Starting phenix.real_space_refine on Wed Jul 1 22:44:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ij2_60613/07_2026/9ij2_60613.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ij2_60613/07_2026/9ij2_60613.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ij2_60613/07_2026/9ij2_60613.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ij2_60613/07_2026/9ij2_60613.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ij2_60613/07_2026/9ij2_60613.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ij2_60613/07_2026/9ij2_60613.map" } resolution = 3.9 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= 0.024 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 43 5.49 5 S 25 5.16 5 C 2229 2.51 5 N 644 2.21 5 O 788 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 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: 3729 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2820 Classifications: {'peptide': 351} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 331} Chain breaks: 1 Chain: "B" Number of atoms: 466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 466 Classifications: {'RNA': 22} Modifications used: {'p5*END': 1, 'rna2p_pyr': 3, 'rna3p_pur': 11, 'rna3p_pyr': 8} Link IDs: {'rna2p': 3, 'rna3p': 18} Chain: "C" Number of atoms: 443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 443 Classifications: {'RNA': 21} Modifications used: {'rna3p_pur': 9, 'rna3p_pyr': 11} Link IDs: {'rna3p': 20} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.10, per 1000 atoms: 0.29 Number of scatterers: 3729 At special positions: 0 Unit cell: (66.12, 78.66, 93.48, 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 25 16.00 P 43 15.00 O 788 8.00 N 644 7.00 C 2229 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: 0.22 Conformation dependent library (CDL) restraints added in 73.4 milliseconds 694 Ramachandran restraints generated. 347 Oldfield, 0 Emsley, 347 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 664 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 2 sheets defined 37.3% alpha, 13.7% beta 17 base pairs and 28 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 612 through 625 Processing helix chain 'A' and resid 646 through 652 Processing helix chain 'A' and resid 675 through 688 removed outlier: 3.868A pdb=" N TYR A 679 " --> pdb=" O ARG A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 703 Processing helix chain 'A' and resid 707 through 723 removed outlier: 3.695A pdb=" N VAL A 711 " --> pdb=" O ARG A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 781 through 802 removed outlier: 4.427A pdb=" N SER A 785 " --> pdb=" O GLU A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 819 through 825 removed outlier: 3.661A pdb=" N ASN A 825 " --> pdb=" O LYS A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 826 through 833 removed outlier: 4.632A pdb=" N GLN A 830 " --> pdb=" O TYR A 826 " (cutoff:3.500A) Processing helix chain 'A' and resid 834 through 837 Processing helix chain 'A' and resid 914 through 926 removed outlier: 3.839A pdb=" N MET A 918 " --> pdb=" O SER A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 939 through 953 removed outlier: 3.541A pdb=" N LYS A 943 " --> pdb=" O PRO A 939 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ALA A 945 " --> pdb=" O PRO A 941 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU A 948 " --> pdb=" O TYR A 944 " (cutoff:3.500A) Processing helix chain 'A' and resid 963 through 967 Processing sheet with id=AA1, first strand: chain 'A' and resid 639 through 641 removed outlier: 3.948A pdb=" N GLN A 695 " --> pdb=" O VAL A 667 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N CYS A 669 " --> pdb=" O GLN A 695 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 769 through 774 removed outlier: 3.856A pdb=" N VAL A 756 " --> pdb=" O VAL A 774 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ASP A 743 " --> pdb=" O GLY A 757 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N SER A 761 " --> pdb=" O VAL A 739 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N VAL A 739 " --> pdb=" O SER A 761 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N VAL A 809 " --> pdb=" O MET A 738 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N MET A 742 " --> pdb=" O TYR A 811 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ASP A 813 " --> pdb=" O MET A 742 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N VAL A 744 " --> pdb=" O ASP A 813 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ARG A 812 " --> pdb=" O PHE A 848 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N MET A 845 " --> pdb=" O ASN A 909 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ASN A 909 " --> pdb=" O MET A 845 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N VAL A 847 " --> pdb=" O VAL A 907 " (cutoff:3.500A) 104 hydrogen bonds defined for protein. 297 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 42 hydrogen bonds 84 hydrogen bond angles 0 basepair planarities 17 basepair parallelities 28 stacking parallelities Total time for adding SS restraints: 0.89 Time building geometry restraints manager: 0.