Starting phenix.real_space_refine on Sun Apr 27 21:24:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9evc_19998/04_2025/9evc_19998.cif Found real_map, /net/cci-nas-00/data/ceres_data/9evc_19998/04_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_19998/04_2025/9evc_19998.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9evc_19998/04_2025/9evc_19998.map" model { file = "/net/cci-nas-00/data/ceres_data/9evc_19998/04_2025/9evc_19998.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9evc_19998/04_2025/9evc_19998.cif" } resolution = 3.73 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 1 9.91 5 S 33 5.16 5 C 4156 2.51 5 N 1080 2.21 5 O 1237 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 6507 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 857, 6506 Classifications: {'peptide': 857} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 29, 'TRANS': 827} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.33, per 1000 atoms: 0.82 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: 2.13 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.82 Creating SS restraints... Processing helix chain 'A' and resid 7 through 15 Processing helix chain 'A' and resid 27 through 35 Processing helix chain 'A' and resid 46 through 54 Processing helix chain 'A' and resid 57 through 73 Processing helix chain 'A' and resid 75 through 111 removed outlier: 3.929A pdb=" N SER A 79 " --> pdb=" O GLU A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 218 Processing helix chain 'A' and resid 230 through 261 Processing helix chain 'A' and resid 270 through 273 Processing helix chain 'A' and resid 274 through 290 removed outlier: 4.033A pdb=" N ALA A 278 " --> pdb=" O ALA A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 312 Processing helix chain 'A' and resid 318 through 322 Processing helix chain 'A' and resid 323 through 328 removed outlier: 3.690A pdb=" N GLY A 326 " --> pdb=" O GLU A 323 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N THR A 328 " --> pdb=" O LEU A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 380 Processing helix chain 'A' and resid 394 through 407 Processing helix chain 'A' and resid 412 through 417 removed outlier: 4.342A pdb=" N GLU A 416 " --> pdb=" O ASN A 412 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LYS A 417 " --> pdb=" O GLU A 413 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 412 through 417' Processing helix chain 'A' and resid 450 through 458 Processing helix chain 'A' and resid 471 through 488 removed outlier: 3.539A pdb=" N GLN A 488 " --> pdb=" O GLU A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 541 Processing helix chain 'A' and resid 552 through 564 Processing helix chain 'A' and resid 575 through 579 Processing helix chain 'A' and resid 582 through 591 removed outlier: 3.987A pdb=" N LYS A 588 " --> pdb=" O GLU A 584 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N GLU A 591 " --> pdb=" O ASP A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 614 removed outlier: 3.985A pdb=" N LYS A 614 " --> pdb=" O ALA A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 634 Processing helix chain 'A' and resid 644 through 651 Processing helix chain 'A' and resid 659 through 701 removed outlier: 3.949A pdb=" N ILE A 663 " --> pdb=" O ASN A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 719 Processing helix chain 'A' and resid 721 through 729 Processing helix chain 'A' and resid 735 through 739 removed outlier: 4.066A pdb=" N ARG A 739 " --> pdb=" O VAL A 736 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 777 Processing helix chain 'A' and resid 779 through 802 removed outlier: 4.185A pdb=" N PHE A 800 " --> pdb=" O THR A 796 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA A 801 " --> pdb=" O LEU A 797 " (cutoff:3.500A) Processing helix chain 'A' and resid 808 through 813 Processing helix chain 'A' and resid 817 through 832 Processing helix chain 'A' and resid 836 through 840 Processing helix chain 'A' and resid 851 through 878 removed outlier: 3.821A pdb=" N ILE A 856 " --> pdb=" O HIS A 852 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N ALA A 857 " --> pdb=" O GLU A 853 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 124 through 126 removed outlier: 3.618A pdb=" N ILE A 126 " --> pdb=" O ALA A 115 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LYS A 116 " --> pdb=" O ILE A 138 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N VAL A 136 " --> pdb=" O ILE A 118 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N MET A 203 " --> pdb=" O PHE A 152 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N PHE A 152 " --> pdb=" O MET A 203 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 167 through 172 removed outlier: 6.352A pdb=" N GLU A 169 " --> pdb=" O ILE A 159 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N ILE A 159 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N LYS A 158 " --> pdb=" O VAL A 198 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU A 196 " --> pdb=" O ASP A 160 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 314 through 316 Processing sheet with id=AA4, first strand: chain 'A' and resid 330 through 334 removed outlier: 5.246A pdb=" N ALA A 594 " --> pdb=" O THR A 545 " (cutoff:3.500A) removed outlier: 8.694A pdb=" N ILE A 571 " --> pdb=" O ALA A 594 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N TYR A 596 " --> pdb=" O ILE A 571 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N LEU A 573 " --> pdb=" O TYR A 596 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 345 through 350 removed outlier: 5.789A pdb=" N VAL A 346 " --> pdb=" O ILE A 524 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ILE A 524 " --> pdb=" O VAL A 346 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ASP A 348 " --> pdb=" O ALA A 522 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N GLY A 519 " --> pdb=" O TYR A 495 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N TYR A 495 " --> pdb=" O GLY A 519 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR A 521 " --> pdb=" O LEU A 493 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR A 447 " --> pdb=" O GLY A 496 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 345 through 350 removed outlier: 5.789A pdb=" N VAL A 346 " --> pdb=" O ILE A 524 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ILE A 524 " --> pdb=" O VAL A 346 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ASP A 348 " --> pdb=" O ALA A 522 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N TYR A 460 " --> pdb=" O LEU A 517 " (cutoff:3.500A) removed outlier: 8.920A pdb=" N GLY A 519 " --> pdb=" O TYR A 460 " (cutoff:3.500A) removed outlier: 10.036A pdb=" N PHE A 462 " --> pdb=" O GLY A 519 " (cutoff:3.500A) removed outlier: 13.089A pdb=" N THR A 521 " --> pdb=" O PHE A 462 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS A 468 " --> pdb=" O VAL A 461 " (cutoff:3.500A) 377 hydrogen bonds defined for protein. 