Starting phenix.real_space_refine on Thu Jul 2 04:07:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9evc_19998/07_2026/9evc_19998.cif Found real_map, /net/cci-nas-00/data/ceres_data/9evc_19998/07_2026/9evc_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 { model { file = "/net/cci-nas-00/data/ceres_data/9evc_19998/07_2026/9evc_19998.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9evc_19998/07_2026/9evc_19998.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9evc_19998/07_2026/9evc_19998.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9evc_19998/07_2026/9evc_19998.map" } resolution = 3.73 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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: {'ASP:plan': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CA': 1} Chain breaks: 1 Time building chain proxies: 1.24, per 1000 atoms: 0.19 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: 0.32 Conformation dependent library (CDL) restraints added in 238.6 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: 0.18 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: 0.85 Time building geometry restraints manager: 0.44 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 3.250 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 3.250 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: 5.220 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.050 Find NCS groups from input model: 0.030 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7084 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= 0.198 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 : 16.20 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.002 0.000 ARG A 5 TYR 0.006 0.001 TYR A 497 PHE 0.011 0.001 PHE A 12 TRP 0.012 0.002 TRP A 611 HIS 0.004 0.001 HIS A 437 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.20 ( 6601) covalent geometry : angle 0.79992 / 0.42 ( 8933) hydrogen bonds : bond 0.15039 / 9.28 ( 374) hydrogen bonds : angle 6.30961 / 4.57 ( 1089) *********************** 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 : 0.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 ILE cc_start: 0.8340 (mt) cc_final: 0.8076 (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: 0.5106 (tpp) REVERT: A 433 MET cc_start: 0.7942 (tpt) cc_final: 0.7291 (tpt) REVERT: A 478 LEU cc_start: 0.8505 (mt) cc_final: 0.7893 (mt) REVERT: A 623 ASP cc_start: 0.7614 (p0) cc_final: 0.7394 (p0) REVERT: A 677 ILE cc_start: 0.8500 (mm) cc_final: 0.8293 (mm) REVERT: A 865 VAL cc_start: 0.6774 (m) cc_final: 0.6498 (m) outliers start: 3 outliers final: 3 residues processed: 202 average time/residue: 0.0676 time to fit residues: 18.4583 Evaluate side-chains 147 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 144 time to evaluate : 0.251 ------------------------------------------------------------------------------- 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 49 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 74 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 70 GLN A 277 ASN A 358 ASN ** A 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 603 ASN A 716 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.163661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.135126 restraints weight = 15773.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.139206 restraints weight = 8018.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.141829 restraints weight = 5073.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.143103 restraints weight = 3757.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.144261 restraints weight = 3148.111| |-----------------------------------------------------------------------------| r_work (final): 0.4068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6601 Z= 0.152 Angle : 0.661 14.063 8933 Z= 0.337 Chirality : 0.044 0.193 1070 Planarity : 0.004 0.037 1141 Dihedral : 5.013 51.349 908 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 15.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 7.48 % Allowed : 27.19 % Favored : 65.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.28), residues: 849 helix: 0.50 (0.23), residues: 466 sheet: -2.95 (0.55), residues: 69 loop : -2.19 (0.33), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 528 TYR 0.011 0.002 TYR A 495 PHE 0.029 0.001 PHE A 455 TRP 0.010 0.002 TRP A 854 HIS 0.005 0.001 HIS A 437 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 ( 6601) covalent geometry : angle 0.66104 / 0.34 ( 8933) hydrogen bonds : bond 0.04415 / 2.70 ( 374) hydrogen bonds : angle 4.89623 / 3.53 ( 1089) *********************** 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 211 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 159 time to evaluate : 0.