Starting phenix.real_space_refine on Thu Oct 22 17:11:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pef_71560/10_2026/9pef_71560.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pef_71560/10_2026/9pef_71560.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9pef_71560/10_2026/9pef_71560.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pef_71560/10_2026/9pef_71560.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9pef_71560/10_2026/9pef_71560.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pef_71560/10_2026/9pef_71560.map" } resolution = 3.7 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 456 2.51 5 N 88 2.21 5 O 88 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-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 632 Number of models: 1 Model: "" Number of chains: 16 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: "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: "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: "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} Time building chain proxies: 0.12, per 1000 atoms: 0.19 Number of scatterers: 632 At special positions: 0 Unit cell: (55.61, 64.74, 40.67, 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 88 8.00 N 88 7.00 C 456 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=8, symmetry=0 Number of additional bonds: simple=8, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.05 Conformation dependent library (CDL) restraints added in 114.4 milliseconds 96 Ramachandran restraints generated. 48 Oldfield, 0 Emsley, 48 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 112 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 4 sheets defined 0.0% alpha, 40.6% 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 'J' and resid 3 through 5 removed outlier: 6.229A 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 2 through 6 Processing sheet with id=AA3, first strand: chain 'M' and resid 2 through 6 Processing sheet with id=AA4, first strand: chain 'O' and resid 3 through 6 removed outlier: 6.331A pdb=" N GLU O 4 " --> pdb=" O PHE C 5 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 12 hydrogen bonds defined for protein. 24 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: 0.03 Time building geometry restraints manager: 0.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.25: 80 1.25 - 1.32: 8 1.32 - 1.39: 240 1.39 - 1.46: 78 1.46 - 1.53: 242 Bond restraints: 648 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 5.24e+01 bond pdb=" C PHE J 7 " pdb=" N GLY J 8 " ideal model delta sigma weight residual 1.329 1.430 -0.101 1.40e-02 5.10e+03 5.18e+01 bond pdb=" C PHE K 7 " pdb=" N GLY K 8 " ideal model delta sigma weight residual 1.329 1.430 -0.101 1.40e-02 5.10e+03 5.17e+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 5.17e+01 bond pdb=" C PHE B 7 " pdb=" N GLY B 8 " ideal model delta sigma weight residual 1.329 1.430 -0.101 1.40e-02 5.10e+03 5.16e+01 ... (remaining 643 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.60: 786 5.60 - 11.20: 32 11.20 - 16.81: 5 16.81 - 22.41: 3 22.41 - 28.01: 6 Bond angle restraints: 832 Sorted by residual: angle pdb=" O PHE K 7 " pdb=" C PHE K 7 " pdb=" N GLY K 8 " ideal model delta sigma weight residual 122.59 98.38 24.21 1.33e+00 5.65e-01 3.31e+02 angle pdb=" C PHE M 7 " pdb=" N GLY M 8 " pdb=" CA GLY M 8 " ideal model delta sigma weight residual 121.70 149.71 -28.01 1.80e+00 3.09e-01 2.42e+02 angle pdb=" C PHE B 7 " pdb=" N GLY B 8 " pdb=" CA GLY B 8 " ideal model delta sigma weight residual 121.70 145.99 -24.29 1.80e+00 3.09e-01 1.82e+02 angle pdb=" C PHE N 7 " pdb=" N GLY N 8 " pdb=" CA GLY N 8 " ideal model delta sigma weight residual 121.70 97.60 24.10 1.80e+00 3.09e-01 1.79e+02 angle pdb=" O PHE M 7 " pdb=" C PHE M 7 " pdb=" N GLY M 8 " ideal model delta sigma weight residual 122.34 98.54 23.80 1.80e+00 3.09e-01 1.75e+02 ... (remaining 827 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 35.99: 316 35.99 - 71.98: 12 71.98 - 107.97: 0 107.97 - 143.96: 0 143.96 - 179.95: 8 Dihedral angle restraints: 336 sinusoidal: 168 harmonic: 168 Sorted by residual: dihedral pdb=" CH3 ACE L 0 " pdb=" C ACE L 0 " pdb=" N PHE L 1 " pdb=" CA PHE L 1 " ideal model delta sinusoidal sigma weight residual -180.00 -0.05 -179.95 1 5.00e+00 4.00e-02 7.68e+02 dihedral pdb=" CH3 ACE B 0 " pdb=" C ACE B 0 " pdb=" N PHE B 1 " pdb=" CA PHE B 1 " ideal model delta sinusoidal sigma weight residual -180.00 -0.16 -179.84 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 -0.24 -179.76 1 5.00e+00 4.00e-02 7.68e+02 ... (remaining 333 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.011: 12 0.011 - 0.021: 15 0.021 - 0.032: 16 0.032 - 0.042: 8 0.042 - 0.052: 5 Chirality restraints: 56 Sorted by residual: chirality pdb=" CA LYS L 6 " pdb=" N LYS L 6 " pdb=" C LYS L 6 " pdb=" CB LYS L 6 " both_signs ideal model delta sigma weight residual False 2.51 2.56 -0.05 2.00e-01 2.50e+01 6.88e-02 chirality pdb=" CA PHE C 1 " pdb=" N PHE C 1 " pdb=" C PHE C 1 " pdb=" CB PHE C 1 " both_signs ideal model delta sigma weight residual False 2.51 2.46 0.05 2.00e-01 2.50e+01 5.36e-02 chirality pdb=" CA PHE N 1 " pdb=" N PHE N 1 " pdb=" C PHE N 1 " pdb=" CB PHE N 1 " both_signs ideal model delta sigma weight residual False 2.51 2.47 0.05 2.00e-01 2.50e+01 5.14e-02 ... (remaining 53 not shown) Planarity restraints: 104 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE L 7 " -0.063 2.00e-02 2.50e+03 1.06e-01 1.13e+02 pdb=" C PHE L 7 " 0.184 2.00e-02 2.50e+03 pdb=" O PHE L 7 " -0.064 2.00e-02 2.50e+03 pdb=" N GLY L 8 " -0.058 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE K 7 " -0.048 2.00e-02 2.50e+03 7.58e-02 5.74e+01 pdb=" C PHE K 7 " 0.131 2.00e-02 2.50e+03 pdb=" O PHE K 7 " -0.040 2.00e-02 2.50e+03 pdb=" N GLY K 8 " -0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE J 7 " -0.037 2.00e-02 2.50e+03 6.58e-02 4.33e+01 pdb=" C PHE J 7 " 0.114 2.00e-02 2.50e+03 pdb=" O PHE J 7 " -0.040 2.00e-02 2.50e+03 pdb=" N GLY J 8 " -0.036 2.00e-02 2.50e+03 ... (remaining 101 not shown) Histogram of nonbonded interaction distances: 2.54 - 3.01: 328 3.01 - 3.48: 474 3.48 - 3.95: 750 3.95 - 4.43: 921 4.43 - 4.90: 1465 Nonbonded interactions: 3938 Sorted by model distance: nonbonded pdb=" O PHE N 7 " pdb=" CA GLY N 8 " model vdw 2.535 2.752 nonbonded pdb=" O PHE J 7 " pdb=" CA GLY J 8 " model vdw 2.570 2.752 nonbonded pdb=" O PHE L 7 " pdb=" CA GLY L 8 " model vdw 2.621 2.752 nonbonded pdb=" CG LYS J 2 " pdb=" NZ LYS J 2 " model vdw 2.638 2.816 nonbonded pdb=" CG LYS B 2 " pdb=" NZ LYS B 2 " model vdw 2.639 2.816 ... (remaining 3933 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 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' } 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: 1.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.020 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 1.790 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: 4.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 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 0.135 656 Z= 1.172 Angle : 3.129 28.011 832 Z= 1.824 Chirality : 0.026 0.052 56 Planarity : 0.015 0.106 104 Dihedral : 37.697 179.950 224 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 2.08 % Allowed : 12.50 % Favored : 85.42 % Rotamer: Outliers : 0.00 % Allowed : 16.07 % Favored : 83.93 % 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: -4.60 (0.81), residues: 48 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.50 (0.62), residues: 48 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.011 0.001 PHE M 3 Details of bonding type rmsd/Z covalent geometry : bond 0.02011 / 1.15 ( 648) covalent geometry : angle 3.12874 / 1.82 ( 832) hydrogen bonds : bond 0.25559 / 13.12 ( 12) hydrogen bonds : angle 21.15051 / 11.33 ( 24) Misc. bond : bond 0.02164 / 1.15 ( 8) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 96 Ramachandran restraints generated. 48 Oldfield, 0 Emsley, 48 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 96 Ramachandran restraints generated. 48 Oldfield, 0 Emsley, 48 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 4 residues out of total 56 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.013 Fit side-chains REVERT: N 2 LYS cc_start: 0.7664 (mttt) cc_final: 0.6824 (tptt) outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.1088 time to fit residues: 0.4626 Evaluate side-chains 3 residues out of total 56 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.120835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.108471 restraints weight = 894.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.111365 restraints weight = 457.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.113292 restraints weight = 283.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.114299 restraints weight = 196.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.115224 restraints weight = 155.333| |-----------------------------------------------------------------------------| r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 656 Z= 0.140 Angle : 1.303 10.668 832 Z= 0.459 Chirality : 0.037 0.087 56 Planarity : 0.002 0.009 104 Dihedral : 59.656 179.985 72 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.79 % Allowed : 14.29 % Favored : 83.93 % 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: -4.19 (0.79), residues: 48 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.19 (0.60), residues: 48 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.006 0.001 PHE N 3 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 ( 648) covalent geometry : angle 1.30297 / 0.46 ( 832) hydrogen bonds : bond 0.02090 / 1.02 ( 12) hydrogen bonds : angle 12.87491 / 6.86 ( 24) Misc. bond : bond 0.00045 / 0.02 ( 8) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 96 Ramachandran restraints generated. 48 Oldfield, 0 Emsley, 48 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 96 Ramachandran restraints generated. 48 Oldfield, 0 Emsley, 48 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 5 residues out of total 56 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 4 time to evaluate : 0.014 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 4 average time/residue: 0.0755 time to fit residues: 0.3292 Evaluate side-chains 5 residues out of total 56 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 4 time to evaluate : 0.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 6 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 = 0.3625 r_free = 0.3625 target = 0.108181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.095639 restraints weight = 968.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.098214 restraints weight = 548.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.100038 restraints weight = 358.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.101179 restraints weight = 257.