Starting phenix.real_space_refine on Tue Aug 4 18:08:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ymb_73101/08_2026/9ymb_73101.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ymb_73101/08_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_73101/08_2026/9ymb_73101.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ymb_73101/08_2026/9ymb_73101.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ymb_73101/08_2026/9ymb_73101.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ymb_73101/08_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-2.2rc3-6140/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: 0.94, per 1000 atoms: 0.17 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: 0.33 Conformation dependent library (CDL) restraints added in 249.3 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: 0.48 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: 0.98 Time building geometry restraints manager: 0.45 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=" P A C 17 " pdb=" O5' A C 17 " ideal model delta sigma weight residual 1.593 1.615 -0.022 1.00e-02 1.00e+04 4.76e+00 bond pdb=" P U C 23 " pdb=" O5' U C 23 " ideal model delta sigma weight residual 1.593 1.614 -0.021 1.00e-02 1.00e+04 4.59e+00 bond pdb=" P U C 16 " pdb=" O5' U C 16 " ideal model delta sigma weight residual 1.593 1.613 -0.020 1.00e-02 1.00e+04 4.10e+00 bond pdb=" P U C 24 " pdb=" O5' U C 24 " ideal model delta sigma weight residual 1.593 1.613 -0.020 1.00e-02 1.00e+04 4.05e+00 bond pdb=" P U C 25 " pdb=" O5' U C 25 " ideal model delta sigma weight residual 1.593 1.613 -0.020 1.00e-02 1.00e+04 3.96e+00 ... (remaining 5790 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.76: 7856 2.76 - 5.53: 60 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=" C3' A C 17 " pdb=" C2' A C 17 " pdb=" C1' A C 17 " ideal model delta sigma weight residual 101.30 104.06 -2.76 7.00e-01 2.04e+00 1.55e+01 angle pdb=" C3' U B 6 " pdb=" O3' U B 6 " pdb=" P G B 7 " ideal model delta sigma weight residual 119.70 123.97 -4.27 1.20e+00 6.94e-01 1.27e+01 angle pdb=" C2' C C 22 " pdb=" C1' C C 22 " pdb=" N1 C C 22 " ideal model delta sigma weight residual 112.00 115.55 -3.55 1.10e+00 8.26e-01 1.04e+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: 848 0.112 - 0.225: 35 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: 12.250 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: 0.280 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.230 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 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:1.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.390 ------------------------------------------------------------------------------- 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= 0.203 Angle : 0.693 13.825 7928 Z= 0.412 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 / 0.20 ( 5795) covalent geometry : angle 0.69268 / 0.41 ( 7928) hydrogen bonds : bond 0.20565 / 22.24 ( 241) hydrogen bonds : angle 7.62574 / 9.33 ( 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 : 0.296 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: 0.7027 (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: 0.0829 time to fit residues: 12.0371 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 : 0.255 ------------------------------------------------------------------------------- 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 = 0.4481 r_free = 0.4481 target = 0.180363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.146962 restraints weight = 10913.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.152502 restraints weight = 6155.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.154251 restraints weight = 4249.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.154538 restraints weight = 3570.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.154855 restraints weight = 3380.597| |-----------------------------------------------------------------------------| r_work (final): 0.4188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7054 moved from start: 0.1032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 5795 Z= 0.178 Angle : 0.632 6.583 7928 Z= 0.336 Chirality : 0.046 0.176 890 Planarity : 0.006 0.067 961 Dihedral : 15.110 89.144 1004 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 4.17 % Allowed : 11.13 % Favored : 84.70 % 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: -0.09 (0.34), residues: 646 helix: 0.97 (0.36), residues: 205 sheet: -0.52 (0.42), residues: 155 loop : -0.42 (0.38), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 792 TYR 0.007 0.001 TYR A 393 PHE 0.020 0.002 PHE A 202 TRP 0.010 0.001 TRP A 435 HIS 0.006 0.001 HIS A 466 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.18 ( 5795) covalent geometry : angle 0.63187 / 0.34 ( 7928) hydrogen bonds : bond 0.05221 / 5.47 ( 241) hydrogen bonds : angle 5.95850 / 7.75 ( 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 : 0.