Starting phenix.real_space_refine on Mon May 12 15:48:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wcw_37450/05_2025/8wcw_37450.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wcw_37450/05_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_37450/05_2025/8wcw_37450.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wcw_37450/05_2025/8wcw_37450.map" model { file = "/net/cci-nas-00/data/ceres_data/8wcw_37450/05_2025/8wcw_37450.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wcw_37450/05_2025/8wcw_37450.cif" } resolution = 3.11 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.066 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 6.56, per 1000 atoms: 0.72 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: 2.19 Conformation dependent library (CDL) restraints added in 937.8 milliseconds 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: 0.75 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: 2.34 Time building geometry restraints manager: 2.52 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: 1.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 23.700 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.040 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.12 (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 TRP 0.008 0.001 TRP A 442 HIS 0.004 0.001 HIS A 152 PHE 0.016 0.002 PHE A 341 TYR 0.019 0.002 TYR A 431 ARG 0.003 0.000 ARG B 27 Details of bonding type rmsd hydrogen bonds : bond 0.12511 ( 571) hydrogen bonds : angle 5.88077 ( 1704) covalent geometry : bond 0.00607 ( 9216) covalent geometry : angle 0.72642 (12546) *********************** 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 : 0.956 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: 0.2896 time to fit residues: 38.8481 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 : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 0.7980 chunk 89 optimal weight: 0.7980 chunk 49 optimal weight: 0.0270 chunk 30 optimal weight: 3.9990 chunk 60 optimal weight: 0.6980 chunk 47 optimal weight: 6.9990 chunk 92 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 56 optimal weight: 6.9990 chunk 68 optimal weight: 0.7980 chunk 107 optimal weight: 0.9990 overall best weight: 0.6238 ------------------------------------------------------------------------------- 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 = 0.3746 r_free = 0.3746 target = 0.136482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.096841 restraints weight = 12567.042| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 2.65 r_work: 0.3068 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.1209 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= 0.137 Angle : 0.604 10.294 12546 Z= 0.319 Chirality : 0.041 0.139 1511 Planarity : 0.004 0.053 1613 Dihedral : 4.824 30.270 1303 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.28 % Favored : 90.72 % Rotamer: Outliers : 1.57 % Allowed : 12.79 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.24), residues: 1185 helix: 0.59 (0.19), residues: 765 sheet: -3.23 (0.79), residues: 28 loop : -3.74 (0.23), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 408 HIS 0.003 0.001 HIS A 337 PHE 0.012 0.001 PHE B 296 TYR 0.017 0.001 TYR B 400 ARG 0.006 0.000 ARG A 433 Details of bonding type rmsd hydrogen bonds : bond 0.05506 ( 571) hydrogen bonds : angle 4.63920 ( 1704) covalent geometry : bond 0.00278 ( 9216) covalent geometry : angle 0.60351 (12546) *********************** 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 113 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 98 time to evaluate : 1.256 Fit side-chains REVERT: A 29 MET cc_start: 0.8242 (mmp) cc_final: 0.7964 (mmm) REVERT: A 310 GLU cc_start: 0.8618 (tt0) cc_final: 0.8262 (tt0) REVERT: A 455 ARG cc_start: 0.8322 (tpm170) cc_final: 0.8070 (ttm110) REVERT: A 489 ARG cc_start: 0.8080 (mtm110) cc_final: 0.7285 (mpt180) REVERT: B 139 ASN cc_start: 0.8212 (t0) cc_final: 0.7944 (t0) REVERT: B 209 MET cc_start: 0.8767 (mtt) cc_final: 0.8473 (mtm) REVERT: B 438 MET cc_start: 0.8658 (mmm) cc_final: 0.8119 (mmt) REVERT: B 509 PHE cc_start: 0.7751 (t80) cc_final: 0.7205 (t80) REVERT: B 594 LEU cc_start: 0.7798 (tp) cc_final: 0.7230 (tp) outliers start: 