Starting phenix.real_space_refine on Wed Sep 17 07:10:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9evc_19998/09_2025/9evc_19998.cif Found real_map, /net/cci-nas-00/data/ceres_data/9evc_19998/09_2025/9evc_19998.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9evc_19998/09_2025/9evc_19998.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9evc_19998/09_2025/9evc_19998.map" model { file = "/net/cci-nas-00/data/ceres_data/9evc_19998/09_2025/9evc_19998.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9evc_19998/09_2025/9evc_19998.cif" } 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-2.0-5805/lib/python3.9/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, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.57, per 1000 atoms: 0.24 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: 0.53 Conformation dependent library (CDL) restraints added in 365.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.20 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: 1.13 Time building geometry restraints manager: 0.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2114 1.34 - 1.46: 1087 1.46 - 1.58: 3339 1.58 - 1.70: 0 1.70 - 1.82: 61 Bond restraints: 6601 Sorted by residual: bond pdb=" N LEU A 15 " pdb=" CA LEU A 15 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.32e-02 5.74e+03 8.33e+00 bond pdb=" N GLU A 292 " pdb=" CA GLU A 292 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.28e-02 6.10e+03 6.21e+00 bond pdb=" N LYS A 468 " pdb=" CA LYS A 468 " ideal model delta sigma weight residual 1.452 1.490 -0.038 1.54e-02 4.22e+03 6.15e+00 bond pdb=" N PHE A 55 " pdb=" CA PHE A 55 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.32e-02 5.74e+03 5.92e+00 bond pdb=" N LEU A 763 " pdb=" CA LEU A 763 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.19e-02 7.06e+03 5.54e+00 ... (remaining 6596 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 8660 2.00 - 4.00: 224 4.00 - 6.00: 31 6.00 - 7.99: 11 7.99 - 9.99: 7 Bond angle restraints: 8933 Sorted by residual: angle pdb=" N GLY A 149 " pdb=" CA GLY A 149 " pdb=" C GLY A 149 " ideal model delta sigma weight residual 110.38 116.09 -5.71 1.48e+00 4.57e-01 1.49e+01 angle pdb=" C THR A 54 " pdb=" N PHE A 55 " pdb=" CA PHE A 55 " ideal model delta sigma weight residual 122.54 116.89 5.65 1.65e+00 3.67e-01 1.17e+01 angle pdb=" CB MET A 163 " pdb=" CG MET A 163 " pdb=" SD MET A 163 " ideal model delta sigma weight residual 112.70 122.69 -9.99 3.00e+00 1.11e-01 1.11e+01 angle pdb=" CA GLU A 361 " pdb=" CB GLU A 361 " pdb=" CG GLU A 361 " ideal model delta sigma weight residual 114.10 120.05 -5.95 2.00e+00 2.50e-01 8.85e+00 angle pdb=" C LYS A 468 " pdb=" CA LYS A 468 " pdb=" CB LYS A 468 " ideal model delta sigma weight residual 108.84 113.08 -4.24 1.51e+00 4.39e-01 7.90e+00 ... (remaining 8928 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.29: 3403 16.29 - 32.57: 450 32.57 - 48.86: 122 48.86 - 65.14: 34 65.14 - 81.43: 4 Dihedral angle restraints: 4013 sinusoidal: 1554 harmonic: 2459 Sorted by residual: dihedral pdb=" CA LEU A 851 " pdb=" C LEU A 851 " pdb=" N HIS A 852 " pdb=" CA HIS A 852 " ideal model delta harmonic sigma weight residual -180.00 -157.39 -22.61 0 5.00e+00 4.00e-02 2.04e+01 dihedral pdb=" CA ASP A 720 " pdb=" C ASP A 720 " pdb=" N SER A 721 " pdb=" CA SER A 721 " ideal model delta harmonic sigma weight residual -180.00 -162.55 -17.45 0 5.00e+00 4.00e-02 1.22e+01 dihedral pdb=" CA HIS A 552 " pdb=" C HIS A 552 " pdb=" N LYS A 553 " pdb=" CA LYS A 553 " ideal model delta harmonic sigma weight residual -180.00 -163.73 -16.27 0 5.00e+00 4.00e-02 1.06e+01 ... (remaining 4010 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 895 0.065 - 0.130: 158 0.130 - 0.195: 14 0.195 - 0.261: 1 0.261 - 0.326: 2 Chirality restraints: 1070 Sorted by residual: chirality pdb=" CG LEU A 86 " pdb=" CB LEU A 86 " pdb=" CD1 LEU A 86 " pdb=" CD2 LEU A 86 " both_signs ideal model delta sigma weight residual False -2.59 -2.26 -0.33 2.00e-01 2.50e+01 2.65e+00 chirality pdb=" CB VAL A 516 " pdb=" CA VAL A 516 " pdb=" CG1 VAL A 516 " pdb=" CG2 VAL A 516 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.46e+00 chirality pdb=" CG LEU A 73 " pdb=" CB LEU A 73 " pdb=" CD1 LEU A 73 " pdb=" CD2 LEU A 73 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.35e+00 ... (remaining 1067 not shown) Planarity restraints: 1141 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 119 " -0.261 9.50e-02 1.11e+02 1.17e-01 8.37e+00 pdb=" NE ARG A 119 " 0.015 2.00e-02 2.50e+03 pdb=" CZ ARG A 119 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG A 119 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 119 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 467 " -0.013 2.00e-02 2.50e+03 2.56e-02 6.57e+00 pdb=" C GLU A 467 " 0.044 2.00e-02 2.50e+03 pdb=" O GLU A 467 " -0.017 2.00e-02 2.50e+03 pdb=" N LYS A 468 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A 468 " 0.036 5.00e-02 4.00e+02 5.58e-02 4.98e+00 pdb=" N PRO A 469 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO A 469 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 469 " 0.030 5.00e-02 4.00e+02 ... (remaining 1138 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 120 2.66 - 3.22: 6373 3.22 - 3.78: 11183 3.78 - 4.34: 14195 4.34 - 4.90: 22544 Nonbonded interactions: 54415 Sorted by model distance: nonbonded pdb=" O ILE A 290 " pdb="CA CA A 901 " model vdw 2.095 2.510 nonbonded pdb=" O ASP A 334 " pdb=" OG1 THR A 338 " model vdw 2.229 3.040 nonbonded pdb=" O LEU A 107 " pdb=" OG SER A 111 " model vdw 2.243 3.040 nonbonded pdb=" OD1 ASN A 716 " pdb="CA CA A 901 " model vdw 2.253 2.510 nonbonded pdb=" OG1 THR A 789 " pdb=" OH TYR A 831 " model vdw 2.259 3.040 ... (remaining 54410 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.530 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.420 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7161 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6601 Z= 0.198 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 aren 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 covalent geometry : bond 0.00367 ( 6601) covalent geometry : angle 0.79992 ( 8933) hydrogen bonds : bond 0.15039 ( 374) hydrogen bonds : angle 6.30961 ( 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 : 0.233 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: 0.8043 (mt) REVERT: A 105 ASP cc_start: 0.8712 (m-30) cc_final: 0.8462 (m-30) REVERT: A 110 MET cc_start: 0.7166 (ppp) cc_final: 0.6265 (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: 0.7395 (p0) REVERT: A 677 ILE cc_start: 0.8500 (mm) cc_final: 0.8289 (mm) REVERT: A 865 VAL cc_start: 0.6773 (m) cc_final: 0.6498 (m) outliers start: 3 outliers final: 3 residues processed: 202 average time/residue: 0.0761 time to fit residues: 20.4674 Evaluate side-chains 148 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 145 time to evaluate : 0.256 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 70 GLN A 277 ASN A 358 ASN ** A 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 603 ASN ** A 798 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.163392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.135034 restraints weight = 15799.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.139047 restraints weight = 7986.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.141662 restraints weight = 5079.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.143198 restraints weight = 3767.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.143916 restraints weight = 3104.513| |-----------------------------------------------------------------------------| r_work (final): 0.4065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6601 Z= 0.151 Angle : 0.660 14.281 8933 Z= 0.336 Chirality : 0.044 0.192 1070 Planarity : 0.004 0.039 1141 Dihedral : 5.020 51.426 908 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 15.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 7.19 % Allowed : 27.05 % Favored : 65.76 % 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 aren not related in a simple way. whole: -1.16 (0.28), residues: 849 helix: 0.51 (0.23), residues: 466 sheet: -2.95 (0.55), residues: 69 loop : -2.20 (0.33), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 528 TYR 0.012 0.001 TYR A 495 PHE 0.028 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 covalent geometry : bond 0.00330 ( 6601) covalent geometry : angle 0.66038 ( 8933) hydrogen bonds : bond 0.04376 ( 374) hydrogen bonds : angle 4.87594 ( 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 206 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 156 time to evaluate : 0.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 TYR cc_start: 0.7088 (OUTLIER) cc_final: 0.6316 (t80) REVERT: A 105 ASP cc_start: 0.8715 (m-30) cc_final: 0.8212 (m-30) REVERT: A 110 MET cc_start: 0.6879 (ppp) cc_final: 0.6233 (tmm) REVERT: A 152 PHE cc_start: 0.5392 (OUTLIER) cc_final: 0.4449 (p90) REVERT: A 253 LEU cc_start: 0.7237 (OUTLIER) cc_final: 0.5925 (mm) REVERT: A 358 ASN cc_start: 0.6822 (OUTLIER) cc_final: 0.6256 (t0) REVERT: A 397 GLU cc_start: 0.8594 (mp0) cc_final: 0.8135 (mp0) REVERT: A 433 MET cc_start: 0.8005 (tpt) cc_final: 0.7472 (tpt) REVERT: A 455 PHE cc_start: 0.8656 (m-10) cc_final: 0.8441 (m-80) REVERT: A 478 LEU cc_start: 0.8497 (mt) cc_final: 0.7930 (mt) REVERT: A 623 ASP cc_start: 0.8139 (p0) cc_final: 0.7818 (p0) REVERT: A 633 GLN cc_start: 0.7519 (mp10) cc_final: 0.7170 (mp10) REVERT: A 678 LYS cc_start: 0.8361 (mttt) cc_final: 0.7953 (mttm) REVERT: A 689 LEU cc_start: 0.7759 (OUTLIER) cc_final: 0.7337 (tt) outliers start: 50 outliers final: 25 residues processed: 188 average time/residue: 0.0641 time to fit residues: 16.4748 Evaluate side-chains 172 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 142 time to evaluate : 0.154 ------------------------------------------------------------------------------- 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 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 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: 10.0000 chunk 67 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 chunk 80 optimal weight: 0.9980 chunk 71 optimal weight: 5.9990 chunk 51 optimal weight: 0.8980 chunk 41 optimal weight: 0.1980 chunk 35 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 76 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 482 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.162927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.134457 restraints weight = 15393.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.138532 restraints weight = 7663.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.141116 restraints weight = 4794.