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 TYR cc_start: 0.7096 (OUTLIER) cc_final: 0.6244 (t80) REVERT: A 105 ASP cc_start: 0.8720 (m-30) cc_final: 0.8208 (m-30) REVERT: A 110 MET cc_start: 0.6866 (ppp) cc_final: 0.6217 (tmm) REVERT: A 152 PHE cc_start: 0.5414 (OUTLIER) cc_final: 0.4473 (p90) REVERT: A 253 LEU cc_start: 0.7239 (OUTLIER) cc_final: 0.5933 (mm) REVERT: A 358 ASN cc_start: 0.6811 (OUTLIER) cc_final: 0.6238 (t0) REVERT: A 397 GLU cc_start: 0.8602 (mp0) cc_final: 0.8146 (mp0) REVERT: A 433 MET cc_start: 0.8004 (tpt) cc_final: 0.7473 (tpt) REVERT: A 478 LEU cc_start: 0.8500 (mt) cc_final: 0.7983 (mt) REVERT: A 623 ASP cc_start: 0.8154 (p0) cc_final: 0.7842 (p0) REVERT: A 633 GLN cc_start: 0.7543 (OUTLIER) cc_final: 0.7195 (mp10) REVERT: A 678 LYS cc_start: 0.8375 (mttt) cc_final: 0.7957 (mttm) REVERT: A 689 LEU cc_start: 0.7784 (OUTLIER) cc_final: 0.7357 (tt) outliers start: 52 outliers final: 27 residues processed: 190 average time/residue: 0.0599 time to fit residues: 15.7339 Evaluate side-chains 175 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 142 time to evaluate : 0.144 ------------------------------------------------------------------------------- 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 70 GLN 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 292 GLU Chi-restraints excluded: chain A residue 296 SER 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 518 VAL Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 633 GLN 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 727 LEU Chi-restraints excluded: chain A residue 753 THR Chi-restraints excluded: chain A residue 783 SER Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 824 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 12 optimal weight: 9.9990 chunk 67 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 chunk 80 optimal weight: 0.9990 chunk 71 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 41 optimal weight: 20.0000 chunk 35 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 358 ASN ** A 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 482 ASN ** A 716 ASN ** 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 = 0.4337 r_free = 0.4337 target = 0.162097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.133250 restraints weight = 15313.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.137331 restraints weight = 7686.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.139797 restraints weight = 4837.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.141383 restraints weight = 3570.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.142222 restraints weight = 2933.014| |-----------------------------------------------------------------------------| r_work (final): 0.4062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6601 Z= 0.153 Angle : 0.666 14.379 8933 Z= 0.333 Chirality : 0.044 0.182 1070 Planarity : 0.004 0.036 1141 Dihedral : 4.673 50.847 904 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 17.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 6.76 % Allowed : 27.19 % Favored : 66.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.28), residues: 849 helix: 0.67 (0.23), residues: 466 sheet: -2.17 (0.66), residues: 56 loop : -2.21 (0.32), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 528 TYR 0.014 0.001 TYR A 349 PHE 0.028 0.001 PHE A 455 TRP 0.011 0.002 TRP A 854 HIS 0.005 0.001 HIS A 437 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 ( 6601) covalent geometry : angle 0.66594 / 0.33 ( 8933) hydrogen bonds : bond 0.04210 / 2.52 ( 374) hydrogen bonds : angle 4.73110 / 3.41 ( 1089) *********************** 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 197 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 150 time to evaluate : 0.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ASP cc_start: 0.8555 (m-30) cc_final: 0.8195 (m-30) REVERT: A 110 MET cc_start: 0.6847 (ppp) cc_final: 0.6263 (tmm) REVERT: A 136 VAL cc_start: 0.3855 (OUTLIER) cc_final: 0.3484 (t) REVERT: A 152 PHE cc_start: 0.5401 (OUTLIER) cc_final: 0.3477 (p90) REVERT: A 251 CYS cc_start: 0.7855 (m) cc_final: 0.7542 (t) REVERT: A 253 LEU cc_start: 0.7353 (OUTLIER) cc_final: 0.5982 (mm) REVERT: A 292 GLU cc_start: 0.8267 (mp0) cc_final: 0.7678 (pm20) REVERT: A 358 ASN cc_start: 0.6958 (OUTLIER) cc_final: 0.6167 (t0) REVERT: A 397 GLU cc_start: 0.8560 (mp0) cc_final: 0.8120 (mp0) REVERT: A 433 MET cc_start: 0.8161 (tpt) cc_final: 0.7486 (tpt) REVERT: A 478 LEU cc_start: 0.8549 (mt) cc_final: 0.8001 (mt) REVERT: A 484 GLU cc_start: 0.8338 (pt0) cc_final: 0.7755 (pt0) REVERT: A 623 ASP cc_start: 0.8218 (p0) cc_final: 0.7859 (p0) REVERT: A 633 GLN cc_start: 0.7486 (mp10) cc_final: 0.7123 (mp10) REVERT: A 678 LYS cc_start: 0.8373 (mttt) cc_final: 0.8111 (ttmm) REVERT: A 689 LEU cc_start: 0.7863 (OUTLIER) cc_final: 0.7429 (tt) outliers start: 47 outliers final: 23 residues processed: 181 average time/residue: 0.0598 time to fit residues: 14.6548 Evaluate side-chains 166 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 138 time to evaluate : 0.243 ------------------------------------------------------------------------------- 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 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 296 SER Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 358 ASN Chi-restraints excluded: chain A residue 447 THR 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 783 SER Chi-restraints excluded: chain A residue 790 THR 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 60 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 84 optimal weight: 7.9990 chunk 81 optimal weight: 9.9990 chunk 47 optimal weight: 9.9990 chunk 44 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 80 optimal weight: 0.5980 chunk 74 optimal weight: 0.7980 chunk 58 optimal weight: 0.6980 chunk 40 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 358 ASN ** A 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 412 ASN A 817 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.162113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.133146 restraints weight = 15521.