Starting phenix.real_space_refine on Wed Jul 1 21:19:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xbw_38231/07_2026/8xbw_38231.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xbw_38231/07_2026/8xbw_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_38231/07_2026/8xbw_38231.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xbw_38231/07_2026/8xbw_38231.map" model { file = "/net/cci-nas-00/data/ceres_data/8xbw_38231/07_2026/8xbw_38231.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xbw_38231/07_2026/8xbw_38231.cif" } resolution = 2.89 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= 0.000 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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: 0.93, per 1000 atoms: 0.35 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: 0.30 Conformation dependent library (CDL) restraints added in 81.5 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: 0.42 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: 0.39 Time building geometry restraints manager: 0.38 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=" C4 DC I 52 " pdb=" N4 DC I 52 " ideal model delta sigma weight residual 1.335 1.296 0.039 9.00e-03 1.23e+04 1.91e+01 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=" C5' DA I 51 " pdb=" C4' DA I 51 " ideal model delta sigma weight residual 1.512 1.537 -0.025 7.00e-03 2.04e+04 1.24e+01 bond pdb=" N3 DC I 52 " pdb=" C4 DC I 52 " ideal model delta sigma weight residual 1.335 1.312 0.023 7.00e-03 2.04e+04 1.05e+01 bond pdb=" C3' DC I 55 " pdb=" C2' DC I 55 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.21e+00 ... (remaining 2779 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 3445 1.64 - 3.29: 387 3.29 - 4.93: 47 4.93 - 6.57: 11 6.57 - 8.22: 6 Bond angle restraints: 3896 Sorted by residual: angle pdb=" N6 DA I 51 " pdb=" C6 DA I 51 " pdb=" N1 DA I 51 " ideal model delta sigma weight residual 118.60 113.62 4.98 6.00e-01 2.78e+00 6.88e+01 angle pdb=" C5 DA I 51 " pdb=" C6 DA I 51 " pdb=" N1 DA I 51 " ideal model delta sigma weight residual 117.70 121.64 -3.94 5.00e-01 4.00e+00 6.20e+01 angle pdb=" O5' DA I 51 " pdb=" C5' DA I 51 " pdb=" C4' DA I 51 " ideal model delta sigma weight residual 109.40 115.12 -5.72 8.00e-01 1.56e+00 5.11e+01 angle pdb=" C6 DA I 51 " pdb=" C5 DA I 51 " pdb=" C4 DA I 51 " ideal model delta sigma weight residual 117.00 113.77 3.23 5.00e-01 4.00e+00 4.18e+01 angle pdb=" O2 DC I 52 " pdb=" C2 DC I 52 " pdb=" N3 DC I 52 " ideal model delta sigma weight residual 121.90 117.52 4.38 7.00e-01 2.04e+00 3.91e+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 - 0.104: 422 0.104 - 0.208: 20 0.208 - 0.312: 1 0.312 - 0.416: 0 0.416 - 0.519: 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 2.34 -2.85 -0.52 2.00e-01 2.50e+01 6.74e+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 2.34 -2.64 -0.31 2.00e-01 2.50e+01 2.34e+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: 1.780 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: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.170 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7100 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 : 0.007 0.073 2784 Z= 0.565 Angle : 1.128 8.216 3896 Z= 0.917 Chirality : 0.057 0.519 444 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 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: -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 ARG 0.006 0.001 ARG L 27 TYR 0.016 0.002 TYR F 51 PHE 0.009 0.001 PHE F 61 HIS 0.025 0.004 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00698 / 0.56 ( 2784) covalent geometry : angle 1.12784 / 0.92 ( 3896) hydrogen bonds : bond 0.15552 / 10.42 ( 168) hydrogen bonds : angle 5.49253 / 3.94 ( 453) *********************** 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 : 0.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 77 ASP cc_start: 0.9230 (m-30) cc_final: 0.9024 (p0) REVERT: L 73 LYS cc_start: 0.6764 (mttt) cc_final: 0.6410 (tppt) outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.4733 time to fit residues: 55.5656 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 : 0.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 12 optimal weight: 0.5980 chunk 24 optimal weight: 5.9990 chunk 13 optimal weight: 0.5980 chunk 1 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 chunk 9 optimal weight: 5.9990 chunk 11 optimal weight: 0.7980 chunk 18 optimal weight: 5.9990 chunk 6 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 39 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.085140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.058583 restraints weight = 10409.785| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 5.06 r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.4976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 2784 Z= 0.230 Angle : 0.993 14.141 3896 Z= 0.522 Chirality : 0.052 0.223 444 Planarity : 0.007 0.050 371 Dihedral : 27.594 71.665 663 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 32.