Starting phenix.real_space_refine on Tue Aug 4 11:43:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9peg_71561/08_2026/9peg_71561.cif Found real_map, /net/cci-nas-00/data/ceres_data/9peg_71561/08_2026/9peg_71561.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9peg_71561/08_2026/9peg_71561.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9peg_71561/08_2026/9peg_71561.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9peg_71561/08_2026/9peg_71561.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9peg_71561/08_2026/9peg_71561.map" } resolution = 3.4 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= 0.000 sd= 0.007 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 798 2.51 5 N 154 2.21 5 O 154 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.00s 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: 1106 Number of models: 1 Model: "" Number of chains: 28 Chain: "J" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} 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: "M" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "S" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "T" 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: 0.18, per 1000 atoms: 0.16 Number of scatterers: 1106 At special positions: 0 Unit cell: (83, 66.4, 53.12, 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 154 8.00 N 154 7.00 C 798 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=14, symmetry=0 Number of additional bonds: simple=14, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.26 Conformation dependent library (CDL) restraints added in 18.1 milliseconds 168 Ramachandran restraints generated. 84 Oldfield, 0 Emsley, 84 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 196 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 7 sheets defined 0.0% alpha, 41.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.02 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'J' and resid 3 through 5 removed outlier: 6.226A pdb=" N GLU J 4 " --> pdb=" O PHE B 5 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'K' and resid 3 through 6 removed outlier: 6.347A pdb=" N GLU K 4 " --> pdb=" O PHE C 5 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'L' and resid 3 through 5 removed outlier: 6.228A pdb=" N GLU L 4 " --> pdb=" O PHE D 5 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'M' and resid 2 through 6 Processing sheet with id=AA5, first strand: chain 'O' and resid 2 through 6 Processing sheet with id=AA6, first strand: chain 'Q' and resid 2 through 6 Processing sheet with id=AA7, first strand: chain 'S' and resid 2 through 6 24 hydrogen bonds defined for protein. 48 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: 0.07 Time building geometry restraints manager: 0.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.25: 141 1.25 - 1.33: 34 1.33 - 1.40: 401 1.40 - 1.47: 138 1.47 - 1.54: 420 Bond restraints: 1134 Sorted by residual: bond pdb=" C PHE N 7 " pdb=" N GLY N 8 " ideal model delta sigma weight residual 1.329 1.430 -0.101 1.40e-02 5.10e+03 5.22e+01 bond pdb=" C PHE O 7 " pdb=" N GLY O 8 " ideal model delta sigma weight residual 1.329 1.430 -0.101 1.40e-02 5.10e+03 5.21e+01 bond pdb=" C PHE P 7 " pdb=" N GLY P 8 " ideal model delta sigma weight residual 1.329 1.430 -0.101 1.40e-02 5.10e+03 5.19e+01 bond pdb=" C PHE T 7 " pdb=" N GLY T 8 " ideal model delta sigma weight residual 1.329 1.430 -0.101 1.40e-02 5.10e+03 5.19e+01 bond pdb=" C PHE Q 7 " pdb=" N GLY Q 8 " ideal model delta sigma weight residual 1.329 1.430 -0.101 1.40e-02 5.10e+03 5.19e+01 ... (remaining 1129 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.87: 1419 7.87 - 15.74: 19 15.74 - 23.62: 7 23.62 - 31.49: 8 31.49 - 39.36: 3 Bond angle restraints: 1456 Sorted by residual: angle pdb=" O PHE M 7 " pdb=" C PHE M 7 " pdb=" N GLY M 8 " ideal model delta sigma weight residual 122.46 89.03 33.43 1.38e+00 5.25e-01 5.87e+02 angle pdb=" C PHE M 7 " pdb=" N GLY M 8 " pdb=" CA GLY M 8 " ideal model delta sigma weight residual 121.70 161.06 -39.36 1.80e+00 3.09e-01 4.78e+02 angle pdb=" C PHE P 7 " pdb=" N GLY P 8 " pdb=" CA GLY P 8 " ideal model delta sigma weight residual 121.70 82.90 38.80 1.80e+00 3.09e-01 4.65e+02 angle pdb=" O PHE P 7 " pdb=" C PHE P 7 " pdb=" N GLY P 8 " ideal model delta sigma weight residual 123.04 147.93 -24.89 1.17e+00 7.31e-01 4.52e+02 angle pdb=" CA PHE P 7 " pdb=" C PHE P 7 " pdb=" N GLY P 8 " ideal model delta sigma weight residual 116.23 89.21 27.02 1.30e+00 5.92e-01 4.32e+02 ... (remaining 1451 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 36.00: 557 36.00 - 72.00: 17 72.00 - 108.00: 0 108.00 - 143.99: 0 143.99 - 179.99: 14 Dihedral angle restraints: 588 sinusoidal: 294 harmonic: 294 Sorted by residual: dihedral pdb=" CH3 ACE C 0 " pdb=" C ACE C 0 " pdb=" N PHE C 1 " pdb=" CA PHE C 1 " ideal model delta sinusoidal sigma weight residual -180.00 -0.01 -179.99 1 5.00e+00 4.00e-02 7.68e+02 dihedral pdb=" CH3 ACE O 0 " pdb=" C ACE O 0 " pdb=" N PHE O 1 " pdb=" CA PHE O 1 " ideal model delta sinusoidal sigma weight residual 180.00 0.02 179.98 1 5.00e+00 4.00e-02 7.68e+02 dihedral pdb=" CH3 ACE M 0 " pdb=" C ACE M 0 " pdb=" N PHE M 1 " pdb=" CA PHE M 1 " ideal model delta sinusoidal sigma weight residual 180.00 0.13 179.87 1 5.00e+00 4.00e-02 7.68e+02 ... (remaining 585 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.013: 28 0.013 - 0.025: 25 0.025 - 0.038: 28 0.038 - 0.051: 13 0.051 - 0.063: 4 Chirality restraints: 98 Sorted by residual: chirality pdb=" CA LYS B 6 " pdb=" N LYS B 6 " pdb=" C LYS B 6 " pdb=" CB LYS B 6 " both_signs ideal model delta sigma weight residual False 2.51 2.57 -0.06 2.00e-01 2.50e+01 9.98e-02 chirality pdb=" CA LYS M 6 " pdb=" N LYS M 6 " pdb=" C LYS M 6 " pdb=" CB