Starting phenix.real_space_refine on Sun Jun 8 00:35:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wcw_37450/06_2025/8wcw_37450.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wcw_37450/06_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_37450/06_2025/8wcw_37450.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wcw_37450/06_2025/8wcw_37450.map" model { file = "/net/cci-nas-00/data/ceres_data/8wcw_37450/06_2025/8wcw_37450.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wcw_37450/06_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 5.93, per 1000 atoms: 0.65 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: 2.36 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.90 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: 2.46 Time building geometry restraints manager: 2.77 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: 2.260 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: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 23.490 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: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.200 ------------------------------------------------------------------------------- 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 : 0.929 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: 0.2970 time to fit residues: 39.9435 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 : 0.895 ------------------------------------------------------------------------------- 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 = 45)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.096841 restraints weight = 12566.962| |-----------------------------------------------------------------------------| r_work (start): 0.3206 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: 0.7800 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 4.63921 ( 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 : 0.810 Fit side-chains REVERT: A 29 MET cc_start: 0.8224 (mmp) cc_final: 0.7946 (mmm) REVERT: A 310 GLU cc_start: 0.8613 (tt0) cc_final: 0.8254 (tt0) REVERT: A 455 ARG cc_start: 0.8324 (tpm170) cc_final: 0.8069 (ttm110) REVERT: A 489 ARG cc_start: 0.8075 (mtm110) cc_final: 0.7278 (mpt180) REVERT: B 139 ASN cc_start: 0.8198 (t0) cc_final: 0.7929 (t0) REVERT: B 209 MET cc_start: 0.8748 (mtt) cc_final: 0.8454 (mtm) REVERT: B 438 MET cc_start: 0.8643 (mmm) cc_final: 0.8107 (mmt) REVERT: B 509 PHE cc_start: 0.7750 (t80) cc_final: 0.7203 (t80) REVERT: B 594 LEU cc_start: 0.7786 (tp) cc_final: 0.7217 (tp) outliers start: 15 outliers final: 5 residues processed: 108 average time/residue: 0.2531 time to fit residues: 36.8183 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 : 0.926 ------------------------------------------------------------------------------- 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: 6.9990 chunk 51 optimal weight: 7.9990 chunk 70 optimal weight: 0.5980 chunk 40 optimal weight: 0.6980 chunk 95 optimal weight: 5.9990 chunk 14 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 112 optimal weight: 4.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.3736 r_free = 0.3736 target = 0.135482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.096785 restraints weight = 12707.987| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 2.66 r_work: 0.3070 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.1456 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= 0.138 Angle : 0.591 9.889 12546 Z= 0.310 Chirality : 0.040 0.143 1511 Planarity : 0.004 0.051 1613 Dihedral : 4.644 29.336 1303 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.78 % Favored : 91.22 % Rotamer: Outliers : 2.31 % Allowed : 14.88 % Favored : 82.81 % 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: -0.66 (0.25), residues: 1185 helix: 1.10 (0.19), residues: 766 sheet: -2.57 (0.88), residues: 27 loop : -3.57 (0.24), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 159 HIS 0.003 0.000 HIS A 