Starting phenix.real_space_refine on Tue Feb 11 19:48:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9evc_19998/02_2025/9evc_19998.cif Found real_map, /net/cci-nas-00/data/ceres_data/9evc_19998/02_2025/9evc_19998.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9evc_19998/02_2025/9evc_19998.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9evc_19998/02_2025/9evc_19998.map" model { file = "/net/cci-nas-00/data/ceres_data/9evc_19998/02_2025/9evc_19998.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9evc_19998/02_2025/9evc_19998.cif" } resolution = 3.73 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 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: 5 Type Number sf(0) Gaussians Ca 1 9.91 5 S 33 5.16 5 C 4156 2.51 5 N 1080 2.21 5 O 1237 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 6507 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 857, 6506 Classifications: {'peptide': 857} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 29, 'TRANS': 827} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.98, per 1000 atoms: 0.77 Number of scatterers: 6507 At special positions: 0 Unit cell: (73.216, 88.704, 133.76, 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) Ca 1 19.99 S 33 16.00 O 1237 8.00 N 1080 7.00 C 4156 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: 1.65 Conformation dependent library (CDL) restraints added in 985.3 milliseconds 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1590 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 6 sheets defined 55.9% alpha, 10.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.75 Creating SS restraints... Processing helix chain 'A' and resid 7 through 15 Processing helix chain 'A' and resid 27 through 35 Processing helix chain 'A' and resid 46 through 54 Processing helix chain 'A' and resid 57 through 73 Processing helix chain 'A' and resid 75 through 111 removed outlier: 3.929A pdb=" N SER A 79 " --> pdb=" O GLU A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 218 Processing helix chain 'A' and resid 230 through 261 Processing helix chain 'A' and resid 270 through 273 Processing helix chain 'A' and resid 274 through 290 removed outlier: 4.033A pdb=" N ALA A 278 " --> pdb=" O ALA A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 312 Processing helix chain 'A' and resid 318 through 322 Processing helix chain 'A' and resid 323 through 328 removed outlier: 3.690A pdb=" N GLY A 326 " --> pdb=" O GLU A 323 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N THR A 328 " --> pdb=" O LEU A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 380 Processing helix chain 'A' and resid 394 through 407 Processing helix chain 'A' and resid 412 through 417 removed outlier: 4.342A pdb=" N GLU A 416 " --> pdb=" O ASN A 412 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LYS A 417 " --> pdb=" O GLU A 413 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 412 through 417' Processing helix chain 'A' and resid 450 through 458 Processing helix chain 'A' and resid 471 through 488 removed outlier: 3.539A pdb=" N GLN A 488 " --> pdb=" O GLU A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 541 Processing helix chain 'A' and resid 552 through 564 Processing helix chain 'A' and resid 575 through 579 Processing helix chain 'A' and resid 582 through 591 removed outlier: 3.987A pdb=" N LYS A 588 " --> pdb=" O GLU A 584 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N GLU A 591 " --> pdb=" O ASP A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 614 removed outlier: 3.985A pdb=" N LYS A 614 " --> pdb=" O ALA A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 634 Processing helix chain 'A' and resid 644 through 651 Processing helix chain 'A' and resid 659 through 701 removed outlier: 3.949A pdb=" N ILE A 663 " --> pdb=" O ASN A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 719 Processing helix chain 'A' and resid 721 through 729 Processing helix chain 'A' and resid 735 through 739 removed outlier: 4.066A pdb=" N ARG A 739 " --> pdb=" O VAL A 736 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 777 Processing helix chain 'A' and resid 779 through 802 removed outlier: 4.185A pdb=" N PHE A 800 " --> pdb=" O THR A 796 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA A 801 " --> pdb=" O LEU A 797 " (cutoff:3.500A) Processing helix chain 'A' and resid 808 through 813 Processing helix chain 'A' and resid 817 through 832 Processing helix chain 'A' and resid 836 through 840 Processing helix chain 'A' and resid 851 through 878 removed outlier: 3.821A pdb=" N ILE A 856 " --> pdb=" O HIS A 852 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N ALA A 857 " --> pdb=" O GLU A 853 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 124 through 126 removed outlier: 3.618A pdb=" N ILE A 126 " --> pdb=" O ALA A 115 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LYS A 116 " --> pdb=" O ILE A 138 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N VAL A 136 " --> pdb=" O ILE A 118 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N MET A 203 " --> pdb=" O PHE A 152 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N PHE A 152 " --> pdb=" O MET A 203 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 167 through 172 removed outlier: 6.352A pdb=" N GLU A 169 " --> pdb=" O ILE A 159 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N ILE A 159 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N LYS A 158 " --> pdb=" O VAL A 198 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU A 196 " --> pdb=" O ASP A 160 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 314 through 316 Processing sheet with id=AA4, first strand: chain 'A' and resid 330 through 334 removed outlier: 5.246A pdb=" N ALA A 594 " --> pdb=" O THR A 545 " (cutoff:3.500A) removed outlier: 8.694A pdb=" N ILE A 571 " --> pdb=" O ALA A 594 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N TYR A 596 " --> pdb=" O ILE A 571 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N LEU A 573 " --> pdb=" O TYR A 596 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 345 through 350 removed outlier: 5.789A pdb=" N VAL A 346 " --> pdb=" O ILE A 524 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ILE A 524 " --> pdb=" O VAL A 346 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ASP