Starting phenix.real_space_refine on Wed Feb 12 02:41:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9auf_43878/02_2025/9auf_43878.cif Found real_map, /net/cci-nas-00/data/ceres_data/9auf_43878/02_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_43878/02_2025/9auf_43878.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9auf_43878/02_2025/9auf_43878.map" model { file = "/net/cci-nas-00/data/ceres_data/9auf_43878/02_2025/9auf_43878.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9auf_43878/02_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-5592/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: 5.75, per 1000 atoms: 0.79 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: 2.11 Conformation dependent library (CDL) restraints added in 425.2 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: 3.51 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: 3.51 Time building geometry restraints manager: 2.39 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: 3.990 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: 0.030 Extract box with map and model: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 24.970 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 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:13.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.160 ------------------------------------------------------------------------------- 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 : 0.501 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: 1.9089 time to fit residues: 107.1002 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 : 0.517 ------------------------------------------------------------------------------- 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 = 0.190961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 106)---------------| | r_work = 0.3524 r_free = 0.3524 target = 0.138044 restraints weight = 6081.946| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 0.98 r_work: 0.3359 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 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 : 0.504 Fit side-chains revert: symmetry clash REVERT: A 50 GLN cc_start: 0.8631 (OUTLIER) cc_final: 0.8369 (tp40) REVERT: A 159 LYS cc_start: 0.8208 (ttmm) cc_final: 0.7665 (mtmt) REVERT: A 586 GLU cc_start: 0.7859 (mm-30) cc_final: 0.7580 (tt0) REVERT: A 625 VAL cc_start: 0.8312 (OUTLIER) cc_final: 0.8050 (m) REVERT: A 697 LYS cc_start: 0.7750 (mmtp) cc_final: 0.7365 (mptt) REVERT: A 712 ARG cc_start: 0.7116 (OUTLIER) cc_final: 0.6884 (ttm-80) outliers start: 14 outliers final: 4 residues processed: 60 average time/residue: 1.7577 time to fit residues: 109.5630 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 : 0.552 ------------------------------------------------------------------------------- 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: 1.9990 chunk 42 optimal weight: 6.9990 chunk 48 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 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: 1.3786 ------------------------------------------------------------------------------- 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 = 0.4085 r_free = 0.4085 target = 0.188656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 92)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.135188 restraints weight = 6138.453| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 0.99 r_work: 0.3321 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.1125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 7775 Z= 0.331 Angle : 0.629 11.805 11364 Z= 0.346 Chirality : 0.047 0.947 1382 Planarity : 0.005 0.048 747 Dihedral : 22.443 167.895 3169 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 4.26 % Allowed : 12.50 % 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: 0.71 (0.43), residues: 381 helix: 1.49 (0.41), residues: 149 sheet: -0.50 (0.77), residues: 39 loop : -0.03 (0.47), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 653 PHE 0.013 0.002 PHE A 648 TYR 0.015 0.002 TYR A 70 