Starting phenix.real_space_refine on Tue Aug 4 11:43:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pej_71564/08_2026/9pej_71564.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pej_71564/08_2026/9pej_71564.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/9pej_71564/08_2026/9pej_71564.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pej_71564/08_2026/9pej_71564.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9pej_71564/08_2026/9pej_71564.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pej_71564/08_2026/9pej_71564.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= -0.021 sd= 0.363 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 414 2.51 5 N 84 2.21 5 O 114 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 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: 612 Number of models: 1 Model: "" Number of chains: 12 Chain: "B" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 101 Unusual residues: {'ACE': 1} Classifications: {'peptide': 11, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 10} 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: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 101 Unusual residues: {'ACE': 1} Classifications: {'peptide': 11, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 10} 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: "D" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 101 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: "M" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 101 Unusual residues: {'ACE': 1} Classifications: {'peptide': 11, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 10} 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: "E" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 101 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: "N" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 101 Unusual residues: {'ACE': 1} Classifications: {'peptide': 11, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 10} Chain: "N" 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: 0.11, per 1000 atoms: 0.18 Number of scatterers: 612 At special positions: 0 Unit cell: (52.185, 37.275, 29.82, 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 114 8.00 N 84 7.00 C 414 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=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.05 Conformation dependent library (CDL) restraints added in 11.0 milliseconds 108 Ramachandran restraints generated. 54 Oldfield, 0 Emsley, 54 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 132 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 1 sheets defined 0.0% alpha, 3.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.01 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'K' and resid 4 through 5 removed outlier: 7.120A pdb=" N LYS K 4 " --> pdb=" O PHE M 5 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 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: 0.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.29: 78 1.29 - 1.36: 60 1.36 - 1.43: 180 1.43 - 1.49: 85 1.49 - 1.56: 221 Bond restraints: 624 Sorted by residual: bond pdb=" C ACE D 0 " pdb=" O ACE D 0 " ideal model delta sigma weight residual 1.199 1.402 -0.203 2.00e-02 2.50e+03 1.03e+02 bond pdb=" C ACE N 0 " pdb=" O ACE N 0 " ideal model delta sigma weight residual 1.199 1.401 -0.202 2.00e-02 2.50e+03 1.02e+02 bond pdb=" C ACE K 0 " pdb=" O ACE K 0 " ideal model delta sigma weight residual 1.199 1.401 -0.202 2.00e-02 2.50e+03 1.02e+02 bond pdb=" C ACE B 0 " pdb=" O ACE B 0 " ideal model delta sigma weight residual 1.199 1.401 -0.202 2.00e-02 2.50e+03 1.02e+02 bond pdb=" C ACE E 0 " pdb=" O ACE E 0 " ideal model delta sigma weight residual 1.199 1.401 -0.202 2.00e-02 2.50e+03 1.02e+02 ... (remaining 619 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.91: 700 1.91 - 3.81: 74 3.81 - 5.72: 16 5.72 - 7.63: 13 7.63 - 9.53: 7 Bond angle restraints: 810 Sorted by residual: angle pdb=" N SER M 1 " pdb=" CA SER M 1 " pdb=" CB SER M 1 " ideal model delta sigma weight residual 110.50 102.97 7.53 1.70e+00 3.46e-01 1.96e+01 angle pdb=" CB LYS M 4 " pdb=" CG LYS M 4 " pdb=" CD LYS M 4 " ideal model delta sigma weight residual 111.30 120.83 -9.53 2.30e+00 1.89e-01 1.72e+01 angle pdb=" N SER B 1 " pdb=" CA SER B 1 " pdb=" CB SER B 1 " ideal model delta sigma weight residual 110.50 103.52 6.98 1.70e+00 3.46e-01 1.68e+01 angle pdb=" N SER D 1 " pdb=" CA SER D 1 " pdb=" CB SER D 1 " ideal model delta sigma weight residual 110.50 103.60 6.90 1.70e+00 3.46e-01 1.65e+01 angle pdb=" N SER K 1 " pdb=" CA SER K 1 " pdb=" CB SER K 1 " ideal model delta sigma weight residual 110.50 103.74 6.76 1.70e+00 3.46e-01 1.58e+01 ... (remaining 805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.48: 281 17.48 - 34.95: 54 34.95 - 52.42: 17 52.42 - 69.90: 0 69.90 - 87.37: 2 Dihedral angle restraints: 354 sinusoidal: 162 harmonic: 192 Sorted by residual: dihedral pdb=" CA SER B 6 " pdb=" C SER B 6 " pdb=" N PHE B 7 " pdb=" CA PHE B 7 " ideal model delta harmonic sigma weight residual 180.00 163.43 16.57 0 5.00e+00 4.00e-02 1.10e+01 dihedral pdb=" CB GLU M 8 " pdb=" CG GLU M 8 " pdb=" CD GLU M 8 " pdb=" OE1 GLU M 8 " ideal model delta sinusoidal sigma weight residual 0.00 87.37 -87.37 1 3.00e+01 1.11e-03 1.02e+01 dihedral pdb=" CA PHE M 7 " pdb=" C PHE M 7 " pdb=" N GLU M 8 " pdb=" CA GLU M 8 " ideal model delta harmonic sigma weight residual 180.00 164.17 15.83 0 5.00e+00 4.00e-02 1.00e+01 ... (remaining 351 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.056: 