Starting phenix.real_space_refine on Thu Sep 10 19:49:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7e0f_30931/09_2026/7e0f_30931.cif Found real_map, /net/cci-nas-00/data/ceres_data/7e0f_30931/09_2026/7e0f_30931.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7e0f_30931/09_2026/7e0f_30931.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7e0f_30931/09_2026/7e0f_30931.map" model { file = "/net/cci-nas-00/data/ceres_data/7e0f_30931/09_2026/7e0f_30931.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7e0f_30931/09_2026/7e0f_30931.cif" } resolution = 3.02 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 3 Type Number sf(0) Gaussians C 1248 2.51 5 N 354 2.21 5 O 420 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 2022 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 337 Classifications: {'peptide': 49} Link IDs: {'TRANS': 48} Restraints were copied for chains: B, C, D, E, F Time building chain proxies: 0.32, per 1000 atoms: 0.16 Number of scatterers: 2022 At special positions: 0 Unit cell: (79.5, 81.62, 34.98, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 420 8.00 N 354 7.00 C 1248 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: 0.10 Conformation dependent library (CDL) restraints added in 55.2 milliseconds 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 516 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 10 sheets defined 0.0% alpha, 17.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.07 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 54 through 55 Processing sheet with id=AA2, first strand: chain 'A' and resid 61 through 63 Processing sheet with id=AA3, first strand: chain 'A' and resid 69 through 71 removed outlier: 6.582A pdb=" N VAL A 70 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL B 70 " --> pdb=" O VAL C 71 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 75 through 77 removed outlier: 6.344A pdb=" N ALA A 76 " --> pdb=" O VAL B 77 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ALA B 76 " --> pdb=" O VAL C 77 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 93 through 94 Processing sheet with id=AA6, first strand: chain 'D' and resid 54 through 55 Processing sheet with id=AA7, first strand: chain 'D' and resid 61 through 63 Processing sheet with id=AA8, first strand: chain 'D' and resid 69 through 71 removed outlier: 6.613A pdb=" N VAL D 70 " --> pdb=" O VAL E 71 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N VAL E 70 " --> pdb=" O VAL F 71 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'D' and resid 75 through 77 removed outlier: 6.385A pdb=" N ALA D 76 " --> pdb=" O VAL E 77 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ALA E 76 " --> pdb=" O VAL F 77 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'D' and resid 93 through 94 16 hydrogen bonds defined for protein. 48 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: 0.21 Time building geometry restraints manager: 0.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.27: 378 1.27 - 1.34: 312 1.34 - 1.41: 60 1.41 - 1.47: 366 1.47 - 1.54: 912 Bond restraints: 2028 Sorted by residual: bond pdb=" C GLN C 79 " pdb=" N LYS C 80 " ideal model delta sigma weight residual 1.332 1.269 0.064 1.40e-02 5.10e+03 2.06e+01 bond pdb=" C GLN F 79 " pdb=" N LYS F 80 " ideal model delta sigma weight residual 1.332 1.269 0.063 1.40e-02 5.10e+03 2.04e+01 bond pdb=" C GLN D 79 " pdb=" N LYS D 80 " ideal model delta sigma weight residual 1.332 1.269 0.063 1.40e-02 5.10e+03 2.03e+01 bond pdb=" C GLN B 79 " pdb=" N LYS B 80 " ideal model delta sigma weight residual 1.332 1.270 0.063 1.40e-02 5.10e+03 2.02e+01 bond pdb=" C GLN A 79 " pdb=" N LYS A 80 " ideal model delta sigma weight residual 1.332 1.270 0.063 1.40e-02 5.10e+03 2.00e+01 ... (remaining 2023 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.14: 2321 1.14 - 2.28: 337 2.28 - 3.43: 42 3.43 - 4.57: 42 4.57 - 5.71: 6 Bond angle restraints: 2748 Sorted by residual: angle pdb=" C GLY D 93 " pdb=" N PHE D 94 " pdb=" CA PHE D 94 " ideal model delta sigma weight residual 121.58 115.87 5.71 1.62e+00 3.81e-01 1.24e+01 angle pdb=" C GLY B 93 " pdb=" N PHE B 94 " pdb=" CA PHE B 94 " ideal model delta sigma weight residual 