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.137245 restraints weight = 7749.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.139823 restraints weight = 4887.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.141144 restraints weight = 3577.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.142383 restraints weight = 2989.883| |-----------------------------------------------------------------------------| r_work (final): 0.4053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6601 Z= 0.139 Angle : 0.646 15.419 8933 Z= 0.323 Chirality : 0.043 0.178 1070 Planarity : 0.004 0.034 1141 Dihedral : 4.579 50.607 904 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 17.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 7.05 % Allowed : 27.91 % Favored : 65.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.28), residues: 849 helix: 0.73 (0.24), residues: 469 sheet: -2.36 (0.59), residues: 69 loop : -2.08 (0.33), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 528 TYR 0.023 0.001 TYR A 349 PHE 0.025 0.001 PHE A 455 TRP 0.010 0.001 TRP A 854 HIS 0.005 0.001 HIS A 437 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 ( 6601) covalent geometry : angle 0.64555 / 0.32 ( 8933) hydrogen bonds : bond 0.03955 / 2.36 ( 374) hydrogen bonds : angle 4.55241 / 3.30 ( 1089) *********************** 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 196 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 147 time to evaluate : 0.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ASP cc_start: 0.8530 (m-30) cc_final: 0.8177 (m-30) REVERT: A 110 MET cc_start: 0.6641 (ppp) cc_final: 0.6201 (tmm) REVERT: A 136 VAL cc_start: 0.4067 (OUTLIER) cc_final: 0.3758 (t) REVERT: A 152 PHE cc_start: 0.5314 (OUTLIER) cc_final: 0.3845 (p90) REVERT: A 251 CYS cc_start: 0.7881 (m) cc_final: 0.7570 (t) REVERT: A 253 LEU cc_start: 0.7383 (OUTLIER) cc_final: 0.5988 (mm) REVERT: A 292 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.6985 (pm20) REVERT: A 397 GLU cc_start: 0.8476 (mp0) cc_final: 0.8124 (mp0) REVERT: A 433 MET cc_start: 0.8165 (tpt) cc_final: 0.7474 (tpt) REVERT: A 461 VAL cc_start: 0.5800 (OUTLIER) cc_final: 0.5600 (p) REVERT: A 478 LEU cc_start: 0.8529 (mt) cc_final: 0.8025 (mt) REVERT: A 484 GLU cc_start: 0.8264 (pt0) cc_final: 0.7747 (pt0) REVERT: A 623 ASP cc_start: 0.8192 (p0) cc_final: 0.7848 (p0) REVERT: A 633 GLN cc_start: 0.7553 (mp10) cc_final: 0.7195 (mp10) REVERT: A 640 MET cc_start: 0.8782 (mmm) cc_final: 0.8572 (mmm) REVERT: A 658 ASP cc_start: 0.7069 (t0) cc_final: 0.6868 (t70) REVERT: A 678 LYS cc_start: 0.8353 (mttt) cc_final: 0.8128 (ttmm) REVERT: A 689 LEU cc_start: 0.7876 (OUTLIER) cc_final: 0.7419 (tt) outliers start: 49 outliers final: 31 residues processed: 181 average time/residue: 0.0591 time to fit residues: 14.9260 Evaluate side-chains 173 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 136 time to evaluate : 0.166 ------------------------------------------------------------------------------- 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 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 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 340 THR Chi-restraints excluded: chain A residue 358 ASN Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain A residue 458 CYS Chi-restraints excluded: chain A residue 461 VAL 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 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 707 PHE Chi-restraints excluded: chain A residue 730 GLU Chi-restraints excluded: chain A residue 783 SER Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 829 VAL 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 35 optimal weight: 0.9980 chunk 74 optimal weight: 0.8980 chunk 81 optimal weight: 5.9990 chunk 51 optimal weight: 0.4980 chunk 41 optimal weight: 8.9990 chunk 25 optimal weight: 0.7980 chunk 59 optimal weight: 0.7980 chunk 19 optimal weight: 9.9990 chunk 11 optimal weight: 0.4980 chunk 69 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 358 ASN ** A 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 482 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.162566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.133601 restraints weight = 15550.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.137804 restraints weight = 7766.