Starting phenix.real_space_refine on Wed Mar 5 12:17:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5lij_4054/03_2025/5lij_4054.cif Found real_map, /net/cci-nas-00/data/ceres_data/5lij_4054/03_2025/5lij_4054.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/5lij_4054/03_2025/5lij_4054.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5lij_4054/03_2025/5lij_4054.map" model { file = "/net/cci-nas-00/data/ceres_data/5lij_4054/03_2025/5lij_4054.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5lij_4054/03_2025/5lij_4054.cif" } resolution = 4.2 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= 0.625 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 456 2.51 5 N 152 2.21 5 O 153 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 761 Number of models: 1 Model: "" Number of chains: 1 Chain: "P" Number of atoms: 761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 761 Classifications: {'peptide': 152} Modifications used: {'COO': 1} Link IDs: {'TRANS': 151} Time building chain proxies: 0.28, per 1000 atoms: 0.37 Number of scatterers: 761 At special positions: 0 Unit cell: (49.68, 51.06, 48.3, 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 153 8.00 N 152 7.00 C 456 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: 0.13 Conformation dependent library (CDL) restraints added in 85.5 milliseconds 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 304 Finding SS restraints... Secondary structure from input PDB file: 2 helices and 2 sheets defined 14.5% alpha, 8.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.06 Creating SS restraints... Processing helix chain 'P' and resid 42 through 56 removed outlier: 3.746A pdb=" N ALA P 50 " --> pdb=" O ALA P 46 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA P 51 " --> pdb=" O ALA P 47 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA P 52 " --> pdb=" O ALA P 48 " (cutoff:3.500A) Processing helix chain 'P' and resid 142 through 148 Processing sheet with id=AA1, first strand: chain 'P' and resid 12 through 13 Processing sheet with id=AA2, first strand: chain 'P' and resid 21 through 23 removed outlier: 3.541A pdb=" N ALA P 22 " --> pdb=" O ALA P 134 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA P 115 " --> pdb=" O ALA P 135 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA P 104 " --> pdb=" O ALA P 116 " (cutoff:3.500A) 20 hydrogen bonds defined for protein. 45 hydrogen bond angles 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: 0.09 Time building geometry restraints manager: 0.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.27: 153 1.27 - 1.34: 148 1.34 - 1.40: 3 1.40 - 1.47: 150 1.47 - 1.53: 306 Bond restraints: 760 Sorted by residual: bond pdb=" CA ALA P 132 " pdb=" CB ALA P 132 " ideal model delta sigma weight residual 1.529 1.456 0.073 1.66e-02 3.63e+03 1.94e+01 bond pdb=" C ALA P 131 " pdb=" O ALA P 131 " ideal model delta sigma weight residual 1.234 1.208 0.026 1.22e-02 6.72e+03 4.57e+00 bond pdb=" C ALA P 79 " pdb=" N ALA P 80 " ideal model delta sigma weight residual 1.331 1.304 0.027 1.26e-02 6.30e+03 4.44e+00 bond pdb=" CA ALA P 124 " pdb=" C ALA P 124 " ideal model delta sigma weight residual 1.527 1.502 0.025 1.21e-02 6.83e+03 4.23e+00 bond pdb=" CA ALA P 43 " pdb=" C ALA P 43 " ideal model delta sigma weight residual 1.524 1.500 0.024 1.29e-02 6.01e+03 3.46e+00 ... (remaining 755 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.93: 1028 6.93 - 13.85: 30 13.85 - 20.78: 2 20.78 - 27.70: 2 27.70 - 34.63: 1 Bond angle restraints: 1063 Sorted by residual: angle pdb=" N ALA P 66 " pdb=" CA ALA P 66 " pdb=" C ALA P 66 " ideal model delta sigma weight residual 114.56 149.19 -34.63 1.27e+00 6.20e-01 7.43e+02 angle pdb=" N ALA P 2 " pdb=" CA ALA P 2 " pdb=" C ALA P 2 " ideal model delta sigma weight residual 111.24 133.83 -22.59 1.29e+00 6.01e-01 3.07e+02 angle pdb=" N ALA P 67 " pdb=" CA ALA P 67 " pdb=" CB ALA P 67 " ideal model delta sigma weight residual 110.49 137.65 -27.16 1.69e+00 3.50e-01 2.58e+02 angle pdb=" N ALA P 24 " pdb=" CA ALA P 24 " pdb=" C ALA P 24 " ideal model delta sigma weight residual 111.03 124.86 -13.83 1.11e+00 8.12e-01 1.55e+02 angle pdb=" C ALA P 66 " pdb=" CA ALA P 66 " pdb=" CB ALA P 66 " ideal model delta sigma weight residual 109.13 91.02 18.11 1.56e+00 4.11e-01 1.35e+02 ... (remaining 1058 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.84: 382 10.84 - 21.67: 49 21.67 - 32.51: 17 32.51 - 43.35: 6 43.35 - 54.18: 2 Dihedral angle restraints: 456 sinusoidal: 1 harmonic: 455 Sorted by residual: dihedral pdb=" N ALA P 67 " pdb=" C ALA P 67 " pdb=" CA ALA P 67 " pdb=" CB ALA P 67 " ideal model delta harmonic sigma weight residual 122.90 156.76 -33.86 0 2.50e+00 1.60e-01 1.83e+02 dihedral pdb=" CA ALA P 66 " pdb=" C ALA P 66 " pdb=" N ALA P 67 " pdb=" CA ALA P 67 " ideal model delta harmonic sigma weight residual -180.00 -125.82 -54.18 0 5.00e+00 4.00e-02 1.17e+02 dihedral pdb=" C ALA P 67 " pdb=" N ALA P 67 " pdb=" CA ALA P 67 " pdb=" CB ALA P 67 " ideal model delta harmonic sigma weight residual -122.60 -145.83 23.23 0 2.50e+00 1.60e-01 8.64e+01 ... (remaining 453 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.254: 146 0.254 - 0.508: 3 0.508 - 0.762: 1 0.762 - 1.017: 0 1.017 - 1.271: 2 Chirality restraints: 152 Sorted by residual: chirality pdb=" CA ALA P 67 " pdb=" N ALA P 67 " pdb=" C ALA P 67 " pdb=" CB ALA P 67 " both_signs ideal model delta sigma weight residual False 2.48 1.21 1.27 2.00e-01 2.50e+01 4.04e+01 chirality pdb=" CA ALA P 66 " pdb=" N ALA P 66 " pdb=" C ALA P 66 " pdb=" CB ALA P 66 " both_signs ideal model delta sigma weight residual False 2.48 1.40 1.08 2.00e-01 2.50e+01 2.94e+01 chirality pdb=" CA ALA P 2 " pdb=" N ALA P 2 " pdb=" C ALA P 2 " pdb=" CB ALA P 2 " both_signs ideal model delta sigma weight residual False 2.48 1.97 0.52 2.00e-01 2.50e+01 6.74e+00 ... (remaining 149 not shown) Planarity restraints: 152 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA P 71 " -0.011 2.00e-02 2.50e+03 2.31e-02 5.34e+00 pdb=" C ALA P 71 " 0.040 2.00e-02 2.50e+03 pdb=" O ALA P 71 " -0.015 2.00e-02 2.50e+03 pdb=" N ALA P 72 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA P 130 " -0.011 2.00e-02 2.50e+03 2.25e-02 5.08e+00 pdb=" C ALA P 130 " 0.039 2.00e-02 2.50e+03 pdb=" O ALA P 130 " -0.014 2.00e-02 2.50e+03 pdb=" N ALA P 131 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA P 66 " 0.008 2.00e-02 2.50e+03 1.69e-02 2.87e+00 pdb=" C ALA P 66 " -0.029 2.00e-02 2.50e+03 pdb=" O ALA P 66 " 0.011 2.00e-02 2.50e+03 pdb=" N ALA P 67 " 0.010 2.00e-02 2.50e+03 ... (remaining 149 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 233 2.78 - 3.31: 678 3.31 - 3.84: 1040 3.84 - 4.37: 983 4.37 - 4.90: 1539 Nonbonded interactions: 4473 Sorted by model distance: nonbonded pdb=" O ALA P 87 " pdb=" CA ALA P 106 " model vdw 2.254 3.470 nonbonded pdb=" O ALA P 123 " pdb=" CB ALA P 126 " model vdw 2.270 3.460 nonbonded pdb=" O ALA P 13 " pdb=" N ALA P 97 " model vdw 2.272 3.120 nonbonded pdb=" O ALA P 52 " pdb=" N ALA P 55 " model vdw 2.298 3.120 nonbonded pdb=" O ALA P 142 " pdb=" N ALA P 144 " model vdw 2.440 3.120 ... (remaining 4468 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=0.00 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: 0.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.030 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 4.500 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 6.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 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 : 0.009 0.073 760 Z= 0.650 Angle : 2.916 34.627 1063 Z= 1.992 Chirality : 0.170 1.271 152 Planarity : 0.007 0.023 152 Dihedral : 15.824 54.183 152 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 25.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.67 % Favored : 89.33 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 2.63 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 5.96 % 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: -6.36 (0.33), residues: 150 helix: -5.43 (0.38), residues: 14 sheet: -1.78 (1.86), residues: 11 loop : -4.82 (0.20), residues: 125 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.019 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0271 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 12 optimal weight: 20.0000 chunk 11 optimal weight: 8.9990 chunk 6 optimal weight: 7.9990 chunk 3 optimal weight: 0.2980 chunk 7 optimal weight: 8.9990 chunk 4 optimal weight: 20.0000 chunk 8 optimal weight: 20.0000 chunk 13 optimal weight: 10.0000 chunk 9 optimal weight: 10.0000 chunk 14 optimal weight: 20.0000 chunk 10 optimal weight: 30.0000 overall best weight: 7.2590 ------------------------------------------------------------------------------- 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 = 0.3167 r_free = 0.3167 target = 0.078344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.073110 restraints weight = 3846.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.074338 restraints weight = 2410.