Starting phenix.real_space_refine on Fri Dec 27 08:48:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ij2_60613/12_2024/9ij2_60613.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ij2_60613/12_2024/9ij2_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_60613/12_2024/9ij2_60613.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ij2_60613/12_2024/9ij2_60613.map" model { file = "/net/cci-nas-00/data/ceres_data/9ij2_60613/12_2024/9ij2_60613.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ij2_60613/12_2024/9ij2_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-5532/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: 3.02, per 1000 atoms: 0.81 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: 1.04 Conformation dependent library (CDL) restraints added in 367.3 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: 1.28 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: 1.10 Time building geometry restraints manager: 1.14 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: 0.210 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: 14.490 Find NCS groups from input model: 0.040 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:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.940 ------------------------------------------------------------------------------- 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 : 0.378 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: 0.1806 time to fit residues: 11.5109 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 : 0.332 ------------------------------------------------------------------------------- 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: 0.8980 chunk 22 optimal weight: 4.9990 chunk 35 optimal weight: 6.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5075 moved from start: 0.1467 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= 0.186 Angle : 0.718 9.117 5489 Z= 0.358 Chirality : 0.042 0.182 658 Planarity : 0.006 0.069 534 Dihedral : 21.399 158.712 1027 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 16.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.65 % Favored : 91.35 % Rotamer: Outliers : 5.06 % Allowed : 28.48 % 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: -0.45 (0.62), residues: 69 loop : -3.46 (0.44), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 604 HIS 0.001 0.001 HIS A 927 PHE 0.010 0.001 PHE A 923 TYR 0.024 0.002 TYR A 679 ARG 0.003 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: 16 poor density : 54 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 641 GLU cc_start: 0.7660 (tp30) cc_final: 0.7426 (tp30) REVERT: A 773 VAL cc_start: 0.5806 (OUTLIER) cc_final: 0.5503 (t) outliers start: 16 outliers final: 9 residues processed: 66 average time/residue: 0.1920 time to fit residues: 15.1550 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 : 0.338 ------------------------------------------------------------------------------- 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 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 19 optimal weight: 5.9990 chunk 10 optimal weight: 7.9990 chunk 29 optimal weight: 8.9990 chunk 24 optimal weight: 10.0000 chunk 9 optimal weight: 0.0050 chunk 35 optimal weight: 6.9990 chunk 38 optimal weight: 8.9990 chunk 31 optimal weight: 0.8980 chunk 12 optimal weight: 10.0000 chunk 28 optimal weight: 5.9990 chunk 26 optimal weight: 7.9990 overall best weight: 3.9800 ------------------------------------------------------------------------------- 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 801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 931 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5499 moved from start: 0.3598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 3901 Z= 0.399 Angle : 1.008 11.085 5489 Z= 0.502 Chirality : 0.053 0.233 658 Planarity : 0.007 0.065 534 Dihedral : 21.822 174.193 1027 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 32.