Starting phenix.real_space_refine on Wed Mar 5 21:25:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ij2_60613/03_2025/9ij2_60613.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ij2_60613/03_2025/9ij2_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9ij2_60613/03_2025/9ij2_60613.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ij2_60613/03_2025/9ij2_60613.map" model { file = "/net/cci-nas-00/data/ceres_data/9ij2_60613/03_2025/9ij2_60613.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ij2_60613/03_2025/9ij2_60613.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 2.85, per 1000 atoms: 0.76 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: 0.88 Conformation dependent library (CDL) restraints added in 312.7 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: 1.30 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: 1.29 Time building geometry restraints manager: 1.06 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=" 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=" C ILE A 828 " pdb=" N PRO A 829 " ideal model delta sigma weight residual 1.336 1.356 -0.020 1.20e-02 6.94e+03 2.73e+00 bond pdb=" C ALA A 940 " pdb=" N PRO A 941 " ideal model delta sigma weight residual 1.335 1.353 -0.018 1.19e-02 7.06e+03 2.40e+00 bond pdb=" CA TRP A 604 " pdb=" CB TRP A 604 " ideal model delta sigma weight residual 1.531 1.578 -0.048 3.28e-02 9.30e+02 2.12e+00 bond pdb=" CA ILE A 828 " pdb=" C ILE A 828 " ideal model delta sigma weight residual 1.524 1.538 -0.014 1.05e-02 9.07e+03 1.74e+00 ... (remaining 3896 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.52: 5258 2.52 - 5.03: 184 5.03 - 7.55: 33 7.55 - 10.06: 12 10.06 - 12.58: 2 Bond angle restraints: 5489 Sorted by residual: angle pdb=" CA TYR A 679 " pdb=" CB TYR A 679 " pdb=" CG TYR A 679 " ideal model delta sigma weight residual 113.90 121.95 -8.05 1.80e+00 3.09e-01 2.00e+01 angle pdb=" C PRO A 705 " pdb=" N THR A 706 " pdb=" CA THR A 706 " ideal model delta sigma weight residual 121.54 129.59 -8.05 1.91e+00 2.74e-01 1.78e+01 angle pdb=" C3' U B 1 " pdb=" O3' U B 1 " pdb=" P U B 2 " ideal model delta sigma weight residual 120.20 125.86 -5.66 1.50e+00 4.44e-01 1.43e+01 angle pdb=" C ASN A 801 " pdb=" N HIS A 802 " pdb=" CA HIS A 802 " ideal model delta sigma weight residual 121.54 128.51 -6.97 1.91e+00 2.74e-01 1.33e+01 angle pdb=" CA GLN A 830 " pdb=" CB GLN A 830 " pdb=" CG GLN A 830 " ideal model delta sigma weight residual 114.10 121.39 -7.29 2.00e+00 2.50e-01 1.33e+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: 513 0.058 - 0.115: 111 0.115 - 0.173: 26 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: 0.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.210 Find NCS groups from input model: 0.030 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4915 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= 0.288 Angle : 1.126 12.577 5489 Z= 0.563 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.024 0.003 TRP A 604 HIS 0.012 0.002 HIS A 958 PHE 0.029 0.003 PHE A 950 TYR 0.042 0.003 TYR A 679 ARG 0.003 0.001 ARG A 937 *********************** 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 : 0.305 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: 0.1759 time to fit residues: 11.2030 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 : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 7.9990 chunk 29 optimal weight: 6.9990 chunk 16 optimal weight: 0.8980 chunk 10 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 18 optimal weight: 9.9990 chunk 22 optimal weight: 0.9990 chunk 35 optimal weight: 6.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4831 r_free = 0.4831 target = 0.223349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4645 r_free = 0.4645 target = 0.203940 restraints weight = 9975.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4688 r_free = 0.4688 target = 0.208496 restraints weight = 6468.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4719 r_free = 0.4719 target = 0.211720 restraints weight = 4474.763| |-----------------------------------------------------------------------------| r_work (final): 0.4716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5103 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3901 Z= 0.191 Angle : 0.721 9.082 5489 Z= 0.360 Chirality : 0.042 0.183 658 Planarity : 0.006 0.070 534 Dihedral : 21.404 158.679 1027 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 16.