Starting phenix.real_space_refine on Thu Jul 2 06:00:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9auf_43878/07_2026/9auf_43878.cif Found real_map, /net/cci-nas-00/data/ceres_data/9auf_43878/07_2026/9auf_43878.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9auf_43878/07_2026/9auf_43878.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9auf_43878/07_2026/9auf_43878.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9auf_43878/07_2026/9auf_43878.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9auf_43878/07_2026/9auf_43878.map" } resolution = 2.73 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= 0.112 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 192 5.49 5 S 12 5.16 5 C 3838 2.51 5 N 1329 2.21 5 O 1880 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 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: 7251 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 389, 3193 Classifications: {'peptide': 389} Link IDs: {'PTRANS': 12, 'TRANS': 376} Chain breaks: 3 Chain: "B" Number of atoms: 3121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3121 Classifications: {'RNA': 146} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 7, 'rna3p_pur': 76, 'rna3p_pyr': 58} Link IDs: {'rna2p': 12, 'rna3p': 133} Chain: "C" Number of atoms: 325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 325 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "D" Number of atoms: 290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 290 Classifications: {'DNA': 14} Link IDs: {'rna3p': 13} Chain: "c" Number of atoms: 322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 322 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Time building chain proxies: 1.74, per 1000 atoms: 0.24 Number of scatterers: 7251 At special positions: 0 Unit cell: (82.4868, 101.65, 125.813, 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 12 16.00 P 192 15.00 O 1880 8.00 N 1329 7.00 C 3838 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: 0.65 Conformation dependent library (CDL) restraints added in 288.6 milliseconds 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 738 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 4 sheets defined 44.2% alpha, 12.9% beta 81 base pairs and 140 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'A' and resid 44 through 75 Processing helix chain 'A' and resid 80 through 90 Processing helix chain 'A' and resid 91 through 93 No H-bonds generated for 'chain 'A' and resid 91 through 93' Processing helix chain 'A' and resid 136 through 151 Processing helix chain 'A' and resid 154 through 167 Processing helix chain 'A' and resid 193 through 196 Processing helix chain 'A' and resid 197 through 207 removed outlier: 3.556A pdb=" N ILE A 205 " --> pdb=" O LEU A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 225 Processing helix chain 'A' and resid 228 through 240 removed outlier: 3.570A pdb=" N VAL A 232 " --> pdb=" O ARG A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 255 Processing helix chain 'A' and resid 573 through 575 No H-bonds generated for 'chain 'A' and resid 573 through 575' Processing helix chain 'A' and resid 576 through 583 removed outlier: 3.676A pdb=" N GLU A 580 " --> pdb=" O CYS A 577 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N ASP A 581 " --> pdb=" O GLY A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 599 Processing helix chain 'A' and resid 608 through 615 Processing helix chain 'A' and resid 636 through 638 No H-bonds generated for 'chain 'A' and resid 636 through 638' Processing helix chain 'A' and resid 736 through 738 No H-bonds generated for 'chain 'A' and resid 736 through 738' Processing sheet with id=AA1, first strand: chain 'A' and resid 560 through 562 Processing sheet with id=AA2, first strand: chain 'A' and resid 640 through 643 Processing sheet with id=AA3, first strand: chain 'A' and resid 667 through 673 removed outlier: 6.271A pdb=" N VAL A 657 " --> pdb=" O THR A 695 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N THR A 695 " --> pdb=" O VAL A 657 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N VAL A 659 " --> pdb=" O SER A 693 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 733 through 734 removed outlier: 6.212A pdb=" N GLU A 723 " --> pdb=" O ILE A 713 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N ILE A 713 " --> pdb=" O GLU A 723 " (cutoff:3.500A) 139 hydrogen bonds defined for protein. 