Starting phenix.real_space_refine on Tue Aug 4 22:08:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9auf_43878/08_2026/9auf_43878.cif Found real_map, /net/cci-nas-00/data/ceres_data/9auf_43878/08_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_43878/08_2026/9auf_43878.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9auf_43878/08_2026/9auf_43878.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9auf_43878/08_2026/9auf_43878.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9auf_43878/08_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-2.2rc3-6140/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: 1.58, per 1000 atoms: 0.22 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: 0.70 Conformation dependent library (CDL) restraints added in 288.5 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: 1.09 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: 1.38 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: 10961 2.45 - 4.90: 388 4.90 - 7.35: 9 7.35 - 9.80: 3 9.80 - 12.25: 3 Bond angle restraints: 11364 Sorted by residual: 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 8.00e-01 1.56e+00 1.80e+02 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 1.30e+00 5.92e-01 8.88e+01 angle pdb=" C3' U B 92 " pdb=" O3' U B 92 " pdb=" P U B 93 " ideal model delta sigma weight residual 119.70 127.18 -7.48 1.20e+00 6.94e-01 3.89e+01 angle pdb=" C3' G B 142 " pdb=" O3' G B 142 " pdb=" P G B 143 " ideal model delta sigma weight residual 119.70 126.60 -6.90 1.20e+00 6.94e-01 3.31e+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 ... (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 - 0.218: 1377 0.218 - 0.437: 4 0.437 - 0.655: 0 0.655 - 0.873: 0 0.873 - 1.092: 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 2.98e+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: 5.060 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: 0.120 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 8.740 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.550 ------------------------------------------------------------------------------- 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= 0.441 Angle : 0.905 12.254 11364 Z= 0.777 Chirality : 0.069 1.092 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 0.00524 / 0.44 ( 7775) covalent geometry : angle 0.90487 / 0.78 (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 : 0.178 Fit side-chains revert: symmetry clash REVERT: A 48 ARG cc_start: 0.8658 (ttm170) cc_final: 0.8399 (ttm170) REVERT: A 50 GLN cc_start: 0.8606 (OUTLIER) cc_final: 0.8387 (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: 0.7573 (tt0) REVERT: A 697 LYS cc_start: 0.7711 (mmtp) cc_final: 0.7403 (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: 0.8199 time to fit residues: 45.9261 Evaluate side-chains 49 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 47 time to evaluate : 0.176 ------------------------------------------------------------------------------- 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: 0.9990 chunk 48 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 chunk 50 optimal weight: 9.9990 chunk 53 optimal weight: 5.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- 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 = 0.4121 r_free = 0.4121 target = 0.192416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 97)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.139435 restraints weight = 6203.075| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 0.96 r_work: 0.3366 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.0743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7775 Z= 0.171 Angle : 0.592 10.906 11364 Z= 0.359 Chirality : 0.044 0.509 1382 Planarity : 0.005 0.040 747 Dihedral : 22.477 171.215 3169 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.84 % Allowed : 12.22 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.43), residues: 381 helix: 1.25 (0.41), residues: 148 sheet: -0.24 (0.66), residues: 55 loop : -0.09 (0.50), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 589 TYR 0.015 0.002 TYR A 169 PHE 0.013 0.002 PHE A 648 HIS 0.004 0.001 HIS A 680 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.17 ( 7775) covalent geometry : angle 0.59235 / 0.36 (11364) hydrogen bonds : bond 0.05587 / 3.60 ( 336) hydrogen bonds : angle 3.43810 / 2.42 ( 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 56 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 