Starting phenix.real_space_refine on Wed Jul 23 06:46:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8owd_17234/07_2025/8owd_17234.cif Found real_map, /net/cci-nas-00/data/ceres_data/8owd_17234/07_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_17234/07_2025/8owd_17234.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8owd_17234/07_2025/8owd_17234.map" model { file = "/net/cci-nas-00/data/ceres_data/8owd_17234/07_2025/8owd_17234.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8owd_17234/07_2025/8owd_17234.cif" } resolution = 3.28 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: C, B, E, D Time building chain proxies: 0.78, per 1000 atoms: 0.51 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: 0.96 Conformation dependent library (CDL) restraints added in 193.4 milliseconds 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: 0.25 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: 0.36 Time building geometry restraints manager: 1.03 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 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' } 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: 0.750 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: 0.020 Process input model: 9.160 Find NCS groups from input model: 0.040 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:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.120 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 HIS 0.005 0.002 HIS D 14 PHE 0.015 0.005 PHE C 20 TYR 0.005 0.002 TYR D 10 ARG 0.009 0.005 ARG B 5 Details of bonding type rmsd hydrogen bonds : bond 0.09555 ( 24) hydrogen bonds : angle 6.50386 ( 72) covalent geometry : bond 0.01204 ( 1555) covalent geometry : angle 2.43800 ( 2085) *********************** 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 : 0.173 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: 0.1872 time to fit residues: 15.7531 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 : 0.189 ------------------------------------------------------------------------------- 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 16 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 12 optimal weight: 8.9990 chunk 19 optimal weight: 3.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 15 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.093931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.085181 restraints weight = 2926.528| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 2.50 r_work: 0.3522 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3430 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.2871 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= 0.179 Angle : 0.637 7.329 2085 Z= 0.331 Chirality : 0.052 0.129 220 Planarity : 0.002 0.013 275 Dihedral : 17.504 56.288 262 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 11.61 % Allowed : 21.29 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.62 (0.43), residues: 190 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.99 (0.33), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 6 PHE 0.009 0.001 PHE C 4 TYR 0.006 0.002 TYR B 10 ARG 0.003 0.001 ARG E 5 Details of bonding type rmsd hydrogen bonds : bond 0.02692 ( 24) hydrogen bonds : angle 5.15303 ( 72) covalent geometry : bond 0.00383 ( 1555) covalent geometry : angle 0.63703 ( 2085) *********************** 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 65 residues out of total 155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 47 time to evaluate : 0.189 Fit side-chains REVERT: A 13 HIS cc_start: 0.7267 (OUTLIER) cc_final: 0.6906 (m-70) REVERT: A 22 GLU cc_start: 0.8533 (tm-30) cc_final: 0.8295 (tm-30) REVERT: B 11 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7901 (tt0) REVERT: B 13 HIS cc_start: 0.6792 (OUTLIER) cc_final: 0.6441 (m170) REVERT: B 28 LYS cc_start: 0.8392 (OUTLIER) cc_final: 0.8176 (mttm) REVERT: C 13 HIS cc_start: 0.6928 (OUTLIER) cc_final: 0.6527 (m-70) REVERT: C 23 ASP cc_start: 0.8726 (t0) cc_final: 0.8476 (t0) REVERT: D 11 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7477 (tt0) REVERT: E 5 ARG cc_start: 0.8084 (ttp80) cc_final: 0.6556 (tpp-160) REVERT: E 13 HIS cc_start: 0.6978 (OUTLIER) cc_final: 0.6621 (m-70) REVERT: E 28 LYS cc_start: 0.8103 (OUTLIER) cc_final: 0.6483 (mmmt) outliers start: 18 outliers final: 5 residues processed: 64 average time/residue: 0.1752 time to fit residues: 12.2834 Evaluate side-chains 51 residues out of total 155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 38 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 B residue 13 HIS Chi-restraints excluded: chain B residue 28 LYS 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 2 optimal weight: 3.9990 chunk 12 optimal weight: 9.9990 chunk 18 optimal weight: 9.9990 chunk 3 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 17 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 4 optimal weight: 9.9990 chunk 7 optimal weight: 3.