121.58 115.87 5.71 1.62e+00 3.81e-01 1.24e+01 angle pdb=" C GLY F 93 " pdb=" N PHE F 94 " pdb=" CA PHE F 94 " ideal model delta sigma weight residual 121.58 115.88 5.70 1.62e+00 3.81e-01 1.24e+01 angle pdb=" C GLY E 93 " pdb=" N PHE E 94 " pdb=" CA PHE E 94 " ideal model delta sigma weight residual 121.58 115.89 5.69 1.62e+00 3.81e-01 1.23e+01 angle pdb=" C GLY A 93 " pdb=" N PHE A 94 " pdb=" CA PHE A 94 " ideal model delta sigma weight residual 121.58 115.89 5.69 1.62e+00 3.81e-01 1.23e+01 ... (remaining 2743 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.15: 1086 17.15 - 34.29: 84 34.29 - 51.43: 12 51.43 - 68.58: 0 68.58 - 85.72: 12 Dihedral angle restraints: 1194 sinusoidal: 390 harmonic: 804 Sorted by residual: dihedral pdb=" CA GLY A 93 " pdb=" C GLY A 93 " pdb=" N PHE A 94 " pdb=" CA PHE A 94 " ideal model delta harmonic sigma weight residual -180.00 -153.61 -26.39 0 5.00e+00 4.00e-02 2.79e+01 dihedral pdb=" CA GLY B 93 " pdb=" C GLY B 93 " pdb=" N PHE B 94 " pdb=" CA PHE B 94 " ideal model delta harmonic sigma weight residual 180.00 -153.61 -26.39 0 5.00e+00 4.00e-02 2.79e+01 dihedral pdb=" CA GLY E 93 " pdb=" C GLY E 93 " pdb=" N PHE E 94 " pdb=" CA PHE E 94 " ideal model delta harmonic sigma weight residual -180.00 -153.64 -26.36 0 5.00e+00 4.00e-02 2.78e+01 ... (remaining 1191 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 161 0.043 - 0.085: 128 0.085 - 0.127: 54 0.127 - 0.169: 17 0.169 - 0.211: 6 Chirality restraints: 366 Sorted by residual: chirality pdb=" CB VAL A 95 " pdb=" CA VAL A 95 " pdb=" CG1 VAL A 95 " pdb=" CG2 VAL A 95 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CB VAL B 95 " pdb=" CA VAL B 95 " pdb=" CG1 VAL B 95 " pdb=" CG2 VAL B 95 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CB VAL E 95 " pdb=" CA VAL E 95 " pdb=" CG1 VAL E 95 " pdb=" CG2 VAL E 95 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.20 2.00e-01 2.50e+01 1.05e+00 ... (remaining 363 not shown) Planarity restraints: 348 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 90 " 0.007 2.00e-02 2.50e+03 1.47e-02 2.16e+00 pdb=" C ALA A 90 " -0.025 2.00e-02 2.50e+03 pdb=" O ALA A 90 " 0.010 2.00e-02 2.50e+03 pdb=" N ALA A 91 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA D 90 " -0.007 2.00e-02 2.50e+03 1.47e-02 2.15e+00 pdb=" C ALA D 90 " 0.025 2.00e-02 2.50e+03 pdb=" O ALA D 90 " -0.010 2.00e-02 2.50e+03 pdb=" N ALA D 91 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA C 90 " 0.007 2.00e-02 2.50e+03 1.47e-02 2.15e+00 pdb=" C ALA C 90 " -0.025 2.00e-02 2.50e+03 pdb=" O ALA C 90 " 0.010 2.00e-02 2.50e+03 pdb=" N ALA C 91 " 0.009 2.00e-02 2.50e+03 ... (remaining 345 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 770 2.85 - 3.36: 1787 3.36 - 3.88: 2984 3.88 - 4.39: 3268 4.39 - 4.90: 6828 Nonbonded interactions: 15637 Sorted by model distance: nonbonded pdb=" OG1 THR D 54 " pdb=" OG1 THR D 64 " model vdw 2.341 3.040 nonbonded pdb=" OG1 THR E 54 " pdb=" OG1 THR E 64 " model vdw 2.341 3.040 nonbonded pdb=" OG1 THR F 54 " pdb=" OG1 THR F 64 " model vdw 2.341 3.040 nonbonded pdb=" OG1 THR B 54 " pdb=" OG1 THR B 64 " model vdw 2.341 3.040 nonbonded pdb=" OG1 THR A 54 " pdb=" OG1 THR A 64 " model vdw 2.341 3.040 ... (remaining 15632 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 1.280 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: 0.010 Set scattering table: 0.000 Process input model: 2.870 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 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:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 5.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 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 : 0.016 0.086 2028 Z= 0.747 Angle : 0.986 5.709 2748 Z= 0.581 Chirality : 0.069 0.211 366 Planarity : 0.003 0.015 348 Dihedral : 15.885 85.718 678 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.77 % Favored : 87.23 % Rotamer: Outliers : 0.00 % Allowed : 17.65 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.10 (0.40), residues: 282 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.88 (0.31), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.024 0.007 PHE B 94 HIS 0.001 0.000 HIS F 50 Details of bonding type rmsd/Z