1089 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.23 Time building geometry restraints manager: 2.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2114 1.34 - 1.46: 1087 1.46 - 1.58: 3339 1.58 - 1.70: 0 1.70 - 1.82: 61 Bond restraints: 6601 Sorted by residual: bond pdb=" N LEU A 15 " pdb=" CA LEU A 15 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.32e-02 5.74e+03 8.33e+00 bond pdb=" N GLU A 292 " pdb=" CA GLU A 292 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.28e-02 6.10e+03 6.21e+00 bond pdb=" N LYS A 468 " pdb=" CA LYS A 468 " ideal model delta sigma weight residual 1.452 1.490 -0.038 1.54e-02 4.22e+03 6.15e+00 bond pdb=" N PHE A 55 " pdb=" CA PHE A 55 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.32e-02 5.74e+03 5.92e+00 bond pdb=" N LEU A 763 " pdb=" CA LEU A 763 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.19e-02 7.06e+03 5.54e+00 ... (remaining 6596 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 8660 2.00 - 4.00: 224 4.00 - 6.00: 31 6.00 - 7.99: 11 7.99 - 9.99: 7 Bond angle restraints: 8933 Sorted by residual: angle pdb=" N GLY A 149 " pdb=" CA GLY A 149 " pdb=" C GLY A 149 " ideal model delta sigma weight residual 110.38 116.09 -5.71 1.48e+00 4.57e-01 1.49e+01 angle pdb=" C THR A 54 " pdb=" N PHE A 55 " pdb=" CA PHE A 55 " ideal model delta sigma weight residual 122.54 116.89 5.65 1.65e+00 3.67e-01 1.17e+01 angle pdb=" CB MET A 163 " pdb=" CG MET A 163 " pdb=" SD MET A 163 " ideal model delta sigma weight residual 112.70 122.69 -9.99 3.00e+00 1.11e-01 1.11e+01 angle pdb=" CA GLU A 361 " pdb=" CB GLU A 361 " pdb=" CG GLU A 361 " ideal model delta sigma weight residual 114.10 120.05 -5.95 2.00e+00 2.50e-01 8.85e+00 angle pdb=" C LYS A 468 " pdb=" CA LYS A 468 " pdb=" CB LYS A 468 " ideal model delta sigma weight residual 108.84 113.08 -4.24 1.51e+00 4.39e-01 7.90e+00 ... (remaining 8928 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.29: 3403 16.29 - 32.57: 450 32.57 - 48.86: 122 48.86 - 65.14: 34 65.14 - 81.43: 4 Dihedral angle restraints: 4013 sinusoidal: 1554 harmonic: 2459 Sorted by residual: dihedral pdb=" CA LEU A 851 " pdb=" C LEU A 851 " pdb=" N HIS A 852 " pdb=" CA HIS A 852 " ideal model delta harmonic sigma weight residual -180.00 -157.39 -22.61 0 5.00e+00 4.00e-02 2.04e+01 dihedral pdb=" CA ASP A 720 " pdb=" C ASP A 720 " pdb=" N SER A 721 " pdb=" CA SER A 721 " ideal model delta harmonic sigma weight residual -180.00 -162.55 -17.45 0 5.00e+00 4.00e-02 1.22e+01 dihedral pdb=" CA HIS A 552 " pdb=" C HIS A 552 " pdb=" N LYS A 553 " pdb=" CA LYS A 553 " ideal model delta harmonic sigma weight residual -180.00 -163.73 -16.27 0 5.00e+00 4.00e-02 1.06e+01 ... (remaining 4010 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 895 0.065 - 0.130: 158 0.130 - 0.195: 14 0.195 - 0.261: 1 0.261 - 0.326: 2 Chirality restraints: 1070 Sorted by residual: chirality pdb=" CG LEU A 86 " pdb=" CB LEU A 86 " pdb=" CD1 LEU A 86 " pdb=" CD2 LEU A 86 " both_signs ideal model delta sigma weight residual False -2.59 -2.26 -0.33 2.00e-01 2.50e+01 2.65e+00 chirality pdb=" CB VAL A 516 " pdb=" CA VAL A 516 " pdb=" CG1 VAL A 516 " pdb=" CG2 VAL A 516 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.46e+00 chirality pdb=" CG LEU A 73 " pdb=" CB LEU A 73 " pdb=" CD1 LEU A 73 " pdb=" CD2 LEU A 73 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.35e+00 ... (remaining 1067 not shown) Planarity restraints: 1141 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 119 " -0.261 9.50e-02 1.11e+02 1.17e-01 8.37e+00 pdb=" NE ARG A 119 " 0.015 2.00e-02 2.50e+03 pdb=" CZ ARG A 119 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG A 119 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 119 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 467 " -0.013 2.00e-02 2.50e+03 2.56e-02 6.57e+00 pdb=" C GLU A 467 " 0.044 2.00e-02 2.50e+03 pdb=" O GLU A 467 " -0.017 2.00e-02 2.50e+03 pdb=" N LYS A 468 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A 468 " 0.036 5.00e-02 4.00e+02 5.58e-02 4.98e+00 pdb=" N PRO A 469 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO A 469 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 469 " 0.030 5.00e-02 4.00e+02 ... (remaining 1138 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 120 2.66 - 3.22: 6373 3.22 - 3.78: 11183 3.78 - 4.34: 14195 4.34 - 4.90: 22544 Nonbonded interactions: 54415 Sorted by model distance: nonbonded pdb=" O ILE A 290 " pdb="CA CA A 901 " model vdw 2.095 2.510 nonbonded pdb=" O ASP A 334 " pdb=" OG1 THR A 338 " model vdw 2.229 3.040 nonbonded pdb=" O LEU A 107 " pdb=" OG SER A 111 " model vdw 2.243 3.040 nonbonded pdb=" OD1 ASN A 716 " pdb="CA CA A 901 " model vdw 2.253 2.510 nonbonded pdb=" OG1 THR A 789 " pdb=" OH TYR A 831 " model vdw 2.259 3.040 ... (remaining 54410 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 21.700 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.160 ------------------------------------------------------------------------------- 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 : 16.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 0.43 % Allowed : 31.51 % Favored : 68.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.27), residues: 849 helix: -0.01 (0.23), residues: 457 sheet: -3.20 (0.61), residues: 57 loop : -2.12 (0.31), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 611 HIS 0.004 0.001 HIS A 437 PHE 0.011 0.001 PHE A 12 TYR 0.006 0.001 TYR A 497 ARG 0.002 0.000 ARG A 5 Details of bonding type rmsd hydrogen bonds : bond 0.15039 ( 374) hydrogen bonds : angle 6.30961 ( 1089) covalent geometry : bond 0.00367 ( 6601) covalent geometry : angle 0.79992 ( 8933) *********************** 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 : 0.