Starting phenix.real_space_refine on Thu Jul 2 00:16:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ym9_73099/07_2026/9ym9_73099.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ym9_73099/07_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_73099/07_2026/9ym9_73099.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ym9_73099/07_2026/9ym9_73099.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ym9_73099/07_2026/9ym9_73099.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ym9_73099/07_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-dev-6108/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: 1.23, 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: 0.42 Conformation dependent library (CDL) restraints added in 131.0 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: 0.33 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: 0.52 Time building geometry restraints manager: 0.56 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 1.50e-02 4.44e+03 2.06e+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=" 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 bond pdb=" C4 C C 20 " pdb=" C5 C C 20 " ideal model delta sigma weight residual 1.425 1.416 0.009 8.00e-03 1.56e+04 1.23e+00 ... (remaining 4662 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 6312 1.61 - 3.21: 173 3.21 - 4.82: 31 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=" 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 angle pdb=" C3' A C 6 " pdb=" O3' A C 6 " pdb=" P C C 7 " ideal model delta sigma weight residual 120.20 126.69 -6.49 1.50e+00 4.44e-01 1.87e+01 angle pdb=" C1' C B 17 " pdb=" N1 C B 17 " pdb=" C2 C B 17 " ideal model delta sigma weight residual 118.80 123.48 -4.68 1.10e+00 8.26e-01 1.81e+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: 632 0.051 - 0.103: 105 0.103 - 0.154: 20 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 2.46 2.24 0.22 2.00e-01 2.50e+01 1.19e+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 1.10e+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: 12.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 5.440 Find NCS groups from input model: 0.010 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:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.750 ------------------------------------------------------------------------------- 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= 0.185 Angle : 0.677 8.034 6523 Z= 0.500 Chirality : 0.044 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 0.00299 / 0.19 ( 4667) covalent geometry : angle 0.67720 / 0.50 ( 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 : 0.153 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: 0.0925 time to fit residues: 10.3871 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 : 0.147 ------------------------------------------------------------------------------- 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: 1.9990 chunk 22 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 overall best weight: 0.7440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 729 ASN ** A 849 HIS ** 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 = 0.4749 r_free = 0.4749 target = 0.221685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.185140 restraints weight = 7410.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.190785 restraints weight = 4447.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.194681 restraints weight = 3109.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.197101 restraints weight = 2388.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4517 r_free = 0.4517 target = 0.198801 restraints weight = 1982.250| |-----------------------------------------------------------------------------| r_work (final): 0.4530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6210 moved from start: 0.1179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4667 Z= 0.164 Angle : 0.701 8.687 6523 Z= 0.390 Chirality : 0.049 0.256 764 Planarity : 0.006 0.037 690 Dihedral : 22.684 173.161 1133 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 3.56 % Allowed : 13.99 % Favored : 82.44 % 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: -1.30 (0.39), residues: 449 helix: -0.08 (0.43), residues: 144 sheet: -0.12 (0.54), residues: 88 loop : -1.72 (0.41), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 812 TYR 0.009 0.002 TYR A 654 PHE 0.011 0.002 PHE A 666 TRP 0.004 0.001 TRP A 769 HIS 0.003 0.001 HIS A 711 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.16 ( 4667) covalent geometry : angle 0.70108 / 0.39 ( 6523) hydrogen bonds : bond 0.08323 / 5.43 ( 173) hydrogen bonds : angle 5.43550 / 3.73 ( 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 82 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 68 time to evaluate : 0.153 Fit side-chains REVERT: A 534 ARG cc_start: 0.6881 (mtp85) cc_final: 0.6489 (ttp80) REVERT: A 671 VAL cc_start: 0.7585 (OUTLIER) cc_final: 0.7309 (m) outliers start: 14 outliers final: 9 residues processed: 78 average time/residue: 0.0833 time to fit residues: 8.0337 Evaluate side-chains 67 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 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 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 736 VAL Chi-restraints excluded: chain A residue 766 HIS Chi-restraints excluded: chain A residue 778 GLU 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: 0.6980 chunk 37 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 22 optimal weight: 6.9990 chunk 13 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 4 optimal weight: 0.4980 chunk 14 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- 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 = 0.4730 r_free = 0.4730 target = 0.219088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.182208 restraints weight = 7337.