Starting phenix.real_space_refine on Wed Jun 3 09:34:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9obk_70294/06_2026/9obk_70294.cif Found real_map, /net/cci-nas-00/data/ceres_data/9obk_70294/06_2026/9obk_70294.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9obk_70294/06_2026/9obk_70294.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9obk_70294/06_2026/9obk_70294.map" model { file = "/net/cci-nas-00/data/ceres_data/9obk_70294/06_2026/9obk_70294.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9obk_70294/06_2026/9obk_70294.cif" } resolution = 3.01 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= 0.002 sd= 0.009 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: 4 Type Number sf(0) Gaussians S 10 5.16 5 C 1330 2.51 5 N 340 2.21 5 O 360 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-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2040 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 204 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'SME:plan-1': 1} Unresolved non-hydrogen planarities: 1 Restraints were copied for chains: B, C, D, E, F, G, H, I, J Time building chain proxies: 0.52, per 1000 atoms: 0.25 Number of scatterers: 2040 At special positions: 0 Unit cell: (53.535, 81.755, 40.67, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 10 16.00 O 360 8.00 N 340 7.00 C 1330 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: 0.22 Conformation dependent library (CDL) restraints added in 73.9 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 6 sheets defined 0.0% alpha, 32.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'H' and resid 16 through 19 removed outlier: 6.499A pdb=" N LYS A 16 " --> pdb=" O LEU E 17 " (cutoff:3.500A) removed outlier: 8.305A pdb=" N PHE E 19 " --> pdb=" O LYS A 16 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N VAL A 18 " --> pdb=" O PHE E 19 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N LYS E 16 " --> pdb=" O LEU I 17 " (cutoff:3.500A) removed outlier: 8.315A pdb=" N PHE I 19 " --> pdb=" O LYS E 16 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL E 18 " --> pdb=" O PHE I 19 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 31 through 36 removed outlier: 6.271A pdb=" N ILE D 31 " --> pdb=" O ILE H 32 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N LEU H 34 " --> pdb=" O ILE D 31 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N GLY D 33 " --> pdb=" O LEU H 34 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N VAL H 36 " --> pdb=" O GLY D 33 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N SME D 35 " --> pdb=" O VAL H 36 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ILE A 31 " --> pdb=" O ILE D 32 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N LEU D 34 " --> pdb=" O ILE A 31 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N GLY A 33 " --> pdb=" O LEU D 34 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N VAL D 36 " --> pdb=" O GLY A 33 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N SME A 35 " --> pdb=" O VAL D 36 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 39 through 40 removed outlier: 6.483A pdb=" N VAL A 39 " --> pdb=" O VAL E 40 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N VAL E 39 " --> pdb=" O VAL I 40 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 16 through 19 removed outlier: 6.503A pdb=" N LYS C 16 " --> pdb=" O LEU G 17 " (cutoff:3.500A) removed outlier: 8.315A pdb=" N PHE G 19 " --> pdb=" O LYS C 16 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N VAL C 18 " --> pdb=" O PHE G 19 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LYS B 16 " --> pdb=" O LEU C 17 " (cutoff:3.500A) removed outlier: 8.315A pdb=" N PHE C 19 " --> pdb=" O LYS B 16 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N VAL B 18 " --> pdb=" O PHE C 19 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 31 through 36 removed outlier: 6.269A pdb=" N ILE B 31 " --> pdb=" O ILE F 32 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N LEU F 34 " --> pdb=" O ILE B 31 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N GLY B 33 " --> pdb=" O LEU F 34 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N VAL F 36 " --> pdb=" O GLY B 33 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N SME B 35 " --> pdb=" O VAL F 36 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ILE F 31 " --> pdb=" O ILE J 32 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N LEU J 34 " --> pdb=" O ILE F 31 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N GLY F 33 " --> pdb=" O LEU J 34 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N VAL J 36 " --> pdb=" O GLY F 33 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N SME F 35 " --> pdb=" O VAL J 36 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 39 through 40 removed outlier: 6.493A pdb=" N VAL C 39 " --> pdb=" O VAL G 40 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N VAL B 39 " --> pdb=" O VAL C 40 " (cutoff:3.500A) 36 hydrogen bonds defined for protein. 