Starting phenix.real_space_refine on Tue Aug 4 19:16:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ku4_62574/08_2026/9ku4_62574.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ku4_62574/08_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_62574/08_2026/9ku4_62574.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ku4_62574/08_2026/9ku4_62574.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ku4_62574/08_2026/9ku4_62574.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ku4_62574/08_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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/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: 1.16, per 1000 atoms: 0.19 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: 0.35 Conformation dependent library (CDL) restraints added in 312.9 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: 0.47 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: 0.84 Time building geometry restraints manager: 0.47 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: 8539 1.18 - 2.35: 232 2.35 - 3.53: 102 3.53 - 4.71: 11 4.71 - 5.89: 2 Bond angle restraints: 8886 Sorted by residual: angle pdb=" O5' C C 12 " pdb=" C5' C C 12 " pdb=" C4' C C 12 " ideal model delta sigma weight residual 109.40 112.63 -3.23 8.00e-01 1.56e+00 1.63e+01 angle pdb=" O5' A C 16 " pdb=" C5' A C 16 " pdb=" C4' A C 16 " ideal model delta sigma weight residual 109.40 112.43 -3.03 8.00e-01 1.56e+00 1.44e+01 angle pdb=" O5' A C 53 " pdb=" C5' A C 53 " pdb=" C4' A C 53 " ideal model delta sigma weight residual 109.40 112.36 -2.96 8.00e-01 1.56e+00 1.37e+01 angle pdb=" O5' U C 56 " pdb=" C5' U C 56 " pdb=" C4' U C 56 " ideal model delta sigma weight residual 109.40 112.35 -2.95 8.00e-01 1.56e+00 1.36e+01 angle pdb=" O5' C C 55 " pdb=" C5' C C 55 " pdb=" C4' C C 55 " ideal model delta sigma weight residual 109.40 112.23 -2.83 8.00e-01 1.56e+00 1.25e+01 ... (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 - 0.030: 628 0.030 - 0.059: 231 0.059 - 0.088: 73 0.088 - 0.118: 43 0.118 - 0.147: 50 Chirality restraints: 1025 Sorted by residual: chirality pdb=" C2' A C 16 " pdb=" C3' A C 16 " pdb=" O2' A C 16 " pdb=" C1' A C 16 " both_signs ideal model delta sigma weight residual False -2.62 -2.77 0.15 2.00e-01 2.50e+01 5.43e-01 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=" C2' A C 17 " pdb=" C3' A C 17 " pdb=" O2' A C 17 " pdb=" C1' A C 17 " both_signs ideal model delta sigma weight residual False -2.62 -2.76 0.14 2.00e-01 2.50e+01 5.19e-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: 1.010 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: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.350 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.000 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: 0.010 Load rotamer database and sin/cos tables:6.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.000 ------------------------------------------------------------------------------- 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= 0.126 Angle : 0.540 5.886 8892 Z= 0.377 Chirality : 0.047 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 0.00207 / 0.13 ( 6452) covalent geometry : angle 0.53812 / 0.38 ( 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 : 0.136 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: 0.5287 time to fit residues: 47.9607 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 : 0.214 ------------------------------------------------------------------------------- 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: 1.9990 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 = 0.3827 r_free = 0.3827 target = 0.153238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.115856 restraints weight = 5374.820| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 1.57 r_work: 0.3267 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.0543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 6456 Z= 0.104 Angle : 0.432 4.647 8892 Z= 0.245 Chirality : 0.039 0.154 1025 Planarity : 0.004 0.046 994 Dihedral : 14.582 73.680 1323 Min Nonbonded Distance : 2.595 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: 2.16 (0.32), residues: 671 helix: 2.77 (0.30), residues: 314 sheet: 1.55 (0.47), residues: 115 loop : -0.49 (0.36), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 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 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00184 / 0.10 ( 6452) covalent geometry : angle 0.42889 / 0.24 ( 8886) hydrogen bonds : bond 0.05190 / 3.49 ( 325) hydrogen bonds : angle 3.83942 / 2.68 ( 901) metal coordination : bond 0.00559 / 0.28 ( 4) metal coordination : angle 2.02865 / 1.23 ( 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 : 0.218 Fit side-chains REVERT: B 339 GLU cc_start: 0.7842 (tp30) cc_final: 0.7418 (tp30) REVERT: B 451 GLN cc_start: 0.7687 (tp40) cc_final: 0.7397 (mm110) REVERT: B 811 ARG cc_start: 0.8694 (OUTLIER) cc_final: 0.7674 (ttt180) REVERT: B 896 ASP cc_start: 0.8135 (OUTLIER) cc_final: 0.7733 (m-30) outliers start: 17 outliers final: 9 residues processed: 91 average time/residue: 0.5136 time to fit residues: 48.6230 Evaluate side-chains 94 residues out of total 602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 83 time to evaluate : 0.204 ------------------------------------------------------------------------------- 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: 8.9990 chunk 0 optimal weight: 10.0000 chunk 39 optimal weight: 3.9990 chunk 57 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 chunk 50 optimal weight: 0.4980 chunk 28 optimal weight: 0.7980 chunk 37 optimal weight: 0.6980 chunk 40 optimal weight: 0.6980 chunk 3 optimal weight: 3.9990 chunk 46 optimal weight: 0.4980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3830 r_free = 0.3830 target = 0.153607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.116374 restraints weight = 5301.439| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 1.57 r_work: 0.3270 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.0704 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= 0.097 Angle : 0.417 4.699 8892 Z= 0.235 Chirality : 0.038 0.143 1025 Planarity : 0.004 0.046 994 Dihedral : 14.465 73.876 1318 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.49 % Allowed : 23.59 % 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: 2.22 (0.33), residues: 671 helix: 2.84 (0.29), residues: 315 sheet: 1.47 (0.48), residues: 115 loop : -0.43 (0.38), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 488 TYR 0.011 0.001 TYR B 246 PHE 0.007 0.001 PHE B 471 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 0.00179 / 0.10 ( 6452) covalent geometry : angle 0.41478 / 0.23 ( 8886) hydrogen bonds : bond 0.04693 / 3.15 ( 325) hydrogen bonds : angle 3.62804 / 2.53 ( 901) metal coordination : bond 0.00542 / 0.27 ( 4) metal coordination : angle 1.62939 / 0.94 ( 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 100 residues out of total 602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 85 time to evaluate : 0.161 Fit side-chains revert: symmetry clash REVERT: B 339 GLU cc_start: 0.7806 (tp30) cc_final: 0.7409 (tp30) REVERT: B 451 GLN cc_start: 0.7662 (tp40) cc_final: 0.7372 (mm110) REVERT: B 811 ARG cc_start: 0.8710 (OUTLIER) cc_final: 0.7713 (ttt180) REVERT: B 896 ASP cc_start: 0.8114 (OUTLIER) cc_final: 0.7720 (m-30) outliers start: 15 outliers final: 6 residues processed: 92 average time/residue: 0.5490 time to fit residues: 52.4565 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 : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 457 GLN Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 673 MET Chi-restraints excluded: chain B residue 679 LYS 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: 7.9990 chunk 3 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 65 optimal weight: 6.9990 chunk 69 optimal weight: 10.0000 chunk 11 optimal weight: 0.6980 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 = 0.3791 r_free = 0.3791 target = 0.150774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.112443 restraints weight = 5378.050| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 1.60 r_work: 0.3213 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.0788 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= 0.119 Angle : 0.456 4.688 8892 Z= 0.256 Chirality : 0.040 0.150 1025 Planarity : 0.004 0.046 994 Dihedral : 14.462 73.914 1316 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % 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: 2.11 (0.32), residues: 671 helix: 2.76 (0.29), residues: 315 sheet: 1.37 (0.47), residues: 115 loop : -0.48 (0.37), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 316 TYR 0.015 0.001 TYR B 246 PHE 0.011 0.001 PHE B 295 TRP 0.009 0.001 TRP B 771 HIS 0.003 0.001 HIS B 381 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.12 ( 6452) covalent geometry : angle 0.45405 / 0.26 ( 8886) hydrogen bonds : bond 0.05409 / 3.64 ( 325) hydrogen bonds : angle 3.65343 / 2.55 ( 901) metal coordination : bond 0.00753 / 0.39 ( 4) metal coordination : angle 1.75627 / 1.13 ( 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 99 residues out of total 602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 83 time to evaluate : 0.131 Fit side-chains REVERT: B 339 GLU cc_start: 0.7850 (tp30) cc_final: 0.7436 (tp30) REVERT: B 451 GLN cc_start: 0.7664 (tp40) cc_final: 0.7382 (mm110) REVERT: B 896 ASP cc_start: 0.8114 (OUTLIER) cc_final: 0.7729 (m-30) outliers start: 16 outliers final: 6 residues processed: 90 average time/residue: 0.5267 time to fit residues: 49.2818 Evaluate side-chains 88 residues out of total 602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 81 time to evaluate : 0.151 ------------------------------------------------------------------------------- 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 574 VAL Chi-restraints excluded: chain B residue 673 MET Chi-restraints excluded: chain B residue 780 ILE 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: 9.9990 chunk 69 optimal weight: 10.0000 chunk 47 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 60 optimal weight: 0.0170 chunk 59 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 8 optimal weight: 6.9990 chunk 55 optimal weight: 5.9990 overall best weight: 1.6024 ------------------------------------------------------------------------------- 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 = 0.3776 r_free = 0.3776 target = 0.149528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.110664 restraints weight = 5497.905| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 1.62 r_work: 0.3183 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.0848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6456 Z= 0.133 Angle : 0.482 6.024 8892 Z= 0.269 Chirality : 0.041 0.153 1025 Planarity : 0.004 0.045 994 Dihedral : 14.452 73.899 1316 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.16 % Allowed : 23.09 % Favored : 74.75 % 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: 2.66 (0.29), residues: 315 sheet: 1.24 (0.47), residues: 115 loop : -0.60 (0.37), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 488 TYR 0.016 0.001 TYR B 246 PHE 0.012 0.001 PHE B 295 TRP 0.003 0.001 TRP B 771 HIS 0.004 0.001 HIS B 381 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 ( 6452) covalent geometry : angle 0.47979 / 0.27 ( 8886) hydrogen bonds : bond 0.05812 / 3.90 ( 325) hydrogen bonds : angle 3.71255 / 2.59 ( 901) metal coordination : bond 0.00799 / 0.41 ( 4) metal coordination : angle 1.86245 / 1.21 ( 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 95 residues out of total 602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 0.131 Fit side-chains REVERT: B 339 GLU cc_start: 0.7839 (tp30) cc_final: 0.7459 (tp30) REVERT: B 451 GLN cc_start: 0.7672 (tp40) cc_final: 0.7375 (mm110) REVERT: B 896 ASP cc_start: 0.8136 (OUTLIER) cc_final: 0.7717 (m-30) outliers start: 13 outliers final: 7 residues processed: 87 average time/residue: 0.5275 time to fit residues: 47.6990 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 : 0.155 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 3 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 58 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 chunk 60 optimal weight: 0.2980 chunk 8 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 63 optimal weight: 6.9990 chunk 6 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- 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 = 0.3759 r_free = 0.3759 target = 0.148276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.109532 restraints weight = 5402.098| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 1.61 r_work: 0.3173 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.0956 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= 0.142 Angle : 0.493 5.182 8892 Z= 0.276 Chirality : 0.042 0.159 1025 Planarity : 0.004 0.045 994 Dihedral : 14.462 73.959 1316 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 2.