covalent geometry : bond 0.01578 / 0.75 ( 2028) covalent geometry : angle 0.98648 / 0.58 ( 2748) hydrogen bonds : bond 0.29842 / 22.52 ( 16) hydrogen bonds : angle 11.70191 / 8.07 ( 48) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.081 Fit side-chains REVERT: B 62 GLN cc_start: 0.8853 (pt0) cc_final: 0.8407 (pt0) REVERT: C 62 GLN cc_start: 0.8814 (pt0) cc_final: 0.8532 (pt0) REVERT: C 83 GLU cc_start: 0.8154 (mm-30) cc_final: 0.7340 (pm20) REVERT: E 60 LYS cc_start: 0.7688 (ttmt) cc_final: 0.7419 (mtpt) REVERT: E 62 GLN cc_start: 0.9017 (pt0) cc_final: 0.8721 (pt0) REVERT: F 61 GLU cc_start: 0.8281 (mt-10) cc_final: 0.8048 (mt-10) REVERT: F 62 GLN cc_start: 0.8878 (pt0) cc_final: 0.8589 (pt0) REVERT: F 83 GLU cc_start: 0.8210 (mm-30) cc_final: 0.7547 (pm20) outliers start: 0 outliers final: 0 residues processed: 41 average time/residue: 0.0894 time to fit residues: 4.1339 Evaluate side-chains 22 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 12 optimal weight: 10.0000 chunk 13 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 8 optimal weight: 7.9990 chunk 16 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 9 optimal weight: 5.9990 chunk 11 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 4 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 GLN F 62 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4781 r_free = 0.4781 target = 0.205296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.148360 restraints weight = 1991.252| |-----------------------------------------------------------------------------| r_work (start): 0.4264 rms_B_bonded: 3.04 r_work: 0.4130 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.4130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 2028 Z= 0.138 Angle : 0.600 4.688 2748 Z= 0.336 Chirality : 0.052 0.127 366 Planarity : 0.002 0.009 348 Dihedral : 5.483 25.243 288 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % Rotamer: Outliers : 5.39 % Allowed : 15.20 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.51 (0.44), residues: 282 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.43 (0.33), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.015 0.004 PHE B 94 HIS 0.000 0.000 HIS C 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 ( 2028) covalent geometry : angle 0.60019 / 0.34 ( 2748) hydrogen bonds : bond 0.04894 / 3.54 ( 16) hydrogen bonds : angle 6.98584 / 4.92 ( 48) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 39 time to evaluate : 0.073 Fit side-chains REVERT: B 62 GLN cc_start: 0.8654 (pt0) cc_final: 0.8428 (pt0) REVERT: C 61 GLU cc_start: 0.8366 (mt-10) cc_final: 0.8030 (mt-10) REVERT: C 83 GLU cc_start: 0.8290 (mm-30) cc_final: 0.7340 (pm20) REVERT: E 62 GLN cc_start: 0.8814 (pt0) cc_final: 0.8438 (pt0) REVERT: F 61 GLU cc_start: 0.8252 (mt-10) cc_final: 0.8013 (mt-10) REVERT: F 83 GLU cc_start: 0.8422 (mm-30) cc_final: 0.7513 (pm20) outliers start: 11 outliers final: 8 residues processed: 49 average time/residue: 0.0402 time to fit residues: 2.4491 Evaluate side-chains 37 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 29 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain F residue 52 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 23 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 3 optimal weight: 0.0980 chunk 13 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 5 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 52.5643 > 50:) chunk 20 optimal weight: 0.5980 chunk 16 optimal weight: 6.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 62 GLN C 62 GLN ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 79 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4762 r_free = 0.4762 target = 0.204700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.145950 restraints weight = 1990.098| |-----------------------------------------------------------------------------| r_work (start): 0.4228 rms_B_bonded: 3.10 r_work: 0.4089 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.4089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 2028 Z= 0.183 Angle : 0.592 4.158 2748 Z= 0.334 Chirality : 0.051 0.124 366 Planarity : 0.002 0.009 348 Dihedral : 5.326 25.120 288 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.57 % Favored : 90.43 % Rotamer: Outliers : 5.88 % Allowed : 18.63 % Favored : 75.