Starting phenix.real_space_refine on Tue Mar 3 10:47:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7m64_23688/03_2026/7m64_23688.cif Found real_map, /net/cci-nas-00/data/ceres_data/7m64_23688/03_2026/7m64_23688.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7m64_23688/03_2026/7m64_23688.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7m64_23688/03_2026/7m64_23688.map" model { file = "/net/cci-nas-00/data/ceres_data/7m64_23688/03_2026/7m64_23688.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7m64_23688/03_2026/7m64_23688.cif" } resolution = 4.0 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 ------------------------------------------------------------------------------- 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= 1.000 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 1140 2.51 5 N 330 2.21 5 O 380 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 1850 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 184 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B, C, D, E, F, G, H, I, J Time building chain proxies: 0.16, per 1000 atoms: 0.09 Number of scatterers: 1850 At special positions: 0 Unit cell: (48.53, 66.465, 44.31, 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 380 8.00 N 330 7.00 C 1140 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=10, symmetry=0 Number of additional bonds: simple=10, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.16 Conformation dependent library (CDL) restraints added in 50.0 milliseconds 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 460 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 4 sheets defined 0.0% alpha, 16.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.04 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'H' and resid 14 through 17 removed outlier: 6.145A pdb=" N PHE D 15 " --> pdb=" O LEU H 16 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N PHE A 15 " --> pdb=" O LEU D 16 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE E 15 " --> pdb=" O ASN A 14 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE I 15 " --> pdb=" O ASN E 14 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 27 through 28 removed outlier: 6.871A pdb=" N LEU A 27 " --> pdb=" O SER E 28 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N LEU E 27 " --> pdb=" O SER I 28 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 14 through 17 removed outlier: 3.570A pdb=" N PHE G 15 " --> pdb=" O ASN C 14 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE C 15 " --> pdb=" O ASN B 14 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N PHE B 15 " --> pdb=" O LEU F 16 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N PHE F 15 " --> pdb=" O LEU J 16 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 27 through 28 removed outlier: 6.871A pdb=" N LEU C 27 " --> pdb=" O SER G 28 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N LEU B 27 " --> pdb=" O SER C 28 " (cutoff:3.500A) 12 hydrogen bonds defined for protein. 36 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: 0.14 Time building geometry restraints manager: 0.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.29: 300 1.29 - 1.36: 313 1.36 - 1.43: 267 1.43 - 1.50: 297 1.50 - 1.56: 693 Bond restraints: 1870 Sorted by residual: bond pdb=" N ALA B 13 " pdb=" CA ALA B 13 " ideal model delta sigma weight residual 1.458 1.498 -0.040 1.90e-02 2.77e+03 4.34e+00 bond pdb=" N ALA E 13 " pdb=" CA ALA E 13 " ideal model delta sigma weight residual 1.458 1.498 -0.040 1.90e-02 2.77e+03 4.32e+00 bond pdb=" C ALA C 13 " pdb=" N ASN C 14 " ideal model delta sigma weight residual 1.331 1.357 -0.026 1.25e-02 6.40e+03 4.29e+00 bond pdb=" N ALA F 13 " pdb=" CA ALA F 13 " ideal model delta sigma weight residual 1.458 1.497 -0.039 1.90e-02 2.77e+03 4.27e+00 bond pdb=" N ALA H 13 " pdb=" CA ALA H 13 " ideal model delta sigma weight residual 1.458 1.497 -0.039 1.90e-02 2.77e+03 4.27e+00 ... (remaining 1865 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.17: 1993 1.17 - 2.34: 385 2.34 - 3.51: 114 3.51 - 4.68: 38 4.68 - 5.85: 10 Bond angle restraints: 2540 Sorted by residual: angle pdb=" C ALA H 13 " pdb=" CA ALA H 13 " pdb=" CB ALA H 13 " ideal model delta sigma weight residual 110.50 116.35 -5.85 1.50e+00 4.44e-01 1.52e+01 angle pdb=" C ALA E 13 " pdb=" CA ALA E 13 " pdb=" CB ALA E 13 " ideal model delta sigma weight residual 110.50 116.34 -5.84 1.50e+00 4.44e-01 1.51e+01 angle pdb=" C ALA B 13 " pdb=" CA ALA B 13 " pdb=" CB ALA B 13 " ideal model delta sigma weight residual 110.50 116.33 -5.83 1.50e+00 4.44e-01 1.51e+01 angle pdb=" C ALA C 13 " pdb=" CA ALA C 13 " pdb=" CB ALA C 13 " ideal model delta sigma weight residual 110.50 116.33 -5.83 1.50e+00 4.44e-01 1.51e+01 angle pdb=" C ALA F 13 " pdb=" CA ALA F 13 " pdb=" CB ALA F 13 " ideal model delta sigma weight residual 110.50 116.32 -5.82 1.50e+00 4.44e-01 1.51e+01 ... (remaining 2535 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 5.60: 760 5.60 - 11.20: 140 11.20 - 16.80: 59 16.80 - 22.40: 61 22.40 - 27.99: 20 Dihedral angle restraints: 1040 sinusoidal: 330 harmonic: 710 Sorted by residual: dihedral pdb=" C ALA J 13 " pdb=" N ALA J 13 " pdb=" CA ALA J 13 " pdb=" CB ALA J 13 " ideal model delta harmonic sigma weight residual -122.60 -132.53 9.93 0 2.50e+00 1.60e-01 1.58e+01 dihedral pdb=" C ALA C 13 " pdb=" N ALA C 13 " pdb=" CA ALA C 13 " pdb=" CB ALA C 13 " ideal model delta harmonic sigma weight residual -122.60 -132.51 9.91 0 2.50e+00 1.60e-01 1.57e+01 dihedral pdb=" C ALA E 13 " pdb=" N ALA E 13 " pdb=" CA ALA E 13 " pdb=" CB ALA E 13 " ideal model delta harmonic sigma weight residual -122.60 -132.49 9.89 0 2.50e+00 1.60e-01 1.57e+01 ... (remaining 1037 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 224 0.045 - 0.090: 36 0.090 - 0.135: 11 0.135 - 0.179: 9 0.179 - 0.224: 20 Chirality restraints: 300 Sorted by residual: chirality pdb=" CA ALA J 13 " pdb=" N ALA J 13 " pdb=" C ALA J 13 " pdb=" CB ALA J 13 " both_signs ideal model delta sigma weight residual False 2.48 2.26 0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CA ALA C 13 " pdb=" N ALA C 13 " pdb=" C ALA C 13 " pdb=" CB ALA C 13 " both_signs ideal model delta sigma weight residual False 2.48 2.26 0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CA ALA G 13 " pdb=" N ALA G 13 " pdb=" C ALA G 13 " pdb=" CB ALA G 13 " both_signs ideal model delta sigma weight residual False 2.48 2.26 0.22 2.00e-01 2.50e+01 1.24e+00 ... (remaining 297 not shown) Planarity restraints: 330 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA F 13 " 0.007 2.00e-02 2.50e+03 1.34e-02 1.79e+00 pdb=" C ALA F 13 " -0.023 2.00e-02 2.50e+03 pdb=" O ALA F 13 " 0.009 2.00e-02 2.50e+03 pdb=" N ASN F 14 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA C 13 " -0.007 2.00e-02 2.50e+03 1.34e-02 1.79e+00 pdb=" C ALA C 13 " 0.023 2.00e-02 2.50e+03 pdb=" O ALA C 13 " -0.009 2.00e-02 2.50e+03 pdb=" N ASN C 14 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA H 13 " -0.007 2.00e-02 2.50e+03 1.32e-02 1.75e+00 pdb=" C ALA H 13 " 0.023 2.00e-02 2.50e+03 pdb=" O ALA H 13 " -0.009 2.00e-02 2.50e+03 pdb=" N ASN H 14 " -0.008 2.00e-02 2.50e+03 ... (remaining 327 not shown) Histogram of nonbonded interaction distances: 2.45 - 2.94: 998 2.94 - 3.43: 2256 3.43 - 3.92: 2945 3.92 - 4.41: 3321 4.41 - 4.90: 6387 Nonbonded interactions: 15907 Sorted by model distance: nonbonded pdb=" OG SER I 19 " pdb=" OD1 ASN I 22 " model vdw 2.451 3.040 nonbonded pdb=" OG SER J 19 " pdb=" OD1 ASN J 22 " model vdw 2.451 3.040 nonbonded pdb=" OG SER G 19 " pdb=" OD1 ASN G 22 " model vdw 2.451 3.040 nonbonded pdb=" OG SER A 19 " pdb=" OD1 ASN A 22 " model vdw 2.451 3.040 nonbonded pdb=" OG SER D 19 " pdb=" OD1 ASN D 22 " model vdw 2.451 3.040 ... (remaining 15902 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 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.030 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 2.410 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:0.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 3.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 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 : 0.011 0.103 1880 Z= 0.868 Angle : 1.155 5.847 2540 Z= 0.676 Chirality : 0.068 0.224 300 Planarity : 0.004 0.013 330 Dihedral : 10.068 27.994 580 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 19.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % 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: -3.84 (0.40), residues: 230 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.92 (0.30), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.003 0.001 TYR F 37 PHE 0.009 0.002 PHE F 23 HIS 0.002 0.001 HIS I 18 Details of bonding type rmsd covalent geometry : bond 0.00801 ( 1870) covalent geometry : angle 1.15497 ( 2540) hydrogen bonds : bond 0.32077 ( 12) hydrogen bonds : angle 10.76712 ( 36) Misc. bond : bond 0.10271 ( 10) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.037 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.0139 time to fit residues: 0.6052 Evaluate side-chains 25 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 12 optimal weight: 6.9990 chunk 13 optimal weight: 9.9990 chunk 1 optimal weight: 20.0000 chunk 8 optimal weight: 7.9990 chunk 16 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 chunk 9 optimal weight: 7.9990 chunk 11 optimal weight: 7.9990 chunk 18 optimal weight: 0.7980 chunk 6 optimal weight: 7.9990 chunk 4 optimal weight: 5.9990 overall best weight: 5.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.100763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.090819 restraints weight = 6511.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.092793 restraints weight = 3531.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.094216 restraints weight = 2224.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.095036 restraints weight = 1569.