A 348 " --> pdb=" O ALA A 522 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N GLY A 519 " --> pdb=" O TYR A 495 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N TYR A 495 " --> pdb=" O GLY A 519 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR A 521 " --> pdb=" O LEU A 493 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR A 447 " --> pdb=" O GLY A 496 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 345 through 350 removed outlier: 5.789A pdb=" N VAL A 346 " --> pdb=" O ILE A 524 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ILE A 524 " --> pdb=" O VAL A 346 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ASP A 348 " --> pdb=" O ALA A 522 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N TYR A 460 " --> pdb=" O LEU A 517 " (cutoff:3.500A) removed outlier: 8.920A pdb=" N GLY A 519 " --> pdb=" O TYR A 460 " (cutoff:3.500A) removed outlier: 10.036A pdb=" N PHE A 462 " --> pdb=" O GLY A 519 " (cutoff:3.500A) removed outlier: 13.089A pdb=" N THR A 521 " --> pdb=" O PHE A 462 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS A 468 " --> pdb=" O VAL A 461 " (cutoff:3.500A) 377 hydrogen bonds defined for protein. 1089 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: 2.19 Time building geometry restraints manager: 1.92 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: 2114 1.34 - 1.46: 1087 1.46 - 1.58: 3339 1.58 - 1.70: 0 1.70 - 1.82: 61 Bond restraints: 6601 Sorted by residual: bond pdb=" N LEU A 15 " pdb=" CA LEU A 15 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.32e-02 5.74e+03 8.33e+00 bond pdb=" N GLU A 292 " pdb=" CA GLU A 292 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.28e-02 6.10e+03 6.21e+00 bond pdb=" N LYS A 468 " pdb=" CA LYS A 468 " ideal model delta sigma weight residual 1.452 1.490 -0.038 1.54e-02 4.22e+03 6.15e+00 bond pdb=" N PHE A 55 " pdb=" CA PHE A 55 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.32e-02 5.74e+03 5.92e+00 bond pdb=" N LEU A 763 " pdb=" CA LEU A 763 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.19e-02 7.06e+03 5.54e+00 ... (remaining 6596 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 8660 2.00 - 4.00: 224 4.00 - 6.00: 31 6.00 - 7.99: 11 7.99 - 9.99: 7 Bond angle restraints: 8933 Sorted by residual: angle pdb=" N GLY A 149 " pdb=" CA GLY A 149 " pdb=" C GLY A 149 " ideal model delta sigma weight residual 110.38 116.09 -5.71 1.48e+00 4.57e-01 1.49e+01 angle pdb=" C THR A 54 " pdb=" N PHE A 55 " pdb=" CA PHE A 55 " ideal model delta sigma weight residual 122.54 116.89 5.65 1.65e+00 3.67e-01 1.17e+01 angle pdb=" CB MET A 163 " pdb=" CG MET A 163 " pdb=" SD MET A 163 " ideal model delta sigma weight residual 112.70 122.69 -9.99 3.00e+00 1.11e-01 1.11e+01 angle pdb=" CA GLU A 361 " pdb=" CB GLU A 361 " pdb=" CG GLU A 361 " ideal model delta sigma weight residual 114.10 120.05 -5.95 2.00e+00 2.50e-01 8.85e+00 angle pdb=" C LYS A 468 " pdb=" CA LYS A 468 " pdb=" CB LYS A 468 " ideal model delta sigma weight residual 108.84 113.08 -4.24 1.51e+00 4.39e-01 7.90e+00 ... (remaining 8928 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.29: 3403 16.29 - 32.57: 450 32.57 - 48.86: 122 48.86 - 65.14: 34 65.14 - 81.43: 4 Dihedral angle restraints: 4013 sinusoidal: 1554 harmonic: 2459 Sorted by residual: dihedral pdb=" CA LEU A 851 " pdb=" C LEU A 851 " pdb=" N HIS A 852 " pdb=" CA HIS A 852 " ideal model delta harmonic sigma weight residual -180.00 -157.39 -22.61 0 5.00e+00 4.00e-02 2.04e+01 dihedral pdb=" CA ASP A 720 " pdb=" C ASP A 720 " pdb=" N SER A 721 " pdb=" CA SER A 721 " ideal model delta harmonic sigma weight residual -180.00 -162.55 -17.45 0 5.00e+00 4.00e-02 1.22e+01 dihedral pdb=" CA HIS A 552 " pdb=" C HIS A 552 " pdb=" N LYS A 553 " pdb=" CA LYS A 553 " ideal model delta harmonic sigma weight residual -180.00 -163.73 -16.27 0 5.00e+00 4.00e-02 1.06e+01 ... (remaining 4010 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 895 0.065 - 0.130: 158 0.130 - 0.195: 14 0.195 - 0.261: 1 0.261 - 0.326: 2 Chirality restraints: 1070 Sorted by residual: chirality pdb=" CG LEU A 86 " pdb=" CB LEU A 86 " pdb=" CD1 LEU A 86 " pdb=" CD2 LEU A 86 " both_signs ideal model delta sigma weight residual False -2.59 -2.26 -0.33 2.00e-01 2.50e+01 2.65e+00 chirality pdb=" CB VAL A 516 " pdb=" CA VAL A 516 " pdb=" CG1 VAL A 516 " pdb=" CG2 VAL A 516 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.46e+00 chirality pdb=" CG LEU A 73 " pdb=" CB LEU A 73 " pdb=" CD1 LEU A 73 " pdb=" CD2 LEU A 73 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.35e+00 ... (remaining 1067 not shown) Planarity restraints: 1141 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 119 " -0.261 9.50e-02 1.11e+02 1.17e-01 8.37e+00 pdb=" NE ARG A 119 " 0.015 2.00e-02 2.50e+03 pdb=" CZ ARG A 119 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG A 119 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 119 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 467 " -0.013 2.00e-02 2.50e+03 2.56e-02 6.57e+00 pdb=" C GLU A 467 " 0.044 2.00e-02 2.50e+03 pdb=" O GLU A 467 " -0.017 2.00e-02 2.50e+03 pdb=" N LYS A 468 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A 468 " 0.036 5.00e-02 4.00e+02 5.58e-02 4.98e+00 pdb=" N PRO A 469 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO A 469 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 469 " 0.030 5.00e-02 4.00e+02 ... (remaining 1138 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 120 2.66 - 3.22: 6373 3.22 - 3.78: 11183 3.78 - 4.34: 14195 4.34 - 4.90: 22544 Nonbonded interactions: 54415 Sorted by model distance: nonbonded pdb=" O ILE A 290 " pdb="CA CA A 901 " model vdw 2.095 2.510 nonbonded pdb=" O ASP A 334 " pdb=" OG1 THR A 338 " model vdw 2.229 3.040 nonbonded pdb=" O LEU A 107 " pdb=" OG SER A 111 " model vdw 2.243 3.040 nonbonded pdb=" OD1 ASN A 716 " pdb="CA CA A 901 " model vdw 2.253 2.510 nonbonded pdb=" OG1 THR A 789 " pdb=" OH TYR A 831 " model vdw 2.259 3.040 ... (remaining 54410 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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 group one per residue 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: 3.770 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: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 19.610 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7161 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 : 0.004 0.042 6601 Z= 0.239 Angle : 0.800 9.993 8933 Z= 0.423 Chirality : 0.050 0.326 1070 Planarity : 0.006 0.117 1141 Dihedral : 16.474 81.426 2423 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 16.