Starting phenix.real_space_refine on Tue Aug 4 11:45:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w06_65494/08_2026/9w06_65494.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w06_65494/08_2026/9w06_65494.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9w06_65494/08_2026/9w06_65494.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w06_65494/08_2026/9w06_65494.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9w06_65494/08_2026/9w06_65494.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w06_65494/08_2026/9w06_65494.map" } resolution = 3.6 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= 0.001 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 1035 2.51 5 N 303 2.21 5 O 342 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 1680 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 450 Classifications: {'peptide': 66} Link IDs: {'TRANS': 65} Chain: "s" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 60 Classifications: {'peptide': 12} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'TRANS': 11} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'UNK:plan-1': 12} Unresolved non-hydrogen planarities: 12 Chain: "t" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 50 Classifications: {'peptide': 10} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'TRANS': 9} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'UNK:plan-1': 10} Unresolved non-hydrogen planarities: 10 Restraints were copied for chains: C, D, u, w, v, x Time building chain proxies: 0.58, per 1000 atoms: 0.35 Number of scatterers: 1680 At special positions: 0 Unit cell: (76.36, 82.17, 29.05, 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 342 8.00 N 303 7.00 C 1035 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=0, symmetry=0 Time building additional restraints: 0.14 Conformation dependent library (CDL) restraints added in 58.1 milliseconds 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 462 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 8 sheets defined 0.0% alpha, 27.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.07 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'B' and resid 44 through 46 removed outlier: 6.216A pdb=" N LYS B 45 " --> pdb=" O GLU D 46 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 49 through 52 removed outlier: 6.903A pdb=" N HIS D 50 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N HIS C 50 " --> pdb=" O GLY D 51 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 55 through 57 removed outlier: 6.278A pdb=" N ALA B 56 " --> pdb=" O GLU D 57 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 63 through 65 removed outlier: 6.585A pdb=" N THR C 64 " --> pdb=" O ASN D 65 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 69 through 71 removed outlier: 6.336A pdb=" N ALA C 69 " --> pdb=" O VAL D 70 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 76 through 81 removed outlier: 6.440A pdb=" N ALA B 76 " --> pdb=" O VAL D 77 " (cutoff:3.500A) removed outlier: 8.358A pdb=" N GLN D 79 " --> pdb=" O ALA B 76 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ALA B 78 " --> pdb=" O GLN D 79 " (cutoff:3.500A) removed outlier: 8.657A pdb=" N THR D 81 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N LYS B 80 " --> pdb=" O THR D 81 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 88 through 89 removed outlier: 6.862A pdb=" N ILE C 88 " --> pdb=" O ALA D 89 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 95 through 96 removed outlier: 6.314A pdb=" N VAL B 95 " --> pdb=" O LYS D 96 " (cutoff:3.500A) 17 hydrogen bonds defined for protein. 51 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: 0.18 Time building geometry restraints manager: 0.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.28: 309 1.28 - 1.35: 270 1.35 - 1.41: 30 1.41 - 1.48: 297 1.48 - 1.54: 771 Bond restraints: 1677 Sorted by residual: bond pdb=" C VAL C 66 " pdb=" N GLY C 67 " ideal model delta sigma weight residual 1.335 1.321 0.013 7.50e-03 1.78e+04 3.18e+00 bond pdb=" C VAL D 66 " pdb=" N GLY D 67 " ideal model delta sigma weight residual 1.335 1.322 0.013 7.50e-03 1.78e+04 3.02e+00 bond pdb=" C VAL B 66 " pdb=" N GLY B 67 " ideal model delta sigma weight residual 1.335 1.322 0.013 7.50e-03 1.78e+04 2.87e+00 bond pdb=" C GLY B 67 " pdb=" O GLY B 67 " ideal model delta sigma weight residual 1.236 1.229 0.007 5.30e-03 3.56e+04 1.93e+00 bond pdb=" C GLY D 93 " pdb=" N PHE D 94 " ideal model delta sigma weight residual 1.331 1.313 0.018 1.30e-02 5.92e+03 1.90e+00 ... (remaining 1672 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.86: 1715 0.86 - 1.71: 413 1.71 - 2.57: 96 2.57 - 3.42: 34 3.42 - 4.28: 10 Bond angle restraints: 2268 Sorted by