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.68 % Favored : 87.32 % Rotamer: Outliers : 11.08 % Allowed : 25.32 % Favored : 63.61 % 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: -3.56 (0.42), residues: 347 helix: -0.92 (0.49), residues: 106 sheet: -1.12 (0.63), residues: 61 loop : -3.92 (0.42), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP A 604 HIS 0.006 0.002 HIS A 927 PHE 0.031 0.004 PHE A 923 TYR 0.046 0.003 TYR A 679 ARG 0.005 0.001 ARG A 700 *********************** 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 87 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 52 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 650 TYR cc_start: 0.3768 (OUTLIER) cc_final: 0.0818 (p90) REVERT: A 719 MET cc_start: 0.5893 (mmt) cc_final: 0.5649 (mmm) REVERT: A 735 LYS cc_start: 0.4176 (OUTLIER) cc_final: 0.3346 (pttm) REVERT: A 773 VAL cc_start: 0.5795 (OUTLIER) cc_final: 0.5468 (t) REVERT: A 842 HIS cc_start: 0.8572 (OUTLIER) cc_final: 0.7843 (p90) REVERT: A 928 MET cc_start: 0.7585 (ppp) cc_final: 0.6171 (ppp) outliers start: 35 outliers final: 18 residues processed: 77 average time/residue: 0.1702 time to fit residues: 16.0212 Evaluate side-chains 72 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 50 time to evaluate : 0.369 ------------------------------------------------------------------------------- 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 618 GLU 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 722 LYS Chi-restraints excluded: chain A residue 735 LYS Chi-restraints excluded: chain A residue 743 ASP Chi-restraints excluded: chain A residue 758 PHE 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 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 Chi-restraints excluded: chain A residue 946 HIS Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 956 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 18 optimal weight: 9.9990 chunk 3 optimal weight: 0.9990 chunk 16 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 chunk 35 optimal weight: 6.9990 chunk 37 optimal weight: 10.0000 chunk 33 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 21 optimal weight: 7.9990 chunk 0 optimal weight: 5.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5363 moved from start: 0.3683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3901 Z= 0.247 Angle : 0.799 10.327 5489 Z= 0.396 Chirality : 0.046 0.180 658 Planarity : 0.006 0.065 534 Dihedral : 21.601 173.676 1027 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 23.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.09 % Favored : 89.91 % Rotamer: Outliers : 8.86 % Allowed : 28.16 % 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: -3.26 (0.43), residues: 347 helix: -0.73 (0.47), residues: 106 sheet: -0.77 (0.64), residues: 69 loop : -3.88 (0.43), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 604 HIS 0.003 0.001 HIS A 958 PHE 0.018 0.002 PHE A 923 TYR 0.030 0.003 TYR A 679 ARG 0.010 0.001 ARG A 709 *********************** 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 82 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 54 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 601 MET cc_start: 0.5807 (tpt) cc_final: 0.5460 (tpt) REVERT: A 622 MET cc_start: 0.0289 (tpt) cc_final: -0.0546 (tpt) REVERT: A 650 TYR cc_start: 0.3564 (OUTLIER) cc_final: 0.0749 (p90) REVERT: A 655 GLN cc_start: 0.2525 (OUTLIER) cc_final: 0.1276 (mt0) REVERT: A 719 MET cc_start: 0.5719 (mmt) cc_final: 0.5387 (mmm) REVERT: A 735 LYS cc_start: 0.4189 (OUTLIER) cc_final: 0.3671 (pttm) REVERT: A 773 VAL cc_start: 0.5880 (OUTLIER) cc_final: 0.5565 (t) REVERT: A 842 HIS cc_start: 0.8399 (OUTLIER) cc_final: 0.7635 (p90) outliers start: 28 outliers final: 16 residues processed: 76 average time/residue: 0.1769 time to fit residues: 16.1895 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 : 0.353 ------------------------------------------------------------------------------- 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 604 TRP Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain A residue 650 TYR Chi-restraints excluded: chain A residue 655 GLN Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 672 MET Chi-restraints excluded: chain A residue 722 LYS Chi-restraints excluded: chain A residue 735 LYS Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 773 VAL 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 849 VAL 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 28 optimal weight: 4.9990 chunk 15 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 12 optimal weight: 6.9990 chunk 7 optimal weight: 6.9990 chunk 22 optimal weight: 7.