Starting phenix.real_space_refine on Tue Feb 3 18:21:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9m38_63601/02_2026/9m38_63601.cif Found real_map, /net/cci-nas-00/data/ceres_data/9m38_63601/02_2026/9m38_63601.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9m38_63601/02_2026/9m38_63601.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9m38_63601/02_2026/9m38_63601.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9m38_63601/02_2026/9m38_63601.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9m38_63601/02_2026/9m38_63601.map" } resolution = 3.47 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.017 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: 4 Type Number sf(0) Gaussians S 20 5.16 5 C 3843 2.51 5 N 991 2.21 5 O 1083 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5937 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 5937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 716, 5937 Classifications: {'peptide': 716} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 16, 'TRANS': 699} Chain breaks: 5 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Time building chain proxies: 1.04, per 1000 atoms: 0.18 Number of scatterers: 5937 At special positions: 0 Unit cell: (84.645, 100.035, 94.905, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 20 16.00 O 1083 8.00 N 991 7.00 C 3843 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.36 Conformation dependent library (CDL) restraints added in 333.3 milliseconds 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1392 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 2 sheets defined 75.8% alpha, 0.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 96 through 105 Processing helix chain 'A' and resid 113 through 143 removed outlier: 3.720A pdb=" N LEU A 117 " --> pdb=" O ILE A 113 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU A 143 " --> pdb=" O LEU A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 172 removed outlier: 3.537A pdb=" N GLY A 171 " --> pdb=" O GLN A 167 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLN A 172 " --> pdb=" O THR A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 184 removed outlier: 3.894A pdb=" N ARG A 178 " --> pdb=" O ASN A 174 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N PHE A 179 " --> pdb=" O LYS A 175 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASN A 181 " --> pdb=" O ASP A 177 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N TYR A 182 " --> pdb=" O ARG A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 190 removed outlier: 3.683A pdb=" N LEU A 188 " --> pdb=" O ARG A 185 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU A 189 " --> pdb=" O LYS A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 222 Processing helix chain 'A' and resid 250 through 270 removed outlier: 4.006A pdb=" N LEU A 254 " --> pdb=" O PHE A 250 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N LEU A 270 " --> pdb=" O ASP A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 284 Processing helix chain 'A' and resid 288 through 301 removed outlier: 3.660A pdb=" N ILE A 292 " --> pdb=" O SER A 288 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU A 300 " --> pdb=" O TYR A 296 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE A 301 " --> pdb=" O TYR A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 321 removed outlier: 3.515A pdb=" N GLU A 317 " --> pdb=" O LYS A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 336 removed outlier: 3.529A pdb=" N SER A 335 " --> pdb=" O LYS A 332 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL A 336 " --> pdb=" O TYR A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 356 removed outlier: 4.028A pdb=" N LEU A 343 " --> pdb=" O LYS A 339 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE A 344 " --> pdb=" O LEU A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 368 Processing helix chain 'A' and resid 371 through 399 removed outlier: 6.534A pdb=" N ALA A 392 " --> pdb=" O SER A 388 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ASP A 393 " --> pdb=" O ALA A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 412 removed outlier: 3.617A pdb=" N LYS A 412 " --> pdb=" O ASP A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 442 Processing helix chain 'A' and resid 445 through 473 Processing helix chain 'A' and resid 480 through 485 removed outlier: 4.339A pdb=" N ASP A 485 " --> pdb=" O PRO A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 504 Processing helix chain 'A' and resid 515 through 527 Processing helix chain 'A' and resid 533 through 545 removed outlier: 3.594A pdb=" N ILE A 537 " --> pdb=" O PRO A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 568 removed outlier: 3.697A pdb=" N PHE A 563 " --> pdb=" O GLY A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 581 removed outlier: 3.520A pdb=" N HIS A 575 " --> pdb=" O SER A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 591 removed outlier: 4.164A pdb=" N THR A 586 " --> pdb=" O PRO A 583 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N ARG A 587 " --> pdb=" O HIS A 584 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N THR A 588 " --> pdb=" O LYS A 585 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LYS A 591 " --> pdb=" O THR A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 603 removed outlier: 3.654A pdb=" N ILE A 603 " --> pdb=" O VAL