337 PHE 0.010 0.001 PHE B 296 TYR 0.014 0.001 TYR B 400 ARG 0.005 0.000 ARG B 15 Details of bonding type rmsd hydrogen bonds : bond 0.05372 ( 571) hydrogen bonds : angle 4.47367 ( 1704) covalent geometry : bond 0.00295 ( 9216) covalent geometry : angle 0.59077 (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 113 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 91 time to evaluate : 0.990 Fit side-chains REVERT: A 128 LEU cc_start: 0.8074 (OUTLIER) cc_final: 0.7851 (tp) REVERT: A 310 GLU cc_start: 0.8620 (tt0) cc_final: 0.8289 (tt0) REVERT: A 417 ARG cc_start: 0.7395 (ppt170) cc_final: 0.7093 (ppt170) REVERT: A 455 ARG cc_start: 0.8289 (tpm170) cc_final: 0.7992 (ttm110) REVERT: A 489 ARG cc_start: 0.8042 (mtm110) cc_final: 0.7226 (mpt180) REVERT: A 509 ARG cc_start: 0.8092 (OUTLIER) cc_final: 0.7655 (ptp-110) REVERT: B 139 ASN cc_start: 0.8203 (t0) cc_final: 0.7934 (t0) REVERT: B 209 MET cc_start: 0.8669 (mtt) cc_final: 0.8367 (mtm) REVERT: B 509 PHE cc_start: 0.7740 (t80) cc_final: 0.7213 (t80) REVERT: B 594 LEU cc_start: 0.7751 (tp) cc_final: 0.7386 (tp) outliers start: 22 outliers final: 12 residues processed: 109 average time/residue: 0.2334 time to fit residues: 34.9677 Evaluate side-chains 98 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 84 time to evaluate : 0.992 ------------------------------------------------------------------------------- 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 196 LEU 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: 2.9990 chunk 13 optimal weight: 0.7980 chunk 90 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 61 optimal weight: 0.4980 chunk 65 optimal weight: 2.9990 chunk 46 optimal weight: 0.0270 chunk 40 optimal weight: 5.9990 chunk 2 optimal weight: 0.9980 chunk 94 optimal weight: 8.9990 chunk 48 optimal weight: 0.9980 overall best weight: 0.5838 ------------------------------------------------------------------------------- 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 = 0.3755 r_free = 0.3755 target = 0.137602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.099015 restraints weight = 12515.671| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 2.66 r_work: 0.3092 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.1764 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= 0.125 Angle : 0.572 9.546 12546 Z= 0.298 Chirality : 0.040 0.163 1511 Planarity : 0.004 0.048 1613 Dihedral : 4.482 29.751 1303 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.61 % Favored : 91.39 % Rotamer: Outliers : 2.31 % Allowed : 16.67 % 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 (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: -0.24 (0.25), residues: 1185 helix: 1.39 (0.19), residues: 777 sheet: -2.25 (0.92), residues: 27 loop : -3.46 (0.25), residues: 381 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 0.011 0.001 PHE A 341 TYR 0.014 0.001 TYR B 400 ARG 0.003 0.000 ARG A 433 Details of bonding type rmsd hydrogen bonds : bond 0.04950 ( 571) hydrogen bonds : angle 4.30748 ( 1704) covalent geometry : bond 0.00258 ( 9216) covalent geometry : angle 0.57171 (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 119 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 97 time to evaluate : 1.339 Fit side-chains REVERT: A 310 GLU cc_start: 0.8653 (tt0) cc_final: 0.8344 (tt0) REVERT: A 417 ARG cc_start: 0.7374 (ppt170) cc_final: 0.7010 (ppt170) REVERT: A 431 TYR cc_start: 0.8011 (OUTLIER) cc_final: 0.6600 (m-80) REVERT: A 455 ARG cc_start: 0.8234 (tpm170) cc_final: 0.7956 (ttm110) REVERT: A 489 ARG cc_start: 0.7928 (mtm110) cc_final: 0.7101 (mpt180) REVERT: A 509 ARG cc_start: 0.8041 (OUTLIER) cc_final: 0.7573 (ptp-170) REVERT: B 139 ASN cc_start: 0.8199 (t0) cc_final: 0.7920 (t0) REVERT: B 209 MET cc_start: 0.8684 (mtt) cc_final: 0.8383 (mtm) REVERT: B 509 PHE cc_start: 0.7753 (t80) cc_final: 0.7227 (t80) REVERT: B 594 LEU cc_start: 0.7699 (tp) cc_final: 0.7290 (tp) REVERT: B 622 