108 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: 0.26 Time building geometry restraints manager: 0.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.33: 650 1.33 - 1.44: 160 1.44 - 1.55: 1230 1.55 - 1.65: 0 1.65 - 1.76: 20 Bond restraints: 2060 Sorted by residual: bond pdb=" CA ALA B 21 " pdb=" C ALA B 21 " ideal model delta sigma weight residual 1.519 1.526 -0.007 1.01e-02 9.80e+03 4.34e-01 bond pdb=" CA ILE J 31 " pdb=" CB ILE J 31 " ideal model delta sigma weight residual 1.535 1.527 0.008 1.24e-02 6.50e+03 4.17e-01 bond pdb=" CA ALA J 21 " pdb=" C ALA J 21 " ideal model delta sigma weight residual 1.519 1.526 -0.006 1.01e-02 9.80e+03 4.05e-01 bond pdb=" CA ALA C 21 " pdb=" C ALA C 21 " ideal model delta sigma weight residual 1.519 1.526 -0.006 1.01e-02 9.80e+03 3.99e-01 bond pdb=" CA GLY F 38 " pdb=" C GLY F 38 " ideal model delta sigma weight residual 1.522 1.515 0.007 1.06e-02 8.90e+03 3.99e-01 ... (remaining 2055 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.07: 2529 1.07 - 2.14: 161 2.14 - 3.21: 46 3.21 - 4.28: 14 4.28 - 5.35: 10 Bond angle restraints: 2760 Sorted by residual: angle pdb=" N ASN J 27 " pdb=" CA ASN J 27 " pdb=" C ASN J 27 " ideal model delta sigma weight residual 112.26 109.24 3.02 1.32e+00 5.74e-01 5.22e+00 angle pdb=" N ASN F 27 " pdb=" CA ASN F 27 " pdb=" C ASN F 27 " ideal model delta sigma weight residual 112.26 109.25 3.01 1.32e+00 5.74e-01 5.19e+00 angle pdb=" N ASN H 27 " pdb=" CA ASN H 27 " pdb=" C ASN H 27 " ideal model delta sigma weight residual 112.26 109.26 3.00 1.32e+00 5.74e-01 5.18e+00 angle pdb=" N ASN B 27 " pdb=" CA ASN B 27 " pdb=" C ASN B 27 " ideal model delta sigma weight residual 112.26 109.27 2.99 1.32e+00 5.74e-01 5.14e+00 angle pdb=" N ASN I 27 " pdb=" CA ASN I 27 " pdb=" C ASN I 27 " ideal model delta sigma weight residual 112.26 109.28 2.98 1.32e+00 5.74e-01 5.10e+00 ... (remaining 2755 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 7.85: 912 7.85 - 15.69: 138 15.69 - 23.54: 60 23.54 - 31.39: 20 31.39 - 39.23: 20 Dihedral angle restraints: 1150 sinusoidal: 420 harmonic: 730 Sorted by residual: dihedral pdb=" CA LEU J 34 " pdb=" CB LEU J 34 " pdb=" CG LEU J 34 " pdb=" CD1 LEU J 34 " ideal model delta sinusoidal sigma weight residual 180.00 146.96 33.04 3 1.50e+01 4.44e-03 5.49e+00 dihedral pdb=" CA LEU E 34 " pdb=" CB LEU E 34 " pdb=" CG LEU E 34 " pdb=" CD1 LEU E 34 " ideal model delta sinusoidal sigma weight residual 180.00 146.97 33.03 3 1.50e+01 4.44e-03 5.49e+00 dihedral pdb=" CA LEU I 34 " pdb=" CB LEU I 34 " pdb=" CG LEU I 34 " pdb=" CD1 LEU I 34 " ideal model delta sinusoidal sigma weight residual 180.00 146.98 33.02 3 1.50e+01 4.44e-03 5.49e+00 ... (remaining 1147 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 162 0.024 - 0.047: 78 0.047 - 0.071: 10 0.071 - 0.094: 48 0.094 - 0.118: 32 Chirality restraints: 330 Sorted by residual: chirality pdb=" CA ILE G 31 " pdb=" N ILE G 31 " pdb=" C ILE G 31 " pdb=" CB ILE G 31 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.47e-01 chirality pdb=" CA ILE C 31 " pdb=" N ILE C 31 " pdb=" C ILE C 31 " pdb=" CB ILE C 31 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.43e-01 chirality pdb=" CA ILE A 31 " pdb=" N ILE A 31 " pdb=" C ILE A 31 " pdb=" CB ILE A 31 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.39e-01 ... (remaining 327 not shown) Planarity restraints: 340 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE G 19 " -0.004 2.00e-02 2.50e+03 3.13e-03 1.72e-01 pdb=" CG PHE G 19 " 0.007 2.00e-02 2.50e+03 pdb=" CD1 PHE G 19 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE G 19 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE G 19 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE G 19 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE G 19 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA D 21 " 0.002 2.00e-02 2.50e+03 4.09e-03 1.68e-01 pdb=" C ALA D 21 " -0.007 2.00e-02 2.50e+03 pdb=" O ALA D 21 " 0.003 2.00e-02 2.50e+03 pdb=" N GLU D 22 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA I 21 " 0.002 2.00e-02 2.50e+03 4.09e-03 1.67e-01 pdb=" C ALA I 21 " -0.007 2.00e-02 2.50e+03 pdb=" O ALA I 21 " 0.003 2.00e-02 2.50e+03 pdb=" N GLU I 22 " 0.002 2.00e-02 2.50e+03 ... (remaining 337 not shown) Histogram of nonbonded interaction distances: 2.63 - 3.09: 1402 3.09 - 3.54: 1875 3.54 - 3.99: 3083 3.99 - 4.45: 3622 4.45 - 4.90: 6835 Nonbonded interactions: 16817 Sorted by model distance: nonbonded pdb=" O GLY A 37 " pdb=" O GLY C 25 " model vdw 2.632 3.040 nonbonded pdb=" O GLY A 25 " pdb=" O GLY B 37 " model vdw 2.640 3.040 nonbonded pdb=" O GLY F 25 " pdb=" O GLY H 37 " model vdw 2.647 3.040 nonbonded pdb=" O