Starting phenix.real_space_refine on Tue Aug 4 15:42:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ym9_73099/08_2026/9ym9_73099.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ym9_73099/08_2026/9ym9_73099.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ym9_73099/08_2026/9ym9_73099.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ym9_73099/08_2026/9ym9_73099.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ym9_73099/08_2026/9ym9_73099.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ym9_73099/08_2026/9ym9_73099.map" } resolution = 3.79 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 41 5.49 5 S 20 5.16 5 C 2679 2.51 5 N 814 2.21 5 O 926 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 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: 4480 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 455, 3606 Classifications: {'peptide': 455} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 27, 'TRANS': 427} Chain breaks: 2 Chain: "B" Number of atoms: 496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 496 Classifications: {'RNA': 23} Modifications used: {'p5*END': 1, 'rna2p_pur': 2, 'rna2p_pyr': 1, 'rna3p_pur': 12, 'rna3p_pyr': 8} Link IDs: {'rna2p': 2, 'rna3p': 20} Chain: "C" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 378 Classifications: {'RNA': 18} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 3, 'rna3p_pur': 5, 'rna3p_pyr': 7} Link IDs: {'rna2p': 6, 'rna3p': 11} Time building chain proxies: 1.20, per 1000 atoms: 0.27 Number of scatterers: 4480 At special positions: 0 Unit cell: (95.424, 77.106, 75.828, 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 20 16.00 P 41 15.00 O 926 8.00 N 814 7.00 C 2679 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: 0.41 Conformation dependent library (CDL) restraints added in 78.1 milliseconds 898 Ramachandran restraints generated. 449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 852 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 3 sheets defined 36.3% alpha, 12.5% beta 18 base pairs and 29 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'A' and resid 463 through 481 removed outlier: 3.564A pdb=" N LEU A 467 " --> pdb=" O THR A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 512 Processing helix chain 'A' and resid 527 through 538 removed outlier: 3.536A pdb=" N GLU A 531 " --> pdb=" O PRO A 527 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LYS A 533 " --> pdb=" O TYR A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 554 removed outlier: 3.566A pdb=" N ARG A 554 " --> pdb=" O LYS A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 571 removed outlier: 3.921A pdb=" N VAL A 569 " --> pdb=" O LEU A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 589 removed outlier: 4.159A pdb=" N GLN A 589 " --> pdb=" O VAL A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 657 removed outlier: 3.917A pdb=" N ARG A 647 " --> pdb=" O ALA A 643 " (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: 3.676A pdb=" N LEU A 684 " --> pdb=" O LEU A 680 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N LEU A 685 " --> pdb=" O HIS A 681 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 723 Processing helix chain 'A' and resid 752 through 756 removed outlier: 3.582A pdb=" N GLY A 755 " --> pdb=" O SER A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 775 through 789 Processing helix chain 'A' and resid 800 through 814 Processing helix chain 'A' and resid 839 through 846 removed outlier: 4.067A pdb=" N LYS A 844 " --> pdb=" O GLN A 840 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 854 Processing sheet with id=AA1, first strand: chain 'A' and resid 407 through 409 removed outlier: 3.513A pdb=" N VAL A 408 " --> pdb=" O LEU A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 451 through 455 removed outlier: 6.494A pdb=" N ALA A 452 " --> pdb=" O VAL A 519 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N ILE A 521 " --> pdb=" O ALA A 452 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N ALA A 454 " --> pdb=" O ILE A 521 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 625 through 631 removed outlier: 4.009A pdb=" N ILE A 611 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR A 599 " --> pdb=" O ILE A 611 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N PHE A 593 " --> pdb=" O SER A 617 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ILE A 592 " --> pdb=" O ILE A 665 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N TYR A 667 " --> pdb=" O ILE A 592 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N LEU A 594 " --> pdb=" O TYR A 667 " (cutoff:3.500A) removed outlier: 8.162A pdb=" N ASP A 669 " --> pdb=" O LEU A 594 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ALA A 596 " --> pdb=" O ASP A 669 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N ILE A 702 " --> pdb=" O ASP A 770 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ASP A 770 " --> pdb=" O ILE A 702 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N PHE A 704 " --> pdb=" O LEU A 768 " (cutoff:3.500A) 128 hydrogen bonds defined for protein. 