47 0.056 - 0.111: 10 0.111 - 0.166: 3 0.166 - 0.221: 0 0.221 - 0.276: 6 Chirality restraints: 66 Sorted by residual: chirality pdb=" CA SER D 11 " pdb=" N SER D 11 " pdb=" C SER D 11 " pdb=" CB SER D 11 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" CA SER B 11 " pdb=" N SER B 11 " pdb=" C SER B 11 " pdb=" CB SER B 11 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CA SER E 11 " pdb=" N SER E 11 " pdb=" C SER E 11 " pdb=" CB SER E 11 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.76e+00 ... (remaining 63 not shown) Planarity restraints: 102 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE E 9 " -0.011 2.00e-02 2.50e+03 2.30e-02 5.31e+00 pdb=" C PHE E 9 " 0.040 2.00e-02 2.50e+03 pdb=" O PHE E 9 " -0.015 2.00e-02 2.50e+03 pdb=" N LYS E 10 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE E 3 " -0.013 2.00e-02 2.50e+03 1.51e-02 3.98e+00 pdb=" CG PHE E 3 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 PHE E 3 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE E 3 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE E 3 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE E 3 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE E 3 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS N 4 " 0.008 2.00e-02 2.50e+03 1.54e-02 2.36e+00 pdb=" C LYS N 4 " -0.027 2.00e-02 2.50e+03 pdb=" O LYS N 4 " 0.010 2.00e-02 2.50e+03 pdb=" N PHE N 5 " 0.009 2.00e-02 2.50e+03 ... (remaining 99 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 183 2.83 - 3.34: 517 3.34 - 3.86: 898 3.86 - 4.38: 1013 4.38 - 4.90: 1674 Nonbonded interactions: 4285 Sorted by model distance: nonbonded pdb=" N GLU E 8 " pdb=" OE1 GLU E 8 " model vdw 2.307 3.120 nonbonded pdb=" N SER E 11 " pdb=" OG SER E 11 " model vdw 2.560 2.496 nonbonded pdb=" N SER D 11 " pdb=" OG SER D 11 " model vdw 2.614 2.496 nonbonded pdb=" N LYS K 4 " pdb=" O LYS K 4 " model vdw 2.636 2.496 nonbonded pdb=" O SER M 6 " pdb=" OE1 GLU M 8 " model vdw 2.637 3.040 ... (remaining 4280 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 'D' selection = chain 'E' selection = chain 'K' selection = chain 'M' selection = chain 'N' } 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: 0.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.010 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 1.760 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 3.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6224 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 : 0.034 0.203 630 Z= 1.692 Angle : 1.673 9.532 810 Z= 0.860 Chirality : 0.092 0.276 66 Planarity : 0.005 0.023 102 Dihedral : 20.549 87.372 222 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.81 % Favored : 85.19 % Rotamer: Outliers : 3.03 % Allowed : 45.45 % Favored : 51.52 % 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: -3.37 (0.91), residues: 54 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.56 (0.70), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.035 0.002 PHE E 3 Details of bonding type rmsd/Z covalent geometry : bond 0.03376 / 1.69 ( 624) covalent geometry : angle 1.67278 / 0.86 ( 810) Misc. bond : bond 0.02234 / 1.12 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 108 Ramachandran restraints generated. 54 Oldfield, 0 Emsley, 54 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 108 Ramachandran restraints generated. 54 Oldfield, 0 Emsley, 54 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 66 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 26 time to evaluate : 0.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 3 PHE cc_start: 0.5976 (t80) cc_final: 0.5772 (p90) REVERT: E 10 LYS cc_start: 0.7885 (mmmm) cc_final: 0.7019 (pttm) outliers start: 2 outliers final: 1 residues processed: 27 average time/residue: 0.0689 time to fit residues: 1.9257 Evaluate side-chains 26 residues out of total 66 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 25 time to evaluate : 0.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 6 random chunks: chunk 0 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 overall best weight: 0.7983 ------------------------------------------------------------------------------- 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 = 0.4392 r_free = 0.4392 target = 0.119686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.113060 restraints weight = 2685.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.115143 restraints weight = 1336.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.116497 restraints weight = 765.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.117396 restraints weight = 485.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.118127 restraints weight = 322.360| |-----------------------------------------------------------------------------| r_work (final): 0.4367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6083 moved from start: 0.7124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 630 Z= 0.172 Angle : 0.687 6.179 810 Z= 0.372 Chirality : 0.034 0.070 66 Planarity : 0.003 0.009 102 Dihedral : 6.014 14.988 72 Min Nonbonded Distance : 2.682 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % 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: -2.99 (1.03), residues: 54 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.27 (0.78), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.020 0.003 PHE D 7 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.17 ( 624) covalent geometry : angle 0.68684 / 0.37 ( 810) Misc. bond : bond 0.00028 / 0.01 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 108 Ramachandran restraints generated. 