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.25 (0.45), residues: 282 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.23 (0.34), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.015 0.004 PHE C 94 HIS 0.000 0.000 HIS B 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.18 ( 2028) covalent geometry : angle 0.59190 / 0.33 ( 2748) hydrogen bonds : bond 0.03936 / 2.86 ( 16) hydrogen bonds : angle 6.53728 / 4.55 ( 48) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 31 time to evaluate : 0.071 Fit side-chains REVERT: C 61 GLU cc_start: 0.8403 (mt-10) cc_final: 0.8116 (mt-10) REVERT: C 83 GLU cc_start: 0.8282 (mm-30) cc_final: 0.7301 (pm20) REVERT: F 61 GLU cc_start: 0.8315 (mt-10) cc_final: 0.8069 (mt-10) REVERT: F 83 GLU cc_start: 0.8409 (mm-30) cc_final: 0.7452 (pm20) outliers start: 12 outliers final: 11 residues processed: 43 average time/residue: 0.0389 time to fit residues: 2.0994 Evaluate side-chains 40 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 29 time to evaluate : 0.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain F residue 52 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 9 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 chunk 11 optimal weight: 0.2980 chunk 12 optimal weight: 20.0000 chunk 20 optimal weight: 10.0000 chunk 13 optimal weight: 3.9990 chunk 22 optimal weight: 0.4980 chunk 7 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 62 GLN F 62 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4800 r_free = 0.4800 target = 0.208723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.149758 restraints weight = 1953.489| |-----------------------------------------------------------------------------| r_work (start): 0.4234 rms_B_bonded: 3.13 r_work: 0.4115 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.4115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2028 Z= 0.133 Angle : 0.511 3.834 2748 Z= 0.288 Chirality : 0.049 0.123 366 Planarity : 0.002 0.019 348 Dihedral : 4.948 22.652 288 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 5.88 % Allowed : 19.12 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.92 (0.47), residues: 282 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.98 (0.36), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.013 0.003 PHE E 94 HIS 0.000 0.000 HIS A 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 ( 2028) covalent geometry : angle 0.51119 / 0.29 ( 2748) hydrogen bonds : bond 0.03048 / 2.23 ( 16) hydrogen bonds : angle 5.82521 / 4.04 ( 48) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 30 time to evaluate : 0.125 Fit side-chains REVERT: B 62 GLN cc_start: 0.8593 (pt0) cc_final: 0.8273 (mt0) REVERT: C 61 GLU cc_start: 0.8408 (mt-10) cc_final: 0.8094 (mt-10) REVERT: C 83 GLU cc_start: 0.8302 (mm-30) cc_final: 0.7194 (pm20) REVERT: D 83 GLU cc_start: 0.8234 (mm-30) cc_final: 0.7845 (mm-30) REVERT: F 61 GLU cc_start: 0.8283 (mt-10) cc_final: 0.8056 (mt-10) outliers start: 12 outliers final: 10 residues processed: 41 average time/residue: 0.0472 time to fit residues: 2.3970 Evaluate side-chains 36 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 26 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain F residue 52 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 23 optimal weight: 0.0170 chunk 4 optimal weight: 10.0000 chunk 1 optimal weight: 7.9990 chunk 0 optimal weight: 5.9990 chunk 12 optimal weight: 10.0000 chunk 11 optimal weight: 0.0970 chunk 10 optimal weight: 3.9990 chunk 16 optimal weight: 8.9990 chunk 18 optimal weight: 0.9980 chunk 17 optimal weight: 6.9990 chunk 22 optimal weight: 0.7980 overall best weight: 1.1818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 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 = 0.4710 r_free = 0.4710 target = 0.194246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.133983 restraints weight = 2092.488| |-----------------------------------------------------------------------------| r_work (start): 0.4203 rms_B_bonded: 3.43 r_work: 0.4044 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.4044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 2028 Z= 0.161 Angle : 0.528 4.328 2748 Z= 0.299 Chirality : 0.049 0.124 366 Planarity : 0.002 0.016 348 Dihedral : 5.017 22.876 288 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.51 % Favored : 91.49 % Rotamer: Outliers : 6.86 % Allowed : 18.63 % Favored : 74.