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.075245 restraints weight = 1642.685| |-----------------------------------------------------------------------------| r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 760 Z= 0.275 Angle : 1.003 10.390 1063 Z= 0.603 Chirality : 0.043 0.193 152 Planarity : 0.004 0.012 152 Dihedral : 11.127 33.641 152 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 25.33 % Favored : 74.67 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.66 % 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: -6.16 (0.37), residues: 150 helix: -3.10 (0.97), residues: 21 sheet: -2.55 (1.15), residues: 17 loop : -5.02 (0.21), residues: 112 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.019 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0273 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 8 optimal weight: 20.0000 chunk 3 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 6 optimal weight: 7.9990 chunk 9 optimal weight: 20.0000 chunk 1 optimal weight: 0.5980 chunk 11 optimal weight: 30.0000 chunk 10 optimal weight: 8.9990 chunk 7 optimal weight: 7.9990 chunk 12 optimal weight: 10.0000 chunk 5 optimal weight: 2.9990 overall best weight: 4.5188 ------------------------------------------------------------------------------- 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 = 0.3206 r_free = 0.3206 target = 0.080266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.074614 restraints weight = 3712.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.075950 restraints weight = 2324.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.076852 restraints weight = 1579.416| |-----------------------------------------------------------------------------| r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.3783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 760 Z= 0.181 Angle : 0.816 8.598 1063 Z= 0.486 Chirality : 0.039 0.148 152 Planarity : 0.003 0.008 152 Dihedral : 9.198 30.951 152 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 27.33 % Favored : 72.67 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.66 % 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: -5.92 (0.40), residues: 150 helix: -2.62 (0.99), residues: 21 sheet: -2.87 (1.06), residues: 18 loop : -4.83 (0.26), residues: 111 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.019 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0270 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 8 optimal weight: 9.9990 chunk 1 optimal weight: 9.9990 chunk 14 optimal weight: 20.0000 chunk 10 optimal weight: 30.0000 chunk 4 optimal weight: 20.0000 chunk 9 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 3 optimal weight: 7.9990 chunk 7 optimal weight: 0.9990 chunk 13 optimal weight: 20.0000 chunk 6 optimal weight: 20.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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 = 0.3224 r_free = 0.3224 target = 0.081541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.076177 restraints weight = 3694.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.077424 restraints weight = 2374.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.078317 restraints weight = 1638.017| |-----------------------------------------------------------------------------| r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.4186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.009 760 Z= 0.170 Angle : 0.749 7.815 1063 Z= 0.445 Chirality : 0.038 0.127 152 Planarity : 0.002 0.008 152 Dihedral : 8.658 29.141 152 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 26.00 % Favored : 74.00 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % 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: -5.90 (0.46), residues: 150 helix: -1.89 (1.12), residues: 21 sheet: -4.07 (0.66), residues: 35 loop : -4.61 (0.34), residues: 94 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.019 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0276 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 10 optimal weight: 20.0000 chunk 13 optimal weight: 40.0000 chunk 6 optimal weight: 10.0000 chunk 8 optimal weight: 9.9990 chunk 11 optimal weight: 8.9990 chunk 2 optimal weight: 30.0000 chunk 1 optimal weight: 9.9990 chunk 4 optimal weight: 20.0000 chunk 7 optimal weight: 9.9990 chunk 5 optimal weight: 0.1980 chunk 12 optimal weight: 0.7980 overall best weight: 5.9986 ------------------------------------------------------------------------------- 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 = 0.3196 r_free = 0.3196 target = 0.080244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.074950 restraints weight = 3831.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.076250 restraints weight = 2382.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.077167 restraints weight = 1611.197| |-----------------------------------------------------------------------------| r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.4299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.011 760 Z= 0.228 Angle : 0.805 8.573 1063 Z= 0.481 Chirality : 0.039 0.155 152 Planarity : 0.003 0.011 152 Dihedral : 9.107 27.146 152 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 28.00 % Favored : 72.00 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % 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: -5.97 (0.44), residues: 150 helix: -2.22 (1.03), residues: 21 sheet: -3.97 (0.67), residues: 35 loop : -4.67 (0.33), residues: 94 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.018 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0271 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 2 optimal weight: 30.0000 chunk 10 optimal weight: 40.0000 chunk 3 optimal weight: 9.9990 chunk 7 optimal weight: 30.0000 chunk 13 optimal weight: 3.9990 chunk 5 optimal weight: 10.0000 chunk 11 optimal weight: 5.9990 chunk 9 optimal weight: 9.9990 chunk 1 optimal weight: 3.9990 chunk 14 optimal weight: 20.0000 chunk 6 optimal weight: 9.