Starting phenix.real_space_refine on Wed Mar 5 16:23:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xbw_38231/03_2025/8xbw_38231.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xbw_38231/03_2025/8xbw_38231.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xbw_38231/03_2025/8xbw_38231.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xbw_38231/03_2025/8xbw_38231.map" model { file = "/net/cci-nas-00/data/ceres_data/8xbw_38231/03_2025/8xbw_38231.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xbw_38231/03_2025/8xbw_38231.cif" } resolution = 2.89 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= 0.000 sd= 0.000 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: 5 Type Number sf(0) Gaussians P 36 5.49 5 S 6 5.16 5 C 1573 2.51 5 N 501 2.21 5 O 555 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 2671 Number of models: 1 Model: "" Number of chains: 5 Chain: "E" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 790 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "F" Number of atoms: 678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 678 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 1, 'TRANS': 82} Chain: "I" Number of atoms: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 366 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Chain: "J" Number of atoms: 372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 372 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Chain: "L" Number of atoms: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 465 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 3, 'TRANS': 58} Time building chain proxies: 3.06, per 1000 atoms: 1.15 Number of scatterers: 2671 At special positions: 0 Unit cell: (82.68, 71.02, 77.38, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 6 16.00 P 36 15.00 O 555 8.00 N 501 7.00 C 1573 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: 0.77 Conformation dependent library (CDL) restraints added in 234.2 milliseconds 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 454 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 2 sheets defined 73.6% alpha, 1.7% beta 18 base pairs and 31 stacking pairs defined. Time for finding SS restraints: 1.19 Creating SS restraints... Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 77 removed outlier: 3.807A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'L' and resid 25 through 31 removed outlier: 3.703A pdb=" N GLU L 29 " --> pdb=" O ILE L 25 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLN L 30 " --> pdb=" O SER L 26 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N CYS L 31 " --> pdb=" O ARG L 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 25 through 31' Processing helix chain 'L' and resid 34 through 45 Processing helix chain 'L' and resid 48 through 54 Processing helix chain 'L' and resid 56 through 62 removed outlier: 4.357A pdb=" N LEU L 60 " --> pdb=" O PRO L 56 " (cutoff:3.500A) Processing helix chain 'L' and resid 67 through 82 Processing sheet with id=AA1, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.866A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'E' and resid 118 through 119 123 hydrogen bonds defined for protein. 363 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 45 hydrogen bonds 90 hydrogen bond angles 0 basepair planarities 18 basepair parallelities 31 stacking parallelities Total time for adding SS restraints: 0.79 Time building geometry restraints manager: 0.90 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: 678 1.33 - 1.45: 614 1.45 - 1.57: 1412 1.57 - 1.69: 71 1.69 - 1.81: 9 Bond restraints: 2784 Sorted by residual: bond pdb=" N ASN F 25 " pdb=" CA ASN F 25 " ideal model delta sigma weight residual 1.455 1.504 -0.049 1.29e-02 6.01e+03 1.46e+01 bond pdb=" CA ASN F 25 " pdb=" CB ASN F 25 " ideal model delta sigma weight residual 1.536 1.578 -0.042 1.42e-02 4.96e+03 8.73e+00 bond pdb=" N ILE F 26 " pdb=" CA ILE F 26 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.71e+00 bond pdb=" CZ ARG F 19 " pdb=" NH2 ARG F 19 " ideal model delta sigma weight residual 1.330 1.298 0.032 1.30e-02 5.92e+03 6.05e+00 bond