Starting phenix.real_space_refine on Tue Feb 3 18:43:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ku4_62574/02_2026/9ku4_62574.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ku4_62574/02_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_62574/02_2026/9ku4_62574.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ku4_62574/02_2026/9ku4_62574.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ku4_62574/02_2026/9ku4_62574.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ku4_62574/02_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-2.0-5952/lib/python3.9/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: 1.29, per 1000 atoms: 0.21 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: 0.46 Conformation dependent library (CDL) restraints added in 131.6 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: 0.61 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: 1.06 Time building geometry restraints manager: 0.58 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=" CA VAL B 522 " pdb=" C VAL B 522 " ideal model delta sigma weight residual 1.520 1.530 -0.010 1.47e-02 4.63e+03 4.81e-01 bond pdb=" C ASN B 384 " pdb=" O ASN B 384 " ideal model delta sigma weight residual 1.236 1.228 0.008 1.26e-02 6.30e+03 4.49e-01 bond pdb=" CG PRO B 301 " pdb=" CD PRO B 301 " ideal model delta sigma weight residual 1.503 1.482 0.021 3.40e-02 8.65e+02 3.70e-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=" 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=" CG ARG B 488 " pdb=" CD ARG B 488 " pdb=" NE ARG B 488 " ideal model delta sigma weight residual 112.00 116.55 -4.55 2.20e+00 2.07e-01 4.28e+00 angle pdb=" N VAL B 522 " pdb=" CA VAL B 522 " pdb=" CB VAL B 522 " ideal model delta sigma weight residual 112.21 110.09 2.12 1.10e+00 8.26e-01 3.70e+00 angle pdb=" N GLY B 703 " pdb=" CA GLY B 703 " pdb=" C GLY B 703 " ideal model delta sigma weight residual 113.18 117.62 -4.44 2.37e+00 1.78e-01 3.51e+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: 1.490 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 7.030 Find NCS groups from input model: 0.020 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:7.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 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= 0.107 Angle : 0.459 5.886 8892 Z= 0.255 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 covalent geometry : bond 0.00200 ( 6452) covalent geometry : angle 0.45734 ( 8886) hydrogen bonds : bond 0.14829 ( 325) hydrogen bonds : angle 4.75386 ( 901) metal coordination : bond 0.00540 ( 4) metal coordination : angle 1.68385 ( 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 : 0.135 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: 0.5798 time to fit residues: 52.3106 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 : 0.154 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: B 336 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.154067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.116170 restraints weight = 5398.254| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 1.60 r_work: 0.3266 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.0703 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= 0.095 Angle : 0.428 4.690 8892 Z= 0.231 Chirality : 0.039 0.149 1025 Planarity : 0.004 0.042 994 Dihedral : 14.494 73.738 1323 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.66 % Allowed : 23.75 % 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: 2.13 (0.32), residues: 671 helix: 2.71 (0.29), residues: 316 sheet: 1.52 (0.47), residues: 115 loop : -0.45 (0.37), residues: 240 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 0.008 0.001 PHE B 295 TRP 0.004 0.001 TRP B 771 HIS 0.002 0.001 HIS B 280 Details of bonding type rmsd covalent geometry : bond 0.00177 ( 6452) covalent geometry : angle 0.42591 ( 8886) hydrogen bonds : bond 0.04381 ( 325) hydrogen bonds : angle 3.62121 ( 901) metal coordination : bond 0.00611 ( 4) metal coordination : angle 1.63028 ( 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 104 residues out of total 602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 88 time to evaluate : 0.135 Fit side-chains REVERT: B 339 GLU cc_start: 0.7823 (tp30) cc_final: 0.7424 (tp30) REVERT: B 451 GLN cc_start: 0.7680 (tp40) cc_final: 0.7382 (mm110) REVERT: B 607 GLU cc_start: 0.7462 (tt0) cc_final: 0.7220 (tt0) REVERT: B 811 ARG cc_start: 0.8736 (OUTLIER) cc_final: 0.7690 (ttt180) REVERT: B 896 ASP cc_start: 0.8116 (OUTLIER) cc_final: 0.7734 (m-30) outliers start: 16 outliers final: 6 residues processed: 95 average time/residue: 0.5457 time to fit residues: 53.7608 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 : 0.128 ------------------------------------------------------------------------------- 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 35 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 39 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 27 optimal weight: 6.9990 chunk 50 optimal weight: 0.8980 