A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 615 Processing helix chain 'A' and resid 625 through 639 removed outlier: 3.901A pdb=" N SER A 639 " --> pdb=" O ARG A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 643 through 648 removed outlier: 3.993A pdb=" N ASP A 647 " --> pdb=" O ILE A 644 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N VAL A 648 " --> pdb=" O PHE A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 711 removed outlier: 3.630A pdb=" N LEU A 680 " --> pdb=" O VAL A 676 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE A 686 " --> pdb=" O VAL A 682 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA A 700 " --> pdb=" O ARG A 696 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N PHE A 709 " --> pdb=" O GLU A 705 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU A 710 " --> pdb=" O ARG A 706 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N HIS A 711 " --> pdb=" O ASP A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 733 Processing helix chain 'A' and resid 752 through 761 removed outlier: 3.942A pdb=" N GLN A 761 " --> pdb=" O LYS A 757 " (cutoff:3.500A) Processing helix chain 'A' and resid 764 through 778 Processing helix chain 'A' and resid 778 through 783 removed outlier: 3.722A pdb=" N ARG A 782 " --> pdb=" O ILE A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 787 through 791 removed outlier: 3.757A pdb=" N GLY A 790 " --> pdb=" O TYR A 787 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ILE A 791 " --> pdb=" O ILE A 788 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 787 through 791' Processing helix chain 'A' and resid 796 through 813 removed outlier: 3.631A pdb=" N LEU A 800 " --> pdb=" O SER A 796 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 834 removed outlier: 4.063A pdb=" N TYR A 826 " --> pdb=" O LYS A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 837 through 845 Processing helix chain 'A' and resid 846 through 849 Processing helix chain 'A' and resid 851 through 860 removed outlier: 3.560A pdb=" N TYR A 855 " --> pdb=" O VAL A 851 " (cutoff:3.500A) Processing helix chain 'A' and resid 860 through 866 removed outlier: 4.034A pdb=" N ASP A 865 " --> pdb=" O ASN A 861 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ARG A 866 " --> pdb=" O GLU A 862 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 196 through 197 Processing sheet with id=AA2, first strand: chain 'A' and resid 717 through 718 343 hydrogen bonds defined for protein. 999 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.75 Time building geometry restraints manager: 0.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1878 1.34 - 1.46: 1260 1.46 - 1.58: 2894 1.58 - 1.69: 0 1.69 - 1.81: 32 Bond restraints: 6064 Sorted by residual: bond pdb=" C ILE A 846 " pdb=" N PRO A 847 " ideal model delta sigma weight residual 1.334 1.368 -0.034 2.34e-02 1.83e+03 2.09e+00 bond pdb=" C TYR A 679 " pdb=" O TYR A 679 " ideal model delta sigma weight residual 1.236 1.248 -0.012 1.15e-02 7.56e+03 1.07e+00 bond pdb=" C MET A 683 " pdb=" O MET A 683 " ideal model delta sigma weight residual 1.237 1.249 -0.012 1.19e-02 7.06e+03 1.01e+00 bond pdb=" C LEU A 117 " pdb=" O LEU A 117 " ideal model delta sigma weight residual 1.236 1.247 -0.010 1.15e-02 7.56e+03 7.82e-01 bond pdb=" N MET A 683 " pdb=" CA MET A 683 " ideal model delta sigma weight residual 1.459 1.470 -0.011 1.23e-02 6.61e+03 7.63e-01 ... (remaining 6059 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.54: 8010 1.54 - 3.08: 140 3.08 - 4.62: 24 4.62 - 6.16: 6 6.16 - 7.70: 1 Bond angle restraints: 8181 Sorted by residual: angle pdb=" CA TYR A 679 " pdb=" CB TYR A 679 " pdb=" CG TYR A 679 " ideal model delta sigma weight residual 113.90 119.42 -5.52 1.80e+00 3.09e-01 9.39e+00 angle pdb=" N TYR A 679 " pdb=" CA TYR A 679 " pdb=" CB TYR A 679 " ideal model delta sigma weight residual 110.01 106.58 3.43 1.45e+00 4.76e-01 5.60e+00 angle pdb=" CB LYS A 472 " pdb=" CG LYS A 472 " pdb=" CD LYS A 472 " ideal model delta sigma weight residual 111.30 116.69 -5.39 2.30e+00 1.89e-01 5.50e+00 angle pdb=" N ILE A 846 " pdb=" CA ILE A 846 " pdb=" C ILE A 846 " ideal model delta sigma weight residual 108.88 113.75 -4.87 2.16e+00 2.14e-01 5.08e+00 angle pdb=" CA LEU A 169 " pdb=" CB LEU A 169 " pdb=" CG LEU A 169 " ideal model delta sigma weight residual 116.30 124.00 -7.70 3.50e+00 8.16e-02 4.84e+00 ... (remaining 8176 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 3260 17.67 - 35.34: 325 35.34 - 53.00: 54 53.00 - 70.67: 6 70.67 - 88.34: 5 Dihedral angle restraints: 3650 sinusoidal: 1504 harmonic: 2146 Sorted by residual: dihedral pdb=" CA PHE A 191 " pdb=" C PHE A 191 " pdb=" N GLY A 192 " pdb=" CA GLY A 192 " ideal model delta harmonic sigma weight residual -180.00 -162.72 -17.28 0 5.00e+00 4.00e-02 1.20e+01 dihedral pdb=" CB LYS A 717 " pdb=" CG LYS A 717 " pdb=" CD LYS A 717 " pdb=" CE LYS A 717 " ideal model delta sinusoidal sigma weight residual 180.00 123.12 56.88 3 1.50e+01 4.44e-03 9.42e+00 dihedral pdb=" CA GLN A 650 " pdb=" CB GLN A 650 " pdb=" CG GLN A 650 " pdb=" CD GLN A 650 " ideal model delta sinusoidal sigma weight residual 60.00 113.76 -53.76 3 1.50e+01 4.44e-03 9.23e+00 ... (remaining 3647 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 503 0.028 - 0.056: 267 0.056 - 0.083: 101 0.083 - 0.111: 27 0.111 - 0.139: 10 Chirality restraints: 908 Sorted by residual: chirality pdb=" CA ASN A 567 " pdb=" N ASN A 567 " pdb=" C ASN A 567 " pdb=" CB ASN A 567 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.82e-01 chirality pdb=" CA ILE A 603 " pdb=" N ILE A 603 " pdb=" C ILE A 603 " pdb=" CB ILE A 603 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.65e-01 chirality pdb=" CA ILE A 505 " pdb=" N ILE A 505 " pdb=" C ILE A 505 " pdb=" CB ILE A 505 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.64e-01 ... (remaining 905 not shown) Planarity restraints: 1028 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 679 " 0.017 2.00e-02 2.50e+03 1.22e-02 2.97e+00 pdb=" CG TYR A 679 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 TYR A 679 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR A 679 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR A 679 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR A 679 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR A 679 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR A 679 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 648 " 0.025 5.00e-02 4.00e+02 3.80e-02 2.31e+00 pdb=" N PRO A 649 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 649 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 649 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 480 " -0.023 5.00e-02 4.00e+02 3.56e-02 2.03e+00 pdb=" N PRO A 481 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO A 481 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 481 " -0.020 5.00e-02 4.00e+02 ... (remaining 1025 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 945 2.76 - 3.29: 5723 3.29 - 3.83: 9064 3.83 - 4.36: 10189 4.36 - 4.90: 18047 Nonbonded interactions: 43968 Sorted by model distance: nonbonded pdb=" OH TYR A 190 " pdb=" OD2 ASP A 522 " model vdw 2.223 3.040 nonbonded pdb=" O TYR A 855 " pdb=" OG1 THR A 859 " model vdw 2.238 3.040 nonbonded pdb=" NZ LYS A 721 " pdb=" OG1 THR A 766 " model vdw 2.244 3.120 nonbonded pdb=" OG SER A 512 " pdb=" N ALA A 513 " model vdw 2.292 3.120 nonbonded pdb=" O LYS A 842 " pdb=" OH TYR A 855 " model vdw 2.333 3.040 ... (remaining 43963 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=0.98 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.000 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.520 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6965 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 0.034 6064 Z= 0.161 Angle : 0.521 7.703 8181 Z= 0.286 Chirality : 0.039 0.139 908 Planarity : 0.004 0.038 1028 Dihedral : 14.166 88.339 2258 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 0.15 % Allowed : 0.00 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.33), residues: 704 helix: 1.56 (0.24), residues: 479 sheet: None (None), residues: 0 loop : -1.53 (0.42), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 573 TYR 0.030 0.001 TYR A 679 PHE 0.013 0.001 PHE A 798 TRP 0.006 0.001 TRP A 258 HIS 0.006 0.001 HIS A 197 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 6064) covalent geometry : angle 0.52140 ( 8181) hydrogen bonds : bond 0.18196 ( 343) hydrogen bonds : angle 5.25134 ( 999) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 110 time to evaluate : 0.144 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 99 LYS cc_start: 0.8287 (mmtp) cc_final: 0.8074 (mmtt) REVERT: A 183 ILE cc_start: 0.7804 (tt) cc_final: 0.7548 (tt) REVERT: A 258 TRP cc_start: 0.7720 (t-100) cc_final: 0.7169 (t-100) REVERT: A 350 TYR cc_start: 0.8615 (t80) cc_final: 0.8142 (t80) REVERT: A 525 ARG cc_start: 0.7924 (mmt90) cc_final: 0.7656 (mmt180) REVERT: A 718 MET cc_start: 0.6451 (tmm) cc_final: 0.6103 (tmm) REVERT: A 721 LYS cc_start: 0.7841 (mttt) cc_final: 0.7583 (mmmm) outliers start: 1 outliers final: 0 residues processed: 111 average time/residue: 0.0699 time to fit residues: 9.7635 Evaluate side-chains 99 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 49 optimal weight: 0.0040 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.0870 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.4980 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.5980 chunk 45 optimal weight: 0.2980 chunk 27 optimal weight: 9.9990 overall best weight: 0.2970 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 759 ASN A 806 GLN A 820 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.172238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.131965 restraints weight = 8523.423| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 2.39 r_work: 0.3455 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3280 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3281 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3281 r_free = 0.3281 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.98 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3281 r_free = 0.3281 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3281 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.1311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6064 Z= 0.133 Angle : 0.517 7.436 8181 Z= 0.281 Chirality : 0.038 0.135 908 Planarity : 0.004 0.034 1028 Dihedral : 3.691 16.345 787 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 0.92 % Allowed : 7.03 % Favored : 92.