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.142693 restraints weight = 3491.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.143407 restraints weight = 2862.843| |-----------------------------------------------------------------------------| r_work (final): 0.4082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.2543 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= 0.136 Angle : 0.652 14.737 8933 Z= 0.325 Chirality : 0.043 0.183 1070 Planarity : 0.004 0.035 1141 Dihedral : 4.661 50.666 904 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 15.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 5.76 % Allowed : 28.06 % Favored : 66.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.85 (0.28), residues: 849 helix: 0.73 (0.23), residues: 467 sheet: -2.14 (0.66), residues: 56 loop : -2.21 (0.32), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 528 TYR 0.013 0.001 TYR A 349 PHE 0.010 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 covalent geometry : bond 0.00300 ( 6601) covalent geometry : angle 0.65167 ( 8933) hydrogen bonds : bond 0.04084 ( 374) hydrogen bonds : angle 4.62942 ( 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 192 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 152 time to evaluate : 0.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ASP cc_start: 0.8538 (m-30) cc_final: 0.8186 (m-30) REVERT: A 110 MET cc_start: 0.6776 (ppp) cc_final: 0.6208 (tmm) REVERT: A 136 VAL cc_start: 0.3939 (OUTLIER) cc_final: 0.3651 (t) REVERT: A 152 PHE cc_start: 0.5326 (OUTLIER) cc_final: 0.3413 (p90) REVERT: A 253 LEU cc_start: 0.7278 (OUTLIER) cc_final: 0.5941 (mm) REVERT: A 358 ASN cc_start: 0.6763 (p0) cc_final: 0.6340 (t0) REVERT: A 397 GLU cc_start: 0.8518 (mp0) cc_final: 0.8091 (mp0) REVERT: A 433 MET cc_start: 0.8119 (tpt) cc_final: 0.7448 (tpt) REVERT: A 455 PHE cc_start: 0.8649 (m-10) cc_final: 0.8423 (m-80) REVERT: A 478 LEU cc_start: 0.8537 (mt) cc_final: 0.8025 (mt) REVERT: A 484 GLU cc_start: 0.8304 (pt0) cc_final: 0.7737 (pt0) REVERT: A 623 ASP cc_start: 0.8169 (p0) cc_final: 0.7808 (p0) REVERT: A 633 GLN cc_start: 0.7512 (mp10) cc_final: 0.7142 (mp10) REVERT: A 678 LYS cc_start: 0.8353 (mttt) cc_final: 0.8106 (ttmm) REVERT: A 689 LEU cc_start: 0.7749 (OUTLIER) cc_final: 0.7327 (tt) outliers start: 40 outliers final: 20 residues processed: 180 average time/residue: 0.0687 time to fit residues: 16.9966 Evaluate side-chains 161 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 137 time to evaluate : 0.177 ------------------------------------------------------------------------------- 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 324 THR Chi-restraints excluded: chain A residue 333 THR 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 783 SER Chi-restraints excluded: chain A residue 790 THR 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: 2.9990 chunk 68 optimal weight: 0.4980 chunk 84 optimal weight: 0.8980 chunk 81 optimal weight: 2.9990 chunk 47 optimal weight: 9.9990 chunk 44 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 80 optimal weight: 0.7980 chunk 74 optimal weight: 0.5980 chunk 58 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 412 ASN A 817 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.161527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.133398 restraints weight = 15448.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.137493 restraints weight = 7586.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.139987 restraints weight = 4688.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.141336 restraints weight = 3430.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.142446 restraints weight = 2834.036| |-----------------------------------------------------------------------------| r_work (final): 0.4069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.2878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6601 Z= 0.135 Angle : 0.632 15.331 8933 Z= 0.316 Chirality : 0.043 0.179 1070 Planarity : 0.004 0.033 1141 Dihedral : 4.549 50.271 904 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 16.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 6.33 % Allowed : 28.35 % 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 aren not related in a simple way. whole: -0.79 (0.28), residues: 849 helix: 0.79 (0.23), residues: 469 sheet: -2.36 (0.58), residues: 69 loop : -2.13 (0.32), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 528 TYR 0.013 0.001 TYR A 349 PHE 0.008 0.001 PHE A 674 TRP 0.010 0.001 TRP A 854 HIS 0.005 0.001 HIS A 437 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 6601) covalent geometry : angle 0.63240 ( 8933) hydrogen bonds : bond 0.03896 ( 374) hydrogen bonds : angle 4.49880 ( 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 194 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 150 time to evaluate : 0.245 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: 0.8549 (m-30) cc_final: 0.8207 (m-30) REVERT: A 110 MET cc_start: 0.6602 (ppp) cc_final: 0.6222 (tmm) REVERT: A 152 PHE cc_start: 0.5322 (OUTLIER) cc_final: 0.3814 (p90) REVERT: A 251 CYS cc_start: 0.7869 (m) cc_final: 0.7575 (t) REVERT: A 253 LEU cc_start: 0.7380 (OUTLIER) cc_final: 0.5994 (mm) REVERT: A 358 ASN cc_start: 0.6762 (p0) cc_final: 0.6287 (t0) REVERT: A 397 GLU cc_start: 