Starting phenix.real_space_refine on Thu Jul 2 02:19:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ymb_73101/07_2026/9ymb_73101.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ymb_73101/07_2026/9ymb_73101.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ymb_73101/07_2026/9ymb_73101.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ymb_73101/07_2026/9ymb_73101.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ymb_73101/07_2026/9ymb_73101.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ymb_73101/07_2026/9ymb_73101.map" } resolution = 3.77 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 18 5.49 5 S 31 5.16 5 C 3510 2.51 5 N 1008 2.21 5 O 1059 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5626 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 173 Classifications: {'RNA': 8} Modifications used: {'p5*END': 1, 'rna2p_pyr': 1, 'rna3p_pur': 5, 'rna3p_pyr': 2} Link IDs: {'rna2p': 1, 'rna3p': 6} Chain: "C" Number of atoms: 209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 209 Classifications: {'RNA': 10} Modifications used: {'rna3p_pur': 4, 'rna3p_pyr': 6} Link IDs: {'rna3p': 9} Chain: "A" Number of atoms: 5244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 656, 5244 Classifications: {'peptide': 656} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 41, 'TRANS': 613} Chain breaks: 4 Time building chain proxies: 1.17, per 1000 atoms: 0.21 Number of scatterers: 5626 At special positions: 0 Unit cell: (77.532, 77.958, 106.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 31 16.00 P 18 15.00 O 1059 8.00 N 1008 7.00 C 3510 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.36 Conformation dependent library (CDL) restraints added in 205.8 milliseconds 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1234 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 6 sheets defined 36.9% alpha, 19.5% beta 4 base pairs and 11 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'A' and resid 72 through 82 removed outlier: 3.870A pdb=" N HIS A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 148 Processing helix chain 'A' and resid 155 through 174 removed outlier: 3.526A pdb=" N ILE A 159 " --> pdb=" O PRO A 155 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N HIS A 168 " --> pdb=" O VAL A 164 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N LEU A 169 " --> pdb=" O VAL A 165 " (cutoff:3.500A) Proline residue: A 170 - end of helix Processing helix chain 'A' and resid 371 through 387 Processing helix chain 'A' and resid 391 through 396 Processing helix chain 'A' and resid 458 through 462 Processing helix chain 'A' and resid 463 through 481 removed outlier: 3.506A pdb=" N LEU A 467 " --> pdb=" O THR A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 499 No H-bonds generated for 'chain 'A' and resid 497 through 499' Processing helix chain 'A' and resid 500 through 512 removed outlier: 3.689A pdb=" N ARG A 506 " --> pdb=" O GLU A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 539 removed outlier: 4.350A pdb=" N ALA A 530 " --> pdb=" O THR A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 554 Processing helix chain 'A' and resid 556 through 572 Processing helix chain 'A' and resid 584 through 589 removed outlier: 3.580A pdb=" N PHE A 587 " --> pdb=" O PRO A 584 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLN A 589 " --> pdb=" O VAL A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 658 removed outlier: 4.129A pdb=" N MET A 645 " --> pdb=" O ASP A 641 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N GLN A 652 " --> pdb=" O GLU A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 674 No H-bonds generated for 'chain 'A' and resid 672 through 674' Processing helix chain 'A' and resid 675 through 695 removed outlier: 3.948A pdb=" N LEU A 684 " --> pdb=" O LEU A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 723 Processing helix chain 'A' and resid 775 through 787 removed outlier: 3.885A pdb=" N CYS A 787 " --> pdb=" O THR A 783 " (cutoff:3.500A) Processing helix chain 'A' and resid 800 through 817 removed outlier: 3.994A pdb=" N TYR A 815 " --> pdb=" O PHE A 811 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N HIS A 816 " --> pdb=" O ARG A 812 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU A 817 " --> pdb=" O ALA A 813 " (cutoff:3.500A) Processing helix chain 'A' and resid 836 through 847 removed outlier: 3.657A pdb=" N ALA A 845 " --> pdb=" O ALA A 841 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLN A 847 " --> pdb=" O ALA A 843 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 855 removed outlier: 3.805A pdb=" N ARG A 854 " --> pdb=" O ASP A 851 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 625 through 632 removed outlier: 3.629A pdb=" N VAL A 614 " --> pdb=" O THR A 628 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE A 611 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N SER A 617 " --> pdb=" O PHE A 593 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N PHE A 593 " --> pdb=" O SER A 617 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N VAL A 598 " --> pdb=" O ASP A 669 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ILE A 702 " --> pdb=" O ASP A 770 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ASP A 770 " --> pdb=" O ILE A 702 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N PHE A 704 " --> pdb=" O LEU A 768 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N