46 time to evaluate : 0.145 Fit side-chains REVERT: A 50 GLN cc_start: 0.8629 (OUTLIER) cc_final: 0.8394 (tp40) REVERT: A 148 MET cc_start: 0.8428 (mtp) cc_final: 0.7837 (mtp) REVERT: A 159 LYS cc_start: 0.8221 (ttmm) cc_final: 0.7680 (mtmt) REVERT: A 586 GLU cc_start: 0.7901 (mm-30) cc_final: 0.7575 (tt0) REVERT: A 611 GLU cc_start: 0.7780 (mt-10) cc_final: 0.7370 (mt-10) REVERT: A 697 LYS cc_start: 0.7761 (mmtp) cc_final: 0.7406 (mptt) REVERT: A 712 ARG cc_start: 0.7104 (ptm160) cc_final: 0.6859 (ttm-80) outliers start: 10 outliers final: 4 residues processed: 53 average time/residue: 0.7225 time to fit residues: 39.7815 Evaluate side-chains 50 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 45 time to evaluate : 0.112 ------------------------------------------------------------------------------- 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 581 ASP Chi-restraints excluded: chain A residue 607 LEU 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: 0.5980 chunk 44 optimal weight: 5.9990 chunk 9 optimal weight: 0.6980 chunk 50 optimal weight: 9.9990 chunk 18 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 39 optimal weight: 4.9990 chunk 6 optimal weight: 0.5980 chunk 16 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.4125 r_free = 0.4125 target = 0.192693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.140177 restraints weight = 6138.664| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 0.93 r_work: 0.3380 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3273 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.1027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7775 Z= 0.152 Angle : 0.543 10.122 11364 Z= 0.333 Chirality : 0.042 0.488 1382 Planarity : 0.005 0.040 747 Dihedral : 22.404 170.457 3169 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.84 % Allowed : 12.78 % 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: 0.96 (0.43), residues: 381 helix: 1.81 (0.41), residues: 148 sheet: -0.48 (0.75), residues: 44 loop : 0.06 (0.48), 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 0.012 0.001 PHE A 648 HIS 0.003 0.001 HIS A 680 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.15 ( 7775) covalent geometry : angle 0.54258 / 0.33 (11364) hydrogen bonds : bond 0.04963 / 3.22 ( 336) hydrogen bonds : angle 3.18374 / 2.23 ( 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 60 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 50 time to evaluate : 0.174 Fit side-chains REVERT: A 50 GLN cc_start: 0.8619 (OUTLIER) cc_final: 0.8363 (tp40) REVERT: A 159 LYS cc_start: 0.8177 (ttmm) cc_final: 0.7624 (mtmt) REVERT: A 211 ILE cc_start: 0.7417 (OUTLIER) cc_final: 0.6950 (pp) REVERT: A 586 GLU cc_start: 0.7909 (mm-30) cc_final: 0.7565 (tt0) REVERT: A 611 GLU cc_start: 0.7829 (mt-10) cc_final: 0.7496 (mt-10) REVERT: A 697 LYS cc_start: 0.7707 (mmtp) cc_final: 0.7351 (mptt) REVERT: A 712 ARG cc_start: 0.7144 (ptm160) cc_final: 0.6893 (ttm-80) REVERT: A 714 LYS cc_start: 0.7953 (OUTLIER) cc_final: 0.7654 (tptt) outliers start: 10 outliers final: 4 residues processed: 56 average time/residue: 0.6843 time to fit residues: 39.8948 Evaluate side-chains 52 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 45 time to evaluate : 0.171 ------------------------------------------------------------------------------- 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 714 LYS 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: 0.0270 chunk 15 optimal weight: 0.0870 chunk 31 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 49 optimal weight: 6.9990 chunk 35 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 overall best weight: 0.5816 ------------------------------------------------------------------------------- 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 = 0.4139 r_free = 0.4139 target = 0.194110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.141986 restraints weight = 6230.458| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 0.88 r_work: 0.3400 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3290 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.1196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 7775 Z= 0.135 Angle : 0.511 9.542 11364 Z= 0.317 Chirality : 0.040 0.442 1382 Planarity : 0.004 0.035 747 Dihedral : 22.392 169.690 3169 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.27 % Allowed : 13.92 % Favored : 83.81 % 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: -0.52 (0.76), residues: 44 loop : 0.17 (0.48), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 152 TYR 0.009 0.001 TYR A 169 PHE 0.011 0.001 PHE A 648 HIS 0.003 0.001 HIS A 653 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.14 ( 7775) covalent geometry : angle 0.51100 / 0.32 (11364) hydrogen bonds : bond 0.04731 / 3.07 ( 336) hydrogen bonds : angle 3.05835 / 2.12 ( 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 56 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 48 time to evaluate : 0.113 Fit side-chains REVERT: A 88 SER cc_start: 0.8668 (OUTLIER) cc_final: 0.8323 (t) REVERT: A 159 LYS cc_start: 0.8180 (ttmm) cc_final: 0.7624 (mtmt) REVERT: A 211 ILE cc_start: 0.7394 (OUTLIER) cc_final: 0.6949 (pp) REVERT: A 586 GLU cc_start: 0.7938 (mm-30) cc_final: 0.7533 (tt0) REVERT: A 611 GLU cc_start: 0.7819 (mt-10) cc_final: 0.7294 (mt-10) REVERT: A 697 LYS cc_start: 0.7700 (mmtp) cc_final: 0.7359 (mptt) outliers start: 8 outliers final: 3 residues processed: 52 average time/residue: 0.6581 time to fit residues: 35.5930 Evaluate side-chains 51 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 46 time to evaluate : 0.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 5.9990 chunk 12 optimal weight: 0.9980 chunk 54 optimal weight: 4.9990 chunk 7 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 47 optimal weight: 5.9990 chunk 38 optimal weight: 6.9990 chunk 45 optimal weight: 8.9990 chunk 10 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 = 0.4107 r_free = 0.4107 target = 0.190571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.137795 restraints weight = 6148.158| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 0.87 r_work: 0.3360 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 moved from start: 0.1220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 7775 Z= 0.194 Angle : 0.568 10.190 11364 Z= 0.341 Chirality : 0.044 0.487 1382 Planarity : 0.005 0.047 747 Dihedral : 22.420 170.571 3166 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.84 % Allowed : 14.49 % 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: 1.16 (0.44), residues: 381 helix: 2.03 (0.42), residues: 149 sheet: -0.48 (0.77), residues: 44 loop : 0.13 (0.48), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 163 TYR 0.016 0.001 TYR A 70 PHE 0.010 0.002 PHE A 648 HIS 0.005 0.001 HIS A 653 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.19 ( 7775) covalent geometry : angle 0.56757 / 0.34 (11364) hydrogen bonds : bond 0.05109 / 3.28 ( 336) hydrogen bonds : angle 3.13742 / 2.17 ( 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 57 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.141 Fit side-chains REVERT: A 159 LYS cc_start: 0.8207 (ttmm) cc_final: 0.7676 (mtmt) REVERT: A 211 ILE cc_start: 0.7458 (OUTLIER) cc_final: 0.7018 (pp) REVERT: A 581 ASP cc_start: 0.8261 (OUTLIER) cc_final: 0.8046 (t0) REVERT: A 586 GLU cc_start: 0.7979 (mm-30) cc_final: 0.7640 (tt0) REVERT: A 607 LEU cc_start: 0.7371 (OUTLIER) cc_final: 0.7152 (mt) REVERT: A 611 GLU cc_start: 0.7857 (mt-10) cc_final: 0.7437 (mt-10) REVERT: A 687 GLN cc_start: 0.6718 (OUTLIER) cc_final: 0.6458 (pt0) REVERT: A 697 LYS cc_start: 0.7835 (mmtp) cc_final: 0.7458 (mptt) REVERT: A 714 LYS cc_start: 0.8010 (OUTLIER) cc_final: 0.7667 (tptt) outliers start: 10 outliers final: 4 residues processed: 53 average time/residue: 0.6353 time to fit residues: 35.0503 Evaluate side-chains 54 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 45 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 601 THR Chi-restraints excluded: chain A residue 607 LEU 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: 5.9990 chunk 22 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 9 optimal weight: 0.2980 chunk 45 optimal weight: 8.9990 chunk 14 optimal weight: 0.4980 chunk 15 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 38 optimal weight: 5.9990 chunk 18 optimal weight: 0.6980 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 = 0.4125 r_free = 0.4125 target = 0.192558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 101)---------------| | r_work = 0.3549 r_free = 0.3549 target = 0.139950 restraints weight = 6139.767| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 0.93 r_work: 0.3373 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3263 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.1270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 7775 