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.095825 restraints weight = 1256.095| |-----------------------------------------------------------------------------| r_work (final): 0.4078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 1880 Z= 0.166 Angle : 0.832 7.147 2540 Z= 0.417 Chirality : 0.045 0.122 300 Planarity : 0.003 0.009 330 Dihedral : 4.368 13.202 250 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 0.48 % Allowed : 13.81 % Favored : 85.71 % 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: -4.02 (0.37), residues: 230 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.06 (0.29), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.001 TYR J 37 PHE 0.008 0.002 PHE H 23 HIS 0.002 0.001 HIS A 18 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 1870) covalent geometry : angle 0.83182 ( 2540) hydrogen bonds : bond 0.06127 ( 12) hydrogen bonds : angle 6.11229 ( 36) Misc. bond : bond 0.00016 ( 10) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 27 time to evaluate : 0.037 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 27 average time/residue: 0.0145 time to fit residues: 0.5676 Evaluate side-chains 26 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 25 time to evaluate : 0.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 16 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 11 optimal weight: 8.9990 chunk 7 optimal weight: 9.9990 chunk 5 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 14 optimal weight: 30.0000 chunk 18 optimal weight: 0.8980 chunk 4 optimal weight: 30.0000 chunk 12 optimal weight: 7.9990 chunk 0 optimal weight: 40.0000 chunk 10 optimal weight: 0.0570 chunk 16 optimal weight: 4.9990 overall best weight: 3.1904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.104152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.094221 restraints weight = 6438.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.096443 restraints weight = 3285.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.097997 restraints weight = 1995.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.099040 restraints weight = 1364.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.099547 restraints weight = 1025.541| |-----------------------------------------------------------------------------| r_work (final): 0.4138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.3130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.011 1880 Z= 0.120 Angle : 0.737 6.141 2540 Z= 0.366 Chirality : 0.045 0.130 300 Planarity : 0.002 0.007 330 Dihedral : 3.888 10.866 250 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 0.48 % Allowed : 14.76 % Favored : 84.76 % 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: -4.12 (0.36), residues: 230 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.13 (0.28), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.001 TYR A 37 PHE 0.007 0.001 PHE C 15 HIS 0.001 0.001 HIS I 18 Details of bonding type rmsd covalent geometry : bond 0.00231 ( 1870) covalent geometry : angle 0.73704 ( 2540) hydrogen bonds : bond 0.04805 ( 12) hydrogen bonds : angle 5.47620 ( 36) Misc. bond : bond 0.00014 ( 10) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 26 time to evaluate : 0.041 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 26 average time/residue: 0.0163 time to fit residues: 0.6202 Evaluate side-chains 24 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 23 time to evaluate : 0.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 4 optimal weight: 40.0000 chunk 18 optimal weight: 7.9990 chunk 19 optimal weight: 9.9990 chunk 5 optimal weight: 20.0000 chunk 2 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 chunk 8 optimal weight: 50.0000 chunk 14 optimal weight: 30.0000 chunk 13 optimal weight: 0.7980 chunk 1 optimal weight: 9.9990 chunk 11 optimal weight: 9.9990 overall best weight: 7.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 35 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.098792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.088797 restraints weight = 6379.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.090613 restraints weight = 3332.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.092103 restraints weight = 2139.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.093075 restraints weight = 1517.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.093712 restraints weight = 1174.865| |-----------------------------------------------------------------------------| r_work (final): 0.4050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.3376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 1880 Z= 0.205 Angle : 0.791 5.900 2540 Z= 0.411 Chirality : 0.046 0.134 300 Planarity : 0.003 0.009 330 Dihedral : 4.315 11.660 250 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.38 % Allowed : 15.71 % Favored : 81.90 % 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: -4.06 (0.36), residues: 230 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.09 (0.27), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.001 TYR G 37 PHE 0.013 0.002 PHE E 15 HIS 0.002 0.001 HIS J 18 Details of bonding type rmsd covalent geometry : bond 0.00395 ( 1870) covalent geometry : angle 0.79099 ( 2540) hydrogen bonds : bond 0.04225 ( 12) hydrogen bonds : angle 5.43987 ( 36) Misc. bond : bond 0.00096 ( 10) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 16 time to evaluate : 0.074 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 17 average time/residue: 0.0223 time to fit residues: 0.5918 Evaluate side-chains 20 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 16 time to evaluate : 0.