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.102098 restraints weight = 202.801| |-----------------------------------------------------------------------------| r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.042 656 Z= 0.569 Angle : 1.572 12.308 832 Z= 0.630 Chirality : 0.068 0.199 56 Planarity : 0.008 0.032 104 Dihedral : 57.467 176.647 72 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 22.92 % Favored : 77.08 % Rotamer: Outliers : 0.00 % Allowed : 21.43 % Favored : 78.57 % 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: -5.52 (0.85), residues: 48 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.20 (0.65), residues: 48 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.036 0.005 PHE L 1 Details of bonding type rmsd/Z covalent geometry : bond 0.01343 / 0.57 ( 648) covalent geometry : angle 1.57173 / 0.63 ( 832) hydrogen bonds : bond 0.03729 / 1.94 ( 12) hydrogen bonds : angle 17.41221 / 9.20 ( 24) Misc. bond : bond 0.00046 / 0.02 ( 8) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 96 Ramachandran restraints generated. 48 Oldfield, 0 Emsley, 48 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 96 Ramachandran restraints generated. 48 Oldfield, 0 Emsley, 48 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 4 residues out of total 56 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.017 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0993 time to fit residues: 0.4316 Evaluate side-chains 4 residues out of total 56 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.117606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.104416 restraints weight = 959.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.107390 restraints weight = 499.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.109449 restraints weight = 310.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.110808 restraints weight = 215.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.111809 restraints weight = 163.176| |-----------------------------------------------------------------------------| r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.3169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 656 Z= 0.141 Angle : 1.292 10.677 832 Z= 0.454 Chirality : 0.037 0.074 56 Planarity : 0.002 0.008 104 Dihedral : 59.784 179.975 72 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.79 % Allowed : 16.07 % Favored : 82.14 % 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: -4.85 (0.77), residues: 48 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.69 (0.58), residues: 48 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.006 0.001 PHE L 1 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 ( 648) covalent geometry : angle 1.29191 / 0.45 ( 832) hydrogen bonds : bond 0.01551 / 0.78 ( 12) hydrogen bonds : angle 12.78816 / 6.90 ( 24) Misc. bond : bond 0.00128 / 0.06 ( 8) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 96 Ramachandran restraints generated. 48 Oldfield, 0 Emsley, 48 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 96 Ramachandran restraints generated. 48 Oldfield, 0 Emsley, 48 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 4 residues out of total 56 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 3 time to evaluate : 0.015 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 3 average time/residue: 0.0985 time to fit residues: 0.3235 Evaluate side-chains 3 residues out of total 56 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 2 time to evaluate : 0.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 6 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 = 0.3604 r_free = 0.3604 target = 0.104697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.092040 restraints weight = 1054.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.094066 restraints weight = 681.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.095415 restraints weight = 497.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.096415 restraints weight = 392.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.097294 restraints weight = 327.340| |-----------------------------------------------------------------------------| r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.3637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.043 656 Z= 0.555 Angle : 1.576 12.437 832 Z= 0.627 Chirality : 0.068 0.211 56 Planarity : 0.008 0.034 104 Dihedral : 57.559 176.409 72 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 22.92 % Favored : 77.08 % Rotamer: Outliers : 1.79 % Allowed : 21.43 % Favored : 76.79 % 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: -5.79 (0.85), residues: 48 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.41 (0.65), residues: 48 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.035 0.004 PHE L 1 Details of bonding type rmsd/Z covalent geometry : bond 0.01317 / 0.56 ( 648) covalent geometry : angle 1.57615 / 0.63 ( 832) hydrogen bonds : bond 0.03437 / 1.73 ( 12) hydrogen bonds : angle 17.01356 / 9.07 ( 24) Misc. bond : bond 0.00037 / 0.02 ( 8) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 96 Ramachandran restraints generated. 48 Oldfield, 0 Emsley, 48 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 96 Ramachandran restraints generated. 48 Oldfield, 0 Emsley, 48 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 4 residues out of total 56 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 3 time to evaluate : 0.014 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 3 average time/residue: 0.0987 time to fit residues: 0.3392 Evaluate side-chains 3 residues out of total 56 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.114735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.101437 restraints weight = 998.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.104071 restraints weight = 575.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.105954 restraints weight = 384.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.107241 restraints weight = 280.