LYS M 6 " both_signs ideal model delta sigma weight residual False 2.51 2.57 -0.06 2.00e-01 2.50e+01 8.57e-02 chirality pdb=" CA LYS O 6 " pdb=" N LYS O 6 " pdb=" C LYS O 6 " pdb=" CB LYS O 6 " both_signs ideal model delta sigma weight residual False 2.51 2.56 -0.05 2.00e-01 2.50e+01 6.87e-02 ... (remaining 95 not shown) Planarity restraints: 182 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE K 7 " -0.075 2.00e-02 2.50e+03 1.34e-01 1.81e+02 pdb=" C PHE K 7 " 0.233 2.00e-02 2.50e+03 pdb=" O PHE K 7 " -0.087 2.00e-02 2.50e+03 pdb=" N GLY K 8 " -0.070 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE O 7 " 0.072 2.00e-02 2.50e+03 1.14e-01 1.30e+02 pdb=" C PHE O 7 " -0.197 2.00e-02 2.50e+03 pdb=" O PHE O 7 " 0.061 2.00e-02 2.50e+03 pdb=" N GLY O 8 " 0.064 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE S 7 " -0.069 2.00e-02 2.50e+03 1.11e-01 1.24e+02 pdb=" C PHE S 7 " 0.193 2.00e-02 2.50e+03 pdb=" O PHE S 7 " -0.062 2.00e-02 2.50e+03 pdb=" N GLY S 8 " -0.062 2.00e-02 2.50e+03 ... (remaining 179 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.88: 437 2.88 - 3.39: 746 3.39 - 3.89: 1466 3.89 - 4.40: 1623 4.40 - 4.90: 2814 Nonbonded interactions: 7086 Sorted by model distance: nonbonded pdb=" N GLU R 4 " pdb=" OE1 GLU R 4 " model vdw 2.381 3.120 nonbonded pdb=" O PHE P 7 " pdb=" CA GLY P 8 " model vdw 2.440 2.752 nonbonded pdb=" N GLU P 4 " pdb=" OE1 GLU P 4 " model vdw 2.440 3.120 nonbonded pdb=" O PHE R 7 " pdb=" CA GLY R 8 " model vdw 2.487 2.752 nonbonded pdb=" O PHE K 7 " pdb=" CA GLY K 8 " model vdw 2.530 2.752 ... (remaining 7081 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 'B' selection = chain 'C' selection = chain 'D' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.600 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: 2.090 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:0.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 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 : 0.020 0.134 1148 Z= 1.141 Angle : 3.432 39.361 1456 Z= 2.136 Chirality : 0.028 0.063 98 Planarity : 0.021 0.134 182 Dihedral : 37.714 179.989 392 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 1.02 % Allowed : 18.37 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -3.64 (0.62), residues: 84 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.76 (0.47), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.012 0.001 PHE S 3 Details of bonding type rmsd/Z covalent geometry : bond 0.01988 / 1.12 ( 1134) covalent geometry : angle 3.43204 / 2.14 ( 1456) hydrogen bonds : bond 0.21798 / 10.76 ( 24) hydrogen bonds : angle 19.77486 / 12.46 ( 48) Misc. bond : bond 0.02146 / 1.02 ( 14) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 168 Ramachandran restraints generated. 84 Oldfield, 0 Emsley, 84 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 168 Ramachandran restraints generated. 84 Oldfield, 0 Emsley, 84 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 18 time to evaluate : 0.027 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 19 average time/residue: 0.0648 time to fit residues: 1.3287 Evaluate side-chains 15 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 14 time to evaluate : 0.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 1 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.6980 overall best weight: 50.0000 ------------------------------------------------------------------------------- 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 = 0.3001 r_free = 0.3001 target = 0.068523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.059068 restraints weight = 4182.645| |-----------------------------------------------------------------------------| r_work (start): 0.2812 rms_B_bonded: 2.95 r_work: 0.2697 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9007 moved from start: 0.9517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.109 0.359 1148 Z= 4.653 Angle : 3.822 24.084 1456 Z= 2.086 Chirality : 0.255 0.703 98 Planarity : 0.024 0.062 182 Dihedral : 14.403 32.165 128 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 117.18 Ramachandran Plot: Outliers : 7.14 % Allowed : 47.62 % Favored : 45.24 % Rotamer: Outliers : 15.31 % Allowed : 30.61 % Favored : 54.08 % Cbeta Deviations : 10.20 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.02 % 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: -8.93 (0.47), residues: 84 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.80 (0.36), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.118 0.018 PHE T 3 Details of bonding type rmsd/Z covalent geometry : bond 0.10989 / 4.68 ( 1134) covalent geometry : angle 3.82164 / 2.09 ( 1456) hydrogen bonds : bond 0.34945 / 19.00 ( 24) hydrogen bonds : angle 17.69019 / 10.85 ( 48) Misc. bond : bond 0.00669 / 0.33 ( 14) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 168 Ramachandran restraints generated. 84 Oldfield, 0 Emsley, 84 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 168 Ramachandran restraints generated. 84 Oldfield, 0 Emsley, 84 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 31 time to evaluate : 0.028 Fit side-chains revert: symmetry clash REVERT: J 4 GLU cc_start: 0.8866 (tt0) cc_final: 0.8154 (tm-30) REVERT: J 6 LYS cc_start: 0.7142 (OUTLIER) cc_final: 0.6494 (mmmt) REVERT: B 4 GLU cc_start: 0.8876 (tt0) cc_final: 0.8269 (tm-30) REVERT: B 6 LYS cc_start: 0.9165 (ttpt) cc_final: 0.8023 (pttm) REVERT: K 6 LYS cc_start: 0.9427 (mtpp) cc_final: 0.9226 (ttmm) REVERT: C 4 GLU cc_start: 0.8810 (OUTLIER) cc_final: 0.7664 (pm20) REVERT: C 6 LYS cc_start: 0.9152 (tmtt) cc_final: 0.8312 (tptt) REVERT: D 2 LYS cc_start: 0.9403 (tttm) cc_final: 0.8802 (ttmt) REVERT: O 6 LYS cc_start: 0.8554 (OUTLIER) cc_final: 0.8255 (mttp) REVERT: P 6 LYS cc_start: 0.8884 (mttt) cc_final: 0.8386 (mtpp) REVERT: Q 2 LYS cc_start: 0.8924 (mttt) cc_final: 0.8678 (mttp) REVERT: R 3 PHE cc_start: 0.9370 (OUTLIER) cc_final: 0.9101 (m-10) REVERT: R 6 LYS cc_start: 0.8557 (mttt) cc_final: 0.8274 (mtpp) outliers start: 15 outliers final: 5 residues processed: 39 average time/residue: 0.0929 time to fit residues: 3.7802 Evaluate side-chains 39 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 30 time to evaluate : 0.