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Rotamer: Outliers : 8.91 % Allowed : 27.72 % 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 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: -0.72 (0.47), residues: 236 helix: -0.23 (0.35), residues: 167 sheet: None (None), residues: 0 loop : -0.75 (0.66), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 39 TYR 0.027 0.004 TYR E 54 PHE 0.015 0.002 PHE F 61 HIS 0.012 0.002 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00498 / 0.23 ( 2784) covalent geometry : angle 0.99283 / 0.52 ( 3896) hydrogen bonds : bond 0.07031 / 4.78 ( 168) hydrogen bonds : angle 4.98038 / 3.56 ( 453) *********************** 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 100 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 82 time to evaluate : 0.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 39 HIS cc_start: 0.6860 (OUTLIER) cc_final: 0.6613 (m90) REVERT: E 104 PHE cc_start: 0.9259 (OUTLIER) cc_final: 0.8938 (t80) REVERT: F 88 TYR cc_start: 0.8499 (m-80) cc_final: 0.8261 (m-10) outliers start: 18 outliers final: 6 residues processed: 89 average time/residue: 0.3319 time to fit residues: 30.2872 Evaluate side-chains 75 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 67 time to evaluate : 0.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 39 HIS Chi-restraints excluded: chain E residue 46 VAL 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 46 ILE Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 80 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 4 optimal weight: 0.1980 chunk 8 optimal weight: 0.9980 chunk 17 optimal weight: 6.9990 chunk 21 optimal weight: 10.0000 chunk 24 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 2 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 9 optimal weight: 8.9990 chunk 22 optimal weight: 9.9990 chunk 1 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 39 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.080163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.059151 restraints weight = 11765.685| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 3.79 r_work: 0.3360 rms_B_bonded: 4.88 restraints_weight: 0.5000 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.5818 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= 0.230 Angle : 0.973 15.732 3896 Z= 0.506 Chirality : 0.054 0.326 444 Planarity : 0.006 0.042 371 Dihedral : 27.346 67.036 663 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 31.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 6.44 % Allowed : 34.16 % Favored : 59.41 % 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: -1.65 (0.47), residues: 236 helix: -0.58 (0.36), residues: 174 sheet: None (None), residues: 0 loop : -2.25 (0.58), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 39 TYR 0.018 0.002 TYR E 54 PHE 0.035 0.004 PHE E 67 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00490 / 0.23 ( 2784) covalent geometry : angle 0.97262 / 0.51 ( 3896) hydrogen bonds : bond 0.06339 / 4.44 ( 168) hydrogen bonds : angle 4.73354 / 3.36 ( 453) *********************** 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 90 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 77 time to evaluate : 0.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 39 HIS cc_start: 0.6743 (t-90) cc_final: 0.6271 (m170) REVERT: E 68 GLN cc_start: 0.7647 (OUTLIER) cc_final: 0.7436 (pp30) REVERT: E 84 PHE cc_start: 0.6465 (m-10) cc_final: 0.6169 (m-10) REVERT: E 94 GLU cc_start: 0.8175 (mm-30) cc_final: 0.7959 (mm-30) REVERT: E 104 PHE cc_start: 0.9548 (OUTLIER) cc_final: 0.9087 (t80) REVERT: L 70 LYS cc_start: 0.6501 (mttt) cc_final: 0.6142 (tptp) REVERT: L 74 ILE cc_start: 0.7460 (pp) cc_final: 0.6816 (pp) outliers start: 13 outliers final: 6 residues processed: 81 average time/residue: 0.3755 time to fit residues: 31.3305 Evaluate side-chains 78 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 70 time to evaluate : 0.