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.140423 restraints weight = 4864.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.142079 restraints weight = 3564.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.142835 restraints weight = 2911.184| |-----------------------------------------------------------------------------| r_work (final): 0.4060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.3067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6601 Z= 0.134 Angle : 0.650 15.805 8933 Z= 0.322 Chirality : 0.042 0.173 1070 Planarity : 0.004 0.032 1141 Dihedral : 4.533 49.904 904 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 16.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 6.91 % Allowed : 28.63 % Favored : 64.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.28), residues: 849 helix: 0.76 (0.23), residues: 469 sheet: -2.29 (0.57), residues: 69 loop : -2.05 (0.34), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 528 TYR 0.025 0.001 TYR A 349 PHE 0.017 0.001 PHE A 455 TRP 0.009 0.001 TRP A 854 HIS 0.004 0.001 HIS A 437 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 ( 6601) covalent geometry : angle 0.64985 / 0.32 ( 8933) hydrogen bonds : bond 0.03862 / 2.30 ( 374) hydrogen bonds : angle 4.46675 / 3.23 ( 1089) *********************** 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 191 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 143 time to evaluate : 0.179 Fit side-chains revert: symmetry clash revert: symmetry clash 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: 0.8188 (m-30) REVERT: A 152 PHE cc_start: 0.5272 (OUTLIER) cc_final: 0.3893 (p90) REVERT: A 251 CYS cc_start: 0.7808 (m) cc_final: 0.7581 (t) REVERT: A 253 LEU cc_start: 0.7366 (OUTLIER) cc_final: 0.5974 (mm) REVERT: A 280 MET cc_start: 0.6352 (OUTLIER) cc_final: 0.6056 (ttt) REVERT: A 344 MET cc_start: 0.7186 (mpp) cc_final: 0.6510 (mtm) REVERT: A 397 GLU cc_start: 0.8563 (mp0) cc_final: 0.8160 (mp0) REVERT: A 416 GLU cc_start: 0.6749 (mp0) cc_final: 0.6229 (pm20) REVERT: A 433 MET cc_start: 0.8196 (tpt) cc_final: 0.7862 (tpp) REVERT: A 478 LEU cc_start: 0.8547 (mt) cc_final: 0.7971 (mt) REVERT: A 479 LYS cc_start: 0.8083 (mmmt) cc_final: 0.7869 (mmtp) REVERT: A 483 GLU cc_start: 0.8216 (pp20) cc_final: 0.8000 (pp20) REVERT: A 484 GLU cc_start: 0.8324 (pt0) cc_final: 0.7729 (pt0) REVERT: A 623 ASP cc_start: 0.8191 (p0) cc_final: 0.7813 (p0) REVERT: A 633 GLN cc_start: 0.7514 (mp10) cc_final: 0.7092 (mp10) REVERT: A 658 ASP cc_start: 0.7079 (t70) cc_final: 0.6852 (t70) REVERT: A 678 LYS cc_start: 0.8365 (mttt) cc_final: 0.8138 (ttmm) REVERT: A 833 ILE cc_start: 0.7804 (OUTLIER) cc_final: 0.7337 (mt) outliers start: 48 outliers final: 33 residues processed: 180 average time/residue: 0.0569 time to fit residues: 14.4720 Evaluate side-chains 171 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 134 time to evaluate : 0.223 ------------------------------------------------------------------------------- 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 73 LEU Chi-restraints excluded: chain A residue 86 LEU 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 318 LYS Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 358 ASN Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain A residue 458 CYS 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 574 THR Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 649 ASP Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 707 PHE Chi-restraints excluded: chain A residue 730 GLU Chi-restraints excluded: chain A residue 783 SER Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 833 ILE Chi-restraints excluded: chain A residue 866 VAL 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 15 optimal weight: 10.0000 chunk 24 optimal weight: 0.0770 chunk 51 optimal weight: 0.9990 chunk 84 optimal weight: 0.7980 chunk 22 optimal weight: 6.9990 chunk 19 optimal weight: 0.9990 chunk 10 optimal weight: 5.9990 chunk 67 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 60 optimal weight: 0.5980 chunk 78 optimal weight: 8.9990 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 358 ASN ** A 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.162618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.133800 restraints weight = 15725.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.137986 restraints weight = 7883.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.140573 restraints weight = 4952.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.142014 restraints weight = 3627.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.143162 restraints weight = 3000.415| |-----------------------------------------------------------------------------| r_work (final): 0.4074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.3255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6601 Z= 0.132 Angle : 0.642 16.245 8933 Z= 0.317 Chirality : 0.042 0.170 1070 Planarity : 0.004 0.032 1141 Dihedral : 4.501 49.389 904 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 17.