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 64 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 49 time to evaluate : 0.487 Fit side-chains REVERT: A 48 ARG cc_start: 0.8757 (OUTLIER) cc_final: 0.8463 (ttp-170) REVERT: A 50 GLN cc_start: 0.8622 (OUTLIER) cc_final: 0.8375 (tp-100) REVERT: A 159 LYS cc_start: 0.8182 (ttmm) cc_final: 0.7643 (mtmt) REVERT: A 168 GLN cc_start: 0.8988 (OUTLIER) cc_final: 0.7529 (tp-100) REVERT: A 211 ILE cc_start: 0.7529 (OUTLIER) cc_final: 0.7055 (pp) REVERT: A 586 GLU cc_start: 0.7985 (mm-30) cc_final: 0.7629 (tt0) REVERT: A 611 GLU cc_start: 0.7888 (mt-10) cc_final: 0.7407 (mt-10) REVERT: A 625 VAL cc_start: 0.8339 (OUTLIER) cc_final: 0.8049 (m) REVERT: A 697 LYS cc_start: 0.7858 (mmtp) cc_final: 0.7508 (mptt) REVERT: A 712 ARG cc_start: 0.7206 (OUTLIER) cc_final: 0.6960 (ttm-80) REVERT: A 714 LYS cc_start: 0.8119 (OUTLIER) cc_final: 0.7714 (tptt) REVERT: A 716 LEU cc_start: 0.8071 (OUTLIER) cc_final: 0.7780 (pp) outliers start: 15 outliers final: 6 residues processed: 56 average time/residue: 1.7873 time to fit residues: 104.1266 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 : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ARG 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 168 GLN Chi-restraints excluded: chain A residue 211 ILE 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 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: 0.7980 chunk 50 optimal weight: 6.9990 chunk 19 optimal weight: 0.6980 chunk 18 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.4104 r_free = 0.4104 target = 0.190650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.137832 restraints weight = 6146.150| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 0.93 r_work: 0.3351 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3239 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.1157 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= 0.217 Angle : 0.572 11.279 11364 Z= 0.321 Chirality : 0.042 0.868 1382 Planarity : 0.004 0.034 747 Dihedral : 22.416 167.209 3169 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 4.83 % Allowed : 12.22 % 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 (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: 0.96 (0.43), residues: 381 helix: 1.84 (0.41), residues: 149 sheet: -0.55 (0.76), residues: 44 loop : 0.04 (0.47), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 653 PHE 0.012 0.001 PHE A 648 TYR 0.011 0.001 TYR A 70 ARG 0.004 0.001 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 64 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 47 time to evaluate : 0.512 Fit side-chains revert: symmetry clash REVERT: A 48 ARG cc_start: 0.8742 (OUTLIER) cc_final: 0.8433 (ttp-170) REVERT: A 159 LYS cc_start: 0.8201 (ttmm) cc_final: 0.7648 (mtmt) REVERT: A 211 ILE cc_start: 0.7439 (OUTLIER) cc_final: 0.6982 (pp) REVERT: A 580 GLU cc_start: 0.7535 (OUTLIER) cc_final: 0.7329 (pm20) REVERT: A 586 GLU cc_start: 0.7986 (mm-30) cc_final: 0.7620 (tt0) REVERT: A 625 VAL cc_start: 0.8321 (OUTLIER) cc_final: 0.7998 (m) REVERT: A 697 LYS cc_start: 0.7835 (mmtp) cc_final: 0.7464 (mptt) REVERT: A 712 ARG cc_start: 0.7179 (OUTLIER) cc_final: 0.6948 (ttm-80) REVERT: A 716 LEU cc_start: 0.8041 (OUTLIER) cc_final: 0.7795 (pp) outliers start: 17 outliers final: 6 residues processed: 55 average time/residue: 1.8591 time to fit residues: 106.2778 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 : 0.530 ------------------------------------------------------------------------------- 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 580 GLU 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 712 ARG Chi-restraints excluded: chain A residue 716 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 30 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 chunk 13 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.4114 r_free = 0.4114 target = 0.191576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 100)---------------| | r_work = 0.3536 r_free = 0.3536 target = 0.138883 restraints weight = 