Starting phenix.real_space_refine on Tue Feb 11 02:17:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ij2_60613/02_2025/9ij2_60613.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ij2_60613/02_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_60613/02_2025/9ij2_60613.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ij2_60613/02_2025/9ij2_60613.map" model { file = "/net/cci-nas-00/data/ceres_data/9ij2_60613/02_2025/9ij2_60613.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ij2_60613/02_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 2.93, per 1000 atoms: 0.79 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: 1.33 Conformation dependent library (CDL) restraints added in 678.3 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: 1.11 Time building geometry restraints manager: 1.16 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: 0.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.020 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.180 ------------------------------------------------------------------------------- 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 : 0.318 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: 0.1870 time to fit residues: 11.8435 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 : 0.349 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4831 r_free = 0.4831 target = 0.223382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4645 r_free = 0.4645 target = 0.203939 restraints weight = 9977.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4688 r_free = 0.4688 target = 0.208366 restraints weight = 6498.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4718 r_free = 0.4718 target = 0.211700 restraints weight = 4494.048| |-----------------------------------------------------------------------------| r_work (final): 0.4715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5108 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 : 0.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 641 GLU cc_start: 0.7672 (tp30) cc_final: 0.7466 (tp30) REVERT: A 773 VAL cc_start: 0.5778 (OUTLIER) cc_final: 0.5470 (t) outliers start: 16 outliers final: 9 residues processed: 66 average time/residue: 0.1886 time to fit residues: 14.9720 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 : 0.347 ------------------------------------------------------------------------------- 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 28 optimal weight: 4.9990 chunk 23 optimal weight: 9.9990 chunk 17 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 24 optimal weight: 0.9990 chunk 37 optimal weight: 9.9990 chunk 27 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 29 optimal weight: 7.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4752 r_free = 0.4752 target = 0.213969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4549 r_free = 0.4549 target = 0.194104 restraints weight = 10479.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4591 r_free = 0.4591 target = 0.198369 restraints weight = 6896.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4622 r_free = 0.4622 target = 0.201419 restraints weight = 4833.161| |-----------------------------------------------------------------------------| r_work (final): 0.4609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5426 moved from start: 0.2958 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= 0.315 Angle : 0.877 10.378 5489 Z= 0.433 Chirality : 0.048 0.185 658 Planarity : 0.006 0.065 534 Dihedral : 21.505 170.162 1027 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 27.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.26 % Favored : 86.74 % Rotamer: Outliers : 9.18 % Allowed : 26.27 % Favored : 64.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.01 (0.45), residues: 347 helix: -0.49 (0.51), residues: 100 sheet: -0.63 (0.65), residues: 69 loop : -3.64 (0.44), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP A 604 HIS 0.003 0.001 HIS A 957 PHE 0.027 0.003 PHE A 950 TYR 0.033 0.003 TYR A 679 ARG 0.004 0.001 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 82 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 53 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 613 MET cc_start: 0.6299 (mtt) cc_final: 0.5781 (mtt) REVERT: A 650 TYR cc_start: 0.3393 (OUTLIER) cc_final: 0.0564 (p90) REVERT: A 769 TRP cc_start: 0.6852 (m100) cc_final: 0.6643 (m100) REVERT: A 773 VAL cc_start: 0.5732 (OUTLIER) cc_final: 0.5419 (t) REVERT: A 842 HIS cc_start: 0.8421 (OUTLIER) cc_final: 0.7677 (p90) REVERT: A 928 MET cc_start: 0.7522 (ppp) cc_final: 0.6812 (ppp) outliers start: 29 outliers final: 18 residues processed: 76 average time/residue: 0.1899 time to fit residues: 17.2139 Evaluate side-chains 73 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 52 time to evaluate : 0.345 ------------------------------------------------------------------------------- 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 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 734 LEU 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 771 SER Chi-restraints excluded: chain A residue 773 VAL Chi-restraints excluded: chain A residue 777 MET 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 956 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: 6.9990 chunk 1 optimal weight: 7.9990 chunk 37 optimal weight: 9.9990 chunk 36 optimal weight: 8.9990 chunk 21 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 chunk 32 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4776 r_free = 0.4776 target = 0.216404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4586 r_free = 0.4586 target = 0.197566 restraints weight = 10620.