pdb=" CZ ARG F 23 " pdb=" NH2 ARG F 23 " ideal model delta sigma weight residual 1.330 1.300 0.030 1.30e-02 5.92e+03 5.28e+00 ... (remaining 2779 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 3525 1.64 - 3.29: 311 3.29 - 4.93: 46 4.93 - 6.57: 8 6.57 - 8.22: 6 Bond angle restraints: 3896 Sorted by residual: angle pdb=" CA ASN F 25 " pdb=" CB ASN F 25 " pdb=" CG ASN F 25 " ideal model delta sigma weight residual 112.60 106.96 5.64 1.00e+00 1.00e+00 3.18e+01 angle pdb=" N ASN F 25 " pdb=" CA ASN F 25 " pdb=" C ASN F 25 " ideal model delta sigma weight residual 113.97 121.08 -7.11 1.28e+00 6.10e-01 3.09e+01 angle pdb=" CA ASN F 25 " pdb=" C ASN F 25 " pdb=" N ILE F 26 " ideal model delta sigma weight residual 118.47 125.19 -6.72 1.26e+00 6.30e-01 2.85e+01 angle pdb=" C HIS E 39 " pdb=" CA HIS E 39 " pdb=" CB HIS E 39 " ideal model delta sigma weight residual 109.51 117.73 -8.22 1.71e+00 3.42e-01 2.31e+01 angle pdb=" N VAL E 117 " pdb=" CA VAL E 117 " pdb=" C VAL E 117 " ideal model delta sigma weight residual 113.10 108.70 4.40 9.70e-01 1.06e+00 2.05e+01 ... (remaining 3891 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.98: 1208 16.98 - 33.96: 184 33.96 - 50.94: 153 50.94 - 67.92: 64 67.92 - 84.90: 3 Dihedral angle restraints: 1612 sinusoidal: 911 harmonic: 701 Sorted by residual: dihedral pdb=" CA GLY L 32 " pdb=" C GLY L 32 " pdb=" N ILE L 33 " pdb=" CA ILE L 33 " ideal model delta harmonic sigma weight residual 180.00 155.24 24.76 0 5.00e+00 4.00e-02 2.45e+01 dihedral pdb=" CA ARG F 19 " pdb=" C ARG F 19 " pdb=" N LYS F 20 " pdb=" CA LYS F 20 " ideal model delta harmonic sigma weight residual 180.00 159.26 20.74 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" C HIS E 39 " pdb=" N HIS E 39 " pdb=" CA HIS E 39 " pdb=" CB HIS E 39 " ideal model delta harmonic sigma weight residual -122.60 -131.94 9.34 0 2.50e+00 1.60e-01 1.40e+01 ... (remaining 1609 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.102: 424 0.102 - 0.204: 18 0.204 - 0.305: 1 0.305 - 0.407: 0 0.407 - 0.509: 1 Chirality restraints: 444 Sorted by residual: chirality pdb=" P DA J 97 " pdb=" OP1 DA J 97 " pdb=" OP2 DA J 97 " pdb=" O5' DA J 97 " both_signs ideal model delta sigma weight residual True 2.35 -2.85 -0.51 2.00e-01 2.50e+01 6.48e+00 chirality pdb=" P DA I 51 " pdb=" OP1 DA I 51 " pdb=" OP2 DA I 51 " pdb=" O5' DA I 51 " both_signs ideal model delta sigma weight residual True 2.35 -2.64 -0.30 2.00e-01 2.50e+01 2.19e+00 chirality pdb=" CA ASN F 25 " pdb=" N ASN F 25 " pdb=" C ASN F 25 " pdb=" CB ASN F 25 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.02e+00 ... (remaining 441 not shown) Planarity restraints: 371 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA I 51 " -0.076 2.00e-02 2.50e+03 3.09e-02 2.62e+01 pdb=" N9 DA I 51 " 0.024 2.00e-02 2.50e+03 pdb=" C8 DA I 51 " 0.023 2.00e-02 2.50e+03 pdb=" N7 DA I 51 " 0.010 2.00e-02 2.50e+03 pdb=" C5 DA I 51 " 0.012 2.00e-02 2.50e+03 pdb=" C6 DA I 51 " -0.009 2.00e-02 2.50e+03 pdb=" N6 DA I 51 " -0.041 2.00e-02 2.50e+03 pdb=" N1 DA I 51 " -0.007 2.00e-02 2.50e+03 pdb=" C2 DA I 51 " 0.008 2.00e-02 2.50e+03 pdb=" N3 DA I 51 " 0.025 2.00e-02 2.50e+03 pdb=" C4 DA I 51 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS E 39 " -0.043 2.00e-02 2.50e+03 3.59e-02 1.93e+01 pdb=" CG HIS E 39 " 0.058 2.00e-02 2.50e+03 pdb=" ND1 HIS E 39 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 HIS E 39 " 0.024 2.00e-02 2.50e+03 pdb=" CE1 HIS E 39 " 0.004 2.00e-02 2.50e+03 pdb=" NE2 HIS E 39 " -0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN L 23 " 0.060 5.00e-02 4.00e+02 8.87e-02 1.26e+01 pdb=" N PRO L 24 " -0.153 5.00e-02 4.00e+02 pdb=" CA PRO L 24 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO L 24 " 0.048 5.00e-02 4.00e+02 ... (remaining 368 not shown) Histogram of nonbonded interaction distances: 1.15 - 1.90: 1 1.90 - 2.65: 54 2.65 - 3.40: 3563 3.40 - 4.15: 7271 4.15 - 4.90: 11510 Nonbonded interactions: 22399 Sorted by model distance: nonbonded pdb=" NH2 ARG E 40 " pdb=" O2 DT J 90 " model vdw 1.155 3.120 nonbonded pdb=" NH2 ARG E 40 " pdb=" C2 DT J 90 " model vdw 2.155 3.340 nonbonded pdb=" O GLN L 23 " pdb=" N VAL L 49 " model vdw 2.220 3.120 nonbonded pdb=" OD1 ASP E 77 " pdb=" NZ LYS L 73 " model vdw 2.273 3.120 nonbonded pdb=" NZ LYS L 57 " pdb=" OD1 ASP L 72 " model vdw 2.299 3.120 ... (remaining 22394 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 13.440 Find NCS groups from input model: 0.020 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: 0.010 Load rotamer database and sin/cos tables:16.