Starting phenix.real_space_refine on Tue Aug 4 13:57:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ij2_60613/08_2026/9ij2_60613.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ij2_60613/08_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_60613/08_2026/9ij2_60613.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ij2_60613/08_2026/9ij2_60613.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ij2_60613/08_2026/9ij2_60613.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ij2_60613/08_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-2.2rc3-6140/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: 0.83, per 1000 atoms: 0.22 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: 0.18 Conformation dependent library (CDL) restraints added in 64.0 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: 0.36 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: 0.53 Time building geometry restraints manager: 0.25 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: 5216 2.52 - 5.03: 226 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: 471 0.058 - 0.115: 114 0.115 - 0.173: 65 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: 0.180 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: 0.030 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 3.970 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 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:0.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 5.040 ------------------------------------------------------------------------------- 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= 0.302 Angle : 1.181 12.577 5489 Z= 0.869 Chirality : 0.064 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 0.00477 / 0.30 ( 3901) covalent geometry : angle 1.18100 / 0.87 ( 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 : 0.104 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: 0.0648 time to fit residues: 4.1880 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 : 0.104 ------------------------------------------------------------------------------- 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: 20.0000 overall best weight: 0.5058 ------------------------------------------------------------------------------- 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 = 0.4876 r_free = 0.4876 target = 0.228537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4690 r_free = 0.4690 target = 0.208393 restraints weight = 10509.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4731 r_free = 0.4731 target = 0.213110 restraints weight = 6907.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4763 r_free = 0.4763 target = 0.216461 restraints weight = 4831.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4787 r_free = 0.4787 target = 0.218842 restraints weight = 3510.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4803 r_free = 0.4803 target = 0.220610 restraints weight = 2627.701| |-----------------------------------------------------------------------------| r_work (final): 0.4797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4848 moved from start: 0.0960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3901 Z= 0.131 Angle : 0.668 8.571 5489 Z= 0.366 Chirality : 0.043 0.239 658 Planarity : 0.006 0.076 534 Dihedral : 21.423 151.433 1027 Min Nonbonded Distance : 2.473 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: -2.67 (0.44), residues: 347 helix: -0.39 (0.50), residues: 99 sheet: -0.22 (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 0.017 0.002 TYR A 679 PHE 0.015 0.001 PHE A 607 TRP 0.015 0.002 TRP A 604 HIS 0.003 0.000 HIS A 602 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.13 ( 3901) covalent geometry : angle 0.66833 / 0.37 ( 5489) hydrogen bonds : bond 0.06927 / 4.24 ( 146) hydrogen bonds : angle 5.81284 / 3.91 ( 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 62 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 48 time to evaluate : 0.064 Fit side-chains revert: symmetry clash REVERT: A 710 SER cc_start: 0.7495 (OUTLIER) cc_final: 0.7031 (p) REVERT: A 773 VAL cc_start: 0.5793 (OUTLIER) cc_final: 0.5574 (t) outliers start: 14 outliers final: 7 residues processed: 58 average time/residue: 0.0506 time to fit residues: 3.6292 Evaluate side-chains 56 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 47 time to evaluate : 0.063 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain A residue 946 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 37 optimal weight: 20.0000 chunk 11 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 chunk 6 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 29 optimal weight: 9.9990 chunk 36 optimal weight: 20.0000 chunk 16 optimal weight: 0.8980 chunk 26 optimal weight: 0.0050 chunk 2 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 overall best weight: 1.3800 ------------------------------------------------------------------------------- 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 = 0.4846 r_free = 0.4846 target = 0.225267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4667 r_free = 0.4667 target = 0.206686 restraints weight = 10424.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4709 r_free = 0.4709 target = 0.211093 restraints weight = 6787.