15 outliers final: 5 residues processed: 108 average time/residue: 0.2512 time to fit residues: 36.6332 Evaluate side-chains 91 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 86 time to evaluate : 1.042 ------------------------------------------------------------------------------- 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 8 optimal weight: 3.9990 chunk 87 optimal weight: 0.8980 chunk 9 optimal weight: 4.9990 chunk 51 optimal weight: 7.9990 chunk 70 optimal weight: 0.7980 chunk 40 optimal weight: 0.6980 chunk 95 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 79 optimal weight: 0.9990 chunk 112 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.136231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.096773 restraints weight = 12712.717| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 2.66 r_work: 0.3065 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.1422 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= 0.143 Angle : 0.595 9.894 12546 Z= 0.313 Chirality : 0.041 0.147 1511 Planarity : 0.004 0.052 1613 Dihedral : 4.657 29.279 1303 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.78 % Favored : 91.22 % Rotamer: Outliers : 2.10 % Allowed : 14.88 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.24), residues: 1185 helix: 1.07 (0.19), residues: 766 sheet: -2.60 (0.88), residues: 27 loop : -3.58 (0.24), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 159 HIS 0.002 0.000 HIS A 337 PHE 0.010 0.001 PHE B 296 TYR 0.014 0.001 TYR B 400 ARG 0.004 0.000 ARG B 15 Details of bonding type rmsd hydrogen bonds : bond 0.05472 ( 571) hydrogen bonds : angle 4.49687 ( 1704) covalent geometry : bond 0.00312 ( 9216) covalent geometry : angle 0.59493 (12546) *********************** 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: 20 poor density : 90 time to evaluate : 1.240 Fit side-chains REVERT: A 128 LEU cc_start: 0.8127 (OUTLIER) cc_final: 0.7899 (tp) REVERT: A 310 GLU cc_start: 0.8651 (tt0) cc_final: 0.8317 (tt0) REVERT: A 417 ARG cc_start: 0.7419 (ppt170) cc_final: 0.7122 (ppt170) REVERT: A 455 ARG cc_start: 0.8284 (tpm170) cc_final: 0.7979 (ttm110) REVERT: A 489 ARG cc_start: 0.8062 (mtm110) cc_final: 0.7254 (mpt180) REVERT: A 509 ARG cc_start: 0.8082 (OUTLIER) cc_final: 0.7642 (ptp-110) REVERT: B 139 ASN cc_start: 0.8251 (t0) cc_final: 0.7980 (t0) REVERT: B 509 PHE cc_start: 0.7745 (t80) cc_final: 0.7220 (t80) REVERT: B 594 LEU cc_start: 0.7815 (tp) cc_final: 0.7456 (tp) outliers start: 20 outliers final: 11 residues processed: 107 average time/residue: 0.2428 time to fit residues: 35.7202 Evaluate side-chains 100 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 87 time to evaluate : 0.998 ------------------------------------------------------------------------------- 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 133 VAL 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 222 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 511 HIS Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain B residue 597 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 88 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 27 optimal weight: 0.1980 chunk 61 optimal weight: 0.5980 chunk 65 optimal weight: 2.9990 chunk 46 optimal weight: 0.0170 chunk 40 optimal weight: 5.9990 chunk 2 optimal weight: 0.8980 chunk 94 optimal weight: 10.0000 chunk 48 optimal weight: 1.9990 overall best weight: 0.5420 ------------------------------------------------------------------------------- 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 = 0.3761 r_free = 0.3761 target = 0.138093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.099556 restraints weight = 12496.621| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 2.67 r_work: 0.3099 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.1819 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= 0.124 Angle : 0.567 9.449 12546 Z= 0.296 Chirality : 0.040 0.165 1511 Planarity : 0.004 0.048 1613 Dihedral : 4.460 29.799 1303 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 2.31 % Allowed : 16.77 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.25), residues: 1185 helix: 1.42 (0.19), residues: 775 sheet: -2.35 (0.92), residues: 27 loop : -3.48 (0.25), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 159 HIS 0.002 0.000 HIS A 337 PHE 0.010 0.001 PHE B 296 TYR 0.012 0.001 TYR B 400 ARG 0.003 0.000 ARG A 433 Details of bonding type rmsd hydrogen bonds : bond 0.04856 ( 571) hydrogen bonds : angle 4.29232 ( 1704) covalent geometry : bond 0.00252 ( 9216) covalent geometry : angle 0.56706 (12546) *********************** 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 121 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 99 time to evaluate : 0.975 Fit side-chains REVERT: A 310 GLU cc_start: 0.8667 (tt0) cc_final: 0.8365 (tt0) REVERT: A 417 ARG cc_start: 0.7363 (ppt170) cc_final: 0.6992 (ppt170) REVERT: A 431 TYR cc_start: 0.7981 (OUTLIER) cc_final: 0.6575 (m-80) REVERT: A 455 ARG cc_start: 0.8224 (tpm170) cc_final: 0.7943 (ttm110) REVERT: A 489 ARG cc_start: 0.7889 (mtm110) cc_final: 0.7056 (mpt180) REVERT: A 509 ARG cc_start: 0.8032 (OUTLIER) cc_final: 0.7575 (ptp-170) REVERT: B 139 ASN cc_start: 0.8162 (t0) cc_final: 0.7886 (t0) REVERT: B 209 MET cc_start: 0.8630 (mtt) cc_final: 0.8330 (mtm) REVERT: B 438 MET cc_start: 0.8480 (mmm) cc_final: 0.7979 (mmt) REVERT: B 509 PHE cc_start: 0.7743 (t80) cc_final: 0.7246 (t80) REVERT: B 594 LEU cc_start: 0.7649 (tp) cc_final: 0.7237 (tp) REVERT: B 622 MET cc_start: 0.8664 (tpp) cc_final: 0.8405 (tpt) outliers start: 22 outliers final: 12 residues processed: 115 average time/residue: 0.2473 time to fit residues: 38.9462 Evaluate side-chains 104 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 90 time to evaluate : 1.032 ------------------------------------------------------------------------------- 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 196 LEU 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 42 optimal weight: 0.9980 chunk 87 optimal weight: 0.6980 chunk 72 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 110 optimal weight: 0.7980 chunk 82 optimal weight: 0.7980 chunk 99 optimal weight: 0.7980 chunk 76 optimal weight: 0.8980 chunk 89 optimal weight: 0.8980 chunk 105 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 HIS B 294 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.137460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.098561 restraints weight = 12474.877| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 2.65 r_work: 0.3087 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.1888 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= 0.133 Angle : 0.567 8.954 12546 Z= 0.297 Chirality : 0.040 0.157 1511 Planarity : 0.004 0.049 1613 Dihedral : 4.416 28.949 1303 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 2.41 % Allowed : 16.77 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.25), residues: 1185 helix: 1.46 (0.19), residues: 778 sheet: -2.18 (0.96), residues: 27 loop : -3.43 (0.25), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 159 HIS 0.019 0.001 HIS A 337 PHE 0.011 0.001 PHE A 341 TYR 0.010 0.001 TYR B 400 ARG 0.003 0.000 ARG B 15 Details of bonding type rmsd hydrogen bonds : bond 0.05050 ( 571) hydrogen bonds : angle 4.28439 ( 1704) covalent geometry : bond 0.00287 ( 9216) covalent geometry : angle 0.56711 (12546) *********************** 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 111 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 88 time to evaluate : 1.068 Fit side-chains REVERT: A 297 ILE cc_start: 0.7245 (tp) cc_final: 0.6931 (pt) REVERT: A 310 GLU cc_start: 0.8662 (tt0) cc_final: 0.8395 (tt0) REVERT: A 417 ARG cc_start: 0.7351 (ppt170) cc_final: 0.6926 (ppt170) REVERT: A 431 TYR cc_start: 0.8010 (OUTLIER) cc_final: 0.6601 (m-80) REVERT: A 455 ARG cc_start: 0.8236 (tpm170) cc_final: 0.7951 (ttm110) REVERT: A 489 ARG cc_start: 0.7887 (mtm110) cc_final: 0.7055 (mpt180) REVERT: A 509 ARG cc_start: 0.8017 (OUTLIER) cc_final: 0.7587 (ptp-170) REVERT: B 139 ASN cc_start: 0.8197 (t0) cc_final: 0.7924 (t0) REVERT: B 365 GLU cc_start: 0.7670 (tp30) cc_final: 0.7423 (tp30) REVERT: B 509 PHE cc_start: 0.7747 (t80) cc_final: 0.7233 (t80) REVERT: B 548 LEU cc_start: 0.7349 (OUTLIER) cc_final: 0.7132 (tt) REVERT: B 594 LEU cc_start: 0.7618 (tp) cc_final: 0.7184 (tp) REVERT: B 622 MET cc_start: 0.8628 (tpp) cc_final: 0.8380 (tpt) outliers start: 23 outliers