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 ILE cc_start: 0.8340 (mt) cc_final: 0.8078 (mt) REVERT: A 105 ASP cc_start: 0.8712 (m-30) cc_final: 0.8461 (m-30) REVERT: A 110 MET cc_start: 0.7166 (ppp) cc_final: 0.6264 (tmm) REVERT: A 203 MET cc_start: 0.5577 (tpt) cc_final: 0.5108 (tpp) REVERT: A 433 MET cc_start: 0.7942 (tpt) cc_final: 0.7293 (tpt) REVERT: A 478 LEU cc_start: 0.8505 (mt) cc_final: 0.7902 (mt) REVERT: A 623 ASP cc_start: 0.7614 (p0) cc_final: 0.7395 (p0) REVERT: A 677 ILE cc_start: 0.8500 (mm) cc_final: 0.8292 (mm) outliers start: 3 outliers final: 3 residues processed: 202 average time/residue: 0.2062 time to fit residues: 54.7612 Evaluate side-chains 145 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 142 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 PHE Chi-restraints excluded: chain A residue 707 PHE Chi-restraints excluded: chain A residue 879 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 71 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 chunk 35 optimal weight: 6.9990 chunk 22 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 34 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 77 optimal weight: 0.7980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 GLN A 277 ASN A 358 ASN ** A 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 482 ASN ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 603 ASN ** A 798 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 807 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.158214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.128995 restraints weight = 15517.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.132911 restraints weight = 7903.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.135325 restraints weight = 5050.839| |-----------------------------------------------------------------------------| r_work (final): 0.3952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.2532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 6601 Z= 0.224 Angle : 0.722 13.639 8933 Z= 0.371 Chirality : 0.046 0.191 1070 Planarity : 0.005 0.036 1141 Dihedral : 5.125 52.242 908 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 18.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 8.06 % Allowed : 27.34 % Favored : 64.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.28), residues: 849 helix: 0.34 (0.23), residues: 463 sheet: -2.58 (0.65), residues: 51 loop : -2.20 (0.32), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 854 HIS 0.005 0.001 HIS A 437 PHE 0.028 0.002 PHE A 455 TYR 0.018 0.002 TYR A 495 ARG 0.006 0.001 ARG A 528 Details of bonding type rmsd hydrogen bonds : bond 0.04853 ( 374) hydrogen bonds : angle 5.10331 ( 1089) covalent geometry : bond 0.00488 ( 6601) covalent geometry : angle 0.72160 ( 8933) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 156 time to evaluate : 0.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ASP cc_start: 0.8737 (m-30) cc_final: 0.8225 (m-30) REVERT: A 110 MET cc_start: 0.7035 (ppp) cc_final: 0.6413 (tmm) REVERT: A 152 PHE cc_start: 0.5594 (OUTLIER) cc_final: 0.4692 (p90) REVERT: A 342 ASN cc_start: 0.7292 (m-40) cc_final: 0.7057 (m-40) REVERT: A 358 ASN cc_start: 0.7191 (OUTLIER) cc_final: 0.6457 (t0) REVERT: A 397 GLU cc_start: 0.8746 (mp0) cc_final: 0.8343 (mp0) REVERT: A 420 ARG cc_start: 0.8410 (mpt180) cc_final: 0.8124 (mpt180) REVERT: A 426 PHE cc_start: 0.7177 (t80) cc_final: 0.6288 (t80) REVERT: A 433 MET cc_start: 0.8178 (tpt) cc_final: 0.7489 (tpp) REVERT: A 463 LEU cc_start: 0.7699 (mm) cc_final: 0.7492 (mm) REVERT: A 478 LEU cc_start: 0.8565 (mt) cc_final: 0.8062 (mt) REVERT: A 479 LYS cc_start: 0.8136 (mmmt) cc_final: 0.7851 (mmtp) REVERT: A 484 GLU cc_start: 0.8347 (pt0) cc_final: 0.7843 (pt0) REVERT: A 517 LEU cc_start: 0.8067 (OUTLIER) cc_final: 0.7864 (tt) REVERT: A 623 ASP cc_start: 0.8326 (p0) cc_final: 0.8031 (p0) REVERT: A 633 GLN cc_start: 0.7606 (mp10) cc_final: 0.7206 (mp10) REVERT: A 678 LYS cc_start: 0.8416 (mttt) cc_final: 0.8167 (ttmm) REVERT: A 689 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.7753 (tt) REVERT: A 699 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8204 (mp) REVERT: A 718 VAL cc_start: 0.8742 (t) cc_final: 0.8525 (m) outliers start: 56 outliers final: 31 residues processed: 191 average time/residue: 0.2133 time to fit residues: 56.1126 Evaluate side-chains 177 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 141 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 TYR Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 152 PHE Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 358 ASN Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 636 ILE Chi-restraints excluded: chain A residue 649 ASP Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 720 ASP Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 753 THR Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 871 ILE Chi-restraints excluded: chain A residue 879 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 17 optimal weight: 4.9990 chunk 45 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 11 optimal weight: 10.0000 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 482 ASN A 798 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.159302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.130110 restraints weight = 15548.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.134086 restraints weight = 7756.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.136608 restraints weight = 4934.422| |-----------------------------------------------------------------------------| r_work (final): 0.3966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.2872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6601 Z= 0.173 Angle : 0.674 14.211 8933 Z= 0.339 Chirality : 0.044 0.176 1070 Planarity : 0.004 0.037 1141 Dihedral : 4.767 51.554 904 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 19.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 8.20 % Allowed : 27.34 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.28), residues: 849 helix: 0.52 (0.23), residues: 465 sheet: -2.40 (0.56), residues: 69 loop : -2.16 (0.34), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 854 HIS 0.005 0.001 HIS A 437 PHE 0.029 0.001 PHE A 455 TYR 0.015 0.002 TYR A 349 ARG 0.004 0.000 ARG A 317 Details of bonding type rmsd hydrogen bonds : bond 0.04417 ( 374) hydrogen bonds : angle 4.85934 ( 1089) covalent geometry : bond 0.00382 ( 6601) covalent geometry : angle 0.67414 ( 8933) *********************** 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 204 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 147 time to evaluate : 0.