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 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 : 0.006 0.073 2784 Z= 0.376 Angle : 1.060 8.216 3896 Z= 0.729 Chirality : 0.054 0.509 444 Planarity : 0.009 0.089 371 Dihedral : 23.744 84.903 1158 Min Nonbonded Distance : 1.155 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % 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: -0.65 (0.47), residues: 236 helix: -0.12 (0.36), residues: 159 sheet: None (None), residues: 0 loop : -0.82 (0.62), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.025 0.004 HIS E 39 PHE 0.009 0.001 PHE F 61 TYR 0.016 0.002 TYR F 51 ARG 0.006 0.001 ARG L 27 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 77 ASP cc_start: 0.9230 (m-30) cc_final: 0.8979 (p0) REVERT: F 43 VAL cc_start: 0.7864 (t) cc_final: 0.7433 (t) REVERT: L 73 LYS cc_start: 0.6764 (mttt) cc_final: 0.6412 (tppt) outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 1.2112 time to fit residues: 142.1660 Evaluate side-chains 74 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 21 optimal weight: 7.9990 chunk 18 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 6 optimal weight: 0.5980 chunk 12 optimal weight: 0.5980 chunk 19 optimal weight: 7.9990 chunk 7 optimal weight: 0.0030 chunk 11 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 22 optimal weight: 9.9990 chunk 15 optimal weight: 0.8980 overall best weight: 0.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 39 HIS E 93 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.082409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.056319 restraints weight = 10491.148| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 5.16 r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.5664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 2784 Z= 0.257 Angle : 0.847 13.532 3896 Z= 0.453 Chirality : 0.044 0.183 444 Planarity : 0.006 0.043 371 Dihedral : 26.446 62.566 663 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 26.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Rotamer: Outliers : 7.43 % Allowed : 29.21 % Favored : 63.37 % 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: -0.32 (0.50), residues: 236 helix: 0.32 (0.37), residues: 174 sheet: None (None), residues: 0 loop : -1.53 (0.61), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.002 HIS E 39 PHE 0.018 0.003 PHE F 61 TYR 0.024 0.003 TYR E 99 ARG 0.005 0.001 ARG E 63 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 87 time to evaluate : 0.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 104 PHE cc_start: 0.9025 (OUTLIER) cc_final: 0.8655 (t80) REVERT: E 105 GLU cc_start: 0.8997 (tp30) cc_final: 0.8762 (mm-30) REVERT: F 88 TYR cc_start: 0.8448 (m-10) cc_final: 0.8149 (m-10) REVERT: F 90 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8171 (mm) REVERT: L 61 ILE cc_start: 0.8607 (pp) cc_final: 0.8385 (pp) outliers start: 15 outliers final: 4 residues processed: 94 average time/residue: 1.0600 time to fit residues: 102.0897 Evaluate side-chains 74 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 68 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 104 PHE Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 90 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 23 optimal weight: 9.9990 chunk 11 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 chunk 14 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 chunk 24 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 6 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 GLN ** F 93 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 = 0.3796 r_free = 0.3796 target = 0.076692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.054579 restraints weight = 11760.205| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 4.34 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.7258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 2784 Z= 0.278 Angle : 0.891 11.095 3896 Z= 0.469 Chirality : 0.047 0.222 444 Planarity : 0.006 0.050 371 Dihedral : 25.937 68.607 663 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 25.