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4625 r_free = 0.4625 target = 0.201686 restraints weight = 6925.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4655 r_free = 0.4655 target = 0.204801 restraints weight = 4861.039| |-----------------------------------------------------------------------------| r_work (final): 0.4643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5347 moved from start: 0.3217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3901 Z= 0.235 Angle : 0.758 10.054 5489 Z= 0.375 Chirality : 0.044 0.170 658 Planarity : 0.005 0.065 534 Dihedral : 21.422 171.776 1027 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 21.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.53 % Favored : 88.47 % Rotamer: Outliers : 8.54 % Allowed : 27.22 % 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: -2.99 (0.44), residues: 347 helix: -0.45 (0.49), residues: 109 sheet: -0.66 (0.64), residues: 69 loop : -3.79 (0.44), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 604 HIS 0.005 0.001 HIS A 946 PHE 0.019 0.002 PHE A 607 TYR 0.027 0.002 TYR A 679 ARG 0.004 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 83 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 56 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 601 MET cc_start: 0.5721 (tpt) cc_final: 0.5404 (tpt) REVERT: A 613 MET cc_start: 0.6324 (mtt) cc_final: 0.5906 (mtp) REVERT: A 650 TYR cc_start: 0.3295 (OUTLIER) cc_final: 0.0802 (p90) REVERT: A 709 ARG cc_start: 0.7287 (OUTLIER) cc_final: 0.6670 (mmt-90) REVERT: A 719 MET cc_start: 0.5728 (mmt) cc_final: 0.5465 (mmm) REVERT: A 769 TRP cc_start: 0.6607 (m100) cc_final: 0.6388 (m100) REVERT: A 773 VAL cc_start: 0.5654 (OUTLIER) cc_final: 0.5307 (t) REVERT: A 928 MET cc_start: 0.7703 (ppp) cc_final: 0.7163 (ppp) outliers start: 27 outliers final: 13 residues processed: 77 average time/residue: 0.2147 time to fit residues: 19.6445 Evaluate side-chains 68 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 52 time to evaluate : 0.368 ------------------------------------------------------------------------------- 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 664 ILE Chi-restraints excluded: chain A residue 672 MET Chi-restraints excluded: chain A residue 709 ARG Chi-restraints excluded: chain A residue 771 SER Chi-restraints excluded: chain A residue 773 VAL Chi-restraints excluded: chain A residue 777 MET Chi-restraints excluded: chain A residue 784 ASP Chi-restraints excluded: chain A residue 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 16 optimal weight: 5.9990 chunk 28 optimal weight: 6.9990 chunk 26 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 38 optimal weight: 10.0000 chunk 29 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 37 optimal weight: 9.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- 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 = 0.4781 r_free = 0.4781 target = 0.216710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4580 r_free = 0.4580 target = 0.196369 restraints weight = 10945.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4622 r_free = 0.4622 target = 0.200704 restraints weight = 7202.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4656 r_free = 0.4656 target = 0.204210 restraints weight = 5066.173| |-----------------------------------------------------------------------------| r_work (final): 0.4643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5344 moved from start: 0.3546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3901 Z= 0.214 Angle : 0.743 11.464 5489 Z= 0.363 Chirality : 0.043 0.161 658 Planarity : 0.005 0.063 534 Dihedral : 21.373 172.885 1027 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 20.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.24 % Favored : 88.76 % Rotamer: Outliers : 8.54 % Allowed : 27.85 % 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: -2.90 (0.44), residues: 347 helix: -0.32 (0.49), residues: 109 sheet: -0.78 (0.61), residues: 70 loop : -3.70 (0.45), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 604 HIS 0.006 0.001 HIS A 946 PHE 0.017 0.002 PHE A 950 TYR 0.023 0.002 TYR A 679 ARG 0.002 0.000 ARG A 707 *********************** 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: 27 poor density : 51 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 601 MET cc_start: 0.5782 (tpt) cc_final: 0.5428 (tpt) REVERT: A 613 MET cc_start: 0.6249 (mtt) cc_final: 0.5740 (mtt) REVERT: A 650 TYR cc_start: 0.3197 (OUTLIER) cc_final: 0.0880 (p90) REVERT: A 719 MET cc_start: 0.5835 (mmt) cc_final: 0.5471 (mmm) REVERT: A 773 VAL cc_start: 0.5730 (OUTLIER) cc_final: 0.5398 (t) REVERT: A 842 HIS cc_start: 0.8291 (OUTLIER) cc_final: 0.7482 (p90) outliers start: 27 outliers final: 17 residues processed: 75 average time/residue: 0.1879 time to fit residues: 16.7765 Evaluate side-chains 69 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 49 time to evaluate : 0.352 ------------------------------------------------------------------------------- 