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 0.43 % Allowed : 31.51 % Favored : 68.06 % 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: -1.61 (0.27), residues: 849 helix: -0.01 (0.23), residues: 457 sheet: -3.20 (0.61), residues: 57 loop : -2.12 (0.31), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 611 HIS 0.004 0.001 HIS A 437 PHE 0.011 0.001 PHE A 12 TYR 0.006 0.001 TYR A 497 ARG 0.002 0.000 ARG A 5 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 200 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 ILE cc_start: 0.8340 (mt) cc_final: 0.8078 (mt) REVERT: A 105 ASP cc_start: 0.8712 (m-30) cc_final: 0.8461 (m-30) REVERT: A 110 MET cc_start: 0.7166 (ppp) cc_final: 0.6264 (tmm) REVERT: A 203 MET cc_start: 0.5577 (tpt) cc_final: 0.5108 (tpp) REVERT: A 433 MET cc_start: 0.7942 (tpt) cc_final: 0.7293 (tpt) REVERT: A 478 LEU cc_start: 0.8505 (mt) cc_final: 0.7902 (mt) REVERT: A 623 ASP cc_start: 0.7614 (p0) cc_final: 0.7395 (p0) REVERT: A 677 ILE cc_start: 0.8500 (mm) cc_final: 0.8292 (mm) outliers start: 3 outliers final: 3 residues processed: 202 average time/residue: 0.1895 time to fit residues: 50.1642 Evaluate side-chains 145 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 142 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 PHE Chi-restraints excluded: chain A residue 707 PHE Chi-restraints excluded: chain A residue 879 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 71 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 chunk 35 optimal weight: 6.9990 chunk 22 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 34 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 77 optimal weight: 0.7980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 GLN A 277 ASN A 358 ASN ** A 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 482 ASN ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 603 ASN ** A 798 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 807 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.158214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.129004 restraints weight = 15517.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.132820 restraints weight = 7931.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.135267 restraints weight = 5099.318| |-----------------------------------------------------------------------------| r_work (final): 0.3951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.2532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 6601 Z= 0.317 Angle : 0.722 13.639 8933 Z= 0.371 Chirality : 0.046 0.191 1070 Planarity : 0.005 0.036 1141 Dihedral : 5.125 52.242 908 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 18.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 8.06 % Allowed : 27.34 % Favored : 64.60 % 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: -1.25 (0.28), residues: 849 helix: 0.34 (0.23), residues: 463 sheet: -2.58 (0.65), residues: 51 loop : -2.20 (0.32), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 854 HIS 0.005 0.001 HIS A 437 PHE 0.028 0.002 PHE A 455 TYR 0.018 0.002 TYR A 495 ARG 0.006 0.001 ARG A 528 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 156 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ASP cc_start: 0.8738 (m-30) cc_final: 0.8229 (m-30) REVERT: A 110 MET cc_start: 0.7040 (ppp) cc_final: 0.6420 (tmm) REVERT: A 152 PHE cc_start: 0.5595 (OUTLIER) cc_final: 0.4692 (p90) REVERT: A 342 ASN cc_start: 0.7289 (m-40) cc_final: 0.7055 (m-40) REVERT: A 358 ASN cc_start: 0.7192 (OUTLIER) cc_final: 0.6459 (t0) REVERT: A 397 GLU cc_start: 0.8752 (mp0) cc_final: 0.8347 (mp0) REVERT: A 420 ARG cc_start: 0.8413 (mpt180) cc_final: 0.8126 (mpt180) REVERT: A 426 PHE cc_start: 0.7187 (t80) cc_final: 0.6300 (t80) REVERT: A 433 MET cc_start: 0.8181 (tpt) cc_final: 0.7488 (tpp) REVERT: A 463 LEU cc_start: 0.7702 (mm) cc_final: 0.7495 (mm) REVERT: A 478 LEU cc_start: 0.8567 (mt) cc_final: 0.8064 (mt) REVERT: A 479 LYS cc_start: 0.8136 (mmmt) cc_final: 0.7852 (mmtp) REVERT: A 484 GLU cc_start: 0.8348 (pt0) cc_final: 0.7845 (pt0) REVERT: A 517 LEU cc_start: 0.8074 (OUTLIER) cc_final: 0.7871 (tt) REVERT: A 623 ASP cc_start: 0.8323 (p0) cc_final: 0.8028 (p0) REVERT: A 633 GLN cc_start: 0.7603 (mp10) cc_final: 0.7205 (mp10) REVERT: A 678 LYS cc_start: 0.8417 (mttt) cc_final: 0.8169 (ttmm) REVERT: A 689 LEU cc_start: 0.8226 (OUTLIER) cc_final: 0.7751 (tt) REVERT: A 699 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8202 (mp) REVERT: A 718 VAL cc_start: 0.8744 (t) cc_final: 0.8527 (m) outliers start: 56 outliers final: 31 residues processed: 191 average time/residue: 0.1697 time to fit residues: 43.9319 Evaluate side-chains 177 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 141 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 TYR Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 152 PHE Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 358 ASN Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 636 ILE Chi-restraints excluded: chain A residue 649 ASP Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 720 ASP Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 753 THR Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 871 ILE Chi-restraints excluded: chain A residue 879 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 17 optimal weight: 4.9990 chunk 45 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 chunk 11 optimal weight: 10.0000 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 482 ASN A 798 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.159445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.130314 restraints weight = 15536.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.134341 restraints weight = 7734.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.136865 restraints weight = 4890.726| |-----------------------------------------------------------------------------| r_work (final): 0.3968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6601 Z= 0.243 Angle : 0.671 14.300 8933 Z= 0.338 Chirality : 0.044 0.177 1070 Planarity : 0.004 0.037 1141 Dihedral : 4.762 51.517 904 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 18.