GLY C 37 " pdb=" O GLY E 25 " model vdw 2.647 3.040 nonbonded pdb=" O GLY H 25 " pdb=" O GLY J 37 " model vdw 2.647 3.040 ... (remaining 16812 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 '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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.180 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 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 : 0.004 0.013 2060 Z= 0.216 Angle : 0.760 5.350 2760 Z= 0.432 Chirality : 0.051 0.118 330 Planarity : 0.001 0.004 340 Dihedral : 11.032 39.234 690 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -1.19 (0.48), residues: 230 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.90 (0.37), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.007 0.002 PHE G 19 HIS 0.001 0.000 HIS I 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.22 ( 2060) covalent geometry : angle 0.75983 / 0.43 ( 2760) hydrogen bonds : bond 0.09884 / 7.16 ( 36) hydrogen bonds : angle 7.79014 / 5.21 ( 108) *********************** 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 67 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.080 Fit side-chains REVERT: B 28 LYS cc_start: 0.8649 (tttm) cc_final: 0.8392 (tttp) REVERT: G 28 LYS cc_start: 0.8671 (tttm) cc_final: 0.8351 (tppt) REVERT: I 28 LYS cc_start: 0.8635 (tttm) cc_final: 0.8382 (tppt) outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 0.0680 time to fit residues: 5.2249 Evaluate side-chains 37 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.083 ------------------------------------------------------------------------------- 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: 9.9990 chunk 13 optimal weight: 6.9990 chunk 1 optimal weight: 20.0000 chunk 8 optimal weight: 9.9990 chunk 16 optimal weight: 6.9990 chunk 15 optimal weight: 9.9990 chunk 9 optimal weight: 5.9990 chunk 11 optimal weight: 20.0000 chunk 18 optimal weight: 6.9990 chunk 6 optimal weight: 3.9990 chunk 4 optimal weight: 5.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 15 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.129928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.123989 restraints weight = 3869.929| |-----------------------------------------------------------------------------| r_work (start): 0.4218 rms_B_bonded: 2.68 r_work: 0.4137 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work (final): 0.4137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.018 2060 Z= 0.262 Angle : 0.709 5.760 2760 Z= 0.357 Chirality : 0.051 0.133 330 Planarity : 0.002 0.014 340 Dihedral : 6.847 31.206 290 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 7.00 % Allowed : 17.50 % Favored : 75.50 % 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: -1.04 (0.51), residues: 230 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.79 (0.39), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.012 0.002 PHE A 19 HIS 0.000 0.000 HIS H 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00577 / 0.26 ( 2060) covalent geometry : angle 0.70876 / 0.36 ( 2760) hydrogen bonds : bond 0.01608 / 1.14 ( 36) hydrogen bonds : angle 4.35262 / 2.85 ( 108) *********************** 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 66 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 52 time to evaluate : 0.051 Fit side-chains REVERT: A 34 LEU cc_start: 0.9491 (OUTLIER) cc_final: 0.9243 (mp) REVERT: B 34 LEU cc_start: 0.9490 (OUTLIER) cc_final: 0.9247 (mp) REVERT: C 34 LEU cc_start: 0.9510 (OUTLIER) cc_final: 0.9221 (mp) REVERT: D 34 LEU cc_start: 0.9619 (OUTLIER) cc_final: 0.9403 (mp) REVERT: E 34 LEU cc_start: 0.9516 (OUTLIER) cc_final: 0.9225 (mp) REVERT: F 34 LEU cc_start: 0.9579 (OUTLIER) cc_final: 0.9337 (mp) REVERT: G 28 LYS cc_start: 0.8743 (tttm) cc_final: 0.8307 (tppt) REVERT: G 34 LEU cc_start: 0.9409 (OUTLIER) cc_final: 0.9042 (mp) REVERT: H 34 LEU cc_start: 0.9489 (OUTLIER) cc_final: 0.9283 (mp) REVERT: I 28 LYS cc_start: 0.8674 (tttm) cc_final: 0.8334 (tppt) REVERT: I 34 LEU cc_start: 0.9398 (OUTLIER) cc_final: 0.9095 (mp) outliers start: 14 outliers final: 3 residues processed: 55 average time/residue: 0.0704 time to fit residues: 4.4132 Evaluate side-chains 57 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 45 time to evaluate : 0.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain J residue 40 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 17 optimal weight: 10.0000 chunk 9 optimal weight: 9.9990 chunk 7 optimal weight: 8.9990 chunk 12 optimal weight: 9.9990 chunk 11 optimal weight: 6.9990 chunk 15 optimal weight: 9.9990 chunk 16 optimal weight: 9.9990 chunk 13 optimal weight: 6.9990 chunk 3 optimal weight: 8.9990 chunk 4 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 overall best weight: 8.