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.108103 restraints weight = 219.941| |-----------------------------------------------------------------------------| r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.3725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 656 Z= 0.145 Angle : 1.301 10.647 832 Z= 0.462 Chirality : 0.040 0.089 56 Planarity : 0.002 0.007 104 Dihedral : 59.706 179.638 72 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 0.00 % Allowed : 19.64 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.00 (0.80), residues: 48 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.80 (0.61), residues: 48 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.007 0.001 PHE L 1 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.15 ( 648) covalent geometry : angle 1.30107 / 0.46 ( 832) hydrogen bonds : bond 0.01301 / 0.66 ( 12) hydrogen bonds : angle 13.36391 / 7.28 ( 24) Misc. bond : bond 0.00018 / 0.01 ( 8) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 96 Ramachandran restraints generated. 48 Oldfield, 0 Emsley, 48 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 96 Ramachandran restraints generated. 48 Oldfield, 0 Emsley, 48 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2 residues out of total 56 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 2 time to evaluate : 0.047 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 2 average time/residue: 0.2733 time to fit residues: 0.5898 Evaluate side-chains 2 residues out of total 56 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 2 time to evaluate : 0.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 = 0.3597 r_free = 0.3597 target = 0.104584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.090552 restraints weight = 1100.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.092991 restraints weight = 658.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.094720 restraints weight = 455.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.095845 restraints weight = 344.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.096760 restraints weight = 280.782| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.3984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.044 656 Z= 0.550 Angle : 1.591 12.645 832 Z= 0.633 Chirality : 0.067 0.215 56 Planarity : 0.008 0.036 104 Dihedral : 57.625 177.198 72 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 31.25 % Favored : 68.75 % Rotamer: Outliers : 1.79 % Allowed : 21.43 % Favored : 76.79 % 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: -5.99 (0.91), residues: 48 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.56 (0.69), residues: 48 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.032 0.004 PHE L 1 Details of bonding type rmsd/Z covalent geometry : bond 0.01302 / 0.55 ( 648) covalent geometry : angle 1.59080 / 0.63 ( 832) hydrogen bonds : bond 0.03387 / 1.70 ( 12) hydrogen bonds : angle 17.09921 / 9.15 ( 24) Misc. bond : bond 0.00048 / 0.02 ( 8) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 96 Ramachandran restraints generated. 48 Oldfield, 0 Emsley, 48 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 96 Ramachandran restraints generated. 48 Oldfield, 0 Emsley, 48 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 4 residues out of total 56 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 3 time to evaluate : 0.016 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 3 average time/residue: 0.1005 time to fit residues: 0.3301 Evaluate side-chains 4 residues out of total 56 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 3 time to evaluate : 0.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 6 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.114750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.101585 restraints weight = 958.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.104143 restraints weight = 572.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.105888 restraints weight = 389.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.107098 restraints weight = 289.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.107837 restraints weight = 228.511| |-----------------------------------------------------------------------------| r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.4072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 656 Z= 0.140 Angle : 1.300 10.699 832 Z= 0.464 Chirality : 0.041 0.089 56 Planarity : 0.002 0.007 104 Dihedral : 59.716 179.678 72 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.42 % Favored : 89.58 % Rotamer: Outliers : 0.00 % Allowed : 23.21 % Favored : 76.79 % 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: -5.24 (0.81), residues: 48 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.99 (0.62), residues: 48 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.008 0.001 PHE L 1 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 ( 648) covalent geometry : angle 1.30040 / 0.46 ( 832) hydrogen bonds : bond 0.01408 / 0.70 ( 12) hydrogen bonds : angle 13.32233 / 7.30 ( 24) Misc. bond : bond 0.00011 / 0.01 ( 8) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 96 Ramachandran restraints generated. 48 Oldfield, 0 Emsley, 48 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 96 Ramachandran restraints generated. 48 Oldfield, 0 Emsley, 48 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2 residues out of total 56 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 2 time to evaluate : 0.013 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 2 average time/residue: 0.1336 time to fit residues: 0.2914 Evaluate side-chains 2 residues out of total 56 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 2 time to evaluate : 0.