Z= 0.137 Angle : 0.516 9.602 11364 Z= 0.320 Chirality : 0.040 0.450 1382 Planarity : 0.004 0.035 747 Dihedral : 22.415 169.835 3166 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.41 % Allowed : 13.64 % Favored : 82.95 % 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: 1.31 (0.44), residues: 381 helix: 2.21 (0.41), residues: 149 sheet: -0.47 (0.77), residues: 44 loop : 0.19 (0.48), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 152 TYR 0.011 0.001 TYR A 70 PHE 0.012 0.001 PHE A 599 HIS 0.003 0.001 HIS A 680 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.14 ( 7775) covalent geometry : angle 0.51598 / 0.32 (11364) hydrogen bonds : bond 0.04801 / 3.10 ( 336) hydrogen bonds : angle 3.09939 / 2.14 ( 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 58 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 46 time to evaluate : 0.141 Fit side-chains REVERT: A 88 SER cc_start: 0.8663 (OUTLIER) cc_final: 0.8294 (t) REVERT: A 142 LYS cc_start: 0.8657 (OUTLIER) cc_final: 0.8202 (mtpt) REVERT: A 159 LYS cc_start: 0.8185 (ttmm) cc_final: 0.7613 (mtmt) REVERT: A 211 ILE cc_start: 0.7410 (OUTLIER) cc_final: 0.6939 (pp) REVERT: A 586 GLU cc_start: 0.8000 (mm-30) cc_final: 0.7618 (tt0) REVERT: A 611 GLU cc_start: 0.7845 (mt-10) cc_final: 0.7362 (mt-10) REVERT: A 687 GLN cc_start: 0.6785 (OUTLIER) cc_final: 0.6518 (pt0) REVERT: A 697 LYS cc_start: 0.7843 (mmtp) cc_final: 0.7540 (mptt) REVERT: A 714 LYS cc_start: 0.7989 (OUTLIER) cc_final: 0.7668 (tptt) outliers start: 12 outliers final: 5 residues processed: 54 average time/residue: 0.6778 time to fit residues: 38.0787 Evaluate side-chains 55 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 45 time to evaluate : 0.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 581 ASP Chi-restraints excluded: chain A residue 601 THR Chi-restraints excluded: chain A residue 607 LEU 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: 0.9980 chunk 5 optimal weight: 0.9990 chunk 22 optimal weight: 0.4980 chunk 11 optimal weight: 0.0000 chunk 35 optimal weight: 0.6980 chunk 7 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 chunk 44 optimal weight: 5.9990 chunk 32 optimal weight: 0.4980 chunk 46 optimal weight: 5.9990 overall best weight: 0.4984 ------------------------------------------------------------------------------- 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 = 0.4133 r_free = 0.4133 target = 0.193433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.140755 restraints weight = 6200.552| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 0.92 r_work: 0.3388 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.1315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7775 Z= 0.134 Angle : 0.509 9.462 11364 Z= 0.315 Chirality : 0.040 0.440 1382 Planarity : 0.004 0.034 747 Dihedral : 22.394 169.549 3166 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.12 % Allowed : 13.92 % Favored : 82.95 % 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: 1.33 (0.44), residues: 381 helix: 2.24 (0.41), residues: 149 sheet: -0.47 (0.77), residues: 44 loop : 0.19 (0.48), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 152 TYR 0.010 0.001 TYR A 70 PHE 0.011 0.001 PHE A 599 HIS 0.003 0.001 HIS A 653 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.13 ( 7775) covalent geometry : angle 0.50890 / 0.32 (11364) hydrogen bonds : bond 0.04701 / 3.04 ( 336) hydrogen bonds : angle 3.05507 / 2.12 ( 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 56 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 45 time to evaluate : 0.130 Fit side-chains REVERT: A 88 SER cc_start: 0.8658 (OUTLIER) cc_final: 0.8293 (t) REVERT: A 142 LYS cc_start: 0.8657 (OUTLIER) cc_final: 0.8185 (mtpt) REVERT: A 159 LYS cc_start: 0.8196 (ttmm) cc_final: 0.7635 (mtmt) REVERT: A 211 ILE cc_start: 0.7472 (OUTLIER) cc_final: 0.7008 (pp) REVERT: A 586 GLU cc_start: 0.7987 (mm-30) cc_final: 0.7647 (tt0) REVERT: A 607 LEU cc_start: 0.7379 (OUTLIER) cc_final: 0.7128 (mt) REVERT: A 611 GLU cc_start: 0.7840 (mt-10) cc_final: 0.7388 (mt-10) REVERT: A 687 GLN cc_start: 0.6738 (OUTLIER) cc_final: 0.6477 (pt0) REVERT: A 697 LYS cc_start: 0.7830 (mmtp) cc_final: 0.7543 (mptt) REVERT: A 714 LYS cc_start: 0.7980 (OUTLIER) cc_final: 0.7667 (tptt) outliers start: 11 outliers final: 4 residues processed: 52 average time/residue: 0.6258 time to fit residues: 33.9023 Evaluate side-chains 55 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 