MET cc_start: 0.8618 (tpp) cc_final: 0.8349 (tpt) outliers start: 22 outliers final: 11 residues processed: 114 average time/residue: 0.2651 time to fit residues: 41.4987 Evaluate side-chains 101 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 88 time to evaluate : 1.234 ------------------------------------------------------------------------------- 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 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: 0.6980 chunk 87 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 110 optimal weight: 0.9980 chunk 82 optimal weight: 0.7980 chunk 99 optimal weight: 3.9990 chunk 76 optimal weight: 0.8980 chunk 89 optimal weight: 0.8980 chunk 105 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3754 r_free = 0.3754 target = 0.137391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.098452 restraints weight = 12471.630| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 2.66 r_work: 0.3085 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.1873 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= 0.132 Angle : 0.571 9.203 12546 Z= 0.299 Chirality : 0.040 0.151 1511 Planarity : 0.004 0.049 1613 Dihedral : 4.438 29.085 1303 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer: Outliers : 2.62 % Allowed : 16.98 % Favored : 80.40 % 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: 1.43 (0.19), residues: 780 sheet: -2.07 (0.94), residues: 27 loop : -3.50 (0.24), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 159 HIS 0.019 0.001 HIS A 337 PHE 0.010 0.001 PHE A 77 TYR 0.013 0.001 TYR B 400 ARG 0.003 0.000 ARG B 15 Details of bonding type rmsd hydrogen bonds : bond 0.05077 ( 571) hydrogen bonds : angle 4.29477 ( 1704) covalent geometry : bond 0.00283 ( 9216) covalent geometry : angle 0.57146 (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 113 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 88 time to evaluate : 0.934 Fit side-chains REVERT: A 310 GLU cc_start: 0.8656 (tt0) cc_final: 0.8347 (tt0) REVERT: A 417 ARG cc_start: 0.7338 (ppt170) cc_final: 0.6918 (ppt170) REVERT: A 431 TYR cc_start: 0.8016 (OUTLIER) cc_final: 0.6604 (m-80) REVERT: A 455 ARG cc_start: 0.8240 (tpm170) cc_final: 0.7953 (ttm110) REVERT: A 489 ARG cc_start: 0.7888 (mtm110) cc_final: 0.7052 (mpt180) REVERT: A 509 ARG cc_start: 0.8026 (OUTLIER) cc_final: 0.7591 (ptp-170) REVERT: B 139 ASN cc_start: 0.8195 (t0) cc_final: 0.7922 (t0) REVERT: B 438 MET cc_start: 0.8543 (mmm) cc_final: 0.7949 (mmt) REVERT: B 509 PHE cc_start: 0.7732 (t80) cc_final: 0.7221 (t80) REVERT: B 548 LEU cc_start: 0.7354 (OUTLIER) cc_final: 0.7133 (tt) REVERT: B 594 LEU cc_start: 0.7615 (tp) cc_final: 0.7182 (tp) REVERT: B 622 MET cc_start: 0.8635 (tpp) cc_final: 0.8396 (tpt) outliers start: 25 outliers final: 13 residues processed: 109 average time/residue: 0.2971 time to fit residues: 44.9514 Evaluate side-chains 103 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 87 time to evaluate : 1.015 ------------------------------------------------------------------------------- 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: 1.9990 chunk 97 optimal weight: 9.9990 chunk 9 optimal weight: 0.7980 chunk 93 optimal weight: 0.6980 chunk 75 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 104 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 39 optimal weight: 8.9990 chunk 81 optimal weight: 0.7980 chunk 83 optimal weight: 3.