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ASP cc_start: 0.8567 (m-30) cc_final: 0.8209 (m-30) REVERT: A 110 MET cc_start: 0.6924 (ppp) cc_final: 0.6419 (tmm) REVERT: A 152 PHE cc_start: 0.5493 (OUTLIER) cc_final: 0.4013 (p90) REVERT: A 251 CYS cc_start: 0.7977 (m) cc_final: 0.7647 (t) REVERT: A 342 ASN cc_start: 0.7180 (m-40) cc_final: 0.6886 (m-40) REVERT: A 358 ASN cc_start: 0.7065 (p0) cc_final: 0.6488 (t0) REVERT: A 397 GLU cc_start: 0.8633 (mp0) cc_final: 0.8278 (mp0) REVERT: A 420 ARG cc_start: 0.8456 (mpt180) cc_final: 0.8174 (mpt180) REVERT: A 426 PHE cc_start: 0.7151 (t80) cc_final: 0.6870 (t80) REVERT: A 433 MET cc_start: 0.8237 (tpt) cc_final: 0.7584 (tpt) REVERT: A 463 LEU cc_start: 0.7763 (mm) cc_final: 0.7552 (mm) REVERT: A 478 LEU cc_start: 0.8637 (mt) cc_final: 0.8176 (mt) REVERT: A 484 GLU cc_start: 0.8284 (pt0) cc_final: 0.7736 (pt0) REVERT: A 517 LEU cc_start: 0.8110 (OUTLIER) cc_final: 0.7834 (tt) REVERT: A 566 MET cc_start: 0.7477 (mmt) cc_final: 0.7189 (mmt) REVERT: A 623 ASP cc_start: 0.8328 (p0) cc_final: 0.8002 (p0) REVERT: A 633 GLN cc_start: 0.7590 (mp10) cc_final: 0.7217 (mp10) REVERT: A 678 LYS cc_start: 0.8409 (mttt) cc_final: 0.8160 (ttmm) REVERT: A 689 LEU cc_start: 0.8180 (OUTLIER) cc_final: 0.7705 (tt) REVERT: A 833 ILE cc_start: 0.7896 (OUTLIER) cc_final: 0.7424 (mt) outliers start: 57 outliers final: 31 residues processed: 186 average time/residue: 0.2608 time to fit residues: 67.3471 Evaluate side-chains 173 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 138 time to evaluate : 1.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 TYR Chi-restraints excluded: chain A residue 51 PHE Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 152 PHE Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 458 CYS Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 649 ASP Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 720 ASP Chi-restraints excluded: chain A residue 730 GLU Chi-restraints excluded: chain A residue 753 THR Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 766 ILE Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 833 ILE Chi-restraints excluded: chain A residue 844 SER Chi-restraints excluded: chain A residue 871 ILE Chi-restraints excluded: chain A residue 879 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 12 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 66 optimal weight: 0.5980 chunk 21 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 36 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 412 ASN A 482 ASN A 798 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.158861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.130262 restraints weight = 15618.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.134348 restraints weight = 7686.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.136899 restraints weight = 4788.326| |-----------------------------------------------------------------------------| r_work (final): 0.3974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.3207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6601 Z= 0.161 Angle : 0.661 14.645 8933 Z= 0.331 Chirality : 0.043 0.179 1070 Planarity : 0.004 0.037 1141 Dihedral : 4.720 50.963 904 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 19.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 8.49 % Allowed : 26.47 % Favored : 65.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.28), residues: 849 helix: 0.59 (0.23), residues: 472 sheet: -2.42 (0.55), residues: 74 loop : -2.12 (0.34), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 854 HIS 0.005 0.001 HIS A 437 PHE 0.022 0.001 PHE A 455 TYR 0.025 0.002 TYR A 349 ARG 0.004 0.000 ARG A 317 Details of bonding type rmsd hydrogen bonds : bond 0.04210 ( 374) hydrogen bonds : angle 4.71360 ( 1089) covalent geometry : bond 0.00356 ( 6601) covalent geometry : angle 0.66099 ( 8933) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 146 time to evaluate : 0.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ASP cc_start: 0.8578 (m-30) cc_final: 0.8217 (m-30) REVERT: A 152 PHE cc_start: 0.5579 (OUTLIER) cc_final: 0.4320 (p90) REVERT: A 251 CYS cc_start: 0.7905 (m) cc_final: 0.7688 (t) REVERT: A 342 ASN cc_start: 0.7081 (m-40) cc_final: 0.6865 (m-40) REVERT: A 358 ASN cc_start: 0.6940 (p0) cc_final: 0.6273 (t0) REVERT: A 397 GLU cc_start: 0.8670 (mp0) cc_final: 0.8272 (mp0) REVERT: A 433 MET cc_start: 0.8241 (tpt) cc_final: 0.7943 (tpp) REVERT: A 463 LEU cc_start: 0.7727 (mm) cc_final: 0.7485 (mm) REVERT: A 478 LEU cc_start: 0.8644 (mt) cc_final: 0.8066 (mt) REVERT: A 484 GLU cc_start: 0.8251 (pt0) cc_final: 0.7781 (pt0) REVERT: A 517 LEU cc_start: 0.8049 (OUTLIER) cc_final: 0.7773 (tt) REVERT: A 566 MET cc_start: 0.7367 (mmt) cc_final: 0.7097 (mmt) REVERT: A 623 ASP cc_start: 0.8291 (p0) cc_final: 0.7970 (p0) REVERT: A 633 GLN cc_start: 0.7584 (mp10) cc_final: 0.7202 (mp10) REVERT: A 640 MET cc_start: 0.8705 (mmm) cc_final: 0.8505 (mmm) REVERT: A 658 ASP cc_start: 0.7274 (t70) cc_final: 0.7057 (t0) REVERT: A 678 LYS cc_start: 0.8401 (mttt) cc_final: 0.8177 (ttmm) REVERT: A 689 LEU cc_start: 0.8166 (OUTLIER) cc_final: 0.7683 (tt) REVERT: A 828 PHE cc_start: 0.7252 (OUTLIER) cc_final: 0.6949 (m-80) REVERT: A 833 ILE cc_start: 0.7882 (OUTLIER) cc_final: 0.7548 (mt) outliers start: 59 outliers final: 43 residues processed: 186 average time/residue: 0.1566 time to fit residues: 40.2060 Evaluate side-chains 182 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 134 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 PHE Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 152 PHE Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 280 MET Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 309 MET Chi-restraints excluded: chain A residue 318 LYS Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain A residue 458 CYS Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 636 ILE Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 649 ASP Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 707 PHE Chi-restraints excluded: chain A residue 720 ASP Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 730 GLU Chi-restraints excluded: chain A residue 753 THR Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 766 ILE Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 805 ASN Chi-restraints excluded: chain A residue 828 PHE Chi-restraints excluded: chain A residue 833 ILE Chi-restraints excluded: chain A residue 844 SER Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 871 ILE Chi-restraints excluded: chain A residue 879 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 11 optimal weight: 10.0000 chunk 78 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 59 optimal weight: 0.6980 chunk 47 optimal weight: 9.9990 chunk 17 optimal weight: 10.0000 chunk 46 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- 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 612 GLN ** 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 = 0.4238 r_free = 0.4238 target = 0.154560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.125171 restraints weight = 15616.