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4738 r_free = 0.4738 target = 0.214167 restraints weight = 4686.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4759 r_free = 0.4759 target = 0.216264 restraints weight = 3368.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4770 r_free = 0.4770 target = 0.217489 restraints weight = 2546.240| |-----------------------------------------------------------------------------| r_work (final): 0.4765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4967 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3901 Z= 0.145 Angle : 0.656 8.958 5489 Z= 0.356 Chirality : 0.043 0.235 658 Planarity : 0.005 0.070 534 Dihedral : 21.357 155.200 1027 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.51 % Favored : 90.49 % Rotamer: Outliers : 5.70 % Allowed : 25.95 % Favored : 68.35 % 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: -2.50 (0.45), residues: 347 helix: 0.04 (0.52), residues: 99 sheet: -0.36 (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 707 TYR 0.014 0.002 TYR A 608 PHE 0.012 0.002 PHE A 607 TRP 0.014 0.002 TRP A 604 HIS 0.002 0.001 HIS A 927 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.14 ( 3901) covalent geometry : angle 0.65577 / 0.36 ( 5489) hydrogen bonds : bond 0.06374 / 4.04 ( 146) hydrogen bonds : angle 5.57934 / 3.74 ( 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 68 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 50 time to evaluate : 0.061 Fit side-chains revert: symmetry clash REVERT: A 773 VAL cc_start: 0.5451 (OUTLIER) cc_final: 0.5209 (t) outliers start: 18 outliers final: 11 residues processed: 62 average time/residue: 0.0609 time to fit residues: 4.5562 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 : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 578 PHE Chi-restraints excluded: chain A residue 604 TRP 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 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 Chi-restraints excluded: chain A residue 946 HIS 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: 5.9990 chunk 5 optimal weight: 0.0050 chunk 6 optimal weight: 0.0980 chunk 13 optimal weight: 0.8980 chunk 1 optimal weight: 7.9990 chunk 3 optimal weight: 0.6980 chunk 22 optimal weight: 6.9990 chunk 28 optimal weight: 4.9990 chunk 18 optimal weight: 10.0000 chunk 31 optimal weight: 1.9990 chunk 24 optimal weight: 10.0000 overall best weight: 0.7396 ------------------------------------------------------------------------------- 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 = 0.4855 r_free = 0.4855 target = 0.226047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4678 r_free = 0.4678 target = 0.207890 restraints weight = 10308.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4719 r_free = 0.4719 target = 0.212190 restraints weight = 6655.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4751 r_free = 0.4751 target = 0.215364 restraints weight = 4565.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.4775 r_free = 0.4775 target = 0.217690 restraints weight = 3260.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4789 r_free = 0.4789 target = 0.219121 restraints weight = 2395.917| |-----------------------------------------------------------------------------| r_work (final): 0.4786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4917 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3901 Z= 0.124 Angle : 0.649 8.258 5489 Z= 0.343 Chirality : 0.042 0.230 658 Planarity : 0.005 0.066 534 Dihedral : 21.208 155.896 1027 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.51 % Favored : 90.49 % Rotamer: Outliers : 5.70 % Allowed : 29.11 % 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: -2.32 (0.45), residues: 347 helix: 0.49 (0.55), residues: 98 sheet: -0.50 (0.59), residues: 69 loop : -3.33 (0.44), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 707 TYR 0.014 0.002 TYR A 608 PHE 0.009 0.001 PHE A 607 TRP 0.012 0.001 TRP A 604 HIS 0.003 0.001 HIS A 958 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.12 ( 3901) covalent geometry : angle 0.64927 / 0.34 ( 5489) hydrogen bonds : bond 0.05452 / 3.48 ( 146) hydrogen bonds : angle 5.34463 / 3.59 ( 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 69 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 51 time to evaluate : 0.060 Fit side-chains revert: symmetry clash REVERT: A 719 MET cc_start: 0.5951 (mmm) cc_final: 0.5437 (mmm) REVERT: A 773 VAL cc_start: 0.5735 (OUTLIER) cc_final: 0.5440 (t) outliers start: 18 outliers final: 12 residues processed: 63 average time/residue: 0.0570 time to fit residues: 4.3227 Evaluate side-chains 63 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 50 time to evaluate : 0.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 578 PHE 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 710 SER Chi-restraints excluded: chain A residue 730 VAL Chi-restraints excluded: chain A residue 752 MET Chi-restraints excluded: chain A residue 773 VAL Chi-restraints excluded: chain A residue 777 MET 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: 0.9990 chunk 20 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 13 optimal weight: 7.9990 chunk 25 optimal weight: 0.8980 chunk 8 optimal weight: 5.9990 chunk 31 optimal weight: 0.1980 chunk 17 optimal weight: 8.9990 chunk 35 optimal weight: 9.