Starting phenix.real_space_refine on Wed Mar 12 02:22:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9auf_43878/03_2025/9auf_43878.cif Found real_map, /net/cci-nas-00/data/ceres_data/9auf_43878/03_2025/9auf_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9auf_43878/03_2025/9auf_43878.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9auf_43878/03_2025/9auf_43878.map" model { file = "/net/cci-nas-00/data/ceres_data/9auf_43878/03_2025/9auf_43878.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9auf_43878/03_2025/9auf_43878.cif" } resolution = 2.73 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.112 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 5.59, per 1000 atoms: 0.77 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: 1.98 Conformation dependent library (CDL) restraints added in 371.6 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: 3.37 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: 3.30 Time building geometry restraints manager: 2.36 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=" N ALA A 724 " pdb=" CA ALA A 724 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.22e-02 6.72e+03 7.06e+00 bond pdb=" C3' DG C 8 " pdb=" O3' DG C 8 " ideal model delta sigma weight residual 1.422 1.488 -0.066 3.00e-02 1.11e+03 4.79e+00 bond pdb=" C GLU A 723 " pdb=" N ALA A 724 " ideal model delta sigma weight residual 1.330 1.353 -0.023 1.32e-02 5.74e+03 2.91e+00 bond pdb=" O3' G B 142 " pdb=" P G B 143 " ideal model delta sigma weight residual 1.607 1.631 -0.024 1.50e-02 4.44e+03 2.51e+00 bond pdb=" C3' G B 142 " pdb=" O3' G B 142 " ideal model delta sigma weight residual 1.427 1.450 -0.023 1.50e-02 4.44e+03 2.32e+00 ... (remaining 7770 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.45: 11205 2.45 - 4.90: 146 4.90 - 7.35: 8 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=" C3' U B 92 " pdb=" O3' U B 92 " pdb=" P U B 93 " ideal model delta sigma weight residual 120.20 127.18 -6.98 1.50e+00 4.44e-01 2.17e+01 angle pdb=" C3' G B 142 " pdb=" O3' G B 142 " pdb=" P G B 143 " ideal model delta sigma weight residual 120.20 126.60 -6.40 1.50e+00 4.44e-01 1.82e+01 angle pdb=" O3' G B 122 " pdb=" C3' G B 122 " pdb=" C2' G B 122 " ideal model delta sigma weight residual 113.70 120.06 -6.36 1.50e+00 4.44e-01 1.80e+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 2.35 -2.68 -0.33 2.00e-01 2.50e+01 2.71e+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: 2.590 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: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 24.020 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 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:15.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 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 0.066 7775 Z= 0.270 Angle : 0.731 12.254 11364 Z= 0.403 Chirality : 0.052 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (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 HIS 0.006 0.002 HIS A 680 PHE 0.024 0.003 PHE A 596 TYR 0.020 0.003 TYR A 250 ARG 0.012 0.001 ARG A 163 *********************** 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 : 0.517 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: 1.8177 time to fit residues: 102.0284 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 : 0.487 ------------------------------------------------------------------------------- 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 46 optimal weight: 1.9990 chunk 41 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 28 optimal weight: 0.0970 chunk 22 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 49 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.190960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 98)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.138094 restraints weight = 6081.843| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 0.96 r_work: 0.3360 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.0864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7775 Z= 0.245 Angle : 0.590 11.012 11364 Z= 0.328 Chirality : 0.042 0.820 1382 Planarity : 0.005 0.041 747 Dihedral : 22.364 168.363 3169 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.98 % Allowed : 11.93 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.43), residues: 381 helix: 1.25 (0.41), residues: 148 sheet: -0.26 (0.76), residues: 44 loop : -0.07 (0.47), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 680 PHE 0.013 0.002 PHE A 596 TYR 0.013 0.001 TYR A 169 ARG 0.005 