Starting phenix.real_space_refine on Sun Jun 8 00:43:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kwi_62611/06_2025/9kwi_62611.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kwi_62611/06_2025/9kwi_62611.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9kwi_62611/06_2025/9kwi_62611.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kwi_62611/06_2025/9kwi_62611.map" model { file = "/net/cci-nas-00/data/ceres_data/9kwi_62611/06_2025/9kwi_62611.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kwi_62611/06_2025/9kwi_62611.cif" } resolution = 3.19 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= -0.002 sd= 0.068 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 33 5.16 5 C 5773 2.51 5 N 1611 2.21 5 O 1702 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 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: 9127 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 574, 4348 Classifications: {'peptide': 574} Link IDs: {'PTRANS': 19, 'TRANS': 554} Chain: "B" Number of atoms: 4715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 616, 4715 Classifications: {'peptide': 616} Link IDs: {'PTRANS': 18, 'TRANS': 597} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.21, per 1000 atoms: 0.68 Number of scatterers: 9127 At special positions: 0 Unit cell: (68.224, 89.024, 151.424, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 33 16.00 P 6 15.00 Mg 2 11.99 O 1702 8.00 N 1611 7.00 C 5773 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: 2.83 Conformation dependent library (CDL) restraints added in 1.2 seconds 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2188 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 6 sheets defined 72.4% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'A' and resid -1 through 11 removed outlier: 3.732A pdb=" N TRP A 3 " --> pdb=" O SER A -1 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA A 4 " --> pdb=" O ASN A 0 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ARG A 11 " --> pdb=" O ARG A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 13 through 45 Proline residue: A 35 - end of helix Processing helix chain 'A' and resid 50 through 99 Processing helix chain 'A' and resid 102 through 110 removed outlier: 3.892A pdb=" N PHE A 109 " --> pdb=" O GLU A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 119 Processing helix chain 'A' and resid 119 through 135 removed outlier: 3.814A pdb=" N ILE A 125 " --> pdb=" O ASP A 121 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU A 128 " --> pdb=" O HIS A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 154 Processing helix chain 'A' and resid 157 through 203 removed outlier: 4.052A pdb=" N LEU A 161 " --> pdb=" O LEU A 157 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N VAL A 165 " --> pdb=" O LEU A 161 " (cutoff:3.500A) Proline residue: A 166 - end of helix Proline residue: A 181 - end of helix removed outlier: 3.868A pdb=" N GLY A 192 " --> pdb=" O SER A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 210 Processing helix chain 'A' and resid 212 through 239 removed outlier: 3.611A pdb=" N TRP A 237 " --> pdb=" O GLU A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 266 removed outlier: 3.803A pdb=" N VAL A 248 " --> pdb=" O VAL A 244 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA A 266 " --> pdb=" O LEU A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 294 removed outlier: 3.889A pdb=" N ILE A 275 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N MET A 286 " --> pdb=" O MET A 282 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N MET A 294 " --> pdb=" O MET A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 313 removed outlier: 4.443A pdb=" N ARG A 300 " --> pdb=" O VAL A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 382 Processing helix chain 'A' and resid 393 through 397 removed outlier: 3.563A pdb=" N GLY A 396 " --> pdb=" O ARG A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 Processing helix chain 'A' and resid 425 through 434 removed outlier: 3.579A pdb=" N TYR A 431 " --> pdb=" O GLU A 427 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N GLY A 432 " --> pdb=" O ASN A 428 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ARG A 433 " --> pdb=" O LEU A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 448 Processing helix chain 'A' and resid 451 through 456 Processing helix chain 'A' and resid 459 through 462 Processing helix chain 'A' and resid 473 through 488 removed outlier: 3.778A pdb=" N ARG A 488 " --> pdb=" O ARG A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 518 Processing helix chain 'A' and resid 519 through 521 No H-bonds generated for 'chain 'A' and resid 519 through 521' Processing helix chain 'A' and resid 529 through 533 Processing helix chain 'A' and resid 552 through 560 Processing helix chain 'A' and resid 560 through 571 Processing helix chain 'B' and resid 16 through 29 removed outlier: 3.725A pdb=" N SER B 20 " --> pdb=" O ASP B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 72 removed outlier: 3.665A pdb=" N GLY B 52 " --> pdb=" O ILE B 48 " (cutoff:3.500A) Proline residue: B 53 - end of helix removed outlier: 3.778A pdb=" N GLU B 71 " --> pdb=" O VAL B 67 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU B 72 " --> pdb=" O ILE B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 88 Processing helix chain 'B' and resid 91 through 99 removed outlier: 3.601A pdb=" N ASP B 95 " --> pdb=" O GLY B 91 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLY B 99 " --> pdb=" O ASP