Starting phenix.real_space_refine on Mon Dec 30 08:35:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wsf_32756/12_2024/7wsf_32756.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wsf_32756/12_2024/7wsf_32756.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wsf_32756/12_2024/7wsf_32756.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wsf_32756/12_2024/7wsf_32756.map" model { file = "/net/cci-nas-00/data/ceres_data/7wsf_32756/12_2024/7wsf_32756.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wsf_32756/12_2024/7wsf_32756.cif" } resolution = 2.87 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= -0.001 sd= 0.053 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 6717 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 38 5.16 5 C 4590 2.51 5 N 1192 2.21 5 O 1349 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 7170 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 693, 5677 Classifications: {'peptide': 693} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 659} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 16 Chain: "B" Number of atoms: 1492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1492 Classifications: {'peptide': 186} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 173} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.22, per 1000 atoms: 0.73 Number of scatterers: 7170 At special positions: 0 Unit cell: (72.252, 94.998, 140.49, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 38 16.00 O 1349 8.00 N 1192 7.00 C 4590 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 343 " - pdb=" SG CYS A 360 " distance=2.03 Simple disulfide: pdb=" SG CYS A 529 " - pdb=" SG CYS A 541 " distance=2.03 Simple disulfide: pdb=" SG CYS B 323 " - pdb=" SG CYS B 348 " distance=2.03 Simple disulfide: pdb=" SG CYS B 366 " - pdb=" SG CYS B 419 " distance=2.03 Simple disulfide: pdb=" SG CYS B 467 " - pdb=" SG CYS B 474 " distance=2.03 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: 2.06 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 801 " pdb="ZN ZN A 801 " - pdb=" NE2 HIS A 373 " pdb="ZN ZN A 801 " - pdb=" NE2 HIS A 377 " 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1664 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 7 sheets defined 55.2% alpha, 8.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 Processing helix chain 'A' and resid 56 through 81 removed outlier: 3.614A pdb=" N GLN A 60 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG A 78 " --> pdb=" O GLU A 74 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ILE A 79 " --> pdb=" O GLU A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 101 Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.667A pdb=" N SER A 106 " --> pdb=" O SER A 103 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL A 107 " --> pdb=" O GLY A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 129 removed outlier: 3.700A pdb=" N ASN A 117 " --> pdb=" O SER A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 153 removed outlier: 3.600A pdb=" N ILE A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 193 removed outlier: 4.091A pdb=" N LYS A 173 " --> pdb=" O ALA A 169 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN A 174 " --> pdb=" O GLU A 170 " (cutoff:3.500A) Proline residue: A 177 - end of helix Processing helix chain 'A' and resid 197 through 203 Processing helix chain 'A' and resid 204 through 207 Processing helix chain 'A' and resid 217 through 251 removed outlier: 3.877A pdb=" N ILE A 222 " --> pdb=" O ARG A 218 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU A 231 " --> pdb=" O ARG A 227 " (cutoff:3.500A) Proline residue: A 234 - end of helix Processing helix chain 'A' and resid 264 through 266 No H-bonds generated for 'chain 'A' and resid 264 through 266' Processing helix chain 'A' and resid 274 through 276 No H-bonds generated for 'chain 'A' and resid 274 through 276' Processing helix chain 'A' and resid 277 through 282 Processing helix chain 'A' and resid 292 through 298 removed outlier: 3.546A pdb=" N ASN A 298 " --> pdb=" O LYS A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 317 removed outlier: 3.554A pdb=" N PHE A 314 " --> pdb=" O ALA A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 330 removed outlier: 3.703A pdb=" N TRP A 327 " --> pdb=" O THR A 323 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL A 328 " --> pdb=" O GLN A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 384 removed outlier: 3.618A pdb=" N HIS A 372 " --> pdb=" O PHE A 368 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR A 380 " --> pdb=" O GLY A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 387 No H-bonds generated for 'chain 'A' and resid 385 through 387' Processing helix chain 'A' and resid 388 through 392 Processing helix chain 'A' and resid 398 through 412 removed outlier: 3.625A pdb=" N GLY A 404 " --> pdb=" O HIS A 400 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU A 405 " --> pdb=" O GLU A 401 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N MET A 407 " --> pdb=" O VAL A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 420 Processing helix chain 'A' and resid 430 through 446 removed outlier: 3.640A pdb=" N GLN A 444 " --> pdb=" O LYS A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 464 Processing helix chain 'A' and resid 471 through 481 Processing helix chain 'A' and resid 498 through 501 Processing helix chain 'A' and resid 502 through 507 Processing helix chain 'A' and resid 512 through 532 removed outlier: 3.872A pdb=" N THR A 518 " --> pdb=" O TYR A 514 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE A 522 " --> pdb=" O THR A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 541 removed outlier: 3.519A pdb=" N CYS A 541 " --> pdb=" O LEU A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 558 removed outlier: 3.576A pdb=" N GLY A 550 " --> pdb=" O SER A 546 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N MET A 556 " --> pdb=" O ARG A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 574 removed outlier: 3.739A pdb=" N ILE A 572 " --> pdb=" O ALA A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 587 removed outlier: 3.589A pdb=" N PHE A 587 " --> pdb=" O LEU A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 598 Processing helix chain 'A' and resid 638 through 657 removed outlier: 4.259A pdb=" N PHE A 642 " --> pdb=" O GLU A 638 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLN A 643 " --> pdb=" O MET A 639 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA A 647 " --> pdb=" O GLN A 643 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N TYR A 648 " --> pdb=" O SER A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 706 removed outlier: 3.596A pdb=" N SER A 706 " --> pdb=" O ALA A 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 330 Processing helix chain 'B' and resid 352 through 358 removed outlier: 3.890A pdb=" N TYR B 356 " --> pdb=" O TYR B 352 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASN B 357 " --> pdb=" O SER B 353 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N SER B 358 " --> pdb=" O VAL B 354 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 352 through 358' Processing helix chain 'B' and resid 371 through 375 removed outlier: 4.012A pdb=" N ASN B 375 " --> pdb=" O THR B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 397 Processing helix chain 'B' and resid 403 through 409 Processing helix chain 'B' and resid 425 through 430 Processing helix chain 'B' and resid 488 through 492 removed outlier: 3.501A pdb=" N GLN B 492 " --> pdb=" O ILE B 489 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 131 through 133 Processing sheet with id=AA2, first strand: chain 'A' and resid 261 through 262 removed outlier: 5.840A pdb=" N LEU A 261 " --> pdb=" O VAL A 487 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 346 through 351 removed outlier: 6.502A pdb=" N ASP A 354 " --> pdb=" O LEU A 350 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 617 through 620 removed outlier: 6.987A pdb=" N SER A 679 " --> pdb=" O LEU A 674 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N LEU A 674 " --> pdb=" O SER A 679 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 617 through 620 removed outlier: 12.867A pdb=" N PHE A 682 " --> pdb=" O ILE A 693 " (cutoff:3.500A) removed outlier: 11.089A pdb=" N ILE A 693 " --> pdb=" O PHE A 682 " (cutoff:3.500A) removed outlier: 10.485A pdb=" N VAL A 684 " --> pdb=" O SER A 691 " (cutoff:3.500A) removed outlier: 8.783A pdb=" N SER A 691 " --> pdb=" O VAL A 684 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N THR A 686 " --> pdb=" O ASN A 689 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 341 through 345 removed outlier: 3.504A pdb=" N GLU B 341 " --> pdb=" O SER B 386 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 439 through 441 335 hydrogen bonds defined for protein. 951 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: 2.57 Time building geometry restraints manager: 2.25 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: 2301 1.34 - 1.46: 1884 1.46 - 1.58: 3124 1.58 - 1.70: 0 1.70 - 1.82: 62 Bond restraints: 7371 Sorted by residual: bond pdb=" N PRO A 424 " pdb=" CA PRO A 424 " ideal model delta sigma weight residual 1.457 1.468 -0.011 1.31e-02 5.83e+03 6.81e-01 bond pdb=" C PRO A 424 " pdb=" O PRO A 424 " ideal model delta sigma weight residual 1.246 1.239 0.006 8.50e-03 1.38e+04 5.22e-01 bond pdb=" CB PRO B 470 " pdb=" CG PRO B 470 " ideal model delta sigma weight residual 1.506 1.482 0.024 3.90e-02 6.57e+02 3.74e-01 bond pdb=" CG PRO A 499 " pdb=" CD PRO A 499 " ideal model delta sigma weight residual 1.503 1.483 0.020 3.40e-02 8.65e+02 3.56e-01 bond pdb=" C SER B 461 " pdb=" O