0.001 ARG A 163 *********************** 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 66 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 52 time to evaluate : 0.531 Fit side-chains revert: symmetry clash REVERT: A 50 GLN cc_start: 0.8634 (OUTLIER) cc_final: 0.8374 (tp40) REVERT: A 159 LYS cc_start: 0.8212 (ttmm) cc_final: 0.7675 (mtmt) REVERT: A 586 GLU cc_start: 0.7839 (mm-30) cc_final: 0.7583 (tt0) REVERT: A 625 VAL cc_start: 0.8313 (OUTLIER) cc_final: 0.8056 (m) REVERT: A 697 LYS cc_start: 0.7739 (mmtp) cc_final: 0.7354 (mptt) REVERT: A 712 ARG cc_start: 0.7101 (OUTLIER) cc_final: 0.6869 (ttm-80) outliers start: 14 outliers final: 4 residues processed: 60 average time/residue: 1.7238 time to fit residues: 107.5870 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 : 0.558 ------------------------------------------------------------------------------- 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 100 MET 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 8 optimal weight: 0.0870 chunk 42 optimal weight: 6.9990 chunk 48 optimal weight: 1.9990 chunk 29 optimal weight: 0.2980 chunk 30 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 overall best weight: 1.0764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.189981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 91)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.137025 restraints weight = 6145.223| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 0.95 r_work: 0.3345 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.1091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 7775 Z= 0.269 Angle : 0.591 11.248 11364 Z= 0.328 Chirality : 0.043 0.861 1382 Planarity : 0.005 0.041 747 Dihedral : 22.374 167.432 3169 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.69 % Allowed : 12.78 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.43), residues: 381 helix: 1.61 (0.41), residues: 149 sheet: -0.43 (0.76), residues: 44 loop : 0.02 (0.47), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 653 PHE 0.012 0.002 PHE A 648 TYR 0.013 0.001 TYR A 169 ARG 0.004 0.001 ARG A 163 *********************** 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: 13 poor density : 48 time to evaluate : 0.502 Fit side-chains revert: symmetry clash REVERT: A 48 ARG cc_start: 0.8750 (OUTLIER) cc_final: 0.8449 (ttp-170) REVERT: A 159 LYS cc_start: 0.8189 (ttmm) cc_final: 0.7646 (mtmt) REVERT: A 211 ILE cc_start: 0.7485 (OUTLIER) cc_final: 0.7008 (pp) REVERT: A 586 GLU cc_start: 0.7996 (mm-30) cc_final: 0.7602 (tt0) REVERT: A 625 VAL cc_start: 0.8323 (OUTLIER) cc_final: 0.8028 (m) REVERT: A 697 LYS cc_start: 0.7826 (mmtp) cc_final: 0.7473 (mptt) REVERT: A 712 ARG cc_start: 0.7203 (OUTLIER) cc_final: 0.6960 (ttm-80) REVERT: A 714 LYS cc_start: 0.8071 (OUTLIER) cc_final: 0.7685 (tptt) REVERT: A 716 LEU cc_start: 0.8049 (OUTLIER) cc_final: 0.7826 (pp) outliers start: 13 outliers final: 5 residues processed: 54 average time/residue: 1.7798 time to fit residues: 99.9418 Evaluate side-chains 57 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 46 time to evaluate : 0.504 ------------------------------------------------------------------------------- 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 100 MET Chi-restraints excluded: chain A residue 211 ILE 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 716 LEU 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 7 optimal weight: 0.5980 chunk 50 optimal weight: 6.9990 chunk 19 optimal weight: 0.0370 chunk 18 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 49 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.193862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.141760 restraints weight = 6176.589| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 0.87 r_work: 0.3404 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3297 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.1301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7775 Z= 0.166 Angle : 0.523 10.277 11364 Z= 0.294 Chirality : 0.038 0.720 1382 Planarity : 0.004 0.031 747 Dihedral : 22.228 165.447 3166 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.41 % Allowed : 13.92 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.43), residues: 381 helix: 2.10 (0.41), residues: 149 sheet: -0.42 (0.77), residues: 44 loop : 0.17 (0.47), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 653 PHE 0.010 0.001 PHE A 648 TYR 0.010 0.001 TYR A 169 ARG 0.004 0.000 ARG A 163 *********************** 