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer: Outliers : 5.38 % Allowed : 28.16 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.71 (0.44), residues: 347 helix: -0.25 (0.50), residues: 100 sheet: -0.46 (0.62), residues: 69 loop : -3.45 (0.44), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 604 HIS 0.002 0.001 HIS A 927 PHE 0.010 0.002 PHE A 923 TYR 0.024 0.002 TYR A 679 ARG 0.002 0.000 ARG A 675 *********************** 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 70 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 53 time to evaluate : 0.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 641 GLU cc_start: 0.7676 (tp30) cc_final: 0.7458 (tp30) REVERT: A 773 VAL cc_start: 0.5617 (OUTLIER) cc_final: 0.5305 (t) outliers start: 17 outliers final: 10 residues processed: 65 average time/residue: 0.1762 time to fit residues: 13.8567 Evaluate side-chains 63 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 52 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 735 LYS Chi-restraints excluded: chain A residue 743 ASP 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 921 LEU 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 28 optimal weight: 3.9990 chunk 23 optimal weight: 8.9990 chunk 17 optimal weight: 0.4980 chunk 0 optimal weight: 7.9990 chunk 24 optimal weight: 0.9980 chunk 37 optimal weight: 10.0000 chunk 27 optimal weight: 0.9980 chunk 8 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 29 optimal weight: 6.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4833 r_free = 0.4833 target = 0.222970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4652 r_free = 0.4652 target = 0.204469 restraints weight = 10174.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4696 r_free = 0.4696 target = 0.208838 restraints weight = 6603.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4728 r_free = 0.4728 target = 0.211952 restraints weight = 4561.385| |-----------------------------------------------------------------------------| r_work (final): 0.4719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5103 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3901 Z= 0.170 Angle : 0.694 8.730 5489 Z= 0.338 Chirality : 0.041 0.181 658 Planarity : 0.005 0.065 534 Dihedral : 21.135 161.202 1027 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 16.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.22 % Favored : 90.78 % Rotamer: Outliers : 6.33 % Allowed : 27.53 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.51 (0.45), residues: 347 helix: 0.19 (0.52), residues: 102 sheet: -0.42 (0.64), residues: 69 loop : -3.52 (0.44), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 769 HIS 0.003 0.001 HIS A 958 PHE 0.015 0.002 PHE A 950 TYR 0.029 0.002 TYR A 679 ARG 0.004 0.000 ARG A 617 *********************** 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 73 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 53 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 601 MET cc_start: 0.5676 (tpt) cc_final: 0.5338 (tpt) REVERT: A 650 TYR cc_start: 0.3695 (OUTLIER) cc_final: 0.1393 (p90) REVERT: A 772 ARG cc_start: 0.5885 (mmt180) cc_final: 0.5625 (mmt180) REVERT: A 773 VAL cc_start: 0.5724 (OUTLIER) cc_final: 0.5427 (t) REVERT: A 928 MET cc_start: 0.7217 (ppp) cc_final: 0.5755 (ppp) outliers start: 20 outliers final: 12 residues processed: 68 average time/residue: 0.2071 time to fit residues: 16.7127 Evaluate side-chains 65 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 51 time to evaluate : 0.369 ------------------------------------------------------------------------------- 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 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 710 SER Chi-restraints excluded: chain A residue 722 LYS 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 Chi-restraints excluded: chain A residue 921 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 4 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 1 optimal weight: 5.9990 chunk 37 optimal weight: 10.0000 chunk 36 optimal weight: 8.9990 chunk 21 optimal weight: 6.9990 chunk 5 optimal weight: 7.9990 chunk 3 optimal weight: 3.9990 chunk 32 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4775 r_free = 0.4775 target = 0.216003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4576 r_free = 0.4576 target = 0.196124 restraints weight = 10675.