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 8.06 % Allowed : 27.63 % Favored : 64.32 % 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: -1.05 (0.28), residues: 849 helix: 0.54 (0.23), residues: 465 sheet: -2.39 (0.56), residues: 69 loop : -2.16 (0.34), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 854 HIS 0.005 0.001 HIS A 437 PHE 0.030 0.001 PHE A 455 TYR 0.014 0.002 TYR A 349 ARG 0.004 0.000 ARG A 317 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 147 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ASP cc_start: 0.8565 (m-30) cc_final: 0.8207 (m-30) REVERT: A 110 MET cc_start: 0.6904 (ppp) cc_final: 0.6390 (tmm) REVERT: A 152 PHE cc_start: 0.5496 (OUTLIER) cc_final: 0.4014 (p90) REVERT: A 251 CYS cc_start: 0.7970 (m) cc_final: 0.7659 (t) REVERT: A 342 ASN cc_start: 0.7173 (m-40) cc_final: 0.6876 (m-40) REVERT: A 358 ASN cc_start: 0.7092 (p0) cc_final: 0.6525 (t0) REVERT: A 397 GLU cc_start: 0.8630 (mp0) cc_final: 0.8270 (mp0) REVERT: A 420 ARG cc_start: 0.8454 (mpt180) cc_final: 0.8171 (mpt180) REVERT: A 426 PHE cc_start: 0.7139 (t80) cc_final: 0.6856 (t80) REVERT: A 433 MET cc_start: 0.8234 (tpt) cc_final: 0.7580 (tpt) REVERT: A 463 LEU cc_start: 0.7758 (mm) cc_final: 0.7544 (mm) REVERT: A 478 LEU cc_start: 0.8635 (mt) cc_final: 0.8172 (mt) REVERT: A 484 GLU cc_start: 0.8292 (pt0) cc_final: 0.7750 (pt0) REVERT: A 517 LEU cc_start: 0.8113 (OUTLIER) cc_final: 0.7828 (tt) REVERT: A 566 MET cc_start: 0.7465 (mmt) cc_final: 0.7178 (mmt) REVERT: A 623 ASP cc_start: 0.8321 (p0) cc_final: 0.7999 (p0) REVERT: A 633 GLN cc_start: 0.7588 (mp10) cc_final: 0.7212 (mp10) REVERT: A 678 LYS cc_start: 0.8410 (mttt) cc_final: 0.8161 (ttmm) REVERT: A 689 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7692 (tt) REVERT: A 833 ILE cc_start: 0.7894 (OUTLIER) cc_final: 0.7422 (mt) outliers start: 56 outliers final: 32 residues processed: 186 average time/residue: 0.1735 time to fit residues: 43.7194 Evaluate side-chains 174 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 138 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 TYR Chi-restraints excluded: chain A residue 51 PHE Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 152 PHE Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 458 CYS Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 636 ILE Chi-restraints excluded: chain A residue 649 ASP Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 720 ASP Chi-restraints excluded: chain A residue 730 GLU Chi-restraints excluded: chain A residue 753 THR Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 766 ILE Chi-restraints excluded: chain A residue 783 SER Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 833 ILE Chi-restraints excluded: chain A residue 844 SER Chi-restraints excluded: chain A residue 871 ILE Chi-restraints excluded: chain A residue 879 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 12 optimal weight: 7.9990 chunk 82 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 39 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 chunk 45 optimal weight: 0.6980 chunk 36 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 412 ASN A 482 ASN A 798 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.158922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.129428 restraints weight = 15766.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.133504 restraints weight = 7871.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.136031 restraints weight = 4989.256| |-----------------------------------------------------------------------------| r_work (final): 0.3957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.3221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6601 Z= 0.248 Angle : 0.673 14.636 8933 Z= 0.338 Chirality : 0.044 0.178 1070 Planarity : 0.004 0.037 1141 Dihedral : 4.742 51.100 904 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 19.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 8.78 % Allowed : 26.47 % Favored : 64.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.28), residues: 849 helix: 0.62 (0.23), residues: 467 sheet: -2.44 (0.55), residues: 74 loop : -2.08 (0.34), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 854 HIS 0.005 0.001 HIS A 437 PHE 0.022 0.001 PHE A 455 TYR 0.025 0.002 TYR A 349 ARG 0.004 0.000 ARG A 317 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 144 time to evaluate : 0.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ASP cc_start: 0.8578 (m-30) cc_final: 0.8217 (m-30) REVERT: A 152 PHE cc_start: 0.5624 (OUTLIER) cc_final: 0.4386 (p90) REVERT: A 251 CYS cc_start: 0.7928 (m) cc_final: 0.7665 (t) REVERT: A 318 LYS cc_start: 0.7819 (OUTLIER) cc_final: 0.7485 (tttp) REVERT: A 358 ASN cc_start: 0.7075 (p0) cc_final: 0.6357 (t0) REVERT: A 397 GLU cc_start: 0.8687 (mp0) cc_final: 0.8283 (mp0) REVERT: A 433 MET cc_start: 0.8283 (tpt) cc_final: 0.7978 (tpp) REVERT: A 463 LEU cc_start: 0.7752 (mm) cc_final: 0.7526 (mm) REVERT: A 478 LEU cc_start: 0.8657 (mt) cc_final: 0.8093 (mt) REVERT: A 484 GLU cc_start: 0.8320 (pt0) cc_final: 0.7830 (pt0) REVERT: A 517 LEU cc_start: 0.8088 (OUTLIER) cc_final: 0.7810 (tt) REVERT: A 566 MET cc_start: 0.7359 (mmt) cc_final: 0.7066 (mmm) REVERT: A 623 ASP cc_start: 0.8296 (p0) cc_final: 0.7965 (p0) REVERT: A 633 GLN cc_start: 0.7577 (mp10) cc_final: 0.7215 (mp10) REVERT: A 640 MET cc_start: 0.8711 (mmm) cc_final: 0.8511 (mmm) REVERT: A 658 ASP cc_start: 0.7364 (t70) cc_final: 0.7151 (t0) REVERT: A 678 LYS cc_start: 0.8413 (mttt) cc_final: 0.8190 (ttmm) REVERT: A 689 LEU cc_start: 0.8226 (OUTLIER) cc_final: 0.7743 (tt) REVERT: A 828 PHE cc_start: 0.7282 (OUTLIER) cc_final: 0.6981 (m-80) REVERT: A 833 ILE cc_start: 0.7905 (OUTLIER) cc_final: 0.7565 (mt) outliers start: 61 outliers final: 44 residues processed: 185 average time/residue: 0.1544 time to fit residues: 39.4619 Evaluate side-chains 185 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 135 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 PHE Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 152 PHE Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 309 MET Chi-restraints excluded: chain A residue 318 LYS Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain A residue 458 CYS Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 636 ILE Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 649 ASP Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 707 PHE Chi-restraints excluded: chain A residue 719 ASN Chi-restraints excluded: chain A residue 720 ASP Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 730 GLU Chi-restraints excluded: chain A residue 753 THR Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 766 ILE Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 805 ASN Chi-restraints excluded: chain A residue 828 PHE Chi-restraints excluded: chain A residue 833 ILE Chi-restraints excluded: chain A residue 844 SER Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 871 ILE Chi-restraints excluded: chain A residue 879 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 11 optimal weight: 10.0000 chunk 78 optimal weight: 4.9990 chunk 8 optimal weight: 5.9990 chunk 5 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 59 optimal weight: 0.0470 chunk 47 optimal weight: 1.9990 chunk 17 optimal weight: 8.9990 chunk 46 optimal weight: 0.1980 chunk 34 optimal weight: 2.9990 overall best weight: 1.0482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 798 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.159208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.129809 restraints weight = 15562.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.133880 restraints weight = 7784.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.136350 restraints weight = 4932.005| |-----------------------------------------------------------------------------| r_work (final): 0.3965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.3417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6601 Z= 0.233 Angle : 0.660 15.501 8933 Z= 0.331 Chirality : 0.043 0.174 1070 Planarity : 0.004 0.037 1141 Dihedral : 4.688 50.373 904 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 18.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 9.06 % Allowed : 27.91 % Favored : 63.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.28), residues: 849 helix: 0.63 (0.23), residues: 470 sheet: -2.75 (0.53), residues: 74 loop : -2.06 (0.34), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 854 HIS 0.005 0.001 HIS A 437 PHE 0.016 0.001 PHE A 455 TYR 0.026 0.002 TYR A 349 ARG 0.003 0.000 ARG A 742 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 140 time to evaluate : 0.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ASP cc_start: 0.8544 (m-30) cc_final: 0.8179 (m-30) REVERT: A 152 PHE cc_start: 0.5812 (OUTLIER) cc_final: 0.4622 (p90) REVERT: A 309 MET cc_start: 0.7936 (OUTLIER) cc_final: 0.7626 (mtm) REVERT: A 358 ASN cc_start: 0.7092 (p0) cc_final: 0.6353 (t0) REVERT: A 397 GLU cc_start: 0.8684 (mp0) cc_final: 0.8110 (pm20) REVERT: A 433 MET cc_start: 0.8256 (tpt) cc_final: 0.7980 (tpp) REVERT: A 463 LEU cc_start: 0.7739 (mm) cc_final: 0.7530 (mm) REVERT: A 478 LEU cc_start: 0.8683 (mt) cc_final: 0.8107 (mt) REVERT: A 484 GLU cc_start: 0.8380 (pt0) cc_final: 0.7788 (pt0) REVERT: A 517 LEU cc_start: 0.8145 (OUTLIER) cc_final: 0.7872 (tt) REVERT: A 566 MET cc_start: 0.7366 (mmt) cc_final: 0.7140 (mmt) REVERT: A 623 ASP cc_start: 0.8302 (p0) cc_final: 0.8009 (p0) REVERT: A 633 GLN cc_start: 0.7526 (mp10) cc_final: 0.7125 (mp10) REVERT: A 658 ASP cc_start: 0.7309 (t70) cc_final: 0.7092 (t0) REVERT: A 678 LYS cc_start: 0.8407 (mttt) cc_final: 0.8156 (ttmm) REVERT: A 689 LEU cc_start: 0.8178 (OUTLIER) cc_final: 0.7699 (tt) outliers start: 63 outliers final: 44 residues processed: 183 average time/residue: 0.1640 time to fit residues: 41.3998 Evaluate side-chains 180 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 132 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 TYR Chi-restraints excluded: chain A residue 51 PHE Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 152 PHE Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 280 MET Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 309 MET Chi-restraints excluded: chain A residue 318 LYS Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 458 CYS Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 649 ASP Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 707 PHE Chi-restraints excluded: chain A residue 720 ASP Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 730 GLU Chi-restraints excluded: chain A residue 753 THR Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 766 ILE Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 805 ASN Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 844 SER Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 871 ILE Chi-restraints excluded: chain A residue 879 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 19 optimal weight: 8.9990 chunk 1 optimal weight: 5.9990 chunk 74 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 81 optimal weight: 0.9980 chunk 42 optimal weight: 9.9990 chunk 50 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 482 ASN A 603 ASN A 798 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.156290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.127481 restraints weight = 15465.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.131422 restraints weight = 7666.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.133947 restraints weight = 4852.425| |-----------------------------------------------------------------------------| r_work (final): 0.3936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.3755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 6601 Z= 0.295 Angle : 0.706 15.877 8933 Z= 0.356 Chirality : 0.044 0.165 1070 Planarity : 0.004 0.039 1141 Dihedral : 4.842 50.107 904 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 20.