357 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 45 hydrogen bonds 90 hydrogen bond angles 0 basepair planarities 18 basepair parallelities 29 stacking parallelities Total time for adding SS restraints: 0.55 Time building geometry restraints manager: 0.53 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: 1245 1.34 - 1.45: 975 1.45 - 1.57: 2339 1.57 - 1.69: 80 1.69 - 1.81: 28 Bond restraints: 4667 Sorted by residual: bond pdb=" C3' A C 6 " pdb=" O3' A C 6 " ideal model delta sigma weight residual 1.427 1.449 -0.022 1.20e-02 6.94e+03 3.22e+00 bond pdb=" N1 C C 20 " pdb=" C6 C C 20 " ideal model delta sigma weight residual 1.367 1.359 0.008 6.00e-03 2.78e+04 1.74e+00 bond pdb=" O3' A C 6 " pdb=" P C C 7 " ideal model delta sigma weight residual 1.607 1.621 -0.014 1.20e-02 6.94e+03 1.42e+00 bond pdb=" N VAL A 791 " pdb=" CA VAL A 791 " ideal model delta sigma weight residual 1.474 1.456 0.018 1.57e-02 4.06e+03 1.37e+00 bond pdb=" C8 G B 14 " pdb=" N7 G B 14 " ideal model delta sigma weight residual 1.305 1.298 0.007 6.00e-03 2.78e+04 1.30e+00 ... (remaining 4662 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 6208 1.61 - 3.21: 274 3.21 - 4.82: 34 4.82 - 6.43: 4 6.43 - 8.03: 3 Bond angle restraints: 6523 Sorted by residual: angle pdb=" C GLU A 745 " pdb=" CA GLU A 745 " pdb=" CB GLU A 745 " ideal model delta sigma weight residual 116.54 109.69 6.85 1.15e+00 7.56e-01 3.55e+01 angle pdb=" C3' A C 6 " pdb=" O3' A C 6 " pdb=" P C C 7 " ideal model delta sigma weight residual 119.70 126.69 -6.99 1.20e+00 6.94e-01 3.39e+01 angle pdb=" O5' C C 7 " pdb=" C5' C C 7 " pdb=" C4' C C 7 " ideal model delta sigma weight residual 109.40 113.23 -3.83 8.00e-01 1.56e+00 2.29e+01 angle pdb=" O2 C C 13 " pdb=" C2 C C 13 " pdb=" N3 C C 13 " ideal model delta sigma weight residual 121.90 118.74 3.16 7.00e-01 2.04e+00 2.04e+01 angle pdb=" C1' U B 6 " pdb=" N1 U B 6 " pdb=" C2 U B 6 " ideal model delta sigma weight residual 117.70 123.03 -5.33 1.20e+00 6.94e-01 1.97e+01 ... (remaining 6518 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.99: 2666 34.99 - 69.99: 157 69.99 - 104.98: 19 104.98 - 139.97: 0 139.97 - 174.96: 3 Dihedral angle restraints: 2845 sinusoidal: 1525 harmonic: 1320 Sorted by residual: dihedral pdb=" C4' A C 6 " pdb=" C3' A C 6 " pdb=" O3' A C 6 " pdb=" P C C 7 " ideal model delta sinusoidal sigma weight residual -110.00 64.96 -174.96 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' G C 19 " pdb=" C3' G C 19 " pdb=" O3' G C 19 " pdb=" P C C 20 " ideal model delta sinusoidal sigma weight residual 220.00 61.45 158.55 1 3.50e+01 8.16e-04 1.51e+01 dihedral pdb=" C4' A C 15 " pdb=" C3' A C 15 " pdb=" O3' A C 15 " pdb=" P U C 16 " ideal model delta sinusoidal sigma weight residual 220.00 70.69 149.31 1 3.50e+01 8.16e-04 1.46e+01 ... (remaining 2842 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 592 0.051 - 0.103: 109 0.103 - 0.154: 56 0.154 - 0.205: 4 0.205 - 0.257: 3 Chirality restraints: 764 Sorted by residual: chirality pdb=" C3' A C 6 " pdb=" C4' A C 6 " pdb=" O3' A C 6 " pdb=" C2' A C 6 " both_signs ideal model delta sigma weight residual False -2.74 -2.49 -0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" C1' G B 14 " pdb=" O4' G B 14 " pdb=" C2' G B 14 " pdb=" N9 G B 14 " both_signs ideal model delta sigma weight residual False 2.47 2.24 0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" C1' U B 6 " pdb=" O4' U B 6 " pdb=" C2' U B 6 " pdb=" N1 U B 6 " both_signs ideal model delta sigma weight residual False 2.47 2.26 0.21 2.00e-01 2.50e+01 1.15e+00 ... (remaining 761 not shown) Planarity restraints: 690 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G B 14 " -0.030 2.00e-02 2.50e+03 1.29e-02 5.00e+00 pdb=" N9 G B 14 " 0.030 2.00e-02 2.50e+03 pdb=" C8 G B 14 " 0.004 2.00e-02 2.50e+03 pdb=" N7 G B 14 " 0.004 2.00e-02 2.50e+03 pdb=" C5 G B 14 " 0.001 2.00e-02 2.50e+03 pdb=" C6 G B 14 " -0.001 2.00e-02 2.50e+03 pdb=" O6 G B 14 " -0.011 2.00e-02 2.50e+03 pdb=" N1 G B 14 " -0.004 2.00e-02 2.50e+03 pdb=" C2 G B 14 " -0.001 2.00e-02 2.50e+03 pdb=" N2 G B 14 " 0.006 2.00e-02 2.50e+03 pdb=" N3 G B 14 " 0.004 2.00e-02 2.50e+03 pdb=" C4 G B 14 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C C 20 " 0.025 2.00e-02 2.50e+03 1.24e-02 3.47e+00 pdb=" N1 C C 20 " -0.024 2.00e-02 2.50e+03 pdb=" C2 C C 20 " -0.007 2.00e-02 2.50e+03 pdb=" O2 C C 20 " -0.001 2.00e-02 2.50e+03 pdb=" N3 C C 20 " 0.002 2.00e-02 2.50e+03 pdb=" C4 C C 20 " 0.004 2.00e-02 2.50e+03 pdb=" N4 C C 20 " 0.009 2.00e-02 2.50e+03 pdb=" C5 C C 20 " -0.003 2.00e-02 2.50e+03 pdb=" C6 C C 20 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U B 6 " -0.019 2.00e-02 2.50e+03 1.24e-02 3.46e+00 pdb=" N1 U B 6 " 0.031 2.00e-02 2.50e+03 pdb=" C2 U B 6 " -0.003 2.00e-02 2.50e+03 pdb=" O2 U B 6 " 0.000 2.00e-02 2.50e+03 pdb=" N3 U B 6 " -0.001 2.00e-02 2.50e+03 pdb=" C4 U B 6 " -0.003 2.00e-02 2.50e+03 pdb=" O4 U B 6 " -0.003 2.00e-02 2.50e+03 pdb=" C5 U B 6 " -0.002 2.00e-02 2.50e+03 pdb=" C6 U B 6 " 0.000 2.00e-02 2.50e+03 ... (remaining 687 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 241 2.71 - 3.26: 4504 3.26 - 3.80: 7899 3.80 - 4.35: 9623 4.35 - 4.90: 15039 Nonbonded interactions: 37306 Sorted by model distance: nonbonded pdb=" O2' G C 19 " pdb=" OP1 C C 20 " model vdw 2.162 3.040 nonbonded pdb=" OG SER A 763 " pdb=" OG SER A 798 " model vdw 2.186 3.040 nonbonded pdb=" O2' C C 8 " pdb=" O5' U C 9 " model vdw 2.221 3.040 nonbonded pdb=" O ILE A 38 " pdb=" N GLY A 410 " model vdw 2.244 3.120 nonbonded pdb=" NZ LYS A 570 " pdb=" OXT ALA A 859 " model vdw 2.247 3.120 ... (remaining 37301 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: 8.960 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: 0.260 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 5.670 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:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5411 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 0.022 4667 Z= 0.196 Angle : 0.747 8.034 6523 Z= 0.569 Chirality : 0.052 0.257 764 Planarity : 0.005 0.035 690 Dihedral : 19.957 174.964 1993 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 3.31 % Allowed : 9.92 % Favored : 86.