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 = 0.3747 r_free = 0.3747 target = 0.136675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.097571 restraints weight = 12546.625| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 2.65 r_work: 0.3074 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9216 Z= 0.142 Angle : 0.567 7.834 12546 Z= 0.298 Chirality : 0.040 0.155 1511 Planarity : 0.004 0.050 1613 Dihedral : 4.430 29.165 1303 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 2.73 % Allowed : 17.09 % 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 (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: -0.10 (0.25), residues: 1185 helix: 1.49 (0.19), residues: 774 sheet: -2.43 (0.85), residues: 32 loop : -3.35 (0.25), residues: 379 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 0.012 0.001 TYR B 400 ARG 0.002 0.000 ARG A 433 Details of bonding type rmsd hydrogen bonds : bond 0.05206 ( 571) hydrogen bonds : angle 4.31386 ( 1704) covalent geometry : bond 0.00318 ( 9216) covalent geometry : angle 0.56662 (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: 26 poor density : 89 time to evaluate : 1.015 Fit side-chains REVERT: A 310 GLU cc_start: 0.8687 (tt0) cc_final: 0.8371 (tt0) REVERT: A 417 ARG cc_start: 0.7335 (ppt170) cc_final: 0.6872 (ppt170) REVERT: A 431 TYR cc_start: 0.8079 (OUTLIER) cc_final: 0.6612 (m-80) REVERT: A 455 ARG cc_start: 0.8230 (tpm170) cc_final: 0.7973 (ttm110) REVERT: A 489 ARG cc_start: 0.7888 (mtm110) cc_final: 0.7070 (mpt180) REVERT: A 509 ARG cc_start: 0.8023 (OUTLIER) cc_final: 0.7590 (ptp-170) REVERT: B 139 ASN cc_start: 0.8202 (t0) cc_final: 0.7927 (t0) REVERT: B 358 GLN cc_start: 0.8228 (tp40) cc_final: 0.7955 (tp40) REVERT: B 509 PHE cc_start: 0.7737 (t80) cc_final: 0.7207 (t80) REVERT: B 548 LEU cc_start: 0.7378 (OUTLIER) cc_final: 0.7150 (tt) REVERT: B 594 LEU cc_start: 0.7654 (tp) cc_final: 0.7214 (tp) REVERT: B 622 MET cc_start: 0.8669 (tpp) cc_final: 0.8458 (tpt) outliers start: 26 outliers final: 15 residues processed: 110 average time/residue: 0.2199 time to fit residues: 34.1752 Evaluate side-chains 103 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 85 time to evaluate : 0.922 ------------------------------------------------------------------------------- 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 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 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: 4.9990 chunk 16 optimal weight: 3.9990 chunk 78 optimal weight: 0.0370 chunk 105 optimal weight: 0.4980 chunk 115 optimal weight: 8.9990 chunk 44 optimal weight: 1.9990 chunk 39 optimal weight: 7.9990 chunk 79 optimal weight: 0.8980 chunk 8 optimal weight: 5.9990 chunk 61 optimal weight: 0.5980 overall best weight: 0.8060 ------------------------------------------------------------------------------- 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 = 0.3766 r_free = 0.3766 target = 0.137814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.098616 restraints weight = 12670.482| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 2.69 r_work: 0.3091 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.2020 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= 0.132 Angle : 0.555 7.732 12546 Z= 0.291 Chirality : 0.040 0.148 1511 Planarity : 0.004 0.050 1613 Dihedral : 4.354 29.053 1303 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer: Outliers : 2.73 % Allowed : 18.66 % 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: 0.02 (0.25), residues: 1185 helix: 1.58 (0.19), residues: 780 sheet: -2.44 (0.84), residues: 32 loop : -3.36 (0.25), residues: 373 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 0.013 0.001 PHE A 293 TYR 0.010 0.001 TYR B 400 ARG 0.002 0.000 ARG A 433 Details of bonding type rmsd hydrogen bonds : bond 0.05043 ( 571) hydrogen bonds : angle 4.27294 ( 1704) covalent geometry : bond 0.00284 ( 9216) covalent geometry : angle 0.55458 (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 114 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 88 time to evaluate : 1.096 Fit side-chains REVERT: A 310 GLU cc_start: 0.8722 (tt0) cc_final: 0.8429 (tt0) REVERT: A 417 ARG cc_start: 0.7344 (ppt170) cc_final: 0.6872 (ppt170) REVERT: A 431 TYR cc_start: 0.8138 (OUTLIER) cc_final: 0.6676 (m-80) REVERT: A 455 ARG cc_start: 0.8226 (tpm170) cc_final: 0.7961 (ttm110) REVERT: A 489 ARG cc_start: 0.7888 (mtm110) cc_final: 0.7088 (mpt180) REVERT: A 509 ARG cc_start: 0.8025 (OUTLIER) cc_final: 