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 894 1.33 - 1.45: 963 1.45 - 1.57: 1920 1.57 - 1.69: 85 1.69 - 1.81: 39 Bond restraints: 3901 Sorted by residual: bond pdb=" N1 U B 2 " pdb=" C2 U B 2 " ideal model delta sigma weight residual 1.381 1.402 -0.021 9.00e-03 1.23e+04 5.35e+00 bond pdb=" N9 G C 4 " pdb=" C4 G C 4 " ideal model delta sigma weight residual 1.375 1.391 -0.016 8.00e-03 1.56e+04 3.92e+00 bond pdb=" N1 C B 8 " pdb=" C2 C B 8 " ideal model delta sigma weight residual 1.397 1.416 -0.019 1.00e-02 1.00e+04 3.79e+00 bond pdb=" CB TYR A 679 " pdb=" CG TYR A 679 " ideal model delta sigma weight residual 1.512 1.553 -0.041 2.20e-02 2.07e+03 3.50e+00 bond pdb=" C5 U C 7 " pdb=" C6 U C 7 " ideal model delta sigma weight residual 1.337 1.320 0.017 9.00e-03 1.23e+04 3.45e+00 ... (remaining 3896 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.52: 5257 2.52 - 5.03: 185 5.03 - 7.55: 33 7.55 - 10.06: 12 10.06 - 12.58: 2 Bond angle restraints: 5489 Sorted by residual: angle pdb=" N1 U B 2 " pdb=" C2 U B 2 " pdb=" O2 U B 2 " ideal model delta sigma weight residual 122.80 128.85 -6.05 7.00e-01 2.04e+00 7.46e+01 angle pdb=" O2 U B 2 " pdb=" C2 U B 2 " pdb=" N3 U B 2 " ideal model delta sigma weight residual 122.20 116.45 5.75 7.00e-01 2.04e+00 6.76e+01 angle pdb=" C1' U B 2 " pdb=" N1 U B 2 " pdb=" C2 U B 2 " ideal model delta sigma weight residual 117.70 127.48 -9.78 1.20e+00 6.94e-01 6.64e+01 angle pdb=" O2 U C 6 " pdb=" C2 U C 6 " pdb=" N3 U C 6 " ideal model delta sigma weight residual 122.20 117.99 4.21 7.00e-01 2.04e+00 3.62e+01 angle pdb=" N1 C C 8 " pdb=" C2 C C 8 " pdb=" O2 C C 8 " ideal model delta sigma weight residual 118.90 122.43 -3.53 6.00e-01 2.78e+00 3.46e+01 ... (remaining 5484 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.80: 2127 29.80 - 59.60: 218 59.60 - 89.40: 41 89.40 - 119.19: 2 119.19 - 148.99: 1 Dihedral angle restraints: 2389 sinusoidal: 1363 harmonic: 1026 Sorted by residual: dihedral pdb=" O4' U B 2 " pdb=" C1' U B 2 " pdb=" N1 U B 2 " pdb=" C2 U B 2 " ideal model delta sinusoidal sigma weight residual 232.00 157.80 74.20 1 1.70e+01 3.46e-03 2.42e+01 dihedral pdb=" CA ILE A 654 " pdb=" C ILE A 654 " pdb=" N GLN A 655 " pdb=" CA GLN A 655 " ideal model delta harmonic sigma weight residual 180.00 155.66 24.34 0 5.00e+00 4.00e-02 2.37e+01 dihedral pdb=" CA GLN A 830 " pdb=" C GLN A 830 " pdb=" N LEU A 831 " pdb=" CA LEU A 831 " ideal model delta harmonic sigma weight residual 180.00 155.85 24.15 0 5.00e+00 4.00e-02 2.33e+01 ... (remaining 2386 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 512 0.058 - 0.115: 111 0.115 - 0.173: 27 0.173 - 0.230: 5 0.230 - 0.288: 3 Chirality restraints: 658 Sorted by residual: chirality pdb=" C3' G C 12 " pdb=" C4' G C 12 " pdb=" O3' G C 12 " pdb=" C2' G C 12 " both_signs ideal model delta sigma weight residual False -2.48 -2.19 -0.29 2.00e-01 2.50e+01 2.07e+00 chirality pdb=" CA PHE A 950 " pdb=" N PHE A 950 " pdb=" C PHE A 950 " pdb=" CB PHE A 950 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" CA LYS A 943 " pdb=" N LYS A 943 " pdb=" C LYS A 943 " pdb=" CB LYS A 943 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.59e+00 ... (remaining 655 not shown) Planarity restraints: 534 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 938 " 0.055 5.00e-02 4.00e+02 8.32e-02 1.11e+01 pdb=" N PRO A 939 " -0.144 5.00e-02 4.00e+02 pdb=" CA PRO A 939 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO A 939 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 679 " -0.021 2.00e-02 2.50e+03 1.74e-02 6.07e+00 pdb=" CG TYR A 679 " 0.042 2.00e-02 2.50e+03 pdb=" CD1 TYR A 679 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 TYR A 679 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR A 679 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 679 " -0.009 2.00e-02 2.50e+03 pdb=" CZ TYR A 679 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 679 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 635 " 0.040 5.00e-02 4.00e+02 6.04e-02 5.83e+00 pdb=" N PRO A 636 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO A 636 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 636 " 0.033 5.00e-02 4.00e+02 ... (remaining 531 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 873 2.80 - 3.32: 3261 3.32 - 3.85: 6866 3.85 - 4.37: 7272 4.37 - 4.90: 11285 Nonbonded interactions: 29557 Sorted by model distance: nonbonded pdb=" O MET A 928 " pdb=" OH TYR A 944 " model vdw 2.273 3.040 nonbonded pdb=" O THR A 591 " pdb=" OG1 THR A 591 " model vdw 2.326 3.040 nonbonded pdb=" O THR A 674 " pdb=" OG1 THR A 674 " model vdw 2.326 3.040 nonbonded pdb=" O SER A 656 " pdb=" OG SER A 656 " model vdw 2.358 3.040 nonbonded pdb=" O THR A 765 " pdb=" OG1 THR A 765 " model vdw 2.370 3.040 ... (remaining 29552 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: 0.290 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: 0.040 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.000 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:1.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4873 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 : 0.005 0.048 3901 Z= 0.293 Angle : 1.127 12.577 5489 Z= 0.818 Chirality : 0.056 0.288 658 Planarity : 0.007 0.083 534 Dihedral : 22.169 148.993 1725 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.80 % Favored : 90.20 % Rotamer: Outliers : 0.32 % Allowed : 32.28 % Favored : 67.41 % 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: -3.30 (0.42), residues: 347 helix: -1.18 (0.48), residues: 98 sheet: -0.55 (0.63), residues: 69 loop : -3.62 (0.42), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 937 TYR 0.042 0.003 TYR A 679 PHE 0.029 0.003 PHE A 950 TRP 0.024 0.003 TRP A 604 HIS 0.012 0.002 HIS A 958 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.29 ( 3901) covalent geometry : angle 1.12713 / 0.82 ( 5489) hydrogen bonds : bond 0.17472 / 10.15 ( 146) hydrogen bonds : angle 7.47855 / 5.01 ( 381) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 694 Ramachandran restraints generated. 347 Oldfield, 0 Emsley, 347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 694 Ramachandran restraints generated. 