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 626 ILE Chi-restraints excluded: chain A residue 650 TYR Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 672 MET Chi-restraints excluded: chain A residue 722 LYS Chi-restraints excluded: chain A residue 735 LYS Chi-restraints excluded: chain A residue 771 SER Chi-restraints excluded: chain A residue 773 VAL Chi-restraints excluded: chain A residue 777 MET Chi-restraints excluded: chain A residue 784 ASP Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 842 HIS Chi-restraints excluded: chain A residue 844 LYS Chi-restraints excluded: chain A residue 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 36 optimal weight: 10.0000 chunk 11 optimal weight: 0.0670 chunk 7 optimal weight: 0.4980 chunk 20 optimal weight: 7.9990 chunk 8 optimal weight: 0.1980 chunk 13 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 1 optimal weight: 0.1980 chunk 2 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 overall best weight: 0.3918 ------------------------------------------------------------------------------- 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 = 0.4825 r_free = 0.4825 target = 0.222386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4636 r_free = 0.4636 target = 0.203197 restraints weight = 11018.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4674 r_free = 0.4674 target = 0.207339 restraints weight = 7272.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4706 r_free = 0.4706 target = 0.210736 restraints weight = 5139.319| |-----------------------------------------------------------------------------| r_work (final): 0.4692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5158 moved from start: 0.3565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3901 Z= 0.165 Angle : 0.692 9.919 5489 Z= 0.337 Chirality : 0.041 0.166 658 Planarity : 0.005 0.060 534 Dihedral : 21.007 166.508 1027 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.65 % Favored : 91.35 % Rotamer: Outliers : 6.33 % Allowed : 30.38 % 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: -2.42 (0.45), residues: 347 helix: 0.20 (0.52), residues: 103 sheet: -0.60 (0.60), residues: 70 loop : -3.34 (0.46), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 769 HIS 0.004 0.001 HIS A 927 PHE 0.018 0.002 PHE A 950 TYR 0.027 0.002 TYR A 944 ARG 0.003 0.000 ARG A 617 *********************** 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 70 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 50 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 601 MET cc_start: 0.5671 (tpt) cc_final: 0.5360 (tpt) REVERT: A 613 MET cc_start: 0.5966 (mtt) cc_final: 0.5387 (mtt) REVERT: A 650 TYR cc_start: 0.3061 (OUTLIER) cc_final: 0.1288 (p90) REVERT: A 769 TRP cc_start: 0.6287 (m100) cc_final: 0.5804 (m-10) REVERT: A 773 VAL cc_start: 0.5586 (OUTLIER) cc_final: 0.5236 (t) REVERT: A 951 LEU cc_start: 0.8552 (tp) cc_final: 0.8336 (tp) outliers start: 20 outliers final: 12 residues processed: 67 average time/residue: 0.1981 time to fit residues: 15.8316 Evaluate side-chains 63 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 49 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 586 TRP Chi-restraints excluded: chain A residue 593 ASP Chi-restraints excluded: chain A residue 650 TYR Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 672 MET Chi-restraints excluded: chain A residue 735 LYS Chi-restraints excluded: chain A residue 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 921 LEU Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 956 LEU Chi-restraints excluded: chain A residue 962 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 28 optimal weight: 0.1980 chunk 20 optimal weight: 5.9990 chunk 17 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 29 optimal weight: 0.1980 chunk 26 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 10 optimal weight: 7.9990 chunk 7 optimal weight: 8.9990 overall best weight: 0.6784 ------------------------------------------------------------------------------- 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 = 0.4823 r_free = 0.4823 target = 0.221636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4628 r_free = 0.4628 target = 0.201748 restraints weight = 10832.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4674 r_free = 0.4674 target = 0.206586 restraints weight = 7083.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4708 r_free = 0.4708 target = 0.210149 restraints weight = 4860.821| |-----------------------------------------------------------------------------| r_work (final): 0.4695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5164 moved from start: 0.3853 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= 0.162 Angle : 0.684 9.199 5489 Z= 0.331 Chirality : 0.040 0.169 658 Planarity : 0.005 0.062 534 Dihedral : 20.610 155.644 1027 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 17.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.51 % Favored : 90.49 % Rotamer: Outliers : 4.75 % Allowed : 31.33 % Favored : 63.