SER B 461 " ideal model delta sigma weight residual 1.244 1.236 0.008 1.41e-02 5.03e+03 3.33e-01 ... (remaining 7366 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.42: 9865 1.42 - 2.83: 104 2.83 - 4.25: 25 4.25 - 5.67: 7 5.67 - 7.09: 1 Bond angle restraints: 10002 Sorted by residual: angle pdb=" CA LEU A 583 " pdb=" CB LEU A 583 " pdb=" CG LEU A 583 " ideal model delta sigma weight residual 116.30 123.39 -7.09 3.50e+00 8.16e-02 4.10e+00 angle pdb=" N GLU A 494 " pdb=" CA GLU A 494 " pdb=" C GLU A 494 " ideal model delta sigma weight residual 110.80 114.49 -3.69 2.13e+00 2.20e-01 3.01e+00 angle pdb=" N VAL A 363 " pdb=" CA VAL A 363 " pdb=" C VAL A 363 " ideal model delta sigma weight residual 109.34 112.94 -3.60 2.08e+00 2.31e-01 3.00e+00 angle pdb=" CA TYR A 384 " pdb=" CB TYR A 384 " pdb=" CG TYR A 384 " ideal model delta sigma weight residual 113.90 116.45 -2.55 1.80e+00 3.09e-01 2.00e+00 angle pdb=" N ASP A 493 " pdb=" CA ASP A 493 " pdb=" C ASP A 493 " ideal model delta sigma weight residual 107.48 110.64 -3.16 2.29e+00 1.91e-01 1.90e+00 ... (remaining 9997 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 4146 17.99 - 35.99: 187 35.99 - 53.98: 33 53.98 - 71.97: 12 71.97 - 89.96: 3 Dihedral angle restraints: 4381 sinusoidal: 1788 harmonic: 2593 Sorted by residual: dihedral pdb=" CA ASP A 493 " pdb=" C ASP A 493 " pdb=" N GLU A 494 " pdb=" CA GLU A 494 " ideal model delta harmonic sigma weight residual 180.00 159.89 20.11 0 5.00e+00 4.00e-02 1.62e+01 dihedral pdb=" CA CYS A 343 " pdb=" CB CYS A 343 " pdb=" SG CYS A 343 " pdb=" SG CYS A 360 " ideal model delta sinusoidal sigma weight residual 79.00 19.07 59.93 1 2.00e+01 2.50e-03 1.20e+01 dihedral pdb=" CA PRO A 135 " pdb=" C PRO A 135 " pdb=" N ASN A 136 " pdb=" CA ASN A 136 " ideal model delta harmonic sigma weight residual 180.00 162.79 17.21 0 5.00e+00 4.00e-02 1.19e+01 ... (remaining 4378 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 555 0.026 - 0.052: 309 0.052 - 0.078: 99 0.078 - 0.104: 57 0.104 - 0.130: 14 Chirality restraints: 1034 Sorted by residual: chirality pdb=" CA ILE A 694 " pdb=" N ILE A 694 " pdb=" C ILE A 694 " pdb=" CB ILE A 694 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.24e-01 chirality pdb=" CA VAL A 208 " pdb=" N VAL A 208 " pdb=" C VAL A 208 " pdb=" CB VAL A 208 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 3.93e-01 chirality pdb=" CA VAL B 369 " pdb=" N VAL B 369 " pdb=" C VAL B 369 " pdb=" CB VAL B 369 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.78e-01 ... (remaining 1031 not shown) Planarity restraints: 1293 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A 387 " 0.023 5.00e-02 4.00e+02 3.48e-02 1.94e+00 pdb=" N PRO A 388 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO A 388 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 388 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 144 " 0.023 5.00e-02 4.00e+02 3.45e-02 1.90e+00 pdb=" N PRO A 145 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO A 145 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 145 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 581 " 0.018 5.00e-02 4.00e+02 2.79e-02 1.24e+00 pdb=" N PRO A 582 " -0.048 5.00e-02 4.00e+02 pdb=" CA PRO A 582 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 582 " 0.016 5.00e-02 4.00e+02 ... (remaining 1290 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 60 2.59 - 3.17: 5886 3.17 - 3.75: 11309 3.75 - 4.32: 16500 4.32 - 4.90: 26677 Nonbonded interactions: 60432 Sorted by model distance: nonbonded pdb=" OE2 GLU A 401 " pdb="ZN ZN A 801 " model vdw 2.016 2.230 nonbonded pdb=" OG SER B 336 " pdb=" O LYS B 439 " model vdw 2.158 3.040 nonbonded pdb=" OD2 ASP B 393 " pdb=" OH TYR B 481 " model vdw 2.220 3.040 nonbonded pdb=" O VAL A 432 " pdb=" ND2 ASN A 436 " model vdw 2.233 3.120 nonbonded pdb=" OH TYR B 356 " pdb=" OD1 ASN B 375 " model vdw 2.239 3.040 ... (remaining 60427 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: 2.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.000 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 23.910 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:16.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 43.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 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 0.028 7371 Z= 0.173 Angle : 0.440 7.085 10002 Z= 0.222 Chirality : 0.039 0.130 1034 Planarity : 0.003 0.035 1293 Dihedral : 11.232 89.963 2702 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.87 % Allowed : 7.09 % Favored : 89.