347 Oldfield, 0 Emsley, 347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 51 time to evaluate : 0.110 Fit side-chains revert: symmetry clash REVERT: A 772 ARG cc_start: 0.5834 (mmt180) cc_final: 0.5594 (mmm160) outliers start: 1 outliers final: 0 residues processed: 52 average time/residue: 0.0697 time to fit residues: 4.4688 Evaluate side-chains 48 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 24 optimal weight: 9.9990 chunk 26 optimal weight: 7.9990 chunk 2 optimal weight: 0.0870 chunk 16 optimal weight: 0.5980 chunk 32 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 0.0470 chunk 22 optimal weight: 0.7980 chunk 37 optimal weight: 9.9990 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 621 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4873 r_free = 0.4873 target = 0.228253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4685 r_free = 0.4685 target = 0.207862 restraints weight = 10099.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4728 r_free = 0.4728 target = 0.212692 restraints weight = 6626.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4763 r_free = 0.4763 target = 0.216215 restraints weight = 4586.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4784 r_free = 0.4784 target = 0.218653 restraints weight = 3300.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4800 r_free = 0.4800 target = 0.220323 restraints weight = 2454.384| |-----------------------------------------------------------------------------| r_work (final): 0.4799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4863 moved from start: 0.1024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3901 Z= 0.131 Angle : 0.660 8.102 5489 Z= 0.363 Chirality : 0.042 0.199 658 Planarity : 0.006 0.077 534 Dihedral : 21.456 153.137 1027 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 15.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.65 % Favored : 91.35 % Rotamer: Outliers : 4.43 % Allowed : 26.90 % Favored : 68.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.66 (0.44), residues: 347 helix: -0.35 (0.50), residues: 99 sheet: -0.24 (0.65), residues: 69 loop : -3.40 (0.44), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 617 TYR 0.015 0.002 TYR A 608 PHE 0.016 0.001 PHE A 607 TRP 0.013 0.001 TRP A 586 HIS 0.003 0.001 HIS A 602 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.13 ( 3901) covalent geometry : angle 0.66050 / 0.36 ( 5489) hydrogen bonds : bond 0.06332 / 3.89 ( 146) hydrogen bonds : angle 5.72620 / 3.85 ( 381) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 694 Ramachandran restraints generated. 347 Oldfield, 0 Emsley, 347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 694 Ramachandran restraints generated. 347 Oldfield, 0 Emsley, 347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 47 time to evaluate : 0.106 Fit side-chains revert: symmetry clash REVERT: A 710 SER cc_start: 0.7519 (OUTLIER) cc_final: 0.7074 (p) REVERT: A 773 VAL cc_start: 0.5722 (OUTLIER) cc_final: 0.5493 (t) REVERT: A 944 TYR cc_start: 0.7279 (m-80) cc_final: 0.6962 (m-80) outliers start: 14 outliers final: 6 residues processed: 57 average time/residue: 0.0574 time to fit residues: 4.1959 Evaluate side-chains 54 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain A residue 722 LYS Chi-restraints excluded: chain A residue 752 MET Chi-restraints excluded: chain A residue 771 SER Chi-restraints excluded: chain A residue 773 VAL Chi-restraints excluded: chain A residue 777 MET Chi-restraints excluded: chain A residue 849 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 37 optimal weight: 10.0000 chunk 11 optimal weight: 5.9990 chunk 4 optimal weight: 6.9990 chunk 6 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 chunk 29 optimal weight: 7.9990 chunk 36 optimal weight: 20.0000 chunk 16 optimal weight: 0.0170 chunk 26 optimal weight: 0.0050 chunk 2 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 overall best weight: 0.5032 ------------------------------------------------------------------------------- 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 = 0.4869 r_free = 0.4869 target = 0.227765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4687 r_free = 0.4687 target = 0.208602 restraints weight = 10195.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4730 r_free = 0.4730 target = 0.213159 restraints weight = 6686.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4760 r_free = 0.4760 target = 0.216233 restraints weight = 4618.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.4785 r_free = 0.4785 target = 0.218618 restraints weight = 3341.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.4801 r_free = 0.4801 target = 0.220394 restraints weight = 2477.891| |-----------------------------------------------------------------------------| r_work (final): 0.4798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4853 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 3901 Z= 0.117 Angle : 0.608 7.991 5489 Z= 0.331 Chirality : 0.041 0.189 658 Planarity : 0.005 0.069 534 Dihedral : 21.429 155.795 1027 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.65 % Favored : 91.35 % Rotamer: Outliers : 4.75 % Allowed : 26.58 % Favored : 68.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.38 (0.45), residues: 347 helix: 0.26 (0.53), residues: 99 sheet: -0.33 (0.62), residues: 69 loop : -3.37 (0.44), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 675 TYR 0.017 0.001 TYR A 608 PHE 0.008 0.001 PHE A 607 TRP 0.011 0.002 TRP A 604 HIS 0.003 0.001 HIS A 927 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.12 ( 3901) covalent geometry : angle 0.60756 / 0.33 ( 5489) hydrogen bonds : bond 0.05476 / 3.43 ( 146) hydrogen bonds : angle 5.30855 / 3.51 ( 381) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 694 Ramachandran restraints generated. 347 Oldfield, 0 Emsley, 347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 694 Ramachandran restraints generated. 