SER A 763 " --> pdb=" O LEU A 750 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR A 406 " --> pdb=" O ALA A 42 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 46 removed outlier: 3.674A pdb=" N MET A 214 " --> pdb=" O ARG A 207 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG A 207 " --> pdb=" O MET A 214 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 93 through 94 removed outlier: 6.508A pdb=" N ILE A 54 " --> pdb=" O CYS A 137 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N CYS A 137 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N HIS A 56 " --> pdb=" O VAL A 135 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 175 through 177 removed outlier: 3.532A pdb=" N THR A 175 " --> pdb=" O PHE A 182 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 427 through 428 Processing sheet with id=AA6, first strand: chain 'A' and resid 491 through 494 removed outlier: 3.888A pdb=" N PHE A 491 " --> pdb=" O TRP A 451 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS A 493 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N CYS A 455 " --> pdb=" O LYS A 493 " (cutoff:3.500A) 231 hydrogen bonds defined for protein. 642 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 10 hydrogen bonds 20 hydrogen bond angles 0 basepair planarities 4 basepair parallelities 11 stacking parallelities Total time for adding SS restraints: 0.83 Time building geometry restraints manager: 0.55 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: 1755 1.34 - 1.46: 977 1.46 - 1.57: 2980 1.57 - 1.69: 34 1.69 - 1.81: 49 Bond restraints: 5795 Sorted by residual: bond pdb=" O5' U C 25 " pdb=" C5' U C 25 " ideal model delta sigma weight residual 1.420 1.450 -0.030 1.50e-02 4.44e+03 4.06e+00 bond pdb=" O5' U C 16 " pdb=" C5' U C 16 " ideal model delta sigma weight residual 1.420 1.450 -0.030 1.50e-02 4.44e+03 3.89e+00 bond pdb=" O5' U C 24 " pdb=" C5' U C 24 " ideal model delta sigma weight residual 1.420 1.449 -0.029 1.50e-02 4.44e+03 3.84e+00 bond pdb=" O5' A C 18 " pdb=" C5' A C 18 " ideal model delta sigma weight residual 1.420 1.449 -0.029 1.50e-02 4.44e+03 3.75e+00 bond pdb=" O5' G C 19 " pdb=" C5' G C 19 " ideal model delta sigma weight residual 1.420 1.449 -0.029 1.50e-02 4.44e+03 3.64e+00 ... (remaining 5790 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.76: 7858 2.76 - 5.53: 58 5.53 - 8.29: 10 8.29 - 11.06: 0 11.06 - 13.82: 2 Bond angle restraints: 7928 Sorted by residual: angle pdb=" O3' U C 16 " pdb=" P A C 17 " pdb=" OP1 A C 17 " ideal model delta sigma weight residual 108.00 121.82 -13.82 3.00e+00 1.11e-01 2.12e+01 angle pdb=" O3' U C 24 " pdb=" P U C 25 " pdb=" OP1 U C 25 " ideal model delta sigma weight residual 108.00 120.70 -12.70 3.00e+00 1.11e-01 1.79e+01 angle pdb=" O3' U C 16 " pdb=" P A C 17 " pdb=" O5' A C 17 " ideal model delta sigma weight residual 104.00 98.07 5.93 1.50e+00 4.44e-01 1.56e+01 angle pdb=" O3' G C 19 " pdb=" P C C 20 " pdb=" O5' C C 20 " ideal model delta sigma weight residual 104.00 98.27 5.73 1.50e+00 4.44e-01 1.46e+01 angle pdb=" C1' U B 6 " pdb=" N1 U B 6 " pdb=" C2 U B 6 " ideal model delta sigma weight residual 117.70 121.53 -3.83 1.20e+00 6.94e-01 1.02e+01 ... (remaining 7923 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.25: 3224 19.25 - 38.50: 201 38.50 - 57.75: 64 57.75 - 77.00: 25 77.00 - 96.25: 6 Dihedral angle restraints: 3520 sinusoidal: 1614 harmonic: 1906 Sorted by residual: dihedral pdb=" O4' U C 16 " pdb=" C1' U C 16 " pdb=" N1 U C 16 " pdb=" C2 U C 16 " ideal model delta sinusoidal sigma weight residual -160.00 -63.75 -96.25 1 1.50e+01 4.44e-03 4.73e+01 dihedral pdb=" C4' A C 17 " pdb=" O4' A C 17 " pdb=" C1' A C 17 " pdb=" C2' A C 17 " ideal model delta sinusoidal sigma weight residual 3.00 -24.11 27.11 1 8.00e+00 1.56e-02 1.65e+01 dihedral pdb=" O4' U C 25 " pdb=" C1' U C 25 " pdb=" N1 U C 25 " pdb=" C2 U C 25 " ideal model delta sinusoidal sigma weight residual -160.00 -111.30 -48.70 1 1.50e+01 4.44e-03 1.45e+01 ... (remaining 3517 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 855 0.112 - 0.225: 28 0.225 - 0.337: 0 0.337 - 0.450: 3 0.450 - 0.562: 4 Chirality restraints: 890 Sorted by residual: chirality pdb=" P U C 16 " pdb=" OP1 U C 16 " pdb=" OP2 U C 16 " pdb=" O5' U C 16 " both_signs ideal model delta sigma weight residual True 2.41 -2.97 -0.56 2.00e-01 2.50e+01 7.91e+00 chirality pdb=" P U C 25 " pdb=" OP1 U C 25 " pdb=" OP2 U C 25 " pdb=" O5' U C 25 " both_signs ideal model delta sigma weight residual True 2.41 -2.97 -0.56 2.00e-01 2.50e+01 7.71e+00 chirality pdb=" P A C 17 " pdb=" OP1 A C 17 " pdb=" OP2 A C 17 " pdb=" O5' A C 17 " both_signs ideal model delta sigma weight residual True 2.41 -2.95 -0.54 2.00e-01 2.50e+01 7.36e+00 ... (remaining 887 not shown) Planarity restraints: 961 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 106 " 0.038 5.00e-02 4.00e+02 5.78e-02 5.34e+00 pdb=" N PRO A 107 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO A 107 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 107 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' C C 22 " -0.025 2.00e-02 2.50e+03 1.34e-02 4.03e+00 pdb=" N1 C C 22 " 0.029 2.00e-02 2.50e+03 pdb=" C2 C C 22 " -0.004 2.00e-02 2.50e+03 pdb=" O2 C C 22 " 0.005 2.00e-02 2.50e+03 pdb=" N3 C C 22 " 0.000 2.00e-02 2.50e+03 pdb=" C4 C C 22 " -0.004 2.00e-02 2.50e+03 pdb=" N4 C C 22 " -0.007 2.00e-02 2.50e+03 pdb=" C5 C C 22 " -0.001 2.00e-02 2.50e+03 pdb=" C6 C C 22 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A B 4 " 0.023 2.00e-02 2.50e+03 1.05e-02 3.05e+00 pdb=" N9 A B 4 " -0.023 2.00e-02 2.50e+03 pdb=" C8 A B 4 " -0.006 2.00e-02 2.50e+03 pdb=" N7 A B 4 " 0.004 2.00e-02 2.50e+03 pdb=" C5 A B 4 " 0.001 2.00e-02 2.50e+03 pdb=" C6 A B 4 " 0.004 2.00e-02 2.50e+03 pdb=" N6 A B 4 " 0.004 2.00e-02 2.50e+03 pdb=" N1 A B 4 " 0.002 2.00e-02 2.50e+03 pdb=" C2 A B 4 " -0.002 2.00e-02 2.50e+03 pdb=" N3 A B 4 " -0.004 2.00e-02 2.50e+03 pdb=" C4 A B 4 " -0.003 2.00e-02 2.50e+03 ... (remaining 958 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 567 2.75 - 3.28: 5541 3.28 - 3.82: 9614 3.82 - 4.36: 10853 4.36 - 4.90: 18802 Nonbonded interactions: 45377 Sorted by model distance: nonbonded pdb=" O GLY A 573 " pdb=" NH2 ARG A 624 " model vdw 2.207 3.120 nonbonded pdb=" OG SER A 371 " pdb=" O SER A 727 " model vdw 2.211 3.040 nonbonded pdb=" OP1 G B 5 " pdb=" OG SER A 798 " model vdw 2.232 3.040 nonbonded pdb=" ND2 ASN A 568 " pdb=" OD1 ASN A 575 " model vdw 2.255 3.120 nonbonded pdb=" OP1 A B 3 " pdb=" NH2 ARG A 792 " model vdw 2.260 3.120 ... (remaining 45372 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 12.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.630 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6484 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 : 0.003 0.036 5795 Z= 0.191 Angle : 0.684 13.825 7928 Z= 0.395 Chirality : 0.065 0.562 890 Planarity : 0.005 0.058 961 Dihedral : 15.437 96.251 2286 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 3.65 % Allowed : 8.35 % Favored : 88.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.33), residues: 646 helix: 0.92 (0.35), residues: 206 sheet: -0.34 (0.42), residues: 159 loop : -0.43 (0.39), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 72 TYR 0.008 0.001 TYR A 393 PHE 0.011 0.001 PHE A 774 TRP 0.009 0.001 TRP A 435 HIS 0.004 0.001 HIS A 466 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.19 ( 5795) covalent geometry : angle 0.68379 / 0.40 ( 7928) hydrogen bonds : bond 0.20565 / 20.78 ( 241) hydrogen bonds : angle 7.62574 / 8.95 ( 662) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 96 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 PHE cc_start: 0.7023 (m-80) cc_final: 0.6650 (m-10) REVERT: A 47 MET cc_start: 0.7193 (mtm) cc_final: 0.6823 (mtm) REVERT: A 78 MET cc_start: 0.7884 (OUTLIER) cc_final: 0.7574 (tpt) REVERT: A 100 LEU cc_start: 0.7234 (OUTLIER) cc_final: 0.7029 (tm) REVERT: A 104 MET cc_start: 0.7477 (tmm) cc_final: 0.7124 (tmm) REVERT: A 117 VAL cc_start: 0.7550 (OUTLIER) cc_final: 0.6155 (p) REVERT: A 213 MET cc_start: 0.7787 (mmm) cc_final: 0.7060 (mmm) REVERT: A 534 ARG cc_start: 0.7818 (tmm160) cc_final: 0.7028 (tpt-90) REVERT: A 648 GLU cc_start: 0.7795 (mt-10) cc_final: 0.7386 (tp30) REVERT: A 666 PHE cc_start: 0.7643 (t80) cc_final: 0.7208 (t80) REVERT: A 768 LEU cc_start: 0.8980 (mm) cc_final: 0.8723 (mm) outliers start: 21 outliers final: 8 residues processed: 111 average time/residue: 0.0805 time to fit residues: 11.7104 Evaluate side-chains 84 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 73 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 150 ARG Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 711 HIS Chi-restraints excluded: chain A residue 741 THR Chi-restraints excluded: chain A residue 794 THR Chi-restraints excluded: chain A residue 799 ILE Chi-restraints excluded: chain A residue 804 TYR Chi-restraints excluded: chain A residue 821 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 8.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 0.5980 chunk 45 optimal weight: 5.9990 chunk 27 optimal weight: 7.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 71 ASN ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.180400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.146995 restraints weight = 10920.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.152196 restraints weight = 6174.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.154130 restraints weight = 4312.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.154458 restraints weight = 3614.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.154814 restraints weight = 3411.887| |-----------------------------------------------------------------------------| r_work (final): 0.4188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7056 moved from start: 0.1023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 5795 Z= 0.171 Angle : 0.615 6.179 7928 Z= 0.331 Chirality : 0.046 0.186 890 Planarity : 0.006 0.068 961 Dihedral : 15.285 90.086 1004 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 4.17 % Allowed : 10.96 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.34), residues: 646 helix: 0.97 (0.36), residues: 205 sheet: -0.51 (0.42), residues: 155 loop : -0.42 (0.38), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 384 TYR 0.008 0.001 TYR A 393 PHE 0.020 0.002 PHE A 202 TRP 0.010 0.001 TRP A 435 HIS 0.005 0.001 HIS A 600 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.17 ( 5795) covalent geometry : angle 0.61535 / 0.33 ( 7928) hydrogen bonds : bond 0.05115 / 4.93 ( 241) hydrogen bonds : angle 5.97402 / 7.51 ( 662) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 84 time to evaluate : 0.