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 15 GLN C 15 GLN E 15 GLN H 15 GLN I 15 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.125810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.119905 restraints weight = 4020.703| |-----------------------------------------------------------------------------| r_work (start): 0.4174 rms_B_bonded: 2.63 r_work: 0.4099 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.4011 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.4011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.023 2060 Z= 0.360 Angle : 0.764 5.742 2760 Z= 0.388 Chirality : 0.052 0.131 330 Planarity : 0.002 0.012 340 Dihedral : 6.791 31.323 290 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 8.00 % Allowed : 26.00 % Favored : 66.00 % 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: -1.30 (0.51), residues: 230 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.98 (0.39), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.015 0.003 PHE C 19 HIS 0.000 0.000 HIS J 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00788 / 0.36 ( 2060) covalent geometry : angle 0.76368 / 0.39 ( 2760) hydrogen bonds : bond 0.01583 / 1.14 ( 36) hydrogen bonds : angle 3.74144 / 2.45 ( 108) *********************** 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 61 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 45 time to evaluate : 0.079 Fit side-chains REVERT: A 34 LEU cc_start: 0.9521 (OUTLIER) cc_final: 0.9301 (mp) REVERT: B 34 LEU cc_start: 0.9510 (OUTLIER) cc_final: 0.9290 (mp) REVERT: C 34 LEU cc_start: 0.9569 (OUTLIER) cc_final: 0.9311 (mp) REVERT: E 34 LEU cc_start: 0.9569 (OUTLIER) cc_final: 0.9316 (mp) REVERT: F 34 LEU cc_start: 0.9595 (OUTLIER) cc_final: 0.9392 (mp) REVERT: G 28 LYS cc_start: 0.8800 (tttm) cc_final: 0.8370 (tppt) REVERT: G 34 LEU cc_start: 0.9442 (OUTLIER) cc_final: 0.9090 (mp) REVERT: H 34 LEU cc_start: 0.9481 (OUTLIER) cc_final: 0.9268 (mp) REVERT: I 28 LYS cc_start: 0.8731 (tttm) cc_final: 0.8416 (tppt) REVERT: I 34 LEU cc_start: 0.9454 (OUTLIER) cc_final: 0.9198 (mp) REVERT: J 22 GLU cc_start: 0.9091 (tt0) cc_final: 0.8823 (tt0) REVERT: J 34 LEU cc_start: 0.9569 (OUTLIER) cc_final: 0.9289 (mt) outliers start: 16 outliers final: 5 residues processed: 49 average time/residue: 0.0763 time to fit residues: 4.2446 Evaluate side-chains 58 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 44 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain D residue 28 LYS Chi-restraints excluded: chain E residue 22 GLU Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain G residue 15 GLN Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain J residue 34 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 5 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 chunk 1 optimal weight: 9.9990 chunk 13 optimal weight: 7.9990 chunk 14 optimal weight: 7.9990 chunk 9 optimal weight: 0.9990 chunk 2 optimal weight: 10.0000 chunk 7 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 12 optimal weight: 9.9990 chunk 0 optimal weight: 9.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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 = 0.4325 r_free = 0.4325 target = 0.131117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.125016 restraints weight = 3941.902| |-----------------------------------------------------------------------------| r_work (start): 0.4216 rms_B_bonded: 2.75 r_work: 0.4144 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work (final): 0.4144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.022 2060 Z= 0.214 Angle : 0.665 5.699 2760 Z= 0.331 Chirality : 0.051 0.127 330 Planarity : 0.002 0.011 340 Dihedral : 6.966 36.866 290 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 7.50 % Allowed : 30.00 % Favored : 62.50 % 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: -1.32 (0.49), residues: 230 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.00 (0.38), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.010 0.002 PHE D 19 HIS 0.000 0.000 HIS J 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00468 / 0.21 ( 2060) covalent geometry : angle 0.66541 / 0.33 ( 2760) hydrogen bonds : bond 0.01090 / 0.78 ( 36) hydrogen bonds : angle 3.58820 / 2.32 ( 108) *********************** 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 63 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 48 time to evaluate : 0.095 Fit side-chains REVERT: B 22 GLU cc_start: 0.8672 (OUTLIER) cc_final: 0.8332 (tp30) REVERT: B 34 LEU cc_start: 0.9453 (OUTLIER) cc_final: 0.9228 (mp) REVERT: C 34 LEU cc_start: 0.9503 (OUTLIER) cc_final: 0.9221 (mp) REVERT: E 34 LEU cc_start: 0.9498 (OUTLIER) cc_final: 0.9186 (mp) REVERT: G 28 LYS cc_start: 0.8710 (tttm) cc_final: 0.8238 (tppt) REVERT: G 34 LEU cc_start: 0.9411 (OUTLIER) cc_final: 0.9031 (mp) REVERT: H 34 LEU cc_start: 0.9443 (OUTLIER) cc_final: 0.9142 (mp) REVERT: I 28 LYS cc_start: 0.8660 (tttm) cc_final: 0.8296 (tppt) REVERT: I 34 LEU cc_start: 0.9423 (OUTLIER) cc_final: 0.9056 (mp) REVERT: J 22 GLU cc_start: 0.8948 (tt0) cc_final: 0.8599 (tt0) outliers start: 15 outliers final: 2 residues processed: 51 average time/residue: 0.0768 time to fit residues: 4.4291 Evaluate side-chains 58 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 49 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain G residue 15 GLN Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain I residue 34 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 16 optimal weight: 10.0000 chunk 8 optimal weight: 10.0000 chunk 13 optimal weight: 9.9990 chunk 6 optimal weight: 10.0000 chunk 3 optimal weight: 20.0000 chunk 19 optimal weight: 8.9990 chunk 11 optimal weight: 4.9990 chunk 10 optimal weight: 10.0000 chunk 7 optimal weight: 6.9990 chunk 15 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.126801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.120791 restraints weight = 3976.398| |-----------------------------------------------------------------------------| r_work (start): 0.4188 rms_B_bonded: 2.71 r_work: 0.4120 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.4028 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.4028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.025 2060 Z= 0.270 Angle : 0.697 5.777 2760 Z= 0.348 Chirality : 0.051 0.127 330 Planarity : 0.002 0.010 340 Dihedral : 7.169 42.597 290 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 5.50 % Allowed : 31.00 % Favored : 63.50 % 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: -1.32 (0.49), residues: 230 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.00 (0.38), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.012 0.002 PHE E 19 HIS 0.000 0.000 HIS J 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00591 / 0.27 ( 2060) covalent geometry : angle 0.69665 / 0.35 ( 2760) hydrogen bonds : bond 0.01241 / 0.87 ( 36) hydrogen bonds : angle 3.46876 / 2.23 ( 108) *********************** 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 56 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 45 time to evaluate : 0.084 Fit side-chains REVERT: C 34 LEU cc_start: 0.9527 (OUTLIER) cc_final: 0.9254 (mp) REVERT: E 34 LEU cc_start: 0.9498 (OUTLIER) cc_final: 0.9253 (mp) REVERT: G 28 LYS cc_start: 0.8771 (tttm) cc_final: 0.8290 (tppt) REVERT: G 34 LEU cc_start: 0.9436 (OUTLIER) cc_final: 0.9080 (mp) REVERT: H 34 LEU cc_start: 0.9422 (OUTLIER) cc_final: 0.9203 (mp) REVERT: I 28 LYS cc_start: 0.8696 (tttm) cc_final: 0.8322 (tppt) REVERT: I 34 LEU cc_start: 0.9435 (OUTLIER) cc_final: 0.9074 (mp) REVERT: J 22 GLU cc_start: 0.9033 (tt0) cc_final: 0.8738 (tt0) outliers start: 11 outliers final: 4 residues processed: 49 average time/residue: 0.0758 time to fit residues: 4.2261 Evaluate side-chains 55 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 46 time to evaluate : 0.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain E residue 22 GLU Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain G residue 15 GLN Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain I residue 34 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 11 optimal weight: 7.9990 chunk 3 optimal weight: 5.9990 chunk 6 optimal weight: 0.9980 chunk 7 optimal weight: 5.9990 chunk 4 optimal weight: 9.9990 chunk 8 optimal weight: 8.9990 chunk 16 optimal weight: 6.9990 chunk 15 optimal weight: 0.0670 chunk 9 optimal weight: 10.0000 chunk 14 optimal weight: 5.9990 chunk 10 optimal weight: 7.9990 overall best weight: 3.8124 ------------------------------------------------------------------------------- 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 = 0.4359 r_free = 0.4359 target = 0.133661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.127630 restraints weight = 3837.791| |-----------------------------------------------------------------------------| r_work (start): 0.4242 rms_B_bonded: 2.72 r_work: 0.4174 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.4081 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.4081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.018 2060 Z= 0.172 Angle : 0.646 5.678 2760 Z= 0.317 Chirality : 0.052 0.124 330 Planarity : 0.001 0.010 340 Dihedral : 7.102 41.940 290 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 4.50 % Allowed : 32.50 % Favored : 63.00 % 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: -1.24 (0.49), residues: 230 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.94 (0.37), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.009 0.002 PHE E 19 HIS 0.000 0.000 HIS G 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.17 ( 2060) covalent geometry : angle 0.64623 / 0.32 ( 2760) hydrogen bonds : bond 0.01041 / 0.74 ( 36) hydrogen bonds : angle 3.42763 / 2.18 ( 108) *********************** 