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- 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 780 GLN ** A 801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 931 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5530 moved from start: 0.4793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 3901 Z= 0.354 Angle : 0.938 13.126 5489 Z= 0.464 Chirality : 0.051 0.249 658 Planarity : 0.007 0.070 534 Dihedral : 21.812 178.766 1027 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 32.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.70 % Favored : 85.30 % Rotamer: Outliers : 9.18 % Allowed : 27.85 % 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: -3.76 (0.42), residues: 347 helix: -1.32 (0.44), residues: 108 sheet: -1.11 (0.61), residues: 69 loop : -4.05 (0.44), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 604 HIS 0.005 0.002 HIS A 957 PHE 0.029 0.003 PHE A 923 TYR 0.032 0.003 TYR A 679 ARG 0.009 0.001 ARG A 709 *********************** 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 81 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 52 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 622 MET cc_start: 0.0743 (tpt) cc_final: -0.0421 (tpt) REVERT: A 650 TYR cc_start: 0.3739 (OUTLIER) cc_final: 0.0735 (p90) REVERT: A 666 MET cc_start: 0.0887 (mmm) cc_final: 0.0616 (mmm) REVERT: A 735 LYS cc_start: 0.4111 (OUTLIER) cc_final: 0.2966 (pttm) REVERT: A 773 VAL cc_start: 0.5769 (OUTLIER) cc_final: 0.5438 (t) REVERT: A 842 HIS cc_start: 0.8502 (OUTLIER) cc_final: 0.7675 (p90) REVERT: A 928 MET cc_start: 0.7496 (ppp) cc_final: 0.7261 (ppp) outliers start: 29 outliers final: 17 residues processed: 75 average time/residue: 0.1782 time to fit residues: 16.2563 Evaluate side-chains 71 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 50 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 572 ASN Chi-restraints excluded: chain A residue 586 TRP Chi-restraints excluded: chain A residue 604 TRP Chi-restraints excluded: chain A residue 618 GLU Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain A residue 650 TYR Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 672 MET Chi-restraints excluded: chain A residue 722 LYS Chi-restraints excluded: chain A residue 734 LEU Chi-restraints excluded: chain A residue 735 LYS 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 849 VAL 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 946 HIS Chi-restraints excluded: chain A residue 948 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 9 optimal weight: 7.9990 chunk 37 optimal weight: 9.9990 chunk 31 optimal weight: 7.9990 chunk 17 optimal weight: 8.9990 chunk 3 optimal weight: 0.0980 chunk 12 optimal weight: 0.9990 chunk 19 optimal weight: 6.9990 chunk 36 optimal weight: 8.9990 chunk 4 optimal weight: 0.9980 chunk 21 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5495 moved from start: 0.5108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 3901 Z= 0.301 Angle : 0.848 11.955 5489 Z= 0.423 Chirality : 0.048 0.224 658 Planarity : 0.006 0.062 534 Dihedral : 21.633 172.971 1027 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 28.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.54 % Favored : 86.46 % Rotamer: Outliers : 7.59 % Allowed : 29.75 % Favored : 62.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.58 (0.42), residues: 347 helix: -1.01 (0.45), residues: 108 sheet: -1.16 (0.62), residues: 69 loop : -4.00 (0.44), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 930 HIS 0.005 0.001 HIS A 903 PHE 0.021 0.003 PHE A 923 TYR 0.031 0.003 TYR A 679 ARG 0.009 0.001 ARG A 709 *********************** 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 75 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 51 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 617 ARG cc_start: 0.7369 (tpm170) cc_final: 0.6776 (tpm170) REVERT: A 650 TYR cc_start: 0.3567 (OUTLIER) cc_final: 0.0698 (p90) REVERT: A 655 GLN cc_start: 0.2676 (OUTLIER) cc_final: 0.1967 (mt0) REVERT: A 666 MET cc_start: 0.1017 (mmm) cc_final: 0.0640 (mmm) REVERT: A 735 LYS cc_start: 0.4051 (OUTLIER) cc_final: 0.3242 (pttm) REVERT: A 773 VAL cc_start: 0.5953 (OUTLIER) cc_final: 0.5455 (t) REVERT: A 842 HIS cc_start: 0.8490 (OUTLIER) cc_final: 0.7611 (p90) REVERT: A 844 LYS cc_start: 0.3311 (OUTLIER) cc_final: 0.3108 (ptpt) REVERT: A 928 MET cc_start: 0.7760 (ppp) cc_final: 0.7523 (ppp) REVERT: A 969 PHE cc_start: 0.7446 (OUTLIER) cc_final: 0.6730 (p90) outliers start: 24 outliers final: 13 residues processed: 69 average time/residue: 0.1855 time to fit residues: 15.4591 Evaluate side-chains 70 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 50 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 586 TRP Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain A residue 650 TYR Chi-restraints excluded: chain A residue 655 GLN Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 672 MET Chi-restraints excluded: chain A residue 722 LYS Chi-restraints excluded: chain A residue 735 LYS Chi-restraints excluded: chain A residue 773 VAL Chi-restraints excluded: chain A residue 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 849 VAL 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 946 HIS Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 969 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 21 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 37 optimal weight: 9.9990 chunk 23 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 chunk 17 optimal weight: 6.9990 chunk 15 optimal weight: 0.0980 chunk 11 optimal weight: 6.9990 chunk 7 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5308 moved from start: 0.5043 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= 0.196 Angle : 0.729 10.416 5489 Z= 0.359 Chirality : 0.043 0.170 658 Planarity : 0.006 0.062 534 Dihedral : 21.198 160.325 1027 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 19.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.37 % Favored : 89.63 % Rotamer: Outliers : 5.38 % Allowed : 31.65 % 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: -3.11 (0.44), residues: 347 helix: -0.42 (0.49), residues: 108 sheet: -0.96 (0.63), residues: 69 loop : -3.83 (0.45), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 728 HIS 0.003 0.001 HIS A 903 PHE 0.027 0.002 PHE A 950 TYR 0.033 0.002 TYR A 679 ARG 0.005 0.000 ARG A 709 *********************** 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 70 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 53 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 601 MET cc_start: 0.5482 (tpt) cc_final: 0.5149 (tpt) REVERT: A 650 TYR cc_start: 0.3202 (OUTLIER) cc_final: 0.0551 (p90) REVERT: A 655 GLN cc_start: 0.2270 (OUTLIER) cc_final: 0.1246 (mt0) REVERT: A 735 LYS cc_start: 0.3795 (OUTLIER) cc_final: 0.3307 (pttm) REVERT: A 904 TYR cc_start: -0.0599 (OUTLIER) cc_final: -0.1006 (m-80) REVERT: A 907 VAL cc_start: 0.0762 (OUTLIER) cc_final: 0.0354 (p) REVERT: A 928 MET cc_start: 0.7842 (ppp) cc_final: 0.7308 (tmm) outliers start: 17 outliers final: 8 residues processed: 67 average time/residue: 0.2015 time to fit residues: 16.3884 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 : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 586 TRP Chi-restraints excluded: chain A residue 650 TYR Chi-restraints excluded: chain A residue 655 GLN Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 672 MET Chi-restraints excluded: chain A residue 722 LYS Chi-restraints excluded: chain A residue 735 LYS Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 904 TYR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 5.9990 chunk 29 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 36 optimal weight: 10.0000 chunk 32 optimal weight: 6.9990 chunk 35 optimal weight: 7.9990 chunk 21 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 718 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5344 moved from start: 0.5212 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= 0.214 Angle : 0.753 10.443 5489 Z= 0.372 Chirality : 0.044 0.202 658 Planarity : 0.006 0.062 534 Dihedral : 21.043 158.089 1027 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 22.