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.129102 restraints weight = 7718.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.131510 restraints weight = 4908.770| |-----------------------------------------------------------------------------| r_work (final): 0.3895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.3808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 6601 Z= 0.257 Angle : 0.745 15.143 8933 Z= 0.380 Chirality : 0.046 0.177 1070 Planarity : 0.005 0.041 1141 Dihedral : 4.964 51.092 904 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 21.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.13 % Favored : 91.87 % Rotamer: Outliers : 9.50 % Allowed : 26.76 % Favored : 63.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.28), residues: 849 helix: 0.46 (0.23), residues: 460 sheet: -2.79 (0.55), residues: 75 loop : -2.13 (0.33), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 854 HIS 0.005 0.002 HIS A 437 PHE 0.019 0.002 PHE A 674 TYR 0.027 0.003 TYR A 349 ARG 0.004 0.001 ARG A 317 Details of bonding type rmsd hydrogen bonds : bond 0.04828 ( 374) hydrogen bonds : angle 5.10451 ( 1089) covalent geometry : bond 0.00561 ( 6601) covalent geometry : angle 0.74516 ( 8933) *********************** 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 201 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 135 time to evaluate : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 PHE cc_start: 0.5820 (OUTLIER) cc_final: 0.4680 (p90) REVERT: A 290 ILE cc_start: 0.8852 (mm) cc_final: 0.8593 (pt) REVERT: A 309 MET cc_start: 0.8180 (OUTLIER) cc_final: 0.7854 (mtm) REVERT: A 318 LYS cc_start: 0.7864 (OUTLIER) cc_final: 0.7563 (tttp) REVERT: A 397 GLU cc_start: 0.8652 (mp0) cc_final: 0.8308 (mp0) REVERT: A 407 ASN cc_start: 0.8066 (m-40) cc_final: 0.7652 (m-40) REVERT: A 416 GLU cc_start: 0.7099 (mp0) cc_final: 0.6692 (pm20) REVERT: A 426 PHE cc_start: 0.7567 (t80) cc_final: 0.7055 (t80) REVERT: A 433 MET cc_start: 0.8369 (tpt) cc_final: 0.8104 (tpp) REVERT: A 463 LEU cc_start: 0.7785 (mm) cc_final: 0.7562 (mm) REVERT: A 478 LEU cc_start: 0.8735 (mt) cc_final: 0.8239 (mt) REVERT: A 484 GLU cc_start: 0.8495 (pt0) cc_final: 0.7959 (pt0) REVERT: A 490 LEU cc_start: 0.9315 (mt) cc_final: 0.9036 (mt) REVERT: A 517 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.7996 (tt) REVERT: A 566 MET cc_start: 0.7557 (mmt) cc_final: 0.7277 (mmm) REVERT: A 623 ASP cc_start: 0.8434 (p0) cc_final: 0.8130 (p0) REVERT: A 633 GLN cc_start: 0.7565 (mp10) cc_final: 0.7213 (mp10) REVERT: A 658 ASP cc_start: 0.7706 (t70) cc_final: 0.7495 (t0) REVERT: A 678 LYS cc_start: 0.8426 (mttt) cc_final: 0.8199 (ttmm) REVERT: A 689 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8272 (tp) REVERT: A 693 ILE cc_start: 0.9250 (OUTLIER) cc_final: 0.9042 (tt) REVERT: A 828 PHE cc_start: 0.7417 (OUTLIER) cc_final: 0.7027 (m-80) REVERT: A 833 ILE cc_start: 0.7977 (OUTLIER) cc_final: 0.7687 (mt) outliers start: 66 outliers final: 38 residues processed: 183 average time/residue: 0.1876 time to fit residues: 47.4670 Evaluate side-chains 171 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 125 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 TYR Chi-restraints excluded: chain A residue 51 PHE Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 152 PHE Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 309 MET Chi-restraints excluded: chain A residue 318 LYS Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 458 CYS Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 649 ASP Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 719 ASN Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 730 GLU Chi-restraints excluded: chain A residue 753 THR Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 766 ILE Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 805 ASN Chi-restraints excluded: chain A residue 828 PHE Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 833 ILE Chi-restraints excluded: chain A residue 844 SER Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 879 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 19 optimal weight: 8.9990 chunk 1 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 37 optimal weight: 0.9980 chunk 8 optimal weight: 4.9990 chunk 56 optimal weight: 0.7980 chunk 81 optimal weight: 0.6980 chunk 42 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 46 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 719 ASN A 798 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.159234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.130301 restraints weight = 15470.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.134309 restraints weight = 7698.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.136905 restraints weight = 4859.889| |-----------------------------------------------------------------------------| r_work (final): 0.3965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.3752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 6601 Z= 0.146 Angle : 0.665 16.094 8933 Z= 0.332 Chirality : 0.043 0.174 1070 Planarity : 0.004 0.040 1141 Dihedral : 4.822 49.761 904 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 18.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 8.06 % Allowed : 28.92 % Favored : 63.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.28), residues: 849 helix: 0.77 (0.23), residues: 459 sheet: -2.73 (0.54), residues: 77 loop : -2.03 (0.34), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 854 HIS 0.004 0.001 HIS A 437 PHE 0.027 0.001 PHE A 455 TYR 0.031 0.002 TYR A 349 ARG 0.003 0.000 ARG A 742 Details of bonding type rmsd hydrogen bonds : bond 0.04059 ( 374) hydrogen bonds : angle 4.76590 ( 1089) covalent geometry : bond 0.00328 ( 6601) covalent geometry : angle 0.66538 ( 8933) *********************** 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 199 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 143 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 GLN cc_start: 0.7549 (mm110) cc_final: 0.7097 (mm110) REVERT: A 152 PHE cc_start: 0.5990 (OUTLIER) cc_final: 0.4907 (p90) REVERT: A 290 ILE cc_start: 0.8774 (mm) cc_final: 0.8488 (pt) REVERT: A 397 GLU cc_start: 0.8687 (mp0) cc_final: 0.8008 (mt-10) REVERT: A 413 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7670 (pm20) REVERT: A 433 MET cc_start: 0.8318 (tpt) cc_final: 0.8113 (tpp) REVERT: A 478 LEU cc_start: 0.8660 (mt) cc_final: 0.8155 (mt) REVERT: A 479 LYS cc_start: 0.8259 (mmmt) cc_final: 0.7946 (mmtp) REVERT: A 482 ASN cc_start: 0.9094 (OUTLIER) cc_final: 0.8759 (t160) REVERT: A 484 GLU cc_start: 0.8478 (pt0) cc_final: 0.7944 (pt0) REVERT: A 490 LEU cc_start: 0.9162 (mt) cc_final: 0.8943 (mt) REVERT: A 517 LEU cc_start: 0.8294 (OUTLIER) cc_final: 0.8058 (tt) REVERT: A 623 ASP cc_start: 0.8283 (p0) cc_final: 0.7976 (p0) REVERT: A 633 GLN cc_start: 0.7410 (OUTLIER) cc_final: 0.7029 (mp10) REVERT: A 678 LYS cc_start: 0.8428 (mttt) cc_final: 0.8173 (ttmm) REVERT: A 828 PHE cc_start: 0.7213 (OUTLIER) cc_final: 0.6995 (m-80) REVERT: A 833 ILE cc_start: 0.7866 (OUTLIER) cc_final: 0.7554 (mt) REVERT: A 844 SER cc_start: 0.8742 (OUTLIER) cc_final: 0.8504 (p) outliers start: 56 outliers final: 35 residues processed: 185 average time/residue: 0.2232 time to fit residues: 58.4616 Evaluate side-chains 174 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 131 time to evaluate : 2.