B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 160 Processing helix chain 'B' and resid 161 through 167 removed outlier: 3.868A pdb=" N PHE B 165 " --> pdb=" O PRO B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 178 Processing helix chain 'B' and resid 178 through 213 removed outlier: 5.994A pdb=" N SER B 193 " --> pdb=" O SER B 189 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N GLN B 194 " --> pdb=" O MET B 190 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N PHE B 203 " --> pdb=" O VAL B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 222 Processing helix chain 'B' and resid 222 through 262 removed outlier: 3.593A pdb=" N ALA B 226 " --> pdb=" O VAL B 222 " (cutoff:3.500A) Proline residue: B 240 - end of helix removed outlier: 3.552A pdb=" N GLY B 262 " --> pdb=" O GLU B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 269 Processing helix chain 'B' and resid 271 through 299 Processing helix chain 'B' and resid 299 through 326 removed outlier: 3.602A pdb=" N ALA B 303 " --> pdb=" O LEU B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 372 Proline residue: B 346 - end of helix removed outlier: 4.743A pdb=" N ASN B 355 " --> pdb=" O ALA B 351 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N THR B 356 " --> pdb=" O GLY B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 438 Processing helix chain 'B' and resid 456 through 458 No H-bonds generated for 'chain 'B' and resid 456 through 458' Processing helix chain 'B' and resid 459 through 466 Processing helix chain 'B' and resid 481 through 487 Processing helix chain 'B' and resid 493 through 504 Processing helix chain 'B' and resid 505 through 511 removed outlier: 4.212A pdb=" N PHE B 509 " --> pdb=" O TYR B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 544 removed outlier: 3.796A pdb=" N ALA B 544 " --> pdb=" O ARG B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 576 removed outlier: 3.734A pdb=" N LEU B 565 " --> pdb=" O ARG B 561 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N GLU B 572 " --> pdb=" O HIS B 568 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N LEU B 573 " --> pdb=" O ALA B 569 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N ASP B 576 " --> pdb=" O GLU B 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 585 through 590 removed outlier: 3.655A pdb=" N ILE B 589 " --> pdb=" O ARG B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 615 Processing helix chain 'B' and resid 616 through 628 removed outlier: 3.893A pdb=" N TRP B 620 " --> pdb=" O HIS B 616 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N HIS B 626 " --> pdb=" O MET B 622 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEU B 627 " --> pdb=" O THR B 623 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 351 through 354 removed outlier: 5.391A pdb=" N GLN A 352 " --> pdb=" O PHE A 341 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N PHE A 341 " --> pdb=" O GLN A 352 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N ASP A 338 " --> pdb=" O SER A 391 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N SER A 391 " --> pdb=" O ASP A 338 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 411 through 414 removed outlier: 6.757A pdb=" N VAL A 539 " --> pdb=" O ILE A 550 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ILE A 550 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N VAL A 541 " --> pdb=" O VAL A 548 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 423 through 424 Processing sheet with id=AA4, first strand: chain 'B' and resid 407 through 414 removed outlier: 6.481A pdb=" N GLU B 408 " --> pdb=" O SER B 397 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N SER B 397 " --> pdb=" O GLU B 408 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N LEU B 410 " --> pdb=" O HIS B 395 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N PHE B 393 " --> pdb=" O THR B 449 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N THR B 449 " --> pdb=" O PHE B 393 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N HIS B 395 " --> pdb=" O ARG B 447 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N ARG B 447 " --> pdb=" O HIS B 395 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 467 through 470 removed outlier: 6.447A pdb=" N ALA B 421 " --> pdb=" O LEU B 596 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N MET B 598 " --> pdb=" O ALA B 421 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N VAL B 423 " --> pdb=" O MET B 598 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 479 through 480 648 hydrogen bonds defined for protein. 1905 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: 2.98 Time building geometry restraints manager: 3.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1817 1.33 - 1.45: 2129 1.45 - 1.57: 5266 1.57 - 1.69: 10 1.69 - 1.81: 61 Bond restraints: 9283 Sorted by residual: bond pdb=" CA ALA B 554 " pdb=" CB ALA B 554 " ideal model delta sigma weight residual 1.532 1.467 0.064 1.65e-02 3.67e+03 1.52e+01 bond pdb=" C ALA B 554 " pdb=" O ALA B 554 " ideal model delta sigma weight residual 1.236 1.207 0.029 1.32e-02 5.74e+03 4.90e+00 bond pdb=" C ASP B 552 " pdb=" O ASP B 552 " ideal model delta sigma weight residual 1.233 1.210 0.023 1.26e-02 6.30e+03 3.44e+00 bond pdb=" C ALA B 554 " pdb=" N THR B 555 " ideal model delta sigma weight residual 1.330 1.305 0.026 1.43e-02 4.89e+03 3.19e+00 bond pdb=" C LEU B 551 " pdb=" O LEU B 551 " ideal model delta sigma weight residual 1.234 1.214 0.020 1.20e-02 6.94e+03 2.73e+00 ... (remaining 9278 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.48: 