Starting phenix.real_space_refine on Fri Dec 27 04:02:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c4n_45191/12_2024/9c4n_45191.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c4n_45191/12_2024/9c4n_45191.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9c4n_45191/12_2024/9c4n_45191.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c4n_45191/12_2024/9c4n_45191.map" model { file = "/net/cci-nas-00/data/ceres_data/9c4n_45191/12_2024/9c4n_45191.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c4n_45191/12_2024/9c4n_45191.cif" } resolution = 2.9 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= 0.012 sd= 0.086 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: 3 Type Number sf(0) Gaussians C 41 2.51 5 N 16 2.21 5 O 12 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 69 Number of models: 1 Model: "" Number of chains: 1 Chain: "Y" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 69 Classifications: {'peptide': 9} Link IDs: {'PTRANS': 1, 'TRANS': 7} Time building chain proxies: 0.29, per 1000 atoms: 4.20 Number of scatterers: 69 At special positions: 0 Unit cell: (28.08, 27, 28.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 12 8.00 N 16 7.00 C 41 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.02 Conformation dependent library (CDL) restraints added in 16.4 milliseconds 14 Ramachandran restraints generated. 7 Oldfield, 0 Emsley, 7 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 0 helices and 0 sheets defined 0.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... No hydrogen bonds defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.00 Time building geometry restraints manager: 0.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.28: 10 1.28 - 1.35: 15 1.35 - 1.41: 2 1.41 - 1.48: 11 1.48 - 1.54: 31 Bond restraints: 69 Sorted by residual: bond pdb=" CZ ARG Y 661 " pdb=" NH2 ARG Y 661 " ideal model delta sigma weight residual 1.330 1.297 0.033 1.30e-02 5.92e+03 6.46e+00 bond pdb=" CZ ARG Y 668 " pdb=" NH2 ARG Y 668 " ideal model delta sigma weight residual 1.330 1.298 0.032 1.30e-02 5.92e+03 6.12e+00 bond pdb=" CZ ARG Y 668 " pdb=" NH1 ARG Y 668 " ideal model delta sigma weight residual 1.323 1.292 0.031 1.40e-02 5.10e+03 4.85e+00 bond pdb=" CZ ARG Y 661 " pdb=" NH1 ARG Y 661 " ideal model delta sigma weight residual 1.323 1.297 0.026 1.40e-02 5.10e+03 3.46e+00 bond pdb=" N ARG Y 661 " pdb=" CA ARG Y 661 " ideal model delta sigma weight residual 1.458 1.484 -0.026 1.90e-02 2.77e+03 1.91e+00 ... (remaining 64 not shown) Histogram of bond angle deviations from ideal: 0.01 - 0.88: 28 0.88 - 1.75: 31 1.75 - 2.61: 21 2.61 - 3.48: 9 3.48 - 4.35: 2 Bond angle restraints: 91 Sorted by residual: angle pdb=" OE1 GLN Y 669 " pdb=" CD GLN Y 669 " pdb=" NE2 GLN Y 669 " ideal model delta sigma weight residual 122.60 118.25 4.35 1.00e+00 1.00e+00 1.89e+01 angle pdb=" C ARG Y 661 " pdb=" N PRO Y 662 " pdb=" CA PRO Y 662 " ideal model delta sigma weight residual 119.76 122.97 -3.21 1.00e+00 1.00e+00 1.03e+01 angle pdb=" CD ARG Y 668 " pdb=" NE ARG Y 668 " pdb=" CZ ARG Y 668 " ideal model delta sigma weight residual 124.40 127.65 -3.25 1.40e+00 5.10e-01 5.40e+00 angle pdb=" N PRO Y 662 " pdb=" CD PRO Y 662 " pdb=" CG PRO Y 662 " ideal model delta sigma weight residual 103.20 106.21 -3.01 1.50e+00 4.44e-01 4.04e+00 angle pdb=" N PRO Y 662 " pdb=" CA PRO Y 662 " pdb=" CB PRO Y 662 " ideal model delta sigma weight residual 103.34 105.20 -1.86 9.30e-01 1.16e+00 4.00e+00 ... (remaining 86 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 6.38: 35 6.38 - 12.76: 7 12.76 - 19.14: 1 19.14 - 25.52: 1 25.52 - 31.90: 1 Dihedral angle restraints: 45 sinusoidal: 21 harmonic: 24 Sorted by residual: dihedral pdb=" CG ARG Y 668 " pdb=" CD ARG Y 668 " pdb=" NE ARG Y 668 " pdb=" CZ ARG Y 668 " ideal model delta sinusoidal sigma weight residual 180.00 148.10 31.90 2 1.50e+01 4.44e-03 5.96e+00 dihedral pdb=" CA SER Y 666 " pdb=" C SER Y 666 " pdb=" N SER Y 667 " pdb=" CA SER Y 667 " ideal model delta harmonic sigma weight residual 180.00 168.81 11.19 0 5.00e+00 4.00e-02 5.01e+00 dihedral pdb=" CA SER Y 667 " pdb=" C SER Y 667 " pdb=" N ARG Y 668 " pdb=" CA ARG Y 668 " ideal model delta harmonic sigma weight residual 180.00 171.77 8.23 0 5.00e+00 4.00e-02 2.71e+00 ... (remaining 42 not shown) Histogram of chiral volume deviations from ideal: 0.002 - 0.021: 4 0.021 - 0.040: 2 0.040 - 0.059: 0 0.059 - 0.078: 1 0.078 - 0.097: 3 Chirality restraints: 10 Sorted by residual: chirality pdb=" CG LEU Y 665 " pdb=" CB LEU Y 665 " pdb=" CD1 LEU Y 665 " pdb=" CD2 LEU Y 665 " both_signs ideal model delta sigma weight residual False -2.59 -2.69 0.10 2.00e-01 2.50e+01 2.38e-01 chirality pdb=" CA VAL Y 664 " pdb=" N VAL Y 664 " pdb=" C VAL Y 664 " pdb=" CB VAL Y 664 " both_signs ideal model delta sigma weight residual False 2.44 2.53 -0.09 2.00e-01 2.50e+01 1.93e-01 chirality pdb=" CA PRO Y 662 " pdb=" N PRO Y 662 " pdb=" C PRO Y 662 " pdb=" CB PRO Y 662 " both_signs ideal model delta sigma weight residual False 2.72 2.64 0.08 2.00e-01 2.50e+01 1.63e-01 ... (remaining 7 not shown) Planarity restraints: 12 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU Y 665 " -0.008 2.00e-02 2.50e+03 1.51e-02 2.28e+00 pdb=" C LEU Y 665 " 0.026 2.00e-02 2.50e+03 pdb=" O LEU Y 665 " -0.010 2.00e-02 2.50e+03 pdb=" N SER Y 666 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER Y 666 " 0.005 2.00e-02 2.50e+03 1.06e-02 1.12e+00 pdb=" C SER Y 666 " -0.018 2.00e-02 2.50e+03 pdb=" O SER Y 666 " 0.007 2.00e-02 2.50e+03 pdb=" N SER Y 667 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG Y 668 " -0.059 9.50e-02 1.11e+02 2.66e-02 4.36e-01 pdb=" NE ARG Y 668 " 0.004 2.00e-02 2.50e+03 pdb=" CZ ARG Y 668 " 0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG Y 668 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG Y 668 " -0.002 2.00e-02 2.50e+03 ... (remaining 9 not shown) Histogram of nonbonded interaction distances: 2.78 - 3.20: 48 3.20 - 3.63: 43 3.63 - 4.05: 59 4.05 - 4.48: 64 4.48 - 4.90: 87 Nonbonded interactions: 301 Sorted by model distance: nonbonded pdb=" O PRO Y 662 " pdb=" CA GLY Y 663 " model vdw 2.779 2.752 nonbonded pdb=" O LEU Y 665 " pdb=" CA SER Y 666 " model vdw 2.782 2.776 nonbonded pdb=" O ARG Y 661 " pdb=" CA PRO Y 662 " model vdw 2.792 2.776 nonbonded pdb=" N VAL Y 664 " pdb=" O VAL Y 664 " model vdw 2.794 2.496 nonbonded pdb=" N SER Y 666 " pdb=" O SER Y 666 " model vdw 2.796 2.496 ... (remaining 296 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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 individual isotropic 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: 0.960 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: 0.010 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 6.710 Find NCS groups from input model: 0.000 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:15.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6877 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 : 0.013 0.033 69 Z= 0.798 Angle : 1.696 4.347 91 Z= 1.143 Chirality : 0.057 0.097 10 Planarity : 0.011 0.027 12 Dihedral : 9.184 31.898 29 Min Nonbonded Distance : 2.779 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.29 % Favored : 85.71 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -0.15 (3.46), residues: 7 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.11 (2.64), residues: 7 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG Y 661 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14 Ramachandran restraints generated. 7 Oldfield, 0 Emsley, 7 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14 Ramachandran restraints generated. 7 Oldfield, 0 Emsley, 7 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3 residues out of total 8 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.011 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 2.6652 time to fit residues: 8.0158 Evaluate side-chains 2 residues out of total 8 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 2 time to evaluate : 0.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 4.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- 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: 0.6767 moved from start: 0.6160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.060 0.308 69 Z= 2.181 Angle : 2.309 11.275 91 Z= 1.212 Chirality : 0.223 0.452 10 Planarity : 0.011 0.023 12 Dihedral : 5.595 10.677 10 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 12.50 % Allowed : 12.50 % Favored : 75.00 % Cbeta Deviations : 12.50 % 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: -4.60 (2.29), residues: 7 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.50 (1.75), residues: 7 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.002 ARG Y 661 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14 Ramachandran restraints generated. 7 Oldfield, 0 Emsley, 7 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14 Ramachandran restraints generated. 7 Oldfield, 0 Emsley, 7 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3 residues out of total 8 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 2 time to evaluate : 0.009 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 3 average time/residue: 2.8617 time to fit residues: 8.6030 Evaluate side-chains 1 residues out of total 8 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1 time to evaluate : 0.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 4.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- 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: 0.6910 moved from start: 0.6861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.060 0.312 69 Z= 2.200 Angle : 1.881 8.295 91 Z= 0.929 Chirality : 0.224 0.462 10 Planarity : 0.011 0.029 12 Dihedral : 6.371 11.898 10 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 37.50 % Favored : 62.50 % Cbeta Deviations : 12.50 % 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: -5.63 (1.96), residues: 7 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.29 (1.49), residues: 7 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.002 ARG Y 661 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14 Ramachandran restraints generated. 7 Oldfield, 0 Emsley, 7 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14 Ramachandran restraints generated. 7 Oldfield, 0 Emsley, 7 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2 residues out of total 8 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 2 time to evaluate : 0.011 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 2 average time/residue: 3.2816 time to fit residues: 6.5833 Evaluate side-chains 2 residues out of total 8 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 2 time to evaluate : 0.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 5.