0.7604 (ptp-170) REVERT: B 15 ARG cc_start: 0.8864 (ptm-80) cc_final: 0.8663 (ptm-80) REVERT: B 41 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.7981 (mp) REVERT: B 139 ASN cc_start: 0.8272 (t0) cc_final: 0.8012 (t0) REVERT: B 209 MET cc_start: 0.8714 (mtt) cc_final: 0.8446 (mtm) REVERT: B 438 MET cc_start: 0.8576 (mmm) cc_final: 0.7995 (mmt) REVERT: B 509 PHE cc_start: 0.7730 (t80) cc_final: 0.7220 (t80) REVERT: B 548 LEU cc_start: 0.7430 (OUTLIER) cc_final: 0.7200 (tt) REVERT: B 594 LEU cc_start: 0.7719 (tp) cc_final: 0.7283 (tp) REVERT: B 622 MET cc_start: 0.8591 (tpp) cc_final: 0.8375 (tpt) outliers start: 26 outliers final: 14 residues processed: 109 average time/residue: 0.2599 time to fit residues: 38.5519 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 : 1.038 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 11 optimal weight: 3.9990 chunk 20 optimal weight: 0.0060 chunk 47 optimal weight: 8.9990 chunk 111 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 103 optimal weight: 0.6980 chunk 82 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 overall best weight: 0.6596 ------------------------------------------------------------------------------- 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 = 0.3777 r_free = 0.3777 target = 0.138762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.099540 restraints weight = 12867.410| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 2.72 r_work: 0.3103 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9216 Z= 0.125 Angle : 0.547 7.774 12546 Z= 0.287 Chirality : 0.040 0.138 1511 Planarity : 0.004 0.049 1613 Dihedral : 4.299 29.250 1303 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer: Outliers : 1.99 % Allowed : 19.60 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.25), residues: 1185 helix: 1.67 (0.19), residues: 782 sheet: -1.98 (0.96), residues: 27 loop : -3.24 (0.26), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 159 HIS 0.002 0.000 HIS B 609 PHE 0.013 0.001 PHE A 293 TYR 0.010 0.001 TYR B 400 ARG 0.002 0.000 ARG A 433 Details of bonding type rmsd hydrogen bonds : bond 0.04868 ( 571) hydrogen bonds : angle 4.21214 ( 1704) covalent geometry : bond 0.00264 ( 9216) covalent geometry : angle 0.54699 (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 117 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 98 time to evaluate : 1.781 Fit side-chains REVERT: A 310 GLU cc_start: 0.8709 (tt0) cc_final: 0.8432 (tt0) REVERT: A 417 ARG cc_start: 0.7337 (ppt170) cc_final: 0.6866 (ppt170) REVERT: A 431 TYR cc_start: 0.8125 (OUTLIER) cc_final: 0.6658 (m-80) REVERT: A 455 ARG cc_start: 0.8205 (tpm170) cc_final: 0.7951 (ttm110) REVERT: A 489 ARG cc_start: 0.7864 (mtm110) cc_final: 0.7077 (mpt180) REVERT: A 509 ARG cc_start: 0.8032 (OUTLIER) cc_final: 0.7613 (ptp-170) REVERT: B 15 ARG cc_start: 0.8908 (ptm-80) cc_final: 0.8698 (ptm-80) REVERT: B 41 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.7976 (mp) REVERT: B 95 ASP cc_start: 0.7595 (m-30) cc_final: 0.7193 (m-30) REVERT: B 139 ASN cc_start: 0.8255 (t0) cc_final: 0.7990 (t0) REVERT: B 209 MET cc_start: 0.8709 (mtt) cc_final: 0.8441 (mtm) REVERT: B 345 GLN cc_start: 0.8589 (tp40) cc_final: 0.8377 (tp40) REVERT: B 509 PHE cc_start: 0.7724 (t80) cc_final: 0.7224 (t80) REVERT: B 548 LEU cc_start: 0.7392 (OUTLIER) cc_final: 0.7166 (tt) REVERT: B 594 LEU cc_start: 0.7755 (tp) cc_final: 0.7311 (tp) REVERT: B 622 MET cc_start: 0.8637 (tpp) cc_final: 0.8416 (tpt) outliers start: 19 outliers final: 14 residues processed: 112 average time/residue: 0.3149 time to fit residues: 49.9378 Evaluate side-chains 113 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 95 time to evaluate : 1.116 ------------------------------------------------------------------------------- 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 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: 0.9990 chunk 104 optimal weight: 4.9990 chunk 108 