : 90.63 % Rotamer: Outliers : 1.57 % Allowed : 12.58 % Favored : 85.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 aren not related in a simple way. whole: -1.29 (0.24), residues: 1185 helix: 0.61 (0.19), residues: 761 sheet: -3.23 (0.79), residues: 28 loop : -3.73 (0.23), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 433 TYR 0.017 0.001 TYR B 400 PHE 0.012 0.001 PHE B 296 TRP 0.010 0.001 TRP A 408 HIS 0.003 0.001 HIS A 337 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 9216) covalent geometry : angle 0.59970 (12546) hydrogen bonds : bond 0.05495 ( 571) hydrogen bonds : angle 4.63460 ( 1704) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 97 time to evaluate : 0.349 Fit side-chains REVERT: A 29 MET cc_start: 0.8258 (mmp) cc_final: 0.7980 (mmm) REVERT: A 310 GLU cc_start: 0.8618 (tt0) cc_final: 0.8259 (tt0) REVERT: A 455 ARG cc_start: 0.8322 (tpm170) cc_final: 0.8056 (ttm110) REVERT: A 489 ARG cc_start: 0.8075 (mtm110) cc_final: 0.7282 (mpt180) REVERT: B 15 ARG cc_start: 0.8925 (ptt90) cc_final: 0.8606 (ptt90) REVERT: B 139 ASN cc_start: 0.8209 (t0) cc_final: 0.7946 (t0) REVERT: B 209 MET cc_start: 0.8763 (mtt) cc_final: 0.8470 (mtm) REVERT: B 438 MET cc_start: 0.8657 (mmm) cc_final: 0.8127 (mmt) REVERT: B 509 PHE cc_start: 0.7749 (t80) cc_final: 0.7197 (t80) REVERT: B 594 LEU cc_start: 0.7791 (tp) cc_final: 0.7222 (tp) outliers start: 15 outliers final: 5 residues processed: 107 average time/residue: 0.1146 time to fit residues: 16.5771 Evaluate side-chains 93 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 88 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 ILE Chi-restraints excluded: chain A residue 550 ILE Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 223 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 42 optimal weight: 0.9990 chunk 99 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 111 optimal weight: 8.9990 chunk 88 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 39 optimal weight: 9.9990 chunk 103 optimal weight: 0.4980 chunk 35 optimal weight: 10.0000 chunk 117 optimal weight: 0.0010 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.136163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.097520 restraints weight = 12575.537| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 2.64 r_work: 0.3083 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9216 Z= 0.132 Angle : 0.580 9.708 12546 Z= 0.305 Chirality : 0.040 0.156 1511 Planarity : 0.004 0.051 1613 Dihedral : 4.603 29.387 1303 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.95 % Favored : 91.05 % Rotamer: Outliers : 1.68 % Allowed : 15.83 % Favored : 82.49 % 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 aren not related in a simple way. whole: -0.61 (0.25), residues: 1185 helix: 1.14 (0.19), residues: 766 sheet: -2.80 (0.82), residues: 27 loop : -3.55 (0.24), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 433 TYR 0.014 0.001 TYR B 400 PHE 0.011 0.001 PHE B 296 TRP 0.007 0.001 TRP A 159 HIS 0.003 0.000 HIS A 337 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 9216) covalent geometry : angle 0.57997 (12546) hydrogen bonds : bond 0.05216 ( 571) hydrogen bonds : angle 4.43033 ( 1704) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 94 time to evaluate : 0.349 Fit side-chains REVERT: A 128 LEU cc_start: 0.8106 (OUTLIER) cc_final: 0.7826 (tp) REVERT: A 310 GLU cc_start: 0.8630 (tt0) cc_final: 0.8317 (tt0) REVERT: A 417 ARG cc_start: 0.7404 (ppt170) cc_final: 0.7112 (ppt170) REVERT: A 455 ARG cc_start: 0.8270 (tpm170) cc_final: 0.7982 (ttm110) REVERT: A 489 ARG cc_start: 0.8037 (mtm110) cc_final: 0.7242 (mpt180) REVERT: A 509 ARG cc_start: 0.8125 (OUTLIER) cc_final: 0.7710 (ptp90) REVERT: B 15 ARG cc_start: 0.8969 (ptt90) cc_final: 0.8647 (ptt90) REVERT: B 139 ASN cc_start: 0.8221 (t0) cc_final: 0.7938 (t0) REVERT: B 509 PHE cc_start: 0.7741 (t80) cc_final: 0.7214 (t80) REVERT: B 594 LEU cc_start: 0.7753 (tp) cc_final: 0.7394 (tp) outliers start: 16 outliers final: 7 residues processed: 106 average time/residue: 0.1011 time to fit residues: 14.8318 Evaluate side-chains 95 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 86 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 378 ILE Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 509 ARG Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 511 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 48 optimal weight: 0.9980 chunk 98 optimal weight: 5.9990 chunk 77 optimal weight: 0.9980 chunk 102 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 92 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 chunk 91 optimal weight: 0.9990 chunk 82 optimal weight: 0.7980 chunk 88 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.136414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.097632 restraints weight = 12687.330| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 2.68 r_work: 0.3072 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9216 Z= 0.135 Angle : 0.576 9.511 12546 Z= 0.302 Chirality : 0.040 0.175 1511 Planarity : 0.004 0.049 1613 Dihedral : 4.516 29.316 1303 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.61 % Favored : 91.39 % Rotamer: Outliers : 2.41 % Allowed : 16.46 % Favored : 81.13 % 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 aren not related in a simple way. whole: -0.31 (0.25), residues: 1185 helix: 1.34 (0.19), residues: 771 sheet: -2.52 (0.86), residues: 27 loop : -3.42 (0.25), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 433 TYR 0.014 0.001 TYR B 400 PHE 0.010 0.001 PHE B 296 TRP 0.006 0.001 TRP A 159 HIS 0.017 0.001 HIS A 337 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 9216) covalent geometry : angle 0.57608 (12546) hydrogen bonds : bond 0.05189 ( 571) hydrogen bonds : angle 4.35717 ( 1704) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 91 time to evaluate : 0.218 Fit side-chains REVERT: A 29 MET cc_start: 0.8020 (OUTLIER) cc_final: 0.7654 (mmp) REVERT: A 310 GLU cc_start: 0.8664 (tt0) cc_final: 0.8347 (tt0) REVERT: A 417 ARG cc_start: 0.7364 (ppt170) cc_final: 0.6990 (ppt170) REVERT: A 431 TYR cc_start: 0.8024 (OUTLIER) cc_final: 0.6545 (m-80) REVERT: A 435 ASP cc_start: 0.6179 (OUTLIER) cc_final: 0.5977 (p0) REVERT: A 455 ARG cc_start: 0.8252 (tpm170) cc_final: 0.7957 (ttm110) REVERT: A 489 ARG cc_start: 0.7921 (mtm110) cc_final: 0.7094 (mpt180) REVERT: A 509 ARG cc_start: 0.8074 (OUTLIER) cc_final: 0.7625 (ptp-170) REVERT: B 15 ARG cc_start: 0.9000 (ptt90) cc_final: 0.8660 (ptt90) REVERT: B 139 ASN cc_start: 0.8201 (t0) cc_final: 0.7925 (t0) REVERT: B 430 LYS cc_start: 0.6568 (mtpp) cc_final: 0.6358 (mtpt) REVERT: B 509 PHE cc_start: 0.7744 (t80) cc_final: 0.7248 (t80) REVERT: B 594 LEU cc_start: 0.7600 (tp) cc_final: 0.7188 (tp) REVERT: B 622 MET cc_start: 0.8635 (tpp) cc_final: 0.8392 (tpt) outliers start: 23 outliers final: 13 residues processed: 110 average time/residue: 0.0973 time to fit residues: 14.3816 Evaluate side-chains 104 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 87 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 29 MET Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 378 ILE Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 431 TYR Chi-restraints excluded: chain A residue 435 ASP Chi-restraints excluded: chain A residue 509 ARG Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 400 TYR Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 511 HIS Chi-restraints excluded: chain B residue 519 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 46 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 111 optimal weight: 4.9990 chunk 49 optimal weight: 0.0020 chunk 28 optimal weight: 0.8980 chunk 78 optimal weight: 0.1980 chunk 30 optimal weight: 3.9990 chunk 96 optimal weight: 6.9990 chunk 114 