6074.218| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 0.92 r_work: 0.3370 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3260 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.1302 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 : 0.546 10.727 11364 Z= 0.306 Chirality : 0.040 0.789 1382 Planarity : 0.004 0.031 747 Dihedral : 22.277 166.222 3166 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 4.55 % Allowed : 12.78 % 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: 1.17 (0.43), residues: 381 helix: 2.12 (0.42), residues: 149 sheet: -0.55 (0.78), residues: 42 loop : 0.09 (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 0.011 0.001 TYR A 169 ARG 0.005 0.001 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 64 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 48 time to evaluate : 0.498 Fit side-chains REVERT: A 48 ARG cc_start: 0.8752 (OUTLIER) cc_final: 0.8424 (ttp-170) REVERT: A 88 SER cc_start: 0.8679 (OUTLIER) cc_final: 0.8295 (t) REVERT: A 142 LYS cc_start: 0.8658 (OUTLIER) cc_final: 0.8182 (mtpt) REVERT: A 159 LYS cc_start: 0.8190 (ttmm) cc_final: 0.7637 (mtmt) REVERT: A 211 ILE cc_start: 0.7487 (OUTLIER) cc_final: 0.7062 (pp) REVERT: A 581 ASP cc_start: 0.8306 (OUTLIER) cc_final: 0.8102 (t0) REVERT: A 586 GLU cc_start: 0.7971 (mm-30) cc_final: 0.7593 (tt0) REVERT: A 607 LEU cc_start: 0.7429 (OUTLIER) cc_final: 0.7152 (mt) REVERT: A 611 GLU cc_start: 0.7860 (mt-10) cc_final: 0.7355 (mt-10) REVERT: A 625 VAL cc_start: 0.8317 (OUTLIER) cc_final: 0.7969 (m) REVERT: A 687 GLN cc_start: 0.6719 (OUTLIER) cc_final: 0.6513 (pt0) REVERT: A 697 LYS cc_start: 0.7878 (mmtp) cc_final: 0.7479 (mptt) REVERT: A 714 LYS cc_start: 0.8066 (OUTLIER) cc_final: 0.7644 (tptt) REVERT: A 716 LEU cc_start: 0.7921 (OUTLIER) cc_final: 0.7715 (pp) REVERT: A 742 LYS cc_start: 0.7920 (tttp) cc_final: 0.7469 (tptt) outliers start: 16 outliers final: 2 residues processed: 58 average time/residue: 1.8524 time to fit residues: 111.6589 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 : 0.498 ------------------------------------------------------------------------------- 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 607 LEU Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 687 GLN Chi-restraints excluded: chain A residue 714 LYS Chi-restraints excluded: chain A residue 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: 0.6980 chunk 44 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 33 optimal weight: 6.9990 chunk 3 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 = 0.4044 r_free = 0.4044 target = 0.185566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.132083 restraints weight = 6122.779| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 1.07 r_work: 0.3271 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.1393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 7775 Z= 0.272 Angle : 0.581 11.240 11364 Z= 0.322 Chirality : 0.043 0.862 1382 Planarity : 0.005 0.038 747 Dihedral : 22.332 167.281 3166 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 4.55 % Allowed : 13.07 % 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: 1.15 (0.43), residues: 381 helix: 2.06 (0.42), residues: 149 sheet: -0.49 (0.79), residues: 42 loop : 0.09 (0.47), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 653 PHE 0.012 0.002 PHE A 235 TYR 0.015 0.001 TYR A 70 ARG 0.005 0.001 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 64 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 48 time to evaluate : 0.506 Fit side-chains REVERT: A 48 ARG cc_start: 0.8747 (OUTLIER) cc_final: 0.8421 (ttp-170) REVERT: A 159 LYS cc_start: 0.8184 (ttmm) cc_final: 0.7643 (mtmt) REVERT: A 211 ILE cc_start: 0.7497 (OUTLIER) cc_final: 0.7042 (pp) REVERT: A 581 ASP cc_start: 0.8356 (OUTLIER) cc_final: 0.8124 (t0) REVERT: A 586 GLU cc_start: 0.8028 (mm-30) cc_final: 0.7647 (tt0) REVERT: A 611 GLU cc_start: 0.7874 (mt-10) cc_final: 0.7376 (mt-10) REVERT: A 625 VAL cc_start: 0.8345 (OUTLIER) cc_final: 0.7993 (m) REVERT: A 687 GLN cc_start: 0.6763 (OUTLIER) cc_final: 0.6554 (pt0) REVERT: A 