optimal weight: 0.9990 chunk 46 optimal weight: 4.9990 chunk 116 optimal weight: 7.9990 chunk 14 optimal weight: 0.5980 chunk 60 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 56 optimal weight: 7.9990 chunk 103 optimal weight: 0.0770 chunk 32 optimal weight: 0.0060 overall best weight: 0.5358 ------------------------------------------------------------------------------- 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 = 0.3791 r_free = 0.3791 target = 0.139893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.100874 restraints weight = 12519.982| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 2.68 r_work: 0.3128 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9216 Z= 0.118 Angle : 0.539 7.943 12546 Z= 0.282 Chirality : 0.039 0.161 1511 Planarity : 0.004 0.049 1613 Dihedral : 4.247 29.215 1303 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 2.20 % Allowed : 19.29 % Favored : 78.51 % 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: 0.34 (0.25), residues: 1185 helix: 1.79 (0.19), residues: 781 sheet: -2.01 (0.97), residues: 27 loop : -3.19 (0.26), residues: 377 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 0.010 0.001 PHE A 220 TYR 0.009 0.001 TYR B 400 ARG 0.002 0.000 ARG A 433 Details of bonding type rmsd hydrogen bonds : bond 0.04671 ( 571) hydrogen bonds : angle 4.14559 ( 1704) covalent geometry : bond 0.00243 ( 9216) covalent geometry : angle 0.53901 (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 124 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 103 time to evaluate : 1.191 Fit side-chains REVERT: A 148 PHE cc_start: 0.7758 (m-80) cc_final: 0.7535 (m-80) REVERT: A 151 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8266 (mm) REVERT: A 310 GLU cc_start: 0.8718 (tt0) cc_final: 0.8451 (tt0) REVERT: A 417 ARG cc_start: 0.7359 (ppt170) cc_final: 0.6872 (ppt170) REVERT: A 431 TYR cc_start: 0.8097 (OUTLIER) cc_final: 0.6624 (m-80) REVERT: A 455 ARG cc_start: 0.8185 (tpm170) cc_final: 0.7944 (ttm110) REVERT: A 489 ARG cc_start: 0.7845 (mtm110) cc_final: 0.7080 (mpt180) REVERT: A 509 ARG cc_start: 0.8021 (OUTLIER) cc_final: 0.7607 (ptp-170) REVERT: B 41 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.7966 (mp) REVERT: B 139 ASN cc_start: 0.8237 (t0) cc_final: 0.7987 (t0) REVERT: B 345 GLN cc_start: 0.8608 (tp40) cc_final: 0.8349 (tp40) REVERT: B 349 GLN cc_start: 0.7637 (mm110) cc_final: 0.7279 (mm-40) REVERT: B 438 MET cc_start: 0.8403 (mmm) cc_final: 0.7878 (mmt) REVERT: B 509 PHE cc_start: 0.7720 (t80) cc_final: 0.7210 (t80) REVERT: B 548 LEU cc_start: 0.7378 (OUTLIER) cc_final: 0.7152 (tt) REVERT: B 594 LEU cc_start: 0.7773 (tp) cc_final: 0.7333 (tp) REVERT: B 622 MET cc_start: 0.8639 (tpp) cc_final: 0.8423 (tpt) outliers start: 21 outliers final: 15 residues processed: 118 average time/residue: 0.3073 time to fit residues: 51.4470 Evaluate side-chains 113 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 93 time to evaluate : 1.457 ------------------------------------------------------------------------------- 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 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 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 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: 5.9990 chunk 46 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 97 optimal weight: 9.9990 chunk 68 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 99 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 39 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN A 337 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.137792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.098449 restraints weight = 12694.183| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 2.68 r_work: 0.3097 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.2244 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 : 0.562 8.192 12546 Z= 0.294 Chirality : 0.040 0.173 1511 Planarity : 0.004 