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain I residue 16 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 7 optimal weight: 9.9990 chunk 12 optimal weight: 30.0000 chunk 8 optimal weight: 30.0000 chunk 17 optimal weight: 6.9990 chunk 9 optimal weight: 6.9990 chunk 3 optimal weight: 30.0000 chunk 10 optimal weight: 8.9990 chunk 18 optimal weight: 5.9990 chunk 16 optimal weight: 9.9990 chunk 14 optimal weight: 30.0000 chunk 2 optimal weight: 9.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 35 ASN I 35 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.099106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.089491 restraints weight = 6458.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.091427 restraints weight = 3395.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.092700 restraints weight = 2121.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.093731 restraints weight = 1530.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.094361 restraints weight = 1166.099| |-----------------------------------------------------------------------------| r_work (final): 0.4045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.3907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.019 1880 Z= 0.193 Angle : 0.780 8.197 2540 Z= 0.397 Chirality : 0.045 0.138 300 Planarity : 0.002 0.009 330 Dihedral : 4.472 12.862 250 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.86 % Allowed : 17.14 % Favored : 80.00 % 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: -4.11 (0.35), residues: 230 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.13 (0.27), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR J 37 PHE 0.011 0.002 PHE C 15 HIS 0.003 0.001 HIS H 18 Details of bonding type rmsd covalent geometry : bond 0.00373 ( 1870) covalent geometry : angle 0.78028 ( 2540) hydrogen bonds : bond 0.04183 ( 12) hydrogen bonds : angle 5.51420 ( 36) Misc. bond : bond 0.00027 ( 10) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 15 time to evaluate : 0.077 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 18 average time/residue: 0.0261 time to fit residues: 0.7679 Evaluate side-chains 17 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 14 time to evaluate : 0.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain I residue 16 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 12 optimal weight: 0.0000 chunk 5 optimal weight: 20.0000 chunk 15 optimal weight: 9.9990 chunk 9 optimal weight: 20.0000 chunk 19 optimal weight: 20.0000 chunk 2 optimal weight: 40.0000 chunk 3 optimal weight: 7.9990 chunk 6 optimal weight: 20.0000 chunk 0 optimal weight: 30.0000 chunk 1 optimal weight: 5.9990 chunk 11 optimal weight: 10.0000 overall best weight: 6.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 35 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.100324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.090276 restraints weight = 6400.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.092248 restraints weight = 3326.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.093818 restraints weight = 2087.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.094734 restraints weight = 1449.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.095200 restraints weight = 1121.687| |-----------------------------------------------------------------------------| r_work (final): 0.4073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.4233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 1880 Z= 0.173 Angle : 0.760 7.742 2540 Z= 0.387 Chirality : 0.044 0.136 300 Planarity : 0.002 0.009 330 Dihedral : 4.464 13.094 250 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.90 % Allowed : 19.05 % Favored : 79.05 % 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: -4.04 (0.34), residues: 230 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.07 (0.26), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR G 37 PHE 0.011 0.002 PHE C 15 HIS 0.002 0.001 HIS H 18 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 1870) covalent geometry : angle 0.76045 ( 2540) hydrogen bonds : bond 0.03745 ( 12) hydrogen bonds : angle 5.30570 ( 36) Misc. bond : bond 0.00025 ( 10) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 17 time to evaluate : 0.072 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 19 average time/residue: 0.0245 time to fit residues: 0.7173 Evaluate side-chains 16 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 14 time to evaluate : 0.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain I residue 16 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 7 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 chunk 19 optimal weight: 20.0000 chunk 13 optimal weight: 20.0000 chunk 9 optimal weight: 9.9990 chunk 11 optimal weight: 0.9990 chunk 5 optimal weight: 5.9990 chunk 8 optimal weight: 30.0000 chunk 12 optimal weight: 10.0000 chunk 6 optimal weight: 40.0000 chunk 4 optimal weight: 8.9990 overall best weight: 7.