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- 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 = 0.3186 r_free = 0.3186 target = 0.079362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.073515 restraints weight = 3818.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.074896 restraints weight = 2313.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.075871 restraints weight = 1549.151| |-----------------------------------------------------------------------------| r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.4426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.012 760 Z= 0.252 Angle : 0.815 8.441 1063 Z= 0.490 Chirality : 0.039 0.149 152 Planarity : 0.003 0.012 152 Dihedral : 9.331 29.326 152 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 27.33 % Favored : 72.67 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % 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: -6.07 (0.42), residues: 150 helix: -2.33 (1.01), residues: 21 sheet: -3.92 (0.68), residues: 35 loop : -4.78 (0.29), residues: 94 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.019 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0274 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 9 optimal weight: 20.0000 chunk 3 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 12 optimal weight: 8.9990 chunk 11 optimal weight: 30.0000 chunk 14 optimal weight: 9.9990 chunk 2 optimal weight: 30.0000 chunk 4 optimal weight: 20.0000 chunk 8 optimal weight: 5.9990 chunk 6 optimal weight: 4.9990 chunk 13 optimal weight: 6.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- 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 = 0.3172 r_free = 0.3172 target = 0.079005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.073683 restraints weight = 3706.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.074988 restraints weight = 2270.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.075897 restraints weight = 1514.798| |-----------------------------------------------------------------------------| r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.4551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.012 760 Z= 0.259 Angle : 0.830 8.667 1063 Z= 0.498 Chirality : 0.040 0.153 152 Planarity : 0.003 0.012 152 Dihedral : 9.373 26.961 152 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 28.67 % Favored : 71.33 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % 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: -6.21 (0.41), residues: 150 helix: -2.42 (1.01), residues: 21 sheet: -3.89 (0.70), residues: 35 loop : -4.94 (0.25), residues: 94 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.019 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0272 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 5 optimal weight: 9.9990 chunk 11 optimal weight: 30.0000 chunk 13 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 6 optimal weight: 30.0000 chunk 14 optimal weight: 20.0000 chunk 4 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 3 optimal weight: 9.9990 chunk 8 optimal weight: 10.0000 chunk 1 optimal weight: 4.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- 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 = 0.3158 r_free = 0.3158 target = 0.078270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.072963 restraints weight = 3758.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.074210 restraints weight = 2275.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.075124 restraints weight = 1515.399| |-----------------------------------------------------------------------------| r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.4657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.014 760 Z= 0.272 Angle : 0.839 8.506 1063 Z= 0.506 Chirality : 0.040 0.153 152 Planarity : 0.003 0.013 152 Dihedral : 9.511 30.097 152 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 28.00 % Favored : 72.00 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.66 % 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: -6.31 (0.40), residues: 150 helix: -2.49 (1.01), residues: 21 sheet: -3.98 (0.69), residues: 35 loop : -4.99 (0.24), residues: 94 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.019 