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.33), residues: 704 helix: 1.70 (0.24), residues: 497 sheet: None (None), residues: 0 loop : -1.47 (0.43), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 573 TYR 0.022 0.002 TYR A 679 PHE 0.012 0.001 PHE A 433 TRP 0.009 0.001 TRP A 258 HIS 0.005 0.001 HIS A 802 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 6064) covalent geometry : angle 0.51724 ( 8181) hydrogen bonds : bond 0.05653 ( 343) hydrogen bonds : angle 3.82614 ( 999) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 101 time to evaluate : 0.198 Fit side-chains revert: symmetry clash REVERT: A 112 ASN cc_start: 0.7647 (t0) cc_final: 0.7433 (t0) REVERT: A 170 ARG cc_start: 0.7807 (tpt-90) cc_final: 0.7548 (tpt-90) REVERT: A 180 LYS cc_start: 0.7534 (tppp) cc_final: 0.7327 (tppp) REVERT: A 308 MET cc_start: 0.2174 (OUTLIER) cc_final: 0.1270 (mpp) REVERT: A 508 MET cc_start: 0.4953 (pmm) cc_final: 0.4376 (pmm) REVERT: A 522 ASP cc_start: 0.7952 (m-30) cc_final: 0.7712 (m-30) REVERT: A 525 ARG cc_start: 0.8080 (mmt90) cc_final: 0.7800 (mtt180) REVERT: A 721 LYS cc_start: 0.8252 (mttt) cc_final: 0.7984 (mmmm) outliers start: 6 outliers final: 2 residues processed: 103 average time/residue: 0.0769 time to fit residues: 9.8851 Evaluate side-chains 98 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 95 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 MET Chi-restraints excluded: chain A residue 581 ASN Chi-restraints excluded: chain A residue 676 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 29 optimal weight: 40.0000 chunk 51 optimal weight: 0.9990 chunk 62 optimal weight: 0.4980 chunk 63 optimal weight: 0.9990 chunk 54 optimal weight: 0.6980 chunk 7 optimal weight: 0.6980 chunk 39 optimal weight: 0.8980 chunk 22 optimal weight: 7.9990 chunk 21 optimal weight: 0.7980 chunk 41 optimal weight: 0.8980 chunk 15 optimal weight: 0.0010 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 581 ASN A 759 ASN A 820 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.170442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.131430 restraints weight = 8297.164| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 2.22 r_work: 0.3459 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3288 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3283 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3283 r_free = 0.3283 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3282 r_free = 0.3282 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.68 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3282 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6064 Z= 0.166 Angle : 0.516 6.690 8181 Z= 0.282 Chirality : 0.038 0.133 908 Planarity : 0.003 0.034 1028 Dihedral : 3.638 16.116 787 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.22 % Allowed : 9.79 % Favored : 88.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.33), residues: 704 helix: 1.67 (0.24), residues: 498 sheet: None (None), residues: 0 loop : -1.63 (0.43), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 573 TYR 0.027 0.001 TYR A 679 PHE 0.014 0.001 PHE A 798 TRP 0.011 0.001 TRP A 258 HIS 0.006 0.001 HIS A 802 Details of bonding type rmsd covalent geometry : bond 0.00381 ( 6064) covalent geometry : angle 0.51618 ( 8181) hydrogen bonds : bond 0.06395 ( 343) hydrogen bonds : angle 3.78900 ( 999) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 101 time to evaluate : 0.150 Fit side-chains revert: symmetry clash REVERT: A 102 MET cc_start: 0.7861 (mmm) cc_final: 0.7501 (mmm) REVERT: A 112 ASN cc_start: 0.7592 (t0) cc_final: 0.7238 (t0) REVERT: A 180 LYS cc_start: 0.7481 (tppp) cc_final: 0.7184 (tppp) REVERT: A 308 MET cc_start: 0.2059 (OUTLIER) cc_final: 0.1124 (mpp) REVERT: A 498 GLU cc_start: 0.6767 (mt-10) cc_final: 0.6455 (mp0) REVERT: A 508 MET cc_start: 0.4939 (pmm) cc_final: 0.4318 (pmm) REVERT: A 522 ASP cc_start: 0.7838 (m-30) cc_final: 0.7597 (m-30) REVERT: A 707 ASP cc_start: 0.8439 (m-30) cc_final: 0.8177 (m-30) REVERT: A 718 MET cc_start: 0.7558 (tmm) cc_final: 0.7255 (tmm) REVERT: A 721 LYS cc_start: 0.8266 (mttt) cc_final: 0.7931 (mtpt) REVERT: A 758 ASN cc_start: 0.8526 (t0) cc_final: 0.8106 (t0) outliers start: 8 outliers final: 3 residues processed: 104 average time/residue: 0.0694 time to fit residues: 9.1791 Evaluate side-chains 102 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 98 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 MET Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 676 VAL Chi-restraints excluded: chain A residue 820 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 0 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 22 optimal weight: 0.3980 chunk 38 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 12 optimal weight: 0.6980 chunk 24 optimal weight: 0.8980 chunk 29 optimal weight: 5.9990 chunk 57 optimal weight: 0.0670 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 581 ASN A 759 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.169703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.130748 restraints weight = 8360.740| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 2.21 r_work: 0.3452 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3280 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3271 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3271 r_free = 0.3271 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.68 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3271 r_free = 0.3271 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3271 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6064 Z= 0.178 Angle : 0.518 6.223 8181 Z= 0.283 