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain E residue 89 VAL 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 F residue 63 GLU Chi-restraints excluded: chain F residue 80 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 20 optimal weight: 7.9990 chunk 11 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 4 optimal weight: 0.3980 chunk 2 optimal weight: 0.2980 chunk 24 optimal weight: 5.9990 chunk 14 optimal weight: 0.8980 chunk 12 optimal weight: 0.5980 chunk 15 optimal weight: 0.9980 chunk 10 optimal weight: 0.2980 chunk 19 optimal weight: 10.0000 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.080635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.059452 restraints weight = 11323.181| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 3.53 r_work: 0.3532 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.6188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 2784 Z= 0.184 Angle : 0.970 13.934 3896 Z= 0.488 Chirality : 0.052 0.227 444 Planarity : 0.006 0.046 371 Dihedral : 27.207 66.479 663 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 24.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 4.95 % Allowed : 37.62 % Favored : 57.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.55 (0.48), residues: 236 helix: -0.68 (0.36), residues: 167 sheet: None (None), residues: 0 loop : -1.56 (0.66), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 39 TYR 0.027 0.003 TYR E 54 PHE 0.042 0.004 PHE E 67 HIS 0.005 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.18 ( 2784) covalent geometry : angle 0.97000 / 0.49 ( 3896) hydrogen bonds : bond 0.05949 / 4.11 ( 168) hydrogen bonds : angle 4.47643 / 3.18 ( 453) *********************** 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 85 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 0.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 104 PHE cc_start: 0.9521 (OUTLIER) cc_final: 0.9101 (t80) REVERT: E 110 CYS cc_start: 0.9251 (m) cc_final: 0.8962 (t) REVERT: E 123 ASP cc_start: 0.8611 (m-30) cc_final: 0.8065 (m-30) REVERT: F 50 ILE cc_start: 0.8905 (mm) cc_final: 0.8521 (pp) REVERT: F 92 ARG cc_start: 0.8023 (OUTLIER) cc_final: 0.7664 (ptt180) REVERT: L 70 LYS cc_start: 0.7045 (mttt) cc_final: 0.6670 (tptp) REVERT: L 74 ILE cc_start: 0.7670 (pp) cc_final: 0.7187 (pp) outliers start: 10 outliers final: 5 residues processed: 79 average time/residue: 0.3554 time to fit residues: 29.0218 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 : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 46 VAL 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 F residue 63 GLU Chi-restraints excluded: chain F residue 80 THR 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 10 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 6 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 125 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.078735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.057720 restraints weight = 11489.542| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 3.60 r_work: 0.3358 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.6611 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= 0.188 Angle : 0.940 12.800 3896 Z= 0.487 Chirality : 0.049 0.183 444 Planarity : 0.006 0.049 371 Dihedral : 26.950 67.443 663 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 23.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 7.43 % Allowed : 35.64 % Favored : 56.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.23 (0.49), residues: 236 helix: -0.45 (0.37), residues: 167 sheet: None (None), residues: 0 loop : -1.41 (0.67), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 39 TYR 0.026 0.003 TYR E 54 PHE 0.037 0.003 PHE E 67 HIS 0.003 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.19 ( 2784) covalent geometry : angle 0.94039 / 0.49 ( 3896) hydrogen bonds : bond 0.05670 / 3.96 ( 168) hydrogen bonds : angle 4.42839 / 3.13 ( 453) *********************** 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 88 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 73 time to evaluate : 0.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 68 GLN cc_start: 0.7926 (OUTLIER) cc_final: 0.7689 (pp30) REVERT: E 94 GLU cc_start: 0.8092 (mm-30) cc_final: 0.7876 (mm-30) REVERT: E 99 TYR cc_start: 0.8238 (t80) cc_final: 0.7997 (t80) REVERT: E 104 PHE cc_start: 0.9576 (OUTLIER) cc_final: 0.9194 (t80) REVERT: E 110 CYS cc_start: 0.9368 (m) cc_final: 0.9082 (t) REVERT: E 123 ASP cc_start: 0.8575 (m-30) cc_final: 0.7902 (m-30) REVERT: F 46 ILE cc_start: 0.8835 (mt) cc_final: 0.8629 (mt) REVERT: F 50 ILE cc_start: 0.9006 (mm) cc_final: 0.8802 (pp) REVERT: F 62 LEU cc_start: 0.9410 (mt) cc_final: 0.9131 (pp) REVERT: F 92 ARG cc_start: 0.8127 (OUTLIER) cc_final: 0.7781 (ptt180) REVERT: L 70 LYS cc_start: 0.7187 (mttt) cc_final: 0.6836 (tptp) REVERT: L 74 ILE cc_start: 0.7541 (pp) cc_final: 0.6949 (pp) outliers start: 15 outliers final: 7 residues processed: 81 average time/residue: 0.4100 time to fit residues: 34.1177 Evaluate side-chains 77 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 0.