chunk 28 optimal weight: 0.2980 chunk 37 optimal weight: 6.9990 chunk 40 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 336 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.150613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.112159 restraints weight = 5306.465| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 1.60 r_work: 0.3211 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.0778 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 : 0.474 4.686 8892 Z= 0.255 Chirality : 0.040 0.149 1025 Planarity : 0.004 0.043 994 Dihedral : 14.416 73.936 1316 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.99 % Allowed : 23.09 % 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: 2.05 (0.32), residues: 671 helix: 2.67 (0.29), residues: 315 sheet: 1.40 (0.47), residues: 115 loop : -0.48 (0.37), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 316 TYR 0.015 0.001 TYR B 246 PHE 0.010 0.001 PHE B 295 TRP 0.008 0.001 TRP B 771 HIS 0.003 0.001 HIS B 381 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 6452) covalent geometry : angle 0.47156 ( 8886) hydrogen bonds : bond 0.05305 ( 325) hydrogen bonds : angle 3.65476 ( 901) metal coordination : bond 0.00780 ( 4) metal coordination : angle 1.78889 ( 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 99 residues out of total 602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 81 time to evaluate : 0.169 Fit side-chains REVERT: B 339 GLU cc_start: 0.7841 (tp30) cc_final: 0.7459 (tp30) REVERT: B 451 GLN cc_start: 0.7666 (tp40) cc_final: 0.7391 (mm110) REVERT: B 607 GLU cc_start: 0.7473 (tt0) cc_final: 0.7213 (tt0) REVERT: B 896 ASP cc_start: 0.8135 (OUTLIER) cc_final: 0.7748 (m-30) outliers start: 18 outliers final: 8 residues processed: 91 average time/residue: 0.5283 time to fit residues: 50.0739 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 : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 419 ASN Chi-restraints excluded: chain B residue 457 GLN Chi-restraints excluded: chain B residue 489 ILE 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 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: 6.9990 chunk 2 optimal weight: 4.9990 chunk 49 optimal weight: 8.9990 chunk 3 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 chunk 41 optimal weight: 4.9990 chunk 65 optimal weight: 6.9990 chunk 69 optimal weight: 7.9990 chunk 11 optimal weight: 4.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3729 r_free = 0.3729 target = 0.145545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.106607 restraints weight = 5400.373| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 1.61 r_work: 0.3131 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.1166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 6456 Z= 0.227 Angle : 0.631 7.043 8892 Z= 0.337 Chirality : 0.048 0.171 1025 Planarity : 0.005 0.042 994 Dihedral : 14.648 74.167 1316 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.65 % Allowed : 22.59 % 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: 1.47 (0.32), residues: 671 helix: 2.16 (0.29), residues: 318 sheet: 1.01 (0.47), residues: 115 loop : -0.70 (0.36), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 488 TYR 0.020 0.002 TYR B 246 PHE 0.016 0.002 PHE B 776 TRP 0.004 0.001 TRP B 908 HIS 0.005 0.001 HIS B 381 Details of bonding type rmsd covalent geometry : bond 0.00516 ( 6452) covalent geometry : angle 0.62901 ( 8886) hydrogen bonds : bond 0.07853 ( 325) hydrogen bonds : angle 4.04930 ( 901) metal coordination : bond 0.01235 ( 4) metal coordination : angle 2.05466 ( 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: 22 poor density : 80 time to evaluate : 0.145 Fit side-chains REVERT: B 339 GLU cc_start: 0.7746 (tp30) cc_final: 0.7401 (tp30) REVERT: B 451 GLN cc_start: 0.7707 (OUTLIER) cc_final: 0.7403 (mm110) REVERT: B 804 GLU cc_start: 0.7776 (mp0) cc_final: 0.7283 (tp30) outliers start: 22 outliers final: 13 residues processed: 94 average time/residue: 0.5531 time to fit residues: 54.1661 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 : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 451 GLN Chi-restraints excluded: chain B residue 457 GLN Chi-restraints excluded: chain B residue 489 ILE 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 681 ILE 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 68 optimal weight: 5.9990 chunk 69 optimal weight: 5.9990 chunk 47 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 60 optimal weight: 0.0170 chunk 59 optimal weight: 6.9990 chunk 44 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 chunk 55 optimal weight: 5.9990 overall best weight: 1.3022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 336 GLN B 670 ASN B 805 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.149035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.110152 restraints weight = 5528.272| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 1.62 r_work: 0.3176 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.1035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6456 