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.77 (0.48), residues: 282 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.87 (0.37), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.016 0.004 PHE E 94 HIS 0.000 0.000 HIS B 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 ( 2028) covalent geometry : angle 0.52756 / 0.30 ( 2748) hydrogen bonds : bond 0.03129 / 2.34 ( 16) hydrogen bonds : angle 6.09362 / 4.22 ( 48) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 29 time to evaluate : 0.088 Fit side-chains REVERT: A 79 GLN cc_start: 0.9071 (OUTLIER) cc_final: 0.8109 (mm110) REVERT: A 96 LYS cc_start: 0.8713 (tttm) cc_final: 0.8461 (ttpt) REVERT: B 62 GLN cc_start: 0.8676 (pt0) cc_final: 0.8384 (mt0) REVERT: B 79 GLN cc_start: 0.9075 (OUTLIER) cc_final: 0.7933 (mm110) REVERT: C 61 GLU cc_start: 0.8463 (mt-10) cc_final: 0.8155 (mt-10) REVERT: C 83 GLU cc_start: 0.8331 (mm-30) cc_final: 0.7201 (pm20) REVERT: D 83 GLU cc_start: 0.8322 (mm-30) cc_final: 0.7905 (mm-30) REVERT: F 61 GLU cc_start: 0.8314 (mt-10) cc_final: 0.8084 (mt-10) outliers start: 14 outliers final: 11 residues processed: 42 average time/residue: 0.0466 time to fit residues: 2.4121 Evaluate side-chains 39 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 26 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 79 GLN Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 62 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 21 optimal weight: 6.9990 chunk 10 optimal weight: 0.4980 chunk 8 optimal weight: 10.0000 chunk 19 optimal weight: 4.9990 chunk 4 optimal weight: 6.9990 chunk 23 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 1 optimal weight: 6.9990 chunk 6 optimal weight: 0.6980 chunk 16 optimal weight: 9.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4827 r_free = 0.4827 target = 0.212137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.152916 restraints weight = 1965.025| |-----------------------------------------------------------------------------| r_work (start): 0.4295 rms_B_bonded: 3.31 r_work: 0.4151 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.4151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2028 Z= 0.117 Angle : 0.466 3.848 2748 Z= 0.264 Chirality : 0.048 0.122 366 Planarity : 0.002 0.014 348 Dihedral : 4.687 20.893 288 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 6.37 % Allowed : 18.63 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.61 (0.50), residues: 282 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.75 (0.38), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.013 0.003 PHE E 94 HIS 0.000 0.000 HIS E 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 ( 2028) covalent geometry : angle 0.46580 / 0.26 ( 2748) hydrogen bonds : bond 0.02690 / 1.93 ( 16) hydrogen bonds : angle 5.57259 / 3.83 ( 48) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 29 time to evaluate : 0.077 Fit side-chains REVERT: A 62 GLN cc_start: 0.8648 (pt0) cc_final: 0.8192 (mt0) REVERT: A 79 GLN cc_start: 0.8999 (OUTLIER) cc_final: 0.8053 (mm110) REVERT: A 96 LYS cc_start: 0.8612 (tttm) cc_final: 0.8394 (tttt) REVERT: B 62 GLN cc_start: 0.8627 (pt0) cc_final: 0.8402 (mt0) REVERT: C 61 GLU cc_start: 0.8414 (mt-10) cc_final: 0.8096 (mt-10) REVERT: D 62 GLN cc_start: 0.8753 (mt0) cc_final: 0.8205 (mp10) REVERT: D 83 GLU cc_start: 0.8316 (mm-30) cc_final: 0.7893 (mm-30) REVERT: F 61 GLU cc_start: 0.8334 (mt-10) cc_final: 0.8113 (mt-10) outliers start: 13 outliers final: 9 residues processed: 40 average time/residue: 0.0346 time to fit residues: 1.7628 Evaluate side-chains 38 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 28 time to evaluate : 0.