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % 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: -0.12 (0.27), residues: 875 helix: -0.14 (0.24), residues: 422 sheet: 1.68 (0.65), residues: 60 loop : -0.12 (0.30), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 162 HIS 0.003 0.001 HIS A 240 PHE 0.008 0.001 PHE A 522 TYR 0.014 0.001 TYR A 384 ARG 0.002 0.000 ARG A 176 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 155 time to evaluate : 0.865 Fit side-chains Corrupt residue: chain: A residue: PRO 602 >>> skipping REVERT: A 35 GLU cc_start: 0.8173 (tt0) cc_final: 0.7551 (tp30) REVERT: A 362 LYS cc_start: 0.7336 (OUTLIER) cc_final: 0.6956 (mmtt) REVERT: A 596 GLU cc_start: 0.7789 (mt-10) cc_final: 0.7553 (mm-30) REVERT: A 599 ARG cc_start: 0.7290 (mtm110) cc_final: 0.7012 (ptp90) REVERT: A 634 TRP cc_start: 0.2653 (OUTLIER) cc_final: 0.1487 (m100) REVERT: B 324 PRO cc_start: 0.7678 (Cg_endo) cc_final: 0.7474 (Cg_exo) REVERT: B 395 ARG cc_start: 0.7843 (mtm-85) cc_final: 0.7058 (ttp80) REVERT: B 425 THR cc_start: 0.8914 (p) cc_final: 0.8627 (p) outliers start: 31 outliers final: 2 residues processed: 173 average time/residue: 1.3788 time to fit residues: 250.1882 Evaluate side-chains 88 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 84 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 LYS Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 602 PRO Chi-restraints excluded: chain A residue 634 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 73 optimal weight: 4.9990 chunk 65 optimal weight: 0.1980 chunk 36 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 68 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 79 optimal weight: 2.9990 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 298 ASN A 387 GLN A 637 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7371 Z= 0.210 Angle : 0.531 7.318 10002 Z= 0.277 Chirality : 0.042 0.129 1034 Planarity : 0.004 0.037 1293 Dihedral : 4.728 49.262 980 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.22 % Allowed : 13.02 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % 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: 0.54 (0.27), residues: 875 helix: 0.59 (0.25), residues: 417 sheet: 1.26 (0.65), residues: 61 loop : 0.11 (0.31), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 164 HIS 0.005 0.001 HIS A 240 PHE 0.021 0.001 PHE A 680 TYR 0.016 0.001 TYR A 384 ARG 0.004 0.000 ARG A 305 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 89 time to evaluate : 0.876 Fit side-chains Corrupt residue: chain: A residue: PRO 602 >>> skipping REVERT: A 145 PRO cc_start: 0.8299 (Cg_endo) cc_final: 0.7923 (Cg_exo) REVERT: A 155 GLU cc_start: 0.7038 (OUTLIER) cc_final: 0.6286 (mp0) REVERT: A 362 LYS cc_start: 0.7188 (OUTLIER) cc_final: 0.6824 (mmtt) REVERT: A 634 TRP cc_start: 0.2623 (OUTLIER) cc_final: 0.1524 (m100) REVERT: A 681 ASN cc_start: 0.7111 (m-40) cc_final: 0.6880 (m-40) REVERT: B 324 PRO cc_start: 0.7609 (Cg_endo) cc_final: 0.7405 (Cg_exo) REVERT: B 341 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7570 (mt-10) REVERT: B 395 ARG cc_start: 0.7773 (mtm-85) cc_final: 0.7074 (ttp80) REVERT: B 439 LYS cc_start: 0.8156 (mttp) cc_final: 0.7868 (mttt) outliers start: 26 outliers final: 8 residues processed: 111 average time/residue: 1.3533 time to fit residues: 158.1276 Evaluate side-chains 99 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 87 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLU Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 362 LYS Chi-restraints excluded: chain A residue 517 ARG Chi-restraints excluded: chain A residue 535 GLU Chi-restraints excluded: chain A residue 602 PRO Chi-restraints excluded: chain A residue 634 TRP Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 475 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 43 optimal weight: 0.5980 chunk 24 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 79 optimal weight: 3.9990 chunk 85 optimal weight: 0.9990 chunk 70 optimal weight: 0.4980 chunk 78 optimal weight: 0.9990 chunk 26 optimal weight: 0.0000 chunk 63 optimal weight: 0.9980 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 ASN B 435 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7371 Z= 0.167 Angle : 0.482 6.235 10002 Z= 0.250 Chirality : 0.040 0.127 1034 Planarity : 0.004 0.038 1293 Dihedral : 4.416 49.777 978 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.32 % Allowed : 14.95 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % 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: 0.74 (0.28), residues: 875 helix: 0.85 (0.25), residues: 422 sheet: 0.93 (0.67), residues: 55 loop : 0.20 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 164 HIS 0.004 0.001 HIS A 240 PHE 0.013 0.001 PHE A 680 TYR 0.016 0.001 TYR A 384 ARG 0.003 0.000 ARG A 305 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 96 time to evaluate : 0.780 Fit side-chains Corrupt residue: chain: A residue: PRO 602 >>> skipping REVERT: A 89 GLN cc_start: 0.7872 (tm-30) cc_final: 0.7429 (tp40) REVERT: A 145 PRO cc_start: 0.8302 (Cg_endo) cc_final: 0.7948 (Cg_exo) REVERT: A 155 GLU cc_start: 0.7125 (OUTLIER) cc_final: 0.6511 (mp0) REVERT: A 293 THR cc_start: 0.8242 (OUTLIER) cc_final: 0.7960 (m) REVERT: A 362 LYS cc_start: 0.7225 (OUTLIER) cc_final: 0.6949 (mmtt) REVERT: A 533 LYS cc_start: 0.8619 (mmmm) cc_final: 0.8402 (mmtm) REVERT: A 596 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.7745 (mt-10) REVERT: A 634 TRP cc_start: 0.2691 (OUTLIER) cc_final: 0.1564 (m100) REVERT: B 341 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7553 (mt-10) REVERT: B 395 ARG cc_start: 0.7756 (mtm-85) cc_final: 0.7219 (ptm-80) outliers start: 19 outliers final: 5 residues processed: 114 average time/residue: 1.2325 time to fit residues: 148.5519 Evaluate side-chains 95 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 362 LYS Chi-restraints excluded: chain A residue 517 ARG Chi-restraints excluded: chain A residue 535 GLU Chi-restraints excluded: chain A residue 596 GLU Chi-restraints excluded: chain A residue 602 PRO Chi-restraints excluded: chain A residue 634 TRP Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 475 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 78 optimal weight: 5.9990 chunk 59 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 37 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 79 optimal weight: 0.7980 chunk 84 optimal weight: 0.4980 chunk 75 optimal weight: 0.8980 chunk 22 optimal weight: 4.9990 chunk 70 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 396 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.2676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7371 Z= 0.183 Angle : 0.477 5.232 10002 Z= 0.247 Chirality : 0.041 0.128 1034 Planarity : 0.004 0.053 1293 Dihedral : 4.401 48.904 978 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.32 % Allowed : 15.59 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % 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: 0.84 (0.28), residues: 875 helix: 0.99 (0.25), residues: 424 sheet: 0.94 (0.63), residues: 61 loop : 0.16 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 164 HIS 0.004 0.001 HIS A 240 PHE 0.015 0.001 PHE B 364 TYR 0.018 0.001 TYR A 384 ARG 0.008 0.000 ARG A 599 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 83 time to evaluate : 0.728 Fit side-chains Corrupt residue: chain: A residue: PRO 602 >>> skipping REVERT: A 89 GLN cc_start: 0.7878 (tm-30) cc_final: 0.7436 (tp40) REVERT: A 145 PRO cc_start: 0.8341 (Cg_endo) cc_final: 0.8009 (Cg_exo) REVERT: A 155 GLU cc_start: 0.7155 (OUTLIER) cc_final: 0.6501 (mp0) REVERT: A 362 LYS cc_start: 0.7276 (OUTLIER) cc_final: 0.6905 (mmtt) REVERT: A 634 TRP cc_start: 0.2809 (OUTLIER) cc_final: 0.1582 (m100) REVERT: A 710 ILE cc_start: 0.4108 (OUTLIER) cc_final: 0.3715 (mm) REVERT: B 341 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7555 (mt-10) REVERT: B 395 ARG cc_start: 0.7744 (mtm-85) cc_final: 0.7244 (ptm-80) outliers start: 19 outliers final: 6 residues processed: 99 average time/residue: 1.2868 time to fit residues: 134.5033 Evaluate side-chains 92 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 81 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLU Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 362 LYS Chi-restraints excluded: chain A residue 535 GLU Chi-restraints excluded: chain A residue 602 PRO Chi-restraints excluded: chain A residue 634 TRP Chi-restraints excluded: chain A residue 710 ILE Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 475 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 47 optimal weight: 0.8980 chunk 1 optimal weight: 0.6980 chunk 62 optimal weight: 8.9990 chunk 34 optimal weight: 0.7980 chunk 71 optimal weight: 0.9990 chunk 58 optimal weight: 0.0970 chunk 0 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 chunk 75 optimal weight: 0.8980 chunk 21 optimal weight: 0.6980 chunk 28 optimal weight: 0.7980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN B 435 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7371 Z= 0.164 Angle : 0.466 7.120 10002 Z= 0.242 Chirality : 0.040 0.132 1034 Planarity : 0.004 0.043 1293 Dihedral : 4.325 48.829 978 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.19 % Allowed : 16.24 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % 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: 0.96 (0.28), residues: 875 helix: 1.14 (0.25), residues: 423 sheet: 0.71 (0.66), residues: 55 loop : 0.21 (0.31), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 164 HIS 0.004 0.001 HIS A 240 PHE 0.012 0.001 PHE B 364 TYR 0.017 0.001 TYR A 384 ARG 0.003 0.000 ARG A 599 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 87 time to evaluate : 0.833 Fit side-chains Corrupt residue: chain: A residue: PRO 602 >>> skipping REVERT: A 57 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7755 (pm20) REVERT: A 155 GLU cc_start: 0.7159 (OUTLIER) cc_final: 0.6507 (mp0) REVERT: A 362 LYS cc_start: 0.7308 (OUTLIER) cc_final: 0.7035 (mmtt) REVERT: A 634 TRP cc_start: 0.2878 (OUTLIER) cc_final: 0.1594 (m100) REVERT: B 341 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7518 (mt-10) REVERT: B 395 ARG cc_start: 0.7730 (mtm-85) cc_final: 0.7235 (ptm-80) outliers start: 18 outliers final: 5 residues processed: 103 average time/residue: 1.3534 time to fit residues: 147.1666 Evaluate side-chains 90 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 80 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 362 LYS Chi-restraints excluded: chain A residue 517 ARG Chi-restraints excluded: chain A residue 535 GLU Chi-restraints excluded: chain A residue 602 PRO Chi-restraints excluded: chain A residue 634 TRP Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 475 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 75 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 49 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 84 optimal weight: 0.3980 chunk 69 optimal weight: 0.0030 chunk 38 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 27 optimal weight: 0.0670 chunk 44 optimal weight: 0.6980 chunk 81 optimal weight: 0.2980 overall best weight: 0.2928 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 396 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.2989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 7371 Z= 0.129 Angle : 0.449 7.730 10002 Z= 0.232 Chirality : 0.039 0.148 1034 Planarity : 0.004 0.041 1293 Dihedral : 4.230 48.227 978 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.06 % Allowed : 16.24 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % 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: 1.10 (0.28), residues: 875 helix: 1.36 (0.26), residues: 415 sheet: 0.75 (0.66), residues: 55 loop : 0.17 (0.31), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 164 HIS 0.003 0.001 HIS A 240 PHE 0.010 0.001 PHE B 364 TYR 0.015 0.001 TYR A 384 ARG 0.007 0.000 ARG A 599 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 91 time to evaluate : 1.046 Fit side-chains Corrupt residue: chain: A residue: PRO 602 >>> skipping REVERT: A 57 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7867 (pm20) REVERT: A 155 GLU cc_start: 0.7145 (OUTLIER) cc_final: 0.6503 (mp0) REVERT: A 339 ARG cc_start: 0.8437 (mtm180) cc_final: 0.7908 (mtm110) REVERT: A 362 LYS cc_start: 0.7309 (OUTLIER) cc_final: 0.7026 (mmtt) REVERT: A 581 LYS cc_start: 0.7919 (OUTLIER) cc_final: 0.7409 (mppt) REVERT: A 634 TRP cc_start: 0.2948 (OUTLIER) cc_final: 0.1692 (m100) REVERT: A 710 ILE cc_start: 0.3941 (OUTLIER) cc_final: 0.3570 (mm) REVERT: B 341 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7500 (mt-10) REVERT: B 395 ARG cc_start: 0.7704 (mtm-85) cc_final: 0.7247 (ptm-80) outliers start: 17 outliers final: 5 residues processed: 106 average time/residue: 1.2009 time to fit residues: 134.7880 Evaluate side-chains 99 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 87 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLU Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 362 LYS Chi-restraints excluded: chain A residue 517 ARG Chi-restraints excluded: chain A residue 535 GLU Chi-restraints excluded: chain A residue 581 LYS Chi-restraints excluded: chain A residue 602 PRO Chi-restraints excluded: chain A residue 634 TRP Chi-restraints excluded: chain A residue 710 ILE Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 475 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 9 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 61 optimal weight: 4.9990 chunk 70 optimal weight: 0.2980 chunk 83 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 50 optimal weight: 0.5980 chunk 25 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 396 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.2989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7371 Z= 0.176 Angle : 0.474 6.613 10002 Z= 0.244 Chirality : 0.041 0.132 1034 Planarity : 0.004 0.057 1293 Dihedral : 4.253 47.962 978 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.93 % Allowed : 16.49 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % 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: 1.11 (0.28), residues: 875 helix: 1.33 (0.26), residues: 417 sheet: 0.81 (0.67), residues: 55 loop : 0.21 (0.31), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 477 HIS 0.004 0.001 HIS A 240 PHE 0.012 0.001 PHE A 32 TYR 0.017 0.001 TYR A 384 ARG 0.003 0.000 ARG A 599 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 87 time to evaluate : 0.836 Fit side-chains Corrupt residue: chain: A residue: PRO 602 >>> skipping REVERT: A 57 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7890 (pm20) REVERT: A 155 GLU cc_start: 0.7163 (OUTLIER) cc_final: 0.6503 (mp0) REVERT: A 339 ARG cc_start: 0.8439 (mtm180) cc_final: 0.7901 (mtm110) REVERT: A 362 LYS cc_start: 0.7298 (OUTLIER) cc_final: 0.7043 (mmtt) REVERT: A 581 