387 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 197 hydrogen bonds 354 hydrogen bond angles 0 basepair planarities 81 basepair parallelities 140 stacking parallelities Total time for adding SS restraints: 1.22 Time building geometry restraints manager: 0.82 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: 1174 1.33 - 1.45: 2875 1.45 - 1.57: 3328 1.57 - 1.69: 380 1.69 - 1.81: 18 Bond restraints: 7775 Sorted by residual: bond pdb=" N9 A B 59 " pdb=" C4 A B 59 " ideal model delta sigma weight residual 1.374 1.347 0.027 6.00e-03 2.78e+04 2.07e+01 bond pdb=" C1' DT c 23 " pdb=" N1 DT c 23 " ideal model delta sigma weight residual 1.468 1.527 -0.059 1.40e-02 5.10e+03 1.78e+01 bond pdb=" C3' DG C 8 " pdb=" O3' DG C 8 " ideal model delta sigma weight residual 1.435 1.488 -0.053 1.30e-02 5.92e+03 1.64e+01 bond pdb=" C3' DA D 46 " pdb=" C2' DA D 46 " ideal model delta sigma weight residual 1.516 1.547 -0.031 8.00e-03 1.56e+04 1.46e+01 bond pdb=" C1' DT C 11 " pdb=" N1 DT C 11 " ideal model delta sigma weight residual 1.468 1.509 -0.041 1.40e-02 5.10e+03 8.38e+00 ... (remaining 7770 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.45: 11175 2.45 - 4.90: 175 4.90 - 7.35: 9 7.35 - 9.80: 2 9.80 - 12.25: 3 Bond angle restraints: 11364 Sorted by residual: angle pdb=" C2' G B 142 " pdb=" C1' G B 142 " pdb=" N9 G B 142 " ideal model delta sigma weight residual 114.00 126.25 -12.25 1.50e+00 4.44e-01 6.67e+01 angle pdb=" O4' G B 142 " pdb=" C1' G B 142 " pdb=" N9 G B 142 " ideal model delta sigma weight residual 108.20 118.94 -10.74 1.50e+00 4.44e-01 5.12e+01 angle pdb=" O4' DC c 26 " pdb=" C4' DC c 26 " pdb=" C3' DC c 26 " ideal model delta sigma weight residual 106.00 102.79 3.21 6.00e-01 2.78e+00 2.86e+01 angle pdb=" O4' DT C 10 " pdb=" C4' DT C 10 " pdb=" C3' DT C 10 " ideal model delta sigma weight residual 106.00 102.85 3.15 6.00e-01 2.78e+00 2.75e+01 angle pdb=" C2 A B 59 " pdb=" N3 A B 59 " pdb=" C4 A B 59 " ideal model delta sigma weight residual 110.60 108.04 2.56 5.00e-01 4.00e+00 2.62e+01 ... (remaining 11359 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.45: 4289 34.45 - 68.89: 444 68.89 - 103.34: 40 103.34 - 137.78: 1 137.78 - 172.23: 3 Dihedral angle restraints: 4777 sinusoidal: 3642 harmonic: 1135 Sorted by residual: dihedral pdb=" O4' U B 92 " pdb=" C1' U B 92 " pdb=" N1 U B 92 " pdb=" C2 U B 92 " ideal model delta sinusoidal sigma weight residual -128.00 44.23 -172.23 1 1.70e+01 3.46e-03 6.61e+01 dihedral pdb=" O4' G B 142 " pdb=" C1' G B 142 " pdb=" N9 G B 142 " pdb=" C4 G B 142 " ideal model delta sinusoidal sigma weight residual -106.00 -178.82 72.82 1 1.70e+01 3.46e-03 2.34e+01 dihedral pdb=" CA GLU A 723 " pdb=" C GLU A 723 " pdb=" N ALA A 724 " pdb=" CA ALA A 724 " ideal model delta harmonic sigma weight residual 180.00 158.85 21.15 0 5.00e+00 4.00e-02 1.79e+01 ... (remaining 4774 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.219: 1377 0.219 - 0.437: 4 0.437 - 0.656: 0 0.656 - 0.875: 0 0.875 - 1.093: 1 Chirality restraints: 1382 Sorted by residual: chirality pdb=" C1' G B 142 " pdb=" O4' G B 142 " pdb=" C2' G B 142 " pdb=" N9 G B 142 " both_signs ideal model delta sigma weight residual False 2.44 1.34 1.09 2.00e-01 2.50e+01 2.99e+01 chirality pdb=" P DT c 23 " pdb=" OP1 DT c 23 " pdb=" OP2 DT c 23 " pdb=" O5' DT c 23 " both_signs ideal model delta sigma weight residual True 2.34 -2.68 -0.34 2.00e-01 2.50e+01 2.89e+00 chirality pdb=" C3' U B 92 " pdb=" C4' U B 92 " pdb=" O3' U B 92 " pdb=" C2' U B 92 " both_signs ideal model delta sigma weight residual False -2.74 -2.45 -0.30 2.00e-01 2.50e+01 2.24e+00 ... (remaining 1379 not shown) Planarity restraints: 747 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G B 142 " -0.072 2.00e-02 2.50e+03 3.28e-02 3.23e+01 pdb=" N9 G B 142 " 0.084 2.00e-02 2.50e+03 pdb=" C8 G B 142 " 0.002 2.00e-02 2.50e+03 pdb=" N7 G B 142 " 0.000 2.00e-02 2.50e+03 pdb=" C5 G B 142 " 0.002 2.00e-02 2.50e+03 pdb=" C6 G B 142 " -0.003 2.00e-02 2.50e+03 pdb=" O6 G B 142 " -0.022 2.00e-02 2.50e+03 pdb=" N1 G B 142 " -0.006 2.00e-02 2.50e+03 pdb=" C2 G B 142 " 0.004 2.00e-02 2.50e+03 pdb=" N2 G B 142 " 0.002 2.00e-02 2.50e+03 pdb=" N3 G B 142 " 0.011 2.00e-02 2.50e+03 pdb=" C4 G B 142 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 723 " -0.026 2.00e-02 2.50e+03 5.19e-02 2.70e+01 pdb=" C GLU A 723 " 0.090 2.00e-02 2.50e+03 pdb=" O GLU A 723 " -0.034 2.00e-02 2.50e+03 pdb=" N ALA A 724 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A B 111 " -0.027 2.00e-02 2.50e+03 1.20e-02 3.96e+00 pdb=" N9 A B 111 " 0.026 2.00e-02 2.50e+03 pdb=" C8 A B 111 " 0.003 2.00e-02 2.50e+03 pdb=" N7 A B 111 " 0.002 2.00e-02 2.50e+03 pdb=" C5 A B 111 " -0.000 2.00e-02 2.50e+03 pdb=" C6 A B 111 " -0.003 2.00e-02 2.50e+03 pdb=" N6 A B 111 " -0.008 2.00e-02 2.50e+03 pdb=" N1 A B 111 " -0.004 2.00e-02 2.50e+03 pdb=" C2 A B 111 " 0.007 2.00e-02 2.50e+03 pdb=" N3 A B 111 " 0.004 2.00e-02 2.50e+03 pdb=" C4 A B 111 " 0.003 2.00e-02 2.50e+03 ... (remaining 744 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 2084 2.84 - 3.36: 5888 3.36 - 3.87: 15215 3.87 - 4.39: 17526 4.39 - 4.90: 22950 Nonbonded interactions: 63663 Sorted by model distance: nonbonded pdb=" N2 G B 38 " pdb=" OP2 A B 41 " model