Starting phenix.real_space_refine on Fri Aug 22 12:40:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8owd_17234/08_2025/8owd_17234.cif Found real_map, /net/cci-nas-00/data/ceres_data/8owd_17234/08_2025/8owd_17234.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8owd_17234/08_2025/8owd_17234.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8owd_17234/08_2025/8owd_17234.map" model { file = "/net/cci-nas-00/data/ceres_data/8owd_17234/08_2025/8owd_17234.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8owd_17234/08_2025/8owd_17234.cif" } resolution = 3.28 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= 0.001 sd= 0.005 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 5 5.16 5 C 970 2.51 5 N 265 2.21 5 O 285 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-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 1525 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 305 Classifications: {'peptide': 40} Link IDs: {'TRANS': 39} Restraints were copied for chains: B, C, D, E Time building chain proxies: 0.49, per 1000 atoms: 0.32 Number of scatterers: 1525 At special positions: 0 Unit cell: (45.15, 85.05, 40.95, 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 5 16.00 O 285 8.00 N 265 7.00 C 970 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: 0.13 Conformation dependent library (CDL) restraints added in 55.4 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 380 Ramachandran restraints generated. 190 Oldfield, 0 Emsley, 190 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 340 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 5 sheets defined 0.0% alpha, 32.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.08 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 6 Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 12 Processing sheet with id=AA3, first strand: chain 'A' and resid 17 through 22 removed outlier: 6.204A pdb=" N VAL A 18 " --> pdb=" O PHE B 19 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N ALA B 21 " --> pdb=" O VAL A 18 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N PHE A 20 " --> pdb=" O ALA B 21 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N VAL B 18 " --> pdb=" O PHE C 19 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N ALA C 21 " --> pdb=" O VAL B 18 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N PHE B 20 " --> pdb=" O ALA C 21 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N VAL C 18 " --> pdb=" O PHE D 19 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N ALA D 21 " --> pdb=" O VAL C 18 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N PHE C 20 " --> pdb=" O ALA D 21 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N VAL D 18 " --> pdb=" O PHE E 19 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N ALA E 21 " --> pdb=" O VAL D 18 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N PHE D 20 " --> pdb=" O ALA E 21 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 30 through 32 removed outlier: 6.059A pdb=" N ILE A 31 " --> pdb=" O ILE B 32 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N ILE B 31 " --> pdb=" O ILE C 32 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N ILE C 31 " --> pdb=" O ILE D 32 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N ILE D 31 " --> pdb=" O ILE E 32 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 35 through 36 24 hydrogen bonds defined for protein. 72 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: 0.19 Time building geometry restraints manager: 0.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 507 1.33 - 1.45: 283 1.45 - 1.56: 755 1.56 - 1.68: 0 1.68 - 1.80: 10 Bond restraints: 1555 Sorted by residual: bond pdb=" CA LYS C 16 " pdb=" C LYS C 16 " ideal model delta sigma weight residual 1.526 1.492 0.034 1.03e-02 9.43e+03 1.09e+01 bond pdb=" CA LYS B 16 " pdb=" C LYS B 16 " ideal model delta sigma weight residual 1.526 1.493 0.033 1.03e-02 9.43e+03 1.05e+01 bond pdb=" CA LYS A 16 " pdb=" C LYS A 16 " ideal model delta sigma weight residual 1.526 1.493 0.033 1.03e-02 9.43e+03 1.05e+01 bond pdb=" CA LYS D 16 " pdb=" C LYS D 16 " ideal model delta sigma weight residual 1.526 1.493 0.033 1.03e-02 9.43e+03 1.05e+01 bond pdb=" CA LYS E 16 " pdb=" C LYS E 16 " ideal model delta sigma weight residual 1.526 1.494 0.033 1.03e-02 9.43e+03 1.00e+01 ... (remaining 1550 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.33: 1975 4.33 - 8.66: 80 8.66 - 12.99: 20 12.99 - 17.32: 5 17.32 - 21.65: 5 Bond angle restraints: 2085 Sorted by residual: angle pdb=" N GLY D 25 " pdb=" CA GLY D 25 " pdb=" C GLY D 25 " ideal model delta sigma weight residual 111.54 133.19 -21.65 1.36e+00 5.41e-01 2.53e+02 angle pdb=" N GLY C 25 " pdb=" CA GLY C 25 " pdb=" C GLY C 25 " ideal model delta sigma weight residual 111.54 133.15 -21.61 1.36e+00 5.41e-01 2.52e+02 angle pdb=" N GLY B 25 " pdb=" CA GLY B 25 " pdb=" C GLY B 25 " ideal model delta sigma weight residual 111.54 133.14 -21.60 1.36e+00 5.41e-01 2.52e+02 angle pdb=" N GLY E 25 " pdb=" CA GLY E 25 " pdb=" C GLY E 25 " ideal model delta sigma weight residual 111.54 133.13 -21.59 1.36e+00 5.41e-01 2.52e+02 angle pdb=" N GLY A 25 " pdb=" CA GLY A 25 " pdb=" C GLY A 25 " ideal model delta sigma weight residual 111.54 133.13 -21.59 1.36e+00 