final: 13 residues processed: 107 average time/residue: 0.2309 time to fit residues: 34.5718 Evaluate side-chains 102 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 86 time to evaluate : 1.036 ------------------------------------------------------------------------------- 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 18 optimal weight: 0.7980 chunk 97 optimal weight: 9.9990 chunk 9 optimal weight: 3.9990 chunk 93 optimal weight: 0.5980 chunk 75 optimal weight: 0.9980 chunk 29 optimal weight: 0.5980 chunk 104 optimal weight: 4.9990 chunk 4 optimal weight: 0.3980 chunk 39 optimal weight: 7.9990 chunk 81 optimal weight: 0.8980 chunk 83 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3773 r_free = 0.3773 target = 0.138435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.099403 restraints weight = 12624.320| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 2.68 r_work: 0.3105 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.2006 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= 0.125 Angle : 0.551 8.212 12546 Z= 0.289 Chirality : 0.040 0.158 1511 Planarity : 0.004 0.049 1613 Dihedral : 4.375 29.492 1303 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % Rotamer: Outliers : 2.52 % Allowed : 17.40 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.25), residues: 1185 helix: 1.56 (0.19), residues: 778 sheet: -2.09 (0.97), residues: 27 loop : -3.32 (0.25), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 159 HIS 0.003 0.000 HIS B 609 PHE 0.011 0.001 PHE A 293 TYR 0.009 0.001 TYR B 400 ARG 0.002 0.000 ARG A 433 Details of bonding type rmsd hydrogen bonds : bond 0.04892 ( 571) hydrogen bonds : angle 4.24507 ( 1704) covalent geometry : bond 0.00265 ( 9216) covalent geometry : angle 0.55053 (12546) *********************** 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 115 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 91 time to evaluate : 1.102 Fit side-chains REVERT: A 297 ILE cc_start: 0.7301 (tp) cc_final: 0.7002 (pt) REVERT: A 417 ARG cc_start: 0.7363 (ppt170) cc_final: 0.6906 (ppt170) REVERT: A 431 TYR cc_start: 0.8055 (OUTLIER) cc_final: 0.6665 (m-80) REVERT: A 455 ARG cc_start: 0.8230 (tpm170) cc_final: 0.7969 (ttm110) REVERT: A 489 ARG cc_start: 0.7879 (mtm110) cc_final: 0.7081 (mpt180) REVERT: A 509 ARG cc_start: 0.8010 (OUTLIER) cc_final: 0.7589 (ptp-170) REVERT: B 139 ASN cc_start: 0.8258 (t0) cc_final: 0.7995 (t0) REVERT: B 209 MET cc_start: 0.8700 (mtt) cc_final: 0.8425 (mtm) REVERT: B 345 GLN cc_start: 0.8546 (tp40) cc_final: 0.8320 (tp40) REVERT: B 438 MET cc_start: 0.8572 (mmm) cc_final: 0.7970 (mmt) REVERT: B 509 PHE cc_start: 0.7750 (t80) cc_final: 0.7260 (t80) REVERT: B 548 LEU cc_start: 0.7381 (OUTLIER) cc_final: 0.7160 (tt) REVERT: B 594 LEU cc_start: 0.7690 (tp) cc_final: 0.7258 (tp) REVERT: B 622 MET cc_start: 0.8674 (tpp) cc_final: 0.8443 (tpt) outliers start: 24 outliers final: 15 residues processed: 110 average time/residue: 0.2375 time to fit residues: 36.3326 Evaluate side-chains 104 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 86 time to evaluate : 0.985 ------------------------------------------------------------------------------- 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 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 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 43 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 78 optimal weight: 0.0670 chunk 105 optimal weight: 0.2980 chunk 115 optimal weight: 7.9990 chunk 44 optimal weight: 2.9990 chunk 39 optimal weight: 7.9990 chunk 79 optimal weight: 0.7980 chunk 8 optimal weight: 5.9990 chunk 61 optimal weight: 0.9980 overall best weight: 0.6320 ------------------------------------------------------------------------------- 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 = 0.3781 r_free = 0.3781 target = 0.139038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.099975 restraints weight = 12663.170| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 2.69 r_work: 0.3113 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9216 Z= 0.123 Angle : 0.548 10.178 12546 Z= 0.287 Chirality : 0.040 0.165 1511 Planarity : 0.004 0.049 1613 Dihedral : 4.289 28.469 1303 