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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 = 0.3647 r_free = 0.3647 target = 0.087338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.079037 restraints weight = 3043.230| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 2.61 r_work: 0.3433 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3342 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.3472 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= 0.217 Angle : 0.590 6.240 2085 Z= 0.310 Chirality : 0.051 0.129 220 Planarity : 0.003 0.023 275 Dihedral : 12.963 52.499 234 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.13 (0.41), residues: 190 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.38 (0.32), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 13 PHE 0.009 0.001 PHE A 4 TYR 0.005 0.002 TYR B 10 ARG 0.003 0.001 ARG A 5 Details of bonding type rmsd hydrogen bonds : bond 0.02736 ( 24) hydrogen bonds : angle 4.52963 ( 72) covalent geometry : bond 0.00465 ( 1555) covalent geometry : angle 0.58950 ( 2085) *********************** 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: 12 poor density : 37 time to evaluate : 0.168 Fit side-chains REVERT: B 3 GLU cc_start: 0.7268 (mp0) cc_final: 0.6620 (mp0) REVERT: B 11 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.7802 (tt0) REVERT: B 28 LYS cc_start: 0.8329 (OUTLIER) cc_final: 0.7924 (mttm) REVERT: C 23 ASP cc_start: 0.8860 (t0) cc_final: 0.8273 (t0) REVERT: D 3 GLU cc_start: 0.7384 (mp0) cc_final: 0.7176 (mp0) REVERT: D 11 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.7928 (tt0) REVERT: E 3 GLU cc_start: 0.7330 (mp0) cc_final: 0.7106 (mp0) REVERT: E 5 ARG cc_start: 0.8128 (ttp80) cc_final: 0.6912 (tpm170) REVERT: E 11 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.7882 (tt0) REVERT: E 28 LYS cc_start: 0.8256 (OUTLIER) cc_final: 0.6610 (mmmt) outliers start: 12 outliers final: 6 residues processed: 49 average time/residue: 0.1501 time to fit residues: 8.2499 Evaluate side-chains 43 residues out of total 155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 32 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 B residue 28 LYS 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 13 HIS 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 7 optimal weight: 0.9990 chunk 15 optimal weight: 0.1980 chunk 6 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 3 optimal weight: 0.2980 chunk 12 optimal weight: 9.9990 chunk 11 optimal weight: 1.9990 chunk 9 optimal weight: 6.9990 chunk 4 optimal weight: 10.0000 chunk 14 optimal weight: 6.9990 chunk 2 optimal weight: 0.7980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 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 = 0.3683 r_free = 0.3683 target = 0.089501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.081044 restraints weight = 3022.956| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 2.69 r_work: 0.3457 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3367 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.3711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 1555 Z= 0.107 Angle : 0.547 6.786 2085 Z= 0.269 Chirality : 0.051 0.130 220 Planarity : 0.002 0.014 275 Dihedral : 10.715 48.828 226 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 6.45 % Allowed : 23.23 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.18 (0.42), residues: 190 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.42 (0.32), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 13 PHE 0.005 0.001 PHE E 4 TYR 0.002 0.001 TYR D 10 ARG 0.002 0.000 ARG D 5 Details of bonding type rmsd hydrogen bonds : bond 0.01792 ( 24) hydrogen bonds : angle 4.27445 ( 72) covalent geometry : bond 0.00236 ( 1555) covalent geometry : angle 0.54739 ( 2085) *********************** 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 49 residues out of total 155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 39 time to evaluate : 0.165 Fit side-chains REVERT: B 3 GLU cc_start: 0.7202 (mp0) cc_final: 0.6598 (mp0) REVERT: B 11 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.7972 (tt0) REVERT: C 23 ASP cc_start: 0.8801 (t0) cc_final: 0.8376 (t0) REVERT: D 3 GLU cc_start: 0.7389 (mp0) cc_final: 0.6577 (mp0) REVERT: D 11 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.7984 (tt0) REVERT: E 3 GLU cc_start: 0.7291 (mp0) cc_final: 0.7077 (mp0) REVERT: E 5 ARG cc_start: 0.8051 (ttp80) cc_final: 0.6906 (tpm170) REVERT: E 11 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.7998 (tt0) REVERT: E 23 ASP cc_start: 0.8547 (t0) cc_final: 0.7827 (t0) outliers start: 10 outliers final: 5 residues processed: 49 average time/residue: 0.1507 time to fit residues: 8.2999 Evaluate side-chains 43 residues out of total 155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 35 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 17 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 5 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 18 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 12 optimal weight: 9.9990 chunk 16 optimal weight: 5.9990 chunk 19 optimal weight: 0.6980 overall best weight: 2.1388 ------------------------------------------------------------------------------- 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 = 0.3624 r_free = 0.3624 target = 0.084724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.076311 restraints weight = 3134.332| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 2.73 r_work: 0.3397 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3300 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.3909 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= 0.193 Angle : 0.562 6.269 2085 Z= 0.284 Chirality : 0.050 0.129 220 Planarity : 0.002 0.019 275 Dihedral : 10.945 59.220 218 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer: Outliers : 5.81 % Allowed : 21.94 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.29 (0.41), residues: 190 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.50 (0.32), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 14 PHE 0.007 0.001 PHE A 4 TYR 0.005 0.001 TYR B 10 ARG 0.003 0.001 ARG D 5 Details of bonding type rmsd hydrogen bonds : bond 0.02393 ( 24) hydrogen bonds : angle 4.10363 ( 72) covalent geometry : bond 0.00414 ( 1555) covalent geometry : angle 0.56156 ( 2085) *********************** 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 42 residues out of total 155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 33 time to evaluate : 0.188 Fit side-chains REVERT: B 3 GLU cc_start: 0.7513 (mp0) cc_final: 0.6712 (mp0) REVERT: B 11 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.8074 (tt0) REVERT: C 3 GLU cc_start: 0.7279 (mp0) cc_final: 0.6481 (mp0) REVERT: C 23 ASP cc_start: 0.8868 (t0) cc_final: 0.8298 (t0) REVERT: D 3 GLU cc_start: 0.7454 (mp0) cc_final: 0.6814 (mp0) REVERT: D 11 GLU cc_start: 0.8538 (OUTLIER) cc_final: 0.8099 (tt0) REVERT: E 5 ARG cc_start: 0.8161 (ttp80) cc_final: 0.6923 (tpm170) REVERT: E 11 GLU cc_start: 0.8458 (OUTLIER) cc_final: 0.8194 (tt0) outliers start: 9 outliers final: 6 residues processed: 42 average time/residue: 0.1155 time to fit residues: 5.6363 Evaluate side-chains 39 residues out of total 155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 30 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 16 optimal weight: 10.0000 chunk 7 optimal weight: 0.7980 chunk 12 optimal weight: 9.9990 chunk 13 optimal weight: 8.9990 chunk 5 optimal weight: 8.9990 chunk 8 optimal weight: 9.9990 chunk 11 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 18 optimal weight: 8.9990 chunk 14 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.083090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.074684 restraints weight = 3161.586| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 2.69 r_work: 0.3347 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3252 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.4094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 1555 Z= 0.253 Angle : 0.588 6.569 2085 Z= 0.303 Chirality : 0.051 0.128 220 Planarity : 0.003 0.030 275 Dihedral : 11.316 56.344 218 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer: Outliers : 7.10 % Allowed : 23.23 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.41 (0.41), residues: 190 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.59 (0.31), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 14 PHE 0.008 0.002 PHE B 4 TYR 0.006 0.002 TYR B 10 ARG 0.004 0.001 ARG D 5 Details of bonding type rmsd hydrogen bonds : bond 0.02621 ( 24) hydrogen bonds : angle 3.89872 ( 72) covalent geometry : bond 