Starting phenix.real_space_refine on Tue Aug 4 12:25:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xbw_38231/08_2026/8xbw_38231.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xbw_38231/08_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_38231/08_2026/8xbw_38231.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xbw_38231/08_2026/8xbw_38231.map" model { file = "/net/cci-nas-00/data/ceres_data/8xbw_38231/08_2026/8xbw_38231.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xbw_38231/08_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-2.2rc3-6140/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: 0.62, per 1000 atoms: 0.23 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: 0.19 Conformation dependent library (CDL) restraints added in 42.7 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: 0.25 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: 0.24 Time building geometry restraints manager: 0.20 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: 3436 1.64 - 3.29: 396 3.29 - 4.93: 46 4.93 - 6.57: 12 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: 2.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.030 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 3.450 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.820 ------------------------------------------------------------------------------- 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 : 1.133 8.216 3896 Z= 0.922 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 / 0.57 ( 2784) covalent geometry : angle 1.13273 / 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 : 0.050 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: 0.6411 (tppt) outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.4282 time to fit residues: 50.3229 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 : 0.084 ------------------------------------------------------------------------------- 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: 1.9990 chunk 16 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 chunk 9 optimal weight: 5.9990 chunk 11 optimal weight: 0.9990 chunk 18 optimal weight: 5.9990 chunk 6 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3895 r_free = 0.3895 target = 0.085255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.058601 restraints weight = 10439.717| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 5.05 r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.4860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 2784 Z= 0.237 Angle : 0.966 12.906 3896 Z= 0.511 Chirality : 0.051 0.213 444 Planarity : 0.007 0.042 371 Dihedral : 27.603 71.613 663 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 33.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Rotamer: Outliers : 8.42 % Allowed : 29.70 % Favored : 61.88 % 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: -0.51 (0.48), residues: 236 helix: -0.06 (0.36), residues: 167 sheet: None (None), residues: 0 loop : -0.70 (0.67), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 39 TYR 0.028 0.004 TYR E 54 PHE 0.012 0.003 PHE F 61 HIS 0.012 0.003 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00519 / 0.24 ( 2784) covalent geometry : angle 0.96635 / 0.51 ( 3896) hydrogen bonds : bond 0.07192 / 4.91 ( 168) hydrogen bonds : angle 4.97033 / 3.54 ( 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 99 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 82 time to evaluate : 0.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 39 HIS cc_start: 0.6787 (OUTLIER) cc_final: 0.6513 (m90) REVERT: E 83 ARG cc_start: 0.3416 (OUTLIER) cc_final: 0.2879 (tpt90) REVERT: E 104 PHE cc_start: 0.9235 (OUTLIER) cc_final: 0.8880 (t80) REVERT: F 88 TYR cc_start: 0.8479 (m-80) cc_final: 0.8223 (m-10) REVERT: L 70 LYS cc_start: 0.6207 (mttt) cc_final: 0.5573 (mmmt) REVERT: L 74 ILE cc_start: 0.7937 (OUTLIER) cc_final: 0.7605 (pp) outliers start: 17 outliers final: 6 residues processed: 88 average time/residue: 0.3548 time to fit residues: 32.0395 Evaluate side-chains 75 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 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 83 ARG 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 L residue 74 ILE 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: 1.9990 chunk 17 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 2 optimal weight: 0.1980 chunk 10 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 1 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3897 r_free = 0.3897 target = 0.082066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.060826 restraints weight = 11387.812| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 3.39 r_work: 0.3426 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.5595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 2784 Z= 0.205 Angle : 0.964 16.310 3896 Z= 0.500 Chirality : 0.052 0.315 444 Planarity : 0.007 0.066 371 Dihedral : 27.368 68.091 663 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 28.