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 = 0.4843 r_free = 0.4843 target = 0.224469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4659 r_free = 0.4659 target = 0.205532 restraints weight = 10521.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4703 r_free = 0.4703 target = 0.210039 restraints weight = 6858.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4735 r_free = 0.4735 target = 0.213235 restraints weight = 4740.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4758 r_free = 0.4758 target = 0.215489 restraints weight = 3410.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4773 r_free = 0.4773 target = 0.217051 restraints weight = 2556.666| |-----------------------------------------------------------------------------| r_work (final): 0.4769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4982 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3901 Z= 0.133 Angle : 0.646 8.426 5489 Z= 0.341 Chirality : 0.043 0.226 658 Planarity : 0.005 0.065 534 Dihedral : 21.005 158.359 1027 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 15.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.66 % Favored : 89.34 % Rotamer: Outliers : 7.59 % Allowed : 26.27 % 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: -2.26 (0.46), residues: 347 helix: 0.43 (0.54), residues: 100 sheet: -0.44 (0.60), residues: 69 loop : -3.27 (0.45), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 707 TYR 0.018 0.002 TYR A 944 PHE 0.023 0.002 PHE A 950 TRP 0.012 0.002 TRP A 604 HIS 0.008 0.001 HIS A 946 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 ( 3901) covalent geometry : angle 0.64603 / 0.34 ( 5489) hydrogen bonds : bond 0.05566 / 3.64 ( 146) hydrogen bonds : angle 5.23501 / 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 75 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 51 time to evaluate : 0.064 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 650 TYR cc_start: 0.3762 (OUTLIER) cc_final: 0.1677 (p90) REVERT: A 773 VAL cc_start: 0.5511 (OUTLIER) cc_final: 0.5205 (t) outliers start: 24 outliers final: 16 residues processed: 70 average time/residue: 0.0579 time to fit residues: 4.9600 Evaluate side-chains 69 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 51 time to evaluate : 0.102 ------------------------------------------------------------------------------- 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 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 710 SER Chi-restraints excluded: chain A residue 730 VAL 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 844 LYS 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 21 optimal weight: 0.5980 chunk 19 optimal weight: 6.9990 chunk 38 optimal weight: 20.0000 chunk 12 optimal weight: 2.9990 chunk 14 optimal weight: 10.0000 chunk 37 optimal weight: 20.0000 chunk 25 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 4 optimal weight: 3.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- 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 = 0.4812 r_free = 0.4812 target = 0.220886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4616 r_free = 0.4616 target = 0.200214 restraints weight = 10647.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4660 r_free = 0.4660 target = 0.205099 restraints weight = 6968.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4693 r_free = 0.4693 target = 0.208466 restraints weight = 4827.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4718 r_free = 0.4718 target = 0.210976 restraints weight = 3494.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4734 r_free = 0.4734 target = 0.212688 restraints weight = 2610.563| |-----------------------------------------------------------------------------| r_work (final): 0.4728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5106 moved from start: 0.2414 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= 0.166 Angle : 0.692 9.733 5489 Z= 0.366 Chirality : 0.044 0.221 658 Planarity : 0.005 0.064 534 Dihedral : 20.942 162.100 1027 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 20.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.95 % Favored : 89.05 % Rotamer: Outliers : 7.91 % Allowed : 25.95 % 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: -2.49 (0.45), residues: 347 helix: 0.15 (0.52), residues: 102 sheet: -0.44 (0.62), residues: 69 loop : -3.44 (0.44), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 700 TYR 0.011 0.002 TYR A 826 PHE 0.017 0.003 PHE A 950 TRP 0.023 0.002 TRP A 769 HIS 0.006 0.001 HIS A 946 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.17 ( 3901) covalent geometry : angle 0.69198 / 0.37 ( 5489) hydrogen bonds : bond 0.06019 / 3.96 ( 146) hydrogen bonds : angle 5.26640 / 3.59 ( 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 78 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 53 time to evaluate : 0.106 Fit side-chains revert: symmetry clash REVERT: A 601 MET cc_start: 0.5819 (tpt) cc_final: 0.5350 (tpt) REVERT: A 650 TYR cc_start: 0.3441 (OUTLIER) cc_final: 0.1165 (p90) REVERT: A 773 VAL cc_start: 0.5380 (OUTLIER) cc_final: 0.5045 (t) REVERT: A 842 HIS cc_start: 0.8295 (OUTLIER) cc_final: 0.7674 (p90) outliers start: 25 outliers final: 14 residues processed: 73 average time/residue: 0.0701 time to fit residues: 6.1607 Evaluate side-chains 69 