12393 1.48 - 2.96: 208 2.96 - 4.43: 27 4.43 - 5.91: 19 5.91 - 7.39: 4 Bond angle restraints: 12651 Sorted by residual: angle pdb=" CA ASP B 552 " pdb=" CB ASP B 552 " pdb=" CG ASP B 552 " ideal model delta sigma weight residual 112.60 116.77 -4.17 1.00e+00 1.00e+00 1.74e+01 angle pdb=" N ALA B 554 " pdb=" CA ALA B 554 " pdb=" C ALA B 554 " ideal model delta sigma weight residual 113.23 108.34 4.89 1.24e+00 6.50e-01 1.56e+01 angle pdb=" C GLN B 553 " pdb=" CA GLN B 553 " pdb=" CB GLN B 553 " ideal model delta sigma weight residual 110.42 117.81 -7.39 1.99e+00 2.53e-01 1.38e+01 angle pdb=" CA ASP B 552 " pdb=" C ASP B 552 " pdb=" O ASP B 552 " ideal model delta sigma weight residual 120.92 117.17 3.75 1.04e+00 9.25e-01 1.30e+01 angle pdb=" N GLN B 553 " pdb=" CA GLN B 553 " pdb=" C GLN B 553 " ideal model delta sigma weight residual 110.80 104.98 5.82 2.13e+00 2.20e-01 7.46e+00 ... (remaining 12646 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 4790 17.69 - 35.39: 562 35.39 - 53.08: 151 53.08 - 70.77: 30 70.77 - 88.47: 15 Dihedral angle restraints: 5548 sinusoidal: 2148 harmonic: 3400 Sorted by residual: dihedral pdb=" CA ILE A 404 " pdb=" C ILE A 404 " pdb=" N GLU A 405 " pdb=" CA GLU A 405 " ideal model delta harmonic sigma weight residual 180.00 152.19 27.81 0 5.00e+00 4.00e-02 3.09e+01 dihedral pdb=" CA ASN A 320 " pdb=" C ASN A 320 " pdb=" N PRO A 321 " pdb=" CA PRO A 321 " ideal model delta harmonic sigma weight residual 180.00 -161.05 -18.95 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" CA VAL B 401 " pdb=" C VAL B 401 " pdb=" N PRO B 402 " pdb=" CA PRO B 402 " ideal model delta harmonic sigma weight residual -180.00 -162.21 -17.79 0 5.00e+00 4.00e-02 1.27e+01 ... (remaining 5545 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1129 0.040 - 0.079: 290 0.079 - 0.119: 93 0.119 - 0.158: 7 0.158 - 0.198: 1 Chirality restraints: 1520 Sorted by residual: chirality pdb=" CB VAL B 188 " pdb=" CA VAL B 188 " pdb=" CG1 VAL B 188 " pdb=" CG2 VAL B 188 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 9.78e-01 chirality pdb=" CA ILE B 407 " pdb=" N ILE B 407 " pdb=" C ILE B 407 " pdb=" CB ILE B 407 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.34e-01 chirality pdb=" CA ALA B 554 " pdb=" N ALA B 554 " pdb=" C ALA B 554 " pdb=" CB ALA B 554 " both_signs ideal model delta sigma weight residual False 2.48 2.61 -0.13 2.00e-01 2.50e+01 4.19e-01 ... (remaining 1517 not shown) Planarity restraints: 1614 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B 52 " -0.032 5.00e-02 4.00e+02 4.90e-02 3.84e+00 pdb=" N PRO B 53 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO B 53 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 53 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 550 " 0.009 2.00e-02 2.50e+03 1.71e-02 2.94e+00 pdb=" C VAL B 550 " -0.030 2.00e-02 2.50e+03 pdb=" O VAL B 550 " 0.011 2.00e-02 2.50e+03 pdb=" N LEU B 551 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 160 " -0.009 2.00e-02 2.50e+03 1.70e-02 2.89e+00 pdb=" C LEU A 160 " 0.029 2.00e-02 2.50e+03 pdb=" O LEU A 160 " -0.011 2.00e-02 2.50e+03 pdb=" N LEU A 161 " -0.010 2.00e-02 2.50e+03 ... (remaining 1611 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 64 2.54 - 3.13: 7072 3.13 - 3.72: 15174 3.72 - 4.31: 19713 4.31 - 4.90: 34331 Nonbonded interactions: 76354 Sorted by model distance: nonbonded pdb=" OG SER A 375 " pdb="MG MG A 602 " model vdw 1.952 2.170 nonbonded pdb=" OG1 THR B 431 " pdb="MG MG B 701 " model vdw 1.963 2.170 nonbonded pdb=" OE1 GLN A 416 " pdb="MG MG A 602 " model vdw 2.015 2.170 nonbonded pdb=" OE1 GLN B 472 " pdb="MG MG B 701 " model vdw 2.021 2.170 nonbonded pdb=" O3G ATP A 601 " pdb="MG MG A 602 " model vdw 2.065 2.170 ... (remaining 76349 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: 1.650 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: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 26.350 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 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 : 0.003 0.064 9283 Z= 0.138 Angle : 0.518 7.390 12651 Z= 0.287 Chirality : 0.039 0.198 1520 Planarity : 0.003 0.049 1614 Dihedral : 16.984 88.467 3360 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.95 % Favored : 96.88 % Rotamer: Outliers : 2.94 % Allowed : 22.96 % Favored : 74.11 % 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: 1.98 (0.25), residues: 1186 helix: 2.04 (0.19), residues: 793 sheet: 1.82 (0.80), residues: 47 loop : -0.48 (0.32), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 246 HIS 0.009 0.001 HIS A 152 PHE 0.013 0.001 PHE A 453 TYR 0.011 0.001 TYR B 400 ARG 0.008 0.000 ARG A 417 Details of bonding type rmsd hydrogen bonds : bond 0.12354 ( 648) hydrogen bonds : angle 5.12894 ( 1905) covalent geometry : bond 0.00258 ( 9283) covalent geometry : angle 0.51820 (12651) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 110 time to evaluate : 0.996 Fit side-chains revert: symmetry clash REVERT: A 159 TRP cc_start: 0.7998 (p-90) cc_final: 0.7733 (p-90) REVERT: A 315 GLN cc_start: 0.8466 (OUTLIER) cc_final: 0.8262 (pt0) REVERT: B 208 MET cc_start: 0.9069 (tpp) cc_final: 0.8716 (mmt) REVERT: B 227 SER cc_start: 0.8518 (t) cc_final: 0.8273 (m) REVERT: B 287 GLN cc_start: 0.7624 (OUTLIER) cc_final: 0.7302 (tt0) outliers start: 28 outliers final: 19 residues processed: 129 average time/residue: 0.1875 time to fit residues: 35.4927 Evaluate side-chains 127 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 106 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain A residue 315 GLN Chi-restraints excluded: chain A residue 333 ASP Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 287 GLN Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 372 ASP Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain B residue 553 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 0.6980 chunk 89 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 68 optimal weight: 0.9990 chunk 107 optimal weight: 3.