Z= 0.126 Angle : 0.486 4.683 8892 Z= 0.263 Chirality : 0.041 0.154 1025 Planarity : 0.004 0.042 994 Dihedral : 14.397 74.071 1316 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.49 % Allowed : 23.26 % 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: 1.75 (0.32), residues: 671 helix: 2.51 (0.29), residues: 315 sheet: 1.00 (0.47), residues: 116 loop : -0.63 (0.36), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 316 TYR 0.013 0.001 TYR B 246 PHE 0.010 0.001 PHE B 295 TRP 0.004 0.001 TRP B 771 HIS 0.004 0.001 HIS B 381 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 6452) covalent geometry : angle 0.48240 ( 8886) hydrogen bonds : bond 0.05597 ( 325) hydrogen bonds : angle 3.74342 ( 901) metal coordination : bond 0.00782 ( 4) metal coordination : angle 2.20229 ( 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: 15 poor density : 80 time to evaluate : 0.218 Fit side-chains REVERT: B 339 GLU cc_start: 0.7735 (tp30) cc_final: 0.7394 (tp30) REVERT: B 451 GLN cc_start: 0.7685 (tp40) cc_final: 0.7388 (mm110) REVERT: B 607 GLU cc_start: 0.7471 (tt0) cc_final: 0.7207 (tt0) REVERT: B 804 GLU cc_start: 0.7683 (mp0) cc_final: 0.7265 (tp30) REVERT: B 896 ASP cc_start: 0.8150 (OUTLIER) cc_final: 0.7722 (m-30) outliers start: 15 outliers final: 7 residues processed: 87 average time/residue: 0.5624 time to fit residues: 50.8903 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 : 0.214 ------------------------------------------------------------------------------- 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: 1.9990 chunk 58 optimal weight: 8.9990 chunk 39 optimal weight: 4.9990 chunk 60 optimal weight: 0.5980 chunk 8 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 25 optimal weight: 0.3980 chunk 13 optimal weight: 4.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 336 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.150640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.112078 restraints weight = 5428.487| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 1.60 r_work: 0.3201 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.0996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6456 Z= 0.112 Angle : 0.469 6.192 8892 Z= 0.253 Chirality : 0.040 0.151 1025 Planarity : 0.004 0.042 994 Dihedral : 14.346 73.756 1316 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.66 % Allowed : 23.42 % 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: 1.86 (0.32), residues: 671 helix: 2.66 (0.29), residues: 315 sheet: 0.99 (0.47), residues: 116 loop : -0.62 (0.37), residues: 240 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 0.005 0.001 TRP B 771 HIS 0.003 0.001 HIS B 381 Details of bonding type rmsd covalent geometry : bond 0.00223 ( 6452) covalent geometry : angle 0.46612 ( 8886) hydrogen bonds : bond 0.04942 ( 325) hydrogen bonds : angle 3.61169 ( 901) metal coordination : bond 0.00701 ( 4) metal coordination : angle 1.98311 ( 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: 16 poor density : 80 time to evaluate : 0.211 Fit side-chains REVERT: B 339 GLU cc_start: 0.7736 (tp30) cc_final: 0.7394 (tp30) REVERT: B 451 GLN cc_start: 0.7656 (tp40) cc_final: 0.7357 (mm110) REVERT: B 607 GLU cc_start: 0.7461 (tt0) cc_final: 0.7244 (tt0) REVERT: B 670 ASN cc_start: 0.7168 (OUTLIER) cc_final: 0.6703 (t0) REVERT: B 804 GLU cc_start: 0.7633 (mp0) cc_final: 0.7240 (tp30) REVERT: B 811 ARG cc_start: 0.8755 (OUTLIER) cc_final: 0.7659 (ttt180) REVERT: B 896 ASP cc_start: 0.8141 (OUTLIER) cc_final: 0.7739 (m-30) outliers start: 16 outliers final: 10 residues processed: 89 average time/residue: 0.6323 time to fit residues: 58.4805 Evaluate side-chains 91 residues out of total 602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 78 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 419 ASN Chi-restraints excluded: chain B residue 457 GLN Chi-restraints excluded: chain B residue 489 ILE 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 11 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 chunk 28 optimal weight: 7.9990 chunk 22 optimal weight: 3.9990 chunk 60 optimal weight: 0.0070 chunk 20 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 55 optimal weight: 9.9990 chunk 19 optimal weight: 0.6980 overall best weight: 0.8200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 336 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.151578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.113409 restraints weight = 5447.934| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 1.59 r_work: 0.3220 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.1036 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= 0.101 Angle : 0.441 4.779 8892 Z= 0.238 Chirality : 0.039 0.148 1025 Planarity : 0.004 0.042 994 Dihedral : 14.317 73.737 1316 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.33 % Allowed : 23.75 % 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: 1.93 (0.32), residues: 671 helix: 2.75 (0.29), residues: 