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 61 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 49 time to evaluate : 0.503 Fit side-chains REVERT: A 88 SER cc_start: 0.8676 (OUTLIER) cc_final: 0.8318 (t) REVERT: A 159 LYS cc_start: 0.8199 (ttmm) cc_final: 0.7642 (mtmt) REVERT: A 211 ILE cc_start: 0.7481 (OUTLIER) cc_final: 0.7010 (pp) REVERT: A 580 GLU cc_start: 0.7523 (OUTLIER) cc_final: 0.7265 (pm20) REVERT: A 586 GLU cc_start: 0.8010 (mm-30) cc_final: 0.7584 (tt0) REVERT: A 611 GLU cc_start: 0.7856 (mt-10) cc_final: 0.7370 (mt-10) REVERT: A 625 VAL cc_start: 0.8321 (OUTLIER) cc_final: 0.7979 (m) REVERT: A 697 LYS cc_start: 0.7735 (mmtp) cc_final: 0.7451 (mptt) outliers start: 12 outliers final: 4 residues processed: 54 average time/residue: 1.6888 time to fit residues: 95.0508 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 : 0.505 ------------------------------------------------------------------------------- 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 580 GLU 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 741 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 30 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 16 optimal weight: 0.6980 chunk 45 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.191883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.139275 restraints weight = 6074.594| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 0.87 r_work: 0.3380 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3270 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.1352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7775 Z= 0.212 Angle : 0.542 10.492 11364 Z= 0.302 Chirality : 0.039 0.751 1382 Planarity : 0.004 0.031 747 Dihedral : 22.235 166.565 3166 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 4.26 % Allowed : 13.35 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.44), residues: 381 helix: 2.18 (0.42), residues: 149 sheet: -0.34 (0.80), residues: 42 loop : 0.16 (0.47), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 653 PHE 0.011 0.001 PHE A 648 TYR 0.012 0.001 TYR A 70 ARG 0.004 0.000 ARG A 163 *********************** 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 : 0.491 Fit side-chains REVERT: A 48 ARG cc_start: 0.8748 (OUTLIER) cc_final: 0.8401 (ttp-170) REVERT: A 88 SER cc_start: 0.8673 (OUTLIER) cc_final: 0.8292 (t) REVERT: A 159 LYS cc_start: 0.8203 (ttmm) cc_final: 0.7650 (mtmt) REVERT: A 211 ILE cc_start: 0.7490 (OUTLIER) cc_final: 0.7060 (pp) REVERT: A 581 ASP cc_start: 0.8294 (OUTLIER) cc_final: 0.8084 (t0) REVERT: A 586 GLU cc_start: 0.7961 (mm-30) cc_final: 0.7583 (tt0) REVERT: A 607 LEU cc_start: 0.7343 (OUTLIER) cc_final: 0.7108 (mt) REVERT: A 611 GLU cc_start: 0.7835 (mt-10) cc_final: 0.7330 (mt-10) REVERT: A 625 VAL cc_start: 0.8300 (OUTLIER) cc_final: 0.7960 (m) REVERT: A 697 LYS cc_start: 0.7835 (mmtp) cc_final: 0.7566 (mptt) REVERT: A 712 ARG cc_start: 0.7310 (ttm-80) cc_final: 0.7014 (ttt180) REVERT: A 714 LYS cc_start: 0.8050 (OUTLIER) cc_final: 0.7632 (tptt) REVERT: A 716 LEU cc_start: 0.7916 (OUTLIER) cc_final: 0.7698 (pp) REVERT: A 742 LYS cc_start: 0.7941 (tttp) cc_final: 0.7492 (tptt) outliers start: 15 outliers final: 3 residues processed: 57 average time/residue: 1.8015 time to fit residues: 106.8552 Evaluate side-chains 55 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 44 time to evaluate : 0.544 ------------------------------------------------------------------------------- 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 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 714 LYS Chi-restraints excluded: chain A residue 716 LEU 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 20 optimal weight: 0.0470 chunk 44 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 33 optimal weight: 7.9990 chunk 3 optimal weight: 1.9990 overall best weight: 0.8082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN A 168 GLN A 687 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.191785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.139292 restraints weight = 6113.562| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 0.95 r_work: 0.3362 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3256 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.1442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7775 Z= 0.215 Angle : 0.541 10.488 11364 Z= 0.302 Chirality : 0.039 0.750 1382 Planarity : 0.004 0.034 747 Dihedral : 22.211 166.590 3166 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.01 