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 LEU cc_start: 0.7488 (OUTLIER) cc_final: 0.7226 (tm) REVERT: A 213 MET cc_start: 0.7838 (mmm) cc_final: 0.7492 (mmm) REVERT: A 534 ARG cc_start: 0.7485 (tmm160) cc_final: 0.7104 (tpt-90) REVERT: A 648 GLU cc_start: 0.7688 (mt-10) cc_final: 0.7401 (tp30) REVERT: A 666 PHE cc_start: 0.7733 (t80) cc_final: 0.7486 (t80) REVERT: A 821 GLU cc_start: 0.6351 (OUTLIER) cc_final: 0.4759 (mp0) outliers start: 24 outliers final: 16 residues processed: 100 average time/residue: 0.0791 time to fit residues: 10.3294 Evaluate side-chains 89 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 71 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ASN Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 168 HIS Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 711 HIS Chi-restraints excluded: chain A residue 729 ASN Chi-restraints excluded: chain A residue 741 THR Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 759 THR Chi-restraints excluded: chain A residue 799 ILE Chi-restraints excluded: chain A residue 804 TYR Chi-restraints excluded: chain A residue 821 GLU Chi-restraints excluded: chain A residue 842 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 0 optimal weight: 10.0000 chunk 13 optimal weight: 4.9990 chunk 42 optimal weight: 0.8980 chunk 25 optimal weight: 0.6980 chunk 2 optimal weight: 9.9990 chunk 39 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 14 optimal weight: 8.9990 chunk 66 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 141 GLN ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 466 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.180213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.147026 restraints weight = 10707.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.152483 restraints weight = 6142.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.154360 restraints weight = 4258.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.154547 restraints weight = 3546.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.154784 restraints weight = 3345.232| |-----------------------------------------------------------------------------| r_work (final): 0.4178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7037 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 5795 Z= 0.144 Angle : 0.609 9.206 7928 Z= 0.320 Chirality : 0.046 0.178 890 Planarity : 0.005 0.071 961 Dihedral : 15.078 89.613 995 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 3.48 % Allowed : 12.35 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.34), residues: 646 helix: 0.93 (0.36), residues: 205 sheet: -0.62 (0.42), residues: 155 loop : -0.48 (0.38), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 792 TYR 0.009 0.001 TYR A 420 PHE 0.038 0.002 PHE A 82 TRP 0.009 0.002 TRP A 435 HIS 0.003 0.001 HIS A 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 ( 5795) covalent geometry : angle 0.60859 / 0.32 ( 7928) hydrogen bonds : bond 0.04338 / 4.14 ( 241) hydrogen bonds : angle 5.62224 / 7.14 ( 662) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 82 time to evaluate : 0.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.8046 (ppp) cc_final: 0.7166 (tpt) REVERT: A 100 LEU cc_start: 0.7480 (OUTLIER) cc_final: 0.7153 (tm) REVERT: A 104 MET cc_start: 0.7772 (tmm) cc_final: 0.7406 (tmm) REVERT: A 213 MET cc_start: 0.7867 (mmm) cc_final: 0.7519 (mmm) REVERT: A 534 ARG cc_start: 0.7405 (tmm160) cc_final: 0.7104 (tpt-90) REVERT: A 648 GLU cc_start: 0.7631 (mt-10) cc_final: 0.7395 (tm-30) outliers start: 20 outliers final: 14 residues processed: 94 average time/residue: 0.0765 time to fit residues: 9.3482 Evaluate side-chains 87 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 168 HIS Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 494 TYR Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 711 HIS Chi-restraints excluded: chain A residue 729 ASN Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain A residue 799 ILE Chi-restraints excluded: chain A residue 821 GLU Chi-restraints excluded: chain A residue 842 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 65 optimal weight: 9.9990 chunk 43 optimal weight: 10.0000 chunk 52 optimal weight: 4.9990 chunk 56 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 10 optimal weight: 8.9990 chunk 31 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 71 ASN A 204 GLN ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 466 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4493 r_free = 0.4493 target = 0.181522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.147471 restraints weight = 10670.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.152170 restraints weight = 5987.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.155233 restraints weight = 4153.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.157053 restraints weight = 3279.