5.41e-01 2.52e+02 ... (remaining 2080 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.98: 745 14.98 - 29.96: 40 29.96 - 44.93: 35 44.93 - 59.91: 45 59.91 - 74.89: 5 Dihedral angle restraints: 870 sinusoidal: 330 harmonic: 540 Sorted by residual: dihedral pdb=" C ARG B 5 " pdb=" N ARG B 5 " pdb=" CA ARG B 5 " pdb=" CB ARG B 5 " ideal model delta harmonic sigma weight residual -122.60 -132.38 9.78 0 2.50e+00 1.60e-01 1.53e+01 dihedral pdb=" C ARG C 5 " pdb=" N ARG C 5 " pdb=" CA ARG C 5 " pdb=" CB ARG C 5 " ideal model delta harmonic sigma weight residual -122.60 -132.37 9.77 0 2.50e+00 1.60e-01 1.53e+01 dihedral pdb=" C ARG E 5 " pdb=" N ARG E 5 " pdb=" CA ARG E 5 " pdb=" CB ARG E 5 " ideal model delta harmonic sigma weight residual -122.60 -132.35 9.75 0 2.50e+00 1.60e-01 1.52e+01 ... (remaining 867 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.069: 126 0.069 - 0.136: 54 0.136 - 0.204: 15 0.204 - 0.272: 6 0.272 - 0.339: 19 Chirality restraints: 220 Sorted by residual: chirality pdb=" CB VAL A 12 " pdb=" CA VAL A 12 " pdb=" CG1 VAL A 12 " pdb=" CG2 VAL A 12 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.88e+00 chirality pdb=" CB VAL C 12 " pdb=" CA VAL C 12 " pdb=" CG1 VAL C 12 " pdb=" CG2 VAL C 12 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.83e+00 chirality pdb=" CB VAL E 12 " pdb=" CA VAL E 12 " pdb=" CG1 VAL E 12 " pdb=" CG2 VAL E 12 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.81e+00 ... (remaining 217 not shown) Planarity restraints: 275 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL B 24 " 0.009 2.00e-02 2.50e+03 1.88e-02 3.53e+00 pdb=" C VAL B 24 " -0.033 2.00e-02 2.50e+03 pdb=" O VAL B 24 " 0.012 2.00e-02 2.50e+03 pdb=" N GLY B 25 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 24 " 0.009 2.00e-02 2.50e+03 1.86e-02 3.47e+00 pdb=" C VAL D 24 " -0.032 2.00e-02 2.50e+03 pdb=" O VAL D 24 " 0.012 2.00e-02 2.50e+03 pdb=" N GLY D 25 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 24 " 0.009 2.00e-02 2.50e+03 1.86e-02 3.47e+00 pdb=" C VAL C 24 " -0.032 2.00e-02 2.50e+03 pdb=" O VAL C 24 " 0.012 2.00e-02 2.50e+03 pdb=" N GLY C 25 " 0.011 2.00e-02 2.50e+03 ... (remaining 272 not shown) Histogram of nonbonded interaction distances: 2.51 - 2.98: 776 2.98 - 3.46: 1452 3.46 - 3.94: 2619 3.94 - 4.42: 2948 4.42 - 4.90: 5446 Nonbonded interactions: 13241 Sorted by model distance: nonbonded pdb=" NZ LYS C 28 " pdb=" OD2 ASP D 23 " model vdw 2.506 3.120 nonbonded pdb=" NZ LYS B 28 " pdb=" OD2 ASP C 23 " model vdw 2.517 3.120 nonbonded pdb=" NZ LYS D 28 " pdb=" OD2 ASP E 23 " model vdw 2.543 3.120 nonbonded pdb=" NZ LYS A 28 " pdb=" OD2 ASP B 23 " model vdw 2.586 3.120 nonbonded pdb=" O ASP E 1 " pdb=" OE1 GLU E 3 " model vdw 2.591 3.040 ... (remaining 13236 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' } 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: 1.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.030 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 3.880 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 6.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 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 : 0.012 0.035 1555 Z= 0.934 Angle : 2.438 21.645 2085 Z= 1.629 Chirality : 0.118 0.339 220 Planarity : 0.005 0.019 275 Dihedral : 21.081 74.889 530 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 16.13 % Allowed : 19.35 % Favored : 64.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.81 (0.54), residues: 190 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.61 (0.41), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.005 ARG B 5 TYR 0.005 0.002 TYR D 10 PHE 0.015 0.005 PHE C 20 HIS 0.005 0.002 HIS D 14 Details of bonding type rmsd covalent geometry : bond 0.01204 ( 1555) covalent geometry : angle 2.43800 ( 2085) hydrogen bonds : bond 0.09555 ( 24) hydrogen bonds : angle 6.50386 ( 72) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 380 Ramachandran restraints generated. 190 Oldfield, 0 Emsley, 190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 380 Ramachandran restraints generated. 190 Oldfield, 0 Emsley, 190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 57 time to evaluate : 0.064 Fit side-chains REVERT: A 11 GLU cc_start: 0.7292 (OUTLIER) cc_final: 0.7071 (tt0) REVERT: A 13 HIS cc_start: 0.6825 (OUTLIER) cc_final: 0.6551 (m-70) REVERT: A 22 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.7561 (tm-30) REVERT: A 23 ASP cc_start: 0.8691 (t0) cc_final: 0.8261 (t0) REVERT: B 11 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.7204 (tt0) REVERT: B 13 HIS cc_start: 0.6499 (OUTLIER) cc_final: 0.6124 (m170) REVERT: B 17 LEU cc_start: 0.8770 (mp) cc_final: 0.8437 (mt) REVERT: B 22 GLU cc_start: 0.8709 (OUTLIER) cc_final: 0.7544 (tm-30) REVERT: B 23 ASP cc_start: 0.8988 (t0) cc_final: 0.8316 (t0) REVERT: B 28 LYS cc_start: 0.8217 (OUTLIER) cc_final: 0.7986 (mttt) REVERT: C 11 GLU cc_start: 0.7500 (OUTLIER) cc_final: 0.7229 (tt0) REVERT: C 13 HIS cc_start: 0.6280 (OUTLIER) cc_final: 0.5932 (m-70) REVERT: C 22 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.7672 (tm-30) REVERT: C 23 ASP cc_start: 0.8924 (t0) cc_final: 0.7842 (t0) REVERT: D 11 GLU cc_start: 0.7641 (OUTLIER) cc_final: 0.7212 (tt0) REVERT: D 13 HIS cc_start: 0.6744 (OUTLIER) cc_final: 0.6357 (m170) REVERT: D 22 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.8309 (tm-30) REVERT: D 23 ASP cc_start: 0.8949 (t0) cc_final: 0.8229 (t0) REVERT: D 28 LYS cc_start: 0.8292 (OUTLIER) cc_final: 0.8079 (mttt) REVERT: E 5 ARG cc_start: 0.7617 (ttp80) cc_final: 0.6557 (tpp-160) REVERT: E 11 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7436 (tt0) REVERT: E 13 HIS cc_start: 0.6167 (OUTLIER) cc_final: 0.5802 (m170) REVERT: E 22 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.8331 (tm-30) REVERT: E 23 ASP cc_start: 0.8805 (t0) cc_final: 0.7989 (t0) REVERT: E 28 LYS cc_start: 0.8567 (OUTLIER) cc_final: 0.6245 (mmtt) outliers start: 25 outliers final: 5 residues processed: 77 average time/residue: 0.0858 time to fit residues: 7.1931 Evaluate side-chains 75 residues out of total 155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 52 time to evaluate : 0.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLU Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 13 HIS Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 13 HIS Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain B residue 28 LYS Chi-restraints excluded: chain C residue 11 GLU Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 13 HIS Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain D residue 11 GLU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 13 HIS Chi-restraints excluded: chain D residue 22 GLU Chi-restraints excluded: chain D residue 28 LYS Chi-restraints excluded: chain E residue 11 GLU Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 13 HIS Chi-restraints excluded: chain E residue 22 GLU Chi-restraints excluded: chain E residue 28 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 12 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 1 optimal weight: 4.9990 chunk 8 optimal weight: 7.9990 chunk 16 optimal weight: 7.9990 chunk 15 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 13 HIS E 15 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.090883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.082403 restraints weight = 3030.829| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 2.49 r_work: 0.3476 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3382 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.2870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 1555 Z= 0.228 Angle : 0.663 7.511 2085 Z= 0.347 Chirality : 0.052 0.128 220 Planarity : 0.003 0.021 275 Dihedral : 17.829 56.293 262 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 11.61 % Allowed : 21.94 % Favored : 66.45 % 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 aren not related in a simple way. whole: -2.73 (0.42), residues: 190 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.07 (0.32), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 5 TYR 0.007 0.002 TYR B 10 PHE 0.010 0.001 PHE E 4 HIS 0.003 0.001 HIS E 6 Details of bonding type rmsd covalent geometry : bond 0.00484 ( 1555) covalent geometry : angle 0.66255 ( 2085) hydrogen bonds : bond 0.03106 ( 24) hydrogen bonds : angle 5.11153 ( 72) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 380 Ramachandran restraints generated. 190 Oldfield, 0 Emsley, 190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 380 Ramachandran restraints generated. 190 Oldfield, 0 Emsley, 190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 41 time to evaluate : 0.102 Fit side-chains REVERT: A 11 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7739 (tt0) REVERT: A 13 HIS cc_start: 0.7533 (OUTLIER) cc_final: 0.7161 (m170) REVERT: B 11 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7911 (tt0) REVERT: C 13 HIS cc_start: 0.7283 (OUTLIER) cc_final: 0.7003 (m-70) REVERT: C 23 ASP cc_start: 0.8802 (t0) cc_final: 0.8558 (t0) REVERT: D 11 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7670 (tt0) REVERT: E 5 ARG cc_start: 0.8159 (ttp80) cc_final: 0.6589 (tpp-160) REVERT: E 11 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7718 (tt0) REVERT: E 13 HIS cc_start: 0.7132 (OUTLIER) cc_final: 0.6695 (m170) REVERT: E 28 LYS cc_start: 0.8322 (OUTLIER) cc_final: 0.6701 (mmmt) outliers start: 18 outliers final: 6 residues processed: 59 average time/residue: 0.0893 time to fit residues: 5.7841 Evaluate side-chains 47 residues out of total 155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 33 time to evaluate : 0.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLU Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 13 HIS Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain C residue 11 GLU Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 13 HIS Chi-restraints excluded: chain D residue 11 GLU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain E residue 11 GLU Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 13 HIS Chi-restraints excluded: chain E residue 28 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 8 optimal weight: 10.0000 chunk 9 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 13 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 16 optimal weight: 7.9990 chunk 10 optimal weight: 5.9990 chunk 6 optimal weight: 0.9990 chunk 4 optimal weight: 4.9990 chunk 18 optimal weight: 8.9990 chunk 12 optimal weight: 0.9980 overall best weight: 