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4617 r_free = 0.4617 target = 0.200391 restraints weight = 7092.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4648 r_free = 0.4648 target = 0.203554 restraints weight = 5032.235| |-----------------------------------------------------------------------------| r_work (final): 0.4634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5353 moved from start: 0.2925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3901 Z= 0.262 Angle : 0.798 9.578 5489 Z= 0.394 Chirality : 0.045 0.165 658 Planarity : 0.005 0.056 534 Dihedral : 21.215 170.384 1027 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 24.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.97 % Favored : 87.03 % Rotamer: Outliers : 7.91 % Allowed : 27.22 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.84 (0.45), residues: 347 helix: -0.35 (0.48), residues: 108 sheet: -0.48 (0.63), residues: 69 loop : -3.71 (0.46), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 769 HIS 0.003 0.001 HIS A 946 PHE 0.019 0.002 PHE A 607 TYR 0.027 0.002 TYR A 679 ARG 0.003 0.001 ARG A 617 *********************** 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 80 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 55 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 574 ARG cc_start: 0.8335 (ttm-80) cc_final: 0.8119 (tpp-160) REVERT: A 601 MET cc_start: 0.5918 (tpt) cc_final: 0.5509 (tpt) REVERT: A 613 MET cc_start: 0.6391 (mtt) cc_final: 0.5824 (mtt) REVERT: A 622 MET cc_start: -0.0429 (tpp) cc_final: -0.1191 (tpp) REVERT: A 650 TYR cc_start: 0.3384 (OUTLIER) cc_final: 0.0981 (p90) REVERT: A 652 ARG cc_start: 0.5075 (OUTLIER) cc_final: 0.4741 (tpm-80) REVERT: A 773 VAL cc_start: 0.5648 (OUTLIER) cc_final: 0.5304 (t) REVERT: A 842 HIS cc_start: 0.8368 (OUTLIER) cc_final: 0.7675 (p90) REVERT: A 928 MET cc_start: 0.7963 (ppp) cc_final: 0.7603 (ppp) outliers start: 25 outliers final: 10 residues processed: 76 average time/residue: 0.1925 time to fit residues: 17.4934 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 : 0.264 ------------------------------------------------------------------------------- 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 743 ASP Chi-restraints excluded: chain A residue 773 VAL Chi-restraints excluded: chain A residue 784 ASP 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 921 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 16 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 26 optimal weight: 6.9990 chunk 17 optimal weight: 7.9990 chunk 32 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 9 optimal weight: 0.0030 chunk 38 optimal weight: 9.9990 chunk 29 optimal weight: 5.9990 chunk 14 optimal weight: 0.9990 chunk 37 optimal weight: 9.9990 overall best weight: 1.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4779 r_free = 0.4779 target = 0.216543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4575 r_free = 0.4575 target = 0.196036 restraints weight = 11044.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4617 r_free = 0.4617 target = 0.200352 restraints weight = 7291.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4649 r_free = 0.4649 target = 0.203676 restraints weight = 5147.596| |-----------------------------------------------------------------------------| r_work (final): 0.4635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5358 moved from start: 0.3372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3901 Z= 0.234 Angle : 0.755 11.058 5489 Z= 0.370 Chirality : 0.043 0.163 658 Planarity : 0.005 0.061 534 Dihedral : 21.212 172.605 1027 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 20.