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 35 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.100010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.089861 restraints weight = 6331.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.091856 restraints weight = 3339.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.093260 restraints weight = 2087.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.094328 restraints weight = 1491.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.094946 restraints weight = 1138.734| |-----------------------------------------------------------------------------| r_work (final): 0.4070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.4516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.018 1880 Z= 0.180 Angle : 0.765 7.854 2540 Z= 0.390 Chirality : 0.044 0.137 300 Planarity : 0.002 0.009 330 Dihedral : 4.563 13.580 250 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.86 % Allowed : 17.14 % Favored : 80.00 % 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: -3.97 (0.34), residues: 230 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.02 (0.26), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.001 TYR I 37 PHE 0.011 0.002 PHE C 15 HIS 0.003 0.001 HIS H 18 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 1870) covalent geometry : angle 0.76481 ( 2540) hydrogen bonds : bond 0.03843 ( 12) hydrogen bonds : angle 5.32539 ( 36) Misc. bond : bond 0.00027 ( 10) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 17 time to evaluate : 0.074 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 19 average time/residue: 0.0244 time to fit residues: 0.7176 Evaluate side-chains 18 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 15 time to evaluate : 0.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain H residue 16 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 10 optimal weight: 5.9990 chunk 11 optimal weight: 6.9990 chunk 19 optimal weight: 10.0000 chunk 0 optimal weight: 40.0000 chunk 13 optimal weight: 10.0000 chunk 12 optimal weight: 30.0000 chunk 18 optimal weight: 4.9990 chunk 15 optimal weight: 9.9990 chunk 4 optimal weight: 8.9990 chunk 6 optimal weight: 8.9990 chunk 8 optimal weight: 6.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.100643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.090471 restraints weight = 5980.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.092550 restraints weight = 3000.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.093972 restraints weight = 1842.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.094987 restraints weight = 1308.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.095511 restraints weight = 1012.975| |-----------------------------------------------------------------------------| r_work (final): 0.4140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.4675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 1880 Z= 0.172 Angle : 0.768 7.960 2540 Z= 0.389 Chirality : 0.044 0.135 300 Planarity : 0.002 0.013 330 Dihedral : 4.512 13.598 250 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 0.95 % Allowed : 18.10 % Favored : 80.95 % 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: -3.92 (0.34), residues: 230 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.98 (0.26), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR I 37 PHE 0.010 0.002 PHE C 15 HIS 0.002 0.001 HIS J 18 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 1870) covalent geometry : angle 0.76790 ( 2540) hydrogen bonds : bond 0.03730 ( 12) hydrogen bonds : angle 5.30600 ( 36) Misc. bond : bond 0.00022 ( 10) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 16 time to evaluate : 0.053 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 16 average time/residue: 0.0256 time to fit residues: 0.6464 Evaluate side-chains 15 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 13 time to evaluate : 0.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain H residue 16 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 0 optimal weight: 40.0000 chunk 18 optimal weight: 40.0000 chunk 4 optimal weight: 30.0000 chunk 8 optimal weight: 10.0000 chunk 9 optimal weight: 9.9990 chunk 14 optimal weight: 0.7980 chunk 19 optimal weight: 7.9990 chunk 15 optimal weight: 8.9990 chunk 3 optimal weight: 20.0000 chunk 5 optimal weight: 5.9990 chunk 1 optimal weight: 9.9990 overall best weight: 6.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.100515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.090257 restraints weight = 6048.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.092336 restraints weight = 3023.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.093818 restraints weight = 1855.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.094811 restraints weight = 1304.