1.7584 ------------------------------------------------------------------------------- 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 = 0.3690 r_free = 0.3690 target = 0.091104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.081839 restraints weight = 3037.366| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 2.68 r_work: 0.3462 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3369 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.3410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 1555 Z= 0.173 Angle : 0.564 6.274 2085 Z= 0.295 Chirality : 0.051 0.130 220 Planarity : 0.003 0.026 275 Dihedral : 13.123 51.596 235 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 8.39 % Allowed : 24.52 % Favored : 67.10 % 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 aren not related in a simple way. whole: -3.07 (0.42), residues: 190 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.33 (0.32), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 5 TYR 0.005 0.001 TYR B 10 PHE 0.007 0.001 PHE E 4 HIS 0.002 0.001 HIS C 14 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 1555) covalent geometry : angle 0.56448 ( 2085) hydrogen bonds : bond 0.02472 ( 24) hydrogen bonds : angle 4.47818 ( 72) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 380 Ramachandran restraints generated. 190 Oldfield, 0 Emsley, 190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 380 Ramachandran restraints generated. 190 Oldfield, 0 Emsley, 190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 36 time to evaluate : 0.064 Fit side-chains REVERT: A 11 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.7752 (tt0) REVERT: B 3 GLU cc_start: 0.7475 (mp0) cc_final: 0.6798 (mp0) REVERT: B 11 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7858 (tt0) REVERT: C 5 ARG cc_start: 0.8369 (ttm170) cc_final: 0.8149 (ttm170) REVERT: C 11 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7627 (tt0) REVERT: D 11 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.7741 (tt0) REVERT: E 5 ARG cc_start: 0.8041 (ttp80) cc_final: 0.6980 (tpm170) REVERT: E 11 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7596 (tt0) REVERT: E 28 LYS cc_start: 0.8390 (OUTLIER) cc_final: 0.6700 (mmmt) outliers start: 13 outliers final: 5 residues processed: 49 average time/residue: 0.0749 time to fit residues: 4.0698 Evaluate side-chains 42 residues out of total 155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 31 time to evaluate : 0.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLU Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain C residue 11 GLU Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain D residue 11 GLU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain E residue 11 GLU Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 28 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 4 optimal weight: 10.0000 chunk 2 optimal weight: 6.9990 chunk 12 optimal weight: 10.0000 chunk 18 optimal weight: 8.9990 chunk 7 optimal weight: 9.9990 chunk 1 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 13 optimal weight: 8.9990 chunk 0 optimal weight: 8.9990 chunk 19 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 = 0.3574 r_free = 0.3574 target = 0.084753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.076187 restraints weight = 3206.494| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 2.63 r_work: 0.3359 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3270 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.3650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.028 1555 Z= 0.284 Angle : 0.630 6.748 2085 Z= 0.328 Chirality : 0.051 0.128 220 Planarity : 0.003 0.032 275 Dihedral : 12.941 57.007 229 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer: Outliers : 8.39 % Allowed : 21.29 % Favored : 70.32 % 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 aren not related in a simple way. whole: -3.29 (0.41), residues: 190 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.50 (0.31), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 5 TYR 0.006 0.002 TYR B 10 PHE 0.008 0.002 PHE A 4 HIS 0.003 0.001 HIS C 14 Details of bonding type rmsd covalent geometry : bond 0.00602 ( 1555) covalent geometry : angle 0.63037 ( 2085) hydrogen bonds : bond 0.03020 ( 24) hydrogen bonds : angle 3.95920 ( 72) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 380 Ramachandran restraints generated. 190 Oldfield, 0 Emsley, 190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 380 Ramachandran restraints generated. 190 Oldfield, 0 Emsley, 190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 35 time to evaluate : 0.068 Fit side-chains REVERT: A 3 GLU cc_start: 0.8034 (mp0) cc_final: 0.7137 (mp0) REVERT: A 11 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7842 (tt0) REVERT: B 3 GLU cc_start: 0.7283 (mp0) cc_final: 0.6598 (mp0) REVERT: B 11 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.8043 (tt0) REVERT: C 3 GLU cc_start: 0.6804 (mp0) cc_final: 0.6376 (mp0) REVERT: C 11 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7599 (tt0) REVERT: C 23 ASP cc_start: 0.8910 (t0) cc_final: 0.8554 (t0) REVERT: D 11 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.7888 (tt0) REVERT: E 3 GLU cc_start: 0.7262 (mp0) cc_final: 0.6982 (mp0) REVERT: E 5 ARG cc_start: 0.8119 (ttp80) cc_final: 0.7105 (mmp-170) REVERT: E 11 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.7919 (tt0) REVERT: E 28 LYS cc_start: 0.8067 (OUTLIER) cc_final: 0.6490 (mmmt) outliers start: 13 outliers final: 6 residues processed: 48 average time/residue: 0.0556 time to fit residues: 3.0612 Evaluate side-chains 44 residues out of total 155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 32 time to evaluate : 0.