Starting phenix.real_space_refine on Thu Jul 2 03:24:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ku4_62574/07_2026/9ku4_62574.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ku4_62574/07_2026/9ku4_62574.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ku4_62574/07_2026/9ku4_62574.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ku4_62574/07_2026/9ku4_62574.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ku4_62574/07_2026/9ku4_62574.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ku4_62574/07_2026/9ku4_62574.map" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.042 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: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 39 5.49 5 S 34 5.16 5 C 3831 2.51 5 N 1073 2.21 5 O 1272 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6250 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 5420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 675, 5420 Classifications: {'peptide': 675} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 26, 'TRANS': 648} Chain breaks: 1 Chain: "C" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 829 Classifications: {'RNA': 39} Modifications used: {'rna3p_pur': 20, 'rna3p_pyr': 19} Link IDs: {'rna3p': 38} Chain breaks: 1 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4566 SG CYS B 810 36.339 53.926 77.977 1.00 36.48 S ATOM 4592 SG CYS B 813 36.001 54.004 81.748 1.00 44.13 S ATOM 4911 SG CYS B 864 39.451 54.676 80.129 1.00 48.76 S ATOM 4950 SG CYS B 869 37.865 51.201 80.091 1.00 44.82 S Time building chain proxies: 1.64, per 1000 atoms: 0.26 Number of scatterers: 6250 At special positions: 0 Unit cell: (78.28, 87.4, 99.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 34 16.00 P 39 15.00 O 1272 8.00 N 1073 7.00 C 3831 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: 0.47 Conformation dependent library (CDL) restraints added in 376.2 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B1001 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 869 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 810 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 813 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 864 " Number of angles added : 6 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1286 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 5 sheets defined 52.3% alpha, 12.3% beta 19 base pairs and 31 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'B' and resid 244 through 256 Proline residue: B 253 - end of helix removed outlier: 3.641A pdb=" N LYS B 256 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 284 Processing helix chain 'B' and resid 299 through 315 Processing helix chain 'B' and resid 325 through 329 removed outlier: 4.035A pdb=" N ALA B 329 " --> pdb=" O GLY B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 340 Processing helix chain 'B' and resid 347 through 358 removed outlier: 3.771A pdb=" N LEU B 351 " --> pdb=" O THR B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 377 removed outlier: 3.512A pdb=" N THR B 377 " --> pdb=" O CYS B 374 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 374 through 377' Processing helix chain 'B' and resid 381 through 395 Processing helix chain 'B' and resid 419 through 434 Processing helix chain 'B' and resid 445 through 453 removed outlier: 3.575A pdb=" N LEU B 449 " --> pdb=" O ASN B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 490 removed outlier: 3.611A pdb=" N ILE B 489 " --> pdb=" O LEU B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 496 removed outlier: 3.531A pdb=" N ASN B 495 " --> pdb=" O ASP B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 521 Processing helix chain 'B' and resid 527 through 558 Processing helix chain 'B' and resid 559 through 576 removed outlier: 3.845A pdb=" N ALA B 563 " --> pdb=" O ARG B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 602 removed outlier: 3.850A pdb=" N LYS B 593 " --> pdb=" O ARG B 589 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N GLN B 595 " --> pdb=" O GLU B 591 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N GLU B 596 " --> pdb=" O GLU B 592 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG B 602 " --> pdb=" O GLU B 598 " (cutoff:3.500A) Processing helix chain 'B' and resid 603 through 607 removed outlier: 3.908A pdb=" N GLU B 607 " --> pdb=" O PRO B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 625 removed outlier: 3.837A pdb=" N LEU B 624 " --> pdb=" O GLU B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 650 removed outlier: 3.534A pdb=" N VAL B 640 " --> pdb=" O THR B 636 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ASP B 641 " --> pdb=" O ARG B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 674 