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- 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: 0.6904 moved from start: 0.6926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.061 0.314 69 Z= 2.213 Angle : 1.805 7.871 91 Z= 0.890 Chirality : 0.226 0.462 10 Planarity : 0.017 0.046 12 Dihedral : 6.820 12.216 10 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 12.50 % Allowed : 25.00 % Favored : 62.50 % Cbeta Deviations : 12.50 % 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: -6.06 (1.82), residues: 7 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.62 (1.39), residues: 7 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.002 ARG Y 661 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14 Ramachandran restraints generated. 7 Oldfield, 0 Emsley, 7 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14 Ramachandran restraints generated. 7 Oldfield, 0 Emsley, 7 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3 residues out of total 8 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 2 time to evaluate : 0.011 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 2 average time/residue: 3.1781 time to fit residues: 6.3759 Evaluate side-chains 3 residues out of total 8 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 2 time to evaluate : 0.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 661 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 5.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- 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: 0.6911 moved from start: 0.6958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.060 0.312 69 Z= 2.208 Angle : 1.775 7.899 91 Z= 0.875 Chirality : 0.226 0.461 10 Planarity : 0.016 0.043 12 Dihedral : 6.867 12.437 10 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 12.50 % Allowed : 25.00 % Favored : 62.50 % Cbeta Deviations : 12.50 % 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: -6.24 (1.87), residues: 7 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.75 (1.42), residues: 7 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.002 ARG Y 661 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14 Ramachandran restraints generated. 7 Oldfield, 0 Emsley, 7 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14 Ramachandran restraints generated. 7 Oldfield, 0 Emsley, 7 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3 residues out of total 8 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 2 time to evaluate : 0.017 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 2 average time/residue: 3.4649 time to fit residues: 6.9497 Evaluate side-chains 3 residues out of total 8 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 2 time to evaluate : 0.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 661 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 5.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- 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: 0.6915 moved from start: 0.6979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.060 0.312 69 Z= 2.201 Angle : 1.780 8.003 91 Z= 0.877 Chirality : 0.225 0.460 10 Planarity : 0.016 0.044 12 Dihedral : 6.853 12.530 10 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 12.50 % Allowed : 25.00 % Favored : 62.50 % Cbeta Deviations : 12.50 % 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: -6.28 (1.88), residues: 7 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.78 (1.43), residues: 7 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.002 ARG Y 661 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14 Ramachandran restraints generated. 7 Oldfield, 0 Emsley, 7 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14 Ramachandran restraints generated. 7 Oldfield, 0 Emsley, 7 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3 residues out of total 8 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 2 time to evaluate : 0.011 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 2 average time/residue: 3.2597 time to fit residues: 6.5389 Evaluate side-chains 3 residues out of total 8 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 2 time to evaluate : 0.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 661 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 5.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- 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: 0.6905 moved from start: 0.6937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.060 0.313 69 Z= 2.205 Angle : 1.743 7.793 91 Z= 0.868 Chirality : 0.225 0.462 10 Planarity : 0.016 0.044 12 Dihedral : 6.746 12.464 10 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 25.00 % Allowed : 12.50 % Favored : 62.50 % Cbeta Deviations : 12.50 % 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: -6.35 (1.88), residues: 7 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.83 (1.43), residues: 7 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.002 ARG Y 661 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14 Ramachandran restraints generated. 7 Oldfield, 0 Emsley, 7 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14 Ramachandran restraints generated. 7 Oldfield, 0 Emsley, 7 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 4 residues out of total 8 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 2 time to evaluate : 0.011 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 3 average time/residue: 2.7941 time to fit residues: 8.4033 Evaluate side-chains 3 residues out of total 8 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 2 time to evaluate : 0.