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain E residue 104 PHE Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain L residue 66 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 1 optimal weight: 0.7980 chunk 2 optimal weight: 0.0170 chunk 17 optimal weight: 6.9990 chunk 0 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 chunk 21 optimal weight: 10.0000 chunk 11 optimal weight: 0.7980 chunk 6 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 chunk 18 optimal weight: 7.9990 chunk 23 optimal weight: 6.9990 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 85 GLN ** E 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 = 0.3872 r_free = 0.3872 target = 0.079334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.056211 restraints weight = 11625.979| |-----------------------------------------------------------------------------| r_work (start): 0.3715 rms_B_bonded: 5.08 r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.6861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 2784 Z= 0.184 Angle : 0.938 13.561 3896 Z= 0.484 Chirality : 0.049 0.183 444 Planarity : 0.007 0.060 371 Dihedral : 26.827 68.069 663 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 25.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 7.92 % Allowed : 36.14 % Favored : 55.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.50), residues: 236 helix: -0.43 (0.37), residues: 164 sheet: None (None), residues: 0 loop : -1.23 (0.67), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 36 TYR 0.025 0.003 TYR E 54 PHE 0.022 0.003 PHE F 61 HIS 0.002 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.18 ( 2784) covalent geometry : angle 0.93774 / 0.48 ( 3896) hydrogen bonds : bond 0.05472 / 3.83 ( 168) hydrogen bonds : angle 4.43311 / 3.15 ( 453) *********************** 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: 16 poor density : 73 time to evaluate : 0.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 104 PHE cc_start: 0.9476 (OUTLIER) cc_final: 0.9111 (t80) REVERT: E 110 CYS cc_start: 0.9296 (m) cc_final: 0.8964 (t) REVERT: F 92 ARG cc_start: 0.8152 (OUTLIER) cc_final: 0.7813 (ptt180) REVERT: L 43 GLU cc_start: 0.8248 (tm-30) cc_final: 0.8020 (pp20) REVERT: L 66 ILE cc_start: 0.3968 (OUTLIER) cc_final: 0.3011 (tp) REVERT: L 70 LYS cc_start: 0.7177 (mttt) cc_final: 0.6823 (tptp) REVERT: L 74 ILE cc_start: 0.7506 (pp) cc_final: 0.6820 (pp) outliers start: 16 outliers final: 8 residues processed: 81 average time/residue: 0.3881 time to fit residues: 32.3812 Evaluate side-chains 81 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 70 time to evaluate : 0.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 85 GLN Chi-restraints excluded: chain E residue 104 PHE Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain L residue 66 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 0 optimal weight: 6.9990 chunk 6 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 chunk 24 optimal weight: 7.9990 chunk 16 optimal weight: 0.0030 chunk 18 optimal weight: 6.9990 chunk 21 optimal weight: 5.9990 chunk 14 optimal weight: 0.7980 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 68 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 125 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 = 0.3867 r_free = 0.3867 target = 0.079161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.055568 restraints weight = 12144.286| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 5.33 r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.7085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 2784 Z= 0.182 Angle : 0.987 14.389 3896 Z= 0.498 Chirality : 0.050 0.204 444 Planarity : 0.007 0.055 371 Dihedral : 26.681 68.596 663 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 25.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 4.46 % Allowed : 42.57 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.49), residues: 236 helix: -0.66 (0.36), residues: 166 sheet: None (None), residues: 0 loop : -1.40 (0.67), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 36 TYR 0.027 0.003 TYR E 54 PHE 0.020 0.003 PHE F 61 HIS 0.001 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.18 ( 2784) covalent geometry : angle 0.98744 / 0.50 ( 3896) hydrogen bonds : bond 0.05410 / 3.77 ( 168) hydrogen bonds : angle 4.50802 / 3.15 ( 453) *********************** 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 83 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 74 time to evaluate : 0.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 99 TYR cc_start: 0.8075 (t80) cc_final: 0.7868 (t80) REVERT: E 104 PHE cc_start: 0.9564 (OUTLIER) cc_final: 0.9192 (t80) REVERT: E 110 CYS cc_start: 0.9232 (m) cc_final: 0.8876 (t) REVERT: F 50 ILE cc_start: 0.8933 (mm) cc_final: 0.8630 (pp) REVERT: F 92 ARG cc_start: 0.8214 (OUTLIER) cc_final: 0.7841 (ptt180) REVERT: L 70 LYS cc_start: 0.7303 (mttt) cc_final: 0.6938 (tptp) REVERT: L 74 ILE cc_start: 0.7561 (pp) cc_final: 0.7043 (pp) outliers start: 9 outliers final: 6 residues processed: 77 average time/residue: 0.3753 time to fit residues: 29.8471 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 : 0.