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 2.73 % Allowed : 18.24 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.25), residues: 1185 helix: 1.67 (0.19), residues: 777 sheet: -2.03 (0.95), residues: 27 loop : -3.21 (0.26), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 159 HIS 0.003 0.000 HIS B 609 PHE 0.011 0.001 PHE A 293 TYR 0.007 0.001 TYR A 9 ARG 0.005 0.000 ARG B 15 Details of bonding type rmsd hydrogen bonds : bond 0.04817 ( 571) hydrogen bonds : angle 4.20185 ( 1704) covalent geometry : bond 0.00257 ( 9216) covalent geometry : angle 0.54794 (12546) *********************** 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 124 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 98 time to evaluate : 1.062 Fit side-chains REVERT: A 151 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.8080 (mm) REVERT: A 297 ILE cc_start: 0.7246 (tp) cc_final: 0.7018 (pt) REVERT: A 417 ARG cc_start: 0.7342 (ppt170) cc_final: 0.6884 (ppt170) REVERT: A 431 TYR cc_start: 0.8045 (OUTLIER) cc_final: 0.6657 (m-80) REVERT: A 455 ARG cc_start: 0.8211 (tpm170) cc_final: 0.7951 (ttm110) REVERT: A 489 ARG cc_start: 0.7870 (mtm110) cc_final: 0.7089 (mpt180) REVERT: A 509 ARG cc_start: 0.8000 (OUTLIER) cc_final: 0.7590 (ptp-170) REVERT: B 41 LEU cc_start: 0.8297 (OUTLIER) cc_final: 0.7995 (mp) REVERT: B 95 ASP cc_start: 0.7597 (m-30) cc_final: 0.7212 (m-30) REVERT: B 139 ASN cc_start: 0.8260 (t0) cc_final: 0.7997 (t0) REVERT: B 345 GLN cc_start: 0.8586 (tp40) cc_final: 0.8374 (tp40) REVERT: B 438 MET cc_start: 0.8546 (mmm) cc_final: 0.7951 (mmt) REVERT: B 509 PHE cc_start: 0.7729 (t80) cc_final: 0.7228 (t80) REVERT: B 548 LEU cc_start: 0.7412 (OUTLIER) cc_final: 0.7194 (tt) REVERT: B 594 LEU cc_start: 0.7744 (tp) cc_final: 0.7306 (tp) REVERT: B 622 MET cc_start: 0.8596 (tpp) cc_final: 0.8369 (tpt) outliers start: 26 outliers final: 14 residues processed: 119 average time/residue: 0.2178 time to fit residues: 36.0096 Evaluate side-chains 108 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 89 time to evaluate : 0.980 ------------------------------------------------------------------------------- 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 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 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 548 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 11 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 chunk 47 optimal weight: 7.9990 chunk 111 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 103 optimal weight: 5.9990 chunk 82 optimal weight: 0.6980 chunk 55 optimal weight: 0.8980 chunk 29 optimal weight: 0.0980 chunk 70 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3783 r_free = 0.3783 target = 0.139221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.100178 restraints weight = 12870.510| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 2.71 r_work: 0.3118 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9216 Z= 0.122 Angle : 0.552 10.352 12546 Z= 0.288 Chirality : 0.040 0.147 1511 Planarity : 0.004 0.048 1613 Dihedral : 4.251 28.818 1303 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 2.52 % Allowed : 18.87 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.25), residues: 1185 helix: 1.72 (0.19), residues: 782 sheet: -2.02 (0.96), residues: 27 loop : -3.21 (0.25), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 159 HIS 0.002 0.000 HIS B 609 PHE 0.009 0.001 PHE A 77 TYR 0.007 0.001 TYR A 9 ARG 0.002 0.000 ARG A 433 Details of bonding type rmsd hydrogen bonds : bond 0.04757 ( 571) hydrogen bonds : angle 4.17333 ( 1704) covalent geometry : bond 0.00256 ( 9216) covalent geometry : angle 0.55196 (12546) *********************** 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 119 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 95 time to evaluate : 1.008 Fit side-chains REVERT: A 151 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8234 (mm) REVERT: A 417 ARG cc_start: 0.7344 (ppt170) cc_final: 0.6875 (ppt170) REVERT: A 431 TYR cc_start: 0.8034 (OUTLIER) cc_final: 0.6636 (m-80) REVERT: A 455 ARG cc_start: 0.8196 (tpm170) cc_final: 0.7953 (ttm110) REVERT: A 489 ARG cc_start: 0.7870 (mtm110) cc_final: 0.7092 (mpt180) REVERT: A 509 ARG cc_start: 0.8005 (OUTLIER) cc_final: 0.7589 (ptp-170) REVERT: B 15 ARG cc_start: 0.8722 (ptm-80) cc_final: 0.8515 (ptm-80) REVERT: B 41 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.7991 (mp) REVERT: B 139 ASN cc_start: 0.8259 (t0) cc_final: 0.7993 (t0) REVERT: B 345 GLN cc_start: 0.8602 (tp40) cc_final: 0.8395 (tp40) REVERT: B 509 PHE cc_start: 0.7715 (t80) cc_final: 0.7199 (t80) REVERT: B 548 LEU cc_start: 0.7371 (OUTLIER) cc_final: 0.7143 (tt) REVERT: B 594 LEU cc_start: 0.7736 (tp) cc_final: 0.7290 (tp) REVERT: B 622 MET cc_start: 0.8638 (tpp) cc_final: 0.8416 (tpt) outliers start: 24 outliers final: 15 residues processed: 114 average time/residue: 0.2272 time to fit residues: 36.3984 Evaluate side-chains 111 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 91 time to evaluate : 1.094 ------------------------------------------------------------------------------- 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 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 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 79 optimal weight: 0.7980 chunk 104 optimal weight: 4.9990 chunk 108 optimal weight: 5.9990 chunk 46 optimal weight: 0.5980 chunk 116 optimal weight: 4.9990 chunk 14 optimal weight: 0.5980 chunk 60 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 56 optimal weight: 7.9990 chunk 103 optimal weight: 0.0770 chunk 32 optimal weight: 0.0060 overall best weight: 0.4154 ------------------------------------------------------------------------------- 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 = 0.3805 r_free = 0.3805 target = 0.141159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.102455 restraints weight = 12524.273| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 2.67 r_work: 0.3152 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9216 Z= 0.114 Angle : 0.541 9.952 12546 Z= 0.282 Chirality : 0.039 0.159 1511 Planarity : 0.004 0.049 1613 Dihedral : 4.184 28.662 1303 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 2.52 % Allowed : 19.29 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.26), residues: 1185 helix: 1.82 (0.19), residues: 783 sheet: -2.14 (0.95), residues: 28 loop : -3.13 (0.26), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 159 HIS 0.002 0.000 HIS B 609 PHE 0.010 0.001 PHE A 220 TYR 0.007 0.001 TYR B 400 ARG 0.002 0.000 ARG A 433 Details of bonding type rmsd hydrogen bonds : bond 0.04463 ( 571) hydrogen bonds : angle 4.09374 ( 1704) covalent geometry : bond 0.00228 ( 9216) covalent geometry : angle 0.54059 (12546) *********************** 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 131 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 107 time to evaluate : 1.098 Fit side-chains revert: symmetry clash REVERT: A 148 PHE cc_start: 0.7828 (m-80) cc_final: 0.7586 (m-80) REVERT: A 151 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8195 (mm) REVERT: A 293 PHE cc_start: 0.6427 (t80) cc_final: 0.6072 (t80) REVERT: A 417 ARG cc_start: 0.7377 (ppt170) cc_final: 0.6911 (ppt170) REVERT: A 431 TYR cc_start: 0.7957 (OUTLIER) cc_final: 0.6642 (m-80) REVERT: A 435 ASP cc_start: 0.6148 (OUTLIER) cc_final: 0.5939 (p0) REVERT: A 489 ARG cc_start: 0.7817 (mtm110) cc_final: 0.7057 (mpt180) REVERT: A 509 ARG cc_start: 0.8020 (OUTLIER) cc_final: 0.7601 (ptp-170) REVERT: B 15 ARG cc_start: 0.8763 (ptm-80) cc_final: 0.8538 (ptm-80) REVERT: B 41 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.7945 (mp) REVERT: B 139 ASN cc_start: 0.8233 (t0) cc_final: 0.7968 (t0) REVERT: B 345 GLN cc_start: 0.8630 (tp40) cc_final: 0.8366 (tp40) REVERT: B 349 GLN cc_start: 0.7607 (mm110) cc_final: 0.7277 (mm-40) REVERT: B 438 MET cc_start: 0.8353 (mmm) cc_final: 0.7843 (mmt) REVERT: B 509 PHE cc_start: 0.7736 (t80) cc_final: 0.7214 (t80) REVERT: B 548 LEU cc_start: 0.7356 (OUTLIER) cc_final: 0.7137 (tt) REVERT: B 594 LEU cc_start: 0.7654 (tp) cc_final: 0.7207 (tp) REVERT: B 622 MET cc_start: 0.8635 (tpp) cc_final: 0.8420 (tpt) outliers start: 24 outliers final: 17 residues processed: 123 average time/residue: 0.2152 time to fit residues: 37.1943 Evaluate side-chains 118 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 95 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 76 