Chirality : 0.039 0.133 908 Planarity : 0.003 0.034 1028 Dihedral : 3.657 16.348 787 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 1.38 % Allowed : 11.93 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.33), residues: 704 helix: 1.64 (0.24), residues: 499 sheet: None (None), residues: 0 loop : -1.61 (0.43), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 532 TYR 0.027 0.002 TYR A 679 PHE 0.016 0.001 PHE A 798 TRP 0.007 0.001 TRP A 258 HIS 0.006 0.001 HIS A 802 Details of bonding type rmsd covalent geometry : bond 0.00414 ( 6064) covalent geometry : angle 0.51755 ( 8181) hydrogen bonds : bond 0.06476 ( 343) hydrogen bonds : angle 3.76933 ( 999) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 100 time to evaluate : 0.128 Fit side-chains revert: symmetry clash REVERT: A 102 MET cc_start: 0.7885 (mmm) cc_final: 0.7516 (mmm) REVERT: A 112 ASN cc_start: 0.7634 (t0) cc_final: 0.7264 (t0) REVERT: A 180 LYS cc_start: 0.7461 (tppp) cc_final: 0.7187 (tppp) REVERT: A 308 MET cc_start: 0.1901 (OUTLIER) cc_final: 0.0959 (mpp) REVERT: A 508 MET cc_start: 0.4990 (pmm) cc_final: 0.4369 (pmm) REVERT: A 522 ASP cc_start: 0.7788 (m-30) cc_final: 0.7571 (m-30) REVERT: A 707 ASP cc_start: 0.8433 (m-30) cc_final: 0.8139 (m-30) REVERT: A 718 MET cc_start: 0.7706 (tmm) cc_final: 0.7411 (tmm) REVERT: A 721 LYS cc_start: 0.8282 (mttt) cc_final: 0.7914 (mtpp) REVERT: A 758 ASN cc_start: 0.8558 (t0) cc_final: 0.8141 (t0) outliers start: 9 outliers final: 4 residues processed: 107 average time/residue: 0.0721 time to fit residues: 9.8328 Evaluate side-chains 105 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 100 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 MET Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 676 VAL Chi-restraints excluded: chain A residue 835 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 51 optimal weight: 0.7980 chunk 52 optimal weight: 0.8980 chunk 64 optimal weight: 0.2980 chunk 69 optimal weight: 0.4980 chunk 27 optimal weight: 0.9990 chunk 39 optimal weight: 0.6980 chunk 60 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 44 optimal weight: 0.3980 chunk 28 optimal weight: 8.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 581 ASN A 759 ASN A 820 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.170027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.130791 restraints weight = 8502.141| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 2.23 r_work: 0.3449 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3275 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3269 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3269 r_free = 0.3269 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3269 r_free = 0.3269 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3269 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6064 Z= 0.163 Angle : 0.504 6.856 8181 Z= 0.276 Chirality : 0.038 0.133 908 Planarity : 0.003 0.034 1028 Dihedral : 3.652 15.843 787 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.68 % Allowed : 13.30 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.33), residues: 704 helix: 1.73 (0.24), residues: 498 sheet: None (None), residues: 0 loop : -1.58 (0.43), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 532 TYR 0.025 0.001 TYR A 679 PHE 0.015 0.001 PHE A 798 TRP 0.008 0.001 TRP A 258 HIS 0.006 0.001 HIS A 802 Details of bonding type rmsd covalent geometry : bond 0.00374 ( 6064) covalent geometry : angle 0.50403 ( 8181) hydrogen bonds : bond 0.06155 ( 343) hydrogen bonds : angle 3.70438 ( 999) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 102 time to evaluate : 0.153 Fit side-chains revert: symmetry clash REVERT: A 102 MET cc_start: 0.7900 (mmm) cc_final: 0.7529 (mmm) REVERT: A 112 ASN cc_start: 0.7595 (t0) cc_final: 0.7245 (t0) REVERT: A 180 LYS cc_start: 0.7458 (tppp) cc_final: 0.7218 (tppp) REVERT: A 308 MET cc_start: 0.1864 (OUTLIER) cc_final: 0.0912 (mpp) REVERT: A 508 MET cc_start: 0.4998 (pmm) cc_final: 0.4388 (pmm) REVERT: A 525 ARG cc_start: 0.8080 (mtt90) cc_final: 0.7787 (mtt-85) REVERT: A 707 ASP cc_start: 0.8411 (m-30) cc_final: 0.8088 (m-30) REVERT: A 718 MET cc_start: 0.7741 (tmm) cc_final: 0.7515 (tmm) REVERT: A 721 LYS cc_start: 0.8281 (mttt) cc_final: 0.7977 (mmmt) REVERT: A 758 ASN cc_start: 0.8570 (t0) cc_final: 0.8146 (t0) outliers start: 11 outliers final: 7 residues processed: 108 average time/residue: 0.0754 time to fit residues: 10.4917 Evaluate side-chains 108 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 100 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 MET Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 636 ILE Chi-restraints excluded: chain A residue 676 VAL Chi-restraints excluded: chain A residue 820 GLN Chi-restraints excluded: chain A residue 835 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 29 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 chunk 50 optimal weight: 0.4980 chunk 1 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 44 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 24 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 806 GLN A 820 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.168193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.129114 restraints weight = 8417.574| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 2.20 r_work: 0.3424 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3248 