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 HIS A 270 GLN B 186 ASN ** B 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.140766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.118741 restraints weight = 12870.532| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 1.97 r_work: 0.3295 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.0706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9283 Z= 0.157 Angle : 0.510 5.463 12651 Z= 0.274 Chirality : 0.041 0.147 1520 Planarity : 0.004 0.050 1614 Dihedral : 8.204 79.692 1408 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.12 % Favored : 96.71 % Rotamer: Outliers : 4.40 % Allowed : 20.55 % Favored : 75.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.03 (0.25), residues: 1186 helix: 2.08 (0.18), residues: 800 sheet: 1.27 (0.78), residues: 47 loop : -0.42 (0.33), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 246 HIS 0.007 0.001 HIS A 152 PHE 0.014 0.001 PHE A 453 TYR 0.011 0.001 TYR B 400 ARG 0.005 0.000 ARG A 417 Details of bonding type rmsd hydrogen bonds : bond 0.04615 ( 648) hydrogen bonds : angle 4.33092 ( 1905) covalent geometry : bond 0.00358 ( 9283) covalent geometry : angle 0.51002 (12651) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 124 time to evaluate : 1.067 Fit side-chains REVERT: A 159 TRP cc_start: 0.8052 (p-90) cc_final: 0.7796 (p-90) REVERT: A 256 LEU cc_start: 0.8517 (tp) cc_final: 0.8236 (tt) REVERT: A 315 GLN cc_start: 0.8654 (OUTLIER) cc_final: 0.8448 (pt0) REVERT: A 427 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.8138 (mt-10) REVERT: A 515 ARG cc_start: 0.8091 (ttm-80) cc_final: 0.7752 (mtp85) REVERT: B 208 MET cc_start: 0.9118 (tpp) cc_final: 0.8564 (mmt) REVERT: B 287 GLN cc_start: 0.7950 (OUTLIER) cc_final: 0.7679 (tt0) REVERT: B 325 THR cc_start: 0.7905 (m) cc_final: 0.7458 (p) REVERT: B 620 TRP cc_start: 0.8892 (t60) cc_final: 0.8619 (t-100) outliers start: 42 outliers final: 27 residues processed: 159 average time/residue: 0.1966 time to fit residues: 44.8518 Evaluate side-chains 141 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 111 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 LEU Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 212 ARG Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 315 GLN Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 342 CYS Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 422 SER Chi-restraints excluded: chain A residue 427 GLU Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 287 GLN Chi-restraints excluded: chain B residue 372 ASP Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 473 ASP Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain B residue 553 GLN Chi-restraints excluded: chain B residue 625 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 9 optimal weight: 0.9990 chunk 93 optimal weight: 6.9990 chunk 99 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 64 optimal weight: 9.9990 chunk 74 optimal weight: 0.9980 chunk 86 optimal weight: 0.7980 chunk 72 optimal weight: 0.8980 chunk 58 optimal weight: 5.9990 chunk 88 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 HIS A 194 ASN ** B 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 568 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.140985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.117488 restraints weight = 12973.665| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 2.25 r_work: 0.3291 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.0944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9283 Z= 0.135 Angle : 0.483 5.546 12651 Z= 0.258 Chirality : 0.040 0.143 1520 Planarity : 0.004 0.051 1614 Dihedral : 7.647 82.762 1391 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.20 % Favored : 96.63 % Rotamer: Outliers : 4.30 % Allowed : 20.96 % Favored : 74.74 % 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: 2.12 (0.25), residues: 1186 helix: 2.20 (0.18), residues: 798 sheet: 0.92 (0.76), residues: 47 loop : -0.45 (0.33), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 246 HIS 0.008 0.001 HIS A 152 PHE 0.012 0.001 PHE A 453 TYR 0.013 0.001 TYR B 339 ARG 0.005 0.000 ARG A 417 Details of bonding type rmsd hydrogen bonds : bond 0.04362 ( 648) hydrogen bonds : angle 4.16967 ( 1905) covalent geometry : bond 0.00296 ( 9283) covalent geometry : angle 0.48303 (12651) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 123 time to evaluate : 1.214 Fit side-chains REVERT: A 159 TRP cc_start: 0.8049 (p-90) cc_final: 0.7803 (p-90) REVERT: A 256 LEU cc_start: 0.8452 (tp) cc_final: 0.8232 (tt) REVERT: A 427 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.7959 (mt-10) REVERT: A 515 ARG cc_start: 0.7948 (ttm-80) cc_final: 0.7662 (mtp85) REVERT: B 325 THR cc_start: 0.8011 (m) cc_final: 0.7579 (p) REVERT: B 620 TRP cc_start: 0.8832 (t60) cc_final: 0.8540 (t-100) outliers start: 41 outliers final: 24 residues processed: 158 average time/residue: 0.2446 time to fit residues: 55.0805 Evaluate side-chains 140 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 115 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 