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 7.34 % Allowed : 28.20 % Favored : 64.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.28), residues: 849 helix: 0.83 (0.23), residues: 468 sheet: -2.33 (0.57), residues: 69 loop : -2.04 (0.34), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 528 TYR 0.024 0.001 TYR A 349 PHE 0.022 0.001 PHE A 455 TRP 0.009 0.001 TRP A 854 HIS 0.004 0.001 HIS A 437 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 ( 6601) covalent geometry : angle 0.64190 / 0.32 ( 8933) hydrogen bonds : bond 0.03775 / 2.24 ( 374) hydrogen bonds : angle 4.42990 / 3.18 ( 1089) *********************** 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 195 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 144 time to evaluate : 0.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ASP cc_start: 0.8530 (m-30) cc_final: 0.8163 (m-30) REVERT: A 152 PHE cc_start: 0.5322 (OUTLIER) cc_final: 0.3860 (p90) REVERT: A 253 LEU cc_start: 0.7317 (OUTLIER) cc_final: 0.5937 (mm) REVERT: A 280 MET cc_start: 0.6317 (OUTLIER) cc_final: 0.6027 (ttt) REVERT: A 344 MET cc_start: 0.7121 (mpp) cc_final: 0.6453 (mtm) REVERT: A 397 GLU cc_start: 0.8573 (mp0) cc_final: 0.8192 (mp0) REVERT: A 416 GLU cc_start: 0.6723 (mp0) cc_final: 0.6325 (pm20) REVERT: A 433 MET cc_start: 0.8221 (tpt) cc_final: 0.7902 (tpp) REVERT: A 478 LEU cc_start: 0.8498 (mt) cc_final: 0.8028 (mt) REVERT: A 484 GLU cc_start: 0.8283 (pt0) cc_final: 0.7743 (pt0) REVERT: A 623 ASP cc_start: 0.8165 (p0) cc_final: 0.7781 (p0) REVERT: A 633 GLN cc_start: 0.7518 (OUTLIER) cc_final: 0.7083 (mp10) REVERT: A 678 LYS cc_start: 0.8369 (mttt) cc_final: 0.8121 (ttmm) REVERT: A 689 LEU cc_start: 0.7853 (OUTLIER) cc_final: 0.7396 (tt) REVERT: A 833 ILE cc_start: 0.7825 (OUTLIER) cc_final: 0.7464 (mt) outliers start: 51 outliers final: 33 residues processed: 179 average time/residue: 0.0576 time to fit residues: 14.5244 Evaluate side-chains 169 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 130 time to evaluate : 0.201 ------------------------------------------------------------------------------- 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 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 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 318 LYS Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 358 ASN Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain A residue 458 CYS 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 574 THR Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 620 MET Chi-restraints excluded: chain A residue 633 GLN 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 707 PHE Chi-restraints excluded: chain A residue 730 GLU Chi-restraints excluded: chain A residue 783 SER Chi-restraints excluded: chain A residue 790 THR 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 879 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 9 optimal weight: 4.9990 chunk 74 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 12 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 chunk 44 optimal weight: 0.1980 chunk 46 optimal weight: 0.5980 chunk 59 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 407 ASN ** 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 = 0.4325 r_free = 0.4325 target = 0.161990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.133398 restraints weight = 15643.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.137462 restraints weight = 7885.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.140018 restraints weight = 5017.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.141431 restraints weight = 3695.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.142475 restraints weight = 3066.502| |-----------------------------------------------------------------------------| r_work (final): 0.4058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.3448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6601 Z= 0.137 Angle : 0.667 17.126 8933 Z= 0.330 Chirality : 0.043 0.217 1070 Planarity : 0.004 0.031 1141 Dihedral : 4.558 48.900 904 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 16.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 7.63 % Allowed : 29.06 % Favored : 63.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.28), residues: 849 helix: 0.88 (0.23), residues: 468 sheet: -2.48 (0.54), residues: 80 loop : -2.07 (0.34), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 420 TYR 0.025 0.001 TYR A 349 PHE 0.022 0.001 PHE A 455 TRP 0.007 0.001 TRP A 854 HIS 0.004 0.001 HIS A 437 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 ( 6601) covalent geometry : angle 0.66742 / 0.33 ( 8933) hydrogen bonds : bond 0.03799 / 2.23 ( 374) hydrogen bonds : angle 4.43337 / 3.19 ( 1089) *********************** 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 196 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 143 time to evaluate : 0.