Starting phenix.real_space_refine on Tue Mar 11 23:28:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uo2_26638/03_2025/7uo2_26638.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uo2_26638/03_2025/7uo2_26638.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7uo2_26638/03_2025/7uo2_26638.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uo2_26638/03_2025/7uo2_26638.map" model { file = "/net/cci-nas-00/data/ceres_data/7uo2_26638/03_2025/7uo2_26638.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uo2_26638/03_2025/7uo2_26638.cif" } resolution = 3.1 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= 0.012 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: 6 Type Number sf(0) Gaussians P 270 5.49 5 Mg 3 5.21 5 S 2 5.16 5 C 3171 2.51 5 N 1258 2.21 5 O 2031 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 6735 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 922 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 6, 'TRANS': 105} Chain: "B" Number of atoms: 5810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 5810 Classifications: {'RNA': 271} Modifications used: {'5*END': 1, 'rna2p_pur': 29, 'rna2p_pyr': 26, 'rna3p_pur': 122, 'rna3p_pyr': 94} Link IDs: {'rna2p': 55, 'rna3p': 215} Chain breaks: 1 Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 4.90, per 1000 atoms: 0.73 Number of scatterers: 6735 At special positions: 0 Unit cell: (88.5636, 124.96, 127.386, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 2 16.00 P 270 15.00 Mg 3 11.99 O 2031 8.00 N 1258 7.00 C 3171 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: 1.89 Conformation dependent library (CDL) restraints added in 283.5 milliseconds 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 214 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 1 sheets defined 40.2% alpha, 9.8% beta 81 base pairs and 119 stacking pairs defined. Time for finding SS restraints: 3.11 Creating SS restraints... Processing helix chain 'A' and resid 6 through 10 removed outlier: 3.850A pdb=" N LEU A 9 " --> pdb=" O PRO A 6 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG A 10 " --> pdb=" O ARG A 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 6 through 10' Processing helix chain 'A' and resid 13 through 23 removed outlier: 4.134A pdb=" N PHE A 17 " --> pdb=" O THR A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 73 removed outlier: 3.956A pdb=" N ASN A 62 " --> pdb=" O ALA A 58 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N ILE A 64 " --> pdb=" O GLU A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 108 removed outlier: 3.504A pdb=" N LEU A 100 " --> pdb=" O ASP A 96 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU A 107 " --> pdb=" O ALA A 103 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N TRP A 108 " --> pdb=" O LEU A 104 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 35 removed outlier: 3.850A pdb=" N THR A 33 " --> pdb=" O VAL A 87 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL A 87 " --> pdb=" O THR A 33 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ARG A 45 " --> pdb=" O PHE A 84 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N VAL A 86 " --> pdb=" O ARG A 45 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N GLY A 47 " --> pdb=" O VAL A 86 " (cutoff:3.500A) removed outlier: 8.931A pdb=" N ALA A 88 " --> pdb=" O GLY A 47 " (cutoff:3.500A) 24 hydrogen bonds defined for protein. 72 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 218 hydrogen bonds 400 hydrogen bond angles 0 basepair planarities 81 basepair parallelities 119 stacking parallelities Total time for adding SS restraints: 2.31 Time building geometry restraints manager: 2.