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 overall best weight: 0.7790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.137118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.098243 restraints weight = 12580.782| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 2.65 r_work: 0.3085 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9216 Z= 0.131 Angle : 0.556 7.688 12546 Z= 0.293 Chirality : 0.040 0.185 1511 Planarity : 0.004 0.048 1613 Dihedral : 4.420 29.443 1303 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.35 % Favored : 91.65 % Rotamer: Outliers : 2.41 % Allowed : 16.56 % Favored : 81.03 % 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 aren not related in a simple way. whole: -0.17 (0.25), residues: 1185 helix: 1.42 (0.19), residues: 780 sheet: -2.29 (0.89), residues: 27 loop : -3.41 (0.25), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 433 TYR 0.010 0.001 TYR B 400 PHE 0.010 0.001 PHE B 296 TRP 0.006 0.001 TRP A 159 HIS 0.003 0.000 HIS A 337 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 9216) covalent geometry : angle 0.55629 (12546) hydrogen bonds : bond 0.05075 ( 571) hydrogen bonds : angle 4.29886 ( 1704) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 92 time to evaluate : 0.309 Fit side-chains REVERT: A 135 MET cc_start: 0.7565 (ttm) cc_final: 0.7304 (ttm) REVERT: A 297 ILE cc_start: 0.7235 (tp) cc_final: 0.6935 (pt) REVERT: A 310 GLU cc_start: 0.8685 (tt0) cc_final: 0.8380 (tt0) REVERT: A 417 ARG cc_start: 0.7360 (ppt170) cc_final: 0.6917 (ppt170) REVERT: A 431 TYR cc_start: 0.8070 (OUTLIER) cc_final: 0.6603 (m-80) REVERT: A 455 ARG cc_start: 0.8227 (tpm170) cc_final: 0.7965 (ttm110) REVERT: A 489 ARG cc_start: 0.7885 (mtm110) cc_final: 0.7043 (mpt180) REVERT: A 509 ARG cc_start: 0.8017 (OUTLIER) cc_final: 0.7579 (ptp-170) REVERT: B 15 ARG cc_start: 0.9061 (ptt90) cc_final: 0.8775 (ptt90) REVERT: B 139 ASN cc_start: 0.8206 (t0) cc_final: 0.7941 (t0) REVERT: B 438 MET cc_start: 0.8551 (mmm) cc_final: 0.7959 (mmt) REVERT: B 509 PHE cc_start: 0.7736 (t80) cc_final: 0.7216 (t80) REVERT: B 594 LEU cc_start: 0.7641 (tp) cc_final: 0.7218 (tp) REVERT: B 622 MET cc_start: 0.8629 (tpp) cc_final: 0.8395 (tpt) outliers start: 23 outliers final: 12 residues processed: 110 average time/residue: 0.1065 time to fit residues: 15.8636 Evaluate side-chains 102 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 88 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 378 ILE Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 431 TYR Chi-restraints excluded: chain A residue 509 ARG Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 400 TYR Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 511 HIS Chi-restraints excluded: chain B residue 519 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 21 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 chunk 52 optimal weight: 0.2980 chunk 25 optimal weight: 0.6980 chunk 11 optimal weight: 6.9990 chunk 83 optimal weight: 3.9990 chunk 115 optimal weight: 7.9990 chunk 64 optimal weight: 0.0970 chunk 40 optimal weight: 0.7980 chunk 54 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.138861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.099928 restraints weight = 12720.483| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 2.69 r_work: 0.3112 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9216 Z= 0.123 Angle : 0.543 6.987 12546 Z= 0.286 Chirality : 0.040 0.186 1511 Planarity : 0.004 0.047 1613 Dihedral : 4.346 29.046 1303 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.35 % Favored : 91.65 % Rotamer: Outliers : 2.52 % Allowed : 17.30 % Favored : 80.19 % 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 aren not related in a simple way. whole: 0.06 (0.25), residues: 1185 helix: 1.59 (0.19), residues: 779 sheet: -2.25 (0.88), residues: 27 loop : -3.30 (0.25), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 383 TYR 