Starting phenix.real_space_refine on Tue Aug 4 11:42:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pek_71565/08_2026/9pek_71565.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pek_71565/08_2026/9pek_71565.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9pek_71565/08_2026/9pek_71565.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pek_71565/08_2026/9pek_71565.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9pek_71565/08_2026/9pek_71565.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pek_71565/08_2026/9pek_71565.map" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= -0.025 sd= 0.323 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 300 2.51 5 N 68 2.21 5 O 76 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 444 Number of models: 1 Model: "" Number of chains: 8 Chain: "D" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 110 Unusual residues: {'ACE': 1} Classifications: {'peptide': 11, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 10} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 110 Unusual residues: {'ACE': 1} Classifications: {'peptide': 11, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 10} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 110 Unusual residues: {'ACE': 1} Classifications: {'peptide': 11, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 10} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 110 Unusual residues: {'ACE': 1} Classifications: {'peptide': 11, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 10} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Time building chain proxies: 0.10, per 1000 atoms: 0.23 Number of scatterers: 444 At special positions: 0 Unit cell: (50.055, 48.99, 23.43, 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 76 8.00 N 68 7.00 C 300 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.04 Conformation dependent library (CDL) restraints added in 9.4 milliseconds 72 Ramachandran restraints generated. 36 Oldfield, 0 Emsley, 36 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 88 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: 0.45 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: 0.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.30: 76 1.30 - 1.37: 56 1.37 - 1.43: 96 1.43 - 1.50: 56 1.50 - 1.57: 168 Bond restraints: 452 Sorted by residual: bond pdb=" CB LYS J 10 " pdb=" CG LYS J 10 " ideal model delta sigma weight residual 1.520 1.568 -0.048 3.00e-02 1.11e+03 2.58e+00 bond pdb=" C ACE J 0 " pdb=" O ACE J 0 " ideal model delta sigma weight residual 1.199 1.230 -0.031 2.00e-02 2.50e+03 2.45e+00 bond pdb=" C ACE E 0 " pdb=" O ACE E 0 " ideal model delta sigma weight residual 1.199 1.230 -0.031 2.00e-02 2.50e+03 2.45e+00 bond pdb=" C ACE I 0 " pdb=" O ACE I 0 " ideal model delta sigma weight residual 1.199 1.230 -0.031 2.00e-02 2.50e+03 2.44e+00 bond pdb=" C ACE D 0 " pdb=" O ACE D 0 " ideal model delta sigma weight residual 1.199 1.230 -0.031 2.00e-02 2.50e+03 2.39e+00 ... (remaining 447 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.39: 563 2.39 - 4.77: 15 4.77 - 7.15: 7 7.15 - 9.54: 2 9.54 - 11.92: 1 Bond angle restraints: 588 Sorted by residual: angle pdb=" C ACE E 0 " pdb=" N GLN E 1 " pdb=" CA GLN E 1 " ideal model delta sigma weight residual 121.70 133.62 -11.92 3.00e+00 1.11e-01 1.58e+01 angle pdb=" CB LYS I 4 " pdb=" CG LYS I 4 " pdb=" CD LYS I 4 " ideal model delta sigma weight residual 111.30 118.84 -7.54 2.30e+00 1.89e-01 1.08e+01 angle pdb=" CA LYS J 10 " pdb=" CB LYS J 10 " pdb=" CG LYS J 10 " ideal model delta sigma weight residual 114.10 120.52 -6.42 2.00e+00 2.50e-01 1.03e+01 angle pdb=" CB LYS D 10 " pdb=" CG LYS D 10 " pdb=" CD LYS D 10 " ideal model delta sigma weight residual 111.30 118.59 -7.29 2.30e+00 1.89e-01 1.01e+01 angle pdb=" CB LYS D 4 " pdb=" CG LYS D 4 " pdb=" CD LYS D 4 " ideal model delta sigma weight residual 111.30 118.45 -7.15 2.30e+00 1.89e-01 9.67e+00 ... (remaining 583 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 242 35.97 - 71.93: 17 71.93 - 107.90: 0 107.90 - 143.87: 0 143.87 - 179.83: 1 Dihedral angle restraints: 260 sinusoidal: 132 harmonic: 128 Sorted by residual: dihedral pdb=" CH3 ACE E 0 " pdb=" C ACE E 0 " pdb=" N GLN E 1 " pdb=" CA GLN E 1 " ideal model delta sinusoidal sigma weight residual -180.00 -0.17 -179.83 1 5.00e+00 4.00e-02 7.68e+02 dihedral pdb=" CA PHE J 7 " pdb=" CB PHE J 7 " pdb=" CG PHE J 7 " pdb=" CD1 PHE J 7 " ideal model delta sinusoidal sigma weight residual 90.00 38.23 51.77 2 2.00e+01 2.50e-03 7.40e+00 dihedral pdb=" N GLN E 11 " pdb=" CA GLN E 11 " pdb=" CB GLN E 11 " pdb=" CG GLN E 11 " ideal model delta sinusoidal sigma weight residual 180.00 -138.68 -41.32 3 1.50e+01 4.44e-03 7.39e+00 ... (remaining 257 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.012: 16 0.012 - 0.024: 8 0.024 - 0.036: 6 0.036 - 0.047: 9 0.047 - 0.059: 5 Chirality restraints: 44 Sorted by residual: chirality pdb=" CA LYS J 4 " pdb=" N LYS J 