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 6 LYS Chi-restraints excluded: chain K residue 2 LYS Chi-restraints excluded: chain C residue 4 GLU Chi-restraints excluded: chain M residue 3 PHE Chi-restraints excluded: chain M residue 5 PHE Chi-restraints excluded: chain N residue 4 GLU Chi-restraints excluded: chain O residue 6 LYS Chi-restraints excluded: chain R residue 3 PHE Chi-restraints excluded: chain R residue 7 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- 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 = 0.3011 r_free = 0.3011 target = 0.069447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.060047 restraints weight = 3952.499| |-----------------------------------------------------------------------------| r_work (start): 0.2801 rms_B_bonded: 2.91 r_work: 0.2674 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9015 moved from start: 0.9948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.109 0.342 1148 Z= 4.619 Angle : 3.774 18.109 1456 Z= 2.090 Chirality : 0.246 0.600 98 Planarity : 0.020 0.051 182 Dihedral : 14.586 33.921 126 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 118.58 Ramachandran Plot: Outliers : 1.19 % Allowed : 65.48 % Favored : 33.33 % Rotamer: Outliers : 16.33 % Allowed : 38.78 % Favored : 44.90 % Cbeta Deviations : 9.18 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.02 % 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: -9.62 (0.34), residues: 84 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -7.33 (0.26), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.093 0.014 PHE M 7 Details of bonding type rmsd/Z covalent geometry : bond 0.10933 / 4.65 ( 1134) covalent geometry : angle 3.77399 / 2.09 ( 1456) hydrogen bonds : bond 0.37834 / 20.43 ( 24) hydrogen bonds : angle 17.36338 / 10.67 ( 48) Misc. bond : bond 0.00540 / 0.26 ( 14) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 168 Ramachandran restraints generated. 84 Oldfield, 0 Emsley, 84 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 168 Ramachandran restraints generated. 84 Oldfield, 0 Emsley, 84 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 31 time to evaluate : 0.043 Fit side-chains revert: symmetry clash REVERT: J 4 GLU cc_start: 0.8923 (tt0) cc_final: 0.8234 (tm-30) REVERT: J 6 LYS cc_start: 0.5939 (OUTLIER) cc_final: 0.4737 (mmmt) REVERT: B 4 GLU cc_start: 0.8901 (tt0) cc_final: 0.8256 (tm-30) REVERT: B 6 LYS cc_start: 0.9149 (ttpt) cc_final: 0.8001 (pttm) REVERT: K 6 LYS cc_start: 0.9369 (mtpp) cc_final: 0.9168 (ttmm) REVERT: C 4 GLU cc_start: 0.8845 (tm-30) cc_final: 0.7760 (pm20) REVERT: D 2 LYS cc_start: 0.9413 (tttm) cc_final: 0.8852 (ttmt) REVERT: P 4 GLU cc_start: 0.8548 (mp0) cc_final: 0.7959 (mp0) REVERT: Q 2 LYS cc_start: 0.8822 (mttt) cc_final: 0.8615 (mttp) REVERT: R 3 PHE cc_start: 0.9393 (OUTLIER) cc_final: 0.9125 (m-10) REVERT: R 6 LYS cc_start: 0.8532 (mttt) cc_final: 0.8199 (ttmm) outliers start: 16 outliers final: 10 residues processed: 42 average time/residue: 0.1190 time to fit residues: 5.2315 Evaluate side-chains 43 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 31 time to evaluate : 0.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 6 LYS Chi-restraints excluded: chain B residue 1 PHE Chi-restraints excluded: chain K residue 2 LYS Chi-restraints excluded: chain M residue 5 PHE Chi-restraints excluded: chain N residue 2 LYS Chi-restraints excluded: chain N residue 4 GLU Chi-restraints excluded: chain O residue 4 GLU Chi-restraints excluded: chain P residue 2 LYS Chi-restraints excluded: chain Q residue 1 PHE Chi-restraints excluded: chain R residue 3 PHE Chi-restraints excluded: chain R residue 7 PHE Chi-restraints excluded: chain T residue 1 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9980 overall best weight: 50.0000 ------------------------------------------------------------------------------- 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 = 0.3021 r_free = 0.3021 target = 0.070046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.060515 restraints weight = 3981.707| |-----------------------------------------------------------------------------| r_work (start): 0.2808 rms_B_bonded: 2.91 r_work: 0.2670 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9023 moved from start: 1.0049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.108 0.344 1148 Z= 4.612 Angle : 3.727 20.303 1456 Z= 2.070 Chirality : 0.242 0.596 98 Planarity : 0.020 0.050 182 Dihedral : 14.881 37.103 126 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 116.71 Ramachandran Plot: Outliers : 1.19 % Allowed : 63.10 % Favored : 35.71 % Rotamer: Outliers : 22.45 % Allowed : 34.69 % Favored : 42.86 % Cbeta Deviations : 8.16 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 3.06 % 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: -9.85 (0.30), residues: 84 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -7.50 (0.23), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.085 0.013 PHE N 3 Details of bonding type rmsd/Z covalent geometry : bond 0.10904 / 4.64 ( 1134) covalent geometry : angle 3.72718 / 2.07 ( 1456) hydrogen bonds : bond 0.38392 / 20.98 ( 24) hydrogen bonds : angle 17.50122 / 10.81 ( 48) Misc. bond : bond 0.00543 / 0.26 ( 14) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 168 Ramachandran restraints generated. 