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 79 GLN Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain F residue 52 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 19 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 12 optimal weight: 9.9990 chunk 6 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 chunk 21 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 GLN ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4751 r_free = 0.4751 target = 0.199660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.137301 restraints weight = 1982.645| |-----------------------------------------------------------------------------| r_work (start): 0.4250 rms_B_bonded: 3.40 r_work: 0.4094 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.4094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2028 Z= 0.115 Angle : 0.476 4.688 2748 Z= 0.269 Chirality : 0.048 0.122 366 Planarity : 0.002 0.011 348 Dihedral : 4.624 20.622 288 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 7.35 % Allowed : 18.63 % Favored : 74.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.53 (0.50), residues: 282 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.69 (0.38), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.013 0.003 PHE E 94 HIS 0.000 0.000 HIS B 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 ( 2028) covalent geometry : angle 0.47606 / 0.27 ( 2748) hydrogen bonds : bond 0.02630 / 1.87 ( 16) hydrogen bonds : angle 5.43125 / 3.68 ( 48) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 29 time to evaluate : 0.074 Fit side-chains REVERT: A 62 GLN cc_start: 0.8623 (pt0) cc_final: 0.8111 (mt0) REVERT: A 79 GLN cc_start: 0.8930 (OUTLIER) cc_final: 0.8088 (mm110) REVERT: A 83 GLU cc_start: 0.7840 (mp0) cc_final: 0.7573 (mm-30) REVERT: B 79 GLN cc_start: 0.8983 (OUTLIER) cc_final: 0.7996 (mm110) REVERT: C 61 GLU cc_start: 0.8420 (mt-10) cc_final: 0.8089 (mt-10) REVERT: C 79 GLN cc_start: 0.9039 (OUTLIER) cc_final: 0.8141 (mt0) REVERT: D 62 GLN cc_start: 0.8802 (mt0) cc_final: 0.8027 (mp10) REVERT: D 79 GLN cc_start: 0.8954 (OUTLIER) cc_final: 0.8274 (mm110) REVERT: D 83 GLU cc_start: 0.8270 (mm-30) cc_final: 0.7991 (mm-30) REVERT: E 62 GLN cc_start: 0.8502 (OUTLIER) cc_final: 0.8159 (mt0) REVERT: E 79 GLN cc_start: 0.8897 (OUTLIER) cc_final: 0.8203 (mt0) REVERT: F 61 GLU cc_start: 0.8384 (mt-10) cc_final: 0.8162 (mt-10) outliers start: 15 outliers final: 9 residues processed: 40 average time/residue: 0.0387 time to fit residues: 1.9374 Evaluate side-chains 42 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 27 time to evaluate : 0.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 79 GLN Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 79 GLN Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 62 GLN Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 79 GLN Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain F residue 52 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 21 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 chunk 23 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 13 optimal weight: 4.9990 chunk 11 optimal weight: 0.0170 chunk 10 optimal weight: 0.2980 chunk 15 optimal weight: 1.9990 overall best weight: 0.8624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 62 GLN C 62 GLN E 62 GLN ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4748 r_free = 0.4748 target = 0.199482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.136284 restraints weight = 1993.912| |-----------------------------------------------------------------------------| r_work (start): 0.4245 rms_B_bonded: 3.44 r_work: 0.4089 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.4089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2028 Z= 0.127 Angle : 0.494 4.478 2748 Z= 0.281 Chirality : 0.048 0.122 366 Planarity : 0.002 0.011 348 Dihedral : 4.629 20.305 288 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 7.35 % Allowed : 18.63 % Favored : 74.