through 685 Processing helix chain 'B' and resid 698 through 701 Processing helix chain 'B' and resid 720 through 729 Processing helix chain 'B' and resid 744 through 769 removed outlier: 3.859A pdb=" N ILE B 748 " --> pdb=" O ASN B 744 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS B 759 " --> pdb=" O MET B 755 " (cutoff:3.500A) Processing helix chain 'B' and resid 772 through 794 Processing helix chain 'B' and resid 837 through 840 Processing helix chain 'B' and resid 919 through 923 removed outlier: 3.865A pdb=" N MET B 923 " --> pdb=" O PRO B 920 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 321 through 324 removed outlier: 6.510A pdb=" N VAL B 293 " --> pdb=" O ILE B 344 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N LEU B 346 " --> pdb=" O VAL B 293 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N PHE B 295 " --> pdb=" O LEU B 346 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR B 260 " --> pdb=" O VAL B 405 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ILE B 261 " --> pdb=" O ALA B 440 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 457 through 462 removed outlier: 6.126A pdb=" N GLN B 457 " --> pdb=" O CYS B 738 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N LEU B 740 " --> pdb=" O GLN B 457 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N PHE B 459 " --> pdb=" O LEU B 740 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N THR B 742 " --> pdb=" O PHE B 459 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ARG B 461 " --> pdb=" O THR B 742 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N VAL B 712 " --> pdb=" O PHE B 739 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N LEU B 741 " --> pdb=" O VAL B 712 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N LEU B 714 " --> pdb=" O LEU B 741 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N GLY B 659 " --> pdb=" O ILE B 695 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 816 through 819 removed outlier: 6.990A pdb=" N LEU B 808 " --> pdb=" O ALA B 817 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N TYR B 819 " --> pdb=" O LYS B 806 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N LYS B 806 " --> pdb=" O TYR B 819 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 830 through 833 removed outlier: 4.474A pdb=" N ILE B 916 " --> pdb=" O VAL B 823 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 842 through 845 removed outlier: 6.680A pdb=" N ILE B 862 " --> pdb=" O TRP B 873 " (cutoff:3.500A) 278 hydrogen bonds defined for protein. 807 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 47 hydrogen bonds 94 hydrogen bond angles 0 basepair planarities 19 basepair parallelities 31 stacking parallelities Total time for adding SS restraints: 1.35 Time building geometry restraints manager: 0.68 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: 1710 1.34 - 1.45: 1218 1.45 - 1.57: 3400 1.57 - 1.69: 76 1.69 - 1.81: 48 Bond restraints: 6452 Sorted by residual: bond pdb=" N GLY B 703 " pdb=" CA GLY B 703 " ideal model delta sigma weight residual 1.449 1.464 -0.015 1.45e-02 4.76e+03 1.08e+00 bond pdb=" CB GLU B 581 " pdb=" CG GLU B 581 " ideal model delta sigma weight residual 1.520 1.545 -0.025 3.00e-02 1.11e+03 6.96e-01 bond pdb=" N1 U C 8 " pdb=" C2 U C 8 " ideal model delta sigma weight residual 1.381 1.388 -0.007 9.00e-03 1.23e+04 5.60e-01 bond pdb=" N1 U C 57 " pdb=" C2 U C 57 " ideal model delta sigma weight residual 1.381 1.388 -0.007 9.00e-03 1.23e+04 5.42e-01 bond pdb=" N1 C C 24 " pdb=" C2 C C 24 " ideal model delta sigma weight residual 1.397 1.404 -0.007 1.00e-02 1.00e+04 5.03e-01 ... (remaining 6447 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.18: 8656 1.18 - 2.35: 183 2.35 - 3.53: 34 3.53 - 4.71: 11 4.71 - 5.89: 2 Bond angle restraints: 8886 Sorted by residual: angle pdb=" C1' U C 8 " pdb=" N1 U C 8 " pdb=" C2 U C 8 " ideal model delta sigma weight residual 117.70 121.30 -3.60 1.20e+00 6.94e-01 9.00e+00 angle pdb=" C1' C C 24 " pdb=" N1 C C 24 " pdb=" C2 C C 24 " ideal model delta sigma weight residual 118.80 121.77 -2.97 1.10e+00 8.26e-01 7.28e+00 angle pdb=" CA GLU B 581 " pdb=" CB GLU B 581 " pdb=" CG GLU B 581 " ideal model delta sigma weight residual 114.10 119.27 -5.17 2.00e+00 2.50e-01 6.68e+00 angle pdb=" CB GLU B 581 " pdb=" CG GLU B 581 " pdb=" CD GLU B 581 " ideal model delta sigma weight residual 112.60 116.42 -3.82 1.70e+00 3.46e-01 5.05e+00 angle pdb=" C1' U C 8 " pdb=" N1 U C 8 " pdb=" C6 U C 8 " ideal model delta sigma weight residual 121.20 118.18 3.02 1.40e+00 5.10e-01 4.66e+00 ... (remaining 8881 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.42: 3293 17.42 - 34.85: 430 34.85 - 52.27: 168 52.27 - 69.69: 74 69.69 - 87.12: 18 Dihedral angle