residual: angle pdb=" C VAL B 66 " pdb=" N GLY B 67 " pdb=" CA GLY B 67 " ideal model delta sigma weight residual 122.63 120.31 2.32 1.03e+00 9.43e-01 5.09e+00 angle pdb=" C VAL D 66 " pdb=" N GLY D 67 " pdb=" CA GLY D 67 " ideal model delta sigma weight residual 122.63 120.36 2.27 1.03e+00 9.43e-01 4.88e+00 angle pdb=" C VAL C 66 " pdb=" N GLY C 67 " pdb=" CA GLY C 67 " ideal model delta sigma weight residual 122.63 120.38 2.25 1.03e+00 9.43e-01 4.78e+00 angle pdb=" N GLU D 35 " pdb=" CA GLU D 35 " pdb=" C GLU D 35 " ideal model delta sigma weight residual 108.46 111.20 -2.74 1.51e+00 4.39e-01 3.29e+00 angle pdb=" N GLU B 35 " pdb=" CA GLU B 35 " pdb=" C GLU B 35 " ideal model delta sigma weight residual 108.46 111.18 -2.72 1.51e+00 4.39e-01 3.23e+00 ... (remaining 2263 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 8.99: 840 8.99 - 17.97: 102 17.97 - 26.96: 36 26.96 - 35.94: 6 35.94 - 44.92: 3 Dihedral angle restraints: 987 sinusoidal: 270 harmonic: 717 Sorted by residual: dihedral pdb=" CA ALA B 89 " pdb=" C ALA B 89 " pdb=" N ALA B 90 " pdb=" CA ALA B 90 " ideal model delta harmonic sigma weight residual 180.00 -164.85 -15.15 0 5.00e+00 4.00e-02 9.18e+00 dihedral pdb=" CA ALA D 89 " pdb=" C ALA D 89 " pdb=" N ALA D 90 " pdb=" CA ALA D 90 " ideal model delta harmonic sigma weight residual -180.00 -164.85 -15.15 0 5.00e+00 4.00e-02 9.18e+00 dihedral pdb=" CA ALA C 89 " pdb=" C ALA C 89 " pdb=" N ALA C 90 " pdb=" CA ALA C 90 " ideal model delta harmonic sigma weight residual -180.00 -164.89 -15.11 0 5.00e+00 4.00e-02 9.14e+00 ... (remaining 984 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 126 0.025 - 0.050: 98 0.050 - 0.075: 40 0.075 - 0.100: 20 0.100 - 0.125: 22 Chirality restraints: 306 Sorted by residual: chirality pdb=" CB VAL D 82 " pdb=" CA VAL D 82 " pdb=" CG1 VAL D 82 " pdb=" CG2 VAL D 82 " both_signs ideal model delta sigma weight residual False -2.63 -2.50 -0.13 2.00e-01 2.50e+01 3.93e-01 chirality pdb=" CB VAL B 82 " pdb=" CA VAL B 82 " pdb=" CG1 VAL B 82 " pdb=" CG2 VAL B 82 " both_signs ideal model delta sigma weight residual False -2.63 -2.51 -0.12 2.00e-01 2.50e+01 3.83e-01 chirality pdb=" CB VAL C 82 " pdb=" CA VAL C 82 " pdb=" CG1 VAL C 82 " pdb=" CG2 VAL C 82 " both_signs ideal model delta sigma weight residual False -2.63 -2.51 -0.12 2.00e-01 2.50e+01 3.66e-01 ... (remaining 303 not shown) Planarity restraints: 288 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 94 " 0.012 2.00e-02 2.50e+03 9.04e-03 1.43e+00 pdb=" CG PHE B 94 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 PHE B 94 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE B 94 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE B 94 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 94 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE B 94 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 94 " 0.012 2.00e-02 2.50e+03 8.87e-03 1.38e+00 pdb=" CG PHE C 94 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 PHE C 94 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 PHE C 94 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE C 94 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE C 94 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE C 94 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 94 " 0.012 2.00e-02 2.50e+03 8.84e-03 1.37e+00 pdb=" CG PHE D 94 " -0.019 2.00e-02 2.50e+03 pdb=" CD1 PHE D 94 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 PHE D 94 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE D 94 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE D 94 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE D 94 " 0.004 2.00e-02 2.50e+03 ... (remaining 285 not shown) Histogram of nonbonded interaction distances: 2.58 - 3.05: 1092 3.05 - 3.51: 1343 3.51 - 3.97: 2050 3.97 - 4.44: 2424 4.44 - 4.90: 5147 Nonbonded interactions: 12056 Sorted by model distance: nonbonded pdb=" OE1 GLU B 39 " pdb=" OG SER B 42 " model vdw 2.583 3.040 nonbonded pdb=" OE1 GLU D 39 " pdb=" OG SER D 42 " model vdw 2.584 3.040 nonbonded pdb=" OE1 GLU C 39 " pdb=" OG SER C 42 " model vdw 2.584 3.040 nonbonded pdb=" N UNK w 103 " pdb=" O UNK w 103 " model vdw 2.586 2.496 nonbonded pdb=" N UNK u 103 " pdb=" O UNK u 103 " model vdw 2.587 2.496 ... (remaining 12051 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: 0.01 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 's' selection = chain 'u' selection = chain 'w' } ncs_group { reference = chain 't' selection = chain 'v' selection = chain 'x' } 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: 1.710 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: 0.050 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 3.630 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 6.