347 Oldfield, 0 Emsley, 347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 46 time to evaluate : 0.105 Fit side-chains revert: symmetry clash REVERT: A 641 GLU cc_start: 0.7655 (tp30) cc_final: 0.7326 (tp30) REVERT: A 773 VAL cc_start: 0.5623 (OUTLIER) cc_final: 0.5343 (t) REVERT: A 944 TYR cc_start: 0.7064 (m-80) cc_final: 0.6853 (m-80) outliers start: 15 outliers final: 10 residues processed: 55 average time/residue: 0.0784 time to fit residues: 5.2621 Evaluate side-chains 56 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 45 time to evaluate : 0.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 578 PHE Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 672 MET Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain A residue 722 LYS Chi-restraints excluded: chain A residue 752 MET Chi-restraints excluded: chain A residue 771 SER Chi-restraints excluded: chain A residue 773 VAL Chi-restraints excluded: chain A residue 777 MET Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 951 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 19 optimal weight: 6.9990 chunk 5 optimal weight: 1.9990 chunk 6 optimal weight: 6.9990 chunk 13 optimal weight: 3.9990 chunk 1 optimal weight: 6.9990 chunk 3 optimal weight: 0.9990 chunk 22 optimal weight: 5.9990 chunk 28 optimal weight: 6.9990 chunk 18 optimal weight: 9.9990 chunk 31 optimal weight: 3.9990 chunk 24 optimal weight: 10.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 946 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4769 r_free = 0.4769 target = 0.216239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4571 r_free = 0.4571 target = 0.196531 restraints weight = 10266.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4614 r_free = 0.4614 target = 0.200852 restraints weight = 6765.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4646 r_free = 0.4646 target = 0.203963 restraints weight = 4757.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4669 r_free = 0.4669 target = 0.206160 restraints weight = 3496.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4683 r_free = 0.4683 target = 0.207703 restraints weight = 2662.104| |-----------------------------------------------------------------------------| r_work (final): 0.4678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5246 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 3901 Z= 0.256 Angle : 0.803 10.285 5489 Z= 0.437 Chirality : 0.048 0.192 658 Planarity : 0.006 0.065 534 Dihedral : 21.313 163.941 1027 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 26.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.39 % Favored : 87.61 % Rotamer: Outliers : 9.18 % Allowed : 24.37 % Favored : 66.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.63 (0.45), residues: 347 helix: -0.10 (0.50), residues: 100 sheet: -0.40 (0.63), residues: 69 loop : -3.46 (0.45), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 700 TYR 0.014 0.003 TYR A 826 PHE 0.022 0.004 PHE A 923 TRP 0.018 0.003 TRP A 604 HIS 0.016 0.002 HIS A 946 Details of bonding type rmsd/Z covalent geometry : bond 0.00531 / 0.26 ( 3901) covalent geometry : angle 0.80281 / 0.44 ( 5489) hydrogen bonds : bond 0.08472 / 5.61 ( 146) hydrogen bonds : angle 5.75954 / 3.93 ( 381) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 694 Ramachandran restraints generated. 347 Oldfield, 0 Emsley, 347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 694 Ramachandran restraints generated. 347 Oldfield, 0 Emsley, 347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 57 time to evaluate : 0.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 617 ARG cc_start: 0.7122 (tpm170) cc_final: 0.6792 (tpm170) REVERT: A 650 TYR cc_start: 0.3422 (OUTLIER) cc_final: 0.0892 (p90) REVERT: A 723 LEU cc_start: 0.6353 (OUTLIER) cc_final: 0.6075 (mm) REVERT: A 769 TRP cc_start: 0.6561 (m100) cc_final: 0.6059 (m100) REVERT: A 842 HIS cc_start: 0.8477 (OUTLIER) cc_final: 0.7947 (p90) outliers start: 29 outliers final: 19 residues processed: 77 average time/residue: 0.0463 time to fit residues: 4.3836 Evaluate side-chains 78 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 56 time to evaluate : 0.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 586 TRP Chi-restraints excluded: chain A residue 593 ASP Chi-restraints excluded: chain A residue 604 TRP Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 650 TYR Chi-restraints excluded: chain A residue 652 ARG Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 672 MET Chi-restraints excluded: chain A residue 702 ILE Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 730 VAL Chi-restraints excluded: chain A residue 743 ASP Chi-restraints excluded: chain A residue 758 PHE Chi-restraints excluded: chain A residue 771 SER Chi-restraints excluded: chain A residue 777 MET Chi-restraints excluded: chain A residue 842 HIS Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 951 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 30 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 9 optimal weight: 0.4980 chunk 0 optimal weight: 4.9990 chunk 13 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 31 optimal weight: 6.9990 chunk 17 optimal weight: 0.0970 chunk 35 optimal weight: 10.0000 overall best weight: 0.5578 ------------------------------------------------------------------------------- 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 = 0.4832 r_free = 0.4832 target = 0.223340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4647 r_free = 0.4647 target = 0.203898 restraints weight = 10269.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4690 r_free = 0.4690 target = 0.208524 restraints weight = 6690.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4720 r_free = 0.4720 target = 0.211603 restraints weight = 4657.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4741 r_free = 0.4741 target = 0.213918 restraints weight = 3408.