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 52 time to evaluate : 0.062 ------------------------------------------------------------------------------- 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 730 VAL 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 842 HIS 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 12 optimal weight: 6.9990 chunk 23 optimal weight: 0.9990 chunk 38 optimal weight: 20.0000 chunk 1 optimal weight: 10.0000 chunk 4 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 24 optimal weight: 10.0000 chunk 35 optimal weight: 10.0000 chunk 14 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 832 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4812 r_free = 0.4812 target = 0.221292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4621 r_free = 0.4621 target = 0.200525 restraints weight = 10776.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4664 r_free = 0.4664 target = 0.205245 restraints weight = 7111.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4695 r_free = 0.4695 target = 0.208576 restraints weight = 4978.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4719 r_free = 0.4719 target = 0.211055 restraints weight = 3628.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4733 r_free = 0.4733 target = 0.212654 restraints weight = 2724.746| |-----------------------------------------------------------------------------| r_work (final): 0.4728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5096 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3901 Z= 0.149 Angle : 0.707 12.875 5489 Z= 0.362 Chirality : 0.043 0.224 658 Planarity : 0.005 0.064 534 Dihedral : 20.911 163.044 1027 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 20.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.95 % Favored : 89.05 % Rotamer: Outliers : 6.01 % Allowed : 29.75 % 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 (0.45), residues: 347 helix: 0.32 (0.52), residues: 102 sheet: -0.43 (0.62), residues: 69 loop : -3.43 (0.45), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 707 TYR 0.010 0.002 TYR A 826 PHE 0.030 0.002 PHE A 950 TRP 0.027 0.002 TRP A 769 HIS 0.003 0.001 HIS A 946 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.15 ( 3901) covalent geometry : angle 0.70670 / 0.36 ( 5489) hydrogen bonds : bond 0.05669 / 3.71 ( 146) hydrogen bonds : angle 5.29803 / 3.61 ( 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 73 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 54 time to evaluate : 0.094 Fit side-chains revert: symmetry clash REVERT: A 601 MET cc_start: 0.5805 (tpt) cc_final: 0.5338 (tpt) REVERT: A 650 TYR cc_start: 0.3378 (OUTLIER) cc_final: 0.1117 (p90) REVERT: A 719 MET cc_start: 0.5929 (mmm) cc_final: 0.5687 (mmm) REVERT: A 773 VAL cc_start: 0.5766 (OUTLIER) cc_final: 0.5458 (t) outliers start: 19 outliers final: 14 residues processed: 71 average time/residue: 0.0596 time to fit residues: 5.0385 Evaluate side-chains 67 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 51 time to evaluate : 0.060 ------------------------------------------------------------------------------- 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 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 735 LYS Chi-restraints excluded: chain A residue 771 SER Chi-restraints excluded: chain A residue 773 VAL Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 844 LYS Chi-restraints excluded: chain A residue 903 HIS Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 951 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 17 optimal weight: 5.9990 chunk 23 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 19 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 38 optimal weight: 20.0000 chunk 5 optimal weight: 6.9990 chunk 3 optimal weight: 5.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 832 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4802 r_free = 0.4802 target = 0.219668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4610 r_free = 0.4610 target = 0.198980 restraints weight = 10737.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4652 r_free = 0.4652 target = 0.203658 restraints weight = 7133.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.4683 r_free = 0.4683 target = 0.207134 restraints weight = 5020.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4707 r_free = 0.4707 target = 0.209521 restraints weight = 3670.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4721 r_free = 0.4721 target = 0.211079 restraints weight = 2757.274| |-----------------------------------------------------------------------------| r_work (final): 0.4717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5147 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3901 Z= 0.167 Angle : 0.746 16.963 5489 Z= 0.381 Chirality : 0.044 0.223 658 Planarity : 0.005 0.066 534 Dihedral : 20.928 165.497 1027 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 21.