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 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 : 0.008 0.033 1677 Z= 0.422 Angle : 0.877 4.275 2268 Z= 0.485 Chirality : 0.049 0.125 306 Planarity : 0.003 0.009 288 Dihedral : 10.057 44.922 525 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.06 % Favored : 85.94 % Rotamer: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % 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: -5.26 (0.38), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.00 (0.29), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.020 0.006 PHE B 94 HIS 0.002 0.001 HIS C 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00847 / 0.42 ( 1677) covalent geometry : angle 0.87713 / 0.49 ( 2268) hydrogen bonds : bond 0.19163 / 8.71 ( 17) hydrogen bonds : angle 8.93317 / 5.64 ( 51) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 12 residues out of total 138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.058 Fit side-chains REVERT: B 57 GLU cc_start: 0.7786 (mt-10) cc_final: 0.7547 (tt0) REVERT: B 80 LYS cc_start: 0.8118 (tttt) cc_final: 0.7899 (tttp) REVERT: C 58 LYS cc_start: 0.9018 (mmmm) cc_final: 0.8796 (mmtt) REVERT: D 80 LYS cc_start: 0.8228 (tttt) cc_final: 0.7933 (tttm) outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.1581 time to fit residues: 2.0858 Evaluate side-chains 10 residues out of total 138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 12 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 1 optimal weight: 7.9990 chunk 8 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 15 optimal weight: 10.0000 chunk 9 optimal weight: 6.9990 chunk 11 optimal weight: 6.9990 chunk 18 optimal weight: 5.9990 chunk 6 optimal weight: 9.9990 chunk 4 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 79 GLN C 79 GLN D 79 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.123231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.104927 restraints weight = 2541.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.107355 restraints weight = 1426.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.109037 restraints weight = 995.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.110058 restraints weight = 779.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.110898 restraints weight = 660.611| |-----------------------------------------------------------------------------| r_work (final): 0.3836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.0848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.026 1677 Z= 0.273 Angle : 0.677 4.964 2268 Z= 0.354 Chirality : 0.046 0.120 306 Planarity : 0.002 0.008 288 Dihedral : 4.825 14.678 255 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.46 % Favored : 88.54 % Rotamer: Outliers : 3.62 % Allowed : 12.32 % Favored : 84.06 % 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: -4.61 (0.42), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.51 (0.32), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.018 0.005 PHE B 94 HIS 0.002 0.001 HIS D 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00580 / 0.27 ( 1677) covalent geometry : angle 0.67700 / 0.35 ( 2268) hydrogen bonds : bond 0.03059 / 1.50 ( 17) hydrogen bonds : angle 6.25240 / 3.85 ( 51) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 13 time to evaluate : 0.053 Fit side-chains REVERT: B 80 LYS cc_start: 0.8310 (tttt) cc_final: 0.8084 (tttp) REVERT: C 58 LYS cc_start: 0.9015 (mmmm) cc_final: 0.8800 (mmtt) outliers start: 5 outliers final: 5 residues processed: 18 average time/residue: 0.1084 time to fit residues: 2.1774 Evaluate side-chains 15 residues out of total 138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 10 time to evaluate : 0.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 88 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 18 optimal weight: 10.0000 chunk 2 optimal weight: 0.8980 chunk 17 optimal weight: 8.9990 chunk 5 optimal weight: 6.9990 chunk 8 optimal weight: 7.9990 chunk 6 optimal weight: 10.0000 chunk 10 optimal weight: 0.9980 chunk 22 optimal weight: 8.9990 chunk 16 optimal weight: 2.9990 chunk 14 optimal weight: 6.9990 chunk 4 optimal weight: 6.9990 overall best weight: 3.7786 ------------------------------------------------------------------------------- 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 = 0.3934 r_free = 0.3934 target = 0.123658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.105282 restraints weight = 2548.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.107794 restraints weight = 1416.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.109477 restraints weight = 975.