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.54 % Favored : 86.46 % Rotamer: Outliers : 4.75 % Allowed : 33.23 % 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: -3.14 (0.44), residues: 347 helix: -0.43 (0.48), residues: 108 sheet: -1.07 (0.62), residues: 69 loop : -3.82 (0.45), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 769 HIS 0.004 0.001 HIS A 957 PHE 0.013 0.002 PHE A 923 TYR 0.033 0.002 TYR A 679 ARG 0.006 0.000 ARG A 709 *********************** 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 68 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 53 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 601 MET cc_start: 0.5500 (tpt) cc_final: 0.5079 (tpt) REVERT: A 617 ARG cc_start: 0.7305 (tpm170) cc_final: 0.6854 (tpm170) REVERT: A 650 TYR cc_start: 0.3347 (OUTLIER) cc_final: 0.0473 (p90) REVERT: A 655 GLN cc_start: 0.2321 (OUTLIER) cc_final: 0.1403 (mt0) REVERT: A 714 LYS cc_start: 0.6698 (tppt) cc_final: 0.6358 (tppt) REVERT: A 719 MET cc_start: 0.5947 (mmt) cc_final: 0.5550 (mmm) REVERT: A 735 LYS cc_start: 0.3690 (OUTLIER) cc_final: 0.3181 (pttm) outliers start: 15 outliers final: 11 residues processed: 65 average time/residue: 0.1891 time to fit residues: 14.8319 Evaluate side-chains 66 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 52 time to evaluate : 0.388 ------------------------------------------------------------------------------- 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 655 GLN Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 672 MET Chi-restraints excluded: chain A residue 722 LYS Chi-restraints excluded: chain A residue 735 LYS Chi-restraints excluded: chain A residue 777 MET Chi-restraints excluded: chain A residue 790 LEU 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 967 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 33 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 37 optimal weight: 9.9990 chunk 22 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 25 optimal weight: 0.1980 chunk 38 optimal weight: 8.9990 chunk 35 optimal weight: 7.9990 chunk 30 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- 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 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 931 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5458 moved from start: 0.5704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3901 Z= 0.273 Angle : 0.826 10.971 5489 Z= 0.412 Chirality : 0.047 0.211 658 Planarity : 0.006 0.060 534 Dihedral : 21.092 161.098 1027 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 26.13 Ramachandran Plot: Outliers : 0.29 % Allowed : 14.70 % Favored : 85.01 % Rotamer: Outliers : 5.38 % Allowed : 32.28 % Favored : 62.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.28 (0.44), residues: 347 helix: -0.48 (0.50), residues: 108 sheet: -1.26 (0.61), residues: 69 loop : -3.88 (0.45), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 639 HIS 0.005 0.001 HIS A 957 PHE 0.026 0.003 PHE A 950 TYR 0.032 0.003 TYR A 679 ARG 0.008 0.001 ARG A 709 *********************** 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 71 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 54 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 601 MET cc_start: 0.5336 (tpt) cc_final: 0.4987 (tpt) REVERT: A 650 TYR cc_start: 0.3413 (OUTLIER) cc_final: 0.0473 (p90) REVERT: A 655 GLN cc_start: 0.2295 (OUTLIER) cc_final: 0.1543 (mp10) REVERT: A 710 SER cc_start: 0.8734 (m) cc_final: 0.8363 (p) REVERT: A 714 LYS cc_start: 0.6760 (tppt) cc_final: 0.6383 (tppt) REVERT: A 735 LYS cc_start: 0.4052 (OUTLIER) cc_final: 0.3382 (pttm) REVERT: A 786 LEU cc_start: 0.7265 (mt) cc_final: 0.6882 (pp) REVERT: A 904 TYR cc_start: -0.0885 (OUTLIER) cc_final: -0.1352 (m-80) REVERT: A 928 MET cc_start: 0.7500 (OUTLIER) cc_final: 0.7199 (tmm) outliers start: 17 outliers final: 10 residues processed: 67 average time/residue: 0.1934 time to fit residues: 15.4045 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 : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 586 TRP Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 650 TYR Chi-restraints excluded: chain A residue 655 GLN Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 672 MET Chi-restraints excluded: chain A residue 722 LYS Chi-restraints excluded: chain A residue 735 LYS Chi-restraints excluded: chain A residue 777 MET Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 904 TYR Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 928 MET 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 23 optimal weight: 0.6980 chunk 18 optimal weight: 8.9990 chunk 24 optimal weight: 9.9990 chunk 32 optimal weight: 0.9980 chunk 9 optimal weight: 5.9990 chunk 28 optimal weight: 0.0370 chunk 4 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 