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.82 % Allowed : 22.76 % 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: 1.82 (0.32), residues: 671 helix: 2.58 (0.29), residues: 315 sheet: 1.04 (0.47), residues: 116 loop : -0.63 (0.37), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 488 TYR 0.016 0.002 TYR B 246 PHE 0.013 0.002 PHE B 295 TRP 0.003 0.001 TRP B 771 HIS 0.004 0.001 HIS B 381 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 ( 6452) covalent geometry : angle 0.49020 / 0.28 ( 8886) hydrogen bonds : bond 0.06145 / 4.12 ( 325) hydrogen bonds : angle 3.74881 / 2.61 ( 901) metal coordination : bond 0.00870 / 0.44 ( 4) metal coordination : angle 1.99873 / 1.30 ( 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 96 residues out of total 602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 79 time to evaluate : 0.139 Fit side-chains REVERT: B 339 GLU cc_start: 0.7792 (tp30) cc_final: 0.7407 (tp30) REVERT: B 451 GLN cc_start: 0.7653 (tp40) cc_final: 0.7343 (mm110) REVERT: B 670 ASN cc_start: 0.7234 (OUTLIER) cc_final: 0.6726 (t0) REVERT: B 804 GLU cc_start: 0.7626 (mp0) cc_final: 0.7246 (tp30) REVERT: B 896 ASP cc_start: 0.8134 (OUTLIER) cc_final: 0.7720 (m-30) outliers start: 17 outliers final: 10 residues processed: 88 average time/residue: 0.5705 time to fit residues: 52.2591 Evaluate side-chains 89 residues out of total 602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 266 THR 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 670 ASN 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: 0.9990 chunk 54 optimal weight: 3.9990 chunk 28 optimal weight: 8.9990 chunk 22 optimal weight: 2.9990 chunk 60 optimal weight: 0.0050 chunk 20 optimal weight: 0.1980 chunk 1 optimal weight: 0.4980 chunk 37 optimal weight: 0.9980 chunk 52 optimal weight: 4.9990 chunk 55 optimal weight: 9.9990 chunk 19 optimal weight: 0.9990 overall best weight: 0.5396 ------------------------------------------------------------------------------- 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 = 0.3801 r_free = 0.3801 target = 0.152201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.113724 restraints weight = 5432.883| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 1.61 r_work: 0.3222 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.0902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 6456 Z= 0.102 Angle : 0.434 6.424 8892 Z= 0.246 Chirality : 0.039 0.146 1025 Planarity : 0.004 0.045 994 Dihedral : 14.374 73.835 1316 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.33 % Allowed : 23.42 % 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: 1.97 (0.32), residues: 671 helix: 2.74 (0.29), residues: 315 sheet: 1.10 (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 0.010 0.001 TYR B 566 PHE 0.008 0.001 PHE B 471 TRP 0.006 0.001 TRP B 771 HIS 0.002 0.001 HIS B 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00190 / 0.10 ( 6452) covalent geometry : angle 0.43133 / 0.25 ( 8886) hydrogen bonds : bond 0.04881 / 3.26 ( 325) hydrogen bonds : angle 3.59650 / 2.51 ( 901) metal coordination : bond 0.00540 / 0.27 ( 4) metal coordination : angle 1.91443 / 1.11 ( 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: 14 poor density : 80 time to evaluate : 0.223 Fit side-chains REVERT: B 339 GLU cc_start: 0.7737 (tp30) cc_final: 0.7378 (tp30) REVERT: B 451 GLN cc_start: 0.7623 (tp40) cc_final: 0.7330 (mm110) REVERT: B 804 GLU cc_start: 0.7634 (OUTLIER) cc_final: 0.7255 (tp30) REVERT: B 896 ASP cc_start: 0.8115 (OUTLIER) cc_final: 0.7708 (m-30) outliers start: 14 outliers final: 8 residues processed: 88 average time/residue: 0.5230 time to fit residues: 48.0581 Evaluate side-chains 89 residues out of total 602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 79 time to evaluate : 0.131 ------------------------------------------------------------------------------- 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 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: 0.7980 chunk 29 optimal weight: 0.4980 chunk 57 optimal weight: 0.0980 chunk 46 optimal weight: 0.0970 chunk 15 optimal weight: 0.4980 chunk 18 optimal weight: 5.9990 chunk 44 