LEU Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 212 ARG Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 422 SER Chi-restraints excluded: chain A residue 427 GLU Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 372 ASP Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 473 ASP Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain B residue 553 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 42 optimal weight: 3.9990 chunk 95 optimal weight: 0.0370 chunk 67 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 99 optimal weight: 0.8980 chunk 33 optimal weight: 6.9990 chunk 100 optimal weight: 0.7980 chunk 19 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 29 optimal weight: 10.0000 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 HIS ** B 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.141867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.120201 restraints weight = 12933.938| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 1.95 r_work: 0.3322 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.1121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9283 Z= 0.119 Angle : 0.468 5.470 12651 Z= 0.250 Chirality : 0.039 0.141 1520 Planarity : 0.003 0.051 1614 Dihedral : 7.122 86.112 1384 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.20 % Favored : 96.63 % Rotamer: Outliers : 3.98 % Allowed : 21.07 % Favored : 74.95 % 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: 2.21 (0.25), residues: 1186 helix: 2.27 (0.18), residues: 799 sheet: 1.30 (0.86), residues: 37 loop : -0.42 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 246 HIS 0.008 0.001 HIS A 152 PHE 0.014 0.001 PHE A 281 TYR 0.011 0.001 TYR B 339 ARG 0.006 0.000 ARG B 247 Details of bonding type rmsd hydrogen bonds : bond 0.04108 ( 648) hydrogen bonds : angle 4.06659 ( 1905) covalent geometry : bond 0.00250 ( 9283) covalent geometry : angle 0.46773 (12651) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 123 time to evaluate : 1.090 Fit side-chains REVERT: A 159 TRP cc_start: 0.8043 (p-90) cc_final: 0.7800 (p-90) REVERT: A 348 ARG cc_start: 0.7566 (OUTLIER) cc_final: 0.6897 (ptt-90) REVERT: A 427 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.8045 (mt-10) REVERT: A 515 ARG cc_start: 0.8035 (ttm-80) cc_final: 0.7766 (mtp85) REVERT: B 208 MET cc_start: 0.9106 (tpp) cc_final: 0.8472 (mmt) REVERT: B 325 THR cc_start: 0.8096 (m) cc_final: 0.7647 (p) REVERT: B 518 ASP cc_start: 0.8364 (m-30) cc_final: 0.8103 (m-30) REVERT: B 620 TRP cc_start: 0.8892 (t60) cc_final: 0.8580 (t-100) outliers start: 38 outliers final: 27 residues processed: 155 average time/residue: 0.2244 time to fit residues: 48.4082 Evaluate side-chains 146 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 117 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 LEU Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 212 ARG Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 348 ARG Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 422 SER Chi-restraints excluded: chain A residue 427 GLU Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 267 LYS Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 372 ASP Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 473 ASP Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain B residue 553 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 86 optimal weight: 0.6980 chunk 69 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 109 optimal weight: 0.8980 chunk 55 optimal weight: 6.9990 chunk 98 optimal weight: 0.9990 chunk 68 optimal weight: 4.9990 chunk 108 optimal weight: 0.3980 chunk 96 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 HIS B 80 GLN B 248 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.141420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.119681 restraints weight = 13002.015| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 1.96 r_work: 0.3305 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.1284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9283 Z= 0.125 Angle : 0.473 6.028 12651 Z= 0.250 Chirality : 0.039 0.142 1520 Planarity : 0.003 0.051 1614 Dihedral : 6.985 88.234 1382 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.37 % Favored : 96.54 % Rotamer: Outliers : 4.30 % Allowed : 20.44 % Favored : 75.26 % 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: 2.25 (0.25), residues: 1186 helix: 2.32 (0.18), residues: 798 sheet: 1.23 (0.84), residues: 37 loop : -0.44 (0.34), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 246 HIS 0.007 0.001 HIS A 152 PHE 0.011 0.001 PHE B 336 TYR 0.011 0.001 TYR B 339 ARG 0.008 0.000 ARG B 366 Details of bonding type rmsd hydrogen bonds : bond 0.04078 ( 648) hydrogen bonds : angle 4.01281 ( 1905) covalent geometry : bond 0.00270 ( 9283) covalent geometry : angle 0.47302 (12651) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 122 time to evaluate : 1.093 Fit side-chains revert: symmetry clash REVERT: A 159 TRP cc_start: 0.8045 (p-90) cc_final: 0.7837 (p-90) REVERT: A 348 ARG cc_start: 0.7466 (OUTLIER) cc_final: 0.6790 (ptt-90) REVERT: A 427 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.7923 (mt-10) REVERT: A 515 ARG cc_start: 0.7918 (ttm-80) cc_final: 0.7588 (mtp85) REVERT: A 563 TYR cc_start: 0.8818 (t80) cc_final: 0.8605 (t80) REVERT: B 186 ASN cc_start: 0.7607 (m-40) cc_final: 0.7247 (t0) REVERT: B 208 MET cc_start: 0.9087 (tpp) cc_final: 0.8471 (mmt) REVERT: B 325 THR cc_start: 0.8064 (m) cc_final: 0.7626 (p) REVERT: B 518 ASP cc_start: 0.8209 (m-30) cc_final: 0.7992 (m-30) REVERT: B 620 TRP cc_start: 0.8797 (t60) cc_final: 0.8483 (t-100) outliers start: 41 outliers final: 31 residues processed: 156 average time/residue: 0.2145 time to fit residues: 47.8899 Evaluate side-chains 149 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 116 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 LEU Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 212 ARG Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 342 CYS Chi-restraints excluded: chain A residue 348 ARG Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 422 SER Chi-restraints excluded: chain A residue 427 GLU Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 267 LYS Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 372 ASP Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 473 ASP Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain B residue 553 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 43 optimal weight: 3.9990 chunk 10 optimal weight: 0.5980 chunk 117 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 chunk 21 optimal weight: 0.3980 chunk 6 optimal weight: 0.7980 chunk 112 optimal weight: 0.7980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 HIS B 568 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.141945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.119928 restraints weight = 12819.725| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 1.98 r_work: 0.3292 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.1404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 9283 Z= 0.120 Angle : 0.475 8.746 12651 Z= 0.249 Chirality : 0.039 0.141 1520 Planarity : 0.003 0.050 1614 Dihedral : 6.881 89.434 1382 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.29 % Favored : 96.63 % Rotamer: Outliers : 3.67 % Allowed : 21.91 % Favored : 74.42 % 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: 2.31 (0.25), residues: 1186 helix: 2.37 (0.18), residues: 796 sheet: 1.25 (0.84), residues: 37 loop : -0.43 (0.33), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 233 HIS 0.008 0.001 HIS A 152 PHE 0.013 0.001 PHE B 343 TYR 0.010 0.001 TYR B 339 ARG 0.006 0.000 ARG B 366 Details of bonding type rmsd hydrogen bonds : bond 0.03992 ( 648) hydrogen bonds : angle 3.96519 ( 1905) covalent geometry : bond 0.00258 ( 9283) covalent geometry : angle 0.47473 (12651) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 124 time to evaluate : 1.055 Fit side-chains revert: symmetry clash REVERT: A 159 TRP cc_start: 0.8069 (p-90) cc_final: 0.7867 (p-90) REVERT: A 348 ARG cc_start: 0.7580 (OUTLIER) cc_final: 0.6892 (ptt-90) REVERT: A 427 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.8061 (mt-10) REVERT: A 515 ARG cc_start: 0.8058 (ttm-80) cc_final: 0.7712 (mtp85) REVERT: A 563 TYR cc_start: 0.8901 (t80) cc_final: 0.8686 (t80) REVERT: B 186 ASN cc_start: 0.7656 (m-40) cc_final: 0.7205 (t0) REVERT: B 208 MET cc_start: 0.9138 (tpp) cc_final: 0.8564 (mmt) REVERT: B 325 THR cc_start: 0.8062 (m) cc_final: 0.7619 (p) REVERT: B 518 ASP cc_start: 0.8375 (m-30) cc_final: 0.8143 (m-30) REVERT: B 620 TRP cc_start: 0.8875 (t60) cc_final: 0.8631 (t-100) REVERT: B 624 ARG cc_start: 0.8346 (mmm-85) cc_final: 0.7630 (ttp80) outliers start: 35 outliers final: 30 residues processed: 153 average time/residue: 0.2424 time to fit residues: 52.1142 Evaluate side-chains 152 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 120 time to evaluate : 1.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 LEU Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 212 ARG Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 342 CYS Chi-restraints excluded: chain A residue 348 ARG Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 422 SER Chi-restraints excluded: chain A residue 427 GLU Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 267 LYS Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 372 ASP Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 473 ASP Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain B residue 553 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 67 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 97 optimal weight: 4.9990 chunk 116 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 58 optimal weight: 0.9980 chunk 88 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 HIS B 568 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.139937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.118378 restraints weight = 13149.052| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 1.94 r_work: 0.3282 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.1507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 9283 Z= 0.127 Angle : 0.478 6.878 12651 Z= 0.251 Chirality : 0.040 0.144 1520 Planarity : 0.003 0.050 1614 Dihedral : 6.815 89.866 1381 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.37 % Favored : 96.54 % Rotamer: Outliers : 3.77 % Allowed : 21.17 % Favored : 75.