84 Oldfield, 0 Emsley, 84 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 168 Ramachandran restraints generated. 84 Oldfield, 0 Emsley, 84 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 29 time to evaluate : 0.049 Fit side-chains revert: symmetry clash REVERT: J 4 GLU cc_start: 0.8928 (tt0) cc_final: 0.8224 (tm-30) REVERT: J 6 LYS cc_start: 0.5756 (OUTLIER) cc_final: 0.4327 (mmmt) REVERT: B 4 GLU cc_start: 0.8914 (tt0) cc_final: 0.8380 (tm-30) REVERT: B 6 LYS cc_start: 0.9166 (ttpt) cc_final: 0.8024 (pttm) REVERT: K 6 LYS cc_start: 0.9351 (mtpp) cc_final: 0.9148 (ttmm) REVERT: C 6 LYS cc_start: 0.9209 (tmtt) cc_final: 0.8510 (tptt) REVERT: D 2 LYS cc_start: 0.9420 (tttm) cc_final: 0.8851 (ttmt) REVERT: M 6 LYS cc_start: 0.8564 (OUTLIER) cc_final: 0.8183 (mttm) REVERT: N 1 PHE cc_start: 0.9055 (OUTLIER) cc_final: 0.8661 (m-80) REVERT: N 2 LYS cc_start: 0.8635 (OUTLIER) cc_final: 0.8282 (mttm) REVERT: P 4 GLU cc_start: 0.8596 (mp0) cc_final: 0.8070 (mp0) REVERT: P 6 LYS cc_start: 0.8886 (mtpt) cc_final: 0.8467 (mtpp) REVERT: Q 2 LYS cc_start: 0.8751 (mttt) cc_final: 0.8529 (mttm) REVERT: R 3 PHE cc_start: 0.9404 (OUTLIER) cc_final: 0.9136 (m-10) REVERT: R 6 LYS cc_start: 0.8505 (mtpt) cc_final: 0.8193 (ttmm) outliers start: 22 outliers final: 10 residues processed: 43 average time/residue: 0.1042 time to fit residues: 4.6876 Evaluate side-chains 44 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 29 time to evaluate : 0.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 1 PHE Chi-restraints excluded: chain J residue 6 LYS Chi-restraints excluded: chain B residue 1 PHE Chi-restraints excluded: chain K residue 2 LYS Chi-restraints excluded: chain L residue 6 LYS Chi-restraints excluded: chain M residue 3 PHE Chi-restraints excluded: chain M residue 6 LYS Chi-restraints excluded: chain N residue 1 PHE Chi-restraints excluded: chain N residue 2 LYS Chi-restraints excluded: chain N residue 4 GLU Chi-restraints excluded: chain O residue 4 GLU Chi-restraints excluded: chain P residue 2 LYS Chi-restraints excluded: chain Q residue 1 PHE Chi-restraints excluded: chain R residue 3 PHE Chi-restraints excluded: chain T residue 1 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- 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 = 0.3021 r_free = 0.3021 target = 0.069832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.060468 restraints weight = 3416.296| |-----------------------------------------------------------------------------| r_work (start): 0.2811 rms_B_bonded: 2.68 r_work: 0.2682 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9019 moved from start: 1.0139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.108 0.373 1148 Z= 4.616 Angle : 3.693 19.909 1456 Z= 2.059 Chirality : 0.242 0.600 98 Planarity : 0.020 0.048 182 Dihedral : 14.996 38.819 126 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 116.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 63.10 % Favored : 36.90 % Rotamer: Outliers : 24.49 % Allowed : 36.73 % Favored : 38.78 % Cbeta Deviations : 8.16 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 3.06 % 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: -9.89 (0.30), residues: 84 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -7.53 (0.23), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.082 0.012 PHE R 3 Details of bonding type rmsd/Z covalent geometry : bond 0.10914 / 4.64 ( 1134) covalent geometry : angle 3.69349 / 2.06 ( 1456) hydrogen bonds : bond 0.38777 / 21.19 ( 24) hydrogen bonds : angle 17.38619 / 10.79 ( 48) Misc. bond : bond 0.00545 / 0.27 ( 14) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 168 Ramachandran restraints generated. 84 Oldfield, 0 Emsley, 84 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 168 Ramachandran restraints generated. 84 Oldfield, 0 Emsley, 84 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 28 time to evaluate : 0.046 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 4 GLU cc_start: 0.8920 (tt0) cc_final: 0.8215 (tm-30) REVERT: J 6 LYS cc_start: 0.5717 (OUTLIER) cc_final: 0.4321 (mmmt) REVERT: B 4 GLU cc_start: 0.8887 (tt0) cc_final: 0.8417 (tm-30) REVERT: B 6 LYS cc_start: 0.9160 (tttt) cc_final: 0.8005 (pttm) REVERT: K 6 LYS cc_start: 0.9341 (mtpp) cc_final: 0.9124 (ttmm) REVERT: D 2 LYS cc_start: 0.9408 (tttm) cc_final: 0.8836 (ttmt) REVERT: M 4 GLU cc_start: 0.8246 (mp0) cc_final: 0.7765 (mp0) REVERT: M 6 LYS cc_start: 0.8607 (OUTLIER) cc_final: 0.8199 (mttm) REVERT: N 1 PHE cc_start: 0.9064 (OUTLIER) cc_final: 0.8650 (m-80) REVERT: N 2 LYS cc_start: 0.8604 (OUTLIER) cc_final: 0.8260 (mttm) REVERT: Q 2 LYS cc_start: 0.8724 (mttt) cc_final: 0.8490 (mttm) REVERT: R 3 PHE cc_start: 0.9402 (OUTLIER) cc_final: 0.9136 (m-10) REVERT: R 6 LYS cc_start: 0.8480 (mtpt) cc_final: 0.8107 (ttmm) outliers start: 24 outliers final: 15 residues processed: 42 average time/residue: 0.1315 time to fit residues: 5.7617 Evaluate side-chains 47 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 27 time to evaluate : 0.