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLU Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain C residue 11 GLU Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain D residue 11 GLU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain E residue 11 GLU Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 28 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 9 optimal weight: 5.9990 chunk 10 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 6 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 8 optimal weight: 10.0000 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 = 0.3637 r_free = 0.3637 target = 0.088292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.079528 restraints weight = 3070.799| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 2.70 r_work: 0.3437 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3348 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.3854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 1555 Z= 0.135 Angle : 0.548 7.266 2085 Z= 0.274 Chirality : 0.050 0.129 220 Planarity : 0.002 0.014 275 Dihedral : 12.252 53.971 229 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 9.03 % Allowed : 20.00 % Favored : 70.97 % 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 aren not related in a simple way. whole: -3.27 (0.42), residues: 190 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.49 (0.32), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 5 TYR 0.004 0.001 TYR C 10 PHE 0.005 0.001 PHE E 4 HIS 0.001 0.000 HIS A 14 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 1555) covalent geometry : angle 0.54823 ( 2085) hydrogen bonds : bond 0.01819 ( 24) hydrogen bonds : angle 3.74609 ( 72) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 380 Ramachandran restraints generated. 190 Oldfield, 0 Emsley, 190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 380 Ramachandran restraints generated. 190 Oldfield, 0 Emsley, 190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 37 time to evaluate : 0.064 Fit side-chains REVERT: A 3 GLU cc_start: 0.7931 (mp0) cc_final: 0.7022 (mp0) REVERT: A 22 GLU cc_start: 0.8454 (OUTLIER) cc_final: 0.7463 (tm-30) REVERT: B 3 GLU cc_start: 0.7243 (mp0) cc_final: 0.6604 (mp0) REVERT: B 5 ARG cc_start: 0.8589 (tpp80) cc_final: 0.7119 (ttp-170) REVERT: B 22 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.7375 (tm-30) REVERT: C 11 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7852 (tt0) REVERT: D 3 GLU cc_start: 0.7379 (mp0) cc_final: 0.6717 (mp0) REVERT: D 11 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.8029 (tt0) REVERT: E 5 ARG cc_start: 0.8161 (ttp80) cc_final: 0.7096 (tpm170) REVERT: E 11 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.8100 (tt0) outliers start: 14 outliers final: 6 residues processed: 51 average time/residue: 0.0656 time to fit residues: 3.7258 Evaluate side-chains 45 residues out of total 155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 34 time to evaluate : 0.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain C residue 11 GLU Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain D residue 11 GLU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain E residue 11 GLU Chi-restraints excluded: chain E residue 12 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 10 optimal weight: 10.0000 chunk 8 optimal weight: 3.9990 chunk 16 optimal weight: 7.9990 chunk 7 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 chunk 18 optimal weight: 8.9990 chunk 6 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 13 optimal weight: 8.9990 chunk 19 optimal weight: 0.1980 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 = 0.3681 r_free = 0.3681 target = 0.090239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.081274 restraints weight = 3013.128| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 2.67 r_work: 0.3473 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3379 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.4007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 1555 Z= 0.124 Angle : 0.551 7.627 2085 Z= 0.270 Chirality : 0.050 0.130 220 Planarity : 0.002 0.013 275 Dihedral : 10.620 59.439 219 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer: Outliers : 7.74 % Allowed : 20.00 % Favored : 72.26 % 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 aren not related in a simple way. whole: -3.23 (0.43), residues: 190 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.46 (0.33), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 5 TYR 0.003 0.001 TYR C 10 PHE 0.004 0.001 PHE E 4 HIS 0.001 0.000 HIS A 14 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 1555) covalent geometry : angle 0.55073 ( 2085) hydrogen bonds : bond 0.01671 ( 24) hydrogen bonds : angle 3.59611 ( 72) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 380 Ramachandran restraints generated. 