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 chunk 56 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 overall best weight: 0.3778 ------------------------------------------------------------------------------- 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 = 0.3830 r_free = 0.3830 target = 0.154501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.116848 restraints weight = 5485.605| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 1.60 r_work: 0.3274 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.1002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 6456 Z= 0.089 Angle : 0.398 4.844 8892 Z= 0.226 Chirality : 0.038 0.145 1025 Planarity : 0.004 0.043 994 Dihedral : 14.359 73.891 1316 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.16 % Allowed : 23.92 % 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: 2.07 (0.32), residues: 671 helix: 2.86 (0.29), residues: 314 sheet: 1.11 (0.47), residues: 115 loop : -0.56 (0.37), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 488 TYR 0.009 0.001 TYR B 566 PHE 0.007 0.001 PHE B 918 TRP 0.007 0.001 TRP B 771 HIS 0.002 0.001 HIS B 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00159 / 0.09 ( 6452) covalent geometry : angle 0.39619 / 0.23 ( 8886) hydrogen bonds : bond 0.04078 / 2.73 ( 325) hydrogen bonds : angle 3.43828 / 2.40 ( 901) metal coordination : bond 0.00456 / 0.23 ( 4) metal coordination : angle 1.67830 / 0.90 ( 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 88 residues out of total 602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 75 time to evaluate : 0.132 Fit side-chains REVERT: B 339 GLU cc_start: 0.7716 (tp30) cc_final: 0.7356 (tp30) REVERT: B 451 GLN cc_start: 0.7576 (tp40) cc_final: 0.7271 (mm110) REVERT: B 612 GLU cc_start: 0.7299 (mt-10) cc_final: 0.7017 (mt-10) REVERT: B 804 GLU cc_start: 0.7522 (OUTLIER) cc_final: 0.7214 (tp30) REVERT: B 896 ASP cc_start: 0.8086 (OUTLIER) cc_final: 0.7720 (m-30) outliers start: 13 outliers final: 6 residues processed: 81 average time/residue: 0.5339 time to fit residues: 45.1345 Evaluate side-chains 81 residues out of total 602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 73 time to evaluate : 0.188 ------------------------------------------------------------------------------- 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 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 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: 3.9990 chunk 27 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 69 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 chunk 17 optimal weight: 6.9990 chunk 13 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- 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 = 0.3760 r_free = 0.3760 target = 0.148218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.109704 restraints weight = 5513.131| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 1.61 r_work: 0.3177 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.1028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6456 Z= 0.151 Angle : 0.503 5.414 8892 Z= 0.280 Chirality : 0.043 0.157 1025 Planarity : 0.004 0.045 994 Dihedral : 14.471 73.914 1316 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.66 % Allowed : 23.92 % 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: 1.85 (0.32), residues: 671 helix: 2.62 (0.29), residues: 315 sheet: 1.00 (0.47), residues: 116 loop : -0.60 (0.37), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 488 TYR 0.017 0.002 TYR B 246 PHE 0.013 0.002 PHE B 842 TRP 0.015 0.001 TRP B 771 HIS 0.003 0.001 HIS B 381 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 ( 6452) covalent geometry : angle 0.50086 / 0.28 ( 8886) hydrogen bonds : bond 0.06091 / 4.09 ( 325) hydrogen bonds : angle 3.70710 / 2.59 ( 901) metal coordination : bond 0.00946 / 0.50 ( 4) metal coordination : angle 1.96034 / 1.31 ( 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 89 residues out of total 602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 79 time to evaluate : 0.177 Fit side-chains REVERT: B 339 GLU cc_start: 0.7758 (tp30) cc_final: 0.7391 (tp30) REVERT: B 451 GLN cc_start: 0.7623 (tp40) cc_final: 0.7308 (mm110) REVERT: B 804 GLU cc_start: 0.7658 (mp0) cc_final: 0.7275 (tp30) REVERT: B 896 ASP cc_start: 0.8131 (OUTLIER) cc_final: 