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.27 (0.25), residues: 1186 helix: 2.34 (0.18), residues: 802 sheet: 1.23 (0.84), residues: 37 loop : -0.48 (0.34), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 229 HIS 0.008 0.001 HIS A 152 PHE 0.013 0.001 PHE B 509 TYR 0.011 0.001 TYR B 339 ARG 0.006 0.000 ARG B 366 Details of bonding type rmsd hydrogen bonds : bond 0.04049 ( 648) hydrogen bonds : angle 3.94397 ( 1905) covalent geometry : bond 0.00281 ( 9283) covalent geometry : angle 0.47765 (12651) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 123 time to evaluate : 1.245 Fit side-chains revert: symmetry clash REVERT: A 159 TRP cc_start: 0.8095 (p-90) cc_final: 0.7880 (p-90) REVERT: A 348 ARG cc_start: 0.7626 (OUTLIER) cc_final: 0.6916 (ptt-90) REVERT: A 427 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.8082 (mt-10) REVERT: A 515 ARG cc_start: 0.8113 (ttm-80) cc_final: 0.7767 (mtp85) REVERT: B 208 MET cc_start: 0.9134 (tpp) cc_final: 0.8604 (mmt) REVERT: B 325 THR cc_start: 0.8089 (m) cc_final: 0.7647 (p) REVERT: B 518 ASP cc_start: 0.8387 (m-30) cc_final: 0.8158 (m-30) REVERT: B 620 TRP cc_start: 0.8890 (t60) cc_final: 0.8638 (t-100) REVERT: B 624 ARG cc_start: 0.8328 (mmm-85) cc_final: 0.7628 (ttp80) outliers start: 36 outliers final: 30 residues processed: 153 average time/residue: 0.3150 time to fit residues: 68.6900 Evaluate side-chains 151 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 119 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 LEU Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 212 ARG Chi-restraints excluded: chain A residue 241 MET Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 342 CYS Chi-restraints excluded: chain A residue 348 ARG Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 422 SER Chi-restraints excluded: chain A residue 427 GLU Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 267 LYS Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 473 ASP Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 519 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 76 optimal weight: 0.5980 chunk 53 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 66 optimal weight: 7.9990 chunk 47 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 HIS B 186 ASN B 344 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.141236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.119104 restraints weight = 13231.914| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 2.03 r_work: 0.3280 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 9283 Z= 0.126 Angle : 0.476 6.815 12651 Z= 0.251 Chirality : 0.040 0.149 1520 Planarity : 0.003 0.050 1614 Dihedral : 6.553 89.922 1376 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.37 % Favored : 96.54 % Rotamer: Outliers : 3.77 % Allowed : 21.59 % Favored : 74.63 % 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: 2.27 (0.25), residues: 1186 helix: 2.35 (0.18), residues: 802 sheet: 1.24 (0.84), residues: 37 loop : -0.50 (0.33), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 233 HIS 0.008 0.001 HIS A 152 PHE 0.012 0.001 PHE B 343 TYR 0.010 0.001 TYR B 400 ARG 0.005 0.000 ARG B 366 Details of bonding type rmsd hydrogen bonds : bond 0.04024 ( 648) hydrogen bonds : angle 3.93349 ( 1905) covalent geometry : bond 0.00277 ( 9283) covalent geometry : angle 0.47642 (12651) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 121 time to evaluate : 1.019 Fit side-chains revert: symmetry clash REVERT: A 159 TRP cc_start: 0.8132 (p-90) cc_final: 0.7931 (p-90) REVERT: A 348 ARG cc_start: 0.7467 (OUTLIER) cc_final: 0.6765 (ptt-90) REVERT: A 427 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7900 (mt-10) REVERT: A 515 ARG cc_start: 0.8000 (ttm-80) cc_final: 0.7670 (mtp85) REVERT: B 208 MET cc_start: 0.9070 (tpp) cc_final: 0.8499 (mmt) REVERT: B 325 THR cc_start: 0.8080 (m) cc_final: 0.7662 (p) REVERT: B 620 TRP cc_start: 0.8812 (t60) cc_final: 0.8500 (t-100) outliers start: 36 outliers final: 31 residues processed: 149 average time/residue: 0.3140 time to fit residues: 67.5657 Evaluate side-chains 152 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 119 time to evaluate : 1.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 LEU Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 212 ARG Chi-restraints excluded: chain A residue 241 MET Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 342 CYS Chi-restraints excluded: chain A residue 348 ARG Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 422 SER Chi-restraints excluded: chain A residue 427 GLU Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 267 LYS Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 473 ASP Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 519 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 54 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 chunk 40 optimal weight: 0.4980 chunk 42 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 108 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 HIS B 65 ASN B 344 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.141799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.119925 restraints weight = 12930.231| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 1.98 r_work: 0.3293 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9283 Z= 0.119 Angle : 0.474 6.595 12651 Z= 0.250 Chirality : 0.039 0.141 1520 Planarity : 0.003 0.051 1614 Dihedral : 6.482 88.542 1376 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.29 % Favored : 96.63 % Rotamer: Outliers : 3.67 % Allowed : 22.01 % Favored : 74.