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.095412 restraints weight = 1013.871| |-----------------------------------------------------------------------------| r_work (final): 0.4143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.4868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 1880 Z= 0.172 Angle : 0.774 8.044 2540 Z= 0.390 Chirality : 0.044 0.134 300 Planarity : 0.002 0.012 330 Dihedral : 4.549 13.428 250 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 0.95 % Allowed : 18.57 % Favored : 80.48 % 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: -3.89 (0.34), residues: 230 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.96 (0.26), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR D 37 PHE 0.010 0.002 PHE E 15 HIS 0.002 0.001 HIS F 18 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 1870) covalent geometry : angle 0.77436 ( 2540) hydrogen bonds : bond 0.03744 ( 12) hydrogen bonds : angle 5.18625 ( 36) Misc. bond : bond 0.00023 ( 10) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 15 time to evaluate : 0.071 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 15 average time/residue: 0.0254 time to fit residues: 0.5973 Evaluate side-chains 17 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 15 time to evaluate : 0.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain H residue 16 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 2 optimal weight: 40.0000 chunk 15 optimal weight: 30.0000 chunk 9 optimal weight: 30.0000 chunk 5 optimal weight: 7.9990 chunk 10 optimal weight: 6.9990 chunk 19 optimal weight: 20.0000 chunk 6 optimal weight: 40.0000 chunk 7 optimal weight: 3.9990 chunk 18 optimal weight: 7.9990 chunk 12 optimal weight: 30.0000 chunk 4 optimal weight: 8.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.098141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.088530 restraints weight = 6169.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.090617 restraints weight = 2990.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.092014 restraints weight = 1792.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.092917 restraints weight = 1250.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.093552 restraints weight = 972.037| |-----------------------------------------------------------------------------| r_work (final): 0.4137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.4992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 1880 Z= 0.180 Angle : 0.783 8.220 2540 Z= 0.395 Chirality : 0.044 0.134 300 Planarity : 0.002 0.011 330 Dihedral : 4.607 13.476 250 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 0.95 % Allowed : 18.57 % Favored : 80.48 % 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: -3.88 (0.34), residues: 230 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.95 (0.26), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.001 TYR D 37 PHE 0.009 0.002 PHE C 15 HIS 0.002 0.001 HIS F 18 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 1870) covalent geometry : angle 0.78314 ( 2540) hydrogen bonds : bond 0.03731 ( 12) hydrogen bonds : angle 5.11374 ( 36) Misc. bond : bond 0.00025 ( 10) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 15 time to evaluate : 0.070 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 15 average time/residue: 0.0266 time to fit residues: 0.6175 Evaluate side-chains 17 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 15 time to evaluate : 0.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain H residue 16 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 4 optimal weight: 30.0000 chunk 3 optimal weight: 20.0000 chunk 17 optimal weight: 6.9990 chunk 13 optimal weight: 8.9990 chunk 0 optimal weight: 40.0000 chunk 12 optimal weight: 8.9990 chunk 9 optimal weight: 7.9990 chunk 16 optimal weight: 0.7980 chunk 2 optimal weight: 5.9990 chunk 18 optimal weight: 30.0000 chunk 7 optimal weight: 7.9990 overall best weight: 5.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.098581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.088704 restraints weight = 6189.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.090848 restraints weight = 3003.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.092245 restraints weight = 1801.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.093188 restraints weight = 1273.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.093853 restraints weight = 981.144| |-----------------------------------------------------------------------------| r_work (final): 0.4150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.5117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 1880 Z= 0.155 Angle : 0.758 8.122 2540 Z= 0.379 Chirality : 0.043 0.133 300 Planarity : 0.002 0.010 330 Dihedral : 4.515 13.678 250 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.43 % Allowed : 18.10 % Favored : 80.48 % 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: -3.87 (0.33), residues: 230 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.94 (0.25), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.001 TYR D 37 PHE 0.009 0.002 PHE E 15 HIS 0.002 0.001 HIS H 18 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 1870) covalent geometry : angle 0.75844 ( 2540) hydrogen bonds : bond 0.03672 ( 12) hydrogen bonds : angle 5.03850 ( 36) Misc. bond : bond 0.00019 ( 10) =============================================================================== Job complete usr+sys time: 407.91 seconds wall clock time: 7 minutes 55.42 seconds (475.42 seconds total)