0.00539 ( 1555) covalent geometry : angle 0.58788 ( 2085) *********************** 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 45 residues out of total 155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 34 time to evaluate : 0.183 Fit side-chains REVERT: A 22 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.7525 (tm-30) REVERT: B 3 GLU cc_start: 0.7527 (mp0) cc_final: 0.6744 (mp0) REVERT: B 11 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.8157 (tt0) REVERT: B 22 GLU cc_start: 0.8617 (OUTLIER) cc_final: 0.7315 (tm-30) REVERT: C 3 GLU cc_start: 0.7300 (mp0) cc_final: 0.6415 (mp0) REVERT: C 23 ASP cc_start: 0.8884 (t0) cc_final: 0.8225 (t0) REVERT: D 3 GLU cc_start: 0.7412 (mp0) cc_final: 0.6677 (mp0) REVERT: D 5 ARG cc_start: 0.8680 (tpp80) cc_final: 0.8446 (tpp80) REVERT: D 11 GLU cc_start: 0.8535 (OUTLIER) cc_final: 0.8069 (tt0) REVERT: E 3 GLU cc_start: 0.7286 (mp0) cc_final: 0.6729 (mp0) REVERT: E 5 ARG cc_start: 0.8140 (ttp80) cc_final: 0.6912 (mmp-170) REVERT: E 11 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.8325 (tt0) outliers start: 11 outliers final: 6 residues processed: 45 average time/residue: 0.1361 time to fit residues: 6.9523 Evaluate side-chains 44 residues out of total 155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 33 time to evaluate : 0.187 ------------------------------------------------------------------------------- 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 11 GLU 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 14 optimal weight: 3.9990 chunk 8 optimal weight: 9.9990 chunk 10 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 11 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 3 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.083379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.074837 restraints weight = 3201.982| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 2.71 r_work: 0.3365 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.4229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 1555 Z= 0.209 Angle : 0.569 6.650 2085 Z= 0.288 Chirality : 0.051 0.130 220 Planarity : 0.002 0.024 275 Dihedral : 11.149 59.391 218 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 7.10 % Allowed : 23.87 % Favored : 69.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.51 (0.41), residues: 190 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.66 (0.31), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 14 PHE 0.006 0.001 PHE B 4 TYR 0.005 0.001 TYR B 10 ARG 0.003 0.001 ARG D 5 Details of bonding type rmsd hydrogen bonds : bond 0.02202 ( 24) hydrogen bonds : angle 3.73327 ( 72) covalent geometry : bond 0.00444 ( 1555) covalent geometry : angle 0.56925 ( 2085) *********************** 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 47 residues out of total 155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 36 time to evaluate : 0.160 Fit side-chains REVERT: A 22 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.7564 (tm-30) REVERT: B 3 GLU cc_start: 0.7546 (mp0) cc_final: 0.6748 (mp0) REVERT: B 22 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.7335 (tm-30) REVERT: C 3 GLU cc_start: 0.7358 (mp0) cc_final: 0.6442 (mp0) REVERT: C 23 ASP cc_start: 0.8930 (t0) cc_final: 0.8175 (t0) REVERT: D 3 GLU cc_start: 0.7405 (mp0) cc_final: 0.6699 (mp0) REVERT: D 11 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.8156 (tt0) REVERT: E 3 GLU cc_start: 0.7315 (mp0) cc_final: 0.6719 (mp0) REVERT: E 5 ARG cc_start: 0.8146 (ttp80) cc_final: 0.6877 (tpm170) outliers start: 11 outliers final: 6 residues processed: 46 average time/residue: 0.1271 time to fit residues: 6.6470 Evaluate side-chains 43 residues out of total 155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 34 time to evaluate : 0.159 ------------------------------------------------------------------------------- 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 12 VAL 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 16 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 chunk 14 optimal weight: 7.9990 chunk 11 optimal weight: 6.9990 chunk 13 optimal weight: 6.9990 chunk 15 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 3 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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 = 0.3515 r_free = 0.3515 target = 0.080292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.072206 restraints weight = 3223.190| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 2.67 r_work: 0.3301 