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0277 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 3 optimal weight: 0.0000 chunk 6 optimal weight: 5.9990 chunk 14 optimal weight: 9.9990 chunk 7 optimal weight: 10.0000 chunk 4 optimal weight: 9.9990 chunk 2 optimal weight: 30.0000 chunk 0 optimal weight: 20.0000 chunk 8 optimal weight: 10.0000 chunk 12 optimal weight: 10.0000 chunk 5 optimal weight: 10.0000 chunk 13 optimal weight: 6.9990 overall best weight: 6.5992 ------------------------------------------------------------------------------- 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 = 0.3172 r_free = 0.3172 target = 0.079061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.073829 restraints weight = 3729.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.075065 restraints weight = 2247.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.075976 restraints weight = 1493.463| |-----------------------------------------------------------------------------| r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.4772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.011 760 Z= 0.246 Angle : 0.812 8.339 1063 Z= 0.488 Chirality : 0.039 0.143 152 Planarity : 0.003 0.012 152 Dihedral : 9.265 26.864 152 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 27.33 % Favored : 72.67 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % 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: -6.30 (0.41), residues: 150 helix: -2.44 (1.02), residues: 21 sheet: -3.99 (0.70), residues: 35 loop : -5.00 (0.24), residues: 94 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.019 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0271 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 13 optimal weight: 20.0000 chunk 2 optimal weight: 20.0000 chunk 5 optimal weight: 5.9990 chunk 1 optimal weight: 8.9990 chunk 14 optimal weight: 20.0000 chunk 10 optimal weight: 30.0000 chunk 3 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 12 optimal weight: 9.9990 chunk 6 optimal weight: 30.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- 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 = 0.3194 r_free = 0.3194 target = 0.079678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.074133 restraints weight = 3783.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.075451 restraints weight = 2268.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.076398 restraints weight = 1513.720| |-----------------------------------------------------------------------------| r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.4892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.010 760 Z= 0.226 Angle : 0.784 8.081 1063 Z= 0.471 Chirality : 0.039 0.138 152 Planarity : 0.003 0.012 152 Dihedral : 8.993 28.293 152 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 27.33 % Favored : 72.67 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % 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: -6.03 (0.40), residues: 150 helix: -2.43 (1.02), residues: 21 sheet: -3.29 (0.92), residues: 23 loop : -4.93 (0.24), residues: 106 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.019 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0273 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 4 optimal weight: 20.0000 chunk 12 optimal weight: 10.0000 chunk 5 optimal weight: 2.9990 chunk 1 optimal weight: 6.9990 chunk 10 optimal weight: 50.0000 chunk 2 optimal weight: 30.0000 chunk 13 optimal weight: 20.0000 chunk 11 optimal weight: 0.9990 chunk 14 optimal weight: 20.0000 chunk 6 optimal weight: 7.9990 chunk 9 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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 = 0.3221 r_free = 0.3221 target = 0.081138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.076166 restraints weight = 3985.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.077395 restraints weight = 2414.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.078275 restraints weight = 1601.436| |-----------------------------------------------------------------------------| r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.5071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.009 760 Z= 0.194 Angle : 0.739 7.557 1063 Z= 0.442 Chirality : 0.038 0.124 152 Planarity : 0.003 0.011 152 Dihedral : 8.550 25.298 152 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 26.67 % Favored : 73.33 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % 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: -5.94 (0.39), residues: 150 helix: -2.36 (1.02), residues: 21 sheet: -2.84 (1.08), residues: 18 loop : -4.92 (0.23), residues: 111 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 311.74 seconds wall clock time: 5 minutes 47.28 seconds (347.28 seconds total)