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 435 ASP 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 196 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 25 optimal weight: 0.7980 chunk 115 optimal weight: 7.9990 chunk 46 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 97 optimal weight: 10.0000 chunk 68 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 99 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 435 ASN 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 = 0.135713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.095830 restraints weight = 12733.945| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 2.70 r_work: 0.3060 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9216 Z= 0.168 Angle : 0.591 10.011 12546 Z= 0.309 Chirality : 0.041 0.156 1511 Planarity : 0.004 0.048 1613 Dihedral : 4.336 28.551 1303 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer: Outliers : 2.10 % Allowed : 19.60 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.25), residues: 1185 helix: 1.59 (0.19), residues: 777 sheet: -1.96 (0.96), residues: 27 loop : -3.11 (0.26), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 3 HIS 0.020 0.001 HIS A 337 PHE 0.014 0.002 PHE A 77 TYR 0.011 0.001 TYR A 9 ARG 0.002 0.000 ARG A 383 Details of bonding type rmsd hydrogen bonds : bond 0.05648 ( 571) hydrogen bonds : angle 4.31196 ( 1704) covalent geometry : bond 0.00391 ( 9216) covalent geometry : angle 0.59080 (12546) ********************** 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 110 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 90 time to evaluate : 0.965 Fit side-chains REVERT: A 148 PHE cc_start: 0.7842 (m-80) cc_final: 0.7584 (m-80) REVERT: A 151 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.8180 (mm) REVERT: A 417 ARG cc_start: 0.7331 (ppt170) cc_final: 0.6850 (ppt170) REVERT: A 431 TYR cc_start: 0.8219 (OUTLIER) cc_final: 0.6664 (m-80) REVERT: A 455 ARG cc_start: 0.8237 (tpm170) cc_final: 0.7972 (ttm110) REVERT: A 489 ARG cc_start: 0.7862 (mtm110) cc_final: 0.7103 (mpt180) REVERT: A 509 ARG cc_start: 0.8007 (OUTLIER) cc_final: 0.7591 (ptp-170) REVERT: B 15 ARG cc_start: 0.8786 (ptm-80) cc_final: 0.8562 (ptm-80) REVERT: B 41 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.7949 (mp) REVERT: B 139 ASN cc_start: 0.8254 (t0) cc_final: 0.7971 (t0) REVERT: B 509 PHE cc_start: 0.7703 (t80) cc_final: 0.7178 (t80) REVERT: B 594 LEU cc_start: 0.7818 (tp) cc_final: 0.7583 (tp) REVERT: B 622 MET cc_start: 0.8642 (tpp) cc_final: 0.8433 (tpt) outliers start: 20 outliers final: 13 residues processed: 106 average time/residue: 0.2232 time to fit residues: 32.7609 Evaluate side-chains 106 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 89 time to evaluate : 1.079 ------------------------------------------------------------------------------- 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 112 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 106 optimal weight: 5.9990 chunk 5 optimal weight: 0.9980 chunk 86 optimal weight: 0.5980 chunk 14 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.137493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.097845 restraints weight = 12567.366| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 2.67 r_work: 0.3095 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.2236 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= 0.136 Angle : 0.562 9.800 12546 Z= 0.294 Chirality : 0.040 0.144 1511 Planarity : 0.004 0.048 1613 Dihedral : 4.292 28.951 1303 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 1.89 % Allowed : 20.13 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.25), residues: 1185 helix: 1.66 (0.19), residues: 783 sheet: -1.92 (0.97), residues: 27 loop : -3.10 (0.26), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 159 HIS 0.019 0.001 HIS A 337 PHE 0.013 0.001 PHE A 293 TYR 0.009 0.001 TYR B 400 ARG 0.002 0.000 ARG A 433 Details of bonding type rmsd hydrogen bonds : bond 0.05169 ( 571) hydrogen bonds : angle 4.24399 ( 1704) covalent geometry : bond 0.00299 ( 9216) covalent geometry : angle 0.56154 (12546) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4182.06 seconds wall clock time: 73 minutes 27.73 seconds (4407.73 seconds total)