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.43), residues: 381 helix: 2.23 (0.42), residues: 149 sheet: -0.44 (0.79), residues: 42 loop : 0.19 (0.47), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 653 PHE 0.010 0.001 PHE A 648 TYR 0.012 0.001 TYR A 70 ARG 0.005 0.000 ARG A 163 *********************** 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 62 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 48 time to evaluate : 0.502 Fit side-chains REVERT: A 48 ARG cc_start: 0.8753 (OUTLIER) cc_final: 0.8407 (ttp-170) REVERT: A 142 LYS cc_start: 0.8661 (OUTLIER) cc_final: 0.8192 (mtpt) REVERT: A 159 LYS cc_start: 0.8217 (ttmm) cc_final: 0.7662 (mtmt) REVERT: A 211 ILE cc_start: 0.7526 (OUTLIER) cc_final: 0.7095 (pp) REVERT: A 586 GLU cc_start: 0.8002 (mm-30) cc_final: 0.7637 (tt0) REVERT: A 607 LEU cc_start: 0.7413 (OUTLIER) cc_final: 0.7168 (mt) REVERT: A 611 GLU cc_start: 0.7844 (mt-10) cc_final: 0.7378 (mt-10) REVERT: A 625 VAL cc_start: 0.8321 (OUTLIER) cc_final: 0.7970 (m) REVERT: A 697 LYS cc_start: 0.7839 (mmtp) cc_final: 0.7590 (mptt) REVERT: A 712 ARG cc_start: 0.7270 (ttm-80) cc_final: 0.6954 (ttt180) REVERT: A 714 LYS cc_start: 0.8065 (OUTLIER) cc_final: 0.7644 (tptt) REVERT: A 716 LEU cc_start: 0.7909 (OUTLIER) cc_final: 0.7657 (pp) REVERT: A 742 LYS cc_start: 0.7942 (tttp) cc_final: 0.7512 (tptt) outliers start: 14 outliers final: 5 residues processed: 57 average time/residue: 1.8517 time to fit residues: 109.4900 Evaluate side-chains 59 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 47 time to evaluate : 0.488 ------------------------------------------------------------------------------- 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 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 714 LYS Chi-restraints excluded: chain A residue 716 LEU 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 54 optimal weight: 1.9990 chunk 35 optimal weight: 0.0870 chunk 8 optimal weight: 0.7980 chunk 25 optimal weight: 0.0040 chunk 22 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 overall best weight: 0.5172 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN A 168 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.192856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.140508 restraints weight = 6125.421| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 0.98 r_work: 0.3378 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3271 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.1490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7775 Z= 0.169 Angle : 0.525 10.277 11364 Z= 0.295 Chirality : 0.038 0.725 1382 Planarity : 0.004 0.031 747 Dihedral : 22.212 166.336 3166 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.69 % Allowed : 13.07 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.44), residues: 381 helix: 2.30 (0.42), residues: 149 sheet: -0.47 (0.78), residues: 42 loop : 0.23 (0.47), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 653 PHE 0.017 0.001 PHE A 235 TYR 0.010 0.001 TYR A 70 ARG 0.004 0.000 ARG A 163 *********************** 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 61 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 48 time to evaluate : 0.488 Fit side-chains REVERT: A 48 ARG cc_start: 0.8741 (OUTLIER) cc_final: 0.8394 (ttp-170) REVERT: A 88 SER cc_start: 0.8664 (OUTLIER) cc_final: 0.8292 (t) REVERT: A 142 LYS cc_start: 0.8648 (OUTLIER) cc_final: 0.8166 (mtpt) REVERT: A 159 LYS cc_start: 0.8196 (ttmm) cc_final: 0.7634 (mtmt) REVERT: A 211 ILE cc_start: 0.7470 (OUTLIER) cc_final: 0.7008 (pp) REVERT: A 581 ASP cc_start: 0.8282 (OUTLIER) cc_final: 0.8046 (t0) REVERT: A 586 GLU cc_start: 0.7986 (mm-30) cc_final: 0.7392 (tt0) REVERT: A 590 GLU cc_start: 0.7195 (mm-30) cc_final: 0.6930 (mp0) REVERT: A 607 LEU cc_start: 0.7356 (OUTLIER) cc_final: 0.7109 (mt) REVERT: A 611 GLU cc_start: 0.7810 (mt-10) cc_final: 0.7314 (mt-10) REVERT: A 625 VAL cc_start: 0.8254 (OUTLIER) cc_final: 0.7953 (m) REVERT: A 697 LYS cc_start: 0.7816 (mmtp) cc_final: 0.7567 (mptt) REVERT: A 712 ARG cc_start: 0.7241 (ttm-80) cc_final: 0.7006 (ttt180) REVERT: A 714 LYS cc_start: 0.8036 (OUTLIER) cc_final: 0.7613 (tptt) REVERT: A 716 LEU cc_start: 0.7859 (OUTLIER) cc_final: 0.7630 (pp) REVERT: A 742 LYS cc_start: 0.7909 (tttp) cc_final: 0.7481 (tptt) outliers start: 13 outliers final: 4 residues processed: 55 average time/residue: 1.7124 time to fit residues: 98.0850 Evaluate side-chains 59 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 46 time to evaluate : 