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 104 PHE Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 92 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 1 optimal weight: 0.6980 chunk 3 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 5 optimal weight: 0.6980 chunk 19 optimal weight: 6.9990 chunk 7 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 chunk 23 optimal weight: 0.3980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 68 GLN E 85 GLN ** E 125 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 = 0.3855 r_free = 0.3855 target = 0.078575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.055098 restraints weight = 11814.785| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 5.18 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.7282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 2784 Z= 0.187 Angle : 1.046 19.124 3896 Z= 0.516 Chirality : 0.050 0.189 444 Planarity : 0.006 0.045 371 Dihedral : 26.519 68.678 663 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 26.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 5.45 % Allowed : 43.07 % Favored : 51.49 % 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: -1.75 (0.49), residues: 236 helix: -0.81 (0.36), residues: 167 sheet: None (None), residues: 0 loop : -1.68 (0.67), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 36 TYR 0.026 0.003 TYR E 54 PHE 0.018 0.002 PHE F 61 HIS 0.002 0.001 HIS L 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.19 ( 2784) covalent geometry : angle 1.04614 / 0.52 ( 3896) hydrogen bonds : bond 0.05327 / 3.79 ( 168) hydrogen bonds : angle 4.55965 / 3.22 ( 453) *********************** 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 84 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 73 time to evaluate : 0.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 77 ASP cc_start: 0.9241 (m-30) cc_final: 0.8915 (p0) REVERT: E 104 PHE cc_start: 0.9533 (OUTLIER) cc_final: 0.9173 (t80) REVERT: F 50 ILE cc_start: 0.8633 (mm) cc_final: 0.8415 (pp) REVERT: F 92 ARG cc_start: 0.8255 (OUTLIER) cc_final: 0.7884 (ptt180) REVERT: L 43 GLU cc_start: 0.7027 (pp20) cc_final: 0.6669 (OUTLIER) REVERT: L 70 LYS cc_start: 0.7476 (mttt) cc_final: 0.7106 (tptp) REVERT: L 74 ILE cc_start: 0.7690 (pp) cc_final: 0.7097 (pp) outliers start: 11 outliers final: 7 residues processed: 78 average time/residue: 0.3988 time to fit residues: 32.0606 Evaluate side-chains 77 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 104 PHE Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 80 THR 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 6 optimal weight: 0.6980 chunk 18 optimal weight: 8.9990 chunk 5 optimal weight: 0.7980 chunk 19 optimal weight: 5.9990 chunk 17 optimal weight: 7.9990 chunk 11 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 68 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 125 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 = 0.3827 r_free = 0.3827 target = 0.077320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.055215 restraints weight = 12176.132| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 4.42 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.7640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 2784 Z= 0.199 Angle : 1.035 15.386 3896 Z= 0.520 Chirality : 0.050 0.222 444 Planarity : 0.007 0.050 371 Dihedral : 26.373 68.902 663 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 27.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 4.95 % Allowed : 45.05 % Favored : 50.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.85 (0.48), residues: 236 helix: -0.92 (0.35), residues: 167 sheet: None (None), residues: 0 loop : -1.62 (0.67), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 39 TYR 0.027 0.003 TYR F 88 PHE 0.011 0.002 PHE F 61 HIS 0.002 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.20 ( 2784) covalent geometry : angle 1.03503 / 0.52 ( 3896) hydrogen bonds : bond 0.05393 / 3.85 ( 168) hydrogen bonds : angle 4.67587 / 3.30 ( 453) *********************** 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 88 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 78 time to evaluate : 0.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 104 PHE cc_start: 0.9538 (OUTLIER) cc_final: 0.9198 (t80) REVERT: F 50 ILE cc_start: 0.8900 (mm) cc_final: 0.8684 (pp) REVERT: F 52 GLU cc_start: 0.9172 (pm20) cc_final: 0.8919 (pm20) REVERT: F 92 ARG cc_start: 0.8381 (OUTLIER) cc_final: 0.7978 (ptt180) REVERT: L 66 ILE cc_start: 0.5758 (OUTLIER) cc_final: 0.4739 (tp) REVERT: L 70 LYS cc_start: 0.7583 (mttt) cc_final: 0.7206 (tptp) REVERT: L 74 ILE cc_start: 0.7672 (pp) cc_final: 0.6996 (pp) outliers start: 10 outliers final: 8 residues processed: 82 average time/residue: 0.4019 time to fit residues: 33.9418 Evaluate side-chains 82 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 71 time to evaluate : 0.