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4758 r_free = 0.4758 target = 0.215599 restraints weight = 2573.266| |-----------------------------------------------------------------------------| r_work (final): 0.4757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5023 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3901 Z= 0.134 Angle : 0.669 9.768 5489 Z= 0.358 Chirality : 0.044 0.183 658 Planarity : 0.005 0.064 534 Dihedral : 21.205 162.139 1027 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 17.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.80 % Favored : 90.20 % Rotamer: Outliers : 5.70 % Allowed : 28.16 % Favored : 66.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.42 (0.45), residues: 347 helix: 0.36 (0.53), residues: 102 sheet: -0.57 (0.60), residues: 69 loop : -3.44 (0.44), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 707 TYR 0.017 0.002 TYR A 608 PHE 0.010 0.001 PHE A 950 TRP 0.013 0.002 TRP A 604 HIS 0.007 0.001 HIS A 946 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 ( 3901) covalent geometry : angle 0.66939 / 0.36 ( 5489) hydrogen bonds : bond 0.05316 / 3.32 ( 146) hydrogen bonds : angle 5.25942 / 3.54 ( 381) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 694 Ramachandran restraints generated. 347 Oldfield, 0 Emsley, 347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 694 Ramachandran restraints generated. 347 Oldfield, 0 Emsley, 347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 50 time to evaluate : 0.110 Fit side-chains revert: symmetry clash REVERT: A 601 MET cc_start: 0.5564 (tpt) cc_final: 0.5165 (tpt) REVERT: A 613 MET cc_start: 0.6123 (mtt) cc_final: 0.5547 (mtt) REVERT: A 617 ARG cc_start: 0.7246 (tpm170) cc_final: 0.6817 (tpm170) REVERT: A 650 TYR cc_start: 0.3798 (OUTLIER) cc_final: 0.1412 (p90) REVERT: A 773 VAL cc_start: 0.5704 (OUTLIER) cc_final: 0.5426 (t) REVERT: A 928 MET cc_start: 0.7172 (ppp) cc_final: 0.6071 (ppp) outliers start: 18 outliers final: 10 residues processed: 65 average time/residue: 0.0768 time to fit residues: 6.0002 Evaluate side-chains 64 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 52 time to evaluate : 0.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 586 TRP Chi-restraints excluded: chain A residue 604 TRP Chi-restraints excluded: chain A residue 650 TYR Chi-restraints excluded: chain A residue 652 ARG Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 672 MET Chi-restraints excluded: chain A residue 735 LYS Chi-restraints excluded: chain A residue 752 MET Chi-restraints excluded: chain A residue 773 VAL Chi-restraints excluded: chain A residue 844 LYS Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 951 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 21 optimal weight: 7.9990 chunk 19 optimal weight: 10.0000 chunk 38 optimal weight: 10.0000 chunk 12 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 37 optimal weight: 9.9990 chunk 25 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 4 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 = 0.4831 r_free = 0.4831 target = 0.223140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4639 r_free = 0.4639 target = 0.203006 restraints weight = 10466.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4684 r_free = 0.4684 target = 0.207637 restraints weight = 6922.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4715 r_free = 0.4715 target = 0.210964 restraints weight = 4861.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4738 r_free = 0.4738 target = 0.213407 restraints weight = 3538.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4754 r_free = 0.4754 target = 0.215118 restraints weight = 2652.852| |-----------------------------------------------------------------------------| r_work (final): 0.4752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5041 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3901 Z= 0.135 Angle : 0.658 9.744 5489 Z= 0.354 Chirality : 0.043 0.185 658 Planarity : 0.005 0.069 534 Dihedral : 21.153 162.684 1027 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 18.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.24 % Favored : 88.76 % Rotamer: Outliers : 4.43 % Allowed : 30.06 % Favored : 65.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.41 (0.45), residues: 347 helix: 0.41 (0.52), residues: 103 sheet: -0.62 (0.58), residues: 69 loop : -3.46 (0.45), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 772 TYR 0.039 0.002 TYR A 944 PHE 0.010 0.001 PHE A 607 TRP 0.013 0.002 TRP A 604 HIS 0.009 0.001 HIS A 946 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.14 ( 3901) covalent geometry : angle 0.65770 / 0.35 ( 5489) hydrogen bonds : bond 0.05437 / 3.53 ( 146) hydrogen bonds : angle 5.42629 / 3.72 ( 381) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 694 Ramachandran restraints generated. 347 Oldfield, 0 Emsley, 347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 694 Ramachandran restraints generated. 