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 570 1.32 - 1.44: 3614 1.44 - 1.56: 2714 1.56 - 1.69: 539 1.69 - 1.81: 3 Bond restraints: 7440 Sorted by residual: bond pdb=" C2' U B 17 " pdb=" C1' U B 17 " ideal model delta sigma weight residual 1.529 1.508 0.021 1.50e-02 4.44e+03 1.88e+00 bond pdb=" C4' U B 17 " pdb=" C3' U B 17 " ideal model delta sigma weight residual 1.521 1.540 -0.019 1.50e-02 4.44e+03 1.62e+00 bond pdb=" O3' U B 17 " pdb=" P C B 18 " ideal model delta sigma weight residual 1.607 1.624 -0.017 1.50e-02 4.44e+03 1.31e+00 bond pdb=" O4' G B 271 " pdb=" C1' G B 271 " ideal model delta sigma weight residual 1.412 1.429 -0.017 1.50e-02 4.44e+03 1.23e+00 bond pdb=" C4' G B 271 " pdb=" C3' G B 271 " ideal model delta sigma weight residual 1.521 1.505 0.016 1.50e-02 4.44e+03 1.17e+00 ... (remaining 7435 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.49: 11105 1.49 - 2.98: 235 2.98 - 4.47: 49 4.47 - 5.96: 10 5.96 - 7.44: 1 Bond angle restraints: 11400 Sorted by residual: angle pdb=" C2' G B 271 " pdb=" C1' G B 271 " pdb=" N9 G B 271 " ideal model delta sigma weight residual 112.00 106.53 5.47 1.50e+00 4.44e-01 1.33e+01 angle pdb=" C4' U B 17 " pdb=" C3' U B 17 " pdb=" O3' U B 17 " ideal model delta sigma weight residual 113.00 117.92 -4.92 1.50e+00 4.44e-01 1.08e+01 angle pdb=" O4' G B 271 " pdb=" C4' G B 271 " pdb=" C3' G B 271 " ideal model delta sigma weight residual 104.00 100.99 3.01 1.00e+00 1.00e+00 9.05e+00 angle pdb=" C4' G B 271 " pdb=" C3' G B 271 " pdb=" O3' G B 271 " ideal model delta sigma weight residual 113.00 117.45 -4.45 1.50e+00 4.44e-01 8.78e+00 angle pdb=" O4' G B 271 " pdb=" C1' G B 271 " pdb=" N9 G B 271 " ideal model delta sigma weight residual 108.50 112.90 -4.40 1.50e+00 4.44e-01 8.59e+00 ... (remaining 11395 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.14: 4005 35.14 - 70.28: 745 70.28 - 105.41: 98 105.41 - 140.55: 4 140.55 - 175.69: 4 Dihedral angle restraints: 4856 sinusoidal: 4531 harmonic: 325 Sorted by residual: dihedral pdb=" O4' U B 257 " pdb=" C1' U B 257 " pdb=" N1 U B 257 " pdb=" C2 U B 257 " ideal model delta sinusoidal sigma weight residual 200.00 51.23 148.77 1 1.50e+01 4.44e-03 7.92e+01 dihedral pdb=" O4' U B 331 " pdb=" C1' U B 331 " pdb=" N1 U B 331 " pdb=" C2 U B 331 " ideal model delta sinusoidal sigma weight residual -128.00 47.69 -175.69 1 1.70e+01 3.46e-03 6.63e+01 dihedral pdb=" O4' U B 302 " pdb=" C1' U B 302 " pdb=" N1 U B 302 " pdb=" C2 U B 302 " ideal model delta sinusoidal sigma weight residual 232.00 58.14 173.86 1 1.70e+01 3.46e-03 6.62e+01 ... (remaining 4853 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1424 0.058 - 0.116: 58 0.116 - 0.174: 9 0.174 - 0.232: 1 0.232 - 0.290: 1 Chirality restraints: 1493 Sorted by residual: chirality pdb=" C3' G B 271 " pdb=" C4' G B 271 " pdb=" O3' G B 271 " pdb=" C2' G B 271 " both_signs ideal model delta sigma weight residual False -2.48 -2.19 -0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" C1' G B 16 " pdb=" O4' G B 16 " pdb=" C2' G B 16 " pdb=" N9 G B 16 " both_signs ideal model delta sigma weight residual False 2.46 2.66 -0.20 2.00e-01 2.50e+01 1.00e+00 chirality pdb=" C1' G B 324 " pdb=" O4' G B 324 " pdb=" C2' G B 324 " pdb=" N9 G B 324 " both_signs ideal model delta sigma weight residual False 2.46 2.29 0.17 2.00e-01 2.50e+01 6.86e-01 ... (remaining 1490 not shown) Planarity restraints: 435 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G B 271 " 0.053 2.00e-02 2.50e+03 2.45e-02 1.81e+01 pdb=" N9 G B 271 " -0.064 2.00e-02 2.50e+03 pdb=" C8 G B 271 " -0.003 2.00e-02 2.50e+03 pdb=" N7 G B 271 " 0.002 2.00e-02 2.50e+03 pdb=" C5 G B 271 " 0.002 2.00e-02 2.50e+03 pdb=" C6 G B 271 " -0.002 2.00e-02 2.50e+03 pdb=" O6 G B 271 " 0.017 2.00e-02 2.50e+03 pdb=" N1 G B 271 " 0.003 2.00e-02 2.50e+03 pdb=" C2 G B 271 " -0.001 2.00e-02 2.50e+03 pdb=" N2 G B 271 " 0.000 2.00e-02 2.50e+03 pdb=" N3 G B 271 " -0.008 2.00e-02 2.50e+03 pdb=" C4 G B 271 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U