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 TYR Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 152 PHE Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 309 MET Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain A residue 458 CYS Chi-restraints excluded: chain A residue 482 ASN Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 633 GLN Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 649 ASP Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 707 PHE Chi-restraints excluded: chain A residue 719 ASN Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 730 GLU Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 766 ILE Chi-restraints excluded: chain A residue 805 ASN Chi-restraints excluded: chain A residue 828 PHE Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 833 ILE Chi-restraints excluded: chain A residue 844 SER Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain A residue 879 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 7 optimal weight: 0.8980 chunk 28 optimal weight: 5.9990 chunk 12 optimal weight: 0.0670 chunk 22 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 35 optimal weight: 8.9990 chunk 51 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 overall best weight: 0.7720 ------------------------------------------------------------------------------- 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 = 0.4299 r_free = 0.4299 target = 0.159730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.130720 restraints weight = 15574.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.134766 restraints weight = 7823.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.137325 restraints weight = 4988.902| |-----------------------------------------------------------------------------| r_work (final): 0.3980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.3837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6601 Z= 0.146 Angle : 0.699 16.594 8933 Z= 0.343 Chirality : 0.043 0.168 1070 Planarity : 0.004 0.038 1141 Dihedral : 4.863 49.023 904 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 18.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 7.77 % Allowed : 28.92 % Favored : 63.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.28), residues: 849 helix: 0.74 (0.23), residues: 465 sheet: -2.39 (0.57), residues: 74 loop : -2.11 (0.33), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 854 HIS 0.004 0.001 HIS A 437 PHE 0.014 0.001 PHE A 455 TYR 0.030 0.002 TYR A 349 ARG 0.003 0.000 ARG A 742 Details of bonding type rmsd hydrogen bonds : bond 0.03974 ( 374) hydrogen bonds : angle 4.67198 ( 1089) covalent geometry : bond 0.00332 ( 6601) covalent geometry : angle 0.69865 ( 8933) *********************** 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 190 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 136 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 GLN cc_start: 0.7492 (mm110) cc_final: 0.7040 (mm110) REVERT: A 152 PHE cc_start: 0.5977 (OUTLIER) cc_final: 0.4855 (p90) REVERT: A 290 ILE cc_start: 0.8767 (OUTLIER) cc_final: 0.8524 (pt) REVERT: A 397 GLU cc_start: 0.8673 (mp0) cc_final: 0.8049 (mt-10) REVERT: A 413 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7676 (pm20) REVERT: A 433 MET cc_start: 0.8206 (tpt) cc_final: 0.7954 (tpp) REVERT: A 478 LEU cc_start: 0.8594 (mt) cc_final: 0.8166 (mt) REVERT: A 484 GLU cc_start: 0.8476 (pt0) cc_final: 0.7919 (pt0) REVERT: A 490 LEU cc_start: 0.9100 (mt) cc_final: 0.8875 (mt) REVERT: A 517 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.8001 (tt) REVERT: A 623 ASP cc_start: 0.8226 (p0) cc_final: 0.7893 (p0) REVERT: A 633 GLN cc_start: 0.7371 (OUTLIER) cc_final: 0.6979 (mp10) REVERT: A 678 LYS cc_start: 0.8399 (mttt) cc_final: 0.8145 (ttmm) REVERT: A 828 PHE cc_start: 0.7155 (OUTLIER) cc_final: 0.6901 (m-80) REVERT: A 844 SER cc_start: 0.8712 (OUTLIER) cc_final: 0.8468 (p) outliers start: 54 outliers final: 38 residues processed: 179 average time/residue: 0.1599 time to fit residues: 39.5687 Evaluate side-chains 170 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 125 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 TYR Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 152 PHE Chi-restraints excluded: chain A residue 187 ARG Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 280 MET Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 309 MET Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain A residue 458 CYS Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 633 GLN 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 707 PHE Chi-restraints excluded: chain A residue 719 ASN Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 766 ILE Chi-restraints excluded: chain A residue 805 ASN Chi-restraints excluded: chain A residue 828 PHE Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 844 SER Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain A residue 879 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 67 optimal weight: 0.0270 chunk 13 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 84 optimal weight: 0.9990 chunk 18 optimal weight: 9.9990 chunk 45 optimal weight: 0.7980 chunk 36 optimal weight: 0.0040 chunk 16 optimal weight: 0.9990 chunk 1 optimal weight: 8.9990 chunk 38 optimal weight: 0.7980 chunk 55 optimal weight: 0.7980 overall best weight: 0.4850 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.161045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.132421 restraints weight = 15412.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.136526 restraints weight = 7831.