vdw 2.331 3.120 nonbonded pdb=" O VAL A 583 " pdb=" NH1 ARG A 589 " model vdw 2.334 3.120 nonbonded pdb=" N2 G B 117 " pdb=" OP2 A B 120 " model vdw 2.363 3.120 nonbonded pdb=" NE ARG A 170 " pdb=" OP1 G B 16 " model vdw 2.365 3.120 nonbonded pdb=" OE1 GLU A 586 " pdb=" NH2 ARG A 589 " model vdw 2.386 3.120 ... (remaining 63658 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: 4.290 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.190 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 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 : 0.005 0.059 7775 Z= 0.426 Angle : 0.772 12.254 11364 Z= 0.665 Chirality : 0.054 1.093 1382 Planarity : 0.007 0.075 747 Dihedral : 21.696 172.226 4039 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.57 % Allowed : 11.65 % Favored : 87.78 % 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: -0.18 (0.40), residues: 381 helix: 0.10 (0.39), residues: 146 sheet: -0.06 (0.72), residues: 46 loop : -0.17 (0.45), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 163 TYR 0.020 0.003 TYR A 250 PHE 0.024 0.003 PHE A 596 HIS 0.006 0.002 HIS A 680 Details of bonding type rmsd/Z covalent geometry : bond 0.00515 / 0.43 ( 7775) covalent geometry : angle 0.77216 / 0.67 (11364) hydrogen bonds : bond 0.11875 / 8.51 ( 336) hydrogen bonds : angle 4.37466 / 3.03 ( 741) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 52 time to evaluate : 0.183 Fit side-chains revert: symmetry clash REVERT: A 50 GLN cc_start: 0.8606 (OUTLIER) cc_final: 0.8391 (tp40) REVERT: A 148 MET cc_start: 0.8397 (mtp) cc_final: 0.7920 (mtp) REVERT: A 159 LYS cc_start: 0.8197 (ttmm) cc_final: 0.7659 (mtmt) REVERT: A 586 GLU cc_start: 0.7787 (mm-30) cc_final: 0.7572 (tt0) REVERT: A 697 LYS cc_start: 0.7711 (mmtp) cc_final: 0.7404 (mptt) REVERT: A 712 ARG cc_start: 0.7047 (ptm160) cc_final: 0.6652 (ttt180) outliers start: 2 outliers final: 1 residues processed: 54 average time/residue: 0.7591 time to fit residues: 42.6042 Evaluate side-chains 48 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 46 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 GLN Chi-restraints excluded: chain A residue 741 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 54 optimal weight: 4.9990 chunk 24 optimal weight: 0.3980 chunk 48 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 50 optimal weight: 9.9990 chunk 53 optimal weight: 5.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- 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 = 0.4103 r_free = 0.4103 target = 0.190590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 93)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.137420 restraints weight = 6192.900| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 0.91 r_work: 0.3350 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 moved from start: 0.0709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7775 Z= 0.213 Angle : 0.610 12.461 11364 Z= 0.369 Chirality : 0.050 0.938 1382 Planarity : 0.006 0.043 747 Dihedral : 22.498 170.713 3169 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.41 % Allowed : 12.22 % Favored : 84.38 % 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: 0.46 (0.43), residues: 381 helix: 1.15 (0.41), residues: 148 sheet: -0.33 (0.74), residues: 44 loop : -0.12 (0.47), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 589 TYR 0.016 0.002 TYR A 169 PHE 0.014 0.002 PHE A 648 HIS 0.004 0.002 HIS A 653 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.21 ( 7775) covalent geometry : angle 0.60995 / 0.37 (11364) hydrogen bonds : bond 0.05740 / 3.72 ( 336) hydrogen bonds : angle 3.47183 / 2.45 ( 741) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 45 time to evaluate : 0.173 Fit side-chains revert: symmetry clash REVERT: A 50 GLN cc_start: 0.8623 (OUTLIER) cc_final: 0.8372 (tp40) REVERT: A 148 MET cc_start: 0.8434 (mtp) cc_final: 0.7903 (mtp) REVERT: A 159 LYS cc_start: 0.8209 (ttmm) cc_final: 0.7679 (mtmt) REVERT: A 168 GLN cc_start: 0.8991 (OUTLIER) cc_final: 0.7917 (tp-100) REVERT: A 586 GLU cc_start: 0.7881 (mm-30) cc_final: 0.7601 (tt0) REVERT: A 625 VAL cc_start: 0.8290 (OUTLIER) cc_final: 0.8090 (m) REVERT: A 697 LYS cc_start: 0.7788 (mmtp) cc_final: 0.7415 (mptt) outliers start: 12 outliers final: 5 residues processed: 53 average time/residue: 0.7271 time to fit residues: 40.0915 Evaluate side-chains 51 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 GLN Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 168 GLN Chi-restraints excluded: chain A residue 581 ASP Chi-restraints excluded: chain A residue 601 THR Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain A residue 741 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 12 optimal weight: 0.8980 chunk 44 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 chunk 50 optimal weight: 10.0000 chunk 18 