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.39), residues: 449 helix: -0.11 (0.45), residues: 143 sheet: 0.00 (0.56), residues: 78 loop : -1.25 (0.41), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 668 TYR 0.008 0.001 TYR A 790 PHE 0.010 0.002 PHE A 666 TRP 0.005 0.001 TRP A 451 HIS 0.003 0.001 HIS A 682 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.20 ( 4667) covalent geometry : angle 0.74668 / 0.57 ( 6523) hydrogen bonds : bond 0.20496 / 13.25 ( 173) hydrogen bonds : angle 7.49560 / 5.51 ( 447) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 898 Ramachandran restraints generated. 449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 898 Ramachandran restraints generated. 449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 0.155 Fit side-chains REVERT: A 419 LEU cc_start: 0.6749 (OUTLIER) cc_final: 0.6498 (tt) REVERT: A 531 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.6717 (tm-30) REVERT: A 534 ARG cc_start: 0.6709 (mtp85) cc_final: 0.6444 (ttp80) REVERT: A 671 VAL cc_start: 0.7236 (OUTLIER) cc_final: 0.6918 (m) REVERT: A 784 TYR cc_start: 0.7597 (t80) cc_final: 0.7141 (t80) outliers start: 13 outliers final: 5 residues processed: 92 average time/residue: 0.0860 time to fit residues: 9.6667 Evaluate side-chains 72 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 531 GLU Chi-restraints excluded: chain A residue 533 LYS Chi-restraints excluded: chain A residue 619 ASP Chi-restraints excluded: chain A residue 671 VAL Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 766 HIS Chi-restraints excluded: chain A residue 778 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 16 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 19 optimal weight: 0.0270 chunk 30 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 37 optimal weight: 4.9990 overall best weight: 0.7440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 849 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4750 r_free = 0.4750 target = 0.221656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.185238 restraints weight = 7407.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.190833 restraints weight = 4452.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.194722 restraints weight = 3115.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.197397 restraints weight = 2391.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.199099 restraints weight = 1960.283| |-----------------------------------------------------------------------------| r_work (final): 0.4534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6202 moved from start: 0.1239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4667 Z= 0.162 Angle : 0.733 8.872 6523 Z= 0.393 Chirality : 0.053 0.495 764 Planarity : 0.006 0.037 690 Dihedral : 22.601 178.783 1133 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 3.82 % Allowed : 14.25 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.31 (0.39), residues: 449 helix: -0.08 (0.43), residues: 144 sheet: -0.15 (0.54), residues: 88 loop : -1.73 (0.41), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 812 TYR 0.009 0.002 TYR A 494 PHE 0.011 0.002 PHE A 666 TRP 0.005 0.001 TRP A 769 HIS 0.003 0.001 HIS A 839 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.16 ( 4667) covalent geometry : angle 0.73288 / 0.39 ( 6523) hydrogen bonds : bond 0.08341 / 5.42 ( 173) hydrogen bonds : angle 5.40831 / 3.70 ( 447) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 898 Ramachandran restraints generated. 449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 898 Ramachandran restraints generated. 449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 68 time to evaluate : 0.182 Fit side-chains revert: symmetry clash REVERT: A 534 ARG cc_start: 0.6886 (mtp85) cc_final: 0.6501 (ttp80) REVERT: A 618 MET cc_start: 0.5454 (tpt) cc_final: 0.5160 (tpt) REVERT: A 671 VAL cc_start: 0.7589 (OUTLIER) cc_final: 0.7312 (m) outliers start: 15 outliers final: 9 residues processed: 79 average time/residue: 0.0816 time to fit residues: 8.0432 Evaluate side-chains 68 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 58 time to evaluate : 0.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 533 LYS Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 619 ASP Chi-restraints excluded: chain A residue 671 VAL Chi-restraints excluded: chain A residue 683 GLU Chi-restraints excluded: chain A residue 697 ASP Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 766 HIS Chi-restraints excluded: chain A residue 791 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 11 optimal weight: 0.0980 chunk 37 optimal weight: 0.8980 chunk 1 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 13 optimal weight: 0.5980 chunk 19 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 4 optimal weight: 0.0030 chunk 14 optimal weight: 0.3980 chunk 6 optimal weight: 3.9990 overall best weight: 0.3790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 849 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4776 r_free = 0.4776 target = 0.224388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.188678 restraints weight = 7327.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.194265 restraints weight = 4392.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.198200 restraints weight = 3043.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.200931 restraints weight = 2319.