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 62 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.088 Fit side-chains REVERT: B 22 GLU cc_start: 0.8717 (OUTLIER) cc_final: 0.8398 (tp30) REVERT: B 34 LEU cc_start: 0.9395 (mp) cc_final: 0.9168 (mt) REVERT: C 34 LEU cc_start: 0.9512 (OUTLIER) cc_final: 0.9241 (mp) REVERT: E 22 GLU cc_start: 0.8604 (OUTLIER) cc_final: 0.8287 (tp30) REVERT: E 34 LEU cc_start: 0.9467 (OUTLIER) cc_final: 0.8966 (mp) REVERT: G 28 LYS cc_start: 0.8754 (tttm) cc_final: 0.8259 (tppt) REVERT: G 34 LEU cc_start: 0.9443 (OUTLIER) cc_final: 0.9083 (mp) REVERT: H 34 LEU cc_start: 0.9325 (OUTLIER) cc_final: 0.9080 (mt) REVERT: I 28 LYS cc_start: 0.8695 (tttm) cc_final: 0.8311 (tppt) REVERT: I 34 LEU cc_start: 0.9425 (OUTLIER) cc_final: 0.9034 (mp) REVERT: J 22 GLU cc_start: 0.8966 (tt0) cc_final: 0.8652 (tt0) outliers start: 9 outliers final: 2 residues processed: 55 average time/residue: 0.0633 time to fit residues: 4.0433 Evaluate side-chains 61 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 52 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain E residue 22 GLU Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain I residue 15 GLN Chi-restraints excluded: chain I residue 34 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 5 optimal weight: 20.0000 chunk 13 optimal weight: 0.9980 chunk 6 optimal weight: 4.9990 chunk 8 optimal weight: 10.0000 chunk 0 optimal weight: 1.9990 chunk 18 optimal weight: 9.9990 chunk 11 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 3 optimal weight: 6.9990 chunk 2 optimal weight: 5.9990 chunk 17 optimal weight: 10.0000 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 15 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.134556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.128576 restraints weight = 3897.365| |-----------------------------------------------------------------------------| r_work (start): 0.4271 rms_B_bonded: 2.71 r_work: 0.4206 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.4118 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.4118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.2665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.014 2060 Z= 0.155 Angle : 0.630 5.655 2760 Z= 0.309 Chirality : 0.052 0.122 330 Planarity : 0.001 0.009 340 Dihedral : 7.131 40.824 290 Min Nonbonded Distance : 2.647 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 5.00 % Allowed : 32.50 % Favored : 62.50 % 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: -1.11 (0.49), residues: 230 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.83 (0.37), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.009 0.002 PHE E 19 HIS 0.000 0.000 HIS G 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.16 ( 2060) covalent geometry : angle 0.62968 / 0.31 ( 2760) hydrogen bonds : bond 0.00966 / 0.69 ( 36) hydrogen bonds : angle 3.33399 / 2.10 ( 108) *********************** 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 63 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 53 time to evaluate : 0.083 Fit side-chains REVERT: B 22 GLU cc_start: 0.8666 (OUTLIER) cc_final: 0.8327 (tp30) REVERT: B 34 LEU cc_start: 0.9361 (OUTLIER) cc_final: 0.9129 (mt) REVERT: C 34 LEU cc_start: 0.9473 (OUTLIER) cc_final: 0.9183 (mp) REVERT: E 34 LEU cc_start: 0.9411 (OUTLIER) cc_final: 0.8902 (mp) REVERT: G 28 LYS cc_start: 0.8692 (tttm) cc_final: 0.8189 (tppt) REVERT: G 34 LEU cc_start: 0.9424 (OUTLIER) cc_final: 0.9045 (mp) REVERT: H 34 LEU cc_start: 0.9293 (OUTLIER) cc_final: 0.9075 (mt) REVERT: I 28 LYS cc_start: 0.8654 (tttm) cc_final: 0.8246 (tppt) REVERT: I 34 LEU cc_start: 0.9408 (OUTLIER) cc_final: 0.9005 (mp) REVERT: J 22 GLU cc_start: 0.8968 (tt0) cc_final: 0.8628 (tt0) outliers start: 10 outliers final: 3 residues processed: 55 average time/residue: 0.0734 time to fit residues: 4.6158 Evaluate side-chains 63 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 53 time to evaluate : 0.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain E residue 22 GLU Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain I residue 15 GLN Chi-restraints excluded: chain I residue 34 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 12 optimal weight: 9.9990 chunk 3 optimal weight: 20.0000 chunk 5 optimal weight: 5.9990 chunk 8 optimal weight: 10.0000 chunk 9 optimal weight: 0.7980 chunk 17 optimal weight: 7.9990 chunk 4 optimal weight: 5.9990 chunk 18 optimal weight: 9.9990 chunk 14 optimal weight: 10.0000 chunk 13 optimal weight: 7.9990 chunk 7 optimal weight: 10.0000 overall best weight: 5.7588 ------------------------------------------------------------------------------- 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 = 0.4322 r_free = 0.4322 target = 0.130451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.124444 restraints weight = 