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 1 PHE Chi-restraints excluded: chain J residue 6 LYS Chi-restraints excluded: chain B residue 1 PHE Chi-restraints excluded: chain K residue 2 LYS Chi-restraints excluded: chain L residue 2 LYS Chi-restraints excluded: chain L residue 6 LYS Chi-restraints excluded: chain M residue 3 PHE Chi-restraints excluded: chain M residue 5 PHE Chi-restraints excluded: chain M residue 6 LYS Chi-restraints excluded: chain M residue 7 PHE Chi-restraints excluded: chain N residue 1 PHE Chi-restraints excluded: chain N residue 2 LYS Chi-restraints excluded: chain N residue 4 GLU Chi-restraints excluded: chain O residue 4 GLU Chi-restraints excluded: chain P residue 2 LYS Chi-restraints excluded: chain P residue 4 GLU Chi-restraints excluded: chain Q residue 1 PHE Chi-restraints excluded: chain R residue 3 PHE Chi-restraints excluded: chain S residue 4 GLU Chi-restraints excluded: chain T residue 1 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9980 overall best weight: 50.0000 ------------------------------------------------------------------------------- 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 = 0.3031 r_free = 0.3031 target = 0.070043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.060565 restraints weight = 3735.870| |-----------------------------------------------------------------------------| r_work (start): 0.2812 rms_B_bonded: 2.86 r_work: 0.2671 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9025 moved from start: 1.0174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.108 0.387 1148 Z= 4.613 Angle : 3.699 20.040 1456 Z= 2.061 Chirality : 0.242 0.604 98 Planarity : 0.020 0.047 182 Dihedral : 15.069 40.119 126 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 112.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 63.10 % Favored : 36.90 % Rotamer: Outliers : 24.49 % Allowed : 37.76 % Favored : 37.76 % Cbeta Deviations : 8.16 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 5.10 % 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: -9.91 (0.30), residues: 84 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -7.55 (0.23), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.082 0.012 PHE R 3 Details of bonding type rmsd/Z covalent geometry : bond 0.10900 / 4.64 ( 1134) covalent geometry : angle 3.69900 / 2.06 ( 1456) hydrogen bonds : bond 0.38862 / 21.19 ( 24) hydrogen bonds : angle 17.36657 / 10.83 ( 48) Misc. bond : bond 0.00532 / 0.26 ( 14) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 168 Ramachandran restraints generated. 84 Oldfield, 0 Emsley, 84 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 168 Ramachandran restraints generated. 84 Oldfield, 0 Emsley, 84 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 27 time to evaluate : 0.030 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 4 GLU cc_start: 0.8966 (tt0) cc_final: 0.8222 (tm-30) REVERT: J 6 LYS cc_start: 0.5792 (OUTLIER) cc_final: 0.4390 (mmmt) REVERT: B 4 GLU cc_start: 0.8888 (tt0) cc_final: 0.8412 (tm-30) REVERT: B 6 LYS cc_start: 0.9172 (tttt) cc_final: 0.8027 (pttm) REVERT: K 6 LYS cc_start: 0.9351 (mtpp) cc_final: 0.9138 (ttmm) REVERT: C 4 GLU cc_start: 0.8878 (OUTLIER) cc_final: 0.7767 (pm20) REVERT: D 2 LYS cc_start: 0.9421 (tttm) cc_final: 0.8856 (ttmt) REVERT: M 4 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7843 (mp0) REVERT: M 6 LYS cc_start: 0.8607 (OUTLIER) cc_final: 0.8191 (mttm) REVERT: N 1 PHE cc_start: 0.9058 (OUTLIER) cc_final: 0.8582 (m-80) REVERT: N 2 LYS cc_start: 0.8636 (OUTLIER) cc_final: 0.8297 (mttm) REVERT: Q 2 LYS cc_start: 0.8737 (mttt) cc_final: 0.8511 (mttm) REVERT: R 3 PHE cc_start: 0.9397 (OUTLIER) cc_final: 0.9134 (m-10) REVERT: R 6 LYS cc_start: 0.8490 (mtpt) cc_final: 0.8127 (ttmm) outliers start: 24 outliers final: 16 residues processed: 40 average time/residue: 0.1410 time to fit residues: 5.9055 Evaluate side-chains 50 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 27 time to evaluate : 0.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 1 PHE Chi-restraints excluded: chain J residue 6 LYS Chi-restraints excluded: chain B residue 1 PHE Chi-restraints excluded: chain K residue 2 LYS Chi-restraints excluded: chain C residue 4 GLU Chi-restraints excluded: chain L residue 6 LYS Chi-restraints excluded: chain M residue 3 PHE Chi-restraints excluded: chain M residue 4 GLU Chi-restraints excluded: chain M residue 5 PHE Chi-restraints excluded: chain M residue 6 LYS Chi-restraints excluded: chain M residue 7 PHE Chi-restraints excluded: chain N residue 1 PHE Chi-restraints excluded: chain N residue 2 LYS Chi-restraints excluded: chain N residue 4 GLU Chi-restraints excluded: chain O residue 1 PHE Chi-restraints excluded: chain O residue 4 GLU Chi-restraints excluded: chain P residue 2 LYS Chi-restraints excluded: chain P residue 4 GLU Chi-restraints excluded: chain Q residue 1 PHE Chi-restraints excluded: chain R residue 3 PHE Chi-restraints excluded: chain S residue 4 GLU Chi-restraints excluded: chain T residue 1 PHE Chi-restraints excluded: chain T residue 4 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- 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 = 0.3017 r_free = 0.3017 target = 0.069262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.059735 restraints weight = 3358.121| |-----------------------------------------------------------------------------| r_work (start): 0.2817 rms_B_bonded: 2.76 r_work: 0.2681 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9021 moved from start: 1.0202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.108 0.371 1148 Z= 4.607 Angle : 3.686 19.914 1456 Z= 2.060 Chirality : 0.242 0.608 98 Planarity : 0.020 0.047 182 Dihedral : 15.110 40.948 126 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 113.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 63.10 % Favored : 36.90 % Rotamer: Outliers : 28.57 % Allowed : 35.71 % Favored : 35.71 % Cbeta Deviations : 8.16 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 5.10 % 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: -9.93 (0.29), residues: 84 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -7.56 (0.22), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.082 0.012 PHE R 3 Details of bonding type rmsd/Z covalent geometry : bond 0.10888 / 4.64 ( 1134) covalent geometry : angle 3.68620 / 2.06 ( 1456) hydrogen bonds : bond 0.38921 / 21.22 ( 24) hydrogen bonds : angle 17.36717 / 10.81 ( 48) Misc. bond : bond 0.00526 / 0.26 ( 14) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 168 Ramachandran restraints generated. 