4 " pdb=" C LYS J 4 " pdb=" CB LYS J 4 " both_signs ideal model delta sigma weight residual False 2.51 2.45 0.06 2.00e-01 2.50e+01 8.74e-02 chirality pdb=" CA LYS E 10 " pdb=" N LYS E 10 " pdb=" C LYS E 10 " pdb=" CB LYS E 10 " both_signs ideal model delta sigma weight residual False 2.51 2.45 0.06 2.00e-01 2.50e+01 8.25e-02 chirality pdb=" CA LYS E 4 " pdb=" N LYS E 4 " pdb=" C LYS E 4 " pdb=" CB LYS E 4 " both_signs ideal model delta sigma weight residual False 2.51 2.46 0.05 2.00e-01 2.50e+01 7.38e-02 ... (remaining 41 not shown) Planarity restraints: 80 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE D 7 " 0.002 2.00e-02 2.50e+03 3.88e-03 2.63e-01 pdb=" CG PHE D 7 " -0.008 2.00e-02 2.50e+03 pdb=" CD1 PHE D 7 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE D 7 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE D 7 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE D 7 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE D 7 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE I 3 " 0.001 2.00e-02 2.50e+03 3.39e-03 2.01e-01 pdb=" CG PHE I 3 " -0.007 2.00e-02 2.50e+03 pdb=" CD1 PHE I 3 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE I 3 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE I 3 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE I 3 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE I 3 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU J 8 " -0.002 2.00e-02 2.50e+03 4.18e-03 1.75e-01 pdb=" C GLU J 8 " 0.007 2.00e-02 2.50e+03 pdb=" O GLU J 8 " -0.003 2.00e-02 2.50e+03 pdb=" N PHE J 9 " -0.002 2.00e-02 2.50e+03 ... (remaining 77 not shown) Histogram of nonbonded interaction distances: 2.64 - 3.09: 270 3.09 - 3.54: 363 3.54 - 3.99: 528 3.99 - 4.45: 631 4.45 - 4.90: 894 Nonbonded interactions: 2686 Sorted by model distance: nonbonded pdb=" N PHE D 7 " pdb=" O PHE D 7 " model vdw 2.638 2.496 nonbonded pdb=" N GLU D 8 " pdb=" O GLU D 8 " model vdw 2.644 2.496 nonbonded pdb=" N GLN J 1 " pdb=" N GLU J 2 " model vdw 2.646 2.560 nonbonded pdb=" N GLN D 11 " pdb=" N NH2 D 12 " model vdw 2.647 2.560 nonbonded pdb=" O ACE D 0 " pdb=" NE2 GLN D 1 " model vdw 2.655 3.120 ... (remaining 2681 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.500 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: 0.020 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 1.830 Find NCS groups from input model: 0.020 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:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 3.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4963 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 : 0.012 0.102 456 Z= 0.986 Angle : 1.200 11.923 588 Z= 0.540 Chirality : 0.030 0.059 44 Planarity : 0.001 0.004 80 Dihedral : 23.101 179.831 172 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 0.00 % Allowed : 29.55 % Favored : 70.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -6.06 (0.84), residues: 36 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.61 (0.64), residues: 36 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.008 0.001 PHE D 7 Details of bonding type rmsd/Z covalent geometry : bond 0.00671 / 0.27 ( 452) covalent geometry : angle 1.20035 / 0.54 ( 588) Misc. bond : bond 0.10134 / 5.14 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 72 Ramachandran restraints generated. 36 Oldfield, 0 Emsley, 36 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 72 Ramachandran restraints generated. 36 Oldfield, 0 Emsley, 36 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 44 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.011 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.0681 time to fit residues: 1.5434 Evaluate side-chains 8 residues out of total 44 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 8 time to evaluate : 0.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 4 random chunks: chunk 0 optimal weight: 3.9990 chunk 1 optimal weight: 0.2980 chunk 2 optimal weight: 0.8980 chunk 3 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.088346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.086534 restraints weight = 2459.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.087106 restraints weight = 1370.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.087536 restraints weight = 836.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.087789 restraints weight = 509.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.087930 restraints weight = 314.479| |-----------------------------------------------------------------------------| r_work (final): 0.4062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4687 moved from start: 1.1013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.018 456 Z= 0.149 Angle : 0.823 11.048 588 Z= 0.372 Chirality : 0.031 0.072 44 Planarity : 0.003 0.009 80 Dihedral : 27.350 179.996 48 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.67 % Favored : 83.33 % Rotamer: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -6.55 (0.74), residues: 36 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.99 (0.57), residues: 36 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.019 0.002 PHE D 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.15 ( 452) covalent geometry : angle 0.82344 / 0.37 ( 588) Misc. bond : bond 0.00043 / 0.02 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 72 Ramachandran restraints generated. 