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 LEU cc_start: 0.7485 (OUTLIER) cc_final: 0.7218 (tm) REVERT: A 213 MET cc_start: 0.7833 (mmm) cc_final: 0.7484 (mmm) REVERT: A 534 ARG cc_start: 0.7471 (tmm160) cc_final: 0.7185 (tpt170) REVERT: A 648 GLU cc_start: 0.7682 (mt-10) cc_final: 0.7391 (tp30) REVERT: A 666 PHE cc_start: 0.7740 (t80) cc_final: 0.7494 (t80) REVERT: A 821 GLU cc_start: 0.6358 (OUTLIER) cc_final: 0.4749 (mp0) outliers start: 24 outliers final: 16 residues processed: 100 average time/residue: 0.0665 time to fit residues: 8.5845 Evaluate side-chains 88 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 70 time to evaluate : 0.113 ------------------------------------------------------------------------------- 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: 9.9990 chunk 13 optimal weight: 6.9990 chunk 42 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 2 optimal weight: 6.9990 chunk 39 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 14 optimal weight: 8.9990 chunk 66 optimal weight: 0.8980 chunk 63 optimal weight: 0.5980 chunk 30 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 466 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.181163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.148865 restraints weight = 10706.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.153532 restraints weight = 5937.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.155385 restraints weight = 4318.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.156040 restraints weight = 3360.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.156860 restraints weight = 3334.731| |-----------------------------------------------------------------------------| r_work (final): 0.4203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6995 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 5795 Z= 0.136 Angle : 0.615 9.236 7928 Z= 0.320 Chirality : 0.045 0.174 890 Planarity : 0.005 0.072 961 Dihedral : 14.940 89.255 995 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 3.48 % Allowed : 12.70 % Favored : 83.83 % 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: 0.93 (0.36), residues: 205 sheet: -0.59 (0.42), residues: 155 loop : -0.45 (0.38), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 150 TYR 0.012 0.001 TYR A 790 PHE 0.047 0.002 PHE A 82 TRP 0.009 0.001 TRP A 435 HIS 0.007 0.001 HIS A 466 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 ( 5795) covalent geometry : angle 0.61525 / 0.32 ( 7928) hydrogen bonds : bond 0.04324 / 4.54 ( 241) hydrogen bonds : angle 5.57802 / 7.33 ( 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 100 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 80 time to evaluate : 0.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 LEU cc_start: 0.7457 (OUTLIER) cc_final: 0.7141 (tm) REVERT: A 213 MET cc_start: 0.7844 (mmm) cc_final: 0.7499 (mmm) REVERT: A 534 ARG cc_start: 0.7408 (tmm160) cc_final: 0.7087 (tpt-90) REVERT: A 648 GLU cc_start: 0.7612 (mt-10) cc_final: 0.7402 (tm-30) REVERT: A 666 PHE cc_start: 0.7722 (t80) cc_final: 0.7508 (t80) outliers start: 20 outliers final: 13 residues processed: 94 average time/residue: 0.0522 time to fit residues: 6.5788 Evaluate side-chains 87 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 73 time to evaluate : 0.118 ------------------------------------------------------------------------------- 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 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: 10.0000 chunk 43 optimal weight: 6.9990 chunk 52 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 10 optimal weight: 7.9990 chunk 31 optimal weight: 0.0170 chunk 46 optimal weight: 3.9990 chunk 25 optimal weight: 0.0060 chunk 4 optimal weight: 0.9990 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 141 GLN 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 = 0.4516 r_free = 0.4516 target = 0.183265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.149501 restraints weight = 10680.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.154230 restraints weight = 5991.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.157386 restraints weight = 4163.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.159484 restraints weight = 3276.