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3237 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3237 r_free = 0.3237 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3237 r_free = 0.3237 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3237 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 6064 Z= 0.218 Angle : 0.546 6.534 8181 Z= 0.299 Chirality : 0.041 0.134 908 Planarity : 0.004 0.037 1028 Dihedral : 3.802 16.105 787 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 1.99 % Allowed : 15.14 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.33), residues: 704 helix: 1.60 (0.24), residues: 498 sheet: None (None), residues: 0 loop : -1.56 (0.44), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 532 TYR 0.025 0.002 TYR A 679 PHE 0.018 0.002 PHE A 798 TRP 0.008 0.001 TRP A 258 HIS 0.007 0.001 HIS A 802 Details of bonding type rmsd covalent geometry : bond 0.00519 ( 6064) covalent geometry : angle 0.54567 ( 8181) hydrogen bonds : bond 0.07072 ( 343) hydrogen bonds : angle 3.84626 ( 999) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 103 time to evaluate : 0.217 Fit side-chains REVERT: A 102 MET cc_start: 0.7915 (mmm) cc_final: 0.7544 (mmm) REVERT: A 112 ASN cc_start: 0.7744 (t0) cc_final: 0.7372 (t0) REVERT: A 180 LYS cc_start: 0.7465 (tppp) cc_final: 0.7243 (tppp) REVERT: A 308 MET cc_start: 0.1929 (OUTLIER) cc_final: 0.0971 (mpp) REVERT: A 498 GLU cc_start: 0.6923 (mt-10) cc_final: 0.6598 (mp0) REVERT: A 508 MET cc_start: 0.5034 (pmm) cc_final: 0.4413 (pmm) REVERT: A 707 ASP cc_start: 0.8462 (m-30) cc_final: 0.8128 (m-30) REVERT: A 718 MET cc_start: 0.7774 (tmm) cc_final: 0.7526 (tmm) REVERT: A 721 LYS cc_start: 0.8291 (mttt) cc_final: 0.7945 (mmtt) REVERT: A 758 ASN cc_start: 0.8593 (t0) cc_final: 0.8172 (t0) REVERT: A 832 LYS cc_start: 0.7938 (tptt) cc_final: 0.7693 (tptt) outliers start: 13 outliers final: 8 residues processed: 113 average time/residue: 0.0954 time to fit residues: 13.6688 Evaluate side-chains 111 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 102 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 MET Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 636 ILE Chi-restraints excluded: chain A residue 676 VAL Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 835 THR Chi-restraints excluded: chain A residue 866 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 25 optimal weight: 6.9990 chunk 67 optimal weight: 0.8980 chunk 63 optimal weight: 0.8980 chunk 12 optimal weight: 0.5980 chunk 69 optimal weight: 0.2980 chunk 20 optimal weight: 2.9990 chunk 48 optimal weight: 0.4980 chunk 57 optimal weight: 1.9990 chunk 41 optimal weight: 0.3980 chunk 8 optimal weight: 0.8980 chunk 11 optimal weight: 0.0980 overall best weight: 0.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 HIS A 759 ASN A 806 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.170099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.131089 restraints weight = 8365.609| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 2.21 r_work: 0.3463 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3289 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3284 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3284 r_free = 0.3284 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3284 r_free = 0.3284 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3284 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6064 Z= 0.137 Angle : 0.490 6.405 8181 Z= 0.269 Chirality : 0.038 0.132 908 Planarity : 0.003 0.039 1028 Dihedral : 3.637 15.886 787 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.68 % Allowed : 16.67 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.33), residues: 704 helix: 1.80 (0.24), residues: 496 sheet: None (None), residues: 0 loop : -1.48 (0.43), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 532 TYR 0.022 0.001 TYR A 679 PHE 0.012 0.001 PHE A 798 TRP 0.012 0.001 TRP A 258 HIS 0.005 0.001 HIS A 802 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 6064) covalent geometry : angle 0.48959 ( 8181) hydrogen bonds : bond 0.05667 ( 343) hydrogen bonds : angle 3.66534 ( 999) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 103 time to evaluate : 0.220 Fit side-chains REVERT: A 112 ASN cc_start: 0.7549 (t0) cc_final: 0.7217 (t0) REVERT: A 180 LYS cc_start: 0.7425 (tppp) cc_final: 0.7200 (tppp) REVERT: A 308 MET cc_start: 0.1943 (OUTLIER) cc_final: 0.0982 (mpp) REVERT: A 478 LYS cc_start: 0.8810 (ptmt) cc_final: 0.8580 (ptmt) REVERT: A 498 GLU cc_start: 0.6849 (mt-10) cc_final: 0.6582 (mp0) REVERT: A 508 MET cc_start: 0.5027 (pmm) cc_final: 0.4410 (pmm) REVERT: A 525 ARG cc_start: 0.8068 (mtt90) cc_final: 0.7820 (tpp80) REVERT: A 721 LYS cc_start: 0.8263 (mttt) cc_final: 0.7985 (mmmt) REVERT: A 758 ASN cc_start: 0.8581 (t0) cc_final: 0.8146 (t0) REVERT: A 817 THR cc_start: 0.8033 (p) cc_final: 0.7663 (t) REVERT: A 832 LYS cc_start: 0.7841 (tptt) cc_final: 0.7581 (tptt) outliers start: 11 outliers final: 6 residues processed: 109 average time/residue: 0.0795 time to fit residues: 11.1592 Evaluate side-chains 107 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 100 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 MET Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 613 ASP Chi-restraints excluded: chain A residue 636 ILE Chi-restraints excluded: chain A residue 676 VAL Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 835 