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.25 (0.46), residues: 347 helix: 0.39 (0.52), residues: 103 sheet: -0.54 (0.61), residues: 70 loop : -3.26 (0.47), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 769 HIS 0.001 0.001 HIS A 917 PHE 0.024 0.002 PHE A 969 TYR 0.018 0.002 TYR A 679 ARG 0.003 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 65 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 50 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 601 MET cc_start: 0.5843 (tpt) cc_final: 0.5415 (tpt) REVERT: A 650 TYR cc_start: 0.3120 (OUTLIER) cc_final: 0.1826 (p90) REVERT: A 666 MET cc_start: 0.0430 (mmm) cc_final: 0.0112 (mmm) REVERT: A 773 VAL cc_start: 0.5431 (OUTLIER) cc_final: 0.5021 (t) REVERT: A 844 LYS cc_start: 0.3161 (OUTLIER) cc_final: 0.2951 (ptpt) outliers start: 15 outliers final: 11 residues processed: 63 average time/residue: 0.2199 time to fit residues: 16.6640 Evaluate side-chains 62 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 48 time to evaluate : 0.324 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain A residue 956 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 13 optimal weight: 0.8980 chunk 1 optimal weight: 0.0970 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 23 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 35 optimal weight: 7.9990 chunk 34 optimal weight: 0.8980 chunk 6 optimal weight: 4.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- 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 = 0.4830 r_free = 0.4830 target = 0.222534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4638 r_free = 0.4638 target = 0.203075 restraints weight = 10793.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4682 r_free = 0.4682 target = 0.207769 restraints weight = 7069.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4716 r_free = 0.4716 target = 0.211157 restraints weight = 4886.841| |-----------------------------------------------------------------------------| r_work (final): 0.4703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5115 moved from start: 0.3918 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= 0.156 Angle : 0.665 9.366 5489 Z= 0.324 Chirality : 0.040 0.174 658 Planarity : 0.005 0.064 534 Dihedral : 20.471 157.968 1027 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 16.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer: Outliers : 4.43 % Allowed : 32.28 % 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: -2.10 (0.47), residues: 347 helix: 0.64 (0.53), residues: 102 sheet: -0.43 (0.61), residues: 70 loop : -3.24 (0.48), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 769 HIS 0.001 0.000 HIS A 903 PHE 0.017 0.002 PHE A 969 TYR 0.012 0.001 TYR A 608 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 66 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 52 time to evaluate : 0.319 Fit side-chains revert: symmetry clash REVERT: A 601 MET cc_start: 0.5768 (tpt) cc_final: 0.5435 (tpt) REVERT: A 650 TYR cc_start: 0.3731 (OUTLIER) cc_final: 0.2730 (p90) REVERT: A 666 MET cc_start: 0.0518 (mmm) cc_final: 0.0058 (mmm) REVERT: A 769 TRP cc_start: 0.6222 (m100) cc_final: 0.5756 (m100) REVERT: A 773 VAL cc_start: 0.5240 (OUTLIER) cc_final: 0.4835 (t) outliers start: 14 outliers final: 11 residues processed: 63 average time/residue: 0.1951 time to fit residues: 14.7444 Evaluate side-chains 62 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 49 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 586 TRP Chi-restraints excluded: chain A residue 593 ASP Chi-restraints excluded: chain A residue 650 TYR Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 672 MET Chi-restraints excluded: chain A residue 735 LYS Chi-restraints excluded: chain A residue 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 948 LEU Chi-restraints excluded: chain A residue 969 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 37 optimal weight: 9.9990 chunk 19 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 chunk 31 optimal weight: 7.9990 chunk 5 optimal weight: 0.0020 chunk 20 optimal weight: 7.9990 chunk 17 optimal weight: 0.2980 chunk 38 optimal weight: 10.0000 chunk 21 optimal weight: 0.9980 chunk 2 optimal weight: 4.9990 overall best weight: 2.0592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 746 HIS ** A 801 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 = 0.4762 r_free = 0.4762 target = 0.215344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4569 r_free = 0.4569 target = 0.196515 restraints weight = 10855.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4610 r_free = 0.4610 target = 0.200795 restraints weight = 7065.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4641 r_free = 0.4641 target = 0.203892 restraints weight = 4885.635| |-----------------------------------------------------------------------------| r_work (final): 0.4628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5337 moved from start: 0.4377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3901 Z= 0.244 Angle : 0.801 14.563 5489 Z= 0.391 Chirality : 0.044 0.192 658 Planarity : 0.005 0.064 534 Dihedral : 20.594 160.573 1027 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 23.73 Ramachandran Plot: Outliers : 0.29 % Allowed : 10.95 % Favored : 88.76 % Rotamer: Outliers : 4.11 % Allowed : 33.54 % 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: -2.68 (0.45), residues: 347 helix: -0.09 (0.52), residues: 107 sheet: -0.57 (0.61), residues: 70 loop : -3.62 (0.46), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 769 HIS 0.006 0.001 HIS A 927 PHE 0.020 0.003 PHE