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.187625 restraints weight = 4480.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.191259 restraints weight = 3157.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.193826 restraints weight = 2454.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.195421 restraints weight = 2038.405| |-----------------------------------------------------------------------------| r_work (final): 0.4497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6282 moved from start: 0.1595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 4667 Z= 0.179 Angle : 0.688 7.174 6523 Z= 0.382 Chirality : 0.048 0.238 764 Planarity : 0.005 0.039 690 Dihedral : 22.583 168.269 1128 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 15.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 3.82 % Allowed : 16.28 % Favored : 79.90 % 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: -1.58 (0.39), residues: 449 helix: -0.34 (0.42), residues: 151 sheet: -0.18 (0.55), residues: 88 loop : -1.97 (0.41), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 812 TYR 0.018 0.002 TYR A 654 PHE 0.012 0.002 PHE A 659 TRP 0.003 0.001 TRP A 435 HIS 0.003 0.001 HIS A 839 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.18 ( 4667) covalent geometry : angle 0.68838 / 0.38 ( 6523) hydrogen bonds : bond 0.07711 / 4.94 ( 173) hydrogen bonds : angle 5.30971 / 3.67 ( 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 80 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 65 time to evaluate : 0.150 Fit side-chains REVERT: A 534 ARG cc_start: 0.7001 (mtp85) cc_final: 0.6578 (ttp80) REVERT: A 663 ARG cc_start: 0.6882 (ttm110) cc_final: 0.6667 (ttm110) REVERT: A 784 TYR cc_start: 0.7220 (t80) cc_final: 0.6747 (t80) outliers start: 15 outliers final: 12 residues processed: 74 average time/residue: 0.0815 time to fit residues: 7.5299 Evaluate side-chains 73 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 61 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR 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 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: 10.0000 chunk 44 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 40 optimal weight: 0.0770 chunk 21 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 overall best weight: 0.7738 ------------------------------------------------------------------------------- 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 = 0.4740 r_free = 0.4740 target = 0.220650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.184203 restraints weight = 7215.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.189604 restraints weight = 4333.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.193442 restraints weight = 3022.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.195789 restraints weight = 2311.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4512 r_free = 0.4512 target = 0.197820 restraints weight = 1916.512| |-----------------------------------------------------------------------------| r_work (final): 0.4521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6221 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4667 Z= 0.153 Angle : 0.659 7.418 6523 Z= 0.366 Chirality : 0.046 0.236 764 Planarity : 0.005 0.038 690 Dihedral : 22.243 164.999 1124 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 5.34 % Allowed : 14.76 % Favored : 79.90 % 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: -0.04 (0.43), residues: 145 sheet: -0.04 (0.59), residues: 82 loop : -1.78 (0.40), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 812 TYR 0.013 0.002 TYR A 654 PHE 0.012 0.002 PHE A 470 TRP 0.003 0.001 TRP A 435 HIS 0.004 0.001 HIS A 682 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 ( 4667) covalent geometry : angle 0.65888 / 0.37 ( 6523) hydrogen bonds : bond 0.06937 / 4.44 ( 173) hydrogen bonds : angle 5.05687 / 3.45 ( 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 85 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 64 time to evaluate : 0.165 Fit side-chains REVERT: A 534 ARG cc_start: 0.6962 (mtp85) cc_final: 0.6259 (ttp80) REVERT: A 538 THR cc_start: 0.7677 (t) cc_final: 0.7433 (p) REVERT: A 671 VAL cc_start: 0.7663 (OUTLIER) cc_final: 0.7367 (m) REVERT: A 697 ASP cc_start: 0.2908 (OUTLIER) cc_final: 0.2281 (m-30) REVERT: A 784 TYR cc_start: 0.7186 (t80) cc_final: 0.6740 (t80) REVERT: A 850 GLN cc_start: 0.6520 (OUTLIER) cc_final: 0.5709 (pp30) outliers start: 21 outliers final: 13 residues processed: 81 average time/residue: 0.0804 time to fit residues: 8.1026 Evaluate side-chains 76 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 60 time to evaluate : 0.183 ------------------------------------------------------------------------------- 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 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 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: 6.9990 chunk 21 optimal weight: 0.0270 chunk 5 optimal weight: 1.9990 chunk 29 optimal weight: 10.0000 chunk 8 optimal weight: 1.9990 chunk 27 optimal weight: 0.0980 chunk 32 optimal weight: 4.9990 chunk 12 optimal weight: 7.9990 chunk 4 optimal weight: 0.0060 chunk 11 optimal weight: 0.2980 chunk 17 optimal weight: 0.9980 overall best weight: 0.2854 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 507 HIS A 568 ASN A 575 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4814 r_free = 0.4814 target = 0.227282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.193268 restraints weight = 7154.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4529 r_free = 0.4529 target = 0.198770 restraints weight = 4190.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4572 r_free = 0.4572 target = 0.202752 restraints weight = 2852.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4601 r_free = 0.4601 target = 0.205400 restraints weight = 2116.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4617 r_free = 0.4617 target = 0.207065 restraints weight = 1690.461| |-----------------------------------------------------------------------------| r_work (final): 0.4630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6086 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4667 Z= 0.128 Angle : 0.638 9.835 6523 Z= 0.351 Chirality : 0.046 0.239 764 Planarity : 0.005 0.037 690 Dihedral : 22.131 165.068 1124 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 5.60 % Allowed : 17.05 % 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: -1.07 (0.39), residues: 449 helix: 0.15 (0.43), residues: 144 sheet: 0.17 (0.60), residues: 74 loop : -1.59 (0.40), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 812 TYR 0.008 0.001 TYR A 654 PHE 0.011 0.001 PHE A 470 TRP 0.003 0.001 TRP A 451 HIS 0.003 0.001 HIS A 507 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.13 ( 4667) covalent geometry : angle 0.63752 / 0.35 ( 6523) hydrogen bonds : bond 0.06585 / 4.23 ( 173) hydrogen bonds : angle 4.78151 / 3.27 ( 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 92 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 70 time to evaluate : 0.160 Fit side-chains revert: symmetry clash REVERT: A 479 ARG cc_start: 0.6722 (ttm110) cc_final: 0.6182 (mtp-110) REVERT: A 534 ARG cc_start: 0.6959 (mtp85) cc_final: 0.6300 (ttp80) REVERT: A 631 VAL cc_start: 0.6754 (OUTLIER) cc_final: 0.6471 (p) REVERT: A 671 VAL cc_start: 0.7675 (OUTLIER) cc_final: 0.7357 (m) REVERT: A 697 ASP cc_start: 0.2565 (OUTLIER) cc_final: 0.1820 (m-30) REVERT: A 784 TYR cc_start: 0.7142 (t80) cc_final: 0.6718 (t80) outliers start: 22 outliers final: 11 residues processed: 84 average time/residue: 0.0750 time to fit residues: 7.8206 Evaluate side-chains 77 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 63 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 560 LEU 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 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: 3.9990 chunk 40 optimal weight: 0.2980 chunk 29 optimal weight: 10.0000 chunk 20 optimal weight: 0.9980 chunk 21 optimal weight: 7.9990 chunk 7 optimal weight: 0.0980 chunk 31 optimal weight: 0.9990 chunk 46 optimal weight: 10.0000 chunk 8 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 551 ASN A 568 ASN ** A 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4798 r_free = 0.4798 target = 0.225815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.189180 restraints weight = 7520.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.194738 restraints weight = 4500.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.198847 restraints weight = 3141.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4554 r_free = 0.4554 target = 0.201588 restraints weight = 2388.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4572 r_free = 0.4572 target = 0.203392 restraints weight = 1946.370| |-----------------------------------------------------------------------------| r_work (final): 0.4587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6164 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4667 Z= 0.145 Angle : 0.655 8.821 6523 Z= 0.360 Chirality : 0.045 0.228 764 Planarity : 0.005 0.037 690 Dihedral : 21.962 164.259 1120 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 15.