12 optimal weight: 0.7980 chunk 31 optimal weight: 8.9990 overall best weight: 1.1060 ------------------------------------------------------------------------------- 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 801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5292 moved from start: 0.5714 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= 0.194 Angle : 0.760 10.263 5489 Z= 0.371 Chirality : 0.043 0.184 658 Planarity : 0.005 0.063 534 Dihedral : 20.864 155.867 1027 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 19.64 Ramachandran Plot: Outliers : 0.29 % Allowed : 10.37 % Favored : 89.34 % Rotamer: Outliers : 4.75 % Allowed : 32.91 % Favored : 62.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.98 (0.45), residues: 347 helix: -0.13 (0.51), residues: 109 sheet: -1.23 (0.60), residues: 69 loop : -3.74 (0.45), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 930 HIS 0.002 0.001 HIS A 957 PHE 0.015 0.002 PHE A 950 TYR 0.023 0.002 TYR A 679 ARG 0.006 0.001 ARG A 675 ********************** 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 67 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 52 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 650 TYR cc_start: 0.3483 (OUTLIER) cc_final: 0.0591 (p90) REVERT: A 655 GLN cc_start: 0.2111 (OUTLIER) cc_final: 0.1201 (mt0) REVERT: A 714 LYS cc_start: 0.6660 (tppt) cc_final: 0.6058 (tppt) REVERT: A 719 MET cc_start: 0.5576 (mmt) cc_final: 0.5136 (mmm) REVERT: A 735 LYS cc_start: 0.4144 (OUTLIER) cc_final: 0.3535 (pttm) REVERT: A 786 LEU cc_start: 0.7158 (mt) cc_final: 0.6840 (pp) REVERT: A 832 GLN cc_start: 0.6983 (OUTLIER) cc_final: 0.6483 (mt0) REVERT: A 904 TYR cc_start: -0.0639 (OUTLIER) cc_final: -0.1084 (m-80) REVERT: A 928 MET cc_start: 0.7405 (tmm) cc_final: 0.7202 (tmm) outliers start: 15 outliers final: 9 residues processed: 62 average time/residue: 0.1657 time to fit residues: 12.6954 Evaluate side-chains 66 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 52 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 586 TRP Chi-restraints excluded: chain A residue 650 TYR Chi-restraints excluded: chain A residue 655 GLN Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 672 MET Chi-restraints excluded: chain A residue 722 LYS Chi-restraints excluded: chain A residue 735 LYS Chi-restraints excluded: chain A residue 777 MET Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 832 GLN Chi-restraints excluded: chain A residue 904 TYR Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 967 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 1 optimal weight: 0.2980 chunk 22 optimal weight: 0.7980 chunk 35 optimal weight: 8.9990 chunk 20 optimal weight: 0.9980 chunk 26 optimal weight: 4.9990 chunk 24 optimal weight: 8.9990 chunk 23 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 718 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4772 r_free = 0.4772 target = 0.219081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4606 r_free = 0.4606 target = 0.201895 restraints weight = 11371.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4642 r_free = 0.4642 target = 0.205742 restraints weight = 7573.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4665 r_free = 0.4665 target = 0.208291 restraints weight = 5349.328| |-----------------------------------------------------------------------------| r_work (final): 0.4652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5266 moved from start: 0.5735 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= 0.174 Angle : 0.728 9.211 5489 Z= 0.354 Chirality : 0.041 0.178 658 Planarity : 0.005 0.062 534 Dihedral : 20.755 156.053 1027 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 19.64 Ramachandran Plot: Outliers : 0.29 % Allowed : 10.66 % Favored : 89.05 % Rotamer: Outliers : 4.75 % Allowed : 32.91 % Favored : 62.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.76 (0.45), residues: 347 helix: 0.04 (0.51), residues: 110 sheet: -1.05 (0.60), residues: 69 loop : -3.64 (0.46), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 930 HIS 0.005 0.001 HIS A 602 PHE 0.017 0.002 PHE A 950 TYR 0.021 0.002 TYR A 679 ARG 0.005 0.001 ARG A 675 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1097.10 seconds wall clock time: 21 minutes 0.55 seconds (1260.55 seconds total)