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 661 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 5.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- 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: 0.6811 moved from start: 0.6691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.061 0.314 69 Z= 2.213 Angle : 1.760 7.729 91 Z= 0.889 Chirality : 0.224 0.462 10 Planarity : 0.018 0.044 12 Dihedral : 7.231 12.889 10 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 12.50 % Allowed : 12.50 % Favored : 75.00 % Cbeta Deviations : 12.50 % 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: -6.32 (1.88), residues: 7 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.81 (1.44), residues: 7 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.002 ARG Y 661 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14 Ramachandran restraints generated. 7 Oldfield, 0 Emsley, 7 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14 Ramachandran restraints generated. 7 Oldfield, 0 Emsley, 7 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3 residues out of total 8 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 2 time to evaluate : 0.009 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 2 average time/residue: 3.5253 time to fit residues: 7.0690 Evaluate side-chains 3 residues out of total 8 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 2 time to evaluate : 0.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 661 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 5.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- 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: 0.6801 moved from start: 0.6690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.061 0.313 69 Z= 2.215 Angle : 1.770 7.765 91 Z= 0.891 Chirality : 0.224 0.462 10 Planarity : 0.017 0.044 12 Dihedral : 7.329 13.484 10 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 12.50 % Allowed : 12.50 % Favored : 75.00 % Cbeta Deviations : 12.50 % 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: -6.35 (1.89), residues: 7 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.83 (1.44), residues: 7 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.002 ARG Y 661 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14 Ramachandran restraints generated. 7 Oldfield, 0 Emsley, 7 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14 Ramachandran restraints generated. 7 Oldfield, 0 Emsley, 7 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3 residues out of total 8 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 2 time to evaluate : 0.010 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 2 average time/residue: 3.1196 time to fit residues: 6.2573 Evaluate side-chains 3 residues out of total 8 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 2 time to evaluate : 0.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 661 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 5.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- 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: 0.6782 moved from start: 0.6680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.061 0.316 69 Z= 2.215 Angle : 1.764 7.777 91 Z= 0.888 Chirality : 0.224 0.466 10 Planarity : 0.017 0.044 12 Dihedral : 7.355 13.591 10 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 12.50 % Allowed : 12.50 % Favored : 75.00 % Cbeta Deviations : 12.50 % 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: -6.32 (1.89), residues: 7 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.81 (1.44), residues: 7 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.002 ARG Y 661 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14 Ramachandran restraints generated. 7 Oldfield, 0 Emsley, 7 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14 Ramachandran restraints generated. 7 Oldfield, 0 Emsley, 7 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3 residues out of total 8 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 2 time to evaluate : 0.011 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 2 average time/residue: 3.2544 time to fit residues: 6.5281 Evaluate side-chains 3 residues out of total 8 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 2 time to evaluate : 0.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 661 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 5.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- 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 = 0.3706 r_free = 0.3706 target = 0.160370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.147160 restraints weight = 109.652| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 2.44 r_work: 0.3402 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.6681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.061 0.312 69 Z= 2.219 Angle : 1.756 7.624 91 Z= 0.876 Chirality : 0.225 0.460 10 Planarity : 0.017 0.044 12 Dihedral : 7.517 14.370 10 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 12.50 % Allowed : 12.50 % Favored : 75.00 % Cbeta Deviations : 12.50 % 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: -6.29 (1.89), residues: 7 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.79 (1.44), residues: 7 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.002 ARG Y 661 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 241.10 seconds wall clock time: 5 minutes 12.14 seconds (312.14 seconds total)