A 969 TYR 0.010 0.002 TYR A 679 ARG 0.002 0.000 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 63 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 50 time to evaluate : 0.337 Fit side-chains revert: symmetry clash REVERT: A 601 MET cc_start: 0.5767 (tpt) cc_final: 0.5442 (tpt) REVERT: A 613 MET cc_start: 0.6238 (mtt) cc_final: 0.5669 (mtt) REVERT: A 650 TYR cc_start: 0.3059 (OUTLIER) cc_final: 0.1532 (p90) REVERT: A 773 VAL cc_start: 0.5429 (OUTLIER) cc_final: 0.5036 (t) outliers start: 13 outliers final: 10 residues processed: 62 average time/residue: 0.1897 time to fit residues: 14.3065 Evaluate side-chains 60 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 48 time to evaluate : 0.352 ------------------------------------------------------------------------------- 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 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 946 HIS Chi-restraints excluded: chain A residue 969 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 23 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 12 optimal weight: 0.0980 chunk 13 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 38 optimal weight: 9.9990 chunk 17 optimal weight: 5.9990 chunk 19 optimal weight: 0.0980 chunk 25 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 16 optimal weight: 2.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 = 0.4819 r_free = 0.4819 target = 0.221842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4628 r_free = 0.4628 target = 0.202715 restraints weight = 10751.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4670 r_free = 0.4670 target = 0.207376 restraints weight = 6934.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4702 r_free = 0.4702 target = 0.210582 restraints weight = 4689.884| |-----------------------------------------------------------------------------| r_work (final): 0.4688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5134 moved from start: 0.4322 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= 0.170 Angle : 0.748 15.665 5489 Z= 0.359 Chirality : 0.041 0.185 658 Planarity : 0.005 0.064 534 Dihedral : 20.395 154.392 1027 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 16.25 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.78 % Favored : 91.93 % Rotamer: Outliers : 3.48 % Allowed : 33.86 % 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: -2.24 (0.46), residues: 347 helix: 0.30 (0.54), residues: 102 sheet: -0.45 (0.60), residues: 70 loop : -3.20 (0.48), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 769 HIS 0.005 0.001 HIS A 927 PHE 0.018 0.001 PHE A 969 TYR 0.014 0.001 TYR A 608 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 61 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 50 time to evaluate : 0.351 Fit side-chains revert: symmetry clash REVERT: A 650 TYR cc_start: 0.3171 (OUTLIER) cc_final: 0.1720 (p90) REVERT: A 719 MET cc_start: 0.5901 (pmm) cc_final: 0.5371 (pmm) REVERT: A 769 TRP cc_start: 0.6115 (m100) cc_final: 0.5555 (m100) REVERT: A 773 VAL cc_start: 0.5229 (OUTLIER) cc_final: 0.4807 (t) outliers start: 11 outliers final: 9 residues processed: 60 average time/residue: 0.2006 time to fit residues: 14.4590 Evaluate side-chains 60 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 49 time to evaluate : 0.344 ------------------------------------------------------------------------------- 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 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 969 PHE 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: 5.9990 chunk 24 optimal weight: 6.9990 chunk 34 optimal weight: 0.9990 chunk 30 optimal weight: 0.0050 chunk 29 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 2 optimal weight: 0.0270 chunk 28 optimal weight: 0.0770 chunk 14 optimal weight: 0.9990 overall best weight: 0.4214 ------------------------------------------------------------------------------- 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 = 0.4832 r_free = 0.4832 target = 0.223317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4647 r_free = 0.4647 target = 0.204689 restraints weight = 11001.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4690 r_free = 0.4690 target = 0.209228 restraints weight = 7167.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4721 r_free = 0.4721 target = 0.212330 restraints weight = 4913.301| |-----------------------------------------------------------------------------| r_work (final): 0.4707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5099 moved from start: 0.4457 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= 0.169 Angle : 0.752 15.934 5489 Z= 0.363 Chirality : 0.042 0.187 658 Planarity : 0.005 0.063 534 Dihedral : 20.363 155.667 1027 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 16.67 Ramachandran Plot: Outliers : 0.29 % Allowed : 8.36 % Favored : 91.35 % 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: -2.19 (0.46), residues: 347 helix: 0.28 (0.53), residues: 102 sheet: -0.33 (0.60), residues: 70 loop : -3.16 (0.48), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 769 HIS 0.004 0.001 HIS A 602 PHE 0.034 0.002 PHE A 950 TYR 0.021 0.002 TYR A 944 ARG 0.003 0.000 ARG A 772 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1471.46 seconds wall clock time: 27 minutes 2.45 seconds (1622.45 seconds total)