restraints: 3983 sinusoidal: 2003 harmonic: 1980 Sorted by residual: dihedral pdb=" CA LEU B 346 " pdb=" C LEU B 346 " pdb=" N THR B 347 " pdb=" CA THR B 347 " ideal model delta harmonic sigma weight residual 180.00 159.08 20.92 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" CG ARG B 488 " pdb=" CD ARG B 488 " pdb=" NE ARG B 488 " pdb=" CZ ARG B 488 " ideal model delta sinusoidal sigma weight residual -90.00 -39.95 -50.05 2 1.50e+01 4.44e-03 1.25e+01 dihedral pdb=" CA ASP B 580 " pdb=" CB ASP B 580 " pdb=" CG ASP B 580 " pdb=" OD1 ASP B 580 " ideal model delta sinusoidal sigma weight residual -30.00 -84.63 54.63 1 2.00e+01 2.50e-03 1.01e+01 ... (remaining 3980 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 672 0.029 - 0.059: 234 0.059 - 0.088: 66 0.088 - 0.118: 42 0.118 - 0.147: 11 Chirality restraints: 1025 Sorted by residual: chirality pdb=" CA VAL B 332 " pdb=" N VAL B 332 " pdb=" C VAL B 332 " pdb=" CB VAL B 332 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.41e-01 chirality pdb=" CA ILE B 406 " pdb=" N ILE B 406 " pdb=" C ILE B 406 " pdb=" CB ILE B 406 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.88e-01 chirality pdb=" CA ILE B 629 " pdb=" N ILE B 629 " pdb=" C ILE B 629 " pdb=" CB ILE B 629 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.34e-01 ... (remaining 1022 not shown) Planarity restraints: 994 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL B 522 " 0.008 2.00e-02 2.50e+03 1.51e-02 2.29e+00 pdb=" C VAL B 522 " -0.026 2.00e-02 2.50e+03 pdb=" O VAL B 522 " 0.010 2.00e-02 2.50e+03 pdb=" N PHE B 523 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET B 525 " 0.023 5.00e-02 4.00e+02 3.55e-02 2.01e+00 pdb=" N PRO B 526 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO B 526 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 526 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 332 " 0.023 5.00e-02 4.00e+02 3.48e-02 1.94e+00 pdb=" N PRO B 333 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO B 333 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 333 " 0.019 5.00e-02 4.00e+02 ... (remaining 991 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1060 2.77 - 3.31: 5384 3.31 - 3.84: 10672 3.84 - 4.37: 12355 4.37 - 4.90: 20390 Nonbonded interactions: 49861 Sorted by model distance: nonbonded pdb=" O THR B 328 " pdb=" OG1 THR B 328 " model vdw 2.242 3.040 nonbonded pdb=" N GLU B 581 " pdb=" OE1 GLU B 581 " model vdw 2.272 3.120 nonbonded pdb=" OG SER B 698 " pdb=" O2' U C 54 " model vdw 2.299 3.040 nonbonded pdb=" NE2 GLN B 524 " pdb=" O GLY B 900 " model vdw 2.342 3.120 nonbonded pdb=" O ASN B 625 " pdb=" OG1 THR B 628 " model vdw 2.362 3.040 ... (remaining 49856 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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 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: 1.570 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: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.070 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 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 : 0.002 0.025 6456 Z= 0.119 Angle : 0.459 5.886 8892 Z= 0.300 Chirality : 0.039 0.147 1025 Planarity : 0.004 0.035 994 Dihedral : 19.521 87.117 2697 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.33 % Allowed : 27.41 % Favored : 71.26 % 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: 1.88 (0.32), residues: 671 helix: 2.58 (0.30), residues: 310 sheet: 1.39 (0.47), residues: 116 loop : -0.63 (0.35), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 488 TYR 0.011 0.001 TYR B 566 PHE 0.008 0.001 PHE B 579 TRP 0.004 0.001 TRP B 771 HIS 0.003 0.001 HIS B 381 Details of bonding type rmsd/Z covalent geometry : bond 0.00200 / 0.12 ( 6452) covalent geometry : angle 0.45740 / 0.30 ( 8886) hydrogen bonds : bond 0.14829 / 9.93 ( 325) hydrogen bonds : angle 4.75386 / 3.28 ( 901) metal coordination : bond 0.00540 / 0.27 ( 4) metal coordination : angle 1.68385 / 1.00 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 81 time to evaluate : 0.265 Fit side-chains revert: symmetry clash REVERT: B 339 GLU cc_start: 0.7545 (tp30) cc_final: 0.7205 (tp30) outliers start: 8 outliers final: 5 residues processed: 87 average time/residue: 0.6656 time to fit residues: 60.2137 Evaluate side-chains 87 residues out of total 602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 82 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 909 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 49 optimal weight: 6.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 8.