0.008 0.001 TYR B 400 PHE 0.011 0.001 PHE A 293 TRP 0.006 0.001 TRP A 159 HIS 0.003 0.000 HIS B 609 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 9216) covalent geometry : angle 0.54335 (12546) hydrogen bonds : bond 0.04802 ( 571) hydrogen bonds : angle 4.20456 ( 1704) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 98 time to evaluate : 0.252 Fit side-chains REVERT: A 297 ILE cc_start: 0.7275 (tp) cc_final: 0.7023 (pt) REVERT: A 417 ARG cc_start: 0.7369 (ppt170) cc_final: 0.6915 (ppt170) REVERT: A 431 TYR cc_start: 0.8079 (OUTLIER) cc_final: 0.6617 (m-80) REVERT: A 455 ARG cc_start: 0.8215 (tpm170) cc_final: 0.7958 (ttm110) REVERT: A 489 ARG cc_start: 0.7883 (mtm110) cc_final: 0.7086 (mpt180) REVERT: B 15 ARG cc_start: 0.9055 (ptt90) cc_final: 0.8819 (ptt90) REVERT: B 139 ASN cc_start: 0.8249 (t0) cc_final: 0.7987 (t0) REVERT: B 209 MET cc_start: 0.8692 (mtt) cc_final: 0.8381 (mtm) REVERT: B 345 GLN cc_start: 0.8562 (tp40) cc_final: 0.8342 (tp40) REVERT: B 509 PHE cc_start: 0.7746 (t80) cc_final: 0.7243 (t80) REVERT: B 548 LEU cc_start: 0.7444 (OUTLIER) cc_final: 0.7226 (tt) REVERT: B 594 LEU cc_start: 0.7661 (tp) cc_final: 0.7224 (tp) REVERT: B 622 MET cc_start: 0.8659 (tpp) cc_final: 0.8430 (tpt) outliers start: 24 outliers final: 14 residues processed: 116 average time/residue: 0.0847 time to fit residues: 13.6473 Evaluate side-chains 110 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 94 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 378 ILE Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 431 TYR Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 400 TYR Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 469 MET Chi-restraints excluded: chain B residue 511 HIS Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain B residue 548 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 116 optimal weight: 6.9990 chunk 88 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 78 optimal weight: 0.0040 chunk 61 optimal weight: 0.5980 overall best weight: 0.9196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.137283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.097813 restraints weight = 12787.772| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 2.71 r_work: 0.3084 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9216 Z= 0.138 Angle : 0.557 7.367 12546 Z= 0.292 Chirality : 0.040 0.183 1511 Planarity : 0.004 0.047 1613 Dihedral : 4.335 28.997 1303 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.35 % Favored : 91.65 % Rotamer: Outliers : 3.04 % Allowed : 17.82 % Favored : 79.14 % 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 aren not related in a simple way. whole: 0.04 (0.25), residues: 1185 helix: 1.56 (0.19), residues: 776 sheet: -2.19 (0.88), residues: 27 loop : -3.25 (0.25), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 433 TYR 0.009 0.001 TYR A 9 PHE 0.011 0.001 PHE A 77 TRP 0.006 0.001 TRP A 159 HIS 0.002 0.000 HIS B 609 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 9216) covalent geometry : angle 0.55707 (12546) hydrogen bonds : bond 0.05144 ( 571) hydrogen bonds : angle 4.26921 ( 1704) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 92 time to evaluate : 0.323 Fit side-chains REVERT: A 151 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.8039 (mm) REVERT: A 297 ILE cc_start: 0.7240 (tp) cc_final: 0.7006 (pt) REVERT: A 417 ARG cc_start: 0.7339 (ppt170) cc_final: 0.6871 (ppt170) REVERT: A 431 TYR cc_start: 0.8174 (OUTLIER) cc_final: 0.6637 (m-80) REVERT: A 455 ARG cc_start: 0.8234 (tpm170) cc_final: 0.7971 (ttm110) REVERT: A 489 ARG cc_start: 0.7893 (mtm110) cc_final: 0.7105 (mpt180) REVERT: A 509 ARG cc_start: 0.8039 (OUTLIER) cc_final: 0.7591 (ptp-170) REVERT: B 13 ARG cc_start: 0.7849 (tpt170) cc_final: 0.7561 (tpp-160) REVERT: B 15 ARG cc_start: 0.9036 (ptt90) cc_final: 0.8799 (ptt90) REVERT: B 41 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.8003 (mp) REVERT: B 139 ASN cc_start: 0.8271 (t0) cc_final: 0.8007 (t0) REVERT: B 509 PHE cc_start: 0.7722 (t80) cc_final: 0.7215 (t80) REVERT: B 548 LEU cc_start: 0.7510 (OUTLIER) cc_final: 0.7262 (tt) REVERT: B 594 LEU cc_start: 0.7754 (tp) cc_final: 0.7307 (tp) REVERT: B 622 MET cc_start: 0.8659 (tpp) cc_final: 0.8441 (tpt) outliers start: 29 outliers final: 17 residues processed: 115 average time/residue: 0.0999 time to fit residues: 15.6717 Evaluate side-chains 111 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 89 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 378 ILE Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 431 TYR Chi-restraints excluded: chain A residue 509 ARG Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 400 TYR Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 469 MET Chi-restraints excluded: chain B residue 511 HIS Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain B residue 548 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 42 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 88 optimal weight: 0.0040 chunk 38 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 90 optimal weight: 0.6980 chunk 20 optimal weight: 0.3980 chunk 47 optimal weight: 5.9990 chunk 95 optimal weight: 5.9990 chunk 45 optimal weight: 0.0370 overall best weight: 0.3670 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.140673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.101977 restraints weight = 12591.698| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 2.69 r_work: 0.3146 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9216 Z= 0.115 Angle : 0.535 7.797 12546 Z= 0.280 Chirality : 0.039 0.180 1511 Planarity : 0.004 0.045 1613 Dihedral : 4.240 29.253 1303 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 2.31 % Allowed : 18.76 % Favored : 78.93 % 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 aren not related in a simple way. whole: 0.34 (0.25), residues: 1185 helix: 1.81 (0.20), residues: 779 sheet: -2.09 (0.88), residues: 27 loop : -3.20 (0.26), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 433 TYR 0.007 0.001 TYR B 400 PHE 0.009 0.001 PHE A 220 TRP 0.005 0.001 TRP A 159 HIS 0.002 0.000 HIS B 609 Details of bonding type rmsd covalent geometry : bond 0.00228 ( 9216) covalent geometry : angle 0.53515 (12546) hydrogen bonds : bond 0.04517 ( 571) hydrogen bonds : angle 4.11968 ( 1704) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 106 time to evaluate : 0.286 Fit side-chains REVERT: A 151 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8247 (mm) REVERT: A 417 ARG cc_start: 0.7377 (ppt170) cc_final: 0.6908 (ppt170) REVERT: A 427 GLU cc_start: 0.7812 (tp30) cc_final: 0.7375 (pt0) REVERT: A 431 TYR cc_start: 0.8050 (OUTLIER) cc_final: 0.6764 (m-80) REVERT: A 455 ARG cc_start: 0.8177 (tpm170) cc_final: 0.7939 (ttm110) REVERT: A 489 ARG cc_start: 0.7850 (mtm110) cc_final: 0.7095 (mpt180) REVERT: B 41 LEU cc_start: 0.8269 (OUTLIER) cc_final: 0.7968 (mp) REVERT: B 139 ASN cc_start: 0.8228 (t0) cc_final: 0.7983 (t0) REVERT: B 209 MET cc_start: 0.8676 (mtt) cc_final: 0.8366 (mtm) REVERT: B 349 GLN cc_start: 0.7612 (mm110) cc_final: 0.7253 (mm-40) REVERT: B 358 GLN cc_start: 0.8276 (tp40) cc_final: 0.8056 (tp40) REVERT: B 430 LYS cc_start: 0.6668 (mtpp) cc_final: 0.6301 (mmmt) REVERT: B 438 MET cc_start: 0.8462 (mmm) cc_final: 0.7930 (mmt) REVERT: B 509 PHE cc_start: 0.7725 (t80) cc_final: 0.7214 (t80) REVERT: B 548 LEU cc_start: 0.7468 (OUTLIER) cc_final: 0.7250 (tt) REVERT: B 594 LEU cc_start: 0.7645 (tp) cc_final: 0.7194 (tp) REVERT: B 622 MET cc_start: 0.8620 (tpp) cc_final: 0.8390 (tpt) outliers start: 22 outliers final: 15 residues processed: 123 average time/residue: 0.0723 time to fit residues: 12.4349 Evaluate side-chains 116 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 97 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 