45 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 581 ASP Chi-restraints excluded: chain A residue 601 THR Chi-restraints excluded: chain A residue 607 LEU 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: 6.9990 chunk 25 optimal weight: 0.0970 chunk 17 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 50 optimal weight: 9.9990 chunk 48 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 4 optimal weight: 0.5980 chunk 30 optimal weight: 0.8980 overall best weight: 0.6578 ------------------------------------------------------------------------------- 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 = 0.4134 r_free = 0.4134 target = 0.193420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 97)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.140849 restraints weight = 6222.446| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 0.94 r_work: 0.3394 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 moved from start: 0.1399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 7775 Z= 0.140 Angle : 0.506 9.224 11364 Z= 0.312 Chirality : 0.040 0.425 1382 Planarity : 0.004 0.034 747 Dihedral : 22.358 169.608 3166 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.84 % Allowed : 14.49 % 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: 1.36 (0.44), residues: 381 helix: 2.30 (0.41), residues: 149 sheet: -0.51 (0.79), residues: 42 loop : 0.18 (0.47), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 163 TYR 0.011 0.001 TYR A 70 PHE 0.010 0.001 PHE A 599 HIS 0.003 0.001 HIS A 653 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.14 ( 7775) covalent geometry : angle 0.50646 / 0.31 (11364) hydrogen bonds : bond 0.04600 / 2.98 ( 336) hydrogen bonds : angle 3.01074 / 2.07 ( 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 56 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 46 time to evaluate : 0.139 Fit side-chains REVERT: A 88 SER cc_start: 0.8648 (OUTLIER) cc_final: 0.8301 (t) REVERT: A 142 LYS cc_start: 0.8649 (OUTLIER) cc_final: 0.8160 (mtpt) REVERT: A 159 LYS cc_start: 0.8202 (ttmm) cc_final: 0.7642 (mtmt) REVERT: A 211 ILE cc_start: 0.7472 (OUTLIER) cc_final: 0.7004 (pp) REVERT: A 586 GLU cc_start: 0.8005 (mm-30) cc_final: 0.7658 (tt0) REVERT: A 611 GLU cc_start: 0.7831 (mt-10) cc_final: 0.7378 (mt-10) REVERT: A 687 GLN cc_start: 0.6764 (OUTLIER) cc_final: 0.6505 (pt0) REVERT: A 697 LYS cc_start: 0.7827 (mmtp) cc_final: 0.7549 (mptt) REVERT: A 714 LYS cc_start: 0.8004 (OUTLIER) cc_final: 0.7664 (tptt) outliers start: 10 outliers final: 2 residues processed: 52 average time/residue: 0.6988 time to fit residues: 37.7186 Evaluate side-chains 51 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 44 time to evaluate : 0.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 9.9990 chunk 45 optimal weight: 10.0000 chunk 47 optimal weight: 5.9990 chunk 13 optimal weight: 0.3980 chunk 15 optimal weight: 0.3980 chunk 50 optimal weight: 10.0000 chunk 20 optimal weight: 1.9990 chunk 52 optimal weight: 10.0000 chunk 43 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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 = 0.4089 r_free = 0.4089 target = 0.188692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.135641 restraints weight = 6104.503| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 0.93 r_work: 0.3332 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8828 moved from start: 0.1402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 7775 Z= 0.258 Angle : 0.630 10.649 11364 Z= 0.368 Chirality : 0.049 0.528 1382 Planarity : 0.006 0.052 747 Dihedral : 22.520 170.521 3166 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.56 % Allowed : 14.49 % Favored : 82.95 % 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: 0.96 (0.43), residues: 381 helix: 1.84 (0.41), residues: 149 sheet: -0.51 (0.77), residues: 42 loop : 0.01 (0.46), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 260 TYR 0.020 0.002 TYR A 70 PHE 0.012 0.002 PHE A 235 HIS 0.007 0.002 HIS A 653 Details of bonding type rmsd/Z covalent geometry : bond 0.00506 / 0.26 ( 7775) covalent geometry : angle 0.63044 / 0.37 (11364) hydrogen bonds : bond 0.05649 / 3.61 ( 336) hydrogen bonds : angle 3.29724 / 2.24 ( 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: 9 poor density : 47 time to evaluate : 0.183 Fit side-chains REVERT: A 159 LYS cc_start: 0.8209 (ttmm) cc_final: 0.7667 (mtmt) REVERT: A 211 ILE cc_start: 0.7505 (OUTLIER) cc_final: 