0.8488 (mp0) cc_final: 0.8120 (mp0) REVERT: A 412 ASN cc_start: 0.6775 (OUTLIER) cc_final: 0.6573 (p0) REVERT: A 433 MET cc_start: 0.8160 (tpt) cc_final: 0.7497 (tpt) REVERT: A 455 PHE cc_start: 0.8700 (m-10) cc_final: 0.8418 (m-80) REVERT: A 461 VAL cc_start: 0.5784 (OUTLIER) cc_final: 0.5573 (p) REVERT: A 478 LEU cc_start: 0.8550 (mt) cc_final: 0.8001 (mt) REVERT: A 484 GLU cc_start: 0.8258 (pt0) cc_final: 0.7725 (pt0) REVERT: A 623 ASP cc_start: 0.8184 (p0) cc_final: 0.7798 (p0) REVERT: A 633 GLN cc_start: 0.7554 (mp10) cc_final: 0.7127 (mp10) REVERT: A 658 ASP cc_start: 0.7070 (t70) cc_final: 0.6846 (t70) REVERT: A 678 LYS cc_start: 0.8334 (mttt) cc_final: 0.8105 (ttmm) REVERT: A 689 LEU cc_start: 0.7839 (OUTLIER) cc_final: 0.7392 (tt) outliers start: 44 outliers final: 26 residues processed: 181 average time/residue: 0.0639 time to fit residues: 15.9656 Evaluate side-chains 167 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 136 time to evaluate : 0.243 ------------------------------------------------------------------------------- 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 71 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 296 SER Chi-restraints excluded: chain A residue 318 LYS Chi-restraints excluded: chain A residue 324 THR 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 412 ASN Chi-restraints excluded: chain A residue 447 THR 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 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 844 SER 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: 10.0000 chunk 74 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 chunk 51 optimal weight: 0.5980 chunk 41 optimal weight: 7.9990 chunk 25 optimal weight: 0.8980 chunk 59 optimal weight: 0.6980 chunk 19 optimal weight: 6.9990 chunk 11 optimal weight: 0.9980 chunk 69 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 412 ASN A 482 ASN ** A 798 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.162142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.133000 restraints weight = 15648.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.136988 restraints weight = 7885.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.139611 restraints weight = 4997.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.141126 restraints weight = 3680.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.142056 restraints weight = 3049.705| |-----------------------------------------------------------------------------| r_work (final): 0.4059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.3102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6601 Z= 0.140 Angle : 0.650 15.909 8933 Z= 0.322 Chirality : 0.044 0.247 1070 Planarity : 0.004 0.033 1141 Dihedral : 4.562 49.660 904 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 16.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 6.76 % Allowed : 28.78 % 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 aren not related in a simple way. whole: -0.76 (0.28), residues: 849 helix: 0.81 (0.23), residues: 469 sheet: -2.39 (0.53), residues: 80 loop : -2.05 (0.34), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 528 TYR 0.015 0.001 TYR A 411 PHE 0.010 0.001 PHE A 674 TRP 0.009 0.001 TRP A 854 HIS 0.004 0.001 HIS A 437 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 6601) covalent geometry : angle 0.65028 ( 8933) hydrogen bonds : bond 0.03866 ( 374) hydrogen bonds : angle 4.52019 ( 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 195 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 148 time to evaluate : 0.249 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: 0.8543 (m-30) cc_final: 0.8194 (m-30) REVERT: A 152 PHE cc_start: 0.5247 (OUTLIER) cc_final: 0.3636 (p90) REVERT: A 251 CYS cc_start: 0.7859 (m) cc_final: 0.7592 (t) REVERT: A 344 MET cc_start: 0.7171 (mpp) cc_final: 0.6502 (mtm) REVERT: A 358 ASN cc_start: 0.6787 (p0) cc_final: 0.6277 (t0) REVERT: A 397 GLU cc_start: 0.8572 (mp0) cc_final: 0.8189 (mp0) REVERT: A 433 MET cc_start: 0.8204 (tpt) cc_final: 0.7917 (tpp) REVERT: A 455 PHE cc_start: 0.8717 (m-10) cc_final: 0.8426 (m-80) REVERT: A 461 VAL cc_start: 0.5812 (OUTLIER) cc_final: 0.5586 (p) REVERT: A 478 LEU cc_start: 0.8508 (mt) cc_final: 0.7996 (mt) REVERT: A 484 GLU cc_start: 0.8328 (pt0) cc_final: 0.7744 (pt0) REVERT: A 623 ASP cc_start: 0.8145 (p0) cc_final: 0.7806 (p0) REVERT: A 678 LYS cc_start: 0.8359 (mttt) cc_final: 0.8134 (ttmm) REVERT: A 689 LEU cc_start: 0.7856 (OUTLIER) cc_final: 0.7397 (tt) REVERT: A 833 ILE cc_start: 0.7807 (OUTLIER) cc_final: 0.7358 (mt) outliers start: 47 outliers final: 35 residues processed: 184 average time/residue: 0.0648 time to fit residues: 16.6749 Evaluate side-chains 176 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 137 time to evaluate : 0.238 ------------------------------------------------------------------------------- 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 136 VAL Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 152 PHE Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 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 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 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 673 VAL Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 707 PHE Chi-restraints excluded: chain A residue 720 ASP 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 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: 0.0570 chunk 51 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 22 optimal weight: 6.9990 chunk 19 optimal weight: 0.7980 chunk 10 optimal weight: 6.9990 chunk 67 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 chunk 78 optimal weight: 7.9990 overall best weight: 0.6902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 798 GLN ** 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 = 0.4327 r_free = 0.4327 target = 0.161990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.133076 restraints weight = 15746.