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.97 % Favored : 87.03 % Rotamer: Outliers : 6.65 % Allowed : 29.11 % 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: -2.41 (0.46), residues: 347 helix: 0.25 (0.52), residues: 103 sheet: -0.49 (0.63), residues: 69 loop : -3.40 (0.46), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 707 TYR 0.026 0.003 TYR A 944 PHE 0.031 0.003 PHE A 950 TRP 0.026 0.003 TRP A 769 HIS 0.006 0.001 HIS A 946 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.17 ( 3901) covalent geometry : angle 0.74577 / 0.38 ( 5489) hydrogen bonds : bond 0.06038 / 4.00 ( 146) hydrogen bonds : angle 5.42778 / 3.71 ( 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 72 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 51 time to evaluate : 0.106 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 601 MET cc_start: 0.5839 (tpt) cc_final: 0.5424 (tpt) REVERT: A 650 TYR cc_start: 0.3571 (OUTLIER) cc_final: 0.1239 (p90) REVERT: A 719 MET cc_start: 0.5990 (mmm) cc_final: 0.5672 (mmm) REVERT: A 773 VAL cc_start: 0.5704 (OUTLIER) cc_final: 0.5391 (t) REVERT: A 842 HIS cc_start: 0.8268 (OUTLIER) cc_final: 0.7597 (p90) REVERT: A 844 LYS cc_start: 0.3101 (OUTLIER) cc_final: 0.2897 (ptpt) outliers start: 21 outliers final: 15 residues processed: 69 average time/residue: 0.0542 time to fit residues: 4.5179 Evaluate side-chains 69 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 50 time to evaluate : 0.061 ------------------------------------------------------------------------------- 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 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 735 LYS 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 784 ASP Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 842 HIS Chi-restraints excluded: chain A residue 844 LYS Chi-restraints excluded: chain A residue 903 HIS Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 951 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 19 optimal weight: 4.9990 chunk 11 optimal weight: 0.6980 chunk 1 optimal weight: 10.0000 chunk 9 optimal weight: 3.9990 chunk 7 optimal weight: 8.9990 chunk 15 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 chunk 22 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 832 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4803 r_free = 0.4803 target = 0.219729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4614 r_free = 0.4614 target = 0.199776 restraints weight = 11096.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4655 r_free = 0.4655 target = 0.204437 restraints weight = 7365.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.4687 r_free = 0.4687 target = 0.207792 restraints weight = 5162.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4709 r_free = 0.4709 target = 0.210024 restraints weight = 3760.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4726 r_free = 0.4726 target = 0.211737 restraints weight = 2843.750| |-----------------------------------------------------------------------------| r_work (final): 0.4722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5134 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 : 0.003 0.034 3901 Z= 0.155 Angle : 0.722 13.710 5489 Z= 0.367 Chirality : 0.042 0.228 658 Planarity : 0.005 0.062 534 Dihedral : 20.922 167.723 1027 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 20.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.10 % Favored : 87.90 % Rotamer: Outliers : 5.70 % Allowed : 30.06 % 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: -2.36 (0.46), residues: 347 helix: 0.37 (0.53), residues: 103 sheet: -0.61 (0.63), residues: 69 loop : -3.36 (0.46), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 707 TYR 0.017 0.002 TYR A 944 PHE 0.032 0.002 PHE A 950 TRP 0.016 0.002 TRP A 769 HIS 0.004 0.001 HIS A 946 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.16 ( 3901) covalent geometry : angle 0.72219 / 0.37 ( 5489) hydrogen bonds : bond 0.05638 / 3.71 ( 146) hydrogen bonds : angle 5.27515 / 3.59 ( 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 67 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 49 time to evaluate : 0.064 Fit side-chains revert: symmetry clash REVERT: A 601 MET cc_start: 0.5844 (tpt) cc_final: 0.5449 (tpt) REVERT: A 613 MET cc_start: 0.6219 (mtt) cc_final: 0.5696 (mtt) REVERT: A 650 TYR cc_start: 0.3548 (OUTLIER) cc_final: 0.1306 (p90) REVERT: A 769 TRP cc_start: 0.6125 (m100) cc_final: 0.5609 (m-10) REVERT: A 773 VAL cc_start: 0.5709 (OUTLIER) cc_final: 0.5395 (t) REVERT: A 842 HIS cc_start: 0.8211 (OUTLIER) cc_final: 0.7528 (p90) REVERT: A 844 LYS cc_start: 0.3149 (OUTLIER) cc_final: 0.2902 (ptpt) outliers start: 18 outliers final: 13 residues processed: 64 average time/residue: 0.0513 time to fit residues: 3.9476 Evaluate side-chains 67 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 50 time to evaluate : 0.061 ------------------------------------------------------------------------------- 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 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 777 MET Chi-restraints excluded: chain A residue 784 ASP Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 842 HIS Chi-restraints excluded: chain A residue 844 LYS Chi-restraints excluded: chain A residue 903 HIS Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 951 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 11 optimal weight: 4.9990 chunk 8 optimal weight: 0.9980 chunk 24 optimal weight: 10.0000 chunk 36 optimal weight: 20.0000 chunk 4 optimal weight: 0.0070 chunk 33 optimal weight: 0.2980 chunk 26 optimal weight: 0.9980 chunk 17 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 9 optimal weight: 9.9990 overall best weight: 1.0600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 832 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4851 r_free = 0.4851 target = 0.222849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4697 r_free = 0.4697 target = 0.206675 restraints weight = 12145.