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.160716 restraints weight = 2790.502| |-----------------------------------------------------------------------------| r_work (final): 0.4246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6934 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5795 Z= 0.120 Angle : 0.592 8.259 7928 Z= 0.309 Chirality : 0.044 0.168 890 Planarity : 0.005 0.037 961 Dihedral : 14.759 87.040 992 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 4.00 % Allowed : 13.39 % Favored : 82.61 % 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: -0.22 (0.34), residues: 646 helix: 0.89 (0.36), residues: 207 sheet: -0.67 (0.42), residues: 157 loop : -0.48 (0.39), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 384 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 0.00262 / 0.12 ( 5795) covalent geometry : angle 0.59199 / 0.31 ( 7928) hydrogen bonds : bond 0.03844 / 3.95 ( 241) hydrogen bonds : angle 5.24880 / 6.92 ( 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 114 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 91 time to evaluate : 0.139 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 PHE cc_start: 0.6886 (m-10) cc_final: 0.6613 (m-10) REVERT: A 100 LEU cc_start: 0.7413 (OUTLIER) cc_final: 0.7084 (tm) REVERT: A 104 MET cc_start: 0.7758 (tmm) cc_final: 0.7415 (tmm) REVERT: A 213 MET cc_start: 0.7790 (mmm) cc_final: 0.7216 (mmm) REVERT: A 534 ARG cc_start: 0.7353 (tmm160) cc_final: 0.7111 (tpt-90) outliers start: 23 outliers final: 13 residues processed: 106 average time/residue: 0.0538 time to fit residues: 7.5603 Evaluate side-chains 92 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 78 time to evaluate : 0.189 ------------------------------------------------------------------------------- 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 65 optimal weight: 9.9990 chunk 52 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 51 optimal weight: 0.7980 chunk 8 optimal weight: 7.9990 chunk 35 optimal weight: 0.6980 chunk 29 optimal weight: 7.9990 chunk 18 optimal weight: 9.9990 chunk 26 optimal weight: 5.9990 chunk 58 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 overall best weight: 1.6582 ------------------------------------------------------------------------------- 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 = 0.4477 r_free = 0.4477 target = 0.179881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.146617 restraints weight = 10913.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.151098 restraints weight = 6294.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.153559 restraints weight = 4468.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.153808 restraints weight = 3753.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.154246 restraints weight = 3601.014| |-----------------------------------------------------------------------------| r_work (final): 0.4191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7063 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5795 Z= 0.170 Angle : 0.605 7.044 7928 Z= 0.318 Chirality : 0.045 0.165 890 Planarity : 0.005 0.036 961 Dihedral : 14.794 85.926 992 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 3.48 % Allowed : 13.91 % Favored : 82.61 % 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: -0.23 (0.34), residues: 646 helix: 1.03 (0.36), residues: 206 sheet: -0.78 (0.41), residues: 158 loop : -0.55 (0.40), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 384 TYR 0.009 0.002 TYR A 667 PHE 0.010 0.002 PHE A 456 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 0.00385 / 0.17 ( 5795) covalent geometry : angle 0.60545 / 0.32 ( 7928) hydrogen bonds : bond 0.03982 / 4.11 ( 241) hydrogen bonds : angle 5.20228 / 6.90 ( 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 103 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 83 time to evaluate : 0.199 Fit side-chains revert: symmetry clash REVERT: A 100 LEU cc_start: 0.7351 (OUTLIER) cc_final: 0.6976 (tm) REVERT: A 104 MET cc_start: 0.7752 (tmm) cc_final: 0.7429 (tmm) REVERT: A 213 MET cc_start: 0.7915 (mmm) cc_final: 0.7201 (mmm) REVERT: A 666 PHE cc_start: 0.7785 (t80) cc_final: 0.7477 (t80) REVERT: A 719 ASP cc_start: 0.3165 (t70) cc_final: 0.2869 (t70) outliers start: 20 outliers final: 16 residues processed: 96 average time/residue: 0.0485 time to fit residues: 6.2500 Evaluate side-chains 95 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 78 time to evaluate : 0.148 ------------------------------------------------------------------------------- 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 401 VAL 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 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 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: 2.9990 chunk 8 optimal weight: 8.9990 chunk 17 optimal weight: 9.9990 chunk 33 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 64 optimal weight: 0.0060 chunk 36 optimal weight: 0.7980 chunk 52 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 20 optimal weight: 6.9990 overall best weight: 0.6596 ------------------------------------------------------------------------------- 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 = 0.4495 r_free = 0.4495 target = 0.181509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.147514 restraints weight = 10741.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.152263 restraints weight = 6055.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.155379 restraints weight = 4213.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.157514 restraints weight = 3326.