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.13 % Favored : 91.87 % Rotamer: Outliers : 10.07 % Allowed : 26.19 % Favored : 63.74 % 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: -0.90 (0.28), residues: 849 helix: 0.65 (0.23), residues: 465 sheet: -2.56 (0.56), residues: 72 loop : -2.02 (0.34), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 854 HIS 0.005 0.001 HIS A 437 PHE 0.025 0.001 PHE A 455 TYR 0.028 0.002 TYR A 349 ARG 0.003 0.000 ARG A 420 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 132 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 PHE cc_start: 0.5989 (OUTLIER) cc_final: 0.4886 (p90) REVERT: A 309 MET cc_start: 0.8104 (OUTLIER) cc_final: 0.7832 (mtm) REVERT: A 318 LYS cc_start: 0.7834 (OUTLIER) cc_final: 0.7501 (tttp) REVERT: A 344 MET cc_start: 0.7556 (mpp) cc_final: 0.6920 (mtm) REVERT: A 397 GLU cc_start: 0.8662 (mp0) cc_final: 0.8304 (mp0) REVERT: A 407 ASN cc_start: 0.8002 (m-40) cc_final: 0.7613 (m-40) REVERT: A 416 GLU cc_start: 0.6920 (mp0) cc_final: 0.6485 (pm20) REVERT: A 426 PHE cc_start: 0.7430 (t80) cc_final: 0.6887 (t80) REVERT: A 433 MET cc_start: 0.8348 (tpt) cc_final: 0.8059 (tpp) REVERT: A 463 LEU cc_start: 0.7738 (mm) cc_final: 0.7530 (mm) REVERT: A 478 LEU cc_start: 0.8647 (mt) cc_final: 0.8133 (mt) REVERT: A 484 GLU cc_start: 0.8359 (pt0) cc_final: 0.7921 (pt0) REVERT: A 517 LEU cc_start: 0.8200 (OUTLIER) cc_final: 0.7939 (tt) REVERT: A 623 ASP cc_start: 0.8341 (p0) cc_final: 0.8005 (p0) REVERT: A 632 LYS cc_start: 0.8231 (mtmt) cc_final: 0.7977 (mtmt) REVERT: A 678 LYS cc_start: 0.8402 (mttt) cc_final: 0.8145 (ttmm) REVERT: A 689 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.8050 (tp) REVERT: A 693 ILE cc_start: 0.9164 (OUTLIER) cc_final: 0.8958 (tt) REVERT: A 833 ILE cc_start: 0.7935 (OUTLIER) cc_final: 0.7471 (mt) REVERT: A 844 SER cc_start: 0.8736 (OUTLIER) cc_final: 0.8486 (p) outliers start: 70 outliers final: 44 residues processed: 183 average time/residue: 0.1606 time to fit residues: 40.4597 Evaluate side-chains 176 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 124 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 TYR Chi-restraints excluded: chain A residue 51 PHE Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 152 PHE Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 280 MET Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 309 MET Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 318 LYS Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 458 CYS Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 649 ASP Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 707 PHE Chi-restraints excluded: chain A residue 719 ASN Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 730 GLU Chi-restraints excluded: chain A residue 753 THR Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 766 ILE Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 805 ASN Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 833 ILE Chi-restraints excluded: chain A residue 844 SER Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain A residue 879 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 7 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 12 optimal weight: 0.0370 chunk 22 optimal weight: 5.9990 chunk 8 optimal weight: 0.4980 chunk 53 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 482 ASN ** A 798 GLN ** 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 = 0.4303 r_free = 0.4303 target = 0.160008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.131504 restraints weight = 15571.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.135468 restraints weight = 7799.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.137924 restraints weight = 4945.754| |-----------------------------------------------------------------------------| r_work (final): 0.3992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.3778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6601 Z= 0.199 Angle : 0.665 16.749 8933 Z= 0.331 Chirality : 0.043 0.172 1070 Planarity : 0.004 0.037 1141 Dihedral : 4.741 48.900 904 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 17.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 6.91 % Allowed : 29.50 % Favored : 63.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.28), residues: 849 helix: 0.77 (0.23), residues: 474 sheet: -2.62 (0.55), residues: 73 loop : -2.08 (0.34), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 854 HIS 0.004 0.001 HIS A 437 PHE 0.014 0.001 PHE A 455 TYR 0.032 0.002 TYR A 349 ARG 0.003 0.000 ARG A 742 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 141 time to evaluate : 0.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 GLN cc_start: 0.7530 (mm110) cc_final: 0.7050 (mm110) REVERT: A 152 PHE cc_start: 0.5931 (OUTLIER) cc_final: 0.4877 (p90) REVERT: A 397 GLU cc_start: 0.8684 (mp0) cc_final: 0.8073 (mt-10) REVERT: A 413 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7632 (pm20) REVERT: A 416 GLU cc_start: 0.6863 (mp0) cc_final: 0.6474 (pm20) REVERT: A 426 PHE cc_start: 0.7342 (t80) cc_final: 0.6771 (t80) REVERT: A 463 LEU cc_start: 0.7656 (mm) cc_final: 0.7443 (mm) REVERT: A 478 LEU cc_start: 0.8599 (mt) cc_final: 0.8140 (mt) REVERT: A 479 LYS cc_start: 0.8214 (mmmt) cc_final: 0.7941 (mmtp) REVERT: A 482 ASN cc_start: 0.9031 (OUTLIER) cc_final: 0.8643 (t160) REVERT: A 484 GLU cc_start: 0.8415 (pt0) cc_final: 0.7922 (pt0) REVERT: A 517 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.7959 (tt) REVERT: A 623 ASP cc_start: 0.8201 (p0) cc_final: 0.7841 (p0) REVERT: A 640 MET cc_start: 0.8291 (mmm) cc_final: 0.8018 (mmm) REVERT: A 658 ASP cc_start: 0.7209 (t0) cc_final: 0.6882 (t0) REVERT: A 678 LYS cc_start: 0.8403 (mttt) cc_final: 0.8161 (ttmm) REVERT: A 833 ILE cc_start: 0.7849 (OUTLIER) cc_final: 0.7419 (mt) REVERT: A 844 SER cc_start: 0.8734 (OUTLIER) cc_final: 0.8524 (p) outliers start: 48 outliers final: 35 residues processed: 179 average time/residue: 0.1747 time to fit residues: 42.3866 Evaluate side-chains 170 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 129 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 TYR Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 152 PHE Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 280 MET Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain A residue 458 CYS Chi-restraints excluded: chain A residue 482 ASN Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 649 ASP Chi-restraints excluded: chain A residue 663 ILE Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 707 PHE Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 730 GLU Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 766 ILE Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 833 ILE Chi-restraints excluded: chain A residue 844 SER Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain A residue 879 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 67 optimal weight: 0.3980 chunk 13 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 chunk 18 optimal weight: 7.9990 chunk 45 optimal weight: 5.9990 chunk 36 optimal weight: 6.9990 chunk 16 optimal weight: 9.9990 chunk 1 optimal weight: 9.9990 chunk 38 optimal weight: 0.5980 chunk 55 optimal weight: 0.8980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 482 ASN ** A 798 GLN ** 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 = 0.4306 r_free = 0.4306 target = 0.160217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.131744 restraints weight = 15432.