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 104 PHE Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain L residue 43 GLU Chi-restraints excluded: chain L residue 66 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 4 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 chunk 11 optimal weight: 0.5980 chunk 13 optimal weight: 0.5980 chunk 14 optimal weight: 0.1980 chunk 9 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 22 optimal weight: 0.0470 chunk 1 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 chunk 17 optimal weight: 6.9990 overall best weight: 0.4478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 68 GLN ** E 125 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 = 0.3825 r_free = 0.3825 target = 0.077430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.055920 restraints weight = 11933.864| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 3.71 r_work: 0.3314 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.7833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 2784 Z= 0.196 Angle : 1.125 15.944 3896 Z= 0.562 Chirality : 0.051 0.215 444 Planarity : 0.008 0.080 371 Dihedral : 26.338 69.732 663 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 25.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 3.96 % Allowed : 47.52 % Favored : 48.51 % 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: -1.73 (0.49), residues: 236 helix: -0.79 (0.36), residues: 167 sheet: None (None), residues: 0 loop : -1.70 (0.68), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG E 52 TYR 0.043 0.003 TYR E 99 PHE 0.024 0.002 PHE F 61 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.20 ( 2784) covalent geometry : angle 1.12480 / 0.56 ( 3896) hydrogen bonds : bond 0.05499 / 3.90 ( 168) hydrogen bonds : angle 4.66684 / 3.30 ( 453) ********************** 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 84 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 0.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 104 PHE cc_start: 0.9580 (OUTLIER) cc_final: 0.9202 (t80) REVERT: F 50 ILE cc_start: 0.9095 (mm) cc_final: 0.8866 (pp) REVERT: F 74 GLU cc_start: 0.8959 (mt-10) cc_final: 0.8702 (mm-30) REVERT: F 92 ARG cc_start: 0.8328 (OUTLIER) cc_final: 0.7945 (ptt180) REVERT: L 70 LYS cc_start: 0.7544 (mttt) cc_final: 0.7215 (tptp) REVERT: L 74 ILE cc_start: 0.7516 (pp) cc_final: 0.6761 (pp) outliers start: 8 outliers final: 6 residues processed: 80 average time/residue: 0.4154 time to fit residues: 34.1765 Evaluate side-chains 79 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 71 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 104 PHE Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 92 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 23 optimal weight: 0.6980 chunk 18 optimal weight: 7.9990 chunk 4 optimal weight: 0.0670 chunk 10 optimal weight: 0.6980 chunk 13 optimal weight: 0.6980 chunk 1 optimal weight: 0.6980 chunk 7 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 21 optimal weight: 6.9990 chunk 12 optimal weight: 0.5980 chunk 24 optimal weight: 6.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 68 GLN ** E 125 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 = 0.3818 r_free = 0.3818 target = 0.077132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.055618 restraints weight = 12149.478| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 3.81 r_work: 0.3510 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.8034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 2784 Z= 0.193 Angle : 1.114 15.139 3896 Z= 0.556 Chirality : 0.051 0.205 444 Planarity : 0.006 0.037 371 Dihedral : 26.266 69.744 663 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 26.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 4.46 % Allowed : 48.02 % Favored : 47.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.81 (0.49), residues: 236 helix: -0.85 (0.36), residues: 167 sheet: None (None), residues: 0 loop : -1.74 (0.69), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 52 TYR 0.014 0.002 TYR E 54 PHE 0.023 0.003 PHE F 61 HIS 0.001 0.000 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.19 ( 2784) covalent geometry : angle 1.11416 / 0.56 ( 3896) hydrogen bonds : bond 0.05363 / 3.76 ( 168) hydrogen bonds : angle 4.66475 / 3.28 ( 453) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1368.74 seconds wall clock time: 24 minutes 7.65 seconds (1447.65 seconds total)