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.158584 restraints weight = 2825.418| |-----------------------------------------------------------------------------| r_work (final): 0.4249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6971 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 5795 Z= 0.136 Angle : 0.595 8.028 7928 Z= 0.314 Chirality : 0.045 0.190 890 Planarity : 0.005 0.037 961 Dihedral : 14.976 87.635 992 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 4.35 % Allowed : 13.22 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.34), residues: 646 helix: 0.87 (0.36), residues: 206 sheet: -0.73 (0.42), residues: 158 loop : -0.53 (0.39), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 792 TYR 0.008 0.001 TYR A 790 PHE 0.010 0.001 PHE A 202 TRP 0.008 0.001 TRP A 435 HIS 0.004 0.001 HIS A 466 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 ( 5795) covalent geometry : angle 0.59509 / 0.31 ( 7928) hydrogen bonds : bond 0.03961 / 3.73 ( 241) hydrogen bonds : angle 5.34495 / 6.82 ( 662) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 91 time to evaluate : 0.212 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.8039 (ppp) cc_final: 0.7140 (tpp) REVERT: A 100 LEU cc_start: 0.7421 (OUTLIER) cc_final: 0.7099 (tm) REVERT: A 213 MET cc_start: 0.7870 (mmm) cc_final: 0.7128 (mmm) REVERT: A 534 ARG cc_start: 0.7399 (tmm160) cc_final: 0.7063 (tpt-90) outliers start: 25 outliers final: 16 residues processed: 108 average time/residue: 0.0740 time to fit residues: 10.4105 Evaluate side-chains 91 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 74 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ASN Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 168 HIS Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 494 TYR Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 611 ILE Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 711 HIS Chi-restraints excluded: chain A residue 729 ASN Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain A residue 799 ILE Chi-restraints excluded: chain A residue 821 GLU Chi-restraints excluded: chain A residue 842 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 65 optimal weight: 20.0000 chunk 52 optimal weight: 0.7980 chunk 21 optimal weight: 0.0870 chunk 51 optimal weight: 1.9990 chunk 8 optimal weight: 9.9990 chunk 35 optimal weight: 0.7980 chunk 29 optimal weight: 10.0000 chunk 18 optimal weight: 6.9990 chunk 26 optimal weight: 0.0020 chunk 58 optimal weight: 6.9990 chunk 23 optimal weight: 0.9980 overall best weight: 0.5366 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 71 ASN A 216 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4510 r_free = 0.4510 target = 0.182697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.150114 restraints weight = 10827.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.155585 restraints weight = 6001.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.157653 restraints weight = 4066.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.157903 restraints weight = 3406.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.158523 restraints weight = 3165.920| |-----------------------------------------------------------------------------| r_work (final): 0.4243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6971 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5795 Z= 0.117 Angle : 0.576 7.602 7928 Z= 0.305 Chirality : 0.044 0.195 890 Planarity : 0.005 0.043 961 Dihedral : 14.836 86.584 992 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 3.65 % Allowed : 14.61 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.34), residues: 646 helix: 0.93 (0.36), residues: 209 sheet: -0.72 (0.42), residues: 158 loop : -0.63 (0.39), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 384 TYR 0.009 0.001 TYR A 790 PHE 0.010 0.001 PHE A 456 TRP 0.008 0.001 TRP A 435 HIS 0.003 0.001 HIS A 466 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 ( 5795) covalent geometry : angle 0.57551 / 0.30 ( 7928) hydrogen bonds : bond 0.03725 / 3.49 ( 241) hydrogen bonds : angle 5.14784 / 6.59 ( 662) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 83 time to evaluate : 0.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 PHE cc_start: 0.6985 (m-10) cc_final: 0.6776 (m-10) REVERT: A 78 MET cc_start: 0.8034 (ppp) cc_final: 0.7183 (tpp) REVERT: A 100 LEU cc_start: 0.7392 (OUTLIER) cc_final: 0.7041 (tm) REVERT: A 104 MET cc_start: 0.7791 (tmm) cc_final: 0.7435 (tmm) REVERT: A 213 MET cc_start: 0.7787 (mmm) cc_final: 0.7128 (mmm) outliers start: 21 outliers final: 13 residues processed: 97 average time/residue: 0.0616 time to fit residues: 7.9781 Evaluate side-chains 93 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 79 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 168 HIS Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 611 ILE Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 711 HIS Chi-restraints excluded: chain A residue 729 ASN Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain A residue 799 ILE Chi-restraints excluded: chain A residue 804 TYR Chi-restraints excluded: chain A residue 821 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 47 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 chunk 17 optimal weight: 9.9990 chunk 33 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 64 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 23 optimal weight: 0.0370 chunk 20 optimal weight: 6.9990 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 71 ASN A 216 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.182620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.148518 restraints weight = 10788.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.153316 restraints weight = 6076.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.156518 restraints weight = 4207.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.158559 restraints weight = 3324.