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 5.60 % Allowed : 17.05 % 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: -1.20 (0.38), residues: 449 helix: -0.03 (0.43), residues: 149 sheet: 0.24 (0.61), residues: 74 loop : -1.71 (0.39), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 554 TYR 0.009 0.001 TYR A 654 PHE 0.009 0.001 PHE A 593 TRP 0.003 0.001 TRP A 451 HIS 0.002 0.001 HIS A 682 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.15 ( 4667) covalent geometry : angle 0.65455 / 0.36 ( 6523) hydrogen bonds : bond 0.06268 / 4.06 ( 173) hydrogen bonds : angle 4.81234 / 3.27 ( 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 85 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 63 time to evaluate : 0.152 Fit side-chains REVERT: A 479 ARG cc_start: 0.6767 (ttm110) cc_final: 0.6258 (mtp-110) REVERT: A 534 ARG cc_start: 0.6692 (mtp85) cc_final: 0.6348 (ttp80) REVERT: A 631 VAL cc_start: 0.6798 (OUTLIER) cc_final: 0.6526 (p) REVERT: A 671 VAL cc_start: 0.7693 (OUTLIER) cc_final: 0.7357 (m) REVERT: A 716 PHE cc_start: 0.5659 (OUTLIER) cc_final: 0.4314 (m-80) REVERT: A 850 GLN cc_start: 0.6395 (OUTLIER) cc_final: 0.5589 (pp30) outliers start: 22 outliers final: 14 residues processed: 80 average time/residue: 0.0754 time to fit residues: 7.5535 Evaluate side-chains 77 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 59 time to evaluate : 0.095 ------------------------------------------------------------------------------- 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 519 VAL 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 21 optimal weight: 7.9990 chunk 37 optimal weight: 0.0470 chunk 7 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 45 optimal weight: 6.9990 chunk 46 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 19 optimal weight: 0.6980 chunk 30 optimal weight: 3.9990 overall best weight: 1.3484 ------------------------------------------------------------------------------- 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 = 0.4744 r_free = 0.4744 target = 0.219781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.182695 restraints weight = 7267.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.187949 restraints weight = 4378.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.191723 restraints weight = 3075.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.194339 restraints weight = 2374.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.195945 restraints weight = 1955.784| |-----------------------------------------------------------------------------| r_work (final): 0.4510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6326 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 4667 Z= 0.200 Angle : 0.704 8.860 6523 Z= 0.386 Chirality : 0.047 0.212 764 Planarity : 0.005 0.038 690 Dihedral : 22.006 162.415 1120 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 17.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 4.83 % Allowed : 18.58 % 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: -1.53 (0.39), residues: 449 helix: -0.16 (0.43), residues: 150 sheet: -0.40 (0.57), residues: 87 loop : -1.92 (0.39), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 583 TYR 0.014 0.002 TYR A 654 PHE 0.014 0.002 PHE A 593 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 0.00452 / 0.20 ( 4667) covalent geometry : angle 0.70419 / 0.39 ( 6523) hydrogen bonds : bond 0.06421 / 4.25 ( 173) hydrogen bonds : angle 5.01124 / 3.39 ( 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 81 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 62 time to evaluate : 0.151 Fit side-chains REVERT: A 479 ARG cc_start: 0.6941 (ttm110) cc_final: 0.6403 (mtp-110) REVERT: A 534 ARG cc_start: 0.6746 (mtp85) cc_final: 0.6390 (ttp80) REVERT: A 671 VAL cc_start: 0.7697 (OUTLIER) cc_final: 0.7354 (m) REVERT: A 716 PHE cc_start: 0.5709 (OUTLIER) cc_final: 0.4295 (m-80) REVERT: A 784 TYR cc_start: 0.7211 (t80) cc_final: 0.6735 (t80) REVERT: A 850 GLN cc_start: 0.6427 (OUTLIER) cc_final: 0.5976 (pp30) outliers start: 19 outliers final: 13 residues processed: 78 average time/residue: 0.0827 time to fit residues: 8.0091 Evaluate side-chains 67 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 51 time to evaluate : 0.101 ------------------------------------------------------------------------------- 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 519 VAL 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 634 HIS Chi-restraints excluded: chain A residue 671 VAL Chi-restraints excluded: chain A residue 683 GLU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 36 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 47 optimal weight: 20.0000 chunk 30 optimal weight: 0.9980 chunk 2 optimal weight: 0.5980 chunk 5 optimal weight: 0.5980 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 = 0.4734 r_free = 0.4734 target = 0.219683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.181272 restraints weight = 7191.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.186714 restraints weight = 4342.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.190426 restraints weight = 3036.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.193245 restraints weight = 2360.