54 Oldfield, 0 Emsley, 54 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 108 Ramachandran restraints generated. 54 Oldfield, 0 Emsley, 54 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 66 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.014 Fit side-chains revert: symmetry clash REVERT: B 3 PHE cc_start: 0.6956 (t80) cc_final: 0.5911 (p90) REVERT: D 8 GLU cc_start: 0.7247 (mp0) cc_final: 0.6834 (mm-30) REVERT: N 8 GLU cc_start: 0.7966 (mt-10) cc_final: 0.7577 (pm20) outliers start: 0 outliers final: 0 residues processed: 27 average time/residue: 0.0708 time to fit residues: 1.9781 Evaluate side-chains 23 residues out of total 66 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 6 random chunks: chunk 0 optimal weight: 3.9990 chunk 1 optimal weight: 0.2980 chunk 2 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 4 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 overall best weight: 0.5647 ------------------------------------------------------------------------------- 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 = 0.4392 r_free = 0.4392 target = 0.118795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.112224 restraints weight = 2608.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.114097 restraints weight = 1478.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.115474 restraints weight = 927.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.116433 restraints weight = 596.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.116986 restraints weight = 384.577| |-----------------------------------------------------------------------------| r_work (final): 0.4361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6165 moved from start: 0.9415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 630 Z= 0.129 Angle : 0.545 4.277 810 Z= 0.282 Chirality : 0.033 0.076 66 Planarity : 0.002 0.009 102 Dihedral : 5.806 28.615 72 Min Nonbonded Distance : 2.682 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % 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: -2.50 (1.04), residues: 54 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.89 (0.79), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.020 0.002 PHE M 3 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 ( 624) covalent geometry : angle 0.54468 / 0.28 ( 810) Misc. bond : bond 0.00027 / 0.01 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 108 Ramachandran restraints generated. 54 Oldfield, 0 Emsley, 54 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 108 Ramachandran restraints generated. 54 Oldfield, 0 Emsley, 54 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 66 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.015 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: M 4 LYS cc_start: 0.8571 (mmpt) cc_final: 0.8282 (mmmt) REVERT: N 8 GLU cc_start: 0.8225 (mt-10) cc_final: 0.7715 (pm20) outliers start: 0 outliers final: 0 residues processed: 27 average time/residue: 0.0808 time to fit residues: 2.2515 Evaluate side-chains 23 residues out of total 66 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 6 random chunks: chunk 0 optimal weight: 4.9990 chunk 1 optimal weight: 0.7980 chunk 2 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 4 optimal weight: 0.2980 chunk 5 optimal weight: 0.0870 overall best weight: 0.3943 ------------------------------------------------------------------------------- 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 = 0.4498 r_free = 0.4498 target = 0.117061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.113031 restraints weight = 2471.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.114272 restraints weight = 1335.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4470 r_free = 0.4470 target = 0.115093 restraints weight = 783.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.115630 restraints weight = 494.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.116089 restraints weight = 334.292| |-----------------------------------------------------------------------------| r_work (final): 0.4487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6080 moved from start: 1.0034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 630 Z= 0.129 Angle : 0.578 4.702 810 Z= 0.299 Chirality : 0.032 0.087 66 Planarity : 0.002 0.009 102 Dihedral : 5.541 27.779 72 Min Nonbonded Distance : 2.642 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % 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: -2.90 (0.95), residues: 54 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.20 (0.72), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.015 0.002 PHE K 9 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 ( 624) covalent geometry : angle 0.57788 / 0.30 ( 810) Misc. bond : bond 0.00013 / 0.01 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 108 Ramachandran restraints generated. 54 Oldfield, 0 Emsley, 54 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 108 Ramachandran restraints generated. 