3903.449| |-----------------------------------------------------------------------------| r_work (start): 0.4236 rms_B_bonded: 2.70 r_work: 0.4163 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.4071 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.4071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.020 2060 Z= 0.250 Angle : 0.682 5.797 2760 Z= 0.337 Chirality : 0.052 0.126 330 Planarity : 0.002 0.009 340 Dihedral : 7.246 45.791 290 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 6.00 % Allowed : 32.00 % Favored : 62.00 % 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: -1.15 (0.49), residues: 230 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.87 (0.38), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.012 0.002 PHE E 19 HIS 0.000 0.000 HIS J 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00548 / 0.25 ( 2060) covalent geometry : angle 0.68208 / 0.34 ( 2760) hydrogen bonds : bond 0.01197 / 0.85 ( 36) hydrogen bonds : angle 3.33221 / 2.11 ( 108) *********************** 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 57 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 45 time to evaluate : 0.109 Fit side-chains REVERT: B 34 LEU cc_start: 0.9447 (OUTLIER) cc_final: 0.9103 (mt) REVERT: C 34 LEU cc_start: 0.9525 (OUTLIER) cc_final: 0.9292 (mp) REVERT: E 34 LEU cc_start: 0.9510 (OUTLIER) cc_final: 0.9206 (mp) REVERT: G 28 LYS cc_start: 0.8790 (tttm) cc_final: 0.8324 (tppt) REVERT: G 34 LEU cc_start: 0.9436 (OUTLIER) cc_final: 0.9086 (mp) REVERT: I 28 LYS cc_start: 0.8718 (tttm) cc_final: 0.8373 (tppt) REVERT: I 34 LEU cc_start: 0.9462 (OUTLIER) cc_final: 0.9106 (mp) outliers start: 12 outliers final: 6 residues processed: 49 average time/residue: 0.0752 time to fit residues: 4.1664 Evaluate side-chains 55 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 44 time to evaluate : 0.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain E residue 22 GLU Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain G residue 15 GLN Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain I residue 15 GLN Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain J residue 24 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 13 optimal weight: 8.9990 chunk 17 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 11 optimal weight: 7.9990 chunk 19 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 18 optimal weight: 10.0000 chunk 12 optimal weight: 0.9990 chunk 4 optimal weight: 10.0000 chunk 15 optimal weight: 9.9990 chunk 1 optimal weight: 0.0870 overall best weight: 2.4166 ------------------------------------------------------------------------------- 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 = 0.4392 r_free = 0.4392 target = 0.135211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.129223 restraints weight = 3821.084| |-----------------------------------------------------------------------------| r_work (start): 0.4343 rms_B_bonded: 2.76 r_work: 0.4275 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work (final): 0.4275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.010 2060 Z= 0.116 Angle : 0.611 5.651 2760 Z= 0.299 Chirality : 0.052 0.121 330 Planarity : 0.001 0.009 340 Dihedral : 7.003 36.662 290 Min Nonbonded Distance : 2.670 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 4.50 % Allowed : 33.50 % Favored : 62.00 % 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: -1.04 (0.49), residues: 230 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.78 (0.37), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.007 0.001 PHE D 19 HIS 0.000 0.000 HIS G 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.12 ( 2060) covalent geometry : angle 0.61079 / 0.30 ( 2760) hydrogen bonds : bond 0.00828 / 0.60 ( 36) hydrogen bonds : angle 3.32698 / 2.10 ( 108) *********************** 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 61 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 52 time to evaluate : 0.064 Fit side-chains REVERT: B 22 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.8336 (tp30) REVERT: B 34 LEU cc_start: 0.9400 (mp) cc_final: 0.9180 (mt) REVERT: C 34 LEU cc_start: 0.9475 (OUTLIER) cc_final: 0.9199 (mp) REVERT: E 34 LEU cc_start: 0.9435 (OUTLIER) cc_final: 0.8939 (mp) REVERT: G 28 LYS cc_start: 0.8679 (tttm) cc_final: 0.8199 (tppt) REVERT: G 34 LEU cc_start: 0.9410 (OUTLIER) cc_final: 0.9035 (mp) REVERT: I 28 LYS cc_start: 0.8644 (tttm) cc_final: 0.8269 (tppt) REVERT: I 34 LEU cc_start: 0.9396 (OUTLIER) cc_final: 0.8990 (mp) outliers start: 9 outliers final: 4 residues processed: 55 average time/residue: 0.0671 time to fit residues: 4.2240 Evaluate side-chains 61 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 52 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain E residue 22 GLU Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain I residue 15 GLN Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain J residue 24 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 12 optimal weight: 10.0000 chunk 13 optimal weight: 3.9990 chunk 9 optimal weight: 6.9990 chunk 19 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 chunk 14 optimal weight: 10.0000 chunk 16 optimal weight: 7.9990 chunk 17 optimal weight: 4.9990 chunk 7 optimal weight: 10.0000 chunk 8 optimal weight: 8.9990 chunk 6 optimal weight: 2.