optimal weight: 0.0970 chunk 34 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 overall best weight: 0.7378 ------------------------------------------------------------------------------- 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 = 0.4123 r_free = 0.4123 target = 0.192637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.140342 restraints weight = 6130.112| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 0.87 r_work: 0.3385 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3276 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 moved from start: 0.0912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7775 Z= 0.156 Angle : 0.531 11.836 11364 Z= 0.332 Chirality : 0.044 0.831 1382 Planarity : 0.004 0.034 747 Dihedral : 22.456 169.072 3169 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 3.41 % Allowed : 12.50 % Favored : 84.09 % 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: 0.83 (0.43), residues: 381 helix: 1.73 (0.41), residues: 148 sheet: -0.54 (0.75), residues: 44 loop : -0.04 (0.47), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 163 TYR 0.011 0.001 TYR A 169 PHE 0.013 0.001 PHE A 648 HIS 0.003 0.001 HIS A 653 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.16 ( 7775) covalent geometry : angle 0.53141 / 0.33 (11364) hydrogen bonds : bond 0.04900 / 3.21 ( 336) hydrogen bonds : angle 3.22635 / 2.27 ( 741) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 49 time to evaluate : 0.135 Fit side-chains REVERT: A 50 GLN cc_start: 0.8636 (OUTLIER) cc_final: 0.8376 (tp40) REVERT: A 159 LYS cc_start: 0.8209 (ttmm) cc_final: 0.7677 (mtmt) REVERT: A 211 ILE cc_start: 0.7422 (OUTLIER) cc_final: 0.6976 (pp) REVERT: A 586 GLU cc_start: 0.7908 (mm-30) cc_final: 0.7625 (tt0) REVERT: A 611 GLU cc_start: 0.7814 (mt-10) cc_final: 0.7496 (mt-10) REVERT: A 625 VAL cc_start: 0.8305 (OUTLIER) cc_final: 0.8056 (m) REVERT: A 697 LYS cc_start: 0.7795 (mmtp) cc_final: 0.7403 (mptt) REVERT: A 712 ARG cc_start: 0.7156 (OUTLIER) cc_final: 0.6891 (ttm-80) outliers start: 12 outliers final: 4 residues processed: 56 average time/residue: 0.6380 time to fit residues: 37.2908 Evaluate side-chains 51 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 GLN Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 581 ASP Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain A residue 712 ARG Chi-restraints excluded: chain A residue 741 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 5 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 15 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 50 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.191084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 94)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.138148 restraints weight = 6200.661| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 0.95 r_work: 0.3357 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 0.1059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7775 Z= 0.174 Angle : 0.538 11.861 11364 Z= 0.334 Chirality : 0.045 0.849 1382 Planarity : 0.005 0.041 747 Dihedral : 22.442 169.085 3169 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.98 % Allowed : 13.35 % Favored : 82.67 % 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: 0.99 (0.44), residues: 381 helix: 1.87 (0.41), residues: 149 sheet: -0.55 (0.76), residues: 44 loop : 0.05 (0.48), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 152 TYR 0.013 0.001 TYR A 70 PHE 0.011 0.001 PHE A 235 HIS 0.003 0.001 HIS A 653 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.17 ( 7775) covalent geometry : angle 0.53752 / 0.33 (11364) hydrogen bonds : bond 0.04944 / 3.21 ( 336) hydrogen bonds : angle 3.14374 / 2.18 ( 741) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 48 time to evaluate : 0.176 Fit side-chains REVERT: A 48 ARG cc_start: 0.8750 (OUTLIER) cc_final: 0.8450 (ttp-170) REVERT: A 159 LYS cc_start: 0.8191 (ttmm) cc_final: 0.7652 (mtmt) REVERT: A 211 ILE cc_start: 0.7435 (OUTLIER) cc_final: 0.6987 (pp) REVERT: A 586 GLU cc_start: 0.7965 (mm-30) cc_final: 0.7600 (tt0) REVERT: A 611 GLU cc_start: 0.7826 (mt-10) cc_final: 0.7295 (mt-10) REVERT: A 625 VAL cc_start: 0.8313 (OUTLIER) cc_final: 0.8032 (m) REVERT: A 697 LYS cc_start: 0.7802 (mmtp) cc_final: 0.7435 (mptt) REVERT: A 712 ARG cc_start: 0.7144 (OUTLIER) cc_final: 0.6865 (ttm-80) REVERT: A 714 LYS cc_start: 0.7973 (OUTLIER) cc_final: 0.7641 (tptt) outliers start: 14 outliers final: 5 residues processed: 55 average time/residue: 0.7604 time to fit residues: 43.4808 Evaluate side-chains 56 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 46 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ARG Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 581 ASP Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 712 ARG Chi-restraints excluded: chain A