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.4407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.045 1555 Z= 0.364 Angle : 0.664 6.757 2085 Z= 0.346 Chirality : 0.052 0.131 220 Planarity : 0.004 0.045 275 Dihedral : 9.432 53.689 212 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 6.45 % Allowed : 23.87 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.53 (0.41), residues: 190 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.68 (0.32), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 14 PHE 0.011 0.002 PHE A 4 TYR 0.008 0.002 TYR D 10 ARG 0.005 0.001 ARG D 5 Details of bonding type rmsd hydrogen bonds : bond 0.02595 ( 24) hydrogen bonds : angle 3.92213 ( 72) covalent geometry : bond 0.00770 ( 1555) covalent geometry : angle 0.66440 ( 2085) *********************** 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 44 residues out of total 155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 34 time to evaluate : 0.181 Fit side-chains REVERT: A 22 GLU cc_start: 0.8509 (OUTLIER) cc_final: 0.7644 (tm-30) REVERT: B 3 GLU cc_start: 0.7592 (mp0) cc_final: 0.6864 (mp0) REVERT: B 22 GLU cc_start: 0.8647 (OUTLIER) cc_final: 0.7354 (tm-30) REVERT: C 3 GLU cc_start: 0.7421 (mp0) cc_final: 0.7022 (mp0) REVERT: C 23 ASP cc_start: 0.8981 (t0) cc_final: 0.8161 (t0) REVERT: D 3 GLU cc_start: 0.7387 (mp0) cc_final: 0.6548 (mp0) REVERT: D 11 GLU cc_start: 0.8766 (OUTLIER) cc_final: 0.8261 (tt0) REVERT: E 3 GLU cc_start: 0.7351 (mp0) cc_final: 0.6451 (mp0) REVERT: E 5 ARG cc_start: 0.8254 (ttp80) cc_final: 0.7060 (mmp-170) REVERT: E 22 GLU cc_start: 0.8607 (OUTLIER) cc_final: 0.8364 (tm-30) outliers start: 10 outliers final: 6 residues processed: 44 average time/residue: 0.1214 time to fit residues: 6.3387 Evaluate side-chains 43 residues out of total 155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 33 time to evaluate : 0.181 ------------------------------------------------------------------------------- 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 12 VAL Chi-restraints excluded: chain E residue 22 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 2 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 17 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 15 optimal weight: 0.9980 chunk 8 optimal weight: 9.9990 chunk 3 optimal weight: 0.2980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3641 r_free = 0.3641 target = 0.086019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.077661 restraints weight = 3181.414| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 2.74 r_work: 0.3430 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3336 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.4578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 1555 Z= 0.106 Angle : 0.558 6.858 2085 Z= 0.270 Chirality : 0.051 0.134 220 Planarity : 0.002 0.024 275 Dihedral : 8.567 54.859 212 Min Nonbonded Distance : 2.643 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 5.81 % Allowed : 24.52 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.65 (0.41), residues: 190 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.77 (0.31), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 13 PHE 0.003 0.000 PHE E 4 TYR 0.009 0.001 TYR E 10 ARG 0.002 0.000 ARG D 5 Details of bonding type rmsd hydrogen bonds : bond 0.01290 ( 24) hydrogen bonds : angle 3.65853 ( 72) covalent geometry : bond 0.00226 ( 1555) covalent geometry : angle 0.55839 ( 2085) *********************** 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: 9 poor density : 39 time to evaluate : 0.182 Fit side-chains REVERT: A 22 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.7439 (tm-30) REVERT: B 3 GLU cc_start: 0.7607 (mp0) cc_final: 0.6826 (mp0) REVERT: B 22 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.7333 (tm-30) REVERT: B 23 ASP cc_start: 0.8703 (t0) cc_final: 0.8444 (t0) REVERT: C 3 GLU cc_start: 0.7342 (mp0) cc_final: 0.6374 (mp0) REVERT: C 5 ARG cc_start: 0.8504 (ttm170) cc_final: 0.8183 (ttm-80) REVERT: C 23 ASP cc_start: 0.8865 (t0) cc_final: 0.8340 (t0) REVERT: D 3 GLU cc_start: 0.7412 (mp0) cc_final: 0.6710 (mp0) REVERT: D 7 ASP cc_start: 0.8701 (m-30) cc_final: 0.8165 (m-30) REVERT: D 11 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.8235 (tt0) REVERT: E 3 GLU cc_start: 0.7360 (mp0) cc_final: 0.6739 (mp0) REVERT: E 5 ARG cc_start: 0.8156 (ttp80) cc_final: 0.7064 (mmp-170) outliers start: 9 outliers final: 5 residues processed: 48 average time/residue: 0.1334 time to fit residues: 7.2714 Evaluate side-chains 46 residues out of total 