0.490 ------------------------------------------------------------------------------- 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 100 MET 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 625 VAL Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 714 LYS Chi-restraints excluded: chain A residue 716 LEU 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 54 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 49 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 4 optimal weight: 0.5980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.185217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.131238 restraints weight = 6157.172| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 1.11 r_work: 0.3264 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.1513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 7775 Z= 0.303 Angle : 0.595 11.262 11364 Z= 0.328 Chirality : 0.044 0.865 1382 Planarity : 0.005 0.039 747 Dihedral : 22.325 167.213 3166 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.43), residues: 381 helix: 2.06 (0.42), residues: 149 sheet: -0.49 (0.79), residues: 42 loop : 0.11 (0.46), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 653 PHE 0.011 0.001 PHE A 235 TYR 0.017 0.002 TYR A 70 ARG 0.004 0.001 ARG A 163 *********************** 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 61 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 48 time to evaluate : 0.525 Fit side-chains REVERT: A 48 ARG cc_start: 0.8748 (OUTLIER) cc_final: 0.8444 (ttp-170) REVERT: A 142 LYS cc_start: 0.8651 (OUTLIER) cc_final: 0.8192 (mtpt) REVERT: A 159 LYS cc_start: 0.8175 (ttmm) cc_final: 0.7619 (mtmt) REVERT: A 211 ILE cc_start: 0.7487 (OUTLIER) cc_final: 0.7032 (pp) REVERT: A 581 ASP cc_start: 0.8348 (OUTLIER) cc_final: 0.8125 (t0) REVERT: A 586 GLU cc_start: 0.8035 (mm-30) cc_final: 0.7641 (tt0) REVERT: A 611 GLU cc_start: 0.7841 (mt-10) cc_final: 0.7322 (mt-10) REVERT: A 625 VAL cc_start: 0.8281 (OUTLIER) cc_final: 0.7916 (m) REVERT: A 697 LYS cc_start: 0.7923 (mmtp) cc_final: 0.7559 (mptt) REVERT: A 712 ARG cc_start: 0.7301 (ttm-80) cc_final: 0.7094 (ttt180) REVERT: A 714 LYS cc_start: 0.8040 (OUTLIER) cc_final: 0.7594 (tptt) REVERT: A 716 LEU cc_start: 0.8029 (OUTLIER) cc_final: 0.7735 (pp) REVERT: A 742 LYS cc_start: 0.7923 (tttp) cc_final: 0.7488 (tptt) outliers start: 13 outliers final: 5 residues processed: 56 average time/residue: 1.6553 time to fit residues: 96.6318 Evaluate side-chains 56 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 44 time to evaluate : 0.501 ------------------------------------------------------------------------------- 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 100 MET 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 625 VAL Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 714 LYS Chi-restraints excluded: chain A residue 716 LEU 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 38 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 2 optimal weight: 0.5980 chunk 21 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 23 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.187220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.132748 restraints weight = 6188.724| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 1.04 r_work: 0.3292 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7775 Z= 0.198 Angle : 0.549 10.795 11364 Z= 0.309 Chirality : 0.040 0.799 1382 Planarity : 0.004 0.041 747 Dihedral : 22.307 167.147 3166 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.98 % Allowed : 13.64 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.44), residues: 381 helix: 2.22 (0.42), residues: 149 sheet: -0.44 (0.80), residues: 42 loop : 0.18 (0.46), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 653 PHE 0.010 0.001 PHE A 235 TYR 0.012 0.001 TYR A 70 ARG 0.006 0.000 ARG A 163 *********************** 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 59 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 45 time to evaluate : 0.499 Fit side-chains revert: symmetry clash REVERT: A 48 ARG cc_start: 0.8727 (OUTLIER) cc_final: 0.8396 (ttp-170) REVERT: A 142 LYS cc_start: 0.8633 (OUTLIER) cc_final: 0.8156 (mtpt) REVERT: A 159 LYS cc_start: 0.8158 (ttmm) cc_final: 0.7597 (mtmt) REVERT: A 211 ILE cc_start: 0.7464 (OUTLIER) cc_final: 0.7012 (pp) REVERT: A 581 ASP cc_start: 0.8333 (OUTLIER) cc_final: 0.8106 (t0) REVERT: A 586 GLU cc_start: 0.8026 (mm-30) cc_final: 0.7417 (tt0) REVERT: A 590 GLU cc_start: 0.7171 (mm-30) cc_final: 