697 LYS cc_start: 0.7925 (mmtp) cc_final: 0.7554 (mptt) REVERT: A 714 LYS cc_start: 0.8112 (OUTLIER) cc_final: 0.7684 (tptt) REVERT: A 716 LEU cc_start: 0.8029 (OUTLIER) cc_final: 0.7734 (pp) REVERT: A 742 LYS cc_start: 0.7922 (tttp) cc_final: 0.7485 (tptt) outliers start: 16 outliers final: 5 residues processed: 58 average time/residue: 1.8129 time to fit residues: 109.3162 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 : 0.549 ------------------------------------------------------------------------------- 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 687 GLN 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: 0.0470 chunk 8 optimal weight: 0.7980 chunk 25 optimal weight: 5.9990 chunk 22 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 20 optimal weight: 0.0870 chunk 38 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 overall best weight: 0.5456 ------------------------------------------------------------------------------- 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 = 0.4069 r_free = 0.4069 target = 0.188184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.134121 restraints weight = 6120.348| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 1.01 r_work: 0.3305 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.1435 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= 0.173 Angle : 0.538 10.716 11364 Z= 0.304 Chirality : 0.040 0.788 1382 Planarity : 0.004 0.037 747 Dihedral : 22.302 166.296 3166 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.98 % Allowed : 13.92 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.31 (0.44), residues: 381 helix: 2.28 (0.42), residues: 149 sheet: -0.55 (0.79), residues: 42 loop : 0.13 (0.46), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 680 PHE 0.011 0.001 PHE A 648 TYR 0.010 0.001 TYR A 70 ARG 0.006 0.001 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 59 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 45 time to evaluate : 0.480 Fit side-chains revert: symmetry clash REVERT: A 48 ARG cc_start: 0.8732 (OUTLIER) cc_final: 0.8407 (ttp-170) REVERT: A 142 LYS cc_start: 0.8629 (OUTLIER) cc_final: 0.8147 (mtpt) REVERT: A 159 LYS cc_start: 0.8173 (ttmm) cc_final: 0.7620 (mtmt) REVERT: A 211 ILE cc_start: 0.7473 (OUTLIER) cc_final: 0.7026 (pp) REVERT: A 581 ASP cc_start: 0.8320 (OUTLIER) cc_final: 0.8087 (t0) REVERT: A 586 GLU cc_start: 0.8002 (mm-30) cc_final: 0.7642 (tt0) REVERT: A 621 LYS cc_start: 0.7566 (OUTLIER) cc_final: 0.6928 (mtmt) REVERT: A 625 VAL cc_start: 0.8325 (OUTLIER) cc_final: 0.7980 (m) REVERT: A 687 GLN cc_start: 0.6720 (OUTLIER) cc_final: 0.6516 (pt0) REVERT: A 697 LYS cc_start: 0.7863 (mmtp) cc_final: 0.7440 (mptt) REVERT: A 716 LEU cc_start: 0.7907 (OUTLIER) cc_final: 0.7682 (pp) REVERT: A 742 LYS cc_start: 0.7890 (tttp) cc_final: 0.7449 (tptt) outliers start: 14 outliers final: 4 residues processed: 53 average time/residue: 1.8060 time to fit residues: 99.6984 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 : 0.540 ------------------------------------------------------------------------------- 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 607 LEU 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 687 GLN 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: 0.9980 chunk 39 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 26 optimal weight: 0.5980 chunk 12 optimal weight: 0.7980 chunk 4 optimal weight: 0.5980 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 = 0.4052 r_free = 0.4052 target = 0.186244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.131620 restraints weight = 6155.879| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 1.07 r_work: 0.3281 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.1471 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= 0.253 Angle : 0.568 11.072 11364 Z= 0.315 Chirality : 0.042 0.839 1382 Planarity : 0.004 0.040 747 Dihedral : 22.307 166.858 3166 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.98 % Allowed : 14.20 % Favored : 81.82 % 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: 