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % 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 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: -1.46 (0.47), residues: 236 helix: -0.47 (0.35), residues: 174 sheet: None (None), residues: 0 loop : -2.09 (0.57), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 53 TYR 0.020 0.003 TYR E 54 PHE 0.038 0.003 PHE E 67 HIS 0.010 0.002 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.21 ( 2784) covalent geometry : angle 0.96379 / 0.50 ( 3896) hydrogen bonds : bond 0.06370 / 4.40 ( 168) hydrogen bonds : angle 4.66981 / 3.31 ( 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 86 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 72 time to evaluate : 0.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 60 LEU cc_start: 0.8881 (mm) cc_final: 0.8608 (mt) REVERT: E 94 GLU cc_start: 0.8123 (mm-30) cc_final: 0.7889 (mm-30) REVERT: E 104 PHE cc_start: 0.9533 (OUTLIER) cc_final: 0.9087 (t80) REVERT: F 88 TYR cc_start: 0.8431 (m-10) cc_final: 0.8204 (m-10) outliers start: 14 outliers final: 8 residues processed: 77 average time/residue: 0.3590 time to fit residues: 28.4444 Evaluate side-chains 74 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 65 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 46 VAL 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 66 ILE Chi-restraints excluded: chain F residue 80 THR 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: 6.9990 chunk 11 optimal weight: 0.9990 chunk 16 optimal weight: 0.3980 chunk 4 optimal weight: 0.0970 chunk 2 optimal weight: 0.9990 chunk 24 optimal weight: 5.9990 chunk 14 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 15 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 19 optimal weight: 0.0030 overall best weight: 0.3588 ------------------------------------------------------------------------------- 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 = 0.3893 r_free = 0.3893 target = 0.082329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.061659 restraints weight = 11257.862| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 3.34 r_work: 0.3439 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.5961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 2784 Z= 0.183 Angle : 0.932 12.975 3896 Z= 0.478 Chirality : 0.051 0.246 444 Planarity : 0.006 0.039 371 Dihedral : 27.084 66.671 663 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 25.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer: Outliers : 5.94 % Allowed : 36.14 % 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 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 (0.47), residues: 236 helix: -0.54 (0.36), residues: 174 sheet: None (None), residues: 0 loop : -2.11 (0.59), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 39 TYR 0.034 0.003 TYR E 54 PHE 0.008 0.002 PHE E 104 HIS 0.003 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.18 ( 2784) covalent geometry : angle 0.93249 / 0.48 ( 3896) hydrogen bonds : bond 0.05985 / 4.11 ( 168) hydrogen bonds : angle 4.39573 / 3.12 ( 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 86 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 74 time to evaluate : 0.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 94 GLU cc_start: 0.8360 (mm-30) cc_final: 0.8029 (mm-30) REVERT: E 104 PHE cc_start: 0.9525 (OUTLIER) cc_final: 0.9063 (t80) REVERT: E 120 MET cc_start: 0.5385 (mpp) cc_final: 0.5176 (mpp) REVERT: F 92 ARG cc_start: 0.8038 (OUTLIER) cc_final: 0.7720 (ptt180) REVERT: L 70 LYS cc_start: 0.6474 (mppt) cc_final: 0.5835 (tptp) REVERT: L 74 ILE cc_start: 0.7357 (pp) cc_final: 0.6742 (pp) outliers start: 12 outliers final: 4 residues processed: 79 average time/residue: 0.3483 time to fit residues: 28.3880 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 : 0.064 ------------------------------------------------------------------------------- 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 92 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 10 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 9 optimal weight: 0.5980 chunk 8 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 22 optimal weight: 8.9990 chunk 2 optimal weight: 0.4980 chunk 13 optimal weight: 0.6980 chunk 6 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.080857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.060503 restraints weight = 11432.535| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 3.43 r_work: 0.3395 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.6320 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= 0.178 Angle : 0.934 12.550 3896 Z= 0.485 Chirality : 0.049 0.199 444 Planarity : 0.005 0.041 371 Dihedral : 26.780 66.358 663 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 25.41 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: -1.06 (0.50), residues: 236 helix: -0.42 (0.37), residues: 168 sheet: None (None), residues: 0 loop : -1.08 (0.69), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 39 TYR 0.036 0.003 TYR