36 Oldfield, 0 Emsley, 36 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 72 Ramachandran restraints generated. 36 Oldfield, 0 Emsley, 36 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 15 residues out of total 44 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.015 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.0355 time to fit residues: 0.5739 Evaluate side-chains 8 residues out of total 44 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 8 time to evaluate : 0.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 4 random chunks: chunk 0 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.089998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.087550 restraints weight = 2257.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.088502 restraints weight = 1008.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.088983 restraints weight = 522.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.089271 restraints weight = 295.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.089482 restraints weight = 179.613| |-----------------------------------------------------------------------------| r_work (final): 0.4083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4708 moved from start: 1.3454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 456 Z= 0.160 Angle : 0.814 11.601 588 Z= 0.364 Chirality : 0.033 0.076 44 Planarity : 0.002 0.007 80 Dihedral : 27.079 178.952 48 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.89 % Favored : 86.11 % Rotamer: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -6.88 (0.76), residues: 36 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.24 (0.58), residues: 36 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.015 0.002 PHE D 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.16 ( 452) covalent geometry : angle 0.81446 / 0.36 ( 588) Misc. bond : bond 0.00026 / 0.01 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 72 Ramachandran restraints generated. 36 Oldfield, 0 Emsley, 36 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 72 Ramachandran restraints generated. 36 Oldfield, 0 Emsley, 36 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 10 residues out of total 44 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.013 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.0582 time to fit residues: 0.6117 Evaluate side-chains 6 residues out of total 44 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 6 time to evaluate : 0.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 4 random chunks: chunk 0 optimal weight: 4.9990 chunk 1 optimal weight: 0.0370 chunk 2 optimal weight: 5.9990 chunk 3 optimal weight: 6.9990 overall best weight: 2.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.086335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.081746 restraints weight = 2479.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.083040 restraints weight = 1428.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.083785 restraints weight = 871.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.084320 restraints weight = 584.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.084629 restraints weight = 398.910| |-----------------------------------------------------------------------------| r_work (final): 0.3964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4969 moved from start: 1.5722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.035 456 Z= 0.312 Angle : 1.090 12.266 588 Z= 0.534 Chirality : 0.054 0.135 44 Planarity : 0.004 0.011 80 Dihedral : 28.195 177.625 48 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 18.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.44 % Favored : 80.56 % Rotamer: Outliers : 0.00 % Allowed : 13.64 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -7.35 (0.74), residues: 36 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.60 (0.56), residues: 36 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.025 0.004 PHE J 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00774 / 0.31 ( 452) covalent geometry : angle 1.09030 / 0.53 ( 588) Misc. bond : bond 0.00054 / 0.03 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 72 Ramachandran restraints generated. 36 Oldfield, 0 Emsley, 36 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 72 Ramachandran restraints generated. 