190 Oldfield, 0 Emsley, 190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 380 Ramachandran restraints generated. 190 Oldfield, 0 Emsley, 190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 37 time to evaluate : 0.073 Fit side-chains REVERT: A 3 GLU cc_start: 0.7978 (mp0) cc_final: 0.7059 (mp0) REVERT: A 22 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.7444 (tm-30) REVERT: B 3 GLU cc_start: 0.7308 (mp0) cc_final: 0.6476 (mp0) REVERT: B 5 ARG cc_start: 0.8572 (tpp80) cc_final: 0.8153 (tpp80) REVERT: B 22 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.7319 (tm-30) REVERT: C 3 GLU cc_start: 0.7095 (mp0) cc_final: 0.6305 (mp0) REVERT: D 3 GLU cc_start: 0.7384 (mp0) cc_final: 0.6727 (mp0) REVERT: D 11 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.8079 (tt0) REVERT: E 3 GLU cc_start: 0.7460 (mp0) cc_final: 0.6895 (mp0) REVERT: E 5 ARG cc_start: 0.8096 (ttp80) cc_final: 0.7010 (tpm170) REVERT: E 11 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.8239 (tt0) REVERT: E 23 ASP cc_start: 0.8619 (t0) cc_final: 0.8062 (t0) outliers start: 12 outliers final: 6 residues processed: 49 average time/residue: 0.0723 time to fit residues: 3.9448 Evaluate side-chains 46 residues out of total 155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 36 time to evaluate : 0.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain D residue 11 GLU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain E residue 11 GLU Chi-restraints excluded: chain E residue 12 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 17 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 19 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 5 optimal weight: 10.0000 chunk 8 optimal weight: 10.0000 chunk 14 optimal weight: 9.9990 chunk 18 optimal weight: 6.9990 chunk 16 optimal weight: 0.0020 chunk 4 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 overall best weight: 1.9992 ------------------------------------------------------------------------------- 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 = 0.3619 r_free = 0.3619 target = 0.085500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.076672 restraints weight = 3072.004| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 2.76 r_work: 0.3385 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3290 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.4131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 1555 Z= 0.183 Angle : 0.565 7.192 2085 Z= 0.280 Chirality : 0.050 0.131 220 Planarity : 0.002 0.020 275 Dihedral : 10.038 53.765 216 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer: Outliers : 7.74 % Allowed : 21.94 % Favored : 70.32 % 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 aren not related in a simple way. whole: -3.21 (0.43), residues: 190 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.44 (0.33), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 5 TYR 0.004 0.001 TYR C 10 PHE 0.006 0.001 PHE E 4 HIS 0.002 0.001 HIS A 14 Details of bonding type rmsd covalent geometry : bond 0.00392 ( 1555) covalent geometry : angle 0.56513 ( 2085) hydrogen bonds : bond 0.02083 ( 24) hydrogen bonds : angle 3.60898 ( 72) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 380 Ramachandran restraints generated. 190 Oldfield, 0 Emsley, 190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 380 Ramachandran restraints generated. 190 Oldfield, 0 Emsley, 190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 37 time to evaluate : 0.060 Fit side-chains REVERT: A 3 GLU cc_start: 0.8078 (mp0) cc_final: 0.7162 (mp0) REVERT: A 22 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.7617 (tm-30) REVERT: B 3 GLU cc_start: 0.7392 (mp0) cc_final: 0.6622 (mp0) REVERT: B 5 ARG cc_start: 0.8601 (tpp80) cc_final: 0.8186 (tpp80) REVERT: B 22 GLU cc_start: 0.8620 (OUTLIER) cc_final: 0.7744 (tm-30) REVERT: C 3 GLU cc_start: 0.7221 (mp0) cc_final: 0.6392 (mp0) REVERT: C 22 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.8202 (tm-30) REVERT: D 3 GLU cc_start: 0.7474 (mp0) cc_final: 0.6832 (mp0) REVERT: D 11 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.8126 (tt0) REVERT: D 22 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.7370 (tm-30) REVERT: E 3 GLU cc_start: 0.7532 (mp0) cc_final: 0.6923 (mp0) REVERT: E 5 ARG cc_start: 0.8179 (ttp80) cc_final: 0.7008 (tpm170) REVERT: E 11 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.8300 (tt0) REVERT: E 23 ASP cc_start: 0.8584 (t0) cc_final: 0.7983 (t0) outliers start: 12 outliers final: 6 residues processed: 49 average time/residue: 0.0688 time to fit residues: 3.7612 Evaluate side-chains 48 residues out of total 155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 36 time to evaluate : 0.