347 Oldfield, 0 Emsley, 347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 53 time to evaluate : 0.105 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 601 MET cc_start: 0.5685 (tpt) cc_final: 0.5246 (tpt) REVERT: A 650 TYR cc_start: 0.3828 (OUTLIER) cc_final: 0.1559 (p90) REVERT: A 719 MET cc_start: 0.5899 (mmm) cc_final: 0.5623 (mmm) REVERT: A 769 TRP cc_start: 0.6028 (m100) cc_final: 0.5733 (m100) REVERT: A 773 VAL cc_start: 0.5812 (OUTLIER) cc_final: 0.5531 (t) outliers start: 14 outliers final: 11 residues processed: 65 average time/residue: 0.0973 time to fit residues: 7.4298 Evaluate side-chains 64 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 51 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 586 TRP Chi-restraints excluded: chain A residue 593 ASP Chi-restraints excluded: chain A residue 604 TRP Chi-restraints excluded: chain A residue 650 TYR Chi-restraints excluded: chain A residue 652 ARG Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 672 MET Chi-restraints excluded: chain A residue 722 LYS Chi-restraints excluded: chain A residue 735 LYS Chi-restraints excluded: chain A residue 752 MET Chi-restraints excluded: chain A residue 773 VAL Chi-restraints excluded: chain A residue 844 LYS Chi-restraints excluded: chain A residue 910 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 12 optimal weight: 5.9990 chunk 23 optimal weight: 0.3980 chunk 38 optimal weight: 10.0000 chunk 1 optimal weight: 0.6980 chunk 4 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 35 optimal weight: 10.0000 chunk 14 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 5 optimal weight: 0.0030 overall best weight: 0.5390 ------------------------------------------------------------------------------- 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 = 0.4844 r_free = 0.4844 target = 0.224495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4659 r_free = 0.4659 target = 0.204450 restraints weight = 10338.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4700 r_free = 0.4700 target = 0.209050 restraints weight = 6743.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4731 r_free = 0.4731 target = 0.212588 restraints weight = 4740.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4754 r_free = 0.4754 target = 0.215062 restraints weight = 3433.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.4769 r_free = 0.4769 target = 0.216747 restraints weight = 2560.792| |-----------------------------------------------------------------------------| r_work (final): 0.4767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4986 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 3901 Z= 0.119 Angle : 0.626 8.915 5489 Z= 0.336 Chirality : 0.042 0.182 658 Planarity : 0.005 0.065 534 Dihedral : 21.051 162.814 1027 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 16.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.09 % Favored : 89.91 % Rotamer: Outliers : 4.75 % Allowed : 30.38 % Favored : 64.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.29 (0.46), residues: 347 helix: 0.68 (0.53), residues: 103 sheet: -0.67 (0.58), residues: 69 loop : -3.43 (0.45), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 772 TYR 0.019 0.002 TYR A 944 PHE 0.007 0.001 PHE A 607 TRP 0.010 0.001 TRP A 604 HIS 0.007 0.001 HIS A 946 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.12 ( 3901) covalent geometry : angle 0.62621 / 0.34 ( 5489) hydrogen bonds : bond 0.04782 / 3.11 ( 146) hydrogen bonds : angle 5.25816 / 3.57 ( 381) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 694 Ramachandran restraints generated. 347 Oldfield, 0 Emsley, 347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 694 Ramachandran restraints generated. 347 Oldfield, 0 Emsley, 347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 50 time to evaluate : 0.108 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 601 MET cc_start: 0.5576 (tpt) cc_final: 0.5153 (tpt) REVERT: A 622 MET cc_start: -0.0845 (tpp) cc_final: -0.1243 (tpp) REVERT: A 650 TYR cc_start: 0.3688 (OUTLIER) cc_final: 0.1743 (p90) REVERT: A 719 MET cc_start: 0.6201 (mmm) cc_final: 0.5784 (mmm) REVERT: A 769 TRP cc_start: 0.5572 (m100) cc_final: 0.5180 (m100) REVERT: A 773 VAL cc_start: 0.5898 (OUTLIER) cc_final: 0.5576 (t) outliers start: 15 outliers final: 10 residues processed: 62 average time/residue: 0.0689 time to fit residues: 5.1683 Evaluate side-chains 60 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 48 time to evaluate : 0.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 586 TRP Chi-restraints excluded: chain A residue 593 ASP Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain A residue 650 TYR Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 672 MET Chi-restraints excluded: chain A residue 722 LYS Chi-restraints excluded: chain A residue 735 LYS Chi-restraints excluded: chain A residue 752 MET Chi-restraints excluded: chain A residue 773 VAL Chi-restraints excluded: chain A residue 844 LYS Chi-restraints excluded: chain A residue 910 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 17 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 19 optimal weight: 0.2980 chunk 30 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 27 optimal weight: 0.8980 chunk 38 optimal weight: 10.0000 chunk 5 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- 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 = 0.4874 r_free = 0.4874 target = 0.226126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4700 r_free = 0.4700 target = 0.207842 restraints weight = 11254.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4736 r_free = 0.4736 target = 0.211773 restraints weight = 7434.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4766 r_free = 0.4766 target = 0.214864 restraints weight = 5279.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4786 r_free = 0.4786 target = 0.216955 restraints weight = 3912.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4797 r_free = 0.4797 target = 0.218219 restraints weight = 3000.515| |-----------------------------------------------------------------------------| r_work (final): 0.4797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4992 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3901 Z= 0.121 Angle : 0.618 9.207 5489 Z= 0.328 Chirality : 0.041 0.175 658 Planarity : 0.005 0.065 534 Dihedral : 20.923 164.499 1027 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 17.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.66 % Favored : 89.34 % Rotamer: Outliers : 4.11 % Allowed : 31.33 % Favored : 64.