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.137156 restraints weight = 7922.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.139732 restraints weight = 5020.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.141295 restraints weight = 3695.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.142019 restraints weight = 3041.502| |-----------------------------------------------------------------------------| r_work (final): 0.4063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.3324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6601 Z= 0.137 Angle : 0.658 16.291 8933 Z= 0.325 Chirality : 0.044 0.210 1070 Planarity : 0.004 0.032 1141 Dihedral : 4.619 49.154 904 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 17.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 6.91 % Allowed : 29.35 % Favored : 63.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.77 (0.28), residues: 849 helix: 0.86 (0.23), residues: 462 sheet: -2.65 (0.51), residues: 90 loop : -1.98 (0.34), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 528 TYR 0.010 0.001 TYR A 349 PHE 0.010 0.001 PHE A 674 TRP 0.007 0.001 TRP A 854 HIS 0.004 0.001 HIS A 437 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 6601) covalent geometry : angle 0.65826 ( 8933) hydrogen bonds : bond 0.03822 ( 374) hydrogen bonds : angle 4.49208 ( 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 193 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 145 time to evaluate : 0.191 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: 0.8543 (m-30) cc_final: 0.8168 (m-30) REVERT: A 152 PHE cc_start: 0.5303 (OUTLIER) cc_final: 0.4047 (p90) REVERT: A 344 MET cc_start: 0.7037 (mpp) cc_final: 0.6358 (mtm) REVERT: A 397 GLU cc_start: 0.8606 (mp0) cc_final: 0.8215 (mp0) REVERT: A 416 GLU cc_start: 0.6767 (mp0) cc_final: 0.6207 (pm20) REVERT: A 433 MET cc_start: 0.8209 (tpt) cc_final: 0.7909 (tpp) REVERT: A 484 GLU cc_start: 0.8301 (pt0) cc_final: 0.7752 (pt0) REVERT: A 623 ASP cc_start: 0.8138 (p0) cc_final: 0.7725 (p0) REVERT: A 678 LYS cc_start: 0.8379 (mttt) cc_final: 0.8065 (mttm) REVERT: A 718 VAL cc_start: 0.8576 (t) cc_final: 0.8358 (m) outliers start: 48 outliers final: 39 residues processed: 179 average time/residue: 0.0612 time to fit residues: 15.3721 Evaluate side-chains 175 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 135 time to evaluate : 0.235 ------------------------------------------------------------------------------- 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 95 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 152 PHE Chi-restraints excluded: chain A residue 203 MET 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 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 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 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 707 PHE Chi-restraints excluded: chain A residue 720 ASP Chi-restraints excluded: chain A residue 730 GLU Chi-restraints excluded: chain A residue 766 ILE Chi-restraints excluded: chain A residue 783 SER Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain A residue 879 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 9 optimal weight: 8.9990 chunk 74 optimal weight: 0.9990 chunk 71 optimal weight: 0.2980 chunk 27 optimal weight: 0.9990 chunk 12 optimal weight: 5.9990 chunk 18 optimal weight: 10.0000 chunk 44 optimal weight: 9.9990 chunk 46 optimal weight: 0.6980 chunk 59 optimal weight: 4.9990 chunk 63 optimal weight: 0.8980 chunk 53 optimal weight: 0.5980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 482 ASN A 798 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.161819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.133457 restraints weight = 16055.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.137517 restraints weight = 8155.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.139987 restraints weight = 5174.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.141248 restraints weight = 3841.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 60)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.142421 restraints weight = 3217.871| |-----------------------------------------------------------------------------| r_work (final): 0.4064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.3523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6601 Z= 0.136 Angle : 0.668 16.978 8933 Z= 0.328 Chirality : 0.044 0.206 1070 Planarity : 0.004 0.033 1141 Dihedral : 4.573 48.494 904 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 16.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 7.34 % Allowed : 30.07 % Favored : 62.