residue 714 LYS Chi-restraints excluded: chain A residue 741 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 25 optimal weight: 5.9990 chunk 46 optimal weight: 4.9990 chunk 12 optimal weight: 0.4980 chunk 54 optimal weight: 4.9990 chunk 7 optimal weight: 0.6980 chunk 1 optimal weight: 0.2980 chunk 47 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 45 optimal weight: 6.9990 chunk 10 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.4123 r_free = 0.4123 target = 0.192629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 97)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.140040 restraints weight = 6161.530| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 0.94 r_work: 0.3380 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.1166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7775 Z= 0.149 Angle : 0.511 11.462 11364 Z= 0.320 Chirality : 0.043 0.795 1382 Planarity : 0.004 0.036 747 Dihedral : 22.408 168.150 3166 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 4.26 % Allowed : 13.07 % Favored : 82.67 % 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 (0.44), residues: 381 helix: 2.03 (0.41), residues: 149 sheet: -0.49 (0.76), residues: 44 loop : 0.11 (0.48), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 163 TYR 0.010 0.001 TYR A 169 PHE 0.010 0.001 PHE A 648 HIS 0.003 0.001 HIS A 653 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.15 ( 7775) covalent geometry : angle 0.51093 / 0.32 (11364) hydrogen bonds : bond 0.04647 / 3.02 ( 336) hydrogen bonds : angle 3.08390 / 2.14 ( 741) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 48 time to evaluate : 0.176 Fit side-chains REVERT: A 48 ARG cc_start: 0.8740 (OUTLIER) cc_final: 0.8436 (ttp-170) REVERT: A 159 LYS cc_start: 0.8178 (ttmm) cc_final: 0.7616 (mtmt) REVERT: A 211 ILE cc_start: 0.7427 (OUTLIER) cc_final: 0.6967 (pp) REVERT: A 586 GLU cc_start: 0.7962 (mm-30) cc_final: 0.7601 (tt0) REVERT: A 611 GLU cc_start: 0.7843 (mt-10) cc_final: 0.7339 (mt-10) REVERT: A 625 VAL cc_start: 0.8322 (OUTLIER) cc_final: 0.8015 (m) REVERT: A 687 GLN cc_start: 0.6766 (OUTLIER) cc_final: 0.6495 (pt0) REVERT: A 697 LYS cc_start: 0.7784 (mmtp) cc_final: 0.7405 (mptt) REVERT: A 714 LYS cc_start: 0.7970 (OUTLIER) cc_final: 0.7622 (tptt) outliers start: 15 outliers final: 7 residues processed: 55 average time/residue: 0.7343 time to fit residues: 42.0888 Evaluate side-chains 57 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 45 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ARG Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 238 LYS Chi-restraints excluded: chain A residue 581 ASP Chi-restraints excluded: chain A residue 601 THR Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 687 GLN Chi-restraints excluded: chain A residue 714 LYS Chi-restraints excluded: chain A residue 741 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 46 optimal weight: 4.9990 chunk 22 optimal weight: 0.7980 chunk 17 optimal weight: 0.4980 chunk 32 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 chunk 45 optimal weight: 7.9990 chunk 14 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.4116 r_free = 0.4116 target = 0.191838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 93)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.138691 restraints weight = 6137.951| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 0.95 r_work: 0.3364 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3254 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.1234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7775 Z= 0.162 Angle : 0.514 11.443 11364 Z= 0.321 Chirality : 0.043 0.798 1382 Planarity : 0.004 0.034 747 Dihedral : 22.393 168.423 3166 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.69 % Allowed : 13.92 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.19 (0.44), residues: 381 helix: 2.09 (0.41), residues: 149 sheet: -0.46 (0.77), residues: 44 loop : 0.12 (0.48), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 163 TYR 0.013 0.001 TYR A 70 PHE 0.011 0.001 PHE A 599 HIS 0.004 0.001 HIS A 653 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.16 ( 7775) covalent geometry : angle 0.51411 / 0.32 (11364) hydrogen bonds : bond 0.04690 / 3.05 ( 336) hydrogen bonds : angle 3.08225 / 2.13 ( 741) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 47 time to evaluate : 0.147 Fit side-chains revert: symmetry clash REVERT: A 48 ARG cc_start: 0.8751 (OUTLIER) cc_final: 0.8434 (ttp-170) REVERT: A 159 LYS cc_start: 0.8192 (ttmm) cc_final: 0.7627 (mtmt) REVERT: A 211 ILE cc_start: 0.7466 (OUTLIER) cc_final: 0.7028 (pp) REVERT: A 581 ASP cc_start: 0.8243 (OUTLIER) cc_final: 0.8036 (t0) REVERT: A 586 GLU cc_start: 0.8008 (mm-30) cc_final: 0.7636 (tt0) REVERT: A 625 VAL cc_start: 0.8312 (OUTLIER) cc_final: 0.7972 (m) REVERT: A 687 GLN cc_start: 