315 sheet: 1.00 (0.47), residues: 116 loop : -0.64 (0.37), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 488 TYR 0.011 0.001 TYR B 246 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 covalent geometry : bond 0.00197 ( 6452) covalent geometry : angle 0.43847 ( 8886) hydrogen bonds : bond 0.04527 ( 325) hydrogen bonds : angle 3.52473 ( 901) metal coordination : bond 0.00637 ( 4) metal coordination : angle 1.85772 ( 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 93 residues out of total 602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 79 time to evaluate : 0.232 Fit side-chains REVERT: B 339 GLU cc_start: 0.7746 (tp30) cc_final: 0.7409 (tp30) REVERT: B 451 GLN cc_start: 0.7624 (tp40) cc_final: 0.7317 (mm110) REVERT: B 607 GLU cc_start: 0.7466 (tt0) cc_final: 0.7233 (tt0) REVERT: B 804 GLU cc_start: 0.7593 (OUTLIER) cc_final: 0.7230 (tp30) REVERT: B 896 ASP cc_start: 0.8123 (OUTLIER) cc_final: 0.7733 (m-30) outliers start: 14 outliers final: 9 residues processed: 86 average time/residue: 0.5816 time to fit residues: 52.1592 Evaluate side-chains 88 residues out of total 602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 77 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 419 ASN 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 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: 4.9990 chunk 35 optimal weight: 1.9990 chunk 29 optimal weight: 0.0980 chunk 57 optimal weight: 0.1980 chunk 46 optimal weight: 0.0670 chunk 15 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 24 optimal weight: 0.9980 chunk 56 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 overall best weight: 0.6720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 336 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.152620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.114528 restraints weight = 5548.450| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 1.61 r_work: 0.3234 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.1031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 6456 Z= 0.098 Angle : 0.441 6.956 8892 Z= 0.238 Chirality : 0.039 0.147 1025 Planarity : 0.004 0.042 994 Dihedral : 14.299 73.688 1316 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.83 % Allowed : 24.58 % 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: 1.98 (0.32), residues: 671 helix: 2.81 (0.29), residues: 315 sheet: 1.00 (0.47), residues: 116 loop : -0.62 (0.37), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 488 TYR 0.010 0.001 TYR B 246 PHE 0.007 0.001 PHE B 471 TRP 0.014 0.001 TRP B 771 HIS 0.002 0.001 HIS B 280 Details of bonding type rmsd covalent geometry : bond 0.00191 ( 6452) covalent geometry : angle 0.43894 ( 8886) hydrogen bonds : bond 0.04227 ( 325) hydrogen bonds : angle 3.46080 ( 901) metal coordination : bond 0.00574 ( 4) metal coordination : angle 1.76542 ( 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 89 residues out of total 602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 78 time to evaluate : 0.219 Fit side-chains REVERT: B 339 GLU cc_start: 0.7762 (tp30) cc_final: 0.7420 (tp30) REVERT: B 451 GLN cc_start: 0.7584 (tp40) cc_final: 0.7269 (mm110) REVERT: B 607 GLU cc_start: 0.7459 (tt0) cc_final: 0.6545 (tt0) REVERT: B 804 GLU cc_start: 0.7516 (OUTLIER) cc_final: 0.7190 (tp30) REVERT: B 811 ARG cc_start: 0.8736 (OUTLIER) cc_final: 0.7694 (ttt180) REVERT: B 896 ASP cc_start: 0.8102 (OUTLIER) cc_final: 0.7739 (m-30) outliers start: 11 outliers final: 6 residues processed: 83 average time/residue: 0.6550 time to fit residues: 56.4960 Evaluate side-chains 84 residues out of total 602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 75 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 419 ASN Chi-restraints excluded: chain B residue 457 GLN Chi-restraints excluded: chain B residue 522 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 829 CYS Chi-restraints excluded: chain B residue 896 ASP 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: 5.9990 chunk 63 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 69 optimal weight: 7.9990 chunk 10 optimal weight: 0.8980 chunk 17 optimal weight: 7.9990 chunk 13 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 chunk 1 optimal weight: 0.8980 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 336 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.148683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.109738 restraints weight = 5508.587| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 1.62 r_work: 0.3170 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.1087 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= 0.145 Angle : 0.508 5.218 8892 Z= 0.273 Chirality : 0.042 0.155 1025 Planarity : 0.004 0.042 994 Dihedral : 14.341 73.802 1315 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.83 % Allowed : 24.58 % 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: 1.76 (0.32), residues: 671 helix: 2.57 (0.29), residues: 319 sheet: 0.97 (0.47), residues: 116 loop : -0.76 (0.37), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 488 TYR 0.016 0.002 TYR B 246 PHE 0.013 0.002 PHE B 295 TRP 0.016 0.001 TRP B 771 HIS 0.003 0.001 HIS B 381 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 6452) covalent geometry : angle 0.50532 ( 8886) hydrogen bonds : bond 0.05834 ( 325) hydrogen bonds : angle 3.68940 ( 901) metal coordination : bond 0.00871 ( 4) metal coordination : angle 1.95546 ( 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 93 residues out of total 602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 82 time to evaluate : 0.227 Fit side-chains REVERT: B 339 GLU cc_start: 0.7750 (tp30) cc_final: 0.7404 (tp30) REVERT: B 451 GLN cc_start: 0.7642 (tp40) cc_final: 0.7320 (mm110) REVERT: B 607 GLU cc_start: 0.7470 (tt0) cc_final: 0.7232 (tt0) REVERT: B 670 ASN cc_start: 0.7134 (OUTLIER) cc_final: 0.6678 (t0) REVERT: B 804 GLU cc_start: 0.7636 (mp0) cc_final: 0.7270 (tp30) REVERT: B 896 ASP cc_start: 0.8140 (OUTLIER) cc_final: 0.7730 (m-30) outliers start: 11 outliers final: 7 residues processed: 87 average time/residue: 0.6512 time to fit residues: 58.9276 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 : 0.195 ------------------------------------------------------------------------------- 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 670 ASN 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 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: 8.9990 chunk 66 optimal weight: 1.9990 chunk 28 optimal weight: 7.9990 chunk 65 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 1 optimal weight: 0.0970 chunk 51 optimal weight: 0.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.149932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.111261 restraints weight = 5440.224| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 1.60 r_work: 0.3191 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.1061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6456 Z= 0.122 Angle : 0.487 7.533 8892 Z= 0.263 Chirality : 0.040 0.152 1025 Planarity : 0.004 0.042 994 Dihedral : 14.285 73.879 1315 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.66 % Allowed : 24.75 % 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: 1.86 (0.32), residues: 671 helix: 2.70 (0.29), residues: 315 sheet: 0.98 (0.47), residues: 116 loop : -0.69 (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 0.019 0.001 TRP B 771 HIS 0.003 0.001 HIS B 876 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 6452) covalent geometry : angle 0.48448 ( 8886) hydrogen bonds : bond 0.05207 ( 325) hydrogen bonds : angle 3.62895 ( 901) metal coordination : bond 0.00752 ( 4) metal coordination : angle 2.02784 ( 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 90 residues out of total 602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 80 time to evaluate : 0.150 Fit side-chains REVERT: B 339 GLU cc_start: 0.7733 (tp30) cc_final: 0.7386 (tp30) REVERT: B 451 GLN cc_start: 0.7641 (tp40) cc_final: 0.7347 (mm110) REVERT: B 607 GLU cc_start: 0.7464 (tt0) cc_final: 0.7232 (tt0) REVERT: B 670 ASN cc_start: 0.7137 (OUTLIER) cc_final: 0.6676 (t0) REVERT: B 804 GLU cc_start: 0.7588 (mp0) cc_final: 0.7221 (tp30) REVERT: B 896 ASP cc_start: 0.8136 (OUTLIER) cc_final: 0.7738 (m-30) outliers start: 10 outliers final: 6 residues processed: 85 average time/residue: 0.6034 time to fit residues: 53.3735 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 : 0.221 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 19 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 13 optimal weight: 4.9990 chunk 63 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 36 optimal weight: 0.0670 chunk 21 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 overall best weight: 0.9522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.150743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.112427 restraints weight = 5483.131| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 1.61 r_work: 0.3208 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.1067 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= 0.107 Angle : 0.454 5.724 8892 Z= 0.245 Chirality : 0.039 0.150 1025 Planarity : 0.004 0.041 994 Dihedral : 14.262 73.775 1315 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % 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: 1.92 (0.32), residues: 671 helix: 2.76 (0.29), residues: 315 sheet: 0.98 (0.47), residues: 116 loop : -0.66 (0.37), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 488 TYR 0.012 0.001 TYR B 246 PHE 0.009 0.001 PHE B 295 TRP 0.018 0.001 TRP B 771 HIS 0.002 0.001 HIS B 876 Details of bonding type rmsd covalent geometry : bond 0.00213 ( 6452) covalent geometry : angle 0.45100 ( 8886) hydrogen bonds : bond 0.04719 ( 325) hydrogen bonds : angle 3.54866 ( 901) metal coordination : bond 0.00673 ( 4) metal coordination : angle 1.90389 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2330.84 seconds wall clock time: 40 minutes 15.35 seconds (2415.35 seconds total)