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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 = 0.4341 r_free = 0.4341 target = 0.131930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.125861 restraints weight = 3912.995| |-----------------------------------------------------------------------------| r_work (start): 0.4226 rms_B_bonded: 2.76 r_work: 0.4155 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work (final): 0.4155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.2751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.017 2060 Z= 0.216 Angle : 0.656 5.769 2760 Z= 0.324 Chirality : 0.051 0.123 330 Planarity : 0.001 0.009 340 Dihedral : 7.147 42.724 290 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 5.00 % Allowed : 32.50 % Favored : 62.50 % 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: -1.02 (0.49), residues: 230 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.77 (0.38), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.011 0.002 PHE C 19 HIS 0.000 0.000 HIS J 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.22 ( 2060) covalent geometry : angle 0.65649 / 0.32 ( 2760) hydrogen bonds : bond 0.01114 / 0.79 ( 36) hydrogen bonds : angle 3.28713 / 2.07 ( 108) ********************** 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 59 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 49 time to evaluate : 0.082 Fit side-chains REVERT: B 22 GLU cc_start: 0.8671 (OUTLIER) cc_final: 0.8368 (tp30) REVERT: B 34 LEU cc_start: 0.9418 (mp) cc_final: 0.9203 (mt) REVERT: C 34 LEU cc_start: 0.9482 (OUTLIER) cc_final: 0.9214 (mp) REVERT: E 34 LEU cc_start: 0.9462 (OUTLIER) cc_final: 0.8962 (mp) REVERT: G 28 LYS cc_start: 0.8703 (tttm) cc_final: 0.8223 (tppt) REVERT: G 34 LEU cc_start: 0.9441 (OUTLIER) cc_final: 0.9072 (mp) REVERT: I 28 LYS cc_start: 0.8662 (tttm) cc_final: 0.8303 (tppt) REVERT: I 34 LEU cc_start: 0.9443 (OUTLIER) cc_final: 0.9054 (mp) outliers start: 10 outliers final: 5 residues processed: 53 average time/residue: 0.0693 time to fit residues: 4.2147 Evaluate side-chains 59 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 49 time to evaluate : 0.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain E residue 22 GLU Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain G residue 15 GLN Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain I residue 15 GLN Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain J residue 24 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 9 optimal weight: 7.9990 chunk 17 optimal weight: 6.9990 chunk 4 optimal weight: 10.0000 chunk 2 optimal weight: 10.0000 chunk 13 optimal weight: 0.4980 chunk 10 optimal weight: 3.9990 chunk 12 optimal weight: 7.9990 chunk 6 optimal weight: 4.9990 chunk 7 optimal weight: 7.9990 chunk 8 optimal weight: 10.0000 chunk 5 optimal weight: 5.9990 overall best weight: 4.4988 ------------------------------------------------------------------------------- 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 = 0.4346 r_free = 0.4346 target = 0.132395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.126293 restraints weight = 3962.161| |-----------------------------------------------------------------------------| r_work (start): 0.4231 rms_B_bonded: 2.76 r_work: 0.4165 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work (final): 0.4165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.2776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.015 2060 Z= 0.198 Angle : 0.651 5.768 2760 Z= 0.320 Chirality : 0.051 0.123 330 Planarity : 0.001 0.009 340 Dihedral : 7.108 43.892 290 Min Nonbonded Distance : 2.643 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 5.50 % Allowed : 32.00 % Favored : 62.50 % 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: -1.07 (0.50), residues: 230 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.81 (0.38), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.010 0.002 PHE C 19 HIS 0.000 0.000 HIS J 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.20 ( 2060) covalent geometry : angle 0.65089 / 0.32 ( 2760) hydrogen bonds : bond 0.01048 / 0.75 ( 36) hydrogen bonds : angle 3.28779 / 2.07 ( 108) =============================================================================== Job complete usr+sys time: 843.37 seconds wall clock time: 15 minutes 23.29 seconds (923.29 seconds total)