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.158657 restraints weight = 2827.799| |-----------------------------------------------------------------------------| r_work (final): 0.4241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6963 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 0.032 5795 Z= 0.122 Angle : 0.595 6.957 7928 Z= 0.311 Chirality : 0.045 0.197 890 Planarity : 0.005 0.037 961 Dihedral : 14.775 83.534 992 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 3.48 % Allowed : 14.26 % Favored : 82.26 % 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: -0.22 (0.34), residues: 646 helix: 0.90 (0.36), residues: 207 sheet: -0.70 (0.41), residues: 158 loop : -0.47 (0.40), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 792 TYR 0.006 0.001 TYR A 790 PHE 0.069 0.002 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 0.00271 / 0.12 ( 5795) covalent geometry : angle 0.59451 / 0.31 ( 7928) hydrogen bonds : bond 0.03723 / 3.81 ( 241) hydrogen bonds : angle 5.01899 / 6.65 ( 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 100 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 80 time to evaluate : 0.121 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 LEU cc_start: 0.7360 (OUTLIER) cc_final: 0.7008 (tm) REVERT: A 104 MET cc_start: 0.7741 (tmm) cc_final: 0.7432 (tmm) REVERT: A 213 MET cc_start: 0.7777 (mmm) cc_final: 0.7351 (mmm) REVERT: A 413 LEU cc_start: 0.5965 (OUTLIER) cc_final: 0.5724 (mm) REVERT: A 719 ASP cc_start: 0.3148 (t70) cc_final: 0.2829 (t70) outliers start: 20 outliers final: 12 residues processed: 94 average time/residue: 0.0465 time to fit residues: 6.0903 Evaluate side-chains 89 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 75 time to evaluate : 0.132 ------------------------------------------------------------------------------- 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 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: 0.7980 chunk 9 optimal weight: 4.9990 chunk 19 optimal weight: 7.9990 chunk 23 optimal weight: 5.9990 chunk 27 optimal weight: 6.9990 chunk 32 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 11 optimal weight: 10.0000 chunk 46 optimal weight: 0.4980 chunk 35 optimal weight: 0.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 = 0.4490 r_free = 0.4490 target = 0.180978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.147066 restraints weight = 10897.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.151802 restraints weight = 6121.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.154872 restraints weight = 4258.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.156918 restraints weight = 3370.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.158074 restraints weight = 2876.568| |-----------------------------------------------------------------------------| r_work (final): 0.4233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6981 moved from start: 0.2459 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= 0.133 Angle : 0.584 6.328 7928 Z= 0.310 Chirality : 0.045 0.207 890 Planarity : 0.005 0.042 961 Dihedral : 14.680 83.466 990 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 4.00 % Allowed : 14.78 % 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: -0.11 (0.34), residues: 646 helix: 1.13 (0.36), residues: 201 sheet: -0.69 (0.41), residues: 158 loop : -0.46 (0.40), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 624 TYR 0.006 0.001 TYR A 393 PHE 0.022 0.002 PHE A 87 TRP 0.008 0.001 TRP A 435 HIS 0.002 0.001 HIS A 466 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 ( 5795) covalent geometry : angle 0.58405 / 0.31 ( 7928) hydrogen bonds : bond 0.03755 / 3.80 ( 241) hydrogen bonds : angle 4.99356 / 6.61 ( 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 98 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 75 time to evaluate : 0.196 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.7726 (tmm) cc_final: 0.7441 (tmm) REVERT: A 213 MET cc_start: 0.7727 (mmm) cc_final: 0.7353 (mmm) REVERT: A 384 ARG cc_start: 0.8714 (mtp-110) cc_final: 0.8155 (tmt170) REVERT: A 413 LEU cc_start: 0.5940 (OUTLIER) cc_final: 0.5706 (mm) REVERT: A 719 ASP cc_start: 0.3132 (t70) cc_final: 0.2800 (t70) outliers start: 23 outliers final: 16 residues processed: 92 average time/residue: 0.0472 time to fit residues: 6.0289 Evaluate side-chains 89 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 72 time to evaluate : 0.146 ------------------------------------------------------------------------------- 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 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 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: 10.0000 chunk 17 optimal weight: 10.0000 chunk 22 optimal weight: 4.9990 chunk 61 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 19 optimal weight: 4.9990 chunk 8 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 32 optimal weight: 5.