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4730 r_free = 0.4730 target = 0.210218 restraints weight = 8125.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4753 r_free = 0.4753 target = 0.212608 restraints weight = 5849.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4771 r_free = 0.4771 target = 0.214353 restraints weight = 4410.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4783 r_free = 0.4783 target = 0.215645 restraints weight = 3450.165| |-----------------------------------------------------------------------------| r_work (final): 0.4785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4996 moved from start: 0.3047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3901 Z= 0.135 Angle : 0.682 11.044 5489 Z= 0.354 Chirality : 0.044 0.287 658 Planarity : 0.005 0.063 534 Dihedral : 20.882 167.831 1027 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 19.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.24 % Favored : 88.76 % Rotamer: Outliers : 4.43 % Allowed : 31.65 % Favored : 63.92 % 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: -2.33 (0.46), residues: 347 helix: 0.44 (0.54), residues: 103 sheet: -0.64 (0.62), residues: 69 loop : -3.35 (0.46), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 707 TYR 0.012 0.002 TYR A 608 PHE 0.024 0.002 PHE A 950 TRP 0.012 0.002 TRP A 604 HIS 0.004 0.001 HIS A 927 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.14 ( 3901) covalent geometry : angle 0.68157 / 0.35 ( 5489) hydrogen bonds : bond 0.05334 / 3.51 ( 146) hydrogen bonds : angle 5.21005 / 3.53 ( 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: 14 poor density : 50 time to evaluate : 0.103 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 613 MET cc_start: 0.5700 (mtt) cc_final: 0.5205 (mtt) REVERT: A 650 TYR cc_start: 0.3609 (OUTLIER) cc_final: 0.1338 (p90) REVERT: A 719 MET cc_start: 0.4779 (mmt) cc_final: 0.4533 (mmm) REVERT: A 773 VAL cc_start: 0.5669 (OUTLIER) cc_final: 0.5366 (t) REVERT: A 844 LYS cc_start: 0.3344 (OUTLIER) cc_final: 0.3141 (ptpt) outliers start: 14 outliers final: 10 residues processed: 61 average time/residue: 0.0772 time to fit residues: 5.6374 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 : 0.071 ------------------------------------------------------------------------------- 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 664 ILE Chi-restraints excluded: chain A residue 672 MET Chi-restraints excluded: chain A residue 735 LYS Chi-restraints excluded: chain A residue 773 VAL Chi-restraints excluded: chain A residue 777 MET Chi-restraints excluded: chain A residue 784 ASP Chi-restraints excluded: chain A residue 844 LYS Chi-restraints excluded: chain A residue 903 HIS Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 951 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 11 optimal weight: 0.7980 chunk 19 optimal weight: 8.9990 chunk 22 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 2 optimal weight: 0.0770 chunk 18 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 overall best weight: 0.6940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 832 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4875 r_free = 0.4875 target = 0.225221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4722 r_free = 0.4722 target = 0.209189 restraints weight = 11937.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4755 r_free = 0.4755 target = 0.212757 restraints weight = 8077.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4779 r_free = 0.4779 target = 0.215146 restraints weight = 5811.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4796 r_free = 0.4796 target = 0.216900 restraints weight = 4367.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4808 r_free = 0.4808 target = 0.218221 restraints weight = 3380.349| |-----------------------------------------------------------------------------| r_work (final): 0.4802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4931 moved from start: 0.3135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3901 Z= 0.122 Angle : 0.663 10.661 5489 Z= 0.341 Chirality : 0.041 0.233 658 Planarity : 0.005 0.064 534 Dihedral : 20.770 167.515 1027 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 17.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.80 % Favored : 90.20 % 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: -2.27 (0.46), residues: 347 helix: 0.61 (0.54), residues: 102 sheet: -0.71 (0.61), residues: 69 loop : -3.31 (0.46), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 772 TYR 0.012 0.002 TYR A 608 PHE 0.024 0.002 PHE A 950 TRP 0.019 0.002 TRP A 604 HIS 0.004 0.001 HIS A 602 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 ( 3901) covalent geometry : angle 0.66345 / 0.34 ( 5489) hydrogen bonds : bond 0.04927 / 3.26 ( 146) hydrogen bonds : angle 5.05133 / 3.39 ( 381) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 595.43 seconds wall clock time: 10 minutes 54.65 seconds (654.65 seconds total)