378 ILE Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 431 TYR Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 400 TYR Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 469 MET Chi-restraints excluded: chain B residue 511 HIS Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain B residue 548 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 49 optimal weight: 0.0270 chunk 21 optimal weight: 2.9990 chunk 101 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 47 optimal weight: 7.9990 chunk 51 optimal weight: 1.9990 chunk 97 optimal weight: 9.9990 chunk 10 optimal weight: 3.9990 overall best weight: 1.3444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.135839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.096212 restraints weight = 12646.322| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 2.69 r_work: 0.3069 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9216 Z= 0.170 Angle : 0.582 8.063 12546 Z= 0.306 Chirality : 0.041 0.158 1511 Planarity : 0.004 0.047 1613 Dihedral : 4.344 28.531 1303 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 2.73 % Allowed : 19.60 % Favored : 77.67 % 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 aren not related in a simple way. whole: 0.15 (0.25), residues: 1185 helix: 1.63 (0.19), residues: 777 sheet: -2.04 (0.89), residues: 27 loop : -3.17 (0.26), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 15 TYR 0.010 0.001 TYR A 9 PHE 0.013 0.002 PHE A 77 TRP 0.005 0.001 TRP A 3 HIS 0.022 0.001 HIS A 337 Details of bonding type rmsd covalent geometry : bond 0.00399 ( 9216) covalent geometry : angle 0.58202 (12546) hydrogen bonds : bond 0.05485 ( 571) hydrogen bonds : angle 4.28437 ( 1704) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 90 time to evaluate : 0.300 Fit side-chains REVERT: A 151 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.8128 (mm) REVERT: A 417 ARG cc_start: 0.7349 (ppt170) cc_final: 0.6838 (ppt170) REVERT: A 431 TYR cc_start: 0.8233 (OUTLIER) cc_final: 0.6597 (m-80) REVERT: A 455 ARG cc_start: 0.8238 (tpm170) cc_final: 0.7973 (ttm110) REVERT: A 489 ARG cc_start: 0.7855 (mtm110) cc_final: 0.7079 (mpt180) REVERT: B 41 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.7943 (mp) REVERT: B 139 ASN cc_start: 0.8245 (t0) cc_final: 0.7966 (t0) REVERT: B 358 GLN cc_start: 0.8254 (tp40) cc_final: 0.8022 (tp40) REVERT: B 430 LYS cc_start: 0.6636 (mtpp) cc_final: 0.6277 (mmmt) REVERT: B 509 PHE cc_start: 0.7723 (t80) cc_final: 0.7194 (t80) REVERT: B 548 LEU cc_start: 0.7487 (OUTLIER) cc_final: 0.7228 (tt) REVERT: B 594 LEU cc_start: 0.7798 (tp) cc_final: 0.7351 (tp) REVERT: B 622 MET cc_start: 0.8630 (tpp) cc_final: 0.8416 (tpt) outliers start: 26 outliers final: 15 residues processed: 110 average time/residue: 0.0916 time to fit residues: 13.7817 Evaluate side-chains 109 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 90 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 378 ILE Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 431 TYR Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 400 TYR Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 469 MET Chi-restraints excluded: chain B residue 511 HIS Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain B residue 548 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 7 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 chunk 95 optimal weight: 6.9990 chunk 83 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 114 optimal weight: 0.8980 chunk 74 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.137497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.098020 restraints weight = 12600.285| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 2.69 r_work: 0.3094 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9216 Z= 0.134 Angle : 0.561 8.073 12546 Z= 0.295 Chirality : 0.040 0.145 1511 Planarity : 0.004 0.048 1613 Dihedral : 4.313 