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.32 (0.25), residues: 1186 helix: 2.40 (0.18), residues: 798 sheet: 1.21 (0.84), residues: 37 loop : -0.50 (0.33), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 233 HIS 0.008 0.001 HIS A 152 PHE 0.011 0.001 PHE B 336 TYR 0.009 0.001 TYR B 400 ARG 0.009 0.000 ARG A 417 Details of bonding type rmsd hydrogen bonds : bond 0.03944 ( 648) hydrogen bonds : angle 3.90829 ( 1905) covalent geometry : bond 0.00259 ( 9283) covalent geometry : angle 0.47413 (12651) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 123 time to evaluate : 1.090 Fit side-chains revert: symmetry clash REVERT: A 159 TRP cc_start: 0.8159 (p-90) cc_final: 0.7958 (p-90) REVERT: A 348 ARG cc_start: 0.7609 (OUTLIER) cc_final: 0.6897 (ptt-90) REVERT: A 427 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.8038 (mt-10) REVERT: A 515 ARG cc_start: 0.8102 (ttm-80) cc_final: 0.7770 (mtp85) REVERT: B 208 MET cc_start: 0.9095 (tpp) cc_final: 0.8856 (mmt) REVERT: B 325 THR cc_start: 0.8065 (m) cc_final: 0.7631 (p) REVERT: B 620 TRP cc_start: 0.8876 (t60) cc_final: 0.8641 (t-100) REVERT: B 624 ARG cc_start: 0.8352 (mmm-85) cc_final: 0.7658 (ttp80) outliers start: 35 outliers final: 29 residues processed: 149 average time/residue: 0.2161 time to fit residues: 44.9514 Evaluate side-chains 151 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 120 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 LEU Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 212 ARG Chi-restraints excluded: chain A residue 241 MET Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 342 CYS Chi-restraints excluded: chain A residue 348 ARG Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 422 SER Chi-restraints excluded: chain A residue 427 GLU Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 267 LYS Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 473 ASP Chi-restraints excluded: chain B residue 510 VAL 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 67 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 chunk 6 optimal weight: 0.5980 chunk 74 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 108 optimal weight: 5.9990 chunk 96 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 26 optimal weight: 4.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 HIS B 344 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.141428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.119509 restraints weight = 13101.333| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 1.99 r_work: 0.3310 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 9283 Z= 0.124 Angle : 0.478 6.482 12651 Z= 0.253 Chirality : 0.039 0.143 1520 Planarity : 0.003 0.051 1614 Dihedral : 6.487 88.121 1376 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.20 % Favored : 96.71 % Rotamer: Outliers : 3.67 % Allowed : 22.43 % Favored : 73.90 % 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: 2.33 (0.25), residues: 1186 helix: 2.42 (0.18), residues: 798 sheet: 1.09 (0.83), residues: 37 loop : -0.50 (0.33), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 159 HIS 0.009 0.001 HIS A 152 PHE 0.011 0.001 PHE B 336 TYR 0.009 0.001 TYR B 400 ARG 0.008 0.000 ARG A 417 Details of bonding type rmsd hydrogen bonds : bond 0.03958 ( 648) hydrogen bonds : angle 3.89621 ( 1905) covalent geometry : bond 0.00271 ( 9283) covalent geometry : angle 0.47848 (12651) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 119 time to evaluate : 1.077 Fit side-chains revert: symmetry clash REVERT: A 348 ARG cc_start: 0.7452 (OUTLIER) cc_final: 0.6756 (ptt-90) REVERT: A 427 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7894 (mt-10) REVERT: A 515 ARG cc_start: 0.8002 (ttm-80) cc_final: 0.7694 (mtp85) REVERT: B 208 MET cc_start: 0.9034 (tpp) cc_final: 0.8797 (mmt) REVERT: B 325 THR cc_start: 0.8072 (m) cc_final: 0.7659 (p) REVERT: B 620 TRP cc_start: 0.8796 (t60) cc_final: 0.8468 (t-100) outliers start: 35 outliers final: 29 residues processed: 146 average time/residue: 0.2202 time to fit residues: 45.2614 Evaluate side-chains 150 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 119 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 LEU Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 212 ARG Chi-restraints excluded: chain A residue 241 MET Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 342 CYS Chi-restraints excluded: chain A residue 348 ARG Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 422 SER Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 427 GLU Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 267 LYS Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 473 ASP Chi-restraints excluded: chain B residue 510 VAL 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 103 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 87 optimal weight: 0.7980 chunk 64 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 46 optimal weight: 0.6980 chunk 65 optimal weight: 0.8980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 HIS B 344 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.135919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.115801 restraints weight = 13109.313| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 1.71 r_work: 0.3209 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9283 Z= 0.131 Angle : 0.491 7.012 12651 Z= 0.261 Chirality : 0.040 0.144 1520 Planarity : 0.004 0.059 1614 Dihedral : 6.493 88.733 1375 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.12 % Favored : 96.80 % Rotamer: Outliers : 3.67 % Allowed : 22.54 % Favored : 73.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.31 (0.25), residues: 1186 helix: 2.41 (0.18), residues: 800 sheet: 1.05 (0.83), residues: 37 loop : -0.55 (0.33), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 159 HIS 0.009 0.001 HIS A 152 PHE 0.012 0.001 PHE B 509 TYR 0.010 0.001 TYR B 400 ARG 0.008 0.000 ARG A 417 Details of bonding type rmsd hydrogen bonds : bond 0.04006 ( 648) hydrogen bonds : angle 3.89876 ( 1905) covalent geometry : bond 0.00292 ( 9283) covalent geometry : angle 0.49075 (12651) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4883.30 seconds wall clock time: 87 minutes 53.02 seconds (5273.02 seconds total)