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4560 r_free = 0.4560 target = 0.202658 restraints weight = 1885.813| |-----------------------------------------------------------------------------| r_work (final): 0.4567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6133 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 4667 Z= 0.139 Angle : 0.670 8.100 6523 Z= 0.363 Chirality : 0.050 0.477 764 Planarity : 0.005 0.037 690 Dihedral : 22.248 175.785 1125 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 3.56 % Allowed : 15.78 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.39), residues: 449 helix: -0.01 (0.44), residues: 144 sheet: 0.19 (0.57), residues: 80 loop : -1.73 (0.40), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 812 TYR 0.013 0.001 TYR A 654 PHE 0.011 0.001 PHE A 659 TRP 0.003 0.001 TRP A 435 HIS 0.004 0.001 HIS A 466 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.14 ( 4667) covalent geometry : angle 0.67030 / 0.36 ( 6523) hydrogen bonds : bond 0.07691 / 4.88 ( 173) hydrogen bonds : angle 5.07238 / 3.49 ( 447) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 898 Ramachandran restraints generated. 449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 898 Ramachandran restraints generated. 449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 68 time to evaluate : 0.092 Fit side-chains revert: symmetry clash REVERT: A 534 ARG cc_start: 0.6916 (mtp85) cc_final: 0.6286 (ttp80) REVERT: A 538 THR cc_start: 0.7573 (t) cc_final: 0.7265 (p) REVERT: A 631 VAL cc_start: 0.6896 (t) cc_final: 0.6645 (p) outliers start: 14 outliers final: 10 residues processed: 77 average time/residue: 0.0713 time to fit residues: 6.8031 Evaluate side-chains 73 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 533 LYS Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 619 ASP Chi-restraints excluded: chain A residue 683 GLU Chi-restraints excluded: chain A residue 697 ASP Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 766 HIS Chi-restraints excluded: chain A residue 791 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 0 optimal weight: 9.9990 chunk 44 optimal weight: 0.8980 chunk 23 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 36 optimal weight: 4.9990 chunk 19 optimal weight: 0.0670 chunk 40 optimal weight: 0.8980 chunk 21 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 overall best weight: 0.6920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 507 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4753 r_free = 0.4753 target = 0.221886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.186130 restraints weight = 7229.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.191644 restraints weight = 4332.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.195496 restraints weight = 3001.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4518 r_free = 0.4518 target = 0.198138 restraints weight = 2280.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.199842 restraints weight = 1856.557| |-----------------------------------------------------------------------------| r_work (final): 0.4538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6176 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 0.030 4667 Z= 0.143 Angle : 0.663 9.081 6523 Z= 0.356 Chirality : 0.049 0.447 764 Planarity : 0.005 0.038 690 Dihedral : 22.104 170.043 1124 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 15.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 5.85 % Allowed : 15.01 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.23 (0.39), residues: 449 helix: 0.12 (0.44), residues: 143 sheet: -0.14 (0.56), residues: 88 loop : -1.75 (0.40), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 812 TYR 0.011 0.002 TYR A 654 PHE 0.010 0.001 PHE A 470 TRP 0.003 0.001 TRP A 435 HIS 0.004 0.001 HIS A 507 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 ( 4667) covalent geometry : angle 0.66263 / 0.36 ( 6523) hydrogen bonds : bond 0.06831 / 4.35 ( 173) hydrogen bonds : angle 4.84567 / 3.32 ( 447) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 898 Ramachandran restraints generated. 449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 898 Ramachandran restraints generated. 449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 68 time to evaluate : 0.153 Fit side-chains revert: symmetry clash REVERT: A 534 ARG cc_start: 0.6950 (mtp85) cc_final: 0.6369 (ttp80) REVERT: A 538 THR cc_start: 0.7638 (t) cc_final: 0.7398 (p) REVERT: A 631 VAL cc_start: 0.6852 (OUTLIER) cc_final: 0.6582 (p) REVERT: A 645 MET cc_start: 0.4067 (mtm) cc_final: 0.3836 (ttm) REVERT: A 671 VAL cc_start: 0.7670 (OUTLIER) cc_final: 0.7396 (m) REVERT: A 850 GLN cc_start: 0.6637 (OUTLIER) cc_final: 0.6012 (pp30) outliers start: 23 outliers final: 16 residues processed: 82 average time/residue: 0.0773 time to fit residues: 8.0046 Evaluate side-chains 82 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 63 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 533 LYS Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 567 ILE Chi-restraints excluded: chain A residue 619 ASP Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 634 HIS Chi-restraints excluded: chain A residue 671 VAL Chi-restraints excluded: chain A residue 683 GLU Chi-restraints excluded: chain A residue 697 ASP Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 766 HIS Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 846 VAL Chi-restraints excluded: chain A residue 850 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 45 optimal weight: 9.9990 chunk 21 optimal weight: 0.0870 chunk 5 optimal weight: 4.9990 chunk 29 optimal weight: 9.9990 chunk 8 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 12 optimal weight: 0.1980 chunk 4 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4791 r_free = 0.4791 target = 0.225468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.190612 restraints weight = 7223.