155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 38 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 12 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 14 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 7 optimal weight: 0.0870 chunk 4 optimal weight: 8.9990 chunk 3 optimal weight: 3.9990 chunk 9 optimal weight: 7.9990 chunk 15 optimal weight: 7.9990 chunk 19 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 overall best weight: 1.7964 ------------------------------------------------------------------------------- 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 = 0.3613 r_free = 0.3613 target = 0.084710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.076162 restraints weight = 3169.836| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 2.74 r_work: 0.3391 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3294 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.4590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 1555 Z= 0.170 Angle : 0.611 7.068 2085 Z= 0.292 Chirality : 0.052 0.135 220 Planarity : 0.002 0.023 275 Dihedral : 8.445 52.608 212 Min Nonbonded Distance : 2.642 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 5.16 % Allowed : 26.45 % Favored : 68.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.59 (0.41), residues: 190 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.73 (0.32), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 14 PHE 0.006 0.001 PHE E 4 TYR 0.006 0.001 TYR E 10 ARG 0.003 0.000 ARG D 5 Details of bonding type rmsd hydrogen bonds : bond 0.01866 ( 24) hydrogen bonds : angle 3.71782 ( 72) covalent geometry : bond 0.00375 ( 1555) covalent geometry : angle 0.61059 ( 2085) ********************** 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 45 residues out of total 155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 37 time to evaluate : 0.180 Fit side-chains REVERT: A 22 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.7596 (tm-30) REVERT: B 3 GLU cc_start: 0.7639 (mp0) cc_final: 0.6857 (mp0) REVERT: B 22 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.7382 (tm-30) REVERT: C 3 GLU cc_start: 0.7442 (mp0) cc_final: 0.6514 (mp0) REVERT: C 23 ASP cc_start: 0.8888 (t0) cc_final: 0.8356 (t0) REVERT: D 3 GLU cc_start: 0.7461 (mp0) cc_final: 0.6768 (mp0) REVERT: D 11 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.8301 (tt0) REVERT: E 3 GLU cc_start: 0.7371 (mp0) cc_final: 0.6754 (mp0) REVERT: E 5 ARG cc_start: 0.8242 (ttp80) cc_final: 0.7120 (mmp-170) REVERT: E 23 ASP cc_start: 0.8589 (t0) cc_final: 0.8074 (t0) outliers start: 8 outliers final: 5 residues processed: 45 average time/residue: 0.1363 time to fit residues: 6.9752 Evaluate side-chains 43 residues out of total 155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 35 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 12 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 7 optimal weight: 4.9990 chunk 11 optimal weight: 0.6980 chunk 13 optimal weight: 7.9990 chunk 6 optimal weight: 0.9990 chunk 14 optimal weight: 10.0000 chunk 18 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 10 optimal weight: 0.0040 chunk 3 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 overall best weight: 0.9398 ------------------------------------------------------------------------------- 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 = 0.3682 r_free = 0.3682 target = 0.087813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.078772 restraints weight = 3202.632| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 2.89 r_work: 0.3459 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.4724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 1555 Z= 0.110 Angle : 0.590 7.082 2085 Z= 0.277 Chirality : 0.052 0.136 220 Planarity : 0.002 0.019 275 Dihedral : 8.108 53.832 212 Min Nonbonded Distance : 2.648 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 5.16 % Allowed : 26.45 % Favored : 68.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.63 (0.42), residues: 190 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.76 (0.32), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 13 PHE 0.005 0.001 PHE E 4 TYR 0.008 0.001 TYR E 10 ARG 0.002 0.000 ARG D 5 Details of bonding type rmsd hydrogen bonds : bond 0.01357 ( 24) hydrogen bonds : angle 3.62440 ( 72) covalent geometry : bond 0.00249 ( 1555) covalent geometry : angle 0.59040 ( 2085) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1283.60 seconds wall clock time: 22 minutes 56.96 seconds (1376.96 seconds total)