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.24 (0.46), residues: 347 helix: 0.68 (0.54), residues: 103 sheet: -0.58 (0.59), residues: 69 loop : -3.41 (0.45), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 772 TYR 0.016 0.002 TYR A 944 PHE 0.009 0.001 PHE A 607 TRP 0.010 0.001 TRP A 604 HIS 0.005 0.001 HIS A 946 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.12 ( 3901) covalent geometry : angle 0.61813 / 0.33 ( 5489) hydrogen bonds : bond 0.05020 / 3.32 ( 146) hydrogen bonds : angle 5.19352 / 3.54 ( 381) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 694 Ramachandran restraints generated. 347 Oldfield, 0 Emsley, 347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 694 Ramachandran restraints generated. 347 Oldfield, 0 Emsley, 347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 49 time to evaluate : 0.108 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 601 MET cc_start: 0.5603 (tpt) cc_final: 0.5226 (tpt) REVERT: A 617 ARG cc_start: 0.6873 (tpm170) cc_final: 0.6564 (tpm170) REVERT: A 650 TYR cc_start: 0.3697 (OUTLIER) cc_final: 0.1931 (p90) REVERT: A 773 VAL cc_start: 0.5781 (OUTLIER) cc_final: 0.5492 (t) outliers start: 13 outliers final: 11 residues processed: 60 average time/residue: 0.0580 time to fit residues: 4.2360 Evaluate side-chains 61 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 48 time to evaluate : 0.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 578 PHE Chi-restraints excluded: chain A residue 586 TRP Chi-restraints excluded: chain A residue 593 ASP Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain A residue 650 TYR Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 672 MET Chi-restraints excluded: chain A residue 722 LYS Chi-restraints excluded: chain A residue 735 LYS Chi-restraints excluded: chain A residue 773 VAL Chi-restraints excluded: chain A residue 784 ASP Chi-restraints excluded: chain A residue 844 LYS Chi-restraints excluded: chain A residue 910 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 19 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 1 optimal weight: 0.0170 chunk 9 optimal weight: 7.9990 chunk 7 optimal weight: 5.9990 chunk 15 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 34 optimal weight: 0.8980 overall best weight: 0.7020 ------------------------------------------------------------------------------- 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 = 0.4881 r_free = 0.4881 target = 0.226702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4710 r_free = 0.4710 target = 0.208337 restraints weight = 11078.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4746 r_free = 0.4746 target = 0.212455 restraints weight = 7273.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4775 r_free = 0.4775 target = 0.215526 restraints weight = 5135.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4795 r_free = 0.4795 target = 0.217614 restraints weight = 3774.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4807 r_free = 0.4807 target = 0.218959 restraints weight = 2898.401| |-----------------------------------------------------------------------------| r_work (final): 0.4805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4957 moved from start: 0.2747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 3901 Z= 0.115 Angle : 0.611 9.005 5489 Z= 0.323 Chirality : 0.041 0.174 658 Planarity : 0.005 0.066 534 Dihedral : 20.831 165.178 1027 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 16.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.51 % Favored : 90.49 % Rotamer: Outliers : 4.75 % Allowed : 30.06 % Favored : 65.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.14 (0.46), residues: 347 helix: 0.82 (0.54), residues: 103 sheet: -0.53 (0.60), residues: 69 loop : -3.38 (0.46), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 772 TYR 0.014 0.002 TYR A 608 PHE 0.008 0.001 PHE A 607 TRP 0.010 0.001 TRP A 586 HIS 0.004 0.001 HIS A 946 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.12 ( 3901) covalent geometry : angle 0.61106 / 0.32 ( 5489) hydrogen bonds : bond 0.04690 / 3.07 ( 146) hydrogen bonds : angle 5.10751 / 3.47 ( 381) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 694 Ramachandran restraints generated. 347 Oldfield, 0 Emsley, 347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 694 Ramachandran restraints generated. 347 Oldfield, 0 Emsley, 347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 50 time to evaluate : 0.125 Fit side-chains revert: symmetry clash REVERT: A 601 MET cc_start: 0.5556 (tpt) cc_final: 0.5210 (tpt) REVERT: A 622 MET cc_start: -0.0898 (tpp) cc_final: -0.1294 (tpt) REVERT: A 650 TYR cc_start: 0.3734 (OUTLIER) cc_final: 0.2127 (p90) REVERT: A 773 VAL cc_start: 0.5685 (OUTLIER) cc_final: 0.5370 (t) REVERT: A 844 LYS cc_start: 0.3105 (OUTLIER) cc_final: 0.2875 (ptpt) outliers start: 15 outliers final: 9 residues processed: 62 average time/residue: 0.0632 time to fit residues: 4.7898 Evaluate side-chains 60 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 48 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 578 PHE Chi-restraints excluded: chain A residue 586 TRP Chi-restraints excluded: chain A residue 593 ASP Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain A residue 650 TYR Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 672 MET Chi-restraints excluded: chain A residue 735 LYS Chi-restraints excluded: chain A residue 771 SER Chi-restraints excluded: chain A residue 773 VAL Chi-restraints excluded: chain A residue 844 LYS Chi-restraints excluded: chain A residue 910 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 11 optimal weight: 0.0770 chunk 8 optimal weight: 4.9990 chunk 24 optimal weight: 9.9990 chunk 36 optimal weight: 20.0000 chunk 4 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 26 optimal weight: 0.7980 chunk 17 optimal weight: 7.9990 chunk 6 optimal weight: 0.9980 chunk 22 optimal weight: 5.9990 chunk 9 optimal weight: 10.0000 overall best weight: 2.1742 ------------------------------------------------------------------------------- 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 = 0.4838 r_free = 0.4838 target = 0.221469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4654 r_free = 0.4654 target = 0.202287 restraints weight = 11278.