0.6896 (mp0) REVERT: A 621 LYS cc_start: 0.7584 (OUTLIER) cc_final: 0.6929 (mtmt) REVERT: A 625 VAL cc_start: 0.8279 (OUTLIER) cc_final: 0.7940 (m) REVERT: A 697 LYS cc_start: 0.7899 (mmtp) cc_final: 0.7488 (mptt) REVERT: A 714 LYS cc_start: 0.8027 (OUTLIER) cc_final: 0.7596 (tptt) REVERT: A 716 LEU cc_start: 0.7934 (OUTLIER) cc_final: 0.7656 (pp) REVERT: A 742 LYS cc_start: 0.7912 (tttp) cc_final: 0.7485 (tptt) outliers start: 14 outliers final: 5 residues processed: 54 average time/residue: 1.8010 time to fit residues: 101.2278 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 : 0.503 ------------------------------------------------------------------------------- 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 100 MET 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 621 LYS Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 714 LYS Chi-restraints excluded: chain A residue 716 LEU 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 54 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 33 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.185038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.130793 restraints weight = 6273.118| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 0.93 r_work: 0.3287 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7775 Z= 0.258 Angle : 0.569 11.086 11364 Z= 0.316 Chirality : 0.042 0.844 1382 Planarity : 0.005 0.042 747 Dihedral : 22.304 166.744 3166 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.41 % Allowed : 13.92 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.44), residues: 381 helix: 2.10 (0.42), residues: 149 sheet: -0.46 (0.81), residues: 42 loop : 0.13 (0.46), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 653 PHE 0.016 0.001 PHE A 235 TYR 0.014 0.002 TYR A 70 ARG 0.006 0.001 ARG A 163 ********************** 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 57 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 45 time to evaluate : 0.534 Fit side-chains REVERT: A 48 ARG cc_start: 0.8752 (OUTLIER) cc_final: 0.8420 (ttp-170) REVERT: A 142 LYS cc_start: 0.8640 (OUTLIER) cc_final: 0.8154 (mtpt) REVERT: A 159 LYS cc_start: 0.8213 (ttmm) cc_final: 0.7648 (mtmt) REVERT: A 211 ILE cc_start: 0.7528 (OUTLIER) cc_final: 0.7107 (pp) REVERT: A 581 ASP cc_start: 0.8314 (OUTLIER) cc_final: 0.8087 (t0) REVERT: A 586 GLU cc_start: 0.7992 (mm-30) cc_final: 0.7421 (tt0) REVERT: A 590 GLU cc_start: 0.7154 (mm-30) cc_final: 0.6880 (mp0) REVERT: A 611 GLU cc_start: 0.7800 (mt-10) cc_final: 0.7299 (mt-10) REVERT: A 625 VAL cc_start: 0.8227 (OUTLIER) cc_final: 0.7947 (m) REVERT: A 697 LYS cc_start: 0.7912 (mmtp) cc_final: 0.7535 (mptt) REVERT: A 714 LYS cc_start: 0.8041 (OUTLIER) cc_final: 0.7610 (tptt) REVERT: A 716 LEU cc_start: 0.7968 (OUTLIER) cc_final: 0.7699 (pp) REVERT: A 742 LYS cc_start: 0.7936 (tttp) cc_final: 0.7509 (tptt) outliers start: 12 outliers final: 5 residues processed: 52 average time/residue: 1.7265 time to fit residues: 93.5131 Evaluate side-chains 55 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 43 time to evaluate : 0.569 ------------------------------------------------------------------------------- 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 100 MET 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 625 VAL Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 714 LYS Chi-restraints excluded: chain A residue 716 LEU 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 36 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 52 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 1 optimal weight: 0.5980 chunk 44 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.186573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.132221 restraints weight = 6064.056| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 1.03 r_work: 0.3285 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7775 Z= 0.226 Angle : 0.559 10.947 11364 Z= 0.312 Chirality : 0.041 0.824 1382 Planarity : 0.004 0.041 747 Dihedral : 22.301 166.819 3166 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 6.08 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.44), residues: 381 helix: 2.10 (0.42), residues: 149 sheet: -0.46 (0.81), residues: 42 loop : 0.17 (0.46), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 653 PHE 0.017 0.001 PHE A 235 TYR 0.013 0.001 TYR A 70 ARG 0.006 0.000 ARG A 163 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5830.25 seconds wall clock time: 99 minutes 54.47 seconds (5994.47 seconds total)