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ASP cc_start: 0.8528 (m-30) cc_final: 0.8158 (m-30) REVERT: A 152 PHE cc_start: 0.5393 (OUTLIER) cc_final: 0.4202 (p90) REVERT: A 280 MET cc_start: 0.6309 (OUTLIER) cc_final: 0.5964 (ttt) REVERT: A 344 MET cc_start: 0.7121 (mpp) cc_final: 0.6439 (mtm) REVERT: A 348 ASP cc_start: 0.7092 (OUTLIER) cc_final: 0.6756 (t70) REVERT: A 397 GLU cc_start: 0.8637 (mp0) cc_final: 0.8238 (mp0) REVERT: A 416 GLU cc_start: 0.6718 (mp0) cc_final: 0.6400 (pm20) REVERT: A 433 MET cc_start: 0.8216 (tpt) cc_final: 0.7910 (tpp) REVERT: A 478 LEU cc_start: 0.8450 (mt) cc_final: 0.8005 (mt) REVERT: A 484 GLU cc_start: 0.8328 (pt0) cc_final: 0.7759 (pt0) REVERT: A 623 ASP cc_start: 0.8189 (p0) cc_final: 0.7808 (p0) REVERT: A 633 GLN cc_start: 0.7493 (mp10) cc_final: 0.7045 (mp10) REVERT: A 678 LYS cc_start: 0.8377 (mttt) cc_final: 0.8129 (ttmm) REVERT: A 689 LEU cc_start: 0.7865 (OUTLIER) cc_final: 0.7399 (tt) REVERT: A 833 ILE cc_start: 0.7827 (OUTLIER) cc_final: 0.7372 (mt) outliers start: 53 outliers final: 37 residues processed: 181 average time/residue: 0.0631 time to fit residues: 16.1704 Evaluate side-chains 175 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 133 time to evaluate : 0.222 ------------------------------------------------------------------------------- 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 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 318 LYS Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 458 CYS 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 574 THR 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 673 VAL Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 707 PHE Chi-restraints excluded: chain A residue 730 GLU Chi-restraints excluded: chain A residue 782 MET Chi-restraints excluded: chain A residue 783 SER Chi-restraints excluded: chain A residue 790 THR 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 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 52 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 18 optimal weight: 9.9990 chunk 65 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 43 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 482 ASN A 603 ASN A 705 ASN ** A 798 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 807 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.157609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.128241 restraints weight = 15592.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.132264 restraints weight = 7852.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.134702 restraints weight = 5011.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.136287 restraints weight = 3712.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.137138 restraints weight = 3069.957| |-----------------------------------------------------------------------------| r_work (final): 0.3973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.3847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 6601 Z= 0.209 Angle : 0.732 16.385 8933 Z= 0.367 Chirality : 0.045 0.163 1070 Planarity : 0.004 0.033 1141 Dihedral : 4.769 49.019 904 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 19.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 6.91 % Allowed : 31.08 % Favored : 62.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.28), residues: 849 helix: 0.65 (0.23), residues: 468 sheet: -2.15 (0.62), residues: 71 loop : -2.05 (0.34), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 420 TYR 0.025 0.002 TYR A 349 PHE 0.026 0.001 PHE A 455 TRP 0.010 0.002 TRP A 854 HIS 0.004 0.001 HIS A 437 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.21 ( 6601) covalent geometry : angle 0.73166 / 0.37 ( 8933) hydrogen bonds : bond 0.04367 / 2.54 ( 374) hydrogen bonds : angle 4.70975 / 3.36 ( 1089) *********************** 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 187 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 139 time to evaluate : 0.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 PHE cc_start: 0.5549 (OUTLIER) cc_final: 0.4455 (p90) REVERT: A 280 MET cc_start: 0.6333 (OUTLIER) cc_final: 0.6022 (ttt) REVERT: A 342 ASN cc_start: 0.7085 (m-40) cc_final: 0.6804 (m-40) REVERT: A 397 GLU cc_start: 0.8683 (mp0) cc_final: 0.8204 (mp0) REVERT: A 433 MET cc_start: 0.8316 (tpt) cc_final: 0.8033 (tpp) REVERT: A 478 LEU cc_start: 0.8529 (mt) cc_final: 0.8068 (mt) REVERT: A 479 LYS cc_start: 0.8127 (mmmt) cc_final: 0.7904 (mmtp) REVERT: A 484 GLU cc_start: 0.8419 (pt0) cc_final: 0.7942 (pt0) REVERT: A 623 ASP cc_start: 0.8220 (p0) cc_final: 0.7921 (p0) REVERT: A 678 LYS cc_start: 0.8384 (mttt) cc_final: 0.8165 (ttmm) REVERT: A 689 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.7809 (tt) REVERT: A 833 ILE cc_start: 0.7942 (OUTLIER) cc_final: 0.7671 (mt) outliers start: 48 outliers final: 35 residues processed: 174 average time/residue: 0.0645 time to fit residues: 15.5261 Evaluate side-chains 172 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 133 time to evaluate : 0.264 ------------------------------------------------------------------------------- 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 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 458 CYS 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 620 