0.049 1613 Dihedral : 4.277 28.776 1303 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 2.31 % Allowed : 19.60 % 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 (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: 0.30 (0.25), residues: 1185 helix: 1.73 (0.19), residues: 782 sheet: -1.99 (0.97), residues: 27 loop : -3.14 (0.26), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 159 HIS 0.018 0.001 HIS A 337 PHE 0.011 0.001 PHE A 77 TYR 0.010 0.001 TYR B 400 ARG 0.002 0.000 ARG A 433 Details of bonding type rmsd hydrogen bonds : bond 0.05107 ( 571) hydrogen bonds : angle 4.22094 ( 1704) covalent geometry : bond 0.00306 ( 9216) covalent geometry : angle 0.56189 (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 116 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 94 time to evaluate : 1.169 Fit side-chains REVERT: A 148 PHE cc_start: 0.7756 (m-80) cc_final: 0.7497 (m-80) REVERT: A 151 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.8166 (mm) REVERT: A 417 ARG cc_start: 0.7317 (ppt170) cc_final: 0.6815 (ppt170) REVERT: A 431 TYR cc_start: 0.8159 (OUTLIER) cc_final: 0.6577 (m-80) REVERT: A 455 ARG cc_start: 0.8208 (tpm170) cc_final: 0.7953 (ttm110) REVERT: A 489 ARG cc_start: 0.7834 (mtm110) cc_final: 0.7062 (mpt180) REVERT: A 509 ARG cc_start: 0.8011 (OUTLIER) cc_final: 0.7595 (ptp-170) REVERT: A 544 ASP cc_start: 0.7905 (m-30) cc_final: 0.7625 (m-30) REVERT: B 41 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.7944 (mp) REVERT: B 95 ASP cc_start: 0.7557 (m-30) cc_final: 0.7159 (m-30) REVERT: B 139 ASN cc_start: 0.8236 (t0) cc_final: 0.7975 (t0) REVERT: B 345 GLN cc_start: 0.8572 (tp40) cc_final: 0.8356 (tp40) REVERT: B 509 PHE cc_start: 0.7721 (t80) cc_final: 0.7191 (t80) REVERT: B 548 LEU cc_start: 0.7352 (OUTLIER) cc_final: 0.7090 (tt) REVERT: B 594 LEU cc_start: 0.7823 (tp) cc_final: 0.7382 (tp) REVERT: B 622 MET cc_start: 0.8648 (tpp) cc_final: 0.8440 (tpt) outliers start: 22 outliers final: 16 residues processed: 112 average time/residue: 0.2768 time to fit residues: 44.6695 Evaluate side-chains 115 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 94 time to evaluate : 1.069 ------------------------------------------------------------------------------- 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 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 112 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 106 optimal weight: 4.9990 chunk 5 optimal weight: 0.7980 chunk 86 optimal weight: 0.3980 chunk 14 optimal weight: 0.7980 chunk 91 optimal weight: 0.8980 chunk 117 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3777 r_free = 0.3777 target = 0.138786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.099362 restraints weight = 12556.015| |-----------------------------------------------------------------------------| r_work (start): 0.3247 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: 0.7774 moved from start: 0.2330 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= 0.127 Angle : 0.551 8.164 12546 Z= 0.289 Chirality : 0.040 0.149 1511 Planarity : 0.004 0.048 1613 Dihedral : 4.243 28.896 1303 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.68 % Favored : 92.32 % Rotamer: Outliers : 2.20 % Allowed : 19.71 % 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 (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 (0.25), residues: 1185 helix: 1.78 (0.19), residues: 783 sheet: -1.91 (0.97), residues: 27 loop : -3.07 (0.26), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 159 HIS 0.005 0.000 HIS A 337 PHE 0.009 0.001 PHE A 77 TYR 0.010 0.001 TYR B 400 ARG 0.002 0.000 ARG A 433 Details of bonding type rmsd hydrogen bonds : bond 0.04893 ( 571) hydrogen bonds : angle 4.18482 ( 1704) covalent geometry : bond 0.00272 ( 9216) covalent geometry : angle 0.55138 (12546) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4616.97 seconds wall clock time: 82 minutes 47.01 seconds (4967.01 seconds total)