E 54 PHE 0.010 0.002 PHE E 67 HIS 0.003 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.18 ( 2784) covalent geometry : angle 0.93384 / 0.49 ( 3896) hydrogen bonds : bond 0.05601 / 3.94 ( 168) hydrogen bonds : angle 4.22132 / 2.99 ( 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 93 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 78 time to evaluate : 0.051 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: E 94 GLU cc_start: 0.8140 (mm-30) cc_final: 0.7914 (mm-30) REVERT: E 104 PHE cc_start: 0.9572 (OUTLIER) cc_final: 0.9146 (t80) REVERT: E 110 CYS cc_start: 0.9309 (m) cc_final: 0.9045 (t) REVERT: E 123 ASP cc_start: 0.8553 (m-30) cc_final: 0.7910 (m-30) REVERT: F 50 ILE cc_start: 0.8979 (mm) cc_final: 0.8747 (pp) REVERT: F 92 ARG cc_start: 0.8083 (OUTLIER) cc_final: 0.7757 (ptt180) REVERT: L 49 VAL cc_start: 0.8483 (t) cc_final: 0.8281 (t) REVERT: L 70 LYS cc_start: 0.6747 (mppt) cc_final: 0.6108 (tptp) REVERT: L 74 ILE cc_start: 0.7277 (pp) cc_final: 0.6717 (pp) outliers start: 15 outliers final: 7 residues processed: 85 average time/residue: 0.3376 time to fit residues: 29.6005 Evaluate side-chains 78 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 69 time to evaluate : 0.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 104 PHE Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain E residue 130 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 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: 0.9990 chunk 17 optimal weight: 7.9990 chunk 0 optimal weight: 5.9990 chunk 10 optimal weight: 0.7980 chunk 21 optimal weight: 5.9990 chunk 11 optimal weight: 0.9990 chunk 6 optimal weight: 0.5980 chunk 15 optimal weight: 0.7980 chunk 18 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 68 GLN E 125 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.079767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.058790 restraints weight = 11440.222| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 3.61 r_work: 0.3379 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.6674 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= 0.193 Angle : 0.946 13.570 3896 Z= 0.487 Chirality : 0.049 0.193 444 Planarity : 0.005 0.041 371 Dihedral : 26.641 66.734 663 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 25.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 6.44 % Allowed : 38.61 % Favored : 54.95 % 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: -1.57 (0.47), residues: 236 helix: -0.78 (0.35), residues: 168 sheet: None (None), residues: 0 loop : -1.32 (0.66), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 39 TYR 0.035 0.004 TYR E 54 PHE 0.008 0.002 PHE E 104 HIS 0.002 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.19 ( 2784) covalent geometry : angle 0.94600 / 0.49 ( 3896) hydrogen bonds : bond 0.05524 / 3.82 ( 168) hydrogen bonds : angle 4.44102 / 3.10 ( 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 88 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 75 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 104 PHE cc_start: 0.9606 (OUTLIER) cc_final: 0.9171 (t80) REVERT: E 110 CYS cc_start: 0.9361 (m) cc_final: 0.9075 (t) REVERT: F 50 ILE cc_start: 0.9014 (mm) cc_final: 0.8710 (pp) REVERT: F 92 ARG cc_start: 0.8177 (OUTLIER) cc_final: 0.7825 (ptt180) REVERT: L 70 LYS cc_start: 0.7130 (mppt) cc_final: 0.6493 (tptp) REVERT: L 74 ILE cc_start: 0.7611 (pp) cc_final: 0.6979 (pp) outliers start: 13 outliers final: 6 residues processed: 80 average time/residue: 0.3455 time to fit residues: 28.4819 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 : 0.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 67 PHE 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 82 THR Chi-restraints excluded: chain F residue 92 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 0 optimal weight: 7.9990 chunk 6 optimal weight: 0.5980 chunk 19 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 1 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 16 optimal weight: 0.8980 chunk 18 optimal weight: 6.9990 chunk 21 optimal weight: 0.0970 chunk 14 optimal weight: 0.9980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.080285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.056606 restraints weight = 11594.176| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 5.24 r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.6944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 2784 Z= 0.189 Angle : 0.997 14.538 3896 Z= 0.506 Chirality : 0.051 0.223 444 Planarity : 0.005 0.040 371 Dihedral : 26.503 67.581 663 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 25.