1.22 (0.44), residues: 381 helix: 2.17 (0.42), residues: 149 sheet: -0.52 (0.79), residues: 42 loop : 0.10 (0.46), 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 0.014 0.001 TYR A 70 ARG 0.005 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: 14 poor density : 47 time to evaluate : 0.493 Fit side-chains REVERT: A 48 ARG cc_start: 0.8740 (OUTLIER) cc_final: 0.8418 (ttp-170) REVERT: A 159 LYS cc_start: 0.8187 (ttmm) cc_final: 0.7629 (mtmt) REVERT: A 211 ILE cc_start: 0.7476 (OUTLIER) cc_final: 0.7019 (pp) REVERT: A 581 ASP cc_start: 0.8340 (OUTLIER) cc_final: 0.8113 (t0) REVERT: A 586 GLU cc_start: 0.8019 (mm-30) cc_final: 0.7629 (tt0) REVERT: A 611 GLU cc_start: 0.7858 (mt-10) cc_final: 0.7376 (mt-10) REVERT: A 625 VAL cc_start: 0.8311 (OUTLIER) cc_final: 0.7946 (m) REVERT: A 687 GLN cc_start: 0.6976 (OUTLIER) cc_final: 0.6758 (pt0) REVERT: A 697 LYS cc_start: 0.7893 (mmtp) cc_final: 0.7497 (mptt) REVERT: A 716 LEU cc_start: 0.7949 (OUTLIER) cc_final: 0.7665 (pp) REVERT: A 742 LYS cc_start: 0.7917 (tttp) cc_final: 0.7484 (tptt) outliers start: 14 outliers final: 5 residues processed: 54 average time/residue: 1.9459 time to fit residues: 109.2563 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 : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ARG Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 142 LYS Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 238 LYS Chi-restraints excluded: chain A residue 581 ASP Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 687 GLN 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: 0.5980 chunk 30 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 12 optimal weight: 0.3980 chunk 23 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 = 0.4058 r_free = 0.4058 target = 0.186990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.132100 restraints weight = 6187.213| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 1.10 r_work: 0.3283 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7775 Z= 0.198 Angle : 0.549 10.897 11364 Z= 0.308 Chirality : 0.040 0.813 1382 Planarity : 0.004 0.038 747 Dihedral : 22.303 166.989 3166 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.98 % Allowed : 14.20 % Favored : 81.82 % 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: 1.28 (0.44), residues: 381 helix: 2.22 (0.42), residues: 149 sheet: -0.51 (0.79), residues: 42 loop : 0.13 (0.47), 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 648 TYR 0.013 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 : 0.593 Fit side-chains REVERT: A 48 ARG cc_start: 0.8733 (OUTLIER) cc_final: 0.8409 (ttp-170) REVERT: A 159 LYS cc_start: 0.8156 (ttmm) cc_final: 0.7591 (mtmt) REVERT: A 211 ILE cc_start: 0.7448 (OUTLIER) cc_final: 0.6999 (pp) REVERT: A 226 LYS cc_start: 0.7975 (ptmm) cc_final: 0.7542 (tppp) REVERT: A 581 ASP cc_start: 0.8338 (OUTLIER) cc_final: 0.8107 (t0) REVERT: A 586 GLU cc_start: 0.8024 (mm-30) cc_final: 0.7613 (tt0) REVERT: A 611 GLU cc_start: 0.7847 (mt-10) cc_final: 0.7349 (mt-10) REVERT: A 621 LYS cc_start: 0.7578 (OUTLIER) cc_final: 0.6926 (mtmt) REVERT: A 625 VAL cc_start: 0.8299 (OUTLIER) cc_final: 0.7930 (m) REVERT: A 687 GLN cc_start: 0.6985 (OUTLIER) cc_final: 0.6768 (pt0) REVERT: A 697 LYS cc_start: 0.7889 (mmtp) cc_final: 0.7483 (mptt) REVERT: A 716 LEU cc_start: 0.7925 (OUTLIER) cc_final: 0.7649 (pp) REVERT: A 742 LYS cc_start: 0.7915 (tttp) cc_final: 0.7482 (tptt) outliers start: 14 outliers final: 6 residues processed: 54 average time/residue: 1.8330 time to fit residues: 103.0964 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 : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ARG Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 142 LYS Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 238 LYS Chi-restraints excluded: chain A residue 581 ASP Chi-restraints excluded: chain A residue 601 THR Chi-restraints excluded: chain A residue 621 LYS Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 687 GLN Chi-restraints excluded: chain A residue 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: 