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer: Outliers : 7.43 % Allowed : 34.65 % Favored : 57.92 % 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: -0.90 (0.50), residues: 236 helix: -0.06 (0.38), residues: 175 sheet: None (None), residues: 0 loop : -1.93 (0.64), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E 39 PHE 0.013 0.002 PHE F 61 TYR 0.040 0.003 TYR E 99 ARG 0.005 0.001 ARG E 63 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 81 time to evaluate : 0.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 77 ASP cc_start: 0.9294 (m-30) cc_final: 0.9023 (p0) REVERT: E 90 MET cc_start: 0.9173 (mmm) cc_final: 0.8618 (mmm) REVERT: E 94 GLU cc_start: 0.9321 (mm-30) cc_final: 0.9104 (mp0) REVERT: E 104 PHE cc_start: 0.9472 (OUTLIER) cc_final: 0.8884 (t80) REVERT: E 109 LEU cc_start: 0.9266 (mm) cc_final: 0.9026 (mm) REVERT: E 126 LEU cc_start: 0.9110 (mt) cc_final: 0.8906 (mp) REVERT: F 43 VAL cc_start: 0.8634 (t) cc_final: 0.8265 (t) REVERT: F 62 LEU cc_start: 0.9486 (mt) cc_final: 0.9138 (pp) REVERT: L 46 PHE cc_start: 0.5668 (m-80) cc_final: 0.5350 (m-80) REVERT: L 70 LYS cc_start: 0.7673 (mttt) cc_final: 0.7352 (tptp) outliers start: 15 outliers final: 8 residues processed: 88 average time/residue: 0.8507 time to fit residues: 77.2283 Evaluate side-chains 79 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 70 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 104 PHE Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain L residue 47 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 20 optimal weight: 5.9990 chunk 7 optimal weight: 0.7980 chunk 9 optimal weight: 8.9990 chunk 17 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 6 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 chunk 14 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 93 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 = 0.3801 r_free = 0.3801 target = 0.075782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.054073 restraints weight = 12148.749| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 3.76 r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.8224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 2784 Z= 0.293 Angle : 0.937 12.284 3896 Z= 0.473 Chirality : 0.048 0.244 444 Planarity : 0.005 0.049 371 Dihedral : 25.453 71.255 663 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 24.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer: Outliers : 6.93 % Allowed : 33.17 % Favored : 59.90 % 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: -0.69 (0.49), residues: 236 helix: -0.05 (0.37), residues: 164 sheet: None (None), residues: 0 loop : -1.14 (0.63), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS E 113 PHE 0.020 0.003 PHE F 61 TYR 0.015 0.002 TYR E 54 ARG 0.008 0.001 ARG E 128 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 81 time to evaluate : 0.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 73 GLU cc_start: 0.9257 (pp20) cc_final: 0.8888 (pp20) REVERT: E 82 LEU cc_start: 0.7831 (OUTLIER) cc_final: 0.7352 (mt) REVERT: E 104 PHE cc_start: 0.9499 (OUTLIER) cc_final: 0.8889 (t80) REVERT: F 43 VAL cc_start: 0.8870 (t) cc_final: 0.8632 (t) REVERT: F 72 TYR cc_start: 0.8549 (m-80) cc_final: 0.8220 (m-80) REVERT: F 92 ARG cc_start: 0.8258 (OUTLIER) cc_final: 0.7694 (tmt170) REVERT: L 46 PHE cc_start: 0.5575 (m-80) cc_final: 0.5346 (m-80) REVERT: L 70 LYS cc_start: 0.7683 (mttt) cc_final: 0.7333 (tptp) REVERT: L 74 ILE cc_start: 0.7212 (pp) cc_final: 0.6373 (pp) outliers start: 14 outliers final: 5 residues processed: 85 average time/residue: 0.7478 time to fit residues: 65.7992 Evaluate side-chains 76 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 68 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 