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 6.44 % Allowed : 41.58 % 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 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: -1.63 (0.47), residues: 236 helix: -0.82 (0.35), residues: 168 sheet: None (None), residues: 0 loop : -1.37 (0.66), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 36 TYR 0.038 0.004 TYR E 54 PHE 0.028 0.002 PHE F 61 HIS 0.002 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.19 ( 2784) covalent geometry : angle 0.99673 / 0.51 ( 3896) hydrogen bonds : bond 0.05391 / 3.72 ( 168) hydrogen bonds : angle 4.39047 / 3.12 ( 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 87 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 0.051 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: E 70 LEU cc_start: 0.9228 (pp) cc_final: 0.8821 (pt) REVERT: E 104 PHE cc_start: 0.9307 (OUTLIER) cc_final: 0.8963 (t80) REVERT: F 92 ARG cc_start: 0.8198 (OUTLIER) cc_final: 0.7833 (ptt180) REVERT: L 70 LYS cc_start: 0.7459 (mppt) cc_final: 0.6768 (tptp) REVERT: L 74 ILE cc_start: 0.7708 (pp) cc_final: 0.7083 (pp) outliers start: 13 outliers final: 7 residues processed: 79 average time/residue: 0.3552 time to fit residues: 28.9306 Evaluate side-chains 78 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 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 67 PHE 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 1 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 4 optimal weight: 0.0980 chunk 20 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 19 optimal weight: 5.9990 chunk 7 optimal weight: 0.5980 chunk 16 optimal weight: 3.9990 chunk 23 optimal weight: 20.0000 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3878 r_free = 0.3878 target = 0.079632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.056303 restraints weight = 11498.681| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 5.13 r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.7251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 2784 Z= 0.188 Angle : 1.050 16.251 3896 Z= 0.526 Chirality : 0.053 0.243 444 Planarity : 0.005 0.038 371 Dihedral : 26.364 67.946 663 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 25.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 5.94 % Allowed : 44.55 % Favored : 49.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.68 (0.48), residues: 236 helix: -0.80 (0.36), residues: 167 sheet: None (None), residues: 0 loop : -1.54 (0.65), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 53 TYR 0.040 0.004 TYR E 54 PHE 0.028 0.002 PHE F 61 HIS 0.001 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.19 ( 2784) covalent geometry : angle 1.05040 / 0.53 ( 3896) hydrogen bonds : bond 0.05394 / 3.73 ( 168) hydrogen bonds : angle 4.47968 / 3.17 ( 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 86 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 74 time to evaluate : 0.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 104 PHE cc_start: 0.9386 (OUTLIER) cc_final: 0.8971 (t80) REVERT: F 92 ARG cc_start: 0.8223 (OUTLIER) cc_final: 0.7856 (ptt180) REVERT: L 43 GLU cc_start: 0.6955 (pp20) cc_final: 0.6735 (pp20) REVERT: L 70 LYS cc_start: 0.7634 (mppt) cc_final: 0.7008 (tptp) REVERT: L 74 ILE cc_start: 0.7737 (pp) cc_final: 0.7222 (pp) outliers start: 12 outliers final: 8 residues processed: 77 average time/residue: 0.3439 time to fit residues: 27.2960 Evaluate side-chains 78 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 68 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 67 PHE 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 50 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 47 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 6 optimal weight: 0.8980 chunk 18 optimal weight: 8.9990 chunk 5 optimal weight: 0.5980 chunk 19 optimal weight: 0.0570 chunk 17 optimal weight: 5.9990 chunk 11 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 15 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 chunk 21 optimal weight: 9.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 85 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 = 0.3839 r_free = 0.3839 target = 0.078219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.056152 restraints weight = 11712.612| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 4.23 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.7545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 2784 Z= 0.196 Angle : 1.104 16.513 3896 Z= 0.548 Chirality : 0.052 0.227 444 Planarity : 0.005 0.039 371 Dihedral : 26.282 67.979 663 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 27.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 5.45 % Allowed : 46.04 % 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: -1.71 (0.47), residues: 236 helix: -0.85 (0.35), residues: 165 sheet: None (None), residues: 0 loop : -1.47 (0.66), residues: 71 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 53 TYR 0.040 0.003 TYR E 54 PHE 0.008 0.001 PHE F 61 HIS 0.001 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.20 ( 2784) covalent geometry : angle 1.10370 / 0.55 ( 3896) hydrogen bonds : bond 0.05462 / 3.77 ( 168) hydrogen bonds : angle 4.64671 / 3.24 ( 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 84 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 73 time to evaluate : 0.052 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: E 94 GLU cc_start: 0.8600 (mm-30) cc_final: 0.8396 (mm-30) REVERT: E 104 PHE cc_start: 0.9569 (OUTLIER) cc_final: 0.9146 (t80) REVERT: F 92 ARG cc_start: 0.8230 (OUTLIER) cc_final: 0.7849 (ptt180) REVERT: L 70 LYS cc_start: 0.7508 (mppt) cc_final: 0.6815 (tptp) REVERT: L 74 ILE cc_start: 0.7601 (pp) cc_final: 0.6889 (pp) outliers start: 11 outliers final: 5 residues processed: 78 average time/residue: 0.2687 time to fit residues: 21.6017 Evaluate side-chains 77 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 0.050 ------------------------------------------------------------------------------- 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 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 47 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 4 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 13 optimal weight: 0.0980 chunk 14 optimal weight: 0.5980 chunk 9 optimal weight: 0.0970 chunk 0 optimal weight: 6.9990 chunk 22 optimal weight: 6.9990 chunk 1 optimal weight: 0.5980 chunk 2 optimal weight: 0.9980 chunk 17 optimal weight: 7.9990 overall best weight: 0.4778 ------------------------------------------------------------------------------- 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 = 0.3839 r_free = 0.3839 target = 0.078166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.055902 restraints weight = 11954.456| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 4.50 r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.7652 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= 0.195 Angle : 1.169 18.384 3896 Z= 0.567 Chirality : 0.052 0.212 444 Planarity : 0.006 0.043 371 Dihedral : 26.226 68.202 663 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 26.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer: Outliers : 3.96 % Allowed : 48.02 % Favored : 48.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.05 (0.47), residues: 236 helix: -1.06 (0.35), residues: 167 sheet: None (None), residues: 0 loop : -1.72 (0.65), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 52 TYR 0.047 0.004 TYR E 54 PHE 0.025 0.003 PHE E 67 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.19 ( 2784) covalent geometry : angle 1.16916 / 0.57 ( 3896) hydrogen bonds : bond 0.05521 / 3.87 ( 168) hydrogen bonds : angle 4.66795 / 3.27 ( 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 83 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 75 time to evaluate : 0.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 49 ARG cc_start: 0.9125 (mtp180) cc_final: 0.8533 (ptp-110) REVERT: E 94 GLU cc_start: 0.8588 (mm-30) cc_final: 0.8385 (mm-30) REVERT: E 104 PHE cc_start: 0.9579 (OUTLIER) cc_final: 0.9188 (t80) REVERT: E 109 LEU cc_start: 0.9255 (mm) cc_final: 0.9048 (mm) REVERT: F 74 GLU cc_start: 0.9046 (mt-10) cc_final: 0.8790 (mm-30) REVERT: F 92 ARG cc_start: 0.8233 (OUTLIER) cc_final: 0.7836 (ptt180) REVERT: L 70 LYS cc_start: 0.7557 (mppt) cc_final: 0.6946 (tptp) REVERT: L 74 ILE cc_start: 0.7546 (pp) cc_final: 0.6904 (pp) outliers start: 8 outliers final: 5 residues processed: 79 average time/residue: 0.3823 time to fit residues: 31.1432 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 : 0.088 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 23 optimal weight: 4.9990 chunk 18 optimal weight: 8.9990 chunk 4 optimal weight: 0.0000 chunk 10 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 1 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 21 optimal weight: 8.9990 chunk 12 optimal weight: 0.7980 chunk 24 optimal weight: 5.9990 overall best weight: 0.5384 ------------------------------------------------------------------------------- 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 = 0.3834 r_free = 0.3834 target = 0.077880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.056602 restraints weight = 11753.865| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 4.08 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.7856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.152 2784 Z= 0.280 Angle : 1.235 18.413 3896 Z= 0.608 Chirality : 0.052 0.212 444 Planarity : 0.006 0.062 371 Dihedral : 26.139 68.081 663 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 28.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Rotamer: Outliers : 5.45 % Allowed : 47.52 % 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 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: -1.98 (0.48), residues: 236 helix: -1.04 (0.36), residues: 167 sheet: None (None), residues: 0 loop : -1.62 (0.67), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 52 TYR 0.042 0.003 TYR E 54 PHE 0.010 0.003 PHE E 67 HIS 0.002 0.001 HIS L 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00599 / 0.28 ( 2784) covalent geometry : angle 1.23511 / 0.61 ( 3896) hydrogen bonds : bond 0.05486 / 3.79 ( 168) hydrogen bonds : angle 4.64952 / 3.26 ( 453) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1175.21 seconds wall clock time: 20 minutes 41.23 seconds (1241.23 seconds total)