36 Oldfield, 0 Emsley, 36 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 9 residues out of total 44 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 9 time to evaluate : 0.010 Fit side-chains REVERT: I 10 LYS cc_start: 0.5520 (mmmt) cc_final: 0.4752 (mmtm) outliers start: 0 outliers final: 0 residues processed: 9 average time/residue: 0.0551 time to fit residues: 0.5240 Evaluate side-chains 6 residues out of total 44 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 6 time to evaluate : 0.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 4 random chunks: chunk 0 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 2 optimal weight: 0.6980 chunk 3 optimal weight: 3.9990 overall best weight: 1.8485 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.078740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.076147 restraints weight = 2508.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.077045 restraints weight = 1183.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.077644 restraints weight = 615.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.077944 restraints weight = 346.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.078165 restraints weight = 218.623| |-----------------------------------------------------------------------------| r_work (final): 0.3984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5070 moved from start: 1.5868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.027 456 Z= 0.238 Angle : 0.977 11.958 588 Z= 0.472 Chirality : 0.047 0.103 44 Planarity : 0.003 0.011 80 Dihedral : 28.132 178.344 48 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 2.78 % Allowed : 19.44 % Favored : 77.78 % Rotamer: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -7.40 (0.84), residues: 36 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.63 (0.64), residues: 36 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.024 0.003 PHE J 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00591 / 0.24 ( 452) covalent geometry : angle 0.97665 / 0.47 ( 588) Misc. bond : bond 0.00206 / 0.10 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 72 Ramachandran restraints generated. 36 Oldfield, 0 Emsley, 36 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 72 Ramachandran restraints generated. 36 Oldfield, 0 Emsley, 36 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 8 residues out of total 44 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 8 time to evaluate : 0.012 Fit side-chains REVERT: I 10 LYS cc_start: 0.5698 (mmmt) cc_final: 0.5050 (mmtm) outliers start: 0 outliers final: 0 residues processed: 8 average time/residue: 0.0569 time to fit residues: 0.4816 Evaluate side-chains 6 residues out of total 44 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 6 time to evaluate : 0.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 4 random chunks: chunk 0 optimal weight: 3.9990 chunk 1 optimal weight: 0.3980 chunk 2 optimal weight: 0.0270 chunk 3 optimal weight: 0.3980 overall best weight: 0.2125 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.086573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.083472 restraints weight = 2305.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.084633 restraints weight = 1188.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.085318 restraints weight = 647.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.085748 restraints weight = 377.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.085995 restraints weight = 222.226| |-----------------------------------------------------------------------------| r_work (final): 0.4029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4757 moved from start: 1.5813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 456 Z= 0.141 Angle : 0.820 11.434 588 Z= 0.378 Chirality : 0.035 0.088 44 Planarity : 0.003 0.012 80 Dihedral : 27.484 179.937 48 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 2.78 % Allowed : 11.11 % Favored : 86.11 % Rotamer: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -7.07 (0.80), residues: 36 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.39 (0.61), residues: 36 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.026 0.002 PHE J 7 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 ( 452) covalent geometry : angle 0.81955 / 0.38 ( 588) Misc. bond : bond 0.00010 / 0.01 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 72 Ramachandran restraints generated. 36 Oldfield, 0 Emsley, 36 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 72 Ramachandran restraints generated. 36 Oldfield, 0 Emsley, 36 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 8 residues out of total 44 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 8 time to evaluate : 0.010 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 8 average time/residue: 0.0672 time to fit residues: 0.5629 Evaluate side-chains 5 residues out of total 44 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 4 random chunks: chunk 0 optimal weight: 3.9990 chunk 1 optimal weight: 0.2980 chunk 2 optimal weight: 0.6980 chunk 3 optimal weight: 0.8980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.087179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.084179 restraints weight = 2334.