54 Oldfield, 0 Emsley, 54 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 66 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.014 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 3 PHE cc_start: 0.6464 (m-10) cc_final: 0.6204 (m-10) REVERT: M 3 PHE cc_start: 0.6692 (m-80) cc_final: 0.6477 (m-80) outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.1027 time to fit residues: 2.6429 Evaluate side-chains 24 residues out of total 66 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 6 random chunks: chunk 0 optimal weight: 4.9990 chunk 1 optimal weight: 0.8980 chunk 2 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 overall best weight: 2.2987 ------------------------------------------------------------------------------- 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 = 0.3988 r_free = 0.3988 target = 0.095535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.091872 restraints weight = 3019.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.093136 restraints weight = 1546.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.093870 restraints weight = 883.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.094342 restraints weight = 553.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.094704 restraints weight = 365.776| |-----------------------------------------------------------------------------| r_work (final): 0.3973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6475 moved from start: 1.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.041 630 Z= 0.309 Angle : 0.911 6.249 810 Z= 0.481 Chirality : 0.046 0.111 66 Planarity : 0.004 0.010 102 Dihedral : 7.191 16.907 72 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.52 % Favored : 81.48 % Rotamer: Outliers : 0.00 % Allowed : 10.61 % Favored : 89.39 % 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: -3.49 (0.88), residues: 54 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.65 (0.68), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.022 0.004 PHE M 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00725 / 0.31 ( 624) covalent geometry : angle 0.91100 / 0.48 ( 810) Misc. bond : bond 0.00081 / 0.04 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 108 Ramachandran restraints generated. 54 Oldfield, 0 Emsley, 54 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 108 Ramachandran restraints generated. 54 Oldfield, 0 Emsley, 54 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 66 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.015 Fit side-chains REVERT: B 10 LYS cc_start: 0.5558 (mmpt) cc_final: 0.5091 (mmtm) REVERT: D 4 LYS cc_start: 0.8340 (mmpt) cc_final: 0.8101 (mmmt) outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.1080 time to fit residues: 2.4497 Evaluate side-chains 21 residues out of total 66 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 6 random chunks: chunk 0 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 4 optimal weight: 0.0270 chunk 5 optimal weight: 1.9990 overall best weight: 1.3417 ------------------------------------------------------------------------------- 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 = 0.4088 r_free = 0.4088 target = 0.097451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.093668 restraints weight = 3826.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.094927 restraints weight = 1808.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.095696 restraints weight = 991.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.096223 restraints weight = 601.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.096500 restraints weight = 402.914| |-----------------------------------------------------------------------------| r_work (final): 0.4075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6471 moved from start: 1.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.020 630 Z= 0.195 Angle : 0.685 4.445 810 Z= 0.368 Chirality : 0.039 0.101 66 Planarity : 0.003 0.011 102 Dihedral : 6.395 22.936 72 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % 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: -3.54 (0.99), residues: 54 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.69 (0.76), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.024 0.003 PHE B 7 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.20 ( 624) covalent geometry : angle 0.68468 / 0.37 ( 810) Misc. bond : bond 0.00037 / 0.02 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 108 Ramachandran restraints generated. 54 Oldfield, 0 Emsley, 54 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 108 Ramachandran restraints generated. 54 Oldfield, 0 Emsley, 54 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 66 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.022 Fit side-chains revert: symmetry clash REVERT: B 10 LYS cc_start: 0.6127 (mmpt) cc_final: 0.5655 (mmpt) REVERT: D 10 LYS cc_start: 0.9157 (mmmm) cc_final: 0.8907 (mmmt) REVERT: M 3 PHE cc_start: 0.7669 (m-80) cc_final: 0.7066 (m-80) REVERT: N 10 LYS cc_start: 0.5508 (pptt) cc_final: 0.4922 (pptt) outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.1150 time to fit residues: 2.6252 Evaluate side-chains 21 residues out of total 66 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 6 random chunks: chunk 0 optimal weight: 4.9990 chunk 1 optimal weight: 0.3980 chunk 2 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 overall best weight: 0.7317 ------------------------------------------------------------------------------- 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 = 0.4121 r_free = 0.4121 target = 0.099857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.095978 restraints weight = 2937.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.097182 restraints weight = 1500.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.097911 restraints weight = 873.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.098424 restraints weight = 580.