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain D residue 11 GLU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 22 GLU Chi-restraints excluded: chain E residue 11 GLU Chi-restraints excluded: chain E residue 12 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 1 optimal weight: 5.9990 chunk 2 optimal weight: 7.9990 chunk 9 optimal weight: 6.9990 chunk 5 optimal weight: 0.9980 chunk 8 optimal weight: 9.9990 chunk 7 optimal weight: 7.9990 chunk 3 optimal weight: 6.9990 chunk 18 optimal weight: 0.9990 chunk 6 optimal weight: 7.9990 chunk 13 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- 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 = 0.3596 r_free = 0.3596 target = 0.084442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.075667 restraints weight = 3082.658| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 2.70 r_work: 0.3379 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.4210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 1555 Z= 0.211 Angle : 0.582 7.265 2085 Z= 0.290 Chirality : 0.050 0.133 220 Planarity : 0.003 0.025 275 Dihedral : 10.176 52.981 216 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer: Outliers : 7.74 % Allowed : 22.58 % Favored : 69.68 % 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 aren not related in a simple way. whole: -3.24 (0.43), residues: 190 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.46 (0.33), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 5 TYR 0.006 0.002 TYR B 10 PHE 0.007 0.001 PHE E 4 HIS 0.002 0.001 HIS A 14 Details of bonding type rmsd covalent geometry : bond 0.00448 ( 1555) covalent geometry : angle 0.58191 ( 2085) hydrogen bonds : bond 0.02264 ( 24) hydrogen bonds : angle 3.71522 ( 72) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 380 Ramachandran restraints generated. 190 Oldfield, 0 Emsley, 190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 380 Ramachandran restraints generated. 190 Oldfield, 0 Emsley, 190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 37 time to evaluate : 0.065 Fit side-chains REVERT: A 3 GLU cc_start: 0.8057 (mp0) cc_final: 0.7146 (mp0) REVERT: A 22 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.7539 (tm-30) REVERT: B 3 GLU cc_start: 0.7318 (mp0) cc_final: 0.6566 (mp0) REVERT: B 5 ARG cc_start: 0.8579 (tpp80) cc_final: 0.8123 (tpp80) REVERT: B 22 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.7660 (tm-30) REVERT: C 3 GLU cc_start: 0.7164 (mp0) cc_final: 0.6325 (mp0) REVERT: C 22 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.8188 (tm-30) REVERT: D 3 GLU cc_start: 0.7369 (mp0) cc_final: 0.6779 (mp0) REVERT: D 11 GLU cc_start: 0.8518 (OUTLIER) cc_final: 0.8161 (tt0) REVERT: D 22 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.7220 (tm-30) REVERT: E 3 GLU cc_start: 0.7475 (mp0) cc_final: 0.7208 (mp0) REVERT: E 5 ARG cc_start: 0.8161 (ttp80) cc_final: 0.7031 (tpm170) REVERT: E 23 ASP cc_start: 0.8595 (t0) cc_final: 0.8017 (t0) outliers start: 12 outliers final: 6 residues processed: 49 average time/residue: 0.0634 time to fit residues: 3.4757 Evaluate side-chains 46 residues out of total 155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 35 time to evaluate : 0.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain D residue 11 GLU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 22 GLU Chi-restraints excluded: chain E residue 12 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 12 optimal weight: 6.9990 chunk 15 optimal weight: 4.9990 chunk 5 optimal weight: 7.9990 chunk 9 optimal weight: 2.9990 chunk 19 optimal weight: 0.2980 chunk 8 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 6 optimal weight: 7.9990 chunk 7 optimal weight: 0.0970 chunk 14 optimal weight: 7.9990 chunk 2 optimal weight: 2.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- 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 = 0.3627 r_free = 0.3627 target = 0.085607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.076812 restraints weight = 3032.426| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 2.68 r_work: 0.3411 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3316 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.4325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 1555 Z= 0.174 Angle : 0.575 7.253 2085 Z= 0.281 Chirality : 0.050 0.132 220 Planarity : 0.002 0.019 275 Dihedral : 9.117 53.325 213 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer: Outliers : 7.10 % Allowed : 21.94 % Favored : 70.97 % 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 aren not related in a simple way. whole: -3.28 (0.43), residues: 190 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.49 (0.33), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 5 TYR 0.005 0.001 TYR B 10 PHE 0.006 0.001 PHE D 4 HIS 0.002 0.000 HIS A 14 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 1555) covalent geometry : angle 0.57472 ( 2085) hydrogen bonds : bond 0.02041 ( 24) hydrogen bonds : angle 3.73107 ( 72) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 380 Ramachandran restraints generated. 190 Oldfield, 0 Emsley, 190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 380 Ramachandran restraints generated. 