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 47 optimal weight: 0.7980 chunk 6 optimal weight: 0.0770 chunk 23 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 64 optimal weight: 0.9980 chunk 68 optimal weight: 0.9980 chunk 66 optimal weight: 0.2980 chunk 14 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 2 optimal weight: 0.9980 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 HIS A 820 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.169136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.129892 restraints weight = 8358.354| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 2.22 r_work: 0.3446 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3271 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3269 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3269 r_free = 0.3269 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3270 r_free = 0.3270 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3270 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6064 Z= 0.162 Angle : 0.516 6.769 8181 Z= 0.282 Chirality : 0.038 0.133 908 Planarity : 0.003 0.039 1028 Dihedral : 3.656 15.954 787 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 1.53 % Allowed : 16.67 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.33), residues: 704 helix: 1.76 (0.24), residues: 496 sheet: None (None), residues: 0 loop : -1.44 (0.44), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 587 TYR 0.014 0.001 TYR A 684 PHE 0.014 0.001 PHE A 798 TRP 0.009 0.001 TRP A 258 HIS 0.005 0.001 HIS A 802 Details of bonding type rmsd covalent geometry : bond 0.00375 ( 6064) covalent geometry : angle 0.51625 ( 8181) hydrogen bonds : bond 0.06074 ( 343) hydrogen bonds : angle 3.69114 ( 999) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 102 time to evaluate : 0.133 Fit side-chains REVERT: A 112 ASN cc_start: 0.7602 (t0) cc_final: 0.7277 (t0) REVERT: A 244 ASP cc_start: 0.7836 (p0) cc_final: 0.7524 (p0) REVERT: A 308 MET cc_start: 0.2018 (OUTLIER) cc_final: 0.1037 (mpp) REVERT: A 350 TYR cc_start: 0.8783 (t80) cc_final: 0.8464 (t80) REVERT: A 477 PHE cc_start: 0.8521 (p90) cc_final: 0.8286 (p90) REVERT: A 478 LYS cc_start: 0.8812 (ptmt) cc_final: 0.8602 (ptmt) REVERT: A 498 GLU cc_start: 0.6892 (mt-10) cc_final: 0.6612 (mp0) REVERT: A 508 MET cc_start: 0.5034 (pmm) cc_final: 0.4422 (pmm) REVERT: A 525 ARG cc_start: 0.8054 (mtt90) cc_final: 0.7828 (mtt-85) REVERT: A 721 LYS cc_start: 0.8250 (mttt) cc_final: 0.8014 (mmtt) REVERT: A 758 ASN cc_start: 0.8610 (t0) cc_final: 0.8184 (t0) REVERT: A 817 THR cc_start: 0.7862 (p) cc_final: 0.7504 (t) REVERT: A 832 LYS cc_start: 0.7853 (tptt) cc_final: 0.7642 (tptt) outliers start: 10 outliers final: 7 residues processed: 107 average time/residue: 0.0740 time to fit residues: 10.0063 Evaluate side-chains 109 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 101 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 MET Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 636 ILE Chi-restraints excluded: chain A residue 676 VAL Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 820 GLN Chi-restraints excluded: chain A residue 835 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 7 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 chunk 42 optimal weight: 0.6980 chunk 44 optimal weight: 0.5980 chunk 40 optimal weight: 0.0970 chunk 3 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 70 optimal weight: 0.0980 chunk 69 optimal weight: 0.2980 chunk 24 optimal weight: 0.6980 overall best weight: 0.3578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.171666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.132598 restraints weight = 8443.042| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 2.24 r_work: 0.3477 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3305 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3294 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3294 r_free = 0.3294 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3294 r_free = 0.3294 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3294 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6064 Z= 0.137 Angle : 0.506 6.485 8181 Z= 0.277 Chirality : 0.038 0.133 908 Planarity : 0.003 0.039 1028 Dihedral : 3.615 15.686 787 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.07 % Allowed : 16.97 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.33), residues: 704 helix: 1.88 (0.24), residues: 494 sheet: None (None), residues: 0 loop : -1.36 (0.43), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 587 TYR 0.025 0.001 TYR A 176 PHE 0.012 0.001 PHE A 798 TRP 0.011 0.001 TRP A 258 HIS 0.005 0.001 HIS A 802 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 6064) covalent geometry : angle 0.50568 ( 8181) hydrogen bonds : bond 0.05511 ( 343) hydrogen bonds : angle 3.61537 ( 999) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 101 time to evaluate : 0.226 Fit side-chains REVERT: A 112 ASN cc_start: 0.7498 (t0) cc_final: 0.7195 (t0) REVERT: A 170 ARG cc_start: 0.7575 (tpt-90) cc_final: 0.7278 (tpt-90) REVERT: A 244 ASP cc_start: 0.7816 (p0) cc_final: 0.7502 (p0) REVERT: A 308 MET cc_start: 0.1926 (OUTLIER) cc_final: 0.0951 (mpp) REVERT: A 350 TYR cc_start: 0.8736 (t80) cc_final: 0.8398 (t80) REVERT: A 478 LYS cc_start: 0.8797 (ptmt) cc_final: 0.8591 (ptmt) REVERT: A 498 GLU cc_start: 0.6860 (mt-10) cc_final: 0.6575 (mp0) REVERT: A 508 MET