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.47 (0.50), residues: 282 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.63 (0.38), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.014 0.003 PHE E 94 HIS 0.000 0.000 HIS B 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 ( 2028) covalent geometry : angle 0.49442 / 0.28 ( 2748) hydrogen bonds : bond 0.02496 / 1.88 ( 16) hydrogen bonds : angle 5.42293 / 3.67 ( 48) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 26 time to evaluate : 0.073 Fit side-chains REVERT: A 79 GLN cc_start: 0.8975 (OUTLIER) cc_final: 0.8070 (mm110) REVERT: A 83 GLU cc_start: 0.7805 (mp0) cc_final: 0.7535 (mm-30) REVERT: B 79 GLN cc_start: 0.9012 (OUTLIER) cc_final: 0.7995 (mm110) REVERT: C 61 GLU cc_start: 0.8450 (mt-10) cc_final: 0.8119 (mt-10) REVERT: C 79 GLN cc_start: 0.9038 (OUTLIER) cc_final: 0.8133 (mt0) REVERT: D 62 GLN cc_start: 0.8810 (mt0) cc_final: 0.7996 (mp10) REVERT: D 79 GLN cc_start: 0.8971 (OUTLIER) cc_final: 0.8281 (mm110) REVERT: D 83 GLU cc_start: 0.8259 (mm-30) cc_final: 0.7831 (mm-30) REVERT: E 79 GLN cc_start: 0.8905 (OUTLIER) cc_final: 0.8207 (mt0) REVERT: F 61 GLU cc_start: 0.8373 (mt-10) cc_final: 0.8159 (mt-10) outliers start: 15 outliers final: 9 residues processed: 37 average time/residue: 0.0334 time to fit residues: 1.6332 Evaluate side-chains 40 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 26 time to evaluate : 0.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 79 GLN Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 62 GLN Chi-restraints excluded: chain C residue 79 GLN Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 79 GLN Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain F residue 52 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 18 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 23 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 20 optimal weight: 0.4980 chunk 5 optimal weight: 6.9990 chunk 2 optimal weight: 0.6980 chunk 12 optimal weight: 10.0000 chunk 15 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 62 GLN C 62 GLN E 62 GLN ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4748 r_free = 0.4748 target = 0.199655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.136317 restraints weight = 1971.372| |-----------------------------------------------------------------------------| r_work (start): 0.4240 rms_B_bonded: 3.43 r_work: 0.4085 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.4085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.2658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2028 Z= 0.143 Angle : 0.493 4.248 2748 Z= 0.281 Chirality : 0.049 0.122 366 Planarity : 0.002 0.017 348 Dihedral : 4.722 20.773 288 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 7.35 % Allowed : 18.14 % Favored : 74.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.44 (0.50), residues: 282 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.62 (0.38), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.014 0.003 PHE E 94 HIS 0.000 0.000 HIS B 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 ( 2028) covalent geometry : angle 0.49276 / 0.28 ( 2748) hydrogen bonds : bond 0.02647 / 1.99 ( 16) hydrogen bonds : angle 5.40087 / 3.66 ( 48) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 24 time to evaluate : 0.078 Fit side-chains REVERT: A 79 GLN cc_start: 0.9030 (OUTLIER) cc_final: 0.8081 (mm110) REVERT: B 79 GLN cc_start: 0.9046 (OUTLIER) cc_final: 0.8008 (mm110) REVERT: C 61 GLU cc_start: 0.8497 (mt-10) cc_final: 0.8167 (mt-10) REVERT: C 79 GLN cc_start: 0.9034 (OUTLIER) cc_final: 0.8081 (mt0) REVERT: D 62 GLN cc_start: 0.8803 (mt0) cc_final: 0.8010 (mp10) REVERT: D 79 GLN cc_start: 0.8998 (OUTLIER) cc_final: 0.8265 (mm110) REVERT: D 83 GLU cc_start: 0.8293 (mm-30) cc_final: 0.7978 (mm-30) REVERT: E 79 GLN cc_start: 0.8900 (OUTLIER) cc_final: 0.8195 (mt0) REVERT: F 61 GLU cc_start: 0.8372 (mt-10) cc_final: 0.8154 (mt-10) outliers start: 15 outliers final: 9 residues processed: 37 average time/residue: 0.0322 time to fit residues: 1.6315 Evaluate side-chains 36 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 22 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 79 GLN Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 62 GLN Chi-restraints excluded: chain C residue 79 GLN Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 79 GLN Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain F residue 52 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 16 optimal weight: 10.0000 chunk 6 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 12 optimal weight: 9.9990 chunk 4 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 11 optimal weight: 