0.7980 chunk 18 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 chunk 3 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 2 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 20 optimal weight: 0.0670 overall best weight: 1.1122 ------------------------------------------------------------------------------- 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 = 0.4043 r_free = 0.4043 target = 0.185452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.130992 restraints weight = 6265.688| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 1.11 r_work: 0.3258 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 7775 Z= 0.276 Angle : 0.586 11.455 11364 Z= 0.324 Chirality : 0.044 0.891 1382 Planarity : 0.005 0.042 747 Dihedral : 22.365 167.086 3166 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 4.26 % Allowed : 13.92 % Favored : 81.82 % 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: 1.15 (0.44), residues: 381 helix: 2.06 (0.42), residues: 149 sheet: -0.49 (0.80), residues: 42 loop : 0.09 (0.46), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 653 PHE 0.010 0.001 PHE A 648 TYR 0.015 0.001 TYR A 70 ARG 0.005 0.000 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 62 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 47 time to evaluate : 0.501 Fit side-chains REVERT: A 48 ARG cc_start: 0.8745 (OUTLIER) cc_final: 0.8445 (ttp-170) REVERT: A 159 LYS cc_start: 0.8236 (ttmm) cc_final: 0.7683 (mtmt) REVERT: A 168 GLN cc_start: 0.8873 (tp40) cc_final: 0.7743 (tp-100) REVERT: A 211 ILE cc_start: 0.7515 (OUTLIER) cc_final: 0.7067 (pp) REVERT: A 581 ASP cc_start: 0.8358 (OUTLIER) cc_final: 0.8135 (t0) REVERT: A 586 GLU cc_start: 0.8044 (mm-30) cc_final: 0.7653 (tt0) REVERT: A 611 GLU cc_start: 0.7842 (mt-10) cc_final: 0.7376 (mt-10) REVERT: A 621 LYS cc_start: 0.7598 (OUTLIER) cc_final: 0.7008 (mtmt) REVERT: A 625 VAL cc_start: 0.8341 (OUTLIER) cc_final: 0.7985 (m) REVERT: A 687 GLN cc_start: 0.6984 (OUTLIER) cc_final: 0.6775 (pt0) REVERT: A 697 LYS cc_start: 0.7963 (mmtp) cc_final: 0.7588 (mptt) REVERT: A 714 LYS cc_start: 0.8043 (OUTLIER) cc_final: 0.7613 (tptt) REVERT: A 716 LEU cc_start: 0.8034 (OUTLIER) cc_final: 0.7736 (pp) REVERT: A 742 LYS cc_start: 0.7939 (tttp) cc_final: 0.7509 (tptt) outliers start: 15 outliers final: 6 residues processed: 56 average time/residue: 1.7631 time to fit residues: 102.6652 Evaluate side-chains 61 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 47 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ARG Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 142 LYS Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 238 LYS Chi-restraints excluded: chain A residue 581 ASP Chi-restraints excluded: chain A residue 601 THR Chi-restraints excluded: chain A residue 621 LYS Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 687 GLN Chi-restraints excluded: chain A residue 714 LYS Chi-restraints excluded: chain A residue 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: 1.9990 chunk 35 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- 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 = 0.4025 r_free = 0.4025 target = 0.183758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.129024 restraints weight = 6067.994| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 1.05 r_work: 0.3252 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 7775 Z= 0.348 Angle : 0.632 12.104 11364 Z= 0.347 Chirality : 0.048 1.022 1382 Planarity : 0.005 0.045 747 Dihedral : 22.379 167.565 3166 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 3.98 % Allowed : 14.20 % Favored : 81.82 % 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: 0.96 (0.43), residues: 381 helix: 1.80 (0.42), residues: 149 sheet: -0.53 (0.80), residues: 42 loop : 0.07 (0.46), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS A 653 PHE 0.009 0.002 PHE A 648 TYR 0.018 0.002 TYR A 70 ARG 0.005 0.001 ARG A 163 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5552.70 seconds wall clock time: 98 minutes 37.99 seconds (5917.99 seconds total)