B 17 " 0.015 2.00e-02 2.50e+03 2.20e-02 1.09e+01 pdb=" N1 U B 17 " 0.014 2.00e-02 2.50e+03 pdb=" C2 U B 17 " -0.028 2.00e-02 2.50e+03 pdb=" O2 U B 17 " -0.013 2.00e-02 2.50e+03 pdb=" N3 U B 17 " 0.037 2.00e-02 2.50e+03 pdb=" C4 U B 17 " -0.029 2.00e-02 2.50e+03 pdb=" O4 U B 17 " 0.021 2.00e-02 2.50e+03 pdb=" C5 U B 17 " -0.018 2.00e-02 2.50e+03 pdb=" C6 U B 17 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G B 16 " -0.042 2.00e-02 2.50e+03 1.73e-02 8.95e+00 pdb=" N9 G B 16 " 0.030 2.00e-02 2.50e+03 pdb=" C8 G B 16 " 0.011 2.00e-02 2.50e+03 pdb=" N7 G B 16 " 0.005 2.00e-02 2.50e+03 pdb=" C5 G B 16 " -0.001 2.00e-02 2.50e+03 pdb=" C6 G B 16 " -0.011 2.00e-02 2.50e+03 pdb=" O6 G B 16 " -0.017 2.00e-02 2.50e+03 pdb=" N1 G B 16 " 0.002 2.00e-02 2.50e+03 pdb=" C2 G B 16 " 0.014 2.00e-02 2.50e+03 pdb=" N2 G B 16 " -0.006 2.00e-02 2.50e+03 pdb=" N3 G B 16 " 0.008 2.00e-02 2.50e+03 pdb=" C4 G B 16 " 0.007 2.00e-02 2.50e+03 ... (remaining 432 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 175 2.61 - 3.18: 5207 3.18 - 3.75: 13421 3.75 - 4.33: 16769 4.33 - 4.90: 22869 Nonbonded interactions: 58441 Sorted by model distance: nonbonded pdb=" OP1 G B 250 " pdb="MG MG B 403 " model vdw 2.033 2.170 nonbonded pdb=" OP1 A B 67 " pdb="MG MG B 401 " model vdw 2.049 2.170 nonbonded pdb=" OP1 A B 351 " pdb="MG MG B 401 " model vdw 2.066 2.170 nonbonded pdb=" O2' A B 112 " pdb=" OP1 C B 115 " model vdw 2.134 3.040 nonbonded pdb=" O2' G B 262 " pdb=" OP1 U B 263 " model vdw 2.221 3.040 ... (remaining 58436 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: 0.010 Normalize map: mean=0, sd=1: 3.550 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: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 21.350 Find NCS groups from input model: 0.050 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: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7109 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 : 0.002 0.023 7440 Z= 0.115 Angle : 0.549 7.444 11400 Z= 0.273 Chirality : 0.027 0.290 1493 Planarity : 0.004 0.035 435 Dihedral : 26.442 175.688 4642 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 1.82 % Allowed : 14.55 % Favored : 83.64 % Rotamer: Outliers : 2.04 % Allowed : 10.20 % Favored : 87.76 % 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: -3.16 (0.70), residues: 110 helix: -0.20 (0.84), residues: 36 sheet: -1.26 (1.44), residues: 14 loop : -3.74 (0.58), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP A 108 HIS 0.002 0.000 HIS A 59 PHE 0.004 0.001 PHE A 5 ARG 0.002 0.000 ARG A 69 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 28 time to evaluate : 0.277 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 30 average time/residue: 0.2597 time to fit residues: 9.8434 Evaluate side-chains 18 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 32 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 29 optimal weight: 10.0000 chunk 11 optimal weight: 7.9990 chunk 18 optimal weight: 3.9990 chunk 22 optimal weight: 9.9990 chunk 34 optimal weight: 3.9990 chunk 10 optimal weight: 0.4980 overall best weight: 3.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.061067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.047540 restraints weight = 54082.527| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 1.45 r_work: 0.3376 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.3976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.076 7440 Z= 0.457 Angle : 0.946 8.602 11400 Z= 0.468 Chirality : 0.047 0.272 1493 Planarity : 0.008 0.046 435 Dihedral : 27.310 175.344 4397 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 21.