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.085230 restraints weight = 1208.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.085912 restraints weight = 675.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.086281 restraints weight = 391.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.086487 restraints weight = 237.108| |-----------------------------------------------------------------------------| r_work (final): 0.4095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4758 moved from start: 1.5997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 456 Z= 0.154 Angle : 0.886 11.475 588 Z= 0.394 Chirality : 0.035 0.112 44 Planarity : 0.002 0.009 80 Dihedral : 27.057 179.776 48 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 2.78 % Allowed : 13.89 % Favored : 83.33 % Rotamer: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -6.66 (0.90), residues: 36 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.07 (0.69), residues: 36 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.013 0.002 PHE J 9 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.15 ( 452) covalent geometry : angle 0.88592 / 0.39 ( 588) Misc. bond : bond 0.00015 / 0.01 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 72 Ramachandran restraints generated. 36 Oldfield, 0 Emsley, 36 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 72 Ramachandran restraints generated. 36 Oldfield, 0 Emsley, 36 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 8 residues out of total 44 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 8 time to evaluate : 0.011 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 8 average time/residue: 0.0361 time to fit residues: 0.3150 Evaluate side-chains 5 residues out of total 44 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 4 random chunks: chunk 0 optimal weight: 3.9990 chunk 1 optimal weight: 0.0770 chunk 2 optimal weight: 0.7980 chunk 3 optimal weight: 0.7980 overall best weight: 0.4375 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.089892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.086349 restraints weight = 2312.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.087550 restraints weight = 1291.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.088317 restraints weight = 783.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.088756 restraints weight = 482.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.089002 restraints weight = 303.692| |-----------------------------------------------------------------------------| r_work (final): 0.4145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4692 moved from start: 1.6624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 456 Z= 0.149 Angle : 0.856 11.430 588 Z= 0.388 Chirality : 0.037 0.111 44 Planarity : 0.002 0.008 80 Dihedral : 26.736 179.968 48 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 2.78 % Allowed : 8.33 % Favored : 88.89 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -6.41 (0.88), residues: 36 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.88 (0.67), residues: 36 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.017 0.001 PHE D 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 ( 452) covalent geometry : angle 0.85559 / 0.39 ( 588) Misc. bond : bond 0.00014 / 0.01 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 72 Ramachandran restraints generated. 36 Oldfield, 0 Emsley, 36 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 72 Ramachandran restraints generated. 36 Oldfield, 0 Emsley, 36 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 8 residues out of total 44 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 8 time to evaluate : 0.019 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 8 average time/residue: 0.0832 time to fit residues: 0.7072 Evaluate side-chains 5 residues out of total 44 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 4 random chunks: chunk 0 optimal weight: 3.9990 chunk 1 optimal weight: 0.3980 chunk 2 optimal weight: 0.9980 chunk 3 optimal weight: 0.4980 overall best weight: 0.4480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.089811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.086676 restraints weight = 2374.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.087739 restraints weight = 1286.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.088455 restraints weight = 746.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.088859 restraints weight = 445.