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.135688 restraints weight = 7818.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.138140 restraints weight = 4975.588| |-----------------------------------------------------------------------------| r_work (final): 0.3996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.3913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6601 Z= 0.211 Angle : 0.695 17.182 8933 Z= 0.344 Chirality : 0.043 0.169 1070 Planarity : 0.004 0.037 1141 Dihedral : 4.762 48.025 904 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 17.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 6.91 % Allowed : 30.50 % Favored : 62.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.28), residues: 849 helix: 1.04 (0.23), residues: 450 sheet: -2.27 (0.61), residues: 67 loop : -2.11 (0.32), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 854 HIS 0.004 0.001 HIS A 437 PHE 0.012 0.001 PHE A 455 TYR 0.030 0.002 TYR A 349 ARG 0.003 0.000 ARG A 420 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 136 time to evaluate : 0.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 GLN cc_start: 0.7537 (mm110) cc_final: 0.7053 (mm110) REVERT: A 152 PHE cc_start: 0.5865 (OUTLIER) cc_final: 0.4837 (p90) REVERT: A 344 MET cc_start: 0.7282 (mpp) cc_final: 0.6608 (mtm) REVERT: A 397 GLU cc_start: 0.8681 (mp0) cc_final: 0.8110 (mt-10) REVERT: A 413 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7699 (pm20) REVERT: A 426 PHE cc_start: 0.7328 (t80) cc_final: 0.6795 (t80) REVERT: A 478 LEU cc_start: 0.8569 (mt) cc_final: 0.8125 (mt) REVERT: A 479 LYS cc_start: 0.8232 (mmmt) cc_final: 0.7968 (mmtp) REVERT: A 482 ASN cc_start: 0.9015 (OUTLIER) cc_final: 0.8722 (t0) REVERT: A 484 GLU cc_start: 0.8382 (pt0) cc_final: 0.7961 (pt0) REVERT: A 517 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.7959 (tt) REVERT: A 623 ASP cc_start: 0.8212 (p0) cc_final: 0.7859 (p0) REVERT: A 640 MET cc_start: 0.8403 (mmm) cc_final: 0.8048 (mmm) REVERT: A 678 LYS cc_start: 0.8426 (mttt) cc_final: 0.8148 (ttmm) REVERT: A 833 ILE cc_start: 0.7858 (OUTLIER) cc_final: 0.7428 (mt) REVERT: A 844 SER cc_start: 0.8709 (OUTLIER) cc_final: 0.8467 (p) outliers start: 48 outliers final: 36 residues processed: 173 average time/residue: 0.1692 time to fit residues: 39.9846 Evaluate side-chains 171 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 129 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 TYR Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 152 PHE Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 280 MET Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain A residue 458 CYS Chi-restraints excluded: chain A residue 482 ASN Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 649 ASP Chi-restraints excluded: chain A residue 663 ILE Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 707 PHE Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 766 ILE Chi-restraints excluded: chain A residue 782 MET Chi-restraints excluded: chain A residue 805 ASN Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 833 ILE Chi-restraints excluded: chain A residue 844 SER Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain A residue 879 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 36 optimal weight: 0.0570 chunk 1 optimal weight: 9.9990 chunk 2 optimal weight: 0.8980 chunk 77 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 20 optimal weight: 0.0970 chunk 45 optimal weight: 7.9990 chunk 54 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 58 optimal weight: 0.3980 overall best weight: 0.4096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 405 ASN A 482 ASN ** A 798 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.161407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.133646 restraints weight = 15438.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.137761 restraints weight = 7671.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.140255 restraints weight = 4804.202| |-----------------------------------------------------------------------------| r_work (final): 0.4026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.3987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6601 Z= 0.184 Angle : 0.690 17.078 8933 Z= 0.338 Chirality : 0.043 0.172 1070 Planarity : 0.004 0.039 1141 Dihedral : 4.681 47.002 904 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 16.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 5.76 % Allowed : 32.81 % Favored : 61.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.28), residues: 849 helix: 1.03 (0.23), residues: 456 sheet: -1.95 (0.64), residues: 67 loop : -2.09 (0.32), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 854 HIS 0.004 0.001 HIS A 437 PHE 0.018 0.001 PHE A 455 TYR 0.030 0.002 TYR A 349 ARG 0.002 0.000 ARG A 742 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 142 time to evaluate : 0.