29.424 1303 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.68 % Favored : 92.32 % Rotamer: Outliers : 1.89 % Allowed : 19.92 % Favored : 78.20 % 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 aren not related in a simple way. whole: 0.29 (0.25), residues: 1185 helix: 1.71 (0.19), residues: 782 sheet: -2.08 (0.90), residues: 27 loop : -3.12 (0.26), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 15 TYR 0.009 0.001 TYR B 400 PHE 0.010 0.001 PHE A 77 TRP 0.005 0.001 TRP A 159 HIS 0.019 0.001 HIS A 337 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 9216) covalent geometry : angle 0.56131 (12546) hydrogen bonds : bond 0.05115 ( 571) hydrogen bonds : angle 4.23250 ( 1704) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 90 time to evaluate : 0.252 Fit side-chains REVERT: A 151 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.8191 (mm) REVERT: A 417 ARG cc_start: 0.7349 (ppt170) cc_final: 0.6866 (ppt170) REVERT: A 431 TYR cc_start: 0.8236 (OUTLIER) cc_final: 0.6604 (m-80) REVERT: A 455 ARG cc_start: 0.8207 (tpm170) cc_final: 0.7954 (ttm110) REVERT: A 489 ARG cc_start: 0.7847 (mtm110) cc_final: 0.7087 (mpt180) REVERT: A 544 ASP cc_start: 0.7927 (m-30) cc_final: 0.7635 (m-30) REVERT: B 41 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.7954 (mp) REVERT: B 139 ASN cc_start: 0.8244 (t0) cc_final: 0.7976 (t0) REVERT: B 209 MET cc_start: 0.8707 (mtt) cc_final: 0.8402 (mtm) REVERT: B 358 GLN cc_start: 0.8253 (tp40) cc_final: 0.8045 (tp40) REVERT: B 509 PHE cc_start: 0.7719 (t80) cc_final: 0.7186 (t80) REVERT: B 548 LEU cc_start: 0.7470 (OUTLIER) cc_final: 0.7197 (tt) REVERT: B 594 LEU cc_start: 0.7704 (tp) cc_final: 0.7246 (tp) REVERT: B 622 MET cc_start: 0.8628 (tpp) cc_final: 0.8410 (tpt) outliers start: 18 outliers final: 14 residues processed: 103 average time/residue: 0.0929 time to fit residues: 13.2098 Evaluate side-chains 106 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 88 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 378 ILE Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 431 TYR Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 400 TYR Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 469 MET Chi-restraints excluded: chain B residue 511 HIS Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain B residue 548 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 66 optimal weight: 0.8980 chunk 110 optimal weight: 0.4980 chunk 79 optimal weight: 0.7980 chunk 61 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 15 optimal weight: 0.6980 chunk 81 optimal weight: 0.4980 chunk 1 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 chunk 97 optimal weight: 4.9990 chunk 25 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.139307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.100074 restraints weight = 12444.278| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.68 r_work: 0.3122 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9216 Z= 0.123 Angle : 0.547 8.017 12546 Z= 0.288 Chirality : 0.039 0.130 1511 Planarity : 0.004 0.050 1613 Dihedral : 4.229 28.113 1303 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % Rotamer: Outliers : 2.10 % Allowed : 19.81 % Favored : 78.09 % 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 aren not related in a simple way. whole: 0.46 (0.26), residues: 1185 helix: 1.84 (0.19), residues: 783 sheet: -2.17 (0.88), residues: 27 loop : -3.06 (0.27), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 195 TYR 0.008 0.001 TYR B 400 PHE 0.014 0.001 PHE A 293 TRP 0.006 0.001 TRP A 159 HIS 0.017 0.001 HIS A 337 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 9216) covalent geometry : angle 0.54720 (12546) hydrogen bonds : bond 0.04756 ( 571) hydrogen bonds : angle 4.14150 ( 1704) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1748.27 seconds wall clock time: 30 minutes 39.15 seconds (1839.15 seconds total)