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- 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 = 0.4478 r_free = 0.4478 target = 0.179182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.145569 restraints weight = 10634.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.150170 restraints weight = 6048.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.153122 restraints weight = 4234.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.155145 restraints weight = 3350.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.156486 restraints weight = 2869.360| |-----------------------------------------------------------------------------| r_work (final): 0.4210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7036 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5795 Z= 0.191 Angle : 0.625 6.196 7928 Z= 0.334 Chirality : 0.046 0.179 890 Planarity : 0.005 0.046 961 Dihedral : 14.810 83.525 990 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 4.00 % Allowed : 15.30 % Favored : 80.70 % 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: -0.27 (0.34), residues: 646 helix: 1.06 (0.36), residues: 202 sheet: -0.70 (0.43), residues: 152 loop : -0.68 (0.39), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 384 TYR 0.016 0.002 TYR A 804 PHE 0.055 0.003 PHE A 82 TRP 0.013 0.002 TRP A 769 HIS 0.003 0.001 HIS A 466 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.19 ( 5795) covalent geometry : angle 0.62490 / 0.33 ( 7928) hydrogen bonds : bond 0.04014 / 4.02 ( 241) hydrogen bonds : angle 5.18947 / 6.85 ( 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 100 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 77 time to evaluate : 0.125 Fit side-chains revert: symmetry clash REVERT: A 104 MET cc_start: 0.7721 (tmm) cc_final: 0.7505 (tmm) REVERT: A 204 GLN cc_start: 0.8481 (tt0) cc_final: 0.8225 (pt0) REVERT: A 384 ARG cc_start: 0.8722 (mtp-110) cc_final: 0.8163 (tmt170) REVERT: A 413 LEU cc_start: 0.6075 (OUTLIER) cc_final: 0.5835 (mm) REVERT: A 719 ASP cc_start: 0.3227 (t70) cc_final: 0.2850 (t70) outliers start: 23 outliers final: 17 residues processed: 92 average time/residue: 0.0477 time to fit residues: 6.0796 Evaluate side-chains 88 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 70 time to evaluate : 0.172 ------------------------------------------------------------------------------- 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 218 ASP 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 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: 1.9990 chunk 18 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 35 optimal weight: 0.1980 chunk 19 optimal weight: 3.9990 chunk 32 optimal weight: 0.2980 chunk 46 optimal weight: 0.0970 chunk 15 optimal weight: 0.8980 chunk 14 optimal weight: 8.9990 chunk 56 optimal weight: 0.7980 chunk 39 optimal weight: 0.7980 overall best weight: 0.4378 ------------------------------------------------------------------------------- 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 = 0.4482 r_free = 0.4482 target = 0.180931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.147162 restraints weight = 10807.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.151223 restraints weight = 6257.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.156108 restraints weight = 4379.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.155358 restraints weight = 3385.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.155681 restraints weight = 3267.128| |-----------------------------------------------------------------------------| r_work (final): 0.4176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6992 moved from start: 0.2842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5795 Z= 0.119 Angle : 0.597 8.477 7928 Z= 0.316 Chirality : 0.045 0.171 890 Planarity : 0.005 0.041 961 Dihedral : 14.735 83.120 990 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 3.30 % Allowed : 15.83 % 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: -0.19 (0.34), residues: 646 helix: 1.02 (0.36), residues: 203 sheet: -0.57 (0.42), residues: 150 loop : -0.60 (0.39), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 624 TYR 0.006 0.001 TYR A 55 PHE 0.016 0.002 PHE A 87 TRP 0.007 0.001 TRP A 134 HIS 0.004 0.001 HIS A 466 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 ( 5795) covalent geometry : angle 0.59709 / 0.32 ( 7928) hydrogen bonds : bond 0.03656 / 3.60 ( 241) hydrogen bonds : angle 4.98787 / 6.58 ( 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 102 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 83 time to evaluate : 0.217 Fit side-chains revert: symmetry clash REVERT: A 384 ARG cc_start: 0.8801 (mtp-110) cc_final: 0.8156 (tmt170) REVERT: A 413 LEU cc_start: 0.5894 (OUTLIER) cc_final: 0.5661 (mm) REVERT: A 719 ASP cc_start: 0.3107 (t70) cc_final: 0.2746 (t70) outliers start: 19 outliers final: 17 residues processed: 97 average time/residue: 0.0574 time to fit residues: 7.6887 Evaluate side-chains 94 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 76 time to evaluate : 0.132 ------------------------------------------------------------------------------- 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 507 HIS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 58 optimal weight: 0.5980 chunk 19 optimal weight: 6.9990 chunk 12 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 38 optimal weight: 9.9990 chunk 22 optimal weight: 0.7980 chunk 43 optimal weight: 0.3980 chunk 20 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 = 0.4474 r_free = 0.4474 target = 0.180171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.146913 restraints weight = 10910.