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 = 0.3593 r_free = 0.3593 target = 0.104495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.091274 restraints weight = 1052.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.093433 restraints weight = 682.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.094954 restraints weight = 492.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.096123 restraints weight = 383.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.096931 restraints weight = 314.034| |-----------------------------------------------------------------------------| r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.4139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.045 656 Z= 0.546 Angle : 1.593 12.702 832 Z= 0.633 Chirality : 0.068 0.219 56 Planarity : 0.007 0.035 104 Dihedral : 57.673 177.335 72 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 33.33 % Favored : 66.67 % Rotamer: Outliers : 0.00 % Allowed : 25.00 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -6.18 (0.91), residues: 48 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.70 (0.70), residues: 48 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.030 0.004 PHE L 1 Details of bonding type rmsd/Z covalent geometry : bond 0.01297 / 0.55 ( 648) covalent geometry : angle 1.59296 / 0.63 ( 832) hydrogen bonds : bond 0.03330 / 1.65 ( 12) hydrogen bonds : angle 16.95923 / 9.09 ( 24) Misc. bond : bond 0.00036 / 0.02 ( 8) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 96 Ramachandran restraints generated. 48 Oldfield, 0 Emsley, 48 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 96 Ramachandran restraints generated. 48 Oldfield, 0 Emsley, 48 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3 residues out of total 56 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.013 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0936 time to fit residues: 0.3066 Evaluate side-chains 3 residues out of total 56 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.115178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.101360 restraints weight = 1003.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.103959 restraints weight = 608.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.105638 restraints weight = 418.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.106944 restraints weight = 318.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.107842 restraints weight = 253.213| |-----------------------------------------------------------------------------| r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.4163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 656 Z= 0.146 Angle : 1.307 10.670 832 Z= 0.470 Chirality : 0.042 0.090 56 Planarity : 0.002 0.007 104 Dihedral : 59.776 179.817 72 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.42 % Favored : 89.58 % Rotamer: Outliers : 1.79 % Allowed : 21.43 % Favored : 76.79 % 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: -5.38 (0.87), residues: 48 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.09 (0.66), residues: 48 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.009 0.001 PHE L 1 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.15 ( 648) covalent geometry : angle 1.30691 / 0.47 ( 832) hydrogen bonds : bond 0.01538 / 0.75 ( 12) hydrogen bonds : angle 13.68005 / 7.48 ( 24) Misc. bond : bond 0.00011 / 0.01 ( 8) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 96 Ramachandran restraints generated. 48 Oldfield, 0 Emsley, 48 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 96 Ramachandran restraints generated. 48 Oldfield, 0 Emsley, 48 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3 residues out of total 56 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 2 time to evaluate : 0.014 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 2 average time/residue: 0.1378 time to fit residues: 0.3004 Evaluate side-chains 2 residues out of total 56 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 2 time to evaluate : 0.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 = 0.3590 r_free = 0.3590 target = 0.104145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.090614 restraints weight = 1110.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.092802 restraints weight = 712.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.094256 restraints weight = 516.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.095403 restraints weight = 408.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.095828 restraints weight = 337.621| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.4235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.045 656 Z= 0.549 Angle : 1.591 12.746 832 Z= 0.633 Chirality : 0.067 0.214 56 Planarity : 0.007 0.033 104 Dihedral : 57.729 177.089 72 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 33.33 % Favored : 66.67 % Rotamer: Outliers : 1.79 % Allowed : 23.21 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -6.18 (0.93), residues: 48 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.70 (0.71), residues: 48 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.030 0.004 PHE L 3 Details of bonding type rmsd/Z covalent geometry : bond 0.01306 / 0.55 ( 648) covalent geometry : angle 1.59120 / 0.63 ( 832) hydrogen bonds : bond 0.03245 / 1.62 ( 12) hydrogen bonds : angle 16.82046 / 9.03 ( 24) Misc. bond : bond 0.00037 / 0.02 ( 8) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 163.07 seconds wall clock time: 3 minutes 42.57 seconds (222.57 seconds total)