84 Oldfield, 0 Emsley, 84 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 168 Ramachandran restraints generated. 84 Oldfield, 0 Emsley, 84 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 27 time to evaluate : 0.051 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 4 GLU cc_start: 0.8959 (tt0) cc_final: 0.8211 (tm-30) REVERT: J 6 LYS cc_start: 0.5746 (OUTLIER) cc_final: 0.4268 (mmmt) REVERT: B 4 GLU cc_start: 0.8904 (tt0) cc_final: 0.8418 (tm-30) REVERT: B 6 LYS cc_start: 0.9179 (tttt) cc_final: 0.7990 (pttm) REVERT: K 6 LYS cc_start: 0.9344 (mtpp) cc_final: 0.9107 (ttmm) REVERT: C 4 GLU cc_start: 0.8866 (OUTLIER) cc_final: 0.7751 (pm20) REVERT: C 6 LYS cc_start: 0.9214 (tttt) cc_final: 0.8445 (tptt) REVERT: D 2 LYS cc_start: 0.9414 (tttm) cc_final: 0.8849 (ttmt) REVERT: M 4 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.7810 (mp0) REVERT: M 6 LYS cc_start: 0.8594 (OUTLIER) cc_final: 0.8173 (mttm) REVERT: N 1 PHE cc_start: 0.9095 (OUTLIER) cc_final: 0.8590 (m-80) REVERT: N 2 LYS cc_start: 0.8636 (OUTLIER) cc_final: 0.8312 (mttm) REVERT: R 3 PHE cc_start: 0.9398 (OUTLIER) cc_final: 0.9129 (m-10) REVERT: R 6 LYS cc_start: 0.8462 (mtpt) cc_final: 0.8095 (ttmm) REVERT: S 1 PHE cc_start: 0.9139 (OUTLIER) cc_final: 0.8836 (m-80) outliers start: 28 outliers final: 17 residues processed: 44 average time/residue: 0.1303 time to fit residues: 6.0235 Evaluate side-chains 52 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 27 time to evaluate : 0.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 1 PHE Chi-restraints excluded: chain J residue 6 LYS Chi-restraints excluded: chain B residue 1 PHE Chi-restraints excluded: chain K residue 2 LYS Chi-restraints excluded: chain C residue 4 GLU Chi-restraints excluded: chain L residue 6 LYS Chi-restraints excluded: chain D residue 5 PHE Chi-restraints excluded: chain M residue 3 PHE Chi-restraints excluded: chain M residue 4 GLU Chi-restraints excluded: chain M residue 5 PHE Chi-restraints excluded: chain M residue 6 LYS Chi-restraints excluded: chain M residue 7 PHE Chi-restraints excluded: chain N residue 1 PHE Chi-restraints excluded: chain N residue 2 LYS Chi-restraints excluded: chain N residue 4 GLU Chi-restraints excluded: chain O residue 1 PHE Chi-restraints excluded: chain O residue 4 GLU Chi-restraints excluded: chain P residue 2 LYS Chi-restraints excluded: chain P residue 4 GLU Chi-restraints excluded: chain Q residue 1 PHE Chi-restraints excluded: chain R residue 3 PHE Chi-restraints excluded: chain S residue 1 PHE Chi-restraints excluded: chain S residue 4 GLU Chi-restraints excluded: chain T residue 1 PHE Chi-restraints excluded: chain T residue 4 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- 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 = 0.3022 r_free = 0.3022 target = 0.069596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.060101 restraints weight = 3789.848| |-----------------------------------------------------------------------------| r_work (start): 0.2824 rms_B_bonded: 2.85 r_work: 0.2683 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9028 moved from start: 1.0237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.108 0.362 1148 Z= 4.603 Angle : 3.755 19.934 1456 Z= 2.079 Chirality : 0.246 0.612 98 Planarity : 0.020 0.047 182 Dihedral : 15.573 53.168 126 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 112.10 Ramachandran Plot: Outliers : 1.19 % Allowed : 61.90 % Favored : 36.90 % Rotamer: Outliers : 29.59 % Allowed : 35.71 % Favored : 34.69 % Cbeta Deviations : 8.16 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 4.08 % 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: -9.92 (0.30), residues: 84 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -7.55 (0.23), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.081 0.012 PHE R 3 Details of bonding type rmsd/Z covalent geometry : bond 0.10892 / 4.63 ( 1134) covalent geometry : angle 3.75547 / 2.08 ( 1456) hydrogen bonds : bond 0.38845 / 21.21 ( 24) hydrogen bonds : angle 17.36362 / 10.81 ( 48) Misc. bond : bond 0.00523 / 0.25 ( 14) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 168 Ramachandran restraints generated. 84 Oldfield, 0 Emsley, 84 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 168 Ramachandran restraints generated. 84 Oldfield, 0 Emsley, 84 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 26 time to evaluate : 0.075 Fit side-chains revert: symmetry clash REVERT: J 4 GLU cc_start: 0.8959 (tt0) cc_final: 0.8235 (tm-30) REVERT: J 6 LYS cc_start: 0.5737 (OUTLIER) cc_final: 0.4265 (mmmt) REVERT: B 4 GLU cc_start: 0.8918 (tt0) cc_final: 0.8416 (tm-30) REVERT: B 6 LYS cc_start: 0.9173 (tttt) cc_final: 0.8019 (pttm) REVERT: K 6 LYS cc_start: 0.9357 (mtpp) cc_final: 0.9121 (ttmm) REVERT: C 4 GLU cc_start: 0.8884 (OUTLIER) cc_final: 0.7775 (pm20) REVERT: D 2 LYS cc_start: 0.9423 (tttm) cc_final: 0.8865 (ttmt) REVERT: M 4 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.7854 (mp0) REVERT: M 6 LYS cc_start: 0.8596 (OUTLIER) cc_final: 0.7934 (mttm) REVERT: N 1 PHE cc_start: 0.9181 (OUTLIER) cc_final: 0.8646 (m-80) REVERT: N 2 LYS cc_start: 0.8627 (OUTLIER) cc_final: 0.7646 (mttm) REVERT: N 4 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.7489 (mp0) REVERT: R 3 PHE cc_start: 0.9394 (OUTLIER) cc_final: 0.9127 (m-10) REVERT: R 6 LYS cc_start: 0.8423 (mtpt) cc_final: 0.8073 (ttmm) REVERT: S 1 PHE cc_start: 0.9131 (OUTLIER) cc_final: 0.8831 (m-80) outliers start: 29 outliers final: 15 residues processed: 42 average time/residue: 0.1217 time to fit residues: 5.3766 Evaluate side-chains 50 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 26 time to evaluate : 0.