0.7714 (m-30) outliers start: 10 outliers final: 6 residues processed: 83 average time/residue: 0.5871 time to fit residues: 50.7203 Evaluate side-chains 84 residues out of total 602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 77 time to evaluate : 0.132 ------------------------------------------------------------------------------- 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 574 VAL Chi-restraints excluded: chain B residue 673 MET Chi-restraints excluded: chain B residue 780 ILE 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: 4.9990 chunk 45 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 28 optimal weight: 8.9990 chunk 65 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 1 optimal weight: 0.1980 chunk 51 optimal weight: 0.8980 overall best weight: 1.4186 ------------------------------------------------------------------------------- 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 = 0.3778 r_free = 0.3778 target = 0.149827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.111138 restraints weight = 5418.440| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 1.61 r_work: 0.3189 rms_B_bonded: 2.29 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: 0.8336 moved from start: 0.0999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6456 Z= 0.126 Angle : 0.471 5.718 8892 Z= 0.264 Chirality : 0.041 0.152 1025 Planarity : 0.004 0.045 994 Dihedral : 14.399 73.915 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 : 1.50 % Allowed : 24.75 % Favored : 73.75 % 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: 2.63 (0.29), residues: 315 sheet: 0.96 (0.47), residues: 116 loop : -0.64 (0.37), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 488 TYR 0.015 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 0.00260 / 0.13 ( 6452) covalent geometry : angle 0.46833 / 0.26 ( 8886) hydrogen bonds : bond 0.05608 / 3.75 ( 325) hydrogen bonds : angle 3.66312 / 2.55 ( 901) metal coordination : bond 0.00757 / 0.38 ( 4) metal coordination : angle 1.86376 / 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 88 residues out of total 602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 79 time to evaluate : 0.240 Fit side-chains REVERT: B 339 GLU cc_start: 0.7709 (tp30) cc_final: 0.7383 (tp30) REVERT: B 451 GLN cc_start: 0.7610 (tp40) cc_final: 0.7300 (mm110) REVERT: B 804 GLU cc_start: 0.7662 (mp0) cc_final: 0.7275 (tp30) REVERT: B 896 ASP cc_start: 0.8126 (OUTLIER) cc_final: 0.7715 (m-30) outliers start: 9 outliers final: 7 residues processed: 83 average time/residue: 0.6764 time to fit residues: 58.4084 Evaluate side-chains 87 residues out of total 602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 79 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 457 GLN 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: 3.9990 chunk 11 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 53 optimal weight: 0.5980 chunk 54 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- 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 = 0.3775 r_free = 0.3775 target = 0.149709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.110863 restraints weight = 5439.524| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 1.62 r_work: 0.3185 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.0998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6456 Z= 0.132 Angle : 0.490 7.542 8892 Z= 0.273 Chirality : 0.041 0.153 1025 Planarity : 0.004 0.045 994 Dihedral : 14.402 73.906 1316 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.83 % Allowed : 24.42 % Favored : 73.75 % 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: 1.80 (0.32), residues: 671 helix: 2.60 (0.29), residues: 315 sheet: 0.95 (0.47), residues: 116 loop : -0.64 (0.37), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 488 TYR 0.015 0.001 TYR B 246 PHE 0.011 0.001 PHE B 295 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 0.00278 / 0.13 ( 6452) covalent geometry : angle 0.48784 / 0.27 ( 8886) hydrogen bonds : bond 0.05698 / 3.82 ( 325) hydrogen bonds : angle 3.67737 / 2.56 ( 901) metal coordination : bond 0.00782 / 0.40 ( 4) metal coordination : angle 1.86737 / 1.19 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2170.37 seconds wall clock time: 37 minutes 30.50 seconds (2250.50 seconds total)