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4693 r_free = 0.4693 target = 0.206458 restraints weight = 7473.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4723 r_free = 0.4723 target = 0.209565 restraints weight = 5332.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4744 r_free = 0.4744 target = 0.211731 restraints weight = 3984.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4758 r_free = 0.4758 target = 0.213281 restraints weight = 3077.845| |-----------------------------------------------------------------------------| r_work (final): 0.4756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5132 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3901 Z= 0.178 Angle : 0.680 9.839 5489 Z= 0.362 Chirality : 0.043 0.157 658 Planarity : 0.005 0.065 534 Dihedral : 20.840 169.285 1027 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 22.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.53 % Favored : 88.47 % Rotamer: Outliers : 4.11 % Allowed : 31.01 % Favored : 64.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.41 (0.46), residues: 347 helix: 0.35 (0.53), residues: 102 sheet: -0.57 (0.61), residues: 69 loop : -3.40 (0.46), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 707 TYR 0.014 0.002 TYR A 944 PHE 0.017 0.002 PHE A 923 TRP 0.012 0.002 TRP A 604 HIS 0.004 0.001 HIS A 946 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.18 ( 3901) covalent geometry : angle 0.68013 / 0.36 ( 5489) hydrogen bonds : bond 0.06077 / 4.06 ( 146) hydrogen bonds : angle 5.29573 / 3.62 ( 381) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 694 Ramachandran restraints generated. 347 Oldfield, 0 Emsley, 347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 694 Ramachandran restraints generated. 347 Oldfield, 0 Emsley, 347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 51 time to evaluate : 0.107 Fit side-chains revert: symmetry clash REVERT: A 601 MET cc_start: 0.5989 (tpt) cc_final: 0.5536 (tpt) REVERT: A 617 ARG cc_start: 0.6777 (tpm170) cc_final: 0.6522 (tpm170) REVERT: A 650 TYR cc_start: 0.3333 (OUTLIER) cc_final: 0.1384 (p90) REVERT: A 769 TRP cc_start: 0.5815 (m100) cc_final: 0.5450 (m100) outliers start: 13 outliers final: 11 residues processed: 61 average time/residue: 0.0638 time to fit residues: 4.7487 Evaluate side-chains 63 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 51 time to evaluate : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 586 TRP Chi-restraints excluded: chain A residue 593 ASP Chi-restraints excluded: chain A residue 650 TYR Chi-restraints excluded: chain A residue 652 ARG Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 672 MET Chi-restraints excluded: chain A residue 735 LYS Chi-restraints excluded: chain A residue 771 SER Chi-restraints excluded: chain A residue 777 MET Chi-restraints excluded: chain A residue 844 LYS Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 962 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 11 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 22 optimal weight: 7.9990 chunk 6 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 18 optimal weight: 6.9990 chunk 13 optimal weight: 0.2980 chunk 3 optimal weight: 0.0030 chunk 0 optimal weight: 4.9990 chunk 27 optimal weight: 0.1980 chunk 28 optimal weight: 1.9990 overall best weight: 0.6994 ------------------------------------------------------------------------------- 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 = 0.4874 r_free = 0.4874 target = 0.225844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4712 r_free = 0.4712 target = 0.209003 restraints weight = 12038.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.4744 r_free = 0.4744 target = 0.212513 restraints weight = 8238.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4771 r_free = 0.4771 target = 0.215122 restraints weight = 6036.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4789 r_free = 0.4789 target = 0.216960 restraints weight = 4626.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4799 r_free = 0.4799 target = 0.218150 restraints weight = 3667.917| |-----------------------------------------------------------------------------| r_work (final): 0.4787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5013 moved from start: 0.3054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3901 Z= 0.127 Angle : 0.662 9.052 5489 Z= 0.352 Chirality : 0.042 0.219 658 Planarity : 0.005 0.063 534 Dihedral : 20.810 167.766 1027 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 18.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.93 % Favored : 91.07 % Rotamer: Outliers : 3.16 % Allowed : 32.59 % Favored : 64.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.39 (0.46), residues: 347 helix: 0.36 (0.53), residues: 102 sheet: -0.66 (0.60), residues: 69 loop : -3.35 (0.46), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 772 TYR 0.013 0.002 TYR A 608 PHE 0.009 0.001 PHE A 607 TRP 0.010 0.001 TRP A 586 HIS 0.004 0.001 HIS A 946 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.13 ( 3901) covalent geometry : angle 0.66171 / 0.35 ( 5489) hydrogen bonds : bond 0.04903 / 3.23 ( 146) hydrogen bonds : angle 5.29946 / 3.60 ( 381) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 726.56 seconds wall clock time: 13 minutes 11.75 seconds (791.75 seconds total)