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.110344 restraints weight = 761.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.111256 restraints weight = 656.767| |-----------------------------------------------------------------------------| r_work (final): 0.3851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.1188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 1677 Z= 0.238 Angle : 0.605 4.314 2268 Z= 0.321 Chirality : 0.045 0.116 306 Planarity : 0.002 0.007 288 Dihedral : 4.479 15.039 255 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.94 % Favored : 89.06 % Rotamer: Outliers : 6.52 % Allowed : 12.32 % Favored : 81.16 % 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: -4.18 (0.46), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.18 (0.35), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.015 0.004 PHE B 94 HIS 0.002 0.001 HIS D 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00503 / 0.24 ( 1677) covalent geometry : angle 0.60467 / 0.32 ( 2268) hydrogen bonds : bond 0.02735 / 1.33 ( 17) hydrogen bonds : angle 5.69633 / 3.51 ( 51) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 11 time to evaluate : 0.069 Fit side-chains REVERT: C 58 LYS cc_start: 0.9028 (mmmm) cc_final: 0.8822 (mmtt) outliers start: 9 outliers final: 6 residues processed: 20 average time/residue: 0.0775 time to fit residues: 1.7868 Evaluate side-chains 15 residues out of total 138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 9 time to evaluate : 0.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 82 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 19 optimal weight: 10.0000 chunk 3 optimal weight: 0.9980 chunk 18 optimal weight: 9.9990 chunk 7 optimal weight: 9.9990 chunk 0 optimal weight: 7.9990 chunk 1 optimal weight: 7.9990 chunk 23 optimal weight: 9.9990 chunk 9 optimal weight: 8.9990 chunk 2 optimal weight: 2.9990 chunk 12 optimal weight: 10.0000 chunk 22 optimal weight: 10.0000 overall best weight: 5.7988 ------------------------------------------------------------------------------- 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 = 0.3906 r_free = 0.3906 target = 0.121250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.102443 restraints weight = 2432.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.105191 restraints weight = 1217.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.106960 restraints weight = 792.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.108006 restraints weight = 600.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.108622 restraints weight = 503.473| |-----------------------------------------------------------------------------| r_work (final): 0.3806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.1382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.035 1677 Z= 0.360 Angle : 0.774 5.435 2268 Z= 0.403 Chirality : 0.047 0.118 306 Planarity : 0.003 0.009 288 Dihedral : 4.955 17.329 255 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.10 % Favored : 84.90 % Rotamer: Outliers : 7.97 % Allowed : 9.42 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.39 (0.45), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.34 (0.35), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.020 0.006 PHE B 94 HIS 0.003 0.002 HIS C 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00758 / 0.36 ( 1677) covalent geometry : angle 0.77387 / 0.40 ( 2268) hydrogen bonds : bond 0.02753 / 1.38 ( 17) hydrogen bonds : angle 5.77909 / 3.56 ( 51) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 16 time to evaluate : 0.060 Fit side-chains outliers start: 11 outliers final: 10 residues processed: 26 average time/residue: 0.0665 time to fit residues: 1.9924 Evaluate side-chains 22 residues out of total 138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 12 time to evaluate : 0.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 88 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 2 optimal weight: 0.4980 chunk 6 optimal weight: 9.9990 chunk 10 optimal weight: 6.9990 chunk 23 optimal weight: 9.9990 chunk 14 optimal weight: 9.9990 chunk 17 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 3 optimal weight: 0.8980 chunk 5 optimal weight: 9.9990 chunk 18 optimal weight: 0.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- 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 = 0.3995 r_free = 0.3995 target = 0.126661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.108502 restraints weight = 2480.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.111190 restraints weight = 1313.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.112995 restraints weight = 868.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.114246 restraints weight = 660.