MET 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 689 LEU Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 707 PHE Chi-restraints excluded: chain A residue 730 GLU Chi-restraints excluded: chain A residue 766 ILE Chi-restraints excluded: chain A residue 782 MET 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 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 35 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 chunk 66 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 36 optimal weight: 10.0000 chunk 33 optimal weight: 0.0040 chunk 55 optimal weight: 1.9990 chunk 44 optimal weight: 10.0000 chunk 22 optimal weight: 0.8980 overall best weight: 0.8996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 89 ASN ** 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 = 0.4284 r_free = 0.4284 target = 0.158736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.130732 restraints weight = 15641.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.134587 restraints weight = 7804.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.137073 restraints weight = 4922.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.138632 restraints weight = 3635.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.139384 restraints weight = 2974.882| |-----------------------------------------------------------------------------| r_work (final): 0.4020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.3974 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= 0.158 Angle : 0.724 17.234 8933 Z= 0.359 Chirality : 0.044 0.157 1070 Planarity : 0.004 0.036 1141 Dihedral : 4.754 48.109 904 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 18.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 5.61 % Allowed : 33.24 % Favored : 61.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.28), residues: 849 helix: 0.70 (0.23), residues: 469 sheet: -2.03 (0.64), residues: 66 loop : -2.20 (0.33), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 528 TYR 0.028 0.002 TYR A 349 PHE 0.015 0.001 PHE A 455 TRP 0.009 0.001 TRP A 854 HIS 0.004 0.001 HIS A 437 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 ( 6601) covalent geometry : angle 0.72440 / 0.36 ( 8933) hydrogen bonds : bond 0.04045 / 2.37 ( 374) hydrogen bonds : angle 4.67239 / 3.34 ( 1089) *********************** 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 173 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 134 time to evaluate : 0.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ASP cc_start: 0.8526 (m-30) cc_final: 0.8149 (m-30) REVERT: A 152 PHE cc_start: 0.5434 (OUTLIER) cc_final: 0.4317 (p90) REVERT: A 280 MET cc_start: 0.6357 (OUTLIER) cc_final: 0.6019 (ttt) REVERT: A 342 ASN cc_start: 0.6827 (m-40) cc_final: 0.6623 (m-40) REVERT: A 397 GLU cc_start: 0.8635 (mp0) cc_final: 0.8156 (mp0) REVERT: A 416 GLU cc_start: 0.6850 (mp0) cc_final: 0.6372 (pm20) REVERT: A 433 MET cc_start: 0.8271 (tpt) cc_final: 0.7991 (tpp) REVERT: A 478 LEU cc_start: 0.8419 (mt) cc_final: 0.8008 (mt) REVERT: A 484 GLU cc_start: 0.8494 (pt0) cc_final: 0.7916 (pt0) REVERT: A 623 ASP cc_start: 0.8171 (p0) cc_final: 0.7852 (p0) REVERT: A 678 LYS cc_start: 0.8358 (mttt) cc_final: 0.8158 (ttmm) REVERT: A 689 LEU cc_start: 0.8146 (OUTLIER) cc_final: 0.7621 (tt) REVERT: A 833 ILE cc_start: 0.7876 (OUTLIER) cc_final: 0.7609 (mt) REVERT: A 844 SER cc_start: 0.8697 (OUTLIER) cc_final: 0.8414 (p) outliers start: 39 outliers final: 29 residues processed: 163 average time/residue: 0.0616 time to fit residues: 13.9838 Evaluate side-chains 163 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 129 time to evaluate : 0.227 ------------------------------------------------------------------------------- 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 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 324 THR Chi-restraints excluded: chain A residue 458 CYS 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 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 689 LEU Chi-restraints excluded: chain A residue 707 PHE Chi-restraints excluded: chain A residue 730 GLU 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 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 45 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 10 optimal weight: 0.2980 chunk 52 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 chunk 78 optimal weight: 6.9990 chunk 60 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 14 optimal weight: 6.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 405 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.160493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.132471 restraints weight = 15377.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.136467 restraints weight = 7567.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.138909 restraints weight = 4754.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.140414 restraints weight = 3497.