0.6767 (OUTLIER) cc_final: 0.6512 (pt0) REVERT: A 697 LYS cc_start: 0.7857 (mmtp) cc_final: 0.7475 (mptt) REVERT: A 714 LYS cc_start: 0.8009 (OUTLIER) cc_final: 0.7662 (tptt) outliers start: 13 outliers final: 5 residues processed: 54 average time/residue: 0.7397 time to fit residues: 41.5241 Evaluate side-chains 56 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 45 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ARG Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 238 LYS Chi-restraints excluded: chain A residue 581 ASP Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 687 GLN Chi-restraints excluded: chain A residue 714 LYS Chi-restraints excluded: chain A residue 741 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 39 optimal weight: 4.9990 chunk 12 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 11 optimal weight: 0.0040 chunk 35 optimal weight: 0.0370 chunk 7 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 44 optimal weight: 4.9990 chunk 32 optimal weight: 0.0470 chunk 46 optimal weight: 4.9990 overall best weight: 0.2968 ------------------------------------------------------------------------------- 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 = 0.4141 r_free = 0.4141 target = 0.194394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 100)---------------| | r_work = 0.3571 r_free = 0.3571 target = 0.141876 restraints weight = 6200.635| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 0.96 r_work: 0.3395 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3282 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.1304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7775 Z= 0.121 Angle : 0.489 10.885 11364 Z= 0.310 Chirality : 0.041 0.739 1382 Planarity : 0.004 0.029 747 Dihedral : 22.403 167.565 3166 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.98 % Allowed : 13.35 % Favored : 82.67 % 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 (0.44), residues: 381 helix: 2.11 (0.42), residues: 149 sheet: -0.51 (0.76), residues: 44 loop : 0.18 (0.48), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 163 TYR 0.008 0.001 TYR A 70 PHE 0.011 0.001 PHE A 648 HIS 0.002 0.001 HIS A 554 Details of bonding type rmsd/Z covalent geometry : bond 0.00194 / 0.12 ( 7775) covalent geometry : angle 0.48924 / 0.31 (11364) hydrogen bonds : bond 0.04470 / 2.91 ( 336) hydrogen bonds : angle 3.10311 / 2.13 ( 741) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 49 time to evaluate : 0.174 Fit side-chains revert: symmetry clash REVERT: A 48 ARG cc_start: 0.8728 (OUTLIER) cc_final: 0.8404 (ttp-170) REVERT: A 88 SER cc_start: 0.8670 (OUTLIER) cc_final: 0.8300 (t) REVERT: A 142 LYS cc_start: 0.8642 (OUTLIER) cc_final: 0.8171 (mtpt) REVERT: A 159 LYS cc_start: 0.8186 (ttmm) cc_final: 0.7617 (mtmt) REVERT: A 211 ILE cc_start: 0.7418 (OUTLIER) cc_final: 0.6972 (pp) REVERT: A 581 ASP cc_start: 0.8240 (OUTLIER) cc_final: 0.8026 (t0) REVERT: A 586 GLU cc_start: 0.7997 (mm-30) cc_final: 0.7618 (tt0) REVERT: A 625 VAL cc_start: 0.8301 (OUTLIER) cc_final: 0.7961 (m) REVERT: A 687 GLN cc_start: 0.6737 (OUTLIER) cc_final: 0.6478 (pt0) REVERT: A 697 LYS cc_start: 0.7838 (mmtp) cc_final: 0.7510 (mptt) REVERT: A 714 LYS cc_start: 0.7950 (OUTLIER) cc_final: 0.7623 (tptt) outliers start: 14 outliers final: 5 residues processed: 56 average time/residue: 0.6777 time to fit residues: 39.6119 Evaluate side-chains 58 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 45 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ARG Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 142 LYS Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 238 LYS Chi-restraints excluded: chain A residue 581 ASP Chi-restraints excluded: chain A residue 601 THR Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 687 GLN Chi-restraints excluded: chain A residue 714 LYS Chi-restraints excluded: chain A residue 741 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 51 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 17 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 31 optimal weight: 0.3980 chunk 50 optimal weight: 10.0000 chunk 48 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 4 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 168 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.192306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 99)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.139650 restraints weight = 6215.269| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 0.94 r_work: 0.3375 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3266 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8774 moved from start: 0.1336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7775 Z= 0.158 Angle : 0.502 11.162 11364 Z= 0.315 Chirality : 0.042 0.766 1382 Planarity : 0.004 0.032 747 