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.114955 restraints weight = 542.003| |-----------------------------------------------------------------------------| r_work (final): 0.3903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 1677 Z= 0.129 Angle : 0.491 3.310 2268 Z= 0.265 Chirality : 0.044 0.118 306 Planarity : 0.001 0.007 288 Dihedral : 3.999 13.708 255 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 5.07 % Allowed : 14.49 % Favored : 80.43 % 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: -3.83 (0.48), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.91 (0.36), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.008 0.002 PHE B 94 HIS 0.001 0.001 HIS D 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.13 ( 1677) covalent geometry : angle 0.49108 / 0.26 ( 2268) hydrogen bonds : bond 0.01776 / 0.86 ( 17) hydrogen bonds : angle 5.34954 / 3.33 ( 51) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 9 time to evaluate : 0.059 Fit side-chains outliers start: 7 outliers final: 7 residues processed: 15 average time/residue: 0.0672 time to fit residues: 1.1998 Evaluate side-chains 16 residues out of total 138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 9 time to evaluate : 0.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 88 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 16 optimal weight: 7.9990 chunk 15 optimal weight: 10.0000 chunk 5 optimal weight: 4.9990 chunk 4 optimal weight: 0.8980 chunk 0 optimal weight: 0.7980 chunk 14 optimal weight: 10.0000 chunk 2 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 20 optimal weight: 5.9990 chunk 22 optimal weight: 8.9990 chunk 10 optimal weight: 9.9990 overall best weight: 4.1386 ------------------------------------------------------------------------------- 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 = 0.3956 r_free = 0.3956 target = 0.124373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.105589 restraints weight = 2369.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.108490 restraints weight = 1127.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.110375 restraints weight = 703.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.111422 restraints weight = 519.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.112285 restraints weight = 431.427| |-----------------------------------------------------------------------------| r_work (final): 0.3856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 1677 Z= 0.258 Angle : 0.626 4.447 2268 Z= 0.329 Chirality : 0.045 0.113 306 Planarity : 0.002 0.007 288 Dihedral : 4.352 16.049 255 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.58 % Favored : 85.42 % Rotamer: Outliers : 8.70 % Allowed : 10.87 % Favored : 80.43 % 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: -3.99 (0.48), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.03 (0.37), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.015 0.004 PHE B 94 HIS 0.002 0.001 HIS C 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00547 / 0.26 ( 1677) covalent geometry : angle 0.62640 / 0.33 ( 2268) hydrogen bonds : bond 0.02205 / 1.11 ( 17) hydrogen bonds : angle 5.34908 / 3.33 ( 51) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 11 time to evaluate : 0.062 Fit side-chains outliers start: 12 outliers final: 11 residues processed: 22 average time/residue: 0.0474 time to fit residues: 1.2758 Evaluate side-chains 21 residues out of total 138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 10 time to evaluate : 0.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain D residue 92 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 8 optimal weight: 7.9990 chunk 23 optimal weight: 10.0000 chunk 12 optimal weight: 4.9990 chunk 10 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 chunk 9 optimal weight: 8.9990 chunk 20 optimal weight: 9.9990 chunk 13 optimal weight: 0.9990 chunk 6 optimal weight: 10.0000 chunk 0 optimal weight: 7.9990 chunk 4 optimal weight: 8.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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 = 0.3924 r_free = 0.3924 target = 0.122068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.103822 restraints weight = 2387.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.106426 restraints weight = 1194.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.108195 restraints weight = 772.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.109249 restraints weight = 577.