0.7039 (pp) REVERT: A 586 GLU cc_start: 0.8044 (mm-30) cc_final: 0.7696 (tt0) REVERT: A 611 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7327 (mt-10) REVERT: A 687 GLN cc_start: 0.6733 (OUTLIER) cc_final: 0.6525 (pt0) REVERT: A 697 LYS cc_start: 0.7960 (mmtp) cc_final: 0.7619 (mptt) REVERT: A 714 LYS cc_start: 0.8037 (OUTLIER) cc_final: 0.7652 (tptt) outliers start: 9 outliers final: 5 residues processed: 54 average time/residue: 0.8559 time to fit residues: 48.0270 Evaluate side-chains 52 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 0.9980 chunk 40 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 2 optimal weight: 0.5980 chunk 3 optimal weight: 0.7980 chunk 38 optimal weight: 5.9990 chunk 32 optimal weight: 0.0060 chunk 34 optimal weight: 2.9990 chunk 41 optimal weight: 9.9990 overall best weight: 0.6796 ------------------------------------------------------------------------------- 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 = 0.4125 r_free = 0.4125 target = 0.192728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.140983 restraints weight = 6144.573| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 0.99 r_work: 0.3369 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3265 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7775 Z= 0.144 Angle : 0.521 9.629 11364 Z= 0.321 Chirality : 0.041 0.454 1382 Planarity : 0.004 0.038 747 Dihedral : 22.433 169.542 3166 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.27 % Allowed : 13.92 % Favored : 83.81 % 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: 1.15 (0.44), residues: 381 helix: 2.03 (0.42), residues: 149 sheet: -0.53 (0.78), residues: 42 loop : 0.13 (0.47), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 163 TYR 0.011 0.001 TYR A 70 PHE 0.013 0.001 PHE A 235 HIS 0.003 0.001 HIS A 653 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.14 ( 7775) covalent geometry : angle 0.52072 / 0.32 (11364) hydrogen bonds : bond 0.04770 / 3.07 ( 336) hydrogen bonds : angle 3.15962 / 2.13 ( 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: 8 poor density : 46 time to evaluate : 0.188 Fit side-chains REVERT: A 142 LYS cc_start: 0.8684 (OUTLIER) cc_final: 0.8222 (mtpt) REVERT: A 159 LYS cc_start: 0.8229 (ttmm) cc_final: 0.7684 (mtmt) REVERT: A 211 ILE cc_start: 0.7501 (OUTLIER) cc_final: 0.7050 (pp) REVERT: A 586 GLU cc_start: 0.8029 (mm-30) cc_final: 0.7659 (tt0) REVERT: A 611 GLU cc_start: 0.7840 (mt-10) cc_final: 0.7401 (mt-10) REVERT: A 697 LYS cc_start: 0.7910 (mmtp) cc_final: 0.7541 (mptt) REVERT: A 714 LYS cc_start: 0.8001 (OUTLIER) cc_final: 0.7632 (tptt) outliers start: 8 outliers final: 4 residues processed: 52 average time/residue: 0.8312 time to fit residues: 44.9341 Evaluate side-chains 50 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 626 MET 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: 0.8980 chunk 9 optimal weight: 0.0970 chunk 1 optimal weight: 0.4980 chunk 31 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 chunk 34 optimal weight: 3.9990 chunk 11 optimal weight: 0.0070 chunk 18 optimal weight: 0.6980 chunk 4 optimal weight: 0.9980 overall best weight: 0.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 687 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.193863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.141953 restraints weight = 6135.806| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 1.05 r_work: 0.3387 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3279 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.1517 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= 0.124 Angle : 0.507 9.358 11364 Z= 0.315 Chirality : 0.039 0.432 1382 Planarity : 0.004 0.035 747 Dihedral : 22.415 169.184 3166 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.99 % Allowed : 14.49 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.44), residues: 381 helix: 2.17 (0.43), residues: 149 sheet: -0.49 (0.79), residues: 42 loop : 0.17 (0.47), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 163 TYR 0.009 0.001 TYR A 70 PHE 0.013 0.001 PHE A 235 HIS 0.003 0.001 HIS A 680 Details of bonding type rmsd/Z covalent geometry : bond 0.00200 / 0.12 ( 7775) covalent geometry : angle 0.50718 / 0.32 (11364) hydrogen bonds : bond 0.04656 / 3.00 ( 336) hydrogen bonds : angle 3.13006 / 2.12 ( 741) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2510.80 seconds wall clock time: 43 minutes 26.54 seconds (2606.54 seconds total)