52 ARG Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 104 PHE Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 92 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 18 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 24 optimal weight: 10.0000 chunk 9 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 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 = 0.3727 r_free = 0.3727 target = 0.071810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.050959 restraints weight = 12343.066| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 3.46 r_work: 0.3247 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.9435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 2784 Z= 0.353 Angle : 0.941 12.745 3896 Z= 0.490 Chirality : 0.050 0.219 444 Planarity : 0.006 0.056 371 Dihedral : 25.454 77.200 663 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 25.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 5.45 % Allowed : 39.11 % Favored : 55.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.38 (0.47), residues: 236 helix: -0.43 (0.36), residues: 164 sheet: None (None), residues: 0 loop : -1.81 (0.58), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS E 39 PHE 0.030 0.003 PHE F 61 TYR 0.020 0.003 TYR E 99 ARG 0.009 0.001 ARG E 49 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 79 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 49 ARG cc_start: 0.9321 (mtp180) cc_final: 0.8756 (ptp-110) REVERT: E 82 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8362 (mt) REVERT: E 90 MET cc_start: 0.9281 (mmm) cc_final: 0.8457 (ttp) REVERT: E 104 PHE cc_start: 0.9527 (OUTLIER) cc_final: 0.9067 (t80) REVERT: E 109 LEU cc_start: 0.9412 (tp) cc_final: 0.9196 (tm) REVERT: F 58 LEU cc_start: 0.9469 (mm) cc_final: 0.9199 (tm) REVERT: F 92 ARG cc_start: 0.8431 (OUTLIER) cc_final: 0.7972 (ttt180) REVERT: L 43 GLU cc_start: 0.8563 (tm-30) cc_final: 0.8321 (pp20) REVERT: L 46 PHE cc_start: 0.5782 (m-80) cc_final: 0.5556 (m-80) REVERT: L 50 GLU cc_start: 0.8853 (tm-30) cc_final: 0.8344 (tp30) REVERT: L 70 LYS cc_start: 0.7911 (mttt) cc_final: 0.7557 (tptp) REVERT: L 74 ILE cc_start: 0.7127 (pp) cc_final: 0.6283 (pp) outliers start: 11 outliers final: 3 residues processed: 82 average time/residue: 0.8640 time to fit residues: 73.0932 Evaluate side-chains 70 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 64 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 104 PHE Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain L residue 47 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 7 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 14 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 chunk 2 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 12 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 24 optimal weight: 5.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 125 GLN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 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 = 0.3694 r_free = 0.3694 target = 0.071574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.050717 restraints weight = 12076.514| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 3.39 r_work: 0.3174 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.9730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 2784 Z= 0.280 Angle : 0.972 14.234 3896 Z= 0.498 Chirality : 0.051 0.270 444 Planarity : 0.006 0.053 371 Dihedral : 25.371 78.998 663 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 22.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer: Outliers : 6.44 % Allowed : 41.09 % Favored : 52.48 % 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: -1.26 (0.48), residues: 236 helix: -0.41 (0.36), residues: 164 sheet: None (None), residues: 0 loop : -1.57 (0.61), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E 39 PHE 0.035 0.003 PHE F 61 TYR 0.015 0.002 TYR E 54 ARG 0.006 0.001 ARG E 49 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 76 time to evaluate : 0.235 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 49 ARG cc_start: 0.9344 (mtp180) cc_final: 0.8884 (mpp80) REVERT: E 70 