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.109693 restraints weight = 479.043| |-----------------------------------------------------------------------------| r_work (final): 0.3825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 1677 Z= 0.296 Angle : 0.687 4.802 2268 Z= 0.359 Chirality : 0.046 0.115 306 Planarity : 0.003 0.007 288 Dihedral : 4.576 17.097 255 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.06 % Favored : 85.94 % Rotamer: Outliers : 10.14 % Allowed : 9.42 % Favored : 80.43 % 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 (0.48), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.08 (0.36), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.016 0.005 PHE B 94 HIS 0.002 0.001 HIS C 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00628 / 0.30 ( 1677) covalent geometry : angle 0.68738 / 0.36 ( 2268) hydrogen bonds : bond 0.02378 / 1.22 ( 17) hydrogen bonds : angle 5.45247 / 3.38 ( 51) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 15 time to evaluate : 0.072 Fit side-chains outliers start: 14 outliers final: 13 residues processed: 25 average time/residue: 0.0611 time to fit residues: 1.7864 Evaluate side-chains 27 residues out of total 138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 14 time to evaluate : 0.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain D residue 92 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 18 optimal weight: 9.9990 chunk 13 optimal weight: 10.0000 chunk 9 optimal weight: 7.9990 chunk 6 optimal weight: 9.9990 chunk 17 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 8 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 19 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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 = 0.3982 r_free = 0.3982 target = 0.127045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.108428 restraints weight = 2315.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.111377 restraints weight = 1071.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.113174 restraints weight = 662.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.114594 restraints weight = 489.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.115377 restraints weight = 389.094| |-----------------------------------------------------------------------------| r_work (final): 0.3901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 1677 Z= 0.155 Angle : 0.497 3.339 2268 Z= 0.266 Chirality : 0.044 0.119 306 Planarity : 0.001 0.005 288 Dihedral : 3.926 14.521 255 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.90 % Favored : 90.10 % Rotamer: Outliers : 6.52 % Allowed : 13.04 % Favored : 80.43 % 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: -3.75 (0.49), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.85 (0.37), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.008 0.002 PHE B 94 HIS 0.001 0.001 HIS D 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 ( 1677) covalent geometry : angle 0.49727 / 0.27 ( 2268) hydrogen bonds : bond 0.01736 / 0.88 ( 17) hydrogen bonds : angle 5.19037 / 3.26 ( 51) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 12 time to evaluate : 0.059 Fit side-chains outliers start: 9 outliers final: 9 residues processed: 20 average time/residue: 0.0680 time to fit residues: 1.5834 Evaluate side-chains 21 residues out of total 138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 12 time to evaluate : 0.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 88 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 13 optimal weight: 10.0000 chunk 1 optimal weight: 9.9990 chunk 9 optimal weight: 10.0000 chunk 0 optimal weight: 8.9990 chunk 2 optimal weight: 8.9990 chunk 19 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 23 optimal weight: 10.0000 chunk 3 optimal weight: 1.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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 = 0.4012 r_free = 0.4012 target = 0.129202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.110756 restraints weight = 2308.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.113740 restraints weight = 1075.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.115699 restraints weight = 663.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.116849 restraints weight = 481.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.117774 restraints weight = 393.644| |-----------------------------------------------------------------------------| r_work (final): 0.3932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 1677 Z= 0.110 Angle : 0.417 2.378 2268 Z= 0.228 Chirality : 0.044 0.118 306 Planarity : 0.001 0.005 288 Dihedral : 3.565 12.859 255 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 6.52 % Allowed : 14.49 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.54 (0.50), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.69 (0.38), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.006 0.002 PHE D 94 HIS 0.001 0.001 HIS D 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.11 ( 1677) covalent geometry : angle 0.41724 / 0.23 ( 2268) hydrogen bonds : bond 0.01473 / 0.74 ( 17) hydrogen bonds : angle 4.93338 / 3.12 ( 51) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 13 time to evaluate : 0.055 Fit side-chains outliers start: 9 outliers final: 9 residues processed: 21 average time/residue: 0.0639 time to fit residues: 1.5693 Evaluate side-chains 20 residues out of total 138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 11 time to evaluate : 0.