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.159830 restraints weight = 2836.484| |-----------------------------------------------------------------------------| r_work (final): 0.4249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6942 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5795 Z= 0.120 Angle : 0.567 6.971 7928 Z= 0.302 Chirality : 0.045 0.198 890 Planarity : 0.005 0.037 961 Dihedral : 14.816 86.667 992 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 3.83 % Allowed : 14.26 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.34), residues: 646 helix: 1.09 (0.36), residues: 204 sheet: -0.72 (0.41), residues: 158 loop : -0.49 (0.40), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 72 TYR 0.005 0.001 TYR A 790 PHE 0.057 0.002 PHE A 82 TRP 0.007 0.001 TRP A 435 HIS 0.003 0.001 HIS A 466 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 ( 5795) covalent geometry : angle 0.56698 / 0.30 ( 7928) hydrogen bonds : bond 0.03673 / 3.49 ( 241) hydrogen bonds : angle 5.05825 / 6.48 ( 662) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 86 time to evaluate : 0.189 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 PHE cc_start: 0.7003 (m-10) cc_final: 0.6781 (m-10) REVERT: A 100 LEU cc_start: 0.7358 (OUTLIER) cc_final: 0.7003 (tm) REVERT: A 104 MET cc_start: 0.7750 (tmm) cc_final: 0.7420 (tmm) REVERT: A 213 MET cc_start: 0.7759 (mmm) cc_final: 0.7319 (mmm) REVERT: A 384 ARG cc_start: 0.8749 (mmm160) cc_final: 0.8257 (tmt170) REVERT: A 413 LEU cc_start: 0.5909 (OUTLIER) cc_final: 0.5670 (mm) REVERT: A 653 PHE cc_start: 0.7149 (t80) cc_final: 0.6817 (t80) outliers start: 22 outliers final: 13 residues processed: 100 average time/residue: 0.0586 time to fit residues: 8.0406 Evaluate side-chains 91 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 76 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 168 HIS Chi-restraints excluded: chain A residue 174 TYR Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 611 ILE Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain A residue 711 HIS Chi-restraints excluded: chain A residue 729 ASN Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain A residue 804 TYR Chi-restraints excluded: chain A residue 821 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 48 optimal weight: 4.9990 chunk 9 optimal weight: 8.9990 chunk 19 optimal weight: 2.9990 chunk 23 optimal weight: 0.4980 chunk 27 optimal weight: 6.9990 chunk 32 optimal weight: 0.4980 chunk 22 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 11 optimal weight: 0.0370 chunk 46 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 216 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.181873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.146982 restraints weight = 10989.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.151813 restraints weight = 6096.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.154952 restraints weight = 4229.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.157058 restraints weight = 3330.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.158038 restraints weight = 2836.741| |-----------------------------------------------------------------------------| r_work (final): 0.4217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6949 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5795 Z= 0.117 Angle : 0.576 7.002 7928 Z= 0.305 Chirality : 0.045 0.198 890 Planarity : 0.005 0.042 961 Dihedral : 14.691 86.764 990 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 3.48 % Allowed : 15.30 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.34), residues: 646 helix: 1.16 (0.36), residues: 203 sheet: -0.65 (0.41), residues: 158 loop : -0.45 (0.39), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 72 TYR 0.005 0.001 TYR A 393 PHE 0.020 0.001 PHE A 87 TRP 0.007 0.001 TRP A 435 HIS 0.003 0.001 HIS A 466 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 ( 5795) covalent geometry : angle 0.57633 / 0.31 ( 7928) hydrogen bonds : bond 0.03588 / 3.37 ( 241) hydrogen bonds : angle 5.04235 / 6.40 ( 662) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 82 time to evaluate : 0.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 PHE cc_start: 0.7036 (m-10) cc_final: 0.6789 (m-10) REVERT: A 100 LEU cc_start: 0.7306 (OUTLIER) cc_final: 0.6921 (tm) REVERT: A 104 MET cc_start: 0.7751 (tmm) cc_final: 0.7444 (tmm) REVERT: A 213 MET cc_start: 0.7733 (mmm) cc_final: 0.7356 (mmm) REVERT: A 384 ARG cc_start: 0.8738 (mmm160) cc_final: 0.8222 (tmt170) REVERT: A 413 LEU cc_start: 0.5895 (OUTLIER) cc_final: 0.5651 (mm) outliers start: 20 outliers final: 14 residues processed: 96 average time/residue: 0.0646 time to fit residues: 8.5148 Evaluate side-chains 94 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 78 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 168 HIS Chi-restraints excluded: chain A residue 174 TYR Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 611 ILE Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 626 CYS Chi-restraints excluded: chain A residue 711 HIS Chi-restraints excluded: chain A residue 729 ASN Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain A residue 799 ILE Chi-restraints excluded: chain A residue 821 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 0 optimal weight: 9.9990 chunk 17 optimal weight: 9.9990 chunk 22 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 37 optimal weight: 0.9990 chunk 19 optimal weight: 4.9990 chunk 8 optimal weight: 10.0000 chunk 34 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 216 ASN A 681 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.180664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.146603 restraints weight = 10744.