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.95 % Favored : 89.05 % Rotamer: Outliers : 7.28 % Allowed : 28.48 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.64 (0.46), residues: 347 helix: -0.13 (0.50), residues: 109 sheet: -0.55 (0.62), residues: 69 loop : -3.55 (0.47), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 769 HIS 0.004 0.001 HIS A 946 PHE 0.015 0.002 PHE A 607 TYR 0.010 0.002 TYR A 650 ARG 0.003 0.000 ARG A 617 *********************** 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 78 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 55 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 574 ARG cc_start: 0.8178 (ttm-80) cc_final: 0.7964 (tpp-160) REVERT: A 601 MET cc_start: 0.5762 (tpt) cc_final: 0.5430 (tpt) REVERT: A 622 MET cc_start: -0.0384 (tpp) cc_final: -0.0696 (tpp) REVERT: A 650 TYR cc_start: 0.3351 (OUTLIER) cc_final: 0.1236 (p90) REVERT: A 666 MET cc_start: 0.0694 (mmm) cc_final: 0.0449 (mmm) REVERT: A 695 GLN cc_start: 0.3430 (OUTLIER) cc_final: 0.3083 (mm-40) REVERT: A 719 MET cc_start: 0.6460 (mmt) cc_final: 0.6078 (mmm) REVERT: A 773 VAL cc_start: 0.5655 (OUTLIER) cc_final: 0.5320 (t) REVERT: A 842 HIS cc_start: 0.8283 (OUTLIER) cc_final: 0.7498 (p90) outliers start: 23 outliers final: 15 residues processed: 74 average time/residue: 0.1863 time to fit residues: 16.5390 Evaluate side-chains 72 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 53 time to evaluate : 0.336 ------------------------------------------------------------------------------- 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 664 ILE Chi-restraints excluded: chain A residue 672 MET Chi-restraints excluded: chain A residue 695 GLN 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 842 HIS Chi-restraints excluded: chain A residue 844 LYS Chi-restraints excluded: chain A residue 903 HIS Chi-restraints excluded: chain A residue 907 VAL Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 962 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 36 optimal weight: 9.9990 chunk 11 optimal weight: 0.6980 chunk 7 optimal weight: 0.7980 chunk 20 optimal weight: 9.9990 chunk 8 optimal weight: 3.9990 chunk 13 optimal weight: 0.0980 chunk 32 optimal weight: 4.9990 chunk 1 optimal weight: 9.9990 chunk 2 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 chunk 25 optimal weight: 7.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4780 r_free = 0.4780 target = 0.216495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4578 r_free = 0.4578 target = 0.196156 restraints weight = 10725.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4618 r_free = 0.4618 target = 0.200488 restraints weight = 7125.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4652 r_free = 0.4652 target = 0.204047 restraints weight = 5035.387| |-----------------------------------------------------------------------------| r_work (final): 0.4640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5351 moved from start: 0.3933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3901 Z= 0.217 Angle : 0.736 10.289 5489 Z= 0.360 Chirality : 0.043 0.160 658 Planarity : 0.005 0.061 534 Dihedral : 20.934 168.796 1027 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 20.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.95 % Favored : 89.05 % Rotamer: Outliers : 5.38 % Allowed : 31.33 % Favored : 63.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.61 (0.46), residues: 347 helix: -0.07 (0.51), residues: 109 sheet: -0.61 (0.61), residues: 69 loop : -3.52 (0.48), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 769 HIS 0.004 0.001 HIS A 946 PHE 0.017 0.002 PHE A 607 TYR 0.017 0.002 TYR A 679 ARG 0.003 0.000 ARG A 707 *********************** 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 73 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 56 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 601 MET cc_start: 0.5771 (tpt) cc_final: 0.5456 (tpt) REVERT: A 613 MET cc_start: 0.6206 (mtt) cc_final: 0.5618 (mtt) REVERT: A 622 MET cc_start: -0.0037 (tpp) cc_final: -0.0289 (tpp) REVERT: A 650 TYR cc_start: 0.3083 (OUTLIER) cc_final: 0.1142 (p90) REVERT: A 719 MET cc_start: 0.6480 (mmt) cc_final: 0.6066 (mmm) REVERT: A 769 TRP cc_start: 0.6448 (m100) cc_final: 0.5907 (m-10) REVERT: A 773 VAL cc_start: 0.5576 (OUTLIER) cc_final: 0.5211 (t) outliers start: 17 outliers final: 12 residues processed: 70 average time/residue: 0.1886 time to fit residues: 15.9097 Evaluate side-chains 68 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 54 time to evaluate : 0.338 ------------------------------------------------------------------------------- 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 766 LEU 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 907 VAL Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 948 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 28 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 29 optimal weight: 6.9990 chunk 26 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 10 optimal weight: 5.9990 chunk 7 optimal weight: 8.