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 GLN cc_start: 0.7499 (mm110) cc_final: 0.7044 (mm110) REVERT: A 152 PHE cc_start: 0.5830 (OUTLIER) cc_final: 0.4828 (p90) REVERT: A 344 MET cc_start: 0.7117 (mpp) cc_final: 0.6447 (mtm) REVERT: A 397 GLU cc_start: 0.8707 (mp0) cc_final: 0.8201 (mt-10) REVERT: A 416 GLU cc_start: 0.6818 (mp0) cc_final: 0.6505 (pm20) REVERT: A 478 LEU cc_start: 0.8536 (mt) cc_final: 0.8130 (mt) REVERT: A 479 LYS cc_start: 0.8227 (mmmt) cc_final: 0.7956 (mmtp) REVERT: A 482 ASN cc_start: 0.9012 (OUTLIER) cc_final: 0.8644 (t160) REVERT: A 484 GLU cc_start: 0.8414 (pt0) cc_final: 0.7856 (pt0) REVERT: A 623 ASP cc_start: 0.8172 (p0) cc_final: 0.7759 (p0) REVERT: A 632 LYS cc_start: 0.7873 (mtmt) cc_final: 0.7481 (mttm) REVERT: A 678 LYS cc_start: 0.8394 (mttt) cc_final: 0.8099 (ttmm) REVERT: A 833 ILE cc_start: 0.7784 (OUTLIER) cc_final: 0.7385 (mt) REVERT: A 844 SER cc_start: 0.8699 (OUTLIER) cc_final: 0.8466 (p) outliers start: 40 outliers final: 29 residues processed: 171 average time/residue: 0.1725 time to fit residues: 40.1630 Evaluate side-chains 164 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 131 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 TYR Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 152 PHE Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 280 MET Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 482 ASN Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 663 ILE Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 707 PHE Chi-restraints excluded: chain A residue 766 ILE Chi-restraints excluded: chain A residue 782 MET Chi-restraints excluded: chain A residue 805 ASN Chi-restraints excluded: chain A residue 833 ILE Chi-restraints excluded: chain A residue 844 SER Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain A residue 879 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 81 optimal weight: 0.9990 chunk 22 optimal weight: 5.9990 chunk 75 optimal weight: 0.7980 chunk 11 optimal weight: 5.9990 chunk 69 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 1 optimal weight: 8.9990 chunk 54 optimal weight: 0.0980 chunk 9 optimal weight: 4.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 482 ASN ** A 798 GLN ** 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 = 0.4292 r_free = 0.4292 target = 0.159225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.130687 restraints weight = 15631.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.134602 restraints weight = 7993.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.137055 restraints weight = 5138.764| |-----------------------------------------------------------------------------| r_work (final): 0.3991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.4154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6601 Z= 0.235 Angle : 0.740 17.130 8933 Z= 0.363 Chirality : 0.043 0.158 1070 Planarity : 0.004 0.040 1141 Dihedral : 4.741 46.550 904 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 18.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 5.47 % Allowed : 34.24 % Favored : 60.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.28), residues: 849 helix: 0.95 (0.23), residues: 462 sheet: -1.93 (0.66), residues: 66 loop : -2.13 (0.33), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 854 HIS 0.004 0.001 HIS A 437 PHE 0.026 0.001 PHE A 455 TYR 0.026 0.002 TYR A 349 ARG 0.003 0.000 ARG A 742 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 133 time to evaluate : 0.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 GLN cc_start: 0.7541 (mm110) cc_final: 0.7048 (mm110) REVERT: A 152 PHE cc_start: 0.5849 (OUTLIER) cc_final: 0.4879 (p90) REVERT: A 344 MET cc_start: 0.7151 (mpp) cc_final: 0.6490 (mtm) REVERT: A 397 GLU cc_start: 0.8649 (mp0) cc_final: 0.8161 (mt-10) REVERT: A 416 GLU cc_start: 0.6795 (mp0) cc_final: 0.6192 (pm20) REVERT: A 426 PHE cc_start: 0.7294 (t80) cc_final: 0.7085 (t80) REVERT: A 461 VAL cc_start: 0.6372 (OUTLIER) cc_final: 0.6124 (p) REVERT: A 478 LEU cc_start: 0.8486 (mt) cc_final: 0.8121 (mt) REVERT: A 479 LYS cc_start: 0.8178 (mmmt) cc_final: 0.7898 (mmtp) REVERT: A 482 ASN cc_start: 0.8987 (OUTLIER) cc_final: 0.8652 (t160) REVERT: A 484 GLU cc_start: 0.8449 (pt0) cc_final: 0.8011 (pt0) REVERT: A 623 ASP cc_start: 0.8142 (p0) cc_final: 0.7794 (p0) REVERT: A 632 LYS cc_start: 0.7915 (mtmt) cc_final: 0.7513 (mttm) REVERT: A 678 LYS cc_start: 0.8409 (mttt) cc_final: 0.8112 (ttmm) REVERT: A 833 ILE cc_start: 0.7883 (OUTLIER) cc_final: 0.7453 (mt) outliers start: 38 outliers final: 32 residues processed: 162 average time/residue: 0.1727 time to fit residues: 38.0757 Evaluate side-chains 163 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 127 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 TYR Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 152 PHE Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 280 MET Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 482 ASN Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 663 ILE Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 707 PHE Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 782 MET Chi-restraints excluded: chain A residue 805 ASN Chi-restraints excluded: chain A residue 833 ILE Chi-restraints excluded: chain A residue 844 SER Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain A residue 879 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 57 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 chunk 9 optimal weight: 4.9990 chunk 6 optimal weight: 0.0870 chunk 48 optimal weight: 10.0000 chunk 34 optimal weight: 0.9980 chunk 35 optimal weight: 6.9990 chunk 60 optimal weight: 0.0870 chunk 70 optimal weight: 0.0170 chunk 63 optimal weight: 0.8980 overall best weight: 0.3974 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 798 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.161835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.134490 restraints weight = 16137.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.138451 restraints weight = 8218.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.141020 restraints weight = 5226.052| |-----------------------------------------------------------------------------| r_work (final): 0.4032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.4187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6601 Z= 0.193 Angle : 0.730 17.054 8933 Z= 0.354 Chirality : 0.043 0.160 1070 Planarity : 0.004 0.042 1141 Dihedral : 4.684 45.856 904 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 17.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 5.04 % Allowed : 34.82 % Favored : 60.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.45 (0.29), residues: 849 helix: 1.08 (0.23), residues: 461 sheet: -1.83 (0.66), residues: 66 loop : -2.05 (0.33), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 854 HIS 0.004 0.001 HIS A 437 PHE 0.021 0.001 PHE A 359 TYR 0.033 0.001 TYR A 349 ARG 0.004 0.000 ARG A 420 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2613.99 seconds wall clock time: 47 minutes 38.76 seconds (2858.76 seconds total)