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.196285 restraints weight = 4259.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4542 r_free = 0.4542 target = 0.200141 restraints weight = 2902.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4565 r_free = 0.4565 target = 0.202638 restraints weight = 2178.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4588 r_free = 0.4588 target = 0.204696 restraints weight = 1770.966| |-----------------------------------------------------------------------------| r_work (final): 0.4605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6122 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4667 Z= 0.136 Angle : 0.659 8.777 6523 Z= 0.353 Chirality : 0.048 0.435 764 Planarity : 0.005 0.038 690 Dihedral : 22.052 168.395 1124 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 6.36 % Allowed : 15.27 % Favored : 78.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.39), residues: 449 helix: 0.19 (0.44), residues: 143 sheet: 0.11 (0.58), residues: 80 loop : -1.62 (0.40), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 554 TYR 0.010 0.001 TYR A 654 PHE 0.011 0.001 PHE A 470 TRP 0.003 0.001 TRP A 435 HIS 0.002 0.001 HIS A 682 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.14 ( 4667) covalent geometry : angle 0.65896 / 0.35 ( 6523) hydrogen bonds : bond 0.06631 / 4.25 ( 173) hydrogen bonds : angle 4.77986 / 3.25 ( 447) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 898 Ramachandran restraints generated. 449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 898 Ramachandran restraints generated. 449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 66 time to evaluate : 0.149 Fit side-chains revert: symmetry clash REVERT: A 534 ARG cc_start: 0.6945 (mtp85) cc_final: 0.6356 (ttp80) REVERT: A 538 THR cc_start: 0.7641 (t) cc_final: 0.7418 (p) REVERT: A 631 VAL cc_start: 0.6780 (t) cc_final: 0.6530 (p) REVERT: A 671 VAL cc_start: 0.7653 (OUTLIER) cc_final: 0.7348 (m) REVERT: A 804 TYR cc_start: 0.7808 (OUTLIER) cc_final: 0.7435 (t80) outliers start: 25 outliers final: 17 residues processed: 83 average time/residue: 0.0784 time to fit residues: 8.2635 Evaluate side-chains 82 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 63 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 533 LYS Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 567 ILE Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 619 ASP Chi-restraints excluded: chain A residue 634 HIS Chi-restraints excluded: chain A residue 671 VAL Chi-restraints excluded: chain A residue 683 GLU Chi-restraints excluded: chain A residue 697 ASP Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 766 HIS Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 804 TYR Chi-restraints excluded: chain A residue 846 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 44 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 40 optimal weight: 0.7980 chunk 29 optimal weight: 10.0000 chunk 20 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 46 optimal weight: 20.0000 chunk 8 optimal weight: 0.7980 chunk 9 optimal weight: 0.1980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 575 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4779 r_free = 0.4779 target = 0.224295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.188821 restraints weight = 7389.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.194377 restraints weight = 4386.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4521 r_free = 0.4521 target = 0.198313 restraints weight = 3018.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.200832 restraints weight = 2273.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4568 r_free = 0.4568 target = 0.202844 restraints weight = 1852.456| |-----------------------------------------------------------------------------| r_work (final): 0.4588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6153 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4667 Z= 0.145 Angle : 0.661 9.275 6523 Z= 0.353 Chirality : 0.048 0.428 764 Planarity : 0.005 0.037 690 Dihedral : 21.999 167.531 1124 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 16.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 5.34 % Allowed : 17.30 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.39), residues: 449 helix: 0.14 (0.44), residues: 143 sheet: 0.08 (0.57), residues: 80 loop : -1.62 (0.40), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 554 TYR 0.010 0.002 TYR A 654 PHE 0.009 0.001 PHE A 470 TRP 0.003 0.001 TRP A 435 HIS 0.002 0.001 HIS A 682 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 ( 4667) covalent geometry : angle 0.66075 / 0.35 ( 6523) hydrogen bonds : bond 0.06410 / 4.13 ( 173) hydrogen bonds : angle 4.71320 / 3.22 ( 447) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 898 Ramachandran restraints generated. 449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 898 Ramachandran restraints generated. 