Dihedral : 22.367 168.240 3166 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.69 % Allowed : 13.92 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.22 (0.44), residues: 381 helix: 2.10 (0.42), residues: 149 sheet: -0.41 (0.77), residues: 44 loop : 0.14 (0.48), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 163 TYR 0.012 0.001 TYR A 70 PHE 0.012 0.001 PHE A 235 HIS 0.004 0.001 HIS A 653 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.16 ( 7775) covalent geometry : angle 0.50153 / 0.31 (11364) hydrogen bonds : bond 0.04565 / 2.96 ( 336) hydrogen bonds : angle 3.09869 / 2.12 ( 741) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 44 time to evaluate : 0.176 Fit side-chains revert: symmetry clash REVERT: A 48 ARG cc_start: 0.8748 (OUTLIER) cc_final: 0.8419 (ttp-170) REVERT: A 88 SER cc_start: 0.8688 (OUTLIER) cc_final: 0.8310 (t) REVERT: A 142 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.8156 (mtpt) REVERT: A 159 LYS cc_start: 0.8189 (ttmm) cc_final: 0.7627 (mtmt) REVERT: A 211 ILE cc_start: 0.7462 (OUTLIER) cc_final: 0.7024 (pp) REVERT: A 586 GLU cc_start: 0.7997 (mm-30) cc_final: 0.7639 (tt0) REVERT: A 625 VAL cc_start: 0.8332 (OUTLIER) cc_final: 0.7970 (m) REVERT: A 687 GLN cc_start: 0.6746 (OUTLIER) cc_final: 0.6491 (pt0) REVERT: A 697 LYS cc_start: 0.7839 (mmtp) cc_final: 0.7530 (mptt) REVERT: A 714 LYS cc_start: 0.7976 (OUTLIER) cc_final: 0.7626 (tptt) outliers start: 13 outliers final: 4 residues processed: 51 average time/residue: 0.8052 time to fit residues: 42.6445 Evaluate side-chains 53 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 42 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ARG Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 142 LYS Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 238 LYS Chi-restraints excluded: chain A residue 601 THR Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 687 GLN Chi-restraints excluded: chain A residue 714 LYS Chi-restraints excluded: chain A residue 741 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 37 optimal weight: 7.9990 chunk 45 optimal weight: 7.9990 chunk 47 optimal weight: 4.9990 chunk 13 optimal weight: 0.8980 chunk 15 optimal weight: 0.0980 chunk 50 optimal weight: 9.9990 chunk 20 optimal weight: 0.0010 chunk 52 optimal weight: 10.0000 chunk 43 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 overall best weight: 0.7988 ------------------------------------------------------------------------------- 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 = 0.4120 r_free = 0.4120 target = 0.192194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.140238 restraints weight = 6112.956| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 0.97 r_work: 0.3365 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7775 Z= 0.156 Angle : 0.501 11.054 11364 Z= 0.314 Chirality : 0.042 0.756 1382 Planarity : 0.004 0.030 747 Dihedral : 22.370 168.190 3166 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.69 % Allowed : 14.20 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.21 (0.44), residues: 381 helix: 2.11 (0.42), residues: 149 sheet: -0.41 (0.79), residues: 42 loop : 0.11 (0.47), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 152 TYR 0.012 0.001 TYR A 70 PHE 0.011 0.001 PHE A 235 HIS 0.004 0.001 HIS A 653 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.16 ( 7775) covalent geometry : angle 0.50120 / 0.31 (11364) hydrogen bonds : bond 0.04534 / 2.95 ( 336) hydrogen bonds : angle 3.08576 / 2.10 ( 741) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 43 time to evaluate : 0.189 Fit side-chains revert: symmetry clash REVERT: A 48 ARG cc_start: 0.8744 (OUTLIER) cc_final: 0.8427 (ttp-170) REVERT: A 88 SER cc_start: 0.8692 (OUTLIER) cc_final: 0.8311 (t) REVERT: A 142 LYS cc_start: 0.8658 (OUTLIER) cc_final: 0.8179 (mtpt) REVERT: A 159 LYS cc_start: 0.8212 (ttmm) cc_final: 0.7659 (mtmt) REVERT: A 211 ILE cc_start: 0.7452 (OUTLIER) cc_final: 0.6983 (pp) REVERT: A 586 GLU cc_start: 0.8022 (mm-30) cc_final: 0.7645 (tt0) REVERT: A 625 VAL cc_start: 0.8311 (OUTLIER) cc_final: 0.7953 (m) REVERT: A 687 GLN cc_start: 0.6756 (OUTLIER) cc_final: 0.6550 (pt0) REVERT: A 697 LYS cc_start: 0.7896 (mmtp) cc_final: 0.7571 (mptt) REVERT: A 714 LYS cc_start: 0.7976 (OUTLIER) cc_final: 0.7586 (tptt) REVERT: A 742 LYS cc_start: 0.7948 (tttp) cc_final: 0.7496 (tptt) outliers start: 13 outliers final: 3 residues processed: 52 average time/residue: 0.8620 time to fit residues: 46.4582 Evaluate side-chains 52 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 42 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ARG Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 142 LYS Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 601 THR Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 687 GLN Chi-restraints excluded: chain A residue 714 LYS Chi-restraints excluded: chain A residue 741 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 42 optimal weight: 10.0000 chunk 19 optimal weight: 0.0040 chunk 40 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 3 optimal weight: 0.4980 chunk 38 optimal weight: 5.9990 chunk 32 optimal weight: 0.8980 chunk 34 optimal weight: 0.0570 chunk 41 optimal weight: 10.0000 overall best weight: 0.4510 ------------------------------------------------------------------------------- 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 = 0.4132 r_free = 0.4132 target = 0.193335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.140529 restraints weight = 6140.880| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 0.93 r_work: 0.3389 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3281 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.1452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7775 Z= 0.131 Angle : 0.490 10.909 11364 Z= 0.310 Chirality : 0.041 0.732 1382 Planarity : 0.004 0.035 747 Dihedral : 22.376 168.192 3166 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.12 % Allowed : 14.20 % Favored : 82.67 % 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: 1.27 (0.44), residues: 381 helix: 2.19 (0.42), residues: 149 sheet: -0.43 (0.80), residues: 42 loop : 0.13 (0.47), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 163 TYR 0.010 0.001 TYR A 70 PHE 0.011 0.001 PHE A 599 HIS 0.002 0.001 HIS A 653 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.13 ( 7775) covalent geometry : angle 0.49014 / 0.31 (11364) hydrogen bonds : bond 0.04440 / 2.90 ( 336) hydrogen bonds : angle 3.07192 / 2.10 ( 741) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 43 time to evaluate : 0.196 Fit side-chains REVERT: A 48 ARG cc_start: 0.8729 (OUTLIER) cc_final: 0.8411 (ttp-170) REVERT: A 88 SER cc_start: 0.8669 (OUTLIER) cc_final: 0.8294 (t) REVERT: A 142 LYS cc_start: 0.8635 (OUTLIER) cc_final: 0.8166 (mtpt) REVERT: A 159 LYS cc_start: 0.8174 (ttmm) cc_final: 0.7615 (mtmt) REVERT: A 211 ILE cc_start: 0.7460 (OUTLIER) cc_final: 0.6995 (pp) REVERT: A 586 GLU cc_start: 0.7990 (mm-30) cc_final: 0.7634 (tt0) REVERT: A 611 GLU cc_start: 0.7788 (mt-10) cc_final: 0.7415 (mt-10) REVERT: A 625 VAL cc_start: 0.8310 (OUTLIER) cc_final: 0.7970 (m) REVERT: A 687 GLN cc_start: 0.6728 (OUTLIER) cc_final: 0.6526 (pt0) REVERT: A 697 LYS cc_start: 0.7855 (mmtp) cc_final: 0.7543 (mptt) REVERT: A 714 LYS cc_start: 0.7950 (OUTLIER) cc_final: 0.7566 (tptt) REVERT: A 742 LYS cc_start: 0.7938 (tttp) cc_final: 0.7495 (tptt) outliers start: 11 outliers final: 3 residues processed: 51 average time/residue: 0.8431 time to fit residues: 44.7154 Evaluate side-chains 51 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 41 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ARG Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 142 LYS Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 601 THR Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 687 GLN Chi-restraints excluded: chain A residue 714 LYS Chi-restraints excluded: chain A residue 741 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 3 optimal weight: 0.7980 chunk 9 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 20 optimal weight: 0.1980 chunk 10 optimal weight: 0.6980 chunk 34 optimal weight: 5.9990 chunk 11 optimal weight: 0.0070 chunk 18 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 overall best weight: 0.4998 ------------------------------------------------------------------------------- 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 = 0.4139 r_free = 0.4139 target = 0.194049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 93)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.142068 restraints weight = 6142.610| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 0.90 r_work: 0.3395 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3284 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7775 Z= 0.130 Angle : 0.484 10.744 11364 Z= 0.306 Chirality : 0.040 0.716 1382 Planarity : 0.004 0.038 747 Dihedral : 22.355 167.642 3166 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.84 % Allowed : 15.06 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.30 (0.44), residues: 381 helix: 2.24 (0.42), residues: 149 sheet: -0.28 (0.81), residues: 41 loop : 0.09 (0.46), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 163 TYR 0.010 0.001 TYR A 70 PHE 0.011 0.001 PHE A 235 HIS 0.002 0.001 HIS A 653 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.13 ( 7775) covalent geometry : angle 0.48423 / 0.31 (11364) hydrogen bonds : bond 0.04337 / 2.83 ( 336) hydrogen bonds : angle 3.03945 / 2.07 ( 741) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2670.19 seconds wall clock time: 46 minutes 12.73 seconds (2772.73 seconds total)