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.151226 restraints weight = 6217.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.154145 restraints weight = 4375.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.155948 restraints weight = 3497.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.157354 restraints weight = 3035.459| |-----------------------------------------------------------------------------| r_work (final): 0.4219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7013 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5795 Z= 0.163 Angle : 0.614 7.467 7928 Z= 0.324 Chirality : 0.045 0.198 890 Planarity : 0.005 0.046 961 Dihedral : 14.805 86.735 990 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 4.35 % Allowed : 14.78 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.34), residues: 646 helix: 1.16 (0.36), residues: 203 sheet: -0.77 (0.41), residues: 152 loop : -0.51 (0.39), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 792 TYR 0.013 0.002 TYR A 804 PHE 0.066 0.003 PHE A 82 TRP 0.010 0.002 TRP A 769 HIS 0.003 0.001 HIS A 466 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 ( 5795) covalent geometry : angle 0.61444 / 0.32 ( 7928) hydrogen bonds : bond 0.03836 / 3.55 ( 241) hydrogen bonds : angle 5.06221 / 6.44 ( 662) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 78 time to evaluate : 0.136 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.7787 (tmm) cc_final: 0.7490 (tmm) REVERT: A 204 GLN cc_start: 0.8491 (tt0) cc_final: 0.8177 (pt0) REVERT: A 213 MET cc_start: 0.7783 (mmm) cc_final: 0.7562 (mmm) REVERT: A 384 ARG cc_start: 0.8726 (mmm160) cc_final: 0.8209 (tmt170) REVERT: A 413 LEU cc_start: 0.5993 (OUTLIER) cc_final: 0.5768 (mm) outliers start: 25 outliers final: 17 residues processed: 94 average time/residue: 0.0585 time to fit residues: 7.4304 Evaluate side-chains 92 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 74 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 168 HIS Chi-restraints excluded: chain A residue 174 TYR Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 611 ILE Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 626 CYS Chi-restraints excluded: chain A residue 711 HIS Chi-restraints excluded: chain A residue 729 ASN Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain A residue 821 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 20 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 35 optimal weight: 0.0170 chunk 19 optimal weight: 6.9990 chunk 32 optimal weight: 0.6980 chunk 46 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 14 optimal weight: 8.9990 chunk 56 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 overall best weight: 0.6820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 80 GLN A 216 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.181997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.147450 restraints weight = 10748.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.152207 restraints weight = 6160.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.155233 restraints weight = 4326.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.157295 restraints weight = 3437.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.158429 restraints weight = 2951.628| |-----------------------------------------------------------------------------| r_work (final): 0.4223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6969 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 5795 Z= 0.125 Angle : 0.602 8.277 7928 Z= 0.319 Chirality : 0.045 0.196 890 Planarity : 0.005 0.037 961 Dihedral : 14.774 86.578 990 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 3.13 % Allowed : 16.00 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.34), residues: 646 helix: 1.08 (0.37), residues: 203 sheet: -0.69 (0.42), residues: 152 loop : -0.55 (0.39), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 792 TYR 0.006 0.001 TYR A 55 PHE 0.020 0.002 PHE A 653 TRP 0.007 0.001 TRP A 435 HIS 0.004 0.001 HIS A 466 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 ( 5795) covalent geometry : angle 0.60218 / 0.32 ( 7928) hydrogen bonds : bond 0.03658 / 3.30 ( 241) hydrogen bonds : angle 5.01030 / 6.39 ( 662) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 82 time to evaluate : 0.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 PHE cc_start: 0.7040 (m-10) cc_final: 0.6764 (m-10) REVERT: A 104 MET cc_start: 0.7756 (tmm) cc_final: 0.7543 (tmm) REVERT: A 213 MET cc_start: 0.7739 (mmm) cc_final: 0.7359 (mmm) REVERT: A 384 ARG cc_start: 0.8725 (mmm160) cc_final: 0.8188 (tmt170) REVERT: A 413 LEU cc_start: 0.5894 (OUTLIER) cc_final: 0.5659 (mm) outliers start: 18 outliers final: 15 residues processed: 96 average time/residue: 0.0504 time to fit residues: 6.7167 Evaluate side-chains 94 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 78 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 168 HIS Chi-restraints excluded: chain A residue 174 TYR Chi-restraints excluded: chain A residue 202 PHE Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 611 ILE Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 626 CYS Chi-restraints excluded: chain A residue 711 HIS Chi-restraints excluded: chain A residue 729 ASN Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain A residue 821 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 58 optimal weight: 4.9990 chunk 19 optimal weight: 8.9990 chunk 12 optimal weight: 9.9990 chunk 25 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 38 optimal weight: 9.9990 chunk 22 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 chunk 20 optimal weight: 4.9990 chunk 32 optimal weight: 0.8980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 216 ASN A 766 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.180004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.144386 restraints weight = 10946.