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 0.0870 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 0.0040 chunk 27 optimal weight: 0.6980 overall best weight: 0.5170 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 336 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.152944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.115481 restraints weight = 5372.347| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 1.58 r_work: 0.3261 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.0513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 6456 Z= 0.104 Angle : 0.431 4.656 8892 Z= 0.243 Chirality : 0.039 0.153 1025 Planarity : 0.004 0.047 994 Dihedral : 14.607 73.679 1323 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.82 % Allowed : 23.59 % Favored : 73.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.15 (0.32), residues: 671 helix: 2.76 (0.30), residues: 314 sheet: 1.56 (0.47), residues: 115 loop : -0.49 (0.36), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 488 TYR 0.010 0.001 TYR B 566 PHE 0.010 0.001 PHE B 295 TRP 0.003 0.000 TRP B 771 HIS 0.002 0.001 HIS B 876 Details of bonding type rmsd/Z covalent geometry : bond 0.00187 / 0.10 ( 6452) covalent geometry : angle 0.42842 / 0.24 ( 8886) hydrogen bonds : bond 0.05232 / 3.51 ( 325) hydrogen bonds : angle 3.85651 / 2.69 ( 901) metal coordination : bond 0.00526 / 0.26 ( 4) metal coordination : angle 2.01069 / 1.22 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 84 time to evaluate : 0.233 Fit side-chains REVERT: B 339 GLU cc_start: 0.7848 (tp30) cc_final: 0.7428 (tp30) REVERT: B 451 GLN cc_start: 0.7693 (tp40) cc_final: 0.7403 (mm110) REVERT: B 811 ARG cc_start: 0.8697 (OUTLIER) cc_final: 0.7575 (ttt180) REVERT: B 896 ASP cc_start: 0.8125 (OUTLIER) cc_final: 0.7723 (m-30) outliers start: 17 outliers final: 9 residues processed: 91 average time/residue: 0.6614 time to fit residues: 62.6072 Evaluate side-chains 91 residues out of total 602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 80 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 457 GLN Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 673 MET Chi-restraints excluded: chain B residue 780 ILE Chi-restraints excluded: chain B residue 811 ARG Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 829 CYS Chi-restraints excluded: chain B residue 896 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 35 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 39 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 chunk 28 optimal weight: 0.0270 chunk 37 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 46 optimal weight: 0.1980 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 336 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.153236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.116048 restraints weight = 5299.474| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 1.56 r_work: 0.3267 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.0652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 6456 Z= 0.096 Angle : 0.417 4.684 8892 Z= 0.234 Chirality : 0.039 0.143 1025 Planarity : 0.004 0.047 994 Dihedral : 14.505 73.723 1318 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.49 % Allowed : 23.92 % Favored : 73.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.21 (0.33), residues: 671 helix: 2.82 (0.29), residues: 315 sheet: 1.50 (0.48), residues: 115 loop : -0.44 (0.37), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 488 TYR 0.011 0.001 TYR B 246 PHE 0.008 0.001 PHE B 295 TRP 0.003 0.000 TRP B 771 HIS 0.002 0.001 HIS B 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00179 / 0.10 ( 6452) covalent geometry : angle 0.41505 / 0.23 ( 8886) hydrogen bonds : bond 0.04691 / 3.15 ( 325) hydrogen bonds : angle 3.66246 / 2.56 ( 901) metal coordination : bond 0.00540 / 0.27 ( 4) metal coordination : angle 1.66710 / 0.97 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 82 time to evaluate : 0.181 Fit side-chains REVERT: B 339 GLU cc_start: 0.7822 (tp30) cc_final: 0.7426 (tp30) REVERT: B 451 GLN cc_start: 0.7680 (tp40) cc_final: 0.7389 (mm110) REVERT: B 811 ARG cc_start: 0.8708 (OUTLIER) cc_final: 0.7677 (ttt180) REVERT: B 896 ASP cc_start: 0.8115 (OUTLIER) cc_final: 0.7720 (m-30) outliers start: 15 outliers final: 6 residues processed: 89 average time/residue: 0.7018 time to fit residues: 64.9231 Evaluate side-chains 88 residues out of total 602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 80 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 457 GLN Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 673 MET Chi-restraints excluded: chain B residue 780 ILE Chi-restraints excluded: chain B residue 811 ARG Chi-restraints excluded: chain B residue 829 CYS Chi-restraints excluded: chain B residue 896 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 13 optimal weight: 5.9990 chunk 2 optimal weight: 6.9990 chunk 49 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 34 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 chunk 41 optimal weight: 4.9990 chunk 65 optimal weight: 6.9990 chunk 69 optimal weight: 10.9990 chunk 11 optimal weight: 5.