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.098681 restraints weight = 398.400| |-----------------------------------------------------------------------------| r_work (final): 0.4106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6333 moved from start: 1.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 630 Z= 0.149 Angle : 0.641 5.844 810 Z= 0.338 Chirality : 0.033 0.083 66 Planarity : 0.002 0.007 102 Dihedral : 6.008 26.383 72 Min Nonbonded Distance : 2.648 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % 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: -3.48 (0.98), residues: 54 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.64 (0.74), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.016 0.002 PHE B 7 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.15 ( 624) covalent geometry : angle 0.64094 / 0.34 ( 810) Misc. bond : bond 0.00030 / 0.01 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 108 Ramachandran restraints generated. 54 Oldfield, 0 Emsley, 54 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 108 Ramachandran restraints generated. 54 Oldfield, 0 Emsley, 54 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 66 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.016 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 10 LYS cc_start: 0.6109 (mmpt) cc_final: 0.5563 (mmpt) REVERT: K 10 LYS cc_start: 0.4912 (mmpt) cc_final: 0.4300 (mmtm) REVERT: D 10 LYS cc_start: 0.9195 (mmmm) cc_final: 0.8908 (mmmt) REVERT: M 3 PHE cc_start: 0.7688 (m-80) cc_final: 0.7294 (m-80) outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.1302 time to fit residues: 2.9532 Evaluate side-chains 22 residues out of total 66 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 6 random chunks: chunk 0 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 3 optimal weight: 0.0980 chunk 4 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 overall best weight: 0.6983 ------------------------------------------------------------------------------- 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 = 0.4173 r_free = 0.4173 target = 0.100781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.096878 restraints weight = 3078.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.098129 restraints weight = 1486.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.098997 restraints weight = 831.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.099378 restraints weight = 530.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.099738 restraints weight = 340.941| |-----------------------------------------------------------------------------| r_work (final): 0.4158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6243 moved from start: 1.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 630 Z= 0.147 Angle : 0.655 6.628 810 Z= 0.335 Chirality : 0.033 0.082 66 Planarity : 0.002 0.006 102 Dihedral : 5.693 23.722 72 Min Nonbonded Distance : 2.656 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.26 % Favored : 90.74 % Rotamer: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % 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: -3.25 (1.02), residues: 54 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.47 (0.78), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.014 0.002 PHE B 7 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.15 ( 624) covalent geometry : angle 0.65464 / 0.34 ( 810) Misc. bond : bond 0.00033 / 0.02 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 108 Ramachandran restraints generated. 54 Oldfield, 0 Emsley, 54 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 108 Ramachandran restraints generated. 54 Oldfield, 0 Emsley, 54 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 66 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.030 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 10 LYS cc_start: 0.6156 (mmpt) cc_final: 0.5688 (mmpt) REVERT: K 10 LYS cc_start: 0.4663 (mmpt) cc_final: 0.4250 (mmtt) REVERT: D 10 LYS cc_start: 0.9164 (mmmm) cc_final: 0.8922 (mmmt) REVERT: M 3 PHE cc_start: 0.7739 (m-80) cc_final: 0.7322 (m-80) REVERT: E 5 PHE cc_start: 0.7272 (t80) cc_final: 0.7014 (t80) outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.1285 time to fit residues: 2.6692 Evaluate side-chains 20 residues out of total 66 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 6 random chunks: chunk 0 optimal weight: 4.9990 chunk 1 optimal weight: 0.0000 chunk 2 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 chunk 4 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 overall best weight: 0.5320 ------------------------------------------------------------------------------- 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 = 0.4168 r_free = 0.4168 target = 0.101515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.097727 restraints weight = 2903.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.098921 restraints weight = 1394.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.099693 restraints weight = 786.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.100151 restraints weight = 487.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.100435 restraints weight = 332.523| |-----------------------------------------------------------------------------| r_work (final): 0.4157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6202 moved from start: 1.