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.149197 restraints weight = 6263.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.152226 restraints weight = 4397.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.154266 restraints weight = 3506.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.155227 restraints weight = 3017.599| |-----------------------------------------------------------------------------| r_work (final): 0.4178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6998 moved from start: 0.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5795 Z= 0.141 Angle : 0.623 9.032 7928 Z= 0.324 Chirality : 0.045 0.195 890 Planarity : 0.005 0.051 961 Dihedral : 14.810 87.024 990 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 4.17 % Allowed : 15.48 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.34), residues: 646 helix: 1.15 (0.37), residues: 203 sheet: -0.66 (0.42), residues: 150 loop : -0.70 (0.38), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 792 TYR 0.007 0.001 TYR A 790 PHE 0.074 0.002 PHE A 82 TRP 0.007 0.001 TRP A 435 HIS 0.004 0.001 HIS A 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 ( 5795) covalent geometry : angle 0.62313 / 0.32 ( 7928) hydrogen bonds : bond 0.03712 / 3.37 ( 241) hydrogen bonds : angle 4.97899 / 6.33 ( 662) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 79 time to evaluate : 0.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 PHE cc_start: 0.7025 (m-10) cc_final: 0.6747 (m-10) REVERT: A 104 MET cc_start: 0.7777 (tmm) cc_final: 0.7564 (tmm) REVERT: A 204 GLN cc_start: 0.8434 (tt0) cc_final: 0.8149 (pt0) REVERT: A 213 MET cc_start: 0.7774 (mmm) cc_final: 0.7209 (mmm) REVERT: A 384 ARG cc_start: 0.8711 (mmm160) cc_final: 0.8182 (tmt170) REVERT: A 413 LEU cc_start: 0.5927 (OUTLIER) cc_final: 0.5695 (mm) REVERT: A 856 MET cc_start: 0.6439 (mtt) cc_final: 0.5941 (mtt) outliers start: 24 outliers final: 19 residues processed: 97 average time/residue: 0.0535 time to fit residues: 7.1210 Evaluate side-chains 96 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 76 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 168 HIS Chi-restraints excluded: chain A residue 174 TYR Chi-restraints excluded: chain A residue 202 PHE Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 507 HIS Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 611 ILE Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 626 CYS Chi-restraints excluded: chain A residue 711 HIS Chi-restraints excluded: chain A residue 729 ASN Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain A residue 804 TYR Chi-restraints excluded: chain A residue 821 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 24 optimal weight: 0.0170 chunk 36 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 40 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 7 optimal weight: 10.0000 chunk 2 optimal weight: 0.0010 chunk 47 optimal weight: 0.3980 chunk 29 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 overall best weight: 0.3624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 216 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4494 r_free = 0.4494 target = 0.182176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.146895 restraints weight = 10823.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.151728 restraints weight = 6130.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.154784 restraints weight = 4281.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.156840 restraints weight = 3402.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.157818 restraints weight = 2920.528| |-----------------------------------------------------------------------------| r_work (final): 0.4211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6933 moved from start: 0.3082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5795 Z= 0.120 Angle : 0.633 10.142 7928 Z= 0.328 Chirality : 0.045 0.221 890 Planarity : 0.005 0.041 961 Dihedral : 14.769 86.419 990 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 3.30 % Allowed : 16.70 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.34), residues: 646 helix: 1.09 (0.37), residues: 204 sheet: -0.56 (0.42), residues: 160 loop : -0.65 (0.39), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 792 TYR 0.009 0.001 TYR A 790 PHE 0.020 0.001 PHE A 716 TRP 0.007 0.001 TRP A 134 HIS 0.003 0.001 HIS A 466 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 ( 5795) covalent geometry : angle 0.63273 / 0.33 ( 7928) hydrogen bonds : bond 0.03594 / 3.24 ( 241) hydrogen bonds : angle 4.89199 / 6.26 ( 662) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1250.49 seconds wall clock time: 22 minutes 19.99 seconds (1339.99 seconds total)