449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 66 time to evaluate : 0.156 Fit side-chains revert: symmetry clash REVERT: A 479 ARG cc_start: 0.6767 (ttm110) cc_final: 0.6233 (mtp-110) REVERT: A 534 ARG cc_start: 0.6962 (mtp85) cc_final: 0.6386 (ttp80) REVERT: A 538 THR cc_start: 0.7659 (t) cc_final: 0.7439 (p) REVERT: A 631 VAL cc_start: 0.6788 (OUTLIER) cc_final: 0.6514 (p) REVERT: A 671 VAL cc_start: 0.7669 (OUTLIER) cc_final: 0.7341 (m) REVERT: A 784 TYR cc_start: 0.7165 (t80) cc_final: 0.6661 (t80) REVERT: A 804 TYR cc_start: 0.7814 (OUTLIER) cc_final: 0.7416 (t80) REVERT: A 850 GLN cc_start: 0.6713 (OUTLIER) cc_final: 0.5830 (pp30) outliers start: 21 outliers final: 16 residues processed: 81 average time/residue: 0.0804 time to fit residues: 8.2234 Evaluate side-chains 80 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 60 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 533 LYS Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 567 ILE Chi-restraints excluded: chain A residue 619 ASP Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 634 HIS Chi-restraints excluded: chain A residue 671 VAL Chi-restraints excluded: chain A residue 683 GLU Chi-restraints excluded: chain A residue 697 ASP Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 766 HIS Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 804 TYR Chi-restraints excluded: chain A residue 846 VAL Chi-restraints excluded: chain A residue 850 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 21 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 chunk 45 optimal weight: 0.7980 chunk 46 optimal weight: 20.0000 chunk 0 optimal weight: 9.9990 chunk 19 optimal weight: 0.9980 chunk 30 optimal weight: 7.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 551 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4774 r_free = 0.4774 target = 0.223713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.187444 restraints weight = 7312.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.193084 restraints weight = 4311.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.197054 restraints weight = 2958.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4535 r_free = 0.4535 target = 0.199725 restraints weight = 2235.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4549 r_free = 0.4549 target = 0.201181 restraints weight = 1817.809| |-----------------------------------------------------------------------------| r_work (final): 0.4559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6191 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 4667 Z= 0.154 Angle : 0.685 11.908 6523 Z= 0.364 Chirality : 0.048 0.422 764 Planarity : 0.005 0.037 690 Dihedral : 21.983 166.730 1124 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 16.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 5.34 % Allowed : 19.08 % Favored : 75.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (0.39), residues: 449 helix: -0.04 (0.43), residues: 149 sheet: 0.10 (0.58), residues: 80 loop : -1.72 (0.40), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 630 TYR 0.011 0.002 TYR A 654 PHE 0.008 0.001 PHE A 505 TRP 0.003 0.001 TRP A 435 HIS 0.003 0.001 HIS A 764 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 ( 4667) covalent geometry : angle 0.68528 / 0.36 ( 6523) hydrogen bonds : bond 0.06281 / 4.08 ( 173) hydrogen bonds : angle 4.78210 / 3.24 ( 447) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 898 Ramachandran restraints generated. 449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 898 Ramachandran restraints generated. 449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 61 time to evaluate : 0.154 Fit side-chains revert: symmetry clash REVERT: A 479 ARG cc_start: 0.6772 (ttm110) cc_final: 0.6259 (mtp-110) REVERT: A 534 ARG cc_start: 0.6990 (mtp85) cc_final: 0.6402 (ttp80) REVERT: A 631 VAL cc_start: 0.6881 (OUTLIER) cc_final: 0.6606 (p) REVERT: A 671 VAL cc_start: 0.7682 (OUTLIER) cc_final: 0.7359 (m) REVERT: A 784 TYR cc_start: 0.7161 (t80) cc_final: 0.6703 (t80) REVERT: A 850 GLN cc_start: 0.6710 (OUTLIER) cc_final: 0.5793 (pp30) outliers start: 21 outliers final: 16 residues processed: 77 average time/residue: 0.0833 time to fit residues: 8.0549 Evaluate side-chains 77 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 58 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 533 LYS Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 567 ILE Chi-restraints excluded: chain A residue 619 ASP Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 634 HIS Chi-restraints excluded: chain A residue 671 VAL Chi-restraints excluded: chain A residue 683 GLU Chi-restraints excluded: chain A residue 697 ASP Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 766 HIS Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 846 VAL Chi-restraints excluded: chain A residue 850 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 36 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 chunk 24 optimal weight: 0.9980 chunk 47 optimal weight: 20.0000 chunk 30 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4756 r_free = 0.4756 target = 0.221828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.184681 restraints weight = 7315.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.190097 restraints weight = 4386.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.193977 restraints weight = 3066.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.196556 restraints weight = 2351.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.198053 restraints weight = 1933.920| |-----------------------------------------------------------------------------| r_work (final): 0.4535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6268 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 4667 Z= 0.171 Angle : 0.708 12.253 6523 Z= 0.375 Chirality : 0.049 0.415 764 Planarity : 0.005 0.036 690 Dihedral : 22.027 165.645 1124 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 16.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 5.60 % Allowed : 18.32 % Favored : 76.