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.141201 restraints weight = 2872.281| |-----------------------------------------------------------------------------| r_work (final): 0.4039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.4077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6601 Z= 0.145 Angle : 0.721 17.776 8933 Z= 0.354 Chirality : 0.043 0.149 1070 Planarity : 0.004 0.045 1141 Dihedral : 4.701 47.092 904 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 17.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 5.32 % Allowed : 33.81 % Favored : 60.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.28), residues: 849 helix: 0.80 (0.23), residues: 469 sheet: -2.31 (0.58), residues: 76 loop : -2.16 (0.33), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 528 TYR 0.029 0.002 TYR A 349 PHE 0.014 0.001 PHE A 455 TRP 0.007 0.001 TRP A 854 HIS 0.004 0.001 HIS A 437 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 ( 6601) covalent geometry : angle 0.72135 / 0.35 ( 8933) hydrogen bonds : bond 0.03919 / 2.29 ( 374) hydrogen bonds : angle 4.64597 / 3.30 ( 1089) ********************** 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 172 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 135 time to evaluate : 0.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ASP cc_start: 0.8540 (m-30) cc_final: 0.8170 (m-30) REVERT: A 152 PHE cc_start: 0.5498 (OUTLIER) cc_final: 0.4457 (p90) REVERT: A 190 MET cc_start: 0.5330 (mpp) cc_final: 0.4422 (mmt) REVERT: A 280 MET cc_start: 0.6423 (OUTLIER) cc_final: 0.6024 (ttt) REVERT: A 317 ARG cc_start: 0.8179 (mtm110) cc_final: 0.7948 (mtp-110) REVERT: A 344 MET cc_start: 0.7316 (mpp) cc_final: 0.6774 (mtm) REVERT: A 397 GLU cc_start: 0.8681 (mp0) cc_final: 0.8204 (mt-10) REVERT: A 416 GLU cc_start: 0.6835 (mp0) cc_final: 0.6312 (pm20) REVERT: A 433 MET cc_start: 0.8286 (tpt) cc_final: 0.8001 (tpp) REVERT: A 478 LEU cc_start: 0.8462 (mt) cc_final: 0.8031 (mt) REVERT: A 484 GLU cc_start: 0.8568 (pt0) cc_final: 0.7969 (pt0) REVERT: A 623 ASP cc_start: 0.8154 (p0) cc_final: 0.7808 (p0) REVERT: A 678 LYS cc_start: 0.8342 (mttt) cc_final: 0.8071 (ttmm) REVERT: A 689 LEU cc_start: 0.8021 (OUTLIER) cc_final: 0.7530 (tt) REVERT: A 833 ILE cc_start: 0.7832 (OUTLIER) cc_final: 0.7532 (mt) outliers start: 37 outliers final: 32 residues processed: 161 average time/residue: 0.0619 time to fit residues: 13.8522 Evaluate side-chains 170 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 134 time to evaluate : 0.245 ------------------------------------------------------------------------------- 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 148 ASP Chi-restraints excluded: chain A residue 152 PHE Chi-restraints excluded: chain A residue 203 MET 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 324 THR Chi-restraints excluded: chain A residue 458 CYS 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 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 689 LEU Chi-restraints excluded: chain A residue 707 PHE Chi-restraints excluded: chain A residue 730 GLU Chi-restraints excluded: chain A residue 766 ILE Chi-restraints excluded: chain A residue 782 MET 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 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 15 optimal weight: 8.9990 chunk 11 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 12 optimal weight: 7.9990 chunk 51 optimal weight: 0.6980 chunk 64 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 chunk 22 optimal weight: 5.9990 chunk 59 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4295 r_free = 0.4295 target = 0.159562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.131534 restraints weight = 15278.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.135410 restraints weight = 7596.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.137950 restraints weight = 4787.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.139469 restraints weight = 3525.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.140231 restraints weight = 2900.848| |-----------------------------------------------------------------------------| r_work (final): 0.4028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.4169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6601 Z= 0.152 Angle : 0.726 17.657 8933 Z= 0.356 Chirality : 0.043 0.150 1070 Planarity : 0.004 0.042 1141 Dihedral : 4.679 46.177 904 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 17.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 5.76 % Allowed : 33.53 % Favored : 60.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.28), residues: 849 helix: 0.89 (0.23), residues: 461 sheet: -2.27 (0.59), residues: 76 loop : -2.19 (0.32), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 528 TYR 0.028 0.002 TYR A 349 PHE 0.020 0.001 PHE A 455 TRP 0.008 0.001 TRP A 854 HIS 0.004 0.001 HIS A 437 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 ( 6601) covalent geometry : angle 0.72563 / 0.36 ( 8933) hydrogen bonds : bond 0.03933 / 2.30 ( 374) hydrogen bonds : angle 4.64692 / 3.30 ( 1089) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1267.73 seconds wall clock time: 22 minutes 35.87 seconds (1355.87 seconds total)