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.151155 restraints weight = 6415.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.153763 restraints weight = 4668.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.153892 restraints weight = 3783.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.155044 restraints weight = 3523.664| |-----------------------------------------------------------------------------| r_work (final): 0.4184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6995 moved from start: 0.3009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5795 Z= 0.126 Angle : 0.626 12.132 7928 Z= 0.324 Chirality : 0.045 0.198 890 Planarity : 0.005 0.034 961 Dihedral : 14.733 83.398 990 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 3.30 % Allowed : 17.91 % Favored : 78.78 % 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: -0.06 (0.34), residues: 646 helix: 1.11 (0.36), residues: 203 sheet: -0.54 (0.42), residues: 154 loop : -0.48 (0.40), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 635 TYR 0.007 0.001 TYR A 790 PHE 0.073 0.002 PHE A 82 TRP 0.008 0.002 TRP A 211 HIS 0.003 0.001 HIS A 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 ( 5795) covalent geometry : angle 0.62559 / 0.32 ( 7928) hydrogen bonds : bond 0.03636 / 3.58 ( 241) hydrogen bonds : angle 4.93680 / 6.53 ( 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 99 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 80 time to evaluate : 0.202 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 204 GLN cc_start: 0.8431 (tt0) cc_final: 0.8184 (pt0) REVERT: A 384 ARG cc_start: 0.8726 (mtp-110) cc_final: 0.8160 (tmt170) REVERT: A 413 LEU cc_start: 0.5888 (OUTLIER) cc_final: 0.5640 (mm) REVERT: A 719 ASP cc_start: 0.3044 (t70) cc_final: 0.2675 (t70) outliers start: 19 outliers final: 17 residues processed: 93 average time/residue: 0.0527 time to fit residues: 6.5704 Evaluate side-chains 95 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 77 time to evaluate : 0.115 ------------------------------------------------------------------------------- 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 507 HIS 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 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: 0.9990 chunk 40 optimal weight: 0.9980 chunk 20 optimal weight: 5.9990 chunk 5 optimal weight: 0.4980 chunk 7 optimal weight: 0.6980 chunk 2 optimal weight: 0.1980 chunk 47 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 overall best weight: 0.4818 ------------------------------------------------------------------------------- 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 = 0.4496 r_free = 0.4496 target = 0.181975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.146563 restraints weight = 10827.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.151519 restraints weight = 6100.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.154613 restraints weight = 4241.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.156758 restraints weight = 3357.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.157971 restraints weight = 2865.886| |-----------------------------------------------------------------------------| r_work (final): 0.4220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6933 moved from start: 0.3140 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= 0.125 Angle : 0.623 8.130 7928 Z= 0.327 Chirality : 0.045 0.192 890 Planarity : 0.005 0.033 961 Dihedral : 14.733 83.149 990 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 3.48 % Allowed : 17.91 % Favored : 78.61 % 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: -0.14 (0.34), residues: 646 helix: 1.06 (0.36), residues: 203 sheet: -0.54 (0.41), residues: 160 loop : -0.55 (0.40), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 207 TYR 0.008 0.001 TYR A 790 PHE 0.023 0.002 PHE A 716 TRP 0.008 0.001 TRP A 134 HIS 0.004 0.001 HIS A 634 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 ( 5795) covalent geometry : angle 0.62311 / 0.33 ( 7928) hydrogen bonds : bond 0.03615 / 3.58 ( 241) hydrogen bonds : angle 4.88981 / 6.51 ( 662) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1085.47 seconds wall clock time: 19 minutes 22.91 seconds (1162.91 seconds total)