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.39), residues: 449 helix: -0.06 (0.43), residues: 149 sheet: -0.03 (0.58), residues: 79 loop : -1.89 (0.39), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 663 TYR 0.013 0.002 TYR A 654 PHE 0.010 0.001 PHE A 666 TRP 0.003 0.001 TRP A 451 HIS 0.003 0.001 HIS A 682 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.17 ( 4667) covalent geometry : angle 0.70800 / 0.38 ( 6523) hydrogen bonds : bond 0.06262 / 4.13 ( 173) hydrogen bonds : angle 4.84290 / 3.29 ( 447) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 898 Ramachandran restraints generated. 449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 898 Ramachandran restraints generated. 449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 60 time to evaluate : 0.154 Fit side-chains revert: symmetry clash REVERT: A 479 ARG cc_start: 0.6879 (ttm110) cc_final: 0.6357 (mtp-110) REVERT: A 534 ARG cc_start: 0.6807 (mtp85) cc_final: 0.6535 (ttp80) REVERT: A 554 ARG cc_start: 0.7103 (mmt180) cc_final: 0.6451 (ttp-170) REVERT: A 671 VAL cc_start: 0.7679 (OUTLIER) cc_final: 0.7354 (m) REVERT: A 716 PHE cc_start: 0.5756 (OUTLIER) cc_final: 0.4374 (m-80) REVERT: A 784 TYR cc_start: 0.7149 (t80) cc_final: 0.6665 (t80) REVERT: A 850 GLN cc_start: 0.6766 (OUTLIER) cc_final: 0.5887 (pp30) outliers start: 22 outliers final: 16 residues processed: 77 average time/residue: 0.0822 time to fit residues: 7.9527 Evaluate side-chains 76 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 57 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 533 LYS Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 619 ASP Chi-restraints excluded: chain A residue 634 HIS Chi-restraints excluded: chain A residue 671 VAL Chi-restraints excluded: chain A residue 683 GLU Chi-restraints excluded: chain A residue 697 ASP Chi-restraints excluded: chain A residue 716 PHE Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 766 HIS Chi-restraints excluded: chain A residue 774 PHE Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 846 VAL Chi-restraints excluded: chain A residue 850 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 34 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 7 optimal weight: 7.9990 chunk 47 optimal weight: 20.0000 chunk 20 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 12 optimal weight: 7.9990 chunk 41 optimal weight: 0.5980 chunk 32 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4761 r_free = 0.4761 target = 0.222529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.185545 restraints weight = 7208.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.191099 restraints weight = 4299.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.194953 restraints weight = 2965.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.197420 restraints weight = 2271.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.199517 restraints weight = 1875.121| |-----------------------------------------------------------------------------| r_work (final): 0.4548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6209 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4667 Z= 0.152 Angle : 0.690 10.606 6523 Z= 0.368 Chirality : 0.048 0.420 764 Planarity : 0.005 0.037 690 Dihedral : 21.996 166.336 1124 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 16.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 5.09 % Allowed : 18.32 % Favored : 76.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.39), residues: 449 helix: -0.07 (0.43), residues: 149 sheet: -0.19 (0.56), residues: 85 loop : -1.84 (0.41), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 663 TYR 0.018 0.002 TYR A 494 PHE 0.011 0.001 PHE A 470 TRP 0.002 0.001 TRP A 435 HIS 0.003 0.001 HIS A 682 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 ( 4667) covalent geometry : angle 0.68954 / 0.37 ( 6523) hydrogen bonds : bond 0.06179 / 4.09 ( 173) hydrogen bonds : angle 4.80803 / 3.26 ( 447) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 898 Ramachandran restraints generated. 449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 898 Ramachandran restraints generated. 449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 57 time to evaluate : 0.158 Fit side-chains revert: symmetry clash REVERT: A 419 LEU cc_start: 0.7300 (OUTLIER) cc_final: 0.6686 (tt) REVERT: A 420 TYR cc_start: 0.8107 (m-80) cc_final: 0.7758 (m-80) REVERT: A 479 ARG cc_start: 0.6856 (ttm110) cc_final: 0.6352 (mtp-110) REVERT: A 534 ARG cc_start: 0.6770 (mtp85) cc_final: 0.6529 (ttp80) REVERT: A 554 ARG cc_start: 0.7160 (mmt180) cc_final: 0.6517 (ttp-170) REVERT: A 671 VAL cc_start: 0.7649 (OUTLIER) cc_final: 0.7355 (m) REVERT: A 716 PHE cc_start: 0.5720 (OUTLIER) cc_final: 0.4354 (m-80) REVERT: A 784 TYR cc_start: 0.7135 (t80) cc_final: 0.6673 (t80) REVERT: A 850 GLN cc_start: 0.6722 (OUTLIER) cc_final: 0.5846 (pp30) outliers start: 20 outliers final: 14 residues processed: 72 average time/residue: 0.0859 time to fit residues: 7.7981 Evaluate side-chains 73 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 55 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 533 LYS Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 619 ASP Chi-restraints excluded: chain A residue 634 HIS Chi-restraints excluded: chain A residue 671 VAL Chi-restraints excluded: chain A residue 697 ASP Chi-restraints excluded: chain A residue 716 PHE Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 766 HIS Chi-restraints excluded: chain A residue 774 PHE Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 846 VAL Chi-restraints excluded: chain A residue 850 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 44 optimal weight: 0.8980 chunk 46 optimal weight: 20.0000 chunk 8 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 12 optimal weight: 0.4980 chunk 35 optimal weight: 0.9990 chunk 19 optimal weight: 0.0770 chunk 41 optimal weight: 0.4980 chunk 38 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 575 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4771 r_free = 0.4771 target = 0.223683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.187184 restraints weight = 7133.