0.4980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 62 GLN C 62 GLN E 62 GLN ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4757 r_free = 0.4757 target = 0.200703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.136727 restraints weight = 2000.414| |-----------------------------------------------------------------------------| r_work (start): 0.4244 rms_B_bonded: 3.48 r_work: 0.4089 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.4089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2028 Z= 0.138 Angle : 0.479 4.173 2748 Z= 0.274 Chirality : 0.049 0.121 366 Planarity : 0.002 0.018 348 Dihedral : 4.738 20.892 288 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 8.33 % Allowed : 16.67 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.43 (0.50), residues: 282 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.60 (0.38), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.014 0.003 PHE E 94 HIS 0.000 0.000 HIS B 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 ( 2028) covalent geometry : angle 0.47935 / 0.27 ( 2748) hydrogen bonds : bond 0.02667 / 2.01 ( 16) hydrogen bonds : angle 5.35247 / 3.62 ( 48) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 25 time to evaluate : 0.044 Fit side-chains REVERT: A 79 GLN cc_start: 0.8992 (OUTLIER) cc_final: 0.8085 (mm110) REVERT: A 83 GLU cc_start: 0.8258 (mm-30) cc_final: 0.7986 (mp0) REVERT: B 79 GLN cc_start: 0.9033 (OUTLIER) cc_final: 0.8002 (mm110) REVERT: C 61 GLU cc_start: 0.8508 (mt-10) cc_final: 0.8192 (mt-10) REVERT: C 79 GLN cc_start: 0.8998 (OUTLIER) cc_final: 0.8067 (mt0) REVERT: D 62 GLN cc_start: 0.8786 (mt0) cc_final: 0.7966 (mp10) REVERT: D 79 GLN cc_start: 0.8980 (OUTLIER) cc_final: 0.8255 (mm110) REVERT: D 83 GLU cc_start: 0.8284 (mm-30) cc_final: 0.7970 (mm-30) REVERT: E 79 GLN cc_start: 0.8890 (OUTLIER) cc_final: 0.8169 (mt0) REVERT: F 61 GLU cc_start: 0.8375 (mt-10) cc_final: 0.7974 (mt-10) outliers start: 17 outliers final: 11 residues processed: 40 average time/residue: 0.0263 time to fit residues: 1.3440 Evaluate side-chains 39 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 23 time to evaluate : 0.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 79 GLN Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 62 GLN Chi-restraints excluded: chain C residue 79 GLN Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 62 GLN Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 79 GLN Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain F residue 52 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 9 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 4 optimal weight: 10.0000 chunk 5 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 3 optimal weight: 0.0570 chunk 21 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 17 optimal weight: 6.9990 chunk 13 optimal weight: 0.9990 overall best weight: 1.2104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 62 GLN ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4761 r_free = 0.4761 target = 0.201019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.137204 restraints weight = 1997.132| |-----------------------------------------------------------------------------| r_work (start): 0.4251 rms_B_bonded: 3.47 r_work: 0.4094 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.4094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.2684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.174 2028 Z= 0.394 Angle : 1.773 59.153 2748 Z= 1.110 Chirality : 0.051 0.328 366 Planarity : 0.007 0.122 348 Dihedral : 4.766 20.889 288 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 7.35 % Allowed : 17.65 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.44 (0.50), residues: 282 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.61 (0.38), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.015 0.004 PHE E 94 HIS 0.000 0.000 HIS B 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00819 / 0.39 ( 2028) covalent geometry : angle 1.77282 / 1.11 ( 2748) hydrogen bonds : bond 0.05568 / 4.64 ( 16) hydrogen bonds : angle 5.53307 / 3.71 ( 48) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 748.66 seconds wall clock time: 13 minutes 45.19 seconds (825.19 seconds total)