LEU cc_start: 0.9497 (pp) cc_final: 0.9213 (pt) REVERT: E 73 GLU cc_start: 0.9014 (pp20) cc_final: 0.8773 (pp20) REVERT: E 82 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8487 (mt) REVERT: E 90 MET cc_start: 0.9159 (mmm) cc_final: 0.8783 (ttp) REVERT: E 104 PHE cc_start: 0.9511 (OUTLIER) cc_final: 0.9066 (t80) REVERT: E 109 LEU cc_start: 0.9337 (tp) cc_final: 0.9127 (tm) REVERT: F 37 LEU cc_start: 0.9312 (mp) cc_final: 0.9042 (tm) REVERT: L 43 GLU cc_start: 0.8602 (tm-30) cc_final: 0.8402 (pp20) REVERT: L 46 PHE cc_start: 0.5751 (m-80) cc_final: 0.5548 (m-80) REVERT: L 50 GLU cc_start: 0.8816 (tm-30) cc_final: 0.8379 (tp30) REVERT: L 70 LYS cc_start: 0.7939 (mttt) cc_final: 0.7549 (tptp) REVERT: L 74 ILE cc_start: 0.7326 (pp) cc_final: 0.6562 (pp) outliers start: 13 outliers final: 7 residues processed: 79 average time/residue: 0.8265 time to fit residues: 67.3343 Evaluate side-chains 80 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 71 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 104 PHE Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain L residue 25 ILE Chi-restraints excluded: chain L residue 47 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 11 optimal weight: 0.8980 chunk 9 optimal weight: 0.0970 chunk 2 optimal weight: 0.1980 chunk 13 optimal weight: 0.5980 chunk 20 optimal weight: 30.0000 chunk 5 optimal weight: 0.7980 chunk 15 optimal weight: 0.0020 chunk 10 optimal weight: 0.5980 chunk 8 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 overall best weight: 0.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 125 GLN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 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 = 0.3737 r_free = 0.3737 target = 0.073013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.051656 restraints weight = 11917.662| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 3.49 r_work: 0.3221 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 1.0037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 2784 Z= 0.252 Angle : 1.046 15.213 3896 Z= 0.510 Chirality : 0.050 0.231 444 Planarity : 0.006 0.052 371 Dihedral : 25.333 78.633 663 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 22.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 4.95 % Allowed : 42.08 % Favored : 52.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.39 (0.47), residues: 236 helix: -0.54 (0.36), residues: 166 sheet: None (None), residues: 0 loop : -1.57 (0.58), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS E 39 PHE 0.026 0.003 PHE F 61 TYR 0.017 0.002 TYR F 88 ARG 0.007 0.001 ARG E 42 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 76 time to evaluate : 0.281 Fit side-chains revert: symmetry clash REVERT: E 52 ARG cc_start: 0.8726 (pmm-80) cc_final: 0.8524 (pmm-80) REVERT: E 70 LEU cc_start: 0.9472 (pp) cc_final: 0.9228 (pt) REVERT: E 90 MET cc_start: 0.9215 (mmm) cc_final: 0.8980 (mmm) REVERT: E 104 PHE cc_start: 0.9468 (OUTLIER) cc_final: 0.8941 (t80) REVERT: F 37 LEU cc_start: 0.9288 (mp) cc_final: 0.9058 (tm) REVERT: F 46 ILE cc_start: 0.8849 (OUTLIER) cc_final: 0.8617 (pp) REVERT: F 52 GLU cc_start: 0.9056 (pm20) cc_final: 0.8788 (pm20) REVERT: L 50 GLU cc_start: 0.8873 (tm-30) cc_final: 0.8471 (tp30) REVERT: L 70 LYS cc_start: 0.8063 (mttt) cc_final: 0.7703 (tptp) REVERT: L 74 ILE cc_start: 0.7341 (pp) cc_final: 0.6554 (pp) outliers start: 10 outliers final: 2 residues processed: 80 average time/residue: 0.7415 time to fit residues: 61.4506 Evaluate side-chains 73 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 69 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 104 PHE Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain L residue 25 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 20 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 8 optimal weight: 0.3980 chunk 14 optimal weight: 1.9990 chunk 7 optimal weight: 0.2980 chunk 10 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 chunk 0 optimal weight: 7.9990 chunk 17 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 19 optimal weight: 6.