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4808 r_free = 0.4808 target = 0.220009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4610 r_free = 0.4610 target = 0.199712 restraints weight = 10806.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4649 r_free = 0.4649 target = 0.204043 restraints weight = 7148.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4681 r_free = 0.4681 target = 0.207559 restraints weight = 5075.552| |-----------------------------------------------------------------------------| r_work (final): 0.4669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5255 moved from start: 0.4000 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= 0.176 Angle : 0.695 9.958 5489 Z= 0.340 Chirality : 0.041 0.171 658 Planarity : 0.005 0.064 534 Dihedral : 20.714 158.017 1027 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 18.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.65 % Favored : 91.35 % Rotamer: Outliers : 4.75 % Allowed : 31.96 % Favored : 63.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.43 (0.46), residues: 347 helix: 0.15 (0.51), residues: 109 sheet: -0.60 (0.61), residues: 69 loop : -3.43 (0.48), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 604 HIS 0.004 0.001 HIS A 946 PHE 0.009 0.001 PHE A 607 TYR 0.028 0.002 TYR A 944 ARG 0.002 0.000 ARG A 617 *********************** 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 68 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 53 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 601 MET cc_start: 0.5757 (tpt) cc_final: 0.5487 (tpt) REVERT: A 650 TYR cc_start: 0.3026 (OUTLIER) cc_final: 0.1385 (p90) REVERT: A 695 GLN cc_start: 0.2881 (OUTLIER) cc_final: 0.2534 (tp40) REVERT: A 719 MET cc_start: 0.6109 (mmt) cc_final: 0.5868 (mmm) REVERT: A 773 VAL cc_start: 0.5649 (OUTLIER) cc_final: 0.5289 (t) outliers start: 15 outliers final: 12 residues processed: 66 average time/residue: 0.1984 time to fit residues: 15.6564 Evaluate side-chains 67 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 52 time to evaluate : 0.339 ------------------------------------------------------------------------------- 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 695 GLN 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 910 THR Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 948 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 13 optimal weight: 5.9990 chunk 1 optimal weight: 0.0070 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 chunk 23 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 35 optimal weight: 7.9990 chunk 34 optimal weight: 1.9990 chunk 6 optimal weight: 0.0570 overall best weight: 0.8120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4824 r_free = 0.4824 target = 0.221701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4629 r_free = 0.4629 target = 0.201652 restraints weight = 11032.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4670 r_free = 0.4670 target = 0.206178 restraints weight = 7368.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4704 r_free = 0.4704 target = 0.209747 restraints weight = 5177.384| |-----------------------------------------------------------------------------| r_work (final): 0.4689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5213 moved from start: 0.4218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3901 Z= 0.164 Angle : 0.675 9.411 5489 Z= 0.328 Chirality : 0.040 0.179 658 Planarity : 0.005 0.064 534 Dihedral : 20.560 157.358 1027 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 17.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.80 % Favored : 90.20 % Rotamer: Outliers : 4.11 % Allowed : 32.91 % Favored : 62.