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.139046 restraints weight = 4978.110| |-----------------------------------------------------------------------------| r_work (final): 0.3998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.3922 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= 0.130 Angle : 0.685 16.975 8933 Z= 0.337 Chirality : 0.043 0.153 1070 Planarity : 0.004 0.039 1141 Dihedral : 4.748 47.764 904 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 16.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 5.76 % Allowed : 32.66 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.28), residues: 849 helix: 0.85 (0.23), residues: 462 sheet: -1.82 (0.65), residues: 62 loop : -2.04 (0.33), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 854 HIS 0.004 0.001 HIS A 437 PHE 0.013 0.001 PHE A 359 TYR 0.031 0.002 TYR A 349 ARG 0.003 0.000 ARG A 742 Details of bonding type rmsd hydrogen bonds : bond 0.03868 ( 374) hydrogen bonds : angle 4.62925 ( 1089) covalent geometry : bond 0.00290 ( 6601) covalent geometry : angle 0.68511 ( 8933) *********************** 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 180 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 140 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 GLN cc_start: 0.7504 (mm110) cc_final: 0.7045 (mm110) REVERT: A 152 PHE cc_start: 0.5700 (OUTLIER) cc_final: 0.4723 (p90) REVERT: A 190 MET cc_start: 0.5262 (mpp) cc_final: 0.4429 (mmt) REVERT: A 290 ILE cc_start: 0.8735 (OUTLIER) cc_final: 0.8450 (pt) REVERT: A 309 MET cc_start: 0.7852 (OUTLIER) cc_final: 0.7486 (mtm) REVERT: A 397 GLU cc_start: 0.8687 (mp0) cc_final: 0.8088 (mt-10) REVERT: A 416 GLU cc_start: 0.6700 (mp0) cc_final: 0.6243 (pm20) REVERT: A 426 PHE cc_start: 0.7398 (t80) cc_final: 0.7138 (t80) REVERT: A 433 MET cc_start: 0.8210 (tpt) cc_final: 0.7960 (tpp) REVERT: A 478 LEU cc_start: 0.8571 (mt) cc_final: 0.8154 (mt) REVERT: A 479 LYS cc_start: 0.8211 (mmmt) cc_final: 0.8005 (mmtp) REVERT: A 484 GLU cc_start: 0.8430 (pt0) cc_final: 0.7935 (pt0) REVERT: A 517 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.7947 (tt) REVERT: A 623 ASP cc_start: 0.7783 (p0) cc_final: 0.7374 (p0) REVERT: A 633 GLN cc_start: 0.7357 (OUTLIER) cc_final: 0.6927 (mp10) REVERT: A 678 LYS cc_start: 0.8412 (mttt) cc_final: 0.8135 (ttmm) REVERT: A 833 ILE cc_start: 0.7830 (OUTLIER) cc_final: 0.7418 (mt) outliers start: 40 outliers final: 26 residues processed: 170 average time/residue: 0.1775 time to fit residues: 40.5287 Evaluate side-chains 165 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 133 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 TYR Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 152 PHE Chi-restraints excluded: chain A residue 187 ARG Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 280 MET Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 309 MET Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 458 CYS Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 633 GLN Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 663 ILE Chi-restraints excluded: chain A residue 707 PHE Chi-restraints excluded: chain A residue 766 ILE Chi-restraints excluded: chain A residue 782 MET Chi-restraints excluded: chain A residue 833 ILE Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain A residue 879 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 36 optimal weight: 0.4980 chunk 1 optimal weight: 9.9990 chunk 2 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.160881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.132506 restraints weight = 15454.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.136360 restraints weight = 7801.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.138698 restraints weight = 4959.740| |-----------------------------------------------------------------------------| r_work (final): 0.3980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.4080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6601 Z= 0.149 Angle : 0.706 17.331 8933 Z= 0.348 Chirality : 0.044 0.198 1070 Planarity : 0.004 0.039 1141 Dihedral : 4.755 46.738 904 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 17.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 5.61 % Allowed : 33.53 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.28), residues: 849 helix: 0.93 (0.23), residues: 462 sheet: -2.12 (0.64), residues: 66 loop : -2.10 (0.33), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 854 HIS 0.004 0.001 HIS A 437 PHE 0.013 0.001 PHE A 455 TYR 0.030 0.002 TYR A 349 ARG 0.008 0.001 ARG A 5 Details of bonding type rmsd hydrogen bonds : bond 0.03952 ( 374) hydrogen bonds : angle 4.63656 ( 1089) covalent geometry : bond 0.00337 ( 6601) covalent geometry : angle 0.70634 ( 8933) *********************** 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 175 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 136 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 GLN cc_start: 0.7472 (mm110) cc_final: 0.6992 (mm110) REVERT: A 152 PHE cc_start: 0.5767 (OUTLIER) cc_final: 0.4867 (p90) REVERT: A 190 MET cc_start: 0.5474 (mpp) cc_final: 0.4587 (mmt) REVERT: A 203 MET cc_start: 0.6150 (tpt) cc_final: 0.5923 (tpt) REVERT: A 309 MET cc_start: 0.7896 (OUTLIER) cc_final: 0.7624 (mtm) REVERT: A 344 MET cc_start: 0.7201 (mpp) cc_final: 0.6547 (mtm) REVERT: A 397 GLU cc_start: 0.8716 (mp0) cc_final: 0.8171 (mt-10) REVERT: A 416 GLU cc_start: 0.6794 (mp0) cc_final: 0.6274 (pm20) REVERT: A 426 PHE cc_start: 0.7435 (t80) cc_final: 0.7174 (t80) REVERT: A 433 MET cc_start: 0.8263 (tpt) cc_final: 0.7999 (tpp) REVERT: A 478 LEU cc_start: 0.8558 (mt) cc_final: 0.8170 (mt) REVERT: A 479 LYS cc_start: 0.8209 (mmmt) cc_final: 0.7989 (mmtp) REVERT: A 484 GLU cc_start: 0.8443 (pt0) cc_final: 0.7945 (pt0) REVERT: A 488 GLN cc_start: 0.8594 (tt0) cc_final: 0.8265 (tt0) REVERT: A 490 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8808 (mt) REVERT: A 517 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.7932 (tt) REVERT: A 623 ASP cc_start: 0.7993 (p0) cc_final: 0.7623 (p0) REVERT: A 633 GLN cc_start: 0.7349 (OUTLIER) cc_final: 0.6896 (mp10) REVERT: A 678 LYS cc_start: 0.8364 (mttt) cc_final: 0.8068 (ttmm) REVERT: A 689 LEU cc_start: 0.8058 (OUTLIER) cc_final: 0.7577 (tt) REVERT: A 833 ILE cc_start: 0.7896 (OUTLIER) cc_final: 0.7550 (mt) outliers start: 39 outliers final: 30 residues processed: 161 average time/residue: 0.1754 time to fit residues: 38.4393 Evaluate side-chains 170 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 133 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 TYR Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 152 PHE Chi-restraints excluded: chain A residue 187 ARG Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 280 MET Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 