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 88 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 7 optimal weight: 9.9990 chunk 5 optimal weight: 6.9990 chunk 8 optimal weight: 10.0000 chunk 2 optimal weight: 9.9990 chunk 10 optimal weight: 9.9990 chunk 18 optimal weight: 1.9990 chunk 20 optimal weight: 8.9990 chunk 3 optimal weight: 5.9990 chunk 22 optimal weight: 10.0000 chunk 17 optimal weight: 9.9990 chunk 6 optimal weight: 7.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- 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 = 0.3914 r_free = 0.3914 target = 0.120730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.102277 restraints weight = 2421.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.104892 restraints weight = 1232.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.106478 restraints weight = 807.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.107678 restraints weight = 615.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.108354 restraints weight = 508.765| |-----------------------------------------------------------------------------| r_work (final): 0.3809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.039 1677 Z= 0.387 Angle : 0.787 5.314 2268 Z= 0.408 Chirality : 0.048 0.128 306 Planarity : 0.003 0.009 288 Dihedral : 4.686 18.263 255 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.75 % Favored : 81.25 % Rotamer: Outliers : 7.25 % Allowed : 14.49 % Favored : 78.26 % 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: -3.99 (0.49), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.04 (0.37), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.020 0.006 PHE B 94 HIS 0.004 0.002 HIS C 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00823 / 0.39 ( 1677) covalent geometry : angle 0.78687 / 0.41 ( 2268) hydrogen bonds : bond 0.02656 / 1.36 ( 17) hydrogen bonds : angle 5.36195 / 3.35 ( 51) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 14 time to evaluate : 0.059 Fit side-chains outliers start: 10 outliers final: 10 residues processed: 24 average time/residue: 0.0618 time to fit residues: 1.7324 Evaluate side-chains 24 residues out of total 138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 14 time to evaluate : 0.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 88 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 16 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 13 optimal weight: 0.0980 chunk 1 optimal weight: 2.9990 chunk 5 optimal weight: 9.9990 chunk 8 optimal weight: 0.6980 chunk 15 optimal weight: 10.0000 chunk 9 optimal weight: 5.9990 chunk 0 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 chunk 7 optimal weight: 10.0000 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.130000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.112425 restraints weight = 2396.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.115130 restraints weight = 1259.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.116599 restraints weight = 828.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.118035 restraints weight = 641.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.118830 restraints weight = 519.115| |-----------------------------------------------------------------------------| r_work (final): 0.3934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 1677 Z= 0.080 Angle : 0.415 2.052 2268 Z= 0.228 Chirality : 0.045 0.120 306 Planarity : 0.001 0.005 288 Dihedral : 3.585 12.839 255 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.17 % Allowed : 20.29 % Favored : 77.54 % 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: -3.60 (0.50), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.74 (0.38), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.003 0.001 PHE C 94 HIS 0.001 0.001 HIS D 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00157 / 0.08 ( 1677) covalent geometry : angle 0.41539 / 0.23 ( 2268) hydrogen bonds : bond 0.01269 / 0.64 ( 17) hydrogen bonds : angle 5.03229 / 3.20 ( 51) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 526.69 seconds wall clock time: 10 minutes 1.19 seconds (601.19 seconds total)