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.63 (0.28), residues: 849 helix: 0.96 (0.23), residues: 460 sheet: -2.29 (0.60), residues: 70 loop : -2.05 (0.33), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 528 TYR 0.009 0.001 TYR A 349 PHE 0.010 0.001 PHE A 674 TRP 0.008 0.001 TRP A 854 HIS 0.004 0.001 HIS A 437 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 6601) covalent geometry : angle 0.66794 ( 8933) hydrogen bonds : bond 0.03817 ( 374) hydrogen bonds : angle 4.47921 ( 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 188 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 137 time to evaluate : 0.188 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: 0.8540 (m-30) cc_final: 0.8173 (m-30) REVERT: A 152 PHE cc_start: 0.5296 (OUTLIER) cc_final: 0.4127 (p90) REVERT: A 344 MET cc_start: 0.7046 (mpp) cc_final: 0.6361 (mtm) REVERT: A 397 GLU cc_start: 0.8638 (mp0) cc_final: 0.8177 (mp0) REVERT: A 416 GLU cc_start: 0.6732 (mp0) cc_final: 0.6349 (pm20) REVERT: A 433 MET cc_start: 0.8236 (tpt) cc_final: 0.7953 (tpp) REVERT: A 455 PHE cc_start: 0.8679 (m-10) cc_final: 0.8244 (m-80) REVERT: A 478 LEU cc_start: 0.8363 (mt) cc_final: 0.8038 (mt) REVERT: A 479 LYS cc_start: 0.8067 (mmmt) cc_final: 0.7788 (mmtp) REVERT: A 484 GLU cc_start: 0.8331 (pt0) cc_final: 0.7867 (pt0) REVERT: A 623 ASP cc_start: 0.7819 (p0) cc_final: 0.7375 (p0) REVERT: A 678 LYS cc_start: 0.8355 (mttt) cc_final: 0.8126 (ttmm) REVERT: A 689 LEU cc_start: 0.7870 (OUTLIER) cc_final: 0.7405 (tt) REVERT: A 718 VAL cc_start: 0.8591 (t) cc_final: 0.8377 (m) REVERT: A 833 ILE cc_start: 0.7847 (OUTLIER) cc_final: 0.7430 (mt) outliers start: 51 outliers final: 38 residues processed: 172 average time/residue: 0.0675 time to fit residues: 16.1874 Evaluate side-chains 171 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 130 time to evaluate : 0.188 ------------------------------------------------------------------------------- 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 95 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 152 PHE Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 262 VAL 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 340 THR 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 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 720 ASP Chi-restraints excluded: chain A residue 730 GLU Chi-restraints excluded: chain A residue 766 ILE Chi-restraints excluded: chain A residue 783 SER Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 52 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 18 optimal weight: 9.9990 chunk 65 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 overall best weight: 0.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 482 ASN A 798 GLN A 807 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.161286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.132163 restraints weight = 15588.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.136285 restraints weight = 7868.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.138822 restraints weight = 4991.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.140403 restraints weight = 3678.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.141122 restraints weight = 3015.737| |-----------------------------------------------------------------------------| r_work (final): 0.4045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.3712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6601 Z= 0.153 Angle : 0.690 17.094 8933 Z= 0.340 Chirality : 0.044 0.198 1070 Planarity : 0.004 0.033 1141 Dihedral : 4.615 48.179 904 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 16.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 7.77 % Allowed : 30.36 % Favored : 61.87 % 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 aren not related in a simple way. whole: -0.71 (0.28), residues: 849 helix: 0.93 (0.23), residues: 467 sheet: -2.35 (0.59), residues: 76 loop : -2.17 (0.33), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 528 TYR 0.010 0.002 TYR A 495 PHE 0.010 0.001 PHE A 674 TRP 0.009 0.001 TRP A 854 HIS 0.005 0.001 HIS A 127 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 6601) covalent geometry : angle 0.68972 ( 8933) hydrogen bonds : bond 0.03881 ( 374) hydrogen bonds : angle 4.48380 ( 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 189 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 135 time to evaluate : 0.518 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: 0.8538 (m-30) cc_final: 0.8167 (m-30) REVERT: A 152 PHE cc_start: 0.5529 (OUTLIER) cc_final: 0.4400 (p90) REVERT: A 344 MET cc_start: 0.7071 (mpp) cc_final: 0.6411 (mtm) REVERT: A 348 ASP cc_start: 0.7241 (OUTLIER) cc_final: 0.6842 (t70) REVERT: A 397 GLU cc_start: 0.8655 (mp0) cc_final: 0.8158 (mp0) REVERT: A 416 GLU cc_start: 0.6766 (mp0) cc_final: 0.6421 (pm20) REVERT: A 433 MET cc_start: 0.8267 (tpt) cc_final: 0.7983 (tpp) REVERT: A 455 PHE cc_start: 0.8644 (m-10) cc_final: 0.8279 (m-80) REVERT: A 478 LEU cc_start: 0.8402 (mt) cc_final: 0.8073 (mt) REVERT: A 479 LYS cc_start: 0.7975 (mmmt) cc_final: 0.7707 (mmtp) REVERT: A 484 GLU cc_start: 0.8474 (pt0) cc_final: 0.7952 (pt0) REVERT: A 623 ASP cc_start: 0.7978 (p0) cc_final: 0.7568 (p0) REVERT: A 678 LYS cc_start: 0.8358 (mttt) cc_final: 0.8122 (ttmm) REVERT: A 689 LEU cc_start: 0.8044 (OUTLIER) cc_final: 0.7549 (tt) REVERT: A 833 ILE cc_start: 0.7847 (OUTLIER) cc_final: 0.7424 (mt) outliers start: 54 outliers final: 42 residues processed: 177 average time/residue: 0.0675 time to fit residues: 16.5895 Evaluate side-chains 178 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 132 time to evaluate : 0.231 ------------------------------------------------------------------------------- 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 95 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 152 PHE Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 262 VAL 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 340 THR Chi-restraints excluded: chain A residue 348 ASP 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 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 693 ILE Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 707 PHE Chi-restraints excluded: chain A residue 720 ASP Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 730 GLU Chi-restraints excluded: chain A residue 782 MET Chi-restraints excluded: chain A residue 783 SER 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: 1.9990 chunk 31 optimal weight: 0.9990 chunk 56 optimal weight: 5.9990 chunk 66 optimal weight: 0.3980 chunk 21 optimal weight: 3.9990 chunk 6 optimal weight: 0.0870 chunk 36 optimal weight: 0.2980 chunk 33 optimal weight: 3.9990 chunk 55 optimal weight: 0.5980 chunk 44 optimal weight: 6.9990 chunk 22 optimal weight: 0.7980 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 798 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.162917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.134932 restraints weight = 16221.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.138929 restraints weight = 8146.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.141434 restraints weight = 5129.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.142998 restraints weight = 3805.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.143571 restraints weight = 3128.753| |-----------------------------------------------------------------------------| r_work (final): 0.4084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.3782 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= 0.127 Angle : 0.700 17.932 8933 Z= 0.341 Chirality : 0.044 0.202 1070 Planarity : 0.004 0.040 1141 Dihedral : 4.611 47.303 904 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 16.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 6.04 % Allowed : 32.37 % Favored : 61.58 % 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 aren not related in a simple way. whole: -0.50 (0.28), residues: 849 helix: 1.04 (0.23), residues: 460 sheet: -1.83 (0.64), residues: 70 loop : -2.05 (0.32), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 420 TYR 0.008 0.001 TYR A 596 PHE 0.009 0.001 PHE A 660 TRP 0.006 0.001 TRP A 854 HIS 0.004 0.001 HIS A 437 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 6601) covalent geometry : angle 0.69996 ( 8933) hydrogen bonds : bond 0.03703 ( 374) hydrogen bonds : angle 4.42040 ( 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 178 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 136 time to evaluate : 0.230 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: 0.5503 (OUTLIER) cc_final: 0.4409 (p90) REVERT: A 344 MET cc_start: 0.6912 (mpp) cc_final: 0.6295 (mtm) REVERT: A 348 ASP cc_start: 0.7133 (OUTLIER) cc_final: 0.6809 (t70) REVERT: A 397 GLU cc_start: 0.8643 (mp0) cc_final: 0.8162 (mt-10) REVERT: A 416 GLU cc_start: 0.6743 (mp0) cc_final: 0.6395 (pm20) REVERT: A 433 MET cc_start: 0.8216 (tpt) cc_final: 0.7930 (tpp) REVERT: A 478 LEU cc_start: 0.8372 (mt) cc_final: 0.7960 (mt) REVERT: A 479 LYS cc_start: 0.7952 (mmmt) cc_final: 0.7727 (mmtp) REVERT: A 484 GLU cc_start: 0.8526 (pt0) cc_final: 0.7975 (pt0) REVERT: A 566 MET cc_start: 0.7201 (mmt) cc_final: 0.6953 (mmt) REVERT: A 623 ASP cc_start: 0.7909 (p0) cc_final: 0.7446 (p0) REVERT: A 678 LYS cc_start: 0.8369 (mttt) cc_final: 0.8127 (ttmm) REVERT: A 833 ILE cc_start: 0.7804 (OUTLIER) cc_final: 0.7408 (mt) outliers start: 42 outliers final: 33 residues processed: 167 average time/residue: 0.0667 time to fit residues: 15.3436 Evaluate side-chains 166 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 130 time to evaluate : 0.205 ------------------------------------------------------------------------------- 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 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 253 LEU Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 318 LYS Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 348 ASP 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 574 THR Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 707 PHE Chi-restraints excluded: chain A residue 720 ASP Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 730 GLU Chi-restraints excluded: chain A residue 782 MET Chi-restraints excluded: chain A residue 783 SER Chi-restraints excluded: chain A residue 799 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 45 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 74 optimal weight: 0.8980 chunk 78 optimal weight: 5.9990 chunk 60 optimal weight: 0.8980 chunk 77 optimal weight: 0.8980 chunk 14 optimal weight: 9.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 603 ASN A 798 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.160569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.131344 restraints weight = 15521.