190 Oldfield, 0 Emsley, 190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 37 time to evaluate : 0.062 Fit side-chains REVERT: A 3 GLU cc_start: 0.8038 (mp0) cc_final: 0.7144 (mp0) REVERT: A 22 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.7632 (tm-30) REVERT: B 3 GLU cc_start: 0.7394 (mp0) cc_final: 0.6578 (mp0) REVERT: B 5 ARG cc_start: 0.8609 (tpp80) cc_final: 0.8227 (tpp80) REVERT: B 22 GLU cc_start: 0.8570 (OUTLIER) cc_final: 0.7671 (tm-30) REVERT: C 3 GLU cc_start: 0.7233 (mp0) cc_final: 0.6385 (mp0) REVERT: C 22 GLU cc_start: 0.8478 (OUTLIER) cc_final: 0.8258 (tm-30) REVERT: D 3 GLU cc_start: 0.7404 (mp0) cc_final: 0.6749 (mp0) REVERT: D 11 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.8191 (tt0) REVERT: D 22 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.7203 (tm-30) REVERT: E 3 GLU cc_start: 0.7497 (mp0) cc_final: 0.6838 (mp0) REVERT: E 5 ARG cc_start: 0.8124 (ttp80) cc_final: 0.7008 (tpm170) REVERT: E 23 ASP cc_start: 0.8649 (t0) cc_final: 0.8079 (t0) outliers start: 11 outliers final: 6 residues processed: 48 average time/residue: 0.0620 time to fit residues: 3.3744 Evaluate side-chains 47 residues out of total 155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 36 time to evaluate : 0.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain D residue 11 GLU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 22 GLU Chi-restraints excluded: chain E residue 12 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 14 optimal weight: 9.9990 chunk 13 optimal weight: 6.9990 chunk 12 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.088520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.079370 restraints weight = 3096.087| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 2.78 r_work: 0.3465 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3369 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.4400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 1555 Z= 0.121 Angle : 0.562 7.638 2085 Z= 0.268 Chirality : 0.050 0.133 220 Planarity : 0.002 0.014 275 Dihedral : 8.656 53.034 213 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 7.74 % Allowed : 21.94 % Favored : 70.32 % 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 aren not related in a simple way. whole: -3.21 (0.44), residues: 190 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.44 (0.33), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 5 TYR 0.005 0.001 TYR C 10 PHE 0.003 0.001 PHE E 4 HIS 0.001 0.000 HIS A 14 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 1555) covalent geometry : angle 0.56193 ( 2085) hydrogen bonds : bond 0.01741 ( 24) hydrogen bonds : angle 3.63852 ( 72) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 380 Ramachandran restraints generated. 190 Oldfield, 0 Emsley, 190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 380 Ramachandran restraints generated. 190 Oldfield, 0 Emsley, 190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 37 time to evaluate : 0.037 Fit side-chains REVERT: A 3 GLU cc_start: 0.8044 (mp0) cc_final: 0.7132 (mp0) REVERT: A 22 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.7563 (tm-30) REVERT: B 3 GLU cc_start: 0.7403 (mp0) cc_final: 0.6643 (mp0) REVERT: B 5 ARG cc_start: 0.8527 (tpp80) cc_final: 0.7345 (ttp-110) REVERT: B 22 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.7928 (tm-30) REVERT: C 3 GLU cc_start: 0.7187 (mp0) cc_final: 0.6302 (mp0) REVERT: D 3 GLU cc_start: 0.7309 (mp0) cc_final: 0.6676 (mp0) REVERT: D 11 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.8232 (tt0) REVERT: D 22 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7177 (tm-30) REVERT: E 3 GLU cc_start: 0.7463 (mp0) cc_final: 0.7150 (mp0) REVERT: E 5 ARG cc_start: 0.8155 (ttp80) cc_final: 0.7060 (tpm170) REVERT: E 23 ASP cc_start: 0.8626 (t0) cc_final: 0.8071 (t0) outliers start: 12 outliers final: 6 residues processed: 49 average time/residue: 0.0575 time to fit residues: 3.1472 Evaluate side-chains 45 residues out of total 155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 35 time to evaluate : 0.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain D residue 11 GLU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 22 GLU Chi-restraints excluded: chain E residue 12 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 5 optimal weight: 7.9990 chunk 4 optimal weight: 7.9990 chunk 1 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 18 optimal weight: 8.9990 chunk 12 optimal weight: 9.9990 chunk 13 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 = 0.3574 r_free = 0.3574 target = 0.082940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.074581 restraints weight = 3138.916| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 2.66 r_work: 0.3355 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3263 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.4362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 1555 Z= 0.285 Angle : 0.637 7.492 2085 Z= 0.317 Chirality : 0.050 0.128 220 Planarity : 0.003 0.031 275 Dihedral : 9.569 58.109 213 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 7.10 % Allowed : 21.94 % Favored : 70.97 % 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 aren not related in a simple way. whole: -3.21 (0.44), residues: 190 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.44 (0.33), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 5 TYR 0.008 0.002 TYR B 10 PHE 0.008 0.002 PHE E 4 HIS 0.003 0.001 HIS C 14 Details of bonding type rmsd covalent geometry : bond 0.00603 ( 1555) covalent geometry : angle 0.63715 ( 2085) hydrogen bonds : bond 0.02611 ( 24) hydrogen bonds : angle 3.87126 ( 72) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 678.07 seconds wall clock time: 12 minutes 10.67 seconds (730.67 seconds total)