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 1 PHE Chi-restraints excluded: chain J residue 6 LYS Chi-restraints excluded: chain B residue 1 PHE Chi-restraints excluded: chain K residue 2 LYS Chi-restraints excluded: chain C residue 4 GLU Chi-restraints excluded: chain L residue 2 LYS Chi-restraints excluded: chain M residue 3 PHE Chi-restraints excluded: chain M residue 4 GLU Chi-restraints excluded: chain M residue 5 PHE Chi-restraints excluded: chain M residue 6 LYS Chi-restraints excluded: chain M residue 7 PHE Chi-restraints excluded: chain N residue 1 PHE Chi-restraints excluded: chain N residue 2 LYS Chi-restraints excluded: chain N residue 4 GLU Chi-restraints excluded: chain O residue 1 PHE Chi-restraints excluded: chain O residue 4 GLU Chi-restraints excluded: chain P residue 2 LYS Chi-restraints excluded: chain P residue 4 GLU Chi-restraints excluded: chain Q residue 1 PHE Chi-restraints excluded: chain R residue 3 PHE Chi-restraints excluded: chain S residue 1 PHE Chi-restraints excluded: chain S residue 4 GLU Chi-restraints excluded: chain T residue 1 PHE Chi-restraints excluded: chain T residue 4 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- 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 = 0.3029 r_free = 0.3029 target = 0.069929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.060092 restraints weight = 4307.520| |-----------------------------------------------------------------------------| r_work (start): 0.2798 rms_B_bonded: 3.11 r_work: 0.2653 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9030 moved from start: 1.0275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.108 0.364 1148 Z= 4.604 Angle : 3.759 20.005 1456 Z= 2.079 Chirality : 0.247 0.615 98 Planarity : 0.020 0.048 182 Dihedral : 15.570 52.855 126 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 110.70 Ramachandran Plot: Outliers : 1.19 % Allowed : 63.10 % Favored : 35.71 % Rotamer: Outliers : 27.55 % Allowed : 37.76 % Favored : 34.69 % Cbeta Deviations : 8.16 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 4.08 % 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: -9.89 (0.30), residues: 84 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -7.54 (0.23), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.082 0.012 PHE R 3 Details of bonding type rmsd/Z covalent geometry : bond 0.10895 / 4.63 ( 1134) covalent geometry : angle 3.75917 / 2.08 ( 1456) hydrogen bonds : bond 0.39028 / 21.32 ( 24) hydrogen bonds : angle 17.46079 / 10.86 ( 48) Misc. bond : bond 0.00523 / 0.25 ( 14) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 168 Ramachandran restraints generated. 84 Oldfield, 0 Emsley, 84 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 168 Ramachandran restraints generated. 84 Oldfield, 0 Emsley, 84 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 26 time to evaluate : 0.045 Fit side-chains revert: symmetry clash REVERT: J 4 GLU cc_start: 0.8989 (tt0) cc_final: 0.8241 (tm-30) REVERT: J 6 LYS cc_start: 0.5736 (OUTLIER) cc_final: 0.4254 (mmmt) REVERT: B 4 GLU cc_start: 0.8970 (tt0) cc_final: 0.8426 (tm-30) REVERT: B 6 LYS cc_start: 0.9163 (tttt) cc_final: 0.7946 (pttm) REVERT: K 6 LYS cc_start: 0.9365 (mtpp) cc_final: 0.9122 (ttmm) REVERT: C 6 LYS cc_start: 0.9217 (tttt) cc_final: 0.8544 (tptt) REVERT: D 2 LYS cc_start: 0.9420 (tttm) cc_final: 0.8860 (ttmt) REVERT: M 4 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.7865 (mp0) REVERT: M 6 LYS cc_start: 0.8588 (OUTLIER) cc_final: 0.7923 (mttm) REVERT: N 1 PHE cc_start: 0.9178 (OUTLIER) cc_final: 0.8652 (m-80) REVERT: N 2 LYS cc_start: 0.8627 (OUTLIER) cc_final: 0.7685 (mttm) REVERT: N 4 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.7442 (mp0) REVERT: R 3 PHE cc_start: 0.9400 (OUTLIER) cc_final: 0.9126 (m-10) REVERT: R 6 LYS cc_start: 0.8384 (mtpt) cc_final: 0.8026 (ttmm) REVERT: S 1 PHE cc_start: 0.9130 (OUTLIER) cc_final: 0.8825 (m-80) outliers start: 27 outliers final: 17 residues processed: 41 average time/residue: 0.1238 time to fit residues: 5.3366 Evaluate side-chains 51 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 26 time to evaluate : 0.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 1 PHE Chi-restraints excluded: chain J residue 5 PHE Chi-restraints excluded: chain J residue 6 LYS Chi-restraints excluded: chain B residue 1 PHE Chi-restraints excluded: chain K residue 2 LYS Chi-restraints excluded: chain L residue 2 LYS Chi-restraints excluded: chain D residue 5 PHE Chi-restraints excluded: chain M residue 3 PHE Chi-restraints excluded: chain M residue 4 GLU Chi-restraints excluded: chain M residue 5 PHE Chi-restraints excluded: chain M residue 6 LYS Chi-restraints excluded: chain M residue 7 PHE Chi-restraints excluded: chain N residue 1 PHE Chi-restraints excluded: chain N residue 2 LYS Chi-restraints excluded: chain N residue 4 GLU Chi-restraints excluded: chain O residue 1 PHE Chi-restraints excluded: chain O residue 4 GLU Chi-restraints excluded: chain P residue 2 LYS Chi-restraints excluded: chain P residue 4 GLU Chi-restraints excluded: chain Q residue 1 PHE Chi-restraints excluded: chain R residue 3 PHE Chi-restraints excluded: chain S residue 1 PHE Chi-restraints excluded: chain S residue 4 GLU Chi-restraints excluded: chain T residue 1 PHE Chi-restraints excluded: chain T residue 4 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9980 overall best weight: 50.0000 ------------------------------------------------------------------------------- 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 = 0.3028 r_free = 0.3028 target = 0.069937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.060496 