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 39 HIS E 125 GLN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.072700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.051343 restraints weight = 11766.045| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 3.36 r_work: 0.3238 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 1.0409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 2784 Z= 0.289 Angle : 1.084 15.508 3896 Z= 0.536 Chirality : 0.054 0.266 444 Planarity : 0.005 0.039 371 Dihedral : 25.207 78.742 663 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 23.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 5.45 % Allowed : 42.57 % Favored : 51.98 % 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: -1.46 (0.47), residues: 236 helix: -0.52 (0.37), residues: 166 sheet: None (None), residues: 0 loop : -1.81 (0.55), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS E 39 PHE 0.026 0.003 PHE F 61 TYR 0.036 0.002 TYR E 99 ARG 0.005 0.001 ARG E 42 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.268 Fit side-chains revert: symmetry clash REVERT: E 49 ARG cc_start: 0.9207 (ptm160) cc_final: 0.8557 (ptp-110) REVERT: E 90 MET cc_start: 0.9134 (mmm) cc_final: 0.8852 (mmm) REVERT: F 47 SER cc_start: 0.5873 (OUTLIER) cc_final: 0.5495 (p) REVERT: F 92 ARG cc_start: 0.8470 (OUTLIER) cc_final: 0.8200 (ttt180) REVERT: L 43 GLU cc_start: 0.7438 (pp20) cc_final: 0.7084 (pp20) REVERT: L 50 GLU cc_start: 0.9050 (tm-30) cc_final: 0.8693 (mm-30) REVERT: L 70 LYS cc_start: 0.8060 (mttt) cc_final: 0.7664 (tptm) REVERT: L 74 ILE cc_start: 0.7408 (pp) cc_final: 0.6641 (pp) outliers start: 11 outliers final: 4 residues processed: 79 average time/residue: 0.9732 time to fit residues: 79.2329 Evaluate side-chains 71 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 65 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 39 HIS Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 92 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 24 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 21 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 22 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 chunk 8 optimal weight: 0.5980 chunk 2 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 23 optimal weight: 9.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 39 HIS E 76 GLN E 125 GLN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 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 = 0.3676 r_free = 0.3676 target = 0.070348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.049582 restraints weight = 12271.479| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 3.41 r_work: 0.3160 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 1.1069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 2784 Z= 0.378 Angle : 1.144 16.201 3896 Z= 0.582 Chirality : 0.054 0.254 444 Planarity : 0.006 0.036 371 Dihedral : 25.367 81.225 663 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 30.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 6.44 % Allowed : 43.07 % Favored : 50.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.97 (0.47), residues: 236 helix: -0.92 (0.37), residues: 166 sheet: None (None), residues: 0 loop : -1.94 (0.57), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS E 39 PHE 0.039 0.005 PHE F 61 TYR 0.053 0.003 TYR E 99 ARG 0.005 0.001 ARG F 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 71 time to evaluate : 0.221 Fit side-chains revert: symmetry clash REVERT: E 52 ARG cc_start: 0.8798 (pmm-80) cc_final: 0.8598 (pmm-80) REVERT: E 67 PHE cc_start: 0.9230 (t80) cc_final: 0.8731 (t80) REVERT: E 90 MET cc_start: 0.9159 (mmm) cc_final: 0.8823 (ttp) REVERT: E 104 PHE cc_start: 0.9405 (OUTLIER) cc_final: 0.9067 (t80) REVERT: E 105 GLU cc_start: 0.9560 (mm-30) cc_final: 0.9302 (mm-30) REVERT: F 43 VAL cc_start: 0.9157 (t) cc_final: 0.8812 (m) REVERT: F 47 SER cc_start: 0.6016 (OUTLIER) cc_final: 0.5702 (p) REVERT: L 43 GLU cc_start: 0.7607 (pp20) cc_final: 0.7218 (pp20) REVERT: L 50 GLU cc_start: 0.9028 (tm-30) cc_final: 0.8720 (tp30) REVERT: L 70 LYS cc_start: 0.7981 (mttt) cc_final: 0.7501 (tptm) REVERT: L 74 ILE cc_start: 0.7419 (pp) cc_final: 0.6606 (pp) outliers start: 13 outliers final: 6 residues processed: 78 average time/residue: 0.7157 time to fit residues: 57.8597 Evaluate side-chains 74 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 39 HIS Chi-restraints excluded: chain E residue 104 PHE Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain L residue 25 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 3 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 9 optimal weight: 2.9990 chunk 21 optimal weight: 6.9990 chunk 2 optimal weight: 0.6980 chunk 5 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 22 optimal weight: 4.9990 chunk 15 optimal weight: 0.5980 chunk 8 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 39 HIS ** E 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.072121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.050733 restraints weight = 12046.052| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 3.78 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 1.1376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 2784 Z= 0.323 Angle : 1.228 19.503 3896 Z= 0.606 Chirality : 0.057 0.283 444 Planarity : 0.006 0.039 371 Dihedral : 25.444 81.627 663 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 26.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.47 % Allowed : 49.50 % Favored : 47.03 % 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: -1.98 (0.47), residues: 236 helix: -0.86 (0.36), residues: 163 sheet: None (None), residues: 0 loop : -2.09 (0.57), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS E 39 PHE 0.030 0.004 PHE E 67 TYR 0.078 0.004 TYR E 99 ARG 0.008 0.001 ARG E 42 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 71 time to evaluate : 0.242 Fit side-chains revert: symmetry clash REVERT: E 90 MET cc_start: 0.8958 (mmm) cc_final: 0.8627 (ttp) REVERT: E 105 GLU cc_start: 0.9467 (mm-30) cc_final: 0.9172 (mm-30) REVERT: E 125 GLN cc_start: 0.8910 (pp30) cc_final: 0.8582 (pm20) REVERT: F 47 SER cc_start: 0.6006 (OUTLIER) cc_final: 0.5674 (p) REVERT: L 43 GLU cc_start: 0.7677 (pp20) cc_final: 0.7325 (pp20) REVERT: L 70 LYS cc_start: 0.7972 (mttt) cc_final: 0.7584 (tptm) REVERT: L 74 ILE cc_start: 0.7407 (pp) cc_final: 0.6668 (pp) outliers start: 7 outliers final: 4 residues processed: 76 average time/residue: 0.7251 time to fit residues: 57.1342 Evaluate side-chains 68 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 63 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 104 PHE Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 49 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 15 optimal weight: 1.9990 chunk 24 optimal weight: 6.9990 chunk 6 optimal weight: 0.0060 chunk 12 optimal weight: 0.9990 chunk 3 optimal weight: 0.0570 chunk 11 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 10 optimal weight: 0.0570 chunk 5 optimal weight: 0.6980 chunk 1 optimal weight: 0.0980 overall best weight: 0.1632 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 125 GLN ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 23 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.074546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.053951 restraints weight = 11718.352| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 3.37 r_work: 0.3336 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 1.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 2784 Z= 0.319 Angle : 1.248 19.202 3896 Z= 0.609 Chirality : 0.058 0.304 444 Planarity : 0.005 0.042 371 Dihedral : 25.409 80.255 663 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 23.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.48 % Allowed : 51.49 % Favored : 46.04 % 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: -1.73 (0.48), residues: 236 helix: -0.64 (0.37), residues: 165 sheet: None (None), residues: 0 loop : -2.10 (0.60), residues: 71 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS E 39 PHE 0.011 0.002 PHE E 78 TYR 0.029 0.002 TYR E 99 ARG 0.005 0.001 ARG F 35 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2890.04 seconds wall clock time: 50 minutes 3.86 seconds (3003.86 seconds total)