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.195068 restraints weight = 1934.908| |-----------------------------------------------------------------------------| r_work (final): 0.4492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6319 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 4667 Z= 0.189 Angle : 0.722 12.850 6523 Z= 0.389 Chirality : 0.047 0.212 764 Planarity : 0.005 0.038 690 Dihedral : 21.989 162.823 1120 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 17.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 4.58 % Allowed : 20.61 % Favored : 74.81 % 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: -1.65 (0.39), residues: 449 helix: -0.23 (0.43), residues: 149 sheet: -0.49 (0.57), residues: 87 loop : -2.00 (0.40), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 812 TYR 0.018 0.002 TYR A 494 PHE 0.015 0.002 PHE A 659 TRP 0.003 0.001 TRP A 435 HIS 0.004 0.001 HIS A 682 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.19 ( 4667) covalent geometry : angle 0.72165 / 0.39 ( 6523) hydrogen bonds : bond 0.06371 / 4.22 ( 173) hydrogen bonds : angle 5.07624 / 3.43 ( 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 72 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 54 time to evaluate : 0.155 Fit side-chains REVERT: A 419 LEU cc_start: 0.7421 (OUTLIER) cc_final: 0.6773 (tt) REVERT: A 479 ARG cc_start: 0.6877 (ttm110) cc_final: 0.6338 (mtp-110) REVERT: A 534 ARG cc_start: 0.6748 (mtp85) cc_final: 0.6513 (ttp80) REVERT: A 554 ARG cc_start: 0.7177 (mmt180) cc_final: 0.6486 (ttp-170) REVERT: A 671 VAL cc_start: 0.7669 (OUTLIER) cc_final: 0.7350 (m) REVERT: A 697 ASP cc_start: 0.2830 (OUTLIER) cc_final: 0.1938 (m-30) REVERT: A 716 PHE cc_start: 0.5714 (OUTLIER) cc_final: 0.4309 (m-80) REVERT: A 784 TYR cc_start: 0.7188 (t80) cc_final: 0.6740 (t80) REVERT: A 850 GLN cc_start: 0.6398 (OUTLIER) cc_final: 0.5965 (pp30) outliers start: 18 outliers final: 12 residues processed: 69 average time/residue: 0.0817 time to fit residues: 7.1519 Evaluate side-chains 68 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 51 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR 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 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: 0.9990 chunk 30 optimal weight: 3.9990 chunk 10 optimal weight: 0.0570 chunk 7 optimal weight: 0.9990 chunk 47 optimal weight: 20.0000 chunk 20 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 41 optimal weight: 0.5980 chunk 32 optimal weight: 0.9980 overall best weight: 0.6900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 545 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4761 r_free = 0.4761 target = 0.222525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.184616 restraints weight = 7159.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.190045 restraints weight = 4310.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.193909 restraints weight = 3014.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.196778 restraints weight = 2315.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4523 r_free = 0.4523 target = 0.198674 restraints weight = 1881.382| |-----------------------------------------------------------------------------| r_work (final): 0.4537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6226 moved from start: 0.3016 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= 0.154 Angle : 0.685 10.336 6523 Z= 0.373 Chirality : 0.046 0.215 764 Planarity : 0.005 0.039 690 Dihedral : 21.950 163.583 1120 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 16.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 4.83 % Allowed : 20.87 % Favored : 74.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.39), residues: 449 helix: -0.21 (0.43), residues: 149 sheet: -0.17 (0.59), residues: 79 loop : -1.84 (0.40), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 812 TYR 0.010 0.002 TYR A 654 PHE 0.012 0.002 PHE A 470 TRP 0.003 0.001 TRP A 451 HIS 0.002 0.001 HIS A 682 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 ( 4667) covalent geometry : angle 0.68486 / 0.37 ( 6523) hydrogen bonds : bond 0.06151 / 4.09 ( 173) hydrogen bonds : angle 4.95816 / 3.36 ( 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: 19 poor density : 58 time to evaluate : 0.152 Fit side-chains revert: symmetry clash REVERT: A 419 LEU cc_start: 0.7311 (OUTLIER) cc_final: 0.6718 (tt) REVERT: A 479 ARG cc_start: 0.6870 (ttm110) cc_final: 0.6320 (mtp-110) REVERT: A 554 ARG cc_start: 0.7167 (mmt180) cc_final: 0.6502 (ttp-170) REVERT: A 671 VAL cc_start: 0.7656 (OUTLIER) cc_final: 0.7361 (m) REVERT: A 697 ASP cc_start: 0.2663 (OUTLIER) cc_final: 0.1746 (m-30) REVERT: A 716 PHE cc_start: 0.5703 (OUTLIER) cc_final: 0.4338 (m-80) REVERT: A 784 TYR cc_start: 0.7191 (t80) cc_final: 0.6728 (t80) REVERT: A 850 GLN cc_start: 0.6304 (OUTLIER) cc_final: 0.5783 (mp10) outliers start: 19 outliers final: 12 residues processed: 73 average time/residue: 0.0783 time to fit residues: 7.1480 Evaluate side-chains 73 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 56 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 519 VAL 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: 0.0570 chunk 46 optimal weight: 10.0000 chunk 8 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 12 optimal weight: 7.9990 chunk 35 optimal weight: 5.9990 chunk 19 optimal weight: 0.6980 chunk 41 optimal weight: 0.5980 chunk 38 optimal weight: 4.9990 chunk 36 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 overall best weight: 0.5298 ------------------------------------------------------------------------------- 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 = 0.4764 r_free = 0.4764 target = 0.223048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.185841 restraints weight = 7115.