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 336 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.148722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.110094 restraints weight = 5357.503| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 1.60 r_work: 0.3183 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.0817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6456 Z= 0.147 Angle : 0.495 5.438 8892 Z= 0.276 Chirality : 0.043 0.158 1025 Planarity : 0.004 0.046 994 Dihedral : 14.509 73.827 1316 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 3.16 % Allowed : 22.59 % Favored : 74.25 % 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: 1.99 (0.32), residues: 671 helix: 2.65 (0.29), residues: 315 sheet: 1.35 (0.47), residues: 115 loop : -0.54 (0.37), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 316 TYR 0.017 0.002 TYR B 246 PHE 0.013 0.002 PHE B 295 TRP 0.007 0.001 TRP B 771 HIS 0.004 0.001 HIS B 381 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.15 ( 6452) covalent geometry : angle 0.49261 / 0.28 ( 8886) hydrogen bonds : bond 0.06165 / 4.14 ( 325) hydrogen bonds : angle 3.78716 / 2.64 ( 901) metal coordination : bond 0.00890 / 0.47 ( 4) metal coordination : angle 1.96699 / 1.31 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 83 time to evaluate : 0.221 Fit side-chains REVERT: B 339 GLU cc_start: 0.7857 (tp30) cc_final: 0.7462 (tp30) REVERT: B 451 GLN cc_start: 0.7710 (tp40) cc_final: 0.7399 (mm110) REVERT: B 896 ASP cc_start: 0.8140 (OUTLIER) cc_final: 0.7720 (m-30) outliers start: 19 outliers final: 8 residues processed: 92 average time/residue: 0.6870 time to fit residues: 65.7346 Evaluate side-chains 90 residues out of total 602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 81 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 457 GLN Chi-restraints excluded: chain B residue 492 ASP Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 673 MET Chi-restraints excluded: chain B residue 780 ILE Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 829 CYS Chi-restraints excluded: chain B residue 896 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 68 optimal weight: 10.0000 chunk 69 optimal weight: 10.0000 chunk 47 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 60 optimal weight: 0.0370 chunk 59 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 overall best weight: 0.9460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 336 GLN B 805 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.150678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.112212 restraints weight = 5532.288| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 1.62 r_work: 0.3204 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.0798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 6456 Z= 0.108 Angle : 0.441 6.051 8892 Z= 0.248 Chirality : 0.040 0.146 1025 Planarity : 0.004 0.045 994 Dihedral : 14.423 73.805 1316 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.99 % Allowed : 23.42 % Favored : 74.58 % 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: 2.01 (0.32), residues: 671 helix: 2.72 (0.29), residues: 315 sheet: 1.26 (0.47), residues: 115 loop : -0.56 (0.37), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 488 TYR 0.012 0.001 TYR B 246 PHE 0.009 0.001 PHE B 295 TRP 0.004 0.001 TRP B 771 HIS 0.003 0.001 HIS B 876 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.11 ( 6452) covalent geometry : angle 0.43805 / 0.25 ( 8886) hydrogen bonds : bond 0.05130 / 3.43 ( 325) hydrogen bonds : angle 3.64953 / 2.55 ( 901) metal coordination : bond 0.00620 / 0.31 ( 4) metal coordination : angle 1.87886 / 1.16 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 82 time to evaluate : 0.226 Fit side-chains REVERT: B 339 GLU cc_start: 0.7836 (tp30) cc_final: 0.7451 (tp30) REVERT: B 451 GLN cc_start: 0.7671 (tp40) cc_final: 0.7363 (mm110) REVERT: B 811 ARG cc_start: 0.8759 (OUTLIER) cc_final: 0.7621 (ttt180) REVERT: B 896 ASP cc_start: 0.8123 (OUTLIER) cc_final: 0.7740 (m-30) outliers start: 12 outliers final: 6 residues processed: 87 average time/residue: 0.6920 time to fit residues: 62.6246 Evaluate side-chains 88 residues out of total 602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 80 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 457 GLN Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 673 MET Chi-restraints excluded: chain B residue 780 ILE Chi-restraints excluded: chain B residue 811 ARG Chi-restraints excluded: chain B residue 829 