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.11 (0.47), residues: 347 helix: 0.52 (0.52), residues: 103 sheet: -0.47 (0.62), residues: 69 loop : -3.15 (0.48), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 769 HIS 0.004 0.001 HIS A 946 PHE 0.012 0.001 PHE A 607 TYR 0.021 0.002 TYR A 944 ARG 0.003 0.000 ARG A 617 *********************** 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 65 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 52 time to evaluate : 0.304 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 601 MET cc_start: 0.5818 (tpt) cc_final: 0.5512 (tpt) REVERT: A 650 TYR cc_start: 0.3185 (OUTLIER) cc_final: 0.1890 (p90) REVERT: A 719 MET cc_start: 0.5882 (mmt) cc_final: 0.5645 (mmm) REVERT: A 925 LEU cc_start: 0.7550 (mt) cc_final: 0.7191 (mt) outliers start: 13 outliers final: 9 residues processed: 63 average time/residue: 0.2014 time to fit residues: 15.1178 Evaluate side-chains 62 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 52 time to evaluate : 0.341 ------------------------------------------------------------------------------- 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 735 LYS Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 844 LYS Chi-restraints excluded: chain A residue 921 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 37 optimal weight: 10.0000 chunk 19 optimal weight: 7.9990 chunk 14 optimal weight: 10.0000 chunk 22 optimal weight: 0.0980 chunk 31 optimal weight: 0.5980 chunk 5 optimal weight: 3.9990 chunk 20 optimal weight: 9.9990 chunk 17 optimal weight: 7.9990 chunk 38 optimal weight: 10.0000 chunk 21 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 746 HIS ** A 801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 931 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4735 r_free = 0.4735 target = 0.212300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4538 r_free = 0.4538 target = 0.193231 restraints weight = 10781.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4579 r_free = 0.4579 target = 0.197436 restraints weight = 7168.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4610 r_free = 0.4610 target = 0.200439 restraints weight = 5044.182| |-----------------------------------------------------------------------------| r_work (final): 0.4596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5464 moved from start: 0.4861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 3901 Z= 0.303 Angle : 0.872 15.111 5489 Z= 0.425 Chirality : 0.046 0.185 658 Planarity : 0.005 0.061 534 Dihedral : 20.839 162.135 1027 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 26.70 Ramachandran Plot: Outliers : 0.29 % Allowed : 12.68 % Favored : 87.03 % Rotamer: Outliers : 5.06 % Allowed : 31.65 % Favored : 63.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.73 (0.46), residues: 347 helix: -0.24 (0.50), residues: 108 sheet: -0.68 (0.62), residues: 69 loop : -3.52 (0.48), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 769 HIS 0.006 0.002 HIS A 946 PHE 0.022 0.002 PHE A 923 TYR 0.015 0.003 TYR A 679 ARG 0.005 0.001 ARG A 772 *********************** 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 74 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 58 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 598 THR cc_start: 0.6850 (p) cc_final: 0.6638 (p) REVERT: A 601 MET cc_start: 0.5877 (tpt) cc_final: 0.5599 (tpt) REVERT: A 613 MET cc_start: 0.6201 (mtt) cc_final: 0.5640 (mtt) REVERT: A 650 TYR cc_start: 0.3094 (OUTLIER) cc_final: 0.1513 (p90) REVERT: A 666 MET cc_start: 0.0925 (mmt) cc_final: 0.0084 (mmt) REVERT: A 695 GLN cc_start: 0.3593 (OUTLIER) cc_final: 0.3243 (tp40) REVERT: A 710 SER cc_start: 0.8520 (m) cc_final: 0.8165 (p) REVERT: A 842 HIS cc_start: 0.8356 (OUTLIER) cc_final: 0.7486 (p90) outliers start: 16 outliers final: 12 residues processed: 71 average time/residue: 0.1901 time to fit residues: 16.2291 Evaluate side-chains 71 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 56 time to evaluate : 0.323 ------------------------------------------------------------------------------- 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 695 GLN Chi-restraints excluded: chain A residue 758 PHE Chi-restraints excluded: chain A residue 777 MET 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 907 VAL Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 921 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 23 optimal weight: 0.7980 chunk 7 optimal weight: 8.9990 chunk 12 optimal weight: 0.7980 chunk 13 optimal weight: 0.4980 chunk 34 optimal weight: 0.6980 chunk 38 optimal weight: 10.0000 chunk 17 optimal weight: 5.9990 chunk 19 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 16 optimal weight: 0.0030 overall best weight: 0.