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.191297 restraints weight = 4292.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.195197 restraints weight = 3010.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.197946 restraints weight = 2312.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4531 r_free = 0.4531 target = 0.199697 restraints weight = 1880.426| |-----------------------------------------------------------------------------| r_work (final): 0.4548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6210 moved from start: 0.3199 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= 0.145 Angle : 0.672 11.937 6523 Z= 0.366 Chirality : 0.046 0.215 764 Planarity : 0.005 0.039 690 Dihedral : 21.929 163.559 1120 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 16.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 3.82 % Allowed : 22.14 % Favored : 74.05 % 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: -1.44 (0.39), residues: 449 helix: -0.22 (0.43), residues: 149 sheet: -0.17 (0.58), residues: 79 loop : -1.79 (0.40), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 812 TYR 0.008 0.001 TYR A 815 PHE 0.015 0.002 PHE A 659 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 0.00314 / 0.15 ( 4667) covalent geometry : angle 0.67189 / 0.37 ( 6523) hydrogen bonds : bond 0.06146 / 4.11 ( 173) hydrogen bonds : angle 4.88628 / 3.30 ( 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 74 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 59 time to evaluate : 0.165 Fit side-chains REVERT: A 419 LEU cc_start: 0.7311 (OUTLIER) cc_final: 0.6706 (tt) REVERT: A 479 ARG cc_start: 0.6852 (ttm110) cc_final: 0.6326 (mtp-110) REVERT: A 554 ARG cc_start: 0.7101 (mmt180) cc_final: 0.6465 (ttp-170) REVERT: A 671 VAL cc_start: 0.7695 (OUTLIER) cc_final: 0.7383 (m) REVERT: A 697 ASP cc_start: 0.2560 (OUTLIER) cc_final: 0.1615 (m-30) REVERT: A 716 PHE cc_start: 0.5717 (OUTLIER) cc_final: 0.4371 (m-80) REVERT: A 784 TYR cc_start: 0.7185 (t80) cc_final: 0.6724 (t80) REVERT: A 850 GLN cc_start: 0.6291 (OUTLIER) cc_final: 0.5776 (mp10) outliers start: 15 outliers final: 9 residues processed: 71 average time/residue: 0.0760 time to fit residues: 6.8254 Evaluate side-chains 68 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 54 time to evaluate : 0.154 ------------------------------------------------------------------------------- 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 519 VAL 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 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: 0.9980 chunk 26 optimal weight: 2.9990 chunk 16 optimal weight: 0.3980 chunk 44 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 23 optimal weight: 0.5980 chunk 7 optimal weight: 6.9990 chunk 35 optimal weight: 0.1980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.4764 r_free = 0.4764 target = 0.223297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.186482 restraints weight = 7177.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.191809 restraints weight = 4409.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.195696 restraints weight = 3116.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4517 r_free = 0.4517 target = 0.198273 restraints weight = 2393.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.199854 restraints weight = 1961.674| |-----------------------------------------------------------------------------| r_work (final): 0.4547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6205 moved from start: 0.3295 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 : 0.683 11.731 6523 Z= 0.371 Chirality : 0.045 0.214 764 Planarity : 0.005 0.039 690 Dihedral : 21.921 163.442 1120 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 17.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 4.07 % Allowed : 22.14 % Favored : 73.79 % 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: -1.45 (0.39), residues: 449 helix: -0.27 (0.43), residues: 149 sheet: -0.16 (0.59), residues: 79 loop : -1.76 (0.40), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 812 TYR 0.008 0.001 TYR A 654 PHE 0.027 0.002 PHE A 666 TRP 0.004 0.001 TRP A 451 HIS 0.002 0.000 HIS A 849 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 ( 4667) covalent geometry : angle 0.68258 / 0.37 ( 6523) hydrogen bonds : bond 0.06238 / 4.19 ( 173) hydrogen bonds : angle 4.98116 / 3.35 ( 447) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1345.62 seconds wall clock time: 23 minutes 56.53 seconds (1436.53 seconds total)