restraints weight = 3699.137| |-----------------------------------------------------------------------------| r_work (start): 0.2801 rms_B_bonded: 2.84 r_work: 0.2669 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9020 moved from start: 1.0282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.108 0.361 1148 Z= 4.604 Angle : 3.760 19.968 1456 Z= 2.080 Chirality : 0.247 0.615 98 Planarity : 0.020 0.050 182 Dihedral : 15.563 52.490 126 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 110.70 Ramachandran Plot: Outliers : 1.19 % Allowed : 61.90 % Favored : 36.90 % Rotamer: Outliers : 26.53 % Allowed : 38.78 % Favored : 34.69 % Cbeta Deviations : 8.16 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 4.08 % 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: -9.90 (0.30), residues: 84 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -7.54 (0.23), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.082 0.012 PHE R 3 Details of bonding type rmsd/Z covalent geometry : bond 0.10895 / 4.63 ( 1134) covalent geometry : angle 3.75967 / 2.08 ( 1456) hydrogen bonds : bond 0.39124 / 21.39 ( 24) hydrogen bonds : angle 17.45247 / 10.85 ( 48) Misc. bond : bond 0.00525 / 0.26 ( 14) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 168 Ramachandran restraints generated. 84 Oldfield, 0 Emsley, 84 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 168 Ramachandran restraints generated. 84 Oldfield, 0 Emsley, 84 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 26 time to evaluate : 0.046 Fit side-chains revert: symmetry clash REVERT: J 4 GLU cc_start: 0.8954 (tt0) cc_final: 0.8217 (tm-30) REVERT: J 6 LYS cc_start: 0.5726 (OUTLIER) cc_final: 0.4241 (mmmt) REVERT: B 4 GLU cc_start: 0.8932 (tt0) cc_final: 0.8399 (tm-30) REVERT: B 6 LYS cc_start: 0.9157 (tttt) cc_final: 0.7947 (pttm) REVERT: K 6 LYS cc_start: 0.9347 (OUTLIER) cc_final: 0.9107 (ttmm) REVERT: C 4 GLU cc_start: 0.8878 (OUTLIER) cc_final: 0.7759 (pm20) REVERT: C 6 LYS cc_start: 0.9204 (tttt) cc_final: 0.8436 (tptt) REVERT: D 2 LYS cc_start: 0.9410 (tttm) cc_final: 0.8843 (ttmt) REVERT: M 4 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.7839 (mp0) REVERT: M 6 LYS cc_start: 0.8577 (OUTLIER) cc_final: 0.7906 (mttm) REVERT: N 1 PHE cc_start: 0.9167 (OUTLIER) cc_final: 0.8640 (m-80) REVERT: N 2 LYS cc_start: 0.8604 (OUTLIER) cc_final: 0.7666 (mttm) REVERT: N 4 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.7399 (mp0) REVERT: R 3 PHE cc_start: 0.9394 (OUTLIER) cc_final: 0.9121 (m-10) REVERT: R 6 LYS cc_start: 0.8365 (mtpt) cc_final: 0.8004 (ttmm) REVERT: S 1 PHE cc_start: 0.9127 (OUTLIER) cc_final: 0.8822 (m-80) outliers start: 26 outliers final: 16 residues processed: 41 average time/residue: 0.1193 time to fit residues: 5.1330 Evaluate side-chains 52 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 26 time to evaluate : 0.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 1 PHE Chi-restraints excluded: chain J residue 5 PHE Chi-restraints excluded: chain J residue 6 LYS Chi-restraints excluded: chain B residue 1 PHE Chi-restraints excluded: chain K residue 2 LYS Chi-restraints excluded: chain K residue 6 LYS Chi-restraints excluded: chain C residue 4 GLU Chi-restraints excluded: chain D residue 5 PHE Chi-restraints excluded: chain M residue 3 PHE Chi-restraints excluded: chain M residue 4 GLU Chi-restraints excluded: chain M residue 5 PHE Chi-restraints excluded: chain M residue 6 LYS Chi-restraints excluded: chain M residue 7 PHE Chi-restraints excluded: chain N residue 1 PHE Chi-restraints excluded: chain N residue 2 LYS Chi-restraints excluded: chain N residue 4 GLU Chi-restraints excluded: chain O residue 1 PHE Chi-restraints excluded: chain O residue 4 GLU Chi-restraints excluded: chain P residue 2 LYS Chi-restraints excluded: chain P residue 4 GLU Chi-restraints excluded: chain Q residue 1 PHE Chi-restraints excluded: chain R residue 3 PHE Chi-restraints excluded: chain S residue 1 PHE Chi-restraints excluded: chain S residue 4 GLU Chi-restraints excluded: chain T residue 1 PHE Chi-restraints excluded: chain T residue 4 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9980 overall best weight: 50.0000 ------------------------------------------------------------------------------- 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 = 0.3028 r_free = 0.3028 target = 0.069912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.059846 restraints weight = 4730.626| |-----------------------------------------------------------------------------| r_work (start): 0.2791 rms_B_bonded: 3.28 r_work: 0.2641 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9036 moved from start: 1.0289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.108 0.362 1148 Z= 4.603 Angle : 3.760 20.007 1456 Z= 2.079 Chirality : 0.247 0.615 98 Planarity : 0.020 0.050 182 Dihedral : 15.572 52.025 126 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 110.70 Ramachandran Plot: Outliers : 1.19 % Allowed : 63.10 % Favored : 35.71 % Rotamer: Outliers : 29.59 % Allowed : 35.71 % Favored : 34.69 % Cbeta Deviations : 8.16 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 4.08 % 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: -9.89 (0.30), residues: 84 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -7.53 (0.23), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.082 0.012 PHE R 3 Details of bonding type rmsd/Z covalent geometry : bond 0.10893 / 4.63 ( 1134) covalent geometry : angle 3.75994 / 2.08 ( 1456) hydrogen bonds : bond 0.39232 / 21.48 ( 24) hydrogen bonds : angle 17.44412 / 10.85 ( 48) Misc. bond : bond 0.00525 / 0.26 ( 14) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 393.23 seconds wall clock time: 7 minutes 38.79 seconds (458.79 seconds total)