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.192704 restraints weight = 4227.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.196706 restraints weight = 2911.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4528 r_free = 0.4528 target = 0.199292 restraints weight = 2199.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4549 r_free = 0.4549 target = 0.201198 restraints weight = 1793.240| |-----------------------------------------------------------------------------| r_work (final): 0.4562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6183 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4667 Z= 0.141 Angle : 0.675 10.392 6523 Z= 0.362 Chirality : 0.048 0.420 764 Planarity : 0.005 0.037 690 Dihedral : 21.962 166.474 1124 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 15.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 4.83 % Allowed : 19.08 % Favored : 76.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.41 (0.39), residues: 449 helix: -0.04 (0.43), residues: 150 sheet: -0.37 (0.57), residues: 87 loop : -1.85 (0.40), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 663 TYR 0.009 0.001 TYR A 654 PHE 0.008 0.001 PHE A 666 TRP 0.003 0.001 TRP A 451 HIS 0.002 0.000 HIS A 753 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.14 ( 4667) covalent geometry : angle 0.67455 / 0.36 ( 6523) hydrogen bonds : bond 0.06073 / 4.06 ( 173) hydrogen bonds : angle 4.74833 / 3.23 ( 447) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 898 Ramachandran restraints generated. 449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 898 Ramachandran restraints generated. 449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 58 time to evaluate : 0.196 Fit side-chains revert: symmetry clash REVERT: A 419 LEU cc_start: 0.7309 (OUTLIER) cc_final: 0.6716 (tt) REVERT: A 420 TYR cc_start: 0.8143 (m-80) cc_final: 0.7832 (m-80) REVERT: A 479 ARG cc_start: 0.6888 (ttm110) cc_final: 0.6357 (mtp-110) REVERT: A 534 ARG cc_start: 0.6733 (mtp85) cc_final: 0.6447 (ttp80) REVERT: A 554 ARG cc_start: 0.7101 (mmt180) cc_final: 0.6505 (ttp-170) REVERT: A 671 VAL cc_start: 0.7664 (OUTLIER) cc_final: 0.7358 (m) REVERT: A 716 PHE cc_start: 0.5730 (OUTLIER) cc_final: 0.4378 (m-80) REVERT: A 784 TYR cc_start: 0.7159 (t80) cc_final: 0.6695 (t80) REVERT: A 850 GLN cc_start: 0.6762 (OUTLIER) cc_final: 0.5829 (pp30) outliers start: 19 outliers final: 13 residues processed: 74 average time/residue: 0.0896 time to fit residues: 8.2743 Evaluate side-chains 72 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 55 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 533 LYS Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 619 ASP Chi-restraints excluded: chain A residue 634 HIS Chi-restraints excluded: chain A residue 671 VAL Chi-restraints excluded: chain A residue 697 ASP Chi-restraints excluded: chain A residue 716 PHE Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 766 HIS Chi-restraints excluded: chain A residue 774 PHE Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 846 VAL Chi-restraints excluded: chain A residue 850 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 30 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 chunk 16 optimal weight: 0.0040 chunk 44 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 35 optimal weight: 4.9990 overall best weight: 0.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4766 r_free = 0.4766 target = 0.223312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.186495 restraints weight = 7182.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.192045 restraints weight = 4253.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.195901 restraints weight = 2943.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.198614 restraints weight = 2253.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.4536 r_free = 0.4536 target = 0.200162 restraints weight = 1833.230| |-----------------------------------------------------------------------------| r_work (final): 0.4544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6208 moved from start: 0.3112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4667 Z= 0.147 Angle : 0.687 10.380 6523 Z= 0.367 Chirality : 0.048 0.416 764 Planarity : 0.005 0.037 690 Dihedral : 21.966 166.010 1124 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 16.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 4.33 % Allowed : 19.34 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.39), residues: 449 helix: 0.06 (0.44), residues: 147 sheet: -0.49 (0.54), residues: 93 loop : -1.82 (0.41), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 663 TYR 0.009 0.001 TYR A 654 PHE 0.012 0.002 PHE A 704 TRP 0.003 0.001 TRP A 451 HIS 0.002 0.000 HIS A 753 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.15 ( 4667) covalent geometry : angle 0.68744 / 0.37 ( 6523) hydrogen bonds : bond 0.06150 / 4.11 ( 173) hydrogen bonds : angle 4.83321 / 3.26 ( 447) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1328.91 seconds wall clock time: 23 minutes 35.42 seconds (1415.42 seconds total)