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 946 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4861 r_free = 0.4861 target = 0.224297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4710 r_free = 0.4710 target = 0.208646 restraints weight = 11948.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4743 r_free = 0.4743 target = 0.212263 restraints weight = 8057.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4766 r_free = 0.4766 target = 0.214649 restraints weight = 5714.274| |-----------------------------------------------------------------------------| r_work (final): 0.4755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5139 moved from start: 0.4763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3901 Z= 0.175 Angle : 0.762 16.338 5489 Z= 0.358 Chirality : 0.042 0.186 658 Planarity : 0.005 0.065 534 Dihedral : 20.550 154.601 1027 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 17.80 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.78 % Favored : 91.93 % Rotamer: Outliers : 3.80 % Allowed : 34.18 % Favored : 62.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.47), residues: 347 helix: 0.51 (0.53), residues: 103 sheet: -0.59 (0.61), residues: 69 loop : -3.11 (0.48), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 728 HIS 0.009 0.001 HIS A 946 PHE 0.010 0.001 PHE A 607 TYR 0.018 0.002 TYR A 944 ARG 0.002 0.000 ARG A 617 ********************** 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 65 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 53 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 601 MET cc_start: 0.5457 (tpt) cc_final: 0.5244 (tpt) REVERT: A 650 TYR cc_start: 0.3272 (OUTLIER) cc_final: 0.1732 (p90) REVERT: A 666 MET cc_start: 0.0853 (mmt) cc_final: 0.0439 (mmt) REVERT: A 714 LYS cc_start: 0.6597 (tppt) cc_final: 0.5656 (mmmt) REVERT: A 769 TRP cc_start: 0.6147 (m100) cc_final: 0.5701 (m100) outliers start: 12 outliers final: 8 residues processed: 61 average time/residue: 0.1904 time to fit residues: 14.0238 Evaluate side-chains 59 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 50 time to evaluate : 0.322 ------------------------------------------------------------------------------- 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 790 LEU Chi-restraints excluded: chain A residue 844 LYS Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 946 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 35 optimal weight: 7.9990 chunk 23 optimal weight: 6.9990 chunk 24 optimal weight: 9.9990 chunk 34 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 2 optimal weight: 5.9990 chunk 28 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 718 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 946 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4848 r_free = 0.4848 target = 0.223021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4701 r_free = 0.4701 target = 0.207445 restraints weight = 11798.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4732 r_free = 0.4732 target = 0.211056 restraints weight = 7847.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4755 r_free = 0.4755 target = 0.213445 restraints weight = 5500.302| |-----------------------------------------------------------------------------| r_work (final): 0.4746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5134 moved from start: 0.4799 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= 0.178 Angle : 0.796 16.583 5489 Z= 0.369 Chirality : 0.042 0.180 658 Planarity : 0.005 0.061 534 Dihedral : 20.493 156.086 1027 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 18.79 Ramachandran Plot: Outliers : 0.29 % Allowed : 9.51 % Favored : 90.20 % Rotamer: Outliers : 4.11 % Allowed : 33.86 % Favored : 62.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.46), residues: 347 helix: 0.35 (0.52), residues: 108 sheet: -0.61 (0.60), residues: 69 loop : -3.35 (0.48), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 769 HIS 0.012 0.001 HIS A 946 PHE 0.010 0.001 PHE A 607 TYR 0.022 0.002 TYR A 944 ARG 0.004 0.000 ARG A 772 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1491.82 seconds wall clock time: 26 minutes 34.40 seconds (1594.40 seconds total)