309 MET Chi-restraints excluded: chain A residue 318 LYS Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 458 CYS Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 566 MET Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 633 GLN 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 689 LEU Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 753 THR Chi-restraints excluded: chain A residue 782 MET Chi-restraints excluded: chain A residue 805 ASN Chi-restraints excluded: chain A residue 833 ILE Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain A residue 879 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 81 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 75 optimal weight: 0.0070 chunk 11 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 31 optimal weight: 0.0020 chunk 40 optimal weight: 3.9990 chunk 1 optimal weight: 10.0000 chunk 54 optimal weight: 0.8980 chunk 9 optimal weight: 0.4980 overall best weight: 0.6808 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.160427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.132324 restraints weight = 16021.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.136272 restraints weight = 8134.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.138764 restraints weight = 5201.275| |-----------------------------------------------------------------------------| r_work (final): 0.4002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.4149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6601 Z= 0.140 Angle : 0.709 17.761 8933 Z= 0.347 Chirality : 0.044 0.182 1070 Planarity : 0.004 0.040 1141 Dihedral : 4.763 45.908 904 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 17.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 5.32 % Allowed : 33.67 % Favored : 61.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.28), residues: 849 helix: 0.95 (0.23), residues: 461 sheet: -2.07 (0.66), residues: 66 loop : -2.03 (0.33), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 854 HIS 0.004 0.001 HIS A 437 PHE 0.011 0.001 PHE A 359 TYR 0.031 0.002 TYR A 349 ARG 0.004 0.000 ARG A 420 Details of bonding type rmsd hydrogen bonds : bond 0.03890 ( 374) hydrogen bonds : angle 4.58215 ( 1089) covalent geometry : bond 0.00320 ( 6601) covalent geometry : angle 0.70894 ( 8933) ********************** 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: 37 poor density : 133 time to evaluate : 0.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 TYR cc_start: 0.7779 (OUTLIER) cc_final: 0.7208 (t80) REVERT: A 70 GLN cc_start: 0.7475 (mm110) cc_final: 0.7013 (mm110) REVERT: A 152 PHE cc_start: 0.5837 (OUTLIER) cc_final: 0.4945 (p90) REVERT: A 187 ARG cc_start: 0.5140 (OUTLIER) cc_final: 0.4879 (mpt180) REVERT: A 190 MET cc_start: 0.5437 (mpp) cc_final: 0.4552 (mmt) REVERT: A 290 ILE cc_start: 0.8657 (OUTLIER) cc_final: 0.8430 (pt) REVERT: A 309 MET cc_start: 0.7849 (OUTLIER) cc_final: 0.7580 (mtm) REVERT: A 344 MET cc_start: 0.6996 (mpp) cc_final: 0.6372 (mtm) REVERT: A 397 GLU cc_start: 0.8661 (mp0) cc_final: 0.8142 (mt-10) REVERT: A 416 GLU cc_start: 0.6659 (mp0) cc_final: 0.6284 (pm20) REVERT: A 426 PHE cc_start: 0.7365 (t80) cc_final: 0.7125 (t80) REVERT: A 433 MET cc_start: 0.8194 (tpt) cc_final: 0.7935 (tpp) REVERT: A 478 LEU cc_start: 0.8568 (mt) cc_final: 0.8170 (mt) REVERT: A 479 LYS cc_start: 0.8199 (mmmt) cc_final: 0.7963 (mmtp) REVERT: A 484 GLU cc_start: 0.8450 (pt0) cc_final: 0.7961 (pt0) REVERT: A 623 ASP cc_start: 0.8043 (p0) cc_final: 0.7646 (p0) REVERT: A 633 GLN cc_start: 0.7318 (OUTLIER) cc_final: 0.6881 (mp10) REVERT: A 678 LYS cc_start: 0.8378 (mttt) cc_final: 0.7925 (mttm) REVERT: A 689 LEU cc_start: 0.8018 (OUTLIER) cc_final: 0.7544 (tt) REVERT: A 833 ILE cc_start: 0.7881 (OUTLIER) cc_final: 0.7468 (mt) outliers start: 37 outliers final: 25 residues processed: 159 average time/residue: 0.1743 time to fit residues: 38.1139 Evaluate side-chains 164 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 131 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 TYR Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 152 PHE Chi-restraints excluded: chain A residue 187 ARG Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 280 MET Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 309 MET Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 566 MET Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 633 GLN 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 689 LEU Chi-restraints excluded: chain A residue 707 PHE Chi-restraints excluded: chain A residue 782 MET Chi-restraints excluded: chain A residue 805 ASN Chi-restraints excluded: chain A residue 833 ILE Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain A residue 879 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 57 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 chunk 71 optimal weight: 4.9990 chunk 9 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 34 optimal weight: 0.0970 chunk 35 optimal weight: 0.8980 chunk 60 optimal weight: 0.9990 chunk 70 optimal weight: 0.7980 chunk 63 optimal weight: 0.8980 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 482 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.160387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.131765 restraints weight = 15783.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.135772 restraints weight = 8082.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.138241 restraints weight = 5158.820| |-----------------------------------------------------------------------------| r_work (final): 0.4002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.4232 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= 0.142 Angle : 0.717 17.470 8933 Z= 0.349 Chirality : 0.043 0.155 1070 Planarity : 0.004 0.046 1141 Dihedral : 4.750 45.027 904 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 17.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 5.61 % Allowed : 33.67 % Favored : 60.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.28), residues: 849 helix: 1.05 (0.23), residues: 455 sheet: -1.96 (0.67), residues: 66 loop : -2.03 (0.32), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 854 HIS 0.004 0.001 HIS A 437 PHE 0.011 0.001 PHE A 403 TYR 0.030 0.002 TYR A 349 ARG 0.006 0.000 ARG A 420 Details of bonding type rmsd hydrogen bonds : bond 0.03899 ( 374) hydrogen bonds : angle 4.56567 ( 1089) covalent geometry : bond 0.00323 ( 6601) covalent geometry : angle 0.71684 ( 8933) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3015.21 seconds wall clock time: 54 minutes 15.16 seconds (3255.16 seconds total)