cc_start: 0.5019 (pmm) cc_final: 0.4409 (pmm) REVERT: A 525 ARG cc_start: 0.8085 (mtt90) cc_final: 0.7872 (mtt-85) REVERT: A 721 LYS cc_start: 0.8225 (mttt) cc_final: 0.8010 (mmtt) REVERT: A 758 ASN cc_start: 0.8620 (t0) cc_final: 0.8168 (t0) REVERT: A 817 THR cc_start: 0.7839 (p) cc_final: 0.7497 (t) outliers start: 7 outliers final: 4 residues processed: 105 average time/residue: 0.0760 time to fit residues: 10.0944 Evaluate side-chains 106 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 101 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 MET Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 676 VAL Chi-restraints excluded: chain A residue 835 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 48 optimal weight: 0.0270 chunk 69 optimal weight: 0.0980 chunk 64 optimal weight: 0.2980 chunk 15 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 51 optimal weight: 0.0980 chunk 9 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 overall best weight: 0.2238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 HIS A 820 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.173543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.134978 restraints weight = 8387.101| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 2.19 r_work: 0.3518 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3349 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3336 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3336 r_free = 0.3336 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3336 r_free = 0.3336 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3336 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6064 Z= 0.122 Angle : 0.517 9.031 8181 Z= 0.281 Chirality : 0.037 0.136 908 Planarity : 0.003 0.040 1028 Dihedral : 3.536 15.499 787 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.61 % Allowed : 18.50 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.54 (0.33), residues: 704 helix: 1.99 (0.24), residues: 497 sheet: None (None), residues: 0 loop : -1.44 (0.43), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 587 TYR 0.026 0.001 TYR A 176 PHE 0.035 0.001 PHE A 477 TRP 0.013 0.001 TRP A 258 HIS 0.005 0.001 HIS A 197 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 6064) covalent geometry : angle 0.51669 ( 8181) hydrogen bonds : bond 0.04748 ( 343) hydrogen bonds : angle 3.51130 ( 999) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 104 time to evaluate : 0.146 Fit side-chains REVERT: A 112 ASN cc_start: 0.7153 (t0) cc_final: 0.6927 (t0) REVERT: A 170 ARG cc_start: 0.7550 (tpt-90) cc_final: 0.7256 (tpt-90) REVERT: A 244 ASP cc_start: 0.7791 (p0) cc_final: 0.7481 (p0) REVERT: A 294 ARG cc_start: 0.7938 (tpp80) cc_final: 0.7685 (tpp80) REVERT: A 308 MET cc_start: 0.2203 (OUTLIER) cc_final: 0.1199 (mpp) REVERT: A 350 TYR cc_start: 0.8679 (t80) cc_final: 0.8388 (t80) REVERT: A 478 LYS cc_start: 0.8804 (ptmt) cc_final: 0.8588 (ptmt) REVERT: A 498 GLU cc_start: 0.6842 (mt-10) cc_final: 0.6640 (mp0) REVERT: A 508 MET cc_start: 0.5014 (pmm) cc_final: 0.4403 (pmm) REVERT: A 758 ASN cc_start: 0.8598 (t0) cc_final: 0.8139 (t0) REVERT: A 817 THR cc_start: 0.7842 (p) cc_final: 0.7522 (t) REVERT: A 832 LYS cc_start: 0.7760 (tptt) cc_final: 0.7458 (tptt) outliers start: 4 outliers final: 2 residues processed: 106 average time/residue: 0.0879 time to fit residues: 11.4474 Evaluate side-chains 105 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 102 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 MET Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 820 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 46 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 39 optimal weight: 0.5980 chunk 6 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 24 optimal weight: 0.0060 chunk 30 optimal weight: 0.5980 chunk 31 optimal weight: 0.3980 chunk 62 optimal weight: 0.0980 chunk 37 optimal weight: 0.6980 chunk 29 optimal weight: 20.0000 overall best weight: 0.3396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.173002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.133867 restraints weight = 8372.949| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 2.21 r_work: 0.3505 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3333 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3324 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3324 r_free = 0.3324 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3324 r_free = 0.3324 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3324 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6064 Z= 0.136 Angle : 0.529 8.270 8181 Z= 0.286 Chirality : 0.038 0.142 908 Planarity : 0.003 0.039 1028 Dihedral : 3.532 15.334 787 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.76 % Allowed : 18.65 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.33), residues: 704 helix: 1.99 (0.24), residues: 497 sheet: None (None), residues: 0 loop : -1.45 (0.43), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 532 TYR 0.027 0.001 TYR A 176 PHE 0.036 0.001 PHE A 477 TRP 0.011 0.001 TRP A 258 HIS 0.005 0.001 HIS A 802 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 6064) covalent geometry : angle 0.52861 ( 8181) hydrogen bonds : bond 0.04930 ( 343) hydrogen bonds : angle 3.52221 ( 999) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1463.06 seconds wall clock time: 25 minutes 41.84 seconds (1541.84 seconds total)