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.089061 restraints weight = 271.818| |-----------------------------------------------------------------------------| r_work (final): 0.4204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4690 moved from start: 1.6845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 456 Z= 0.145 Angle : 0.841 11.399 588 Z= 0.379 Chirality : 0.037 0.110 44 Planarity : 0.002 0.008 80 Dihedral : 26.625 179.951 48 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 2.78 % Allowed : 8.33 % Favored : 88.89 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -6.14 (0.92), residues: 36 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.67 (0.70), residues: 36 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.017 0.001 PHE J 9 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 ( 452) covalent geometry : angle 0.84136 / 0.38 ( 588) Misc. bond : bond 0.00008 / 0.00 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 72 Ramachandran restraints generated. 36 Oldfield, 0 Emsley, 36 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 72 Ramachandran restraints generated. 36 Oldfield, 0 Emsley, 36 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 8 residues out of total 44 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 8 time to evaluate : 0.020 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 8 average time/residue: 0.0812 time to fit residues: 0.6910 Evaluate side-chains 5 residues out of total 44 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 4 random chunks: chunk 0 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 chunk 2 optimal weight: 0.0370 chunk 3 optimal weight: 0.1980 overall best weight: 0.1175 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.093285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.089840 restraints weight = 2321.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.090872 restraints weight = 1346.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.091493 restraints weight = 840.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.091863 restraints weight = 570.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.092243 restraints weight = 422.484| |-----------------------------------------------------------------------------| r_work (final): 0.4201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4559 moved from start: 1.7016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 456 Z= 0.148 Angle : 0.849 11.344 588 Z= 0.380 Chirality : 0.037 0.112 44 Planarity : 0.002 0.008 80 Dihedral : 26.397 179.634 48 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 2.78 % Allowed : 8.33 % Favored : 88.89 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -6.04 (0.91), residues: 36 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.60 (0.70), residues: 36 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.018 0.001 PHE J 9 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 ( 452) covalent geometry : angle 0.84894 / 0.38 ( 588) Misc. bond : bond 0.00006 / 0.00 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 72 Ramachandran restraints generated. 36 Oldfield, 0 Emsley, 36 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 72 Ramachandran restraints generated. 36 Oldfield, 0 Emsley, 36 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 9 residues out of total 44 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 9 time to evaluate : 0.019 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 9 average time/residue: 0.0817 time to fit residues: 0.7824 Evaluate side-chains 6 residues out of total 44 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 6 time to evaluate : 0.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 4 random chunks: chunk 0 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 2 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.088172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.085036 restraints weight = 2253.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.086079 restraints weight = 1261.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.086704 restraints weight = 753.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.087142 restraints weight = 452.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.087457 restraints weight = 277.726| |-----------------------------------------------------------------------------| r_work (final): 0.4075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4751 moved from start: 1.7132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 456 Z= 0.164 Angle : 0.907 11.350 588 Z= 0.415 Chirality : 0.036 0.115 44 Planarity : 0.002 0.009 80 Dihedral : 26.633 179.744 48 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 2.78 % Allowed : 13.89 % Favored : 83.33 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -6.02 (0.92), residues: 36 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.58 (0.70), residues: 36 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.021 0.002 PHE J 9 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.16 ( 452) covalent geometry : angle 0.90716 / 0.41 ( 588) Misc. bond : bond 0.00018 / 0.01 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 213.99 seconds wall clock time: 4 minutes 29.31 seconds (269.31 seconds total)