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.135372 restraints weight = 7870.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.137973 restraints weight = 5019.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.139512 restraints weight = 3704.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.140340 restraints weight = 3055.563| |-----------------------------------------------------------------------------| r_work (final): 0.4047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.3927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6601 Z= 0.153 Angle : 0.725 17.799 8933 Z= 0.355 Chirality : 0.045 0.209 1070 Planarity : 0.004 0.044 1141 Dihedral : 4.676 46.872 904 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 16.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 5.76 % Allowed : 32.95 % Favored : 61.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.63 (0.28), residues: 849 helix: 0.93 (0.23), residues: 466 sheet: -2.22 (0.59), residues: 76 loop : -2.05 (0.33), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 420 TYR 0.011 0.001 TYR A 495 PHE 0.010 0.001 PHE A 674 TRP 0.009 0.001 TRP A 854 HIS 0.004 0.001 HIS A 437 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 6601) covalent geometry : angle 0.72503 ( 8933) hydrogen bonds : bond 0.03885 ( 374) hydrogen bonds : angle 4.54181 ( 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 170 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 130 time to evaluate : 0.198 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: 0.5677 (OUTLIER) cc_final: 0.4642 (p90) REVERT: A 344 MET cc_start: 0.7051 (mpp) cc_final: 0.6434 (mtm) REVERT: A 348 ASP cc_start: 0.7284 (OUTLIER) cc_final: 0.6897 (t70) REVERT: A 397 GLU cc_start: 0.8675 (mp0) cc_final: 0.8222 (mt-10) REVERT: A 416 GLU cc_start: 0.6737 (mp0) cc_final: 0.6452 (pm20) REVERT: A 433 MET cc_start: 0.8301 (tpt) cc_final: 0.8007 (tpp) REVERT: A 478 LEU cc_start: 0.8413 (mt) cc_final: 0.8037 (mt) REVERT: A 479 LYS cc_start: 0.7982 (mmmt) cc_final: 0.7753 (mmtp) REVERT: A 484 GLU cc_start: 0.8576 (pt0) cc_final: 0.8023 (pt0) REVERT: A 490 LEU cc_start: 0.9047 (mt) cc_final: 0.8548 (tp) REVERT: A 623 ASP cc_start: 0.7990 (p0) cc_final: 0.7630 (p0) REVERT: A 678 LYS cc_start: 0.8370 (mttt) cc_final: 0.8133 (ttmm) outliers start: 40 outliers final: 36 residues processed: 159 average time/residue: 0.0789 time to fit residues: 17.0807 Evaluate side-chains 164 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 126 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 TYR Chi-restraints excluded: chain A residue 51 PHE Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 152 PHE Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 318 LYS Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 348 ASP 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 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 701 LEU Chi-restraints excluded: chain A residue 707 PHE Chi-restraints excluded: chain A residue 720 ASP Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 730 GLU Chi-restraints excluded: chain A residue 782 MET Chi-restraints excluded: chain A residue 783 SER Chi-restraints excluded: chain A residue 799 THR Chi-restraints excluded: chain A residue 805 ASN Chi-restraints excluded: chain A residue 829 VAL 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: 10.0000 chunk 11 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 64 optimal weight: 0.5980 chunk 10 optimal weight: 0.9990 chunk 67 optimal weight: 0.7980 chunk 22 optimal weight: 6.9990 chunk 59 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 705 ASN A 798 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.160636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.132421 restraints weight = 15448.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.136355 restraints weight = 7649.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.138843 restraints weight = 4822.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.140402 restraints weight = 3555.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.140688 restraints weight = 2924.864| |-----------------------------------------------------------------------------| r_work (final): 0.4039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.4056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6601 Z= 0.147 Angle : 0.733 17.947 8933 Z= 0.359 Chirality : 0.044 0.205 1070 Planarity : 0.004 0.042 1141 Dihedral : 4.662 46.263 904 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 16.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 6.19 % Allowed : 32.95 % 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 aren not related in a simple way. whole: -0.61 (0.28), residues: 849 helix: 0.93 (0.23), residues: 466 sheet: -2.16 (0.59), residues: 76 loop : -2.01 (0.33), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 420 TYR 0.009 0.001 TYR A 495 PHE 0.010 0.001 PHE A 359 TRP 0.008 0.001 TRP A 854 HIS 0.004 0.001 HIS A 437 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 6601) covalent geometry : angle 0.73252 ( 8933) hydrogen bonds : bond 0.03881 ( 374) hydrogen bonds : angle 4.53706 ( 1089) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1414.35 seconds wall clock time: 25 minutes 8.51 seconds (1508.51 seconds total)