CYS Chi-restraints excluded: chain B residue 896 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 3 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 8 optimal weight: 7.9990 chunk 14 optimal weight: 2.9990 chunk 63 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 336 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.149812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.111298 restraints weight = 5398.930| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 1.60 r_work: 0.3190 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.0890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6456 Z= 0.121 Angle : 0.452 4.684 8892 Z= 0.253 Chirality : 0.041 0.152 1025 Planarity : 0.004 0.045 994 Dihedral : 14.427 73.904 1316 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.66 % Allowed : 22.92 % Favored : 74.42 % 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: 1.94 (0.32), residues: 671 helix: 2.69 (0.29), residues: 315 sheet: 1.17 (0.47), residues: 115 loop : -0.62 (0.37), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 488 TYR 0.014 0.001 TYR B 246 PHE 0.011 0.001 PHE B 295 TRP 0.003 0.001 TRP B 771 HIS 0.003 0.001 HIS B 381 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.12 ( 6452) covalent geometry : angle 0.44950 / 0.25 ( 8886) hydrogen bonds : bond 0.05421 / 3.63 ( 325) hydrogen bonds : angle 3.65373 / 2.55 ( 901) metal coordination : bond 0.00740 / 0.38 ( 4) metal coordination : angle 1.84069 / 1.17 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 81 time to evaluate : 0.242 Fit side-chains REVERT: B 339 GLU cc_start: 0.7825 (tp30) cc_final: 0.7445 (tp30) REVERT: B 451 GLN cc_start: 0.7676 (tp40) cc_final: 0.7383 (mm110) REVERT: B 896 ASP cc_start: 0.8129 (OUTLIER) cc_final: 0.7710 (m-30) outliers start: 16 outliers final: 9 residues processed: 90 average time/residue: 0.6764 time to fit residues: 63.3290 Evaluate side-chains 91 residues out of total 602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 81 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 457 GLN Chi-restraints excluded: chain B residue 492 ASP Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 673 MET Chi-restraints excluded: chain B residue 780 ILE Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 829 CYS Chi-restraints excluded: chain B residue 896 ASP Chi-restraints excluded: chain B residue 909 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 11 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 chunk 28 optimal weight: 7.9990 chunk 22 optimal weight: 9.9990 chunk 60 optimal weight: 0.7980 chunk 20 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 52 optimal weight: 4.9990 chunk 55 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 336 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.150736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.112317 restraints weight = 5415.277| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 1.60 r_work: 0.3205 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.0893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 6456 Z= 0.109 Angle : 0.436 5.585 8892 Z= 0.245 Chirality : 0.040 0.148 1025 Planarity : 0.004 0.045 994 Dihedral : 14.397 73.844 1316 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.99 % Allowed : 24.09 % Favored : 73.92 % 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: 1.97 (0.32), residues: 671 helix: 2.73 (0.29), residues: 315 sheet: 1.12 (0.47), residues: 115 loop : -0.59 (0.37), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 488 TYR 0.012 0.001 TYR B 246 PHE 0.009 0.001 PHE B 295 TRP 0.004 0.001 TRP B 771 HIS 0.003 0.001 HIS B 876 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.11 ( 6452) covalent geometry : angle 0.43328 / 0.24 ( 8886) hydrogen bonds : bond 0.05067 / 3.39 ( 325) hydrogen bonds : angle 3.60031 / 2.51 ( 901) metal coordination : bond 0.00663 / 0.34 ( 4) metal coordination : angle 1.83657 / 1.15 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 82 time to evaluate : 0.223 Fit side-chains REVERT: B 339 GLU cc_start: 0.7823 (tp30) cc_final: 0.7444 (tp30) REVERT: B 451 GLN cc_start: 0.7656 (tp40) cc_final: 0.7351 (mm110) REVERT: B 804 GLU cc_start: 0.7622 (OUTLIER) cc_final: 0.7287 (tp30) REVERT: B 896 ASP cc_start: 0.8122 (OUTLIER) cc_final: 0.7721 (m-30) outliers start: 12 outliers final: 9 residues processed: 87 average time/residue: 0.6195 time to fit residues: 56.1530 Evaluate side-chains 91 residues out of total 602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 80 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 457 GLN Chi-restraints excluded: chain B residue 492 ASP Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 673 MET Chi-restraints excluded: chain B residue 780 ILE