LYS cc_start: 0.7953 (OUTLIER) cc_final: 0.7388 (mppt) REVERT: A 634 TRP cc_start: 0.3058 (OUTLIER) cc_final: 0.1714 (m100) REVERT: A 710 ILE cc_start: 0.3850 (OUTLIER) cc_final: 0.3474 (mm) REVERT: B 341 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7511 (mt-10) REVERT: B 395 ARG cc_start: 0.7719 (mtm-85) cc_final: 0.7237 (ptm-80) outliers start: 16 outliers final: 6 residues processed: 102 average time/residue: 1.3840 time to fit residues: 148.7541 Evaluate side-chains 97 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 84 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLU Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 362 LYS Chi-restraints excluded: chain A residue 400 HIS Chi-restraints excluded: chain A residue 517 ARG Chi-restraints excluded: chain A residue 535 GLU Chi-restraints excluded: chain A residue 581 LYS Chi-restraints excluded: chain A residue 602 PRO Chi-restraints excluded: chain A residue 634 TRP Chi-restraints excluded: chain A residue 710 ILE Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 475 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 16 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 57 optimal weight: 0.1980 chunk 41 optimal weight: 3.9990 chunk 7 optimal weight: 0.0670 chunk 65 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 73 optimal weight: 6.9990 chunk 78 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 overall best weight: 0.5920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.3065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7371 Z= 0.161 Angle : 0.469 7.041 10002 Z= 0.242 Chirality : 0.040 0.133 1034 Planarity : 0.004 0.058 1293 Dihedral : 4.213 47.020 978 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.32 % Allowed : 16.11 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % 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: 1.12 (0.28), residues: 875 helix: 1.37 (0.26), residues: 416 sheet: 0.78 (0.66), residues: 55 loop : 0.20 (0.31), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 164 HIS 0.003 0.001 HIS A 240 PHE 0.010 0.001 PHE A 522 TYR 0.017 0.001 TYR A 384 ARG 0.004 0.000 ARG A 599 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 90 time to evaluate : 0.777 Fit side-chains Corrupt residue: chain: A residue: PRO 602 >>> skipping REVERT: A 57 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7921 (pm20) REVERT: A 155 GLU cc_start: 0.7154 (OUTLIER) cc_final: 0.6493 (mp0) REVERT: A 339 ARG cc_start: 0.8434 (mtm180) cc_final: 0.7894 (mtm110) REVERT: A 362 LYS cc_start: 0.7341 (OUTLIER) cc_final: 0.7094 (mmtt) REVERT: A 634 TRP cc_start: 0.3178 (OUTLIER) cc_final: 0.1758 (m100) REVERT: A 710 ILE cc_start: 0.3814 (OUTLIER) cc_final: 0.3445 (mm) REVERT: B 341 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7496 (mt-10) REVERT: B 395 ARG cc_start: 0.7711 (mtm-85) cc_final: 0.7239 (ptm-80) outliers start: 19 outliers final: 6 residues processed: 106 average time/residue: 1.3553 time to fit residues: 151.3822 Evaluate side-chains 96 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 362 LYS Chi-restraints excluded: chain A residue 400 HIS Chi-restraints excluded: chain A residue 517 ARG Chi-restraints excluded: chain A residue 535 GLU Chi-restraints excluded: chain A residue 602 PRO Chi-restraints excluded: chain A residue 634 TRP Chi-restraints excluded: chain A residue 710 ILE Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 475 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 34 optimal weight: 1.9990 chunk 61 optimal weight: 0.2980 chunk 23 optimal weight: 0.7980 chunk 70 optimal weight: 0.9990 chunk 73 optimal weight: 6.9990 chunk 77 optimal weight: 0.7980 chunk 51 optimal weight: 0.4980 chunk 82 optimal weight: 0.9990 chunk 50 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 57 optimal weight: 0.1980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 396 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7371 Z= 0.153 Angle : 0.475 7.336 10002 Z= 0.243 Chirality : 0.040 0.133 1034 Planarity : 0.004 0.057 1293 Dihedral : 4.207 47.163 978 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.06 % Allowed : 16.37 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % 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: 1.18 (0.28), residues: 875 helix: 1.43 (0.26), residues: 416 sheet: 0.91 (0.63), residues: 61 loop : 0.18 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 164 HIS 0.003 0.001 HIS A 240 PHE 0.011 0.001 PHE B 364 TYR 0.016 0.001 TYR A 384 ARG 0.010 0.000 ARG A 599 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 89 time to evaluate : 0.820 Fit side-chains Corrupt residue: chain: A residue: PRO 602 >>> skipping REVERT: A 57 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7941 (pm20) REVERT: A 155 GLU cc_start: 0.7174 (OUTLIER) cc_final: 0.6513 (mp0) REVERT: A 362 LYS cc_start: 0.7492 (OUTLIER) cc_final: 0.7246 (mmtt) REVERT: A 596 GLU cc_start: 0.8551 (tp30) cc_final: 0.7775 (mp0) REVERT: A 634 TRP cc_start: 0.3181 (OUTLIER) cc_final: 0.1783 (m100) REVERT: A 710 ILE cc_start: 0.3792 (OUTLIER) cc_final: 0.3413 (mm) REVERT: B 341 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7478 (mt-10) REVERT: B 395 ARG cc_start: 0.7715 (mtm-85) cc_final: 0.7245 (ptm-80) outliers start: 17 outliers final: 7 residues processed: 104 average time/residue: 1.3454 time to fit residues: 147.3609 Evaluate side-chains 98 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLU Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 362 LYS Chi-restraints excluded: chain A residue 400 HIS Chi-restraints excluded: chain A residue 517 ARG Chi-restraints excluded: chain A residue 535 GLU Chi-restraints excluded: chain A residue 602 PRO Chi-restraints excluded: chain A residue 634 TRP Chi-restraints excluded: chain A residue 710 ILE Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 475 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 86 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 53 optimal weight: 0.0270 chunk 42 optimal weight: 0.9980 chunk 54 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 63 optimal weight: 7.9990 chunk 10 optimal weight: 2.9990 overall best weight: 0.8040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 396 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.3091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7371 Z= 0.195 Angle : 0.506 9.134 10002 Z= 0.255 Chirality : 0.041 0.134 1034 Planarity : 0.004 0.058 1293 Dihedral : 4.267 45.844 978 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.68 % Allowed : 17.27 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % 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: 1.12 (0.28), residues: 875 helix: 1.34 (0.26), residues: 418 sheet: 0.88 (0.63), residues: 61 loop : 0.19 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 164 HIS 0.004 0.001 HIS A 240 PHE 0.014 0.001 PHE B 361 TYR 0.019 0.001 TYR A 384 ARG 0.008 0.000 ARG A 599 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 85 time to evaluate : 0.840 Fit side-chains Corrupt residue: chain: A residue: PRO 602 >>> skipping REVERT: A 57 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7948 (pm20) REVERT: A 155 GLU cc_start: 0.7166 (OUTLIER) cc_final: 0.6486 (mp0) REVERT: A 362 LYS cc_start: 0.7585 (OUTLIER) cc_final: 0.7332 (mmtt) REVERT: A 596 GLU cc_start: 0.8591 (tp30) cc_final: 0.7857 (mp0) REVERT: A 634 TRP cc_start: 0.3250 (OUTLIER) cc_final: 0.1794 (m100) REVERT: A 710 ILE cc_start: 0.3792 (OUTLIER) cc_final: 0.3390 (mm) REVERT: B 341 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7486 (mt-10) REVERT: B 395 ARG cc_start: 0.7724 (mtm-85) cc_final: 0.7250 (ptm-80) outliers start: 14 outliers final: 5 residues processed: 96 average time/residue: 1.4182 time to fit residues: 143.9935 Evaluate side-chains 95 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 362 LYS Chi-restraints excluded: chain A residue 517 ARG Chi-restraints excluded: chain A residue 535 GLU Chi-restraints excluded: chain A residue 602 PRO Chi-restraints excluded: chain A residue 634 TRP Chi-restraints excluded: chain A residue 710 ILE Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 475 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 19 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 28 optimal weight: 0.6980 chunk 70 optimal weight: 2.9990 chunk 8 optimal weight: 0.0470 chunk 12 optimal weight: 2.9990 chunk 60 optimal weight: 8.9990 chunk 3 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 chunk 46 optimal weight: 0.1980 overall best weight: 0.5680 ------------------------------------------------------------------------------- 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 = 0.3806 r_free = 0.3806 target = 0.150421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.116654 restraints weight = 8979.150| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 1.87 r_work: 0.3249 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.3154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7371 Z= 0.163 Angle : 0.491 9.318 10002 Z= 0.249 Chirality : 0.040 0.134 1034 Planarity : 0.004 0.058 1293 Dihedral : 4.220 45.809 978 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.42 % Allowed : 17.65 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % 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: 1.13 (0.28), residues: 875 helix: 1.36 (0.26), residues: 418 sheet: 0.85 (0.63), residues: 61 loop : 0.20 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 164 HIS 0.003 0.001 HIS A 240 PHE 0.010 0.001 PHE B 361 TYR 0.017 0.001 TYR A 384 ARG 0.008 0.000 ARG A 599 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3183.11 seconds wall clock time: 58 minutes 19.69 seconds (3499.69 seconds total)