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 630 Z= 0.132 Angle : 0.638 7.074 810 Z= 0.321 Chirality : 0.032 0.076 66 Planarity : 0.002 0.006 102 Dihedral : 5.245 19.170 72 Min Nonbonded Distance : 2.679 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % 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: -3.16 (1.02), residues: 54 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.40 (0.78), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.014 0.002 PHE B 7 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.13 ( 624) covalent geometry : angle 0.63759 / 0.32 ( 810) Misc. bond : bond 0.00030 / 0.01 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 108 Ramachandran restraints generated. 54 Oldfield, 0 Emsley, 54 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 108 Ramachandran restraints generated. 54 Oldfield, 0 Emsley, 54 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 66 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 10 LYS cc_start: 0.6102 (mmpt) cc_final: 0.5546 (mmpt) REVERT: K 10 LYS cc_start: 0.4874 (mmpt) cc_final: 0.4386 (mmtm) REVERT: D 7 PHE cc_start: 0.7063 (t80) cc_final: 0.6863 (t80) REVERT: D 10 LYS cc_start: 0.9129 (mmmm) cc_final: 0.8908 (mmmt) REVERT: M 3 PHE cc_start: 0.7705 (m-80) cc_final: 0.7375 (m-80) REVERT: E 5 PHE cc_start: 0.7290 (t80) cc_final: 0.6964 (t80) outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.1178 time to fit residues: 2.6911 Evaluate side-chains 21 residues out of total 66 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 6 random chunks: chunk 0 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 3 optimal weight: 0.9990 chunk 4 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 overall best weight: 1.1987 ------------------------------------------------------------------------------- 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 = 0.4079 r_free = 0.4079 target = 0.097252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.093237 restraints weight = 3372.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.094440 restraints weight = 1625.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.095287 restraints weight = 912.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.095811 restraints weight = 568.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.096145 restraints weight = 386.764| |-----------------------------------------------------------------------------| r_work (final): 0.4062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6325 moved from start: 1.2829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 630 Z= 0.192 Angle : 0.764 7.732 810 Z= 0.386 Chirality : 0.037 0.103 66 Planarity : 0.002 0.006 102 Dihedral : 6.069 16.046 72 Min Nonbonded Distance : 2.649 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.96 % Favored : 87.04 % Rotamer: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % 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: -3.45 (0.98), residues: 54 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.62 (0.75), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.013 0.002 PHE B 7 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.19 ( 624) covalent geometry : angle 0.76388 / 0.39 ( 810) Misc. bond : bond 0.00057 / 0.03 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 108 Ramachandran restraints generated. 54 Oldfield, 0 Emsley, 54 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 108 Ramachandran restraints generated. 54 Oldfield, 0 Emsley, 54 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 66 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.028 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 10 LYS cc_start: 0.3795 (mmpt) cc_final: 0.3366 (mmtm) REVERT: D 10 LYS cc_start: 0.9148 (mmmm) cc_final: 0.8914 (mmmm) outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.1234 time to fit residues: 2.5633 Evaluate side-chains 17 residues out of total 66 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 6 random chunks: chunk 0 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 3 optimal weight: 0.6980 chunk 4 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 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 = 0.4109 r_free = 0.4109 target = 0.097498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.093544 restraints weight = 2985.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.094772 restraints weight = 1462.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.095597 restraints weight = 819.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.096110 restraints weight = 505.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.096378 restraints weight = 337.856| |-----------------------------------------------------------------------------| r_work (final): 0.4092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6252 moved from start: 1.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 630 Z= 0.158 Angle : 0.688 7.260 810 Z= 0.348 Chirality : 0.034 0.084 66 Planarity : 0.002 0.007 102 Dihedral : 5.747 16.397 72 Min Nonbonded Distance : 2.678 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % 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: -3.12 (1.06), residues: 54 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.37 (0.81), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.016 0.002 PHE D 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.16 ( 624) covalent geometry : angle 0.68815 / 0.35 ( 810) Misc. bond : bond 0.00026 / 0.01 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 307.20 seconds wall clock time: 6 minutes 15.10 seconds (375.10 seconds total)