Chi-restraints excluded: chain B residue 804 GLU Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 829 CYS Chi-restraints excluded: chain B residue 896 ASP Chi-restraints excluded: chain B residue 909 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 33 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 chunk 57 optimal weight: 0.9980 chunk 46 optimal weight: 5.9990 chunk 15 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 56 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 336 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.151311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.112856 restraints weight = 5510.878| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 1.61 r_work: 0.3213 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.0903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 6456 Z= 0.104 Angle : 0.426 5.016 8892 Z= 0.240 Chirality : 0.039 0.149 1025 Planarity : 0.004 0.044 994 Dihedral : 14.381 73.792 1316 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.82 % Allowed : 23.09 % Favored : 74.09 % 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: 1.99 (0.32), residues: 671 helix: 2.76 (0.29), residues: 315 sheet: 1.13 (0.47), residues: 115 loop : -0.58 (0.37), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 488 TYR 0.012 0.001 TYR B 246 PHE 0.009 0.001 PHE B 295 TRP 0.005 0.001 TRP B 771 HIS 0.002 0.001 HIS B 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00201 / 0.10 ( 6452) covalent geometry : angle 0.42399 / 0.24 ( 8886) hydrogen bonds : bond 0.04813 / 3.21 ( 325) hydrogen bonds : angle 3.55314 / 2.48 ( 901) metal coordination : bond 0.00634 / 0.32 ( 4) metal coordination : angle 1.78254 / 1.10 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 80 time to evaluate : 0.149 Fit side-chains REVERT: B 339 GLU cc_start: 0.7787 (tp30) cc_final: 0.7433 (tp30) REVERT: B 451 GLN cc_start: 0.7629 (tp40) cc_final: 0.7332 (mm110) REVERT: B 612 GLU cc_start: 0.7332 (mt-10) cc_final: 0.7066 (mt-10) REVERT: B 804 GLU cc_start: 0.7611 (OUTLIER) cc_final: 0.7283 (tp30) REVERT: B 811 ARG cc_start: 0.8751 (OUTLIER) cc_final: 0.7658 (ttt180) REVERT: B 896 ASP cc_start: 0.8112 (OUTLIER) cc_final: 0.7739 (m-30) outliers start: 17 outliers final: 9 residues processed: 90 average time/residue: 0.6672 time to fit residues: 62.5044 Evaluate side-chains 91 residues out of total 602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 79 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 457 GLN Chi-restraints excluded: chain B residue 492 ASP Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 673 MET Chi-restraints excluded: chain B residue 780 ILE Chi-restraints excluded: chain B residue 804 GLU Chi-restraints excluded: chain B residue 811 ARG Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 829 CYS Chi-restraints excluded: chain B residue 896 ASP Chi-restraints excluded: chain B residue 909 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 49 optimal weight: 8.9990 chunk 27 optimal weight: 0.8980 chunk 63 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 69 optimal weight: 10.0000 chunk 10 optimal weight: 7.9990 chunk 17 optimal weight: 7.9990 chunk 13 optimal weight: 4.9990 chunk 64 optimal weight: 4.9990 chunk 1 optimal weight: 0.8980 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 336 GLN B 670 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.148129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.109091 restraints weight = 5482.133| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 1.62 r_work: 0.3160 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.0992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6456 Z= 0.159 Angle : 0.514 5.950 8892 Z= 0.286 Chirality : 0.043 0.159 1025 Planarity : 0.005 0.046 994 Dihedral : 14.472 74.080 1316 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.33 % Allowed : 23.26 % Favored : 74.42 % 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: 1.73 (0.32), residues: 671 helix: 2.47 (0.29), residues: 319 sheet: 1.00 (0.47), residues: 116 loop : -0.67 (0.37), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 488 TYR 0.017 0.002 TYR B 246 PHE 0.013 0.002 PHE B 842 TRP 0.013 0.001 TRP B 771 HIS 0.003 0.001 HIS B 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.16 ( 6452) covalent geometry : angle 0.51123 / 0.29 ( 8886) hydrogen bonds : bond 0.06384 / 4.28 ( 325) hydrogen bonds : angle 3.77769 / 2.63 ( 901) metal coordination : bond 0.01016 / 0.53 ( 4) metal coordination : angle 2.06862 / 1.39 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 81 time to evaluate : 0.161 Fit side-chains REVERT: B 339 GLU cc_start: 0.7726 (tp30) cc_final: 0.7400 (tp30) REVERT: B 451 GLN cc_start: 0.7647 (tp40) cc_final: 0.7332 (mm110) REVERT: B 804 GLU cc_start: 0.7630 (mp0) cc_final: 0.7256 (tp30) REVERT: B 896 ASP cc_start: 0.8138 (OUTLIER) cc_final: 0.7722 (m-30) outliers start: 14 outliers final: 9 residues processed: 88 average time/residue: 0.6705 time to fit residues: 61.4094 Evaluate side-chains 88 residues out of total 602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 78 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 457 GLN Chi-restraints excluded: chain B residue 492 ASP Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 673 MET Chi-restraints excluded: chain B residue 780 ILE Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 829 CYS Chi-restraints excluded: chain B residue 896 ASP Chi-restraints excluded: chain B residue 909 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 40 optimal weight: 1.9990 chunk 50 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 1 optimal weight: 0.0270 chunk 51 optimal weight: 0.7980 overall best weight: 1.1644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 336 GLN B 670 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.150089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.111243 restraints weight = 5419.662| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 1.62 r_work: 0.3190 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.0954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 6456 Z= 0.117 Angle : 0.456 5.632 8892 Z= 0.256 Chirality : 0.040 0.151 1025 Planarity : 0.004 0.044 994 Dihedral : 14.393 73.952 1316 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.99 % Allowed : 23.92 % Favored : 74.09 % 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: 1.82 (0.32), residues: 671 helix: 2.63 (0.29), residues: 315 sheet: 0.98 (0.47), residues: 116 loop : -0.65 (0.37), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 488 TYR 0.013 0.001 TYR B 246 PHE 0.010 0.001 PHE B 295 TRP 0.011 0.001 TRP B 771 HIS 0.003 0.001 HIS B 381 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.12 ( 6452) covalent geometry : angle 0.45335 / 0.26 ( 8886) hydrogen bonds : bond 0.05386 / 3.59 ( 325) hydrogen bonds : angle 3.66213 / 2.56 ( 901) metal coordination : bond 0.00683 / 0.34 ( 4) metal coordination : angle 1.91153 / 1.19 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 79 time to evaluate : 0.263 Fit side-chains REVERT: B 339 GLU cc_start: 0.7728 (tp30) cc_final: 0.7393 (tp30) REVERT: B 451 GLN cc_start: 0.7615 (tp40) cc_final: 0.7310 (mm110) REVERT: B 612 GLU cc_start: 0.7392 (mt-10) cc_final: 0.7137 (mt-10) REVERT: B 804 GLU cc_start: 0.7642 (mp0) cc_final: 0.7269 (tp30) REVERT: B 896 ASP cc_start: 0.8124 (OUTLIER) cc_final: 0.7713 (m-30) outliers start: 12 outliers final: 8 residues processed: 84 average time/residue: 0.6453 time to fit residues: 56.4368 Evaluate side-chains 88 residues out of total 602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 79 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 457 GLN Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 673 MET Chi-restraints excluded: chain B residue 780 ILE Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 829 CYS Chi-restraints excluded: chain B residue 896 ASP Chi-restraints excluded: chain B residue 909 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 19 optimal weight: 0.2980 chunk 11 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 63 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 336 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.150161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.111329 restraints weight = 5443.453| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 1.61 r_work: 0.3189 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.0978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6456 Z= 0.119 Angle : 0.457 5.809 8892 Z= 0.256 Chirality : 0.041 0.152 1025 Planarity : 0.004 0.044 994 Dihedral : 14.384 73.844 1316 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.50 % Allowed : 24.58 % Favored : 73.92 % 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: 1.83 (0.32), residues: 671 helix: 2.62 (0.29), residues: 315 sheet: 0.98 (0.47), residues: 116 loop : -0.62 (0.37), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 488 TYR 0.014 0.001 TYR B 246 PHE 0.012 0.001 PHE B 579 TRP 0.012 0.001 TRP B 771 HIS 0.003 0.001 HIS B 381 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.12 ( 6452) covalent geometry : angle 0.45424 / 0.26 ( 8886) hydrogen bonds : bond 0.05347 / 3.57 ( 325) hydrogen bonds : angle 3.63614 / 2.54 ( 901) metal coordination : bond 0.00720 / 0.37 ( 4) metal coordination : angle 1.84281 / 1.16 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2747.26 seconds wall clock time: 47 minutes 25.83 seconds (2845.83 seconds total)