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.36 % Favored : 83.64 % Rotamer: Outliers : 4.08 % Allowed : 14.29 % Favored : 81.63 % 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: -3.34 (0.69), residues: 110 helix: -0.89 (0.76), residues: 39 sheet: -1.44 (1.27), residues: 14 loop : -3.54 (0.66), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.002 TRP A 108 HIS 0.006 0.003 HIS A 111 PHE 0.024 0.004 PHE A 19 ARG 0.007 0.001 ARG A 10 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 21 time to evaluate : 0.293 Fit side-chains REVERT: A 31 GLN cc_start: 0.8351 (tp-100) cc_final: 0.7995 (tp-100) REVERT: A 105 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7641 (mm-30) outliers start: 4 outliers final: 2 residues processed: 24 average time/residue: 0.2513 time to fit residues: 7.7336 Evaluate side-chains 20 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 17 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 105 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 25 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 23 optimal weight: 9.9990 chunk 6 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 59 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.061415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.047879 restraints weight = 56159.569| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 1.34 r_work: 0.3390 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.4257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 7440 Z= 0.330 Angle : 0.818 7.683 11400 Z= 0.405 Chirality : 0.042 0.257 1493 Planarity : 0.007 0.047 435 Dihedral : 27.199 173.674 4397 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 18.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.73 % Favored : 87.27 % Rotamer: Outliers : 7.14 % Allowed : 14.29 % Favored : 78.57 % 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: -3.61 (0.71), residues: 110 helix: -1.47 (0.73), residues: 45 sheet: -1.64 (1.16), residues: 14 loop : -3.55 (0.74), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 108 HIS 0.004 0.002 HIS A 43 PHE 0.010 0.003 PHE A 17 ARG 0.002 0.001 ARG A 73 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 21 time to evaluate : 0.263 Fit side-chains REVERT: A 31 GLN cc_start: 0.8214 (tp-100) cc_final: 0.7830 (tp-100) outliers start: 7 outliers final: 4 residues processed: 26 average time/residue: 0.2410 time to fit residues: 7.9535 Evaluate side-chains 21 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 17 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 112 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 2 optimal weight: 0.9990 chunk 27 optimal weight: 6.9990 chunk 9 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 26 optimal weight: 10.0000 chunk 29 optimal weight: 5.9990 chunk 10 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.060484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.046920 restraints weight = 57104.316| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 1.48 r_work: 0.3362 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.4856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 7440 Z= 0.384 Angle : 0.893 7.563 11400 Z= 0.441 Chirality : 0.046 0.276 1493 Planarity : 0.007 0.038 435 Dihedral : 27.363 173.037 4397 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 22.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.64 % Favored : 86.36 % Rotamer: Outliers : 9.18 % Allowed : 14.29 % Favored : 76.53 % 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: -3.56 (0.73), residues: 110 helix: -1.54 (0.75), residues: 45 sheet: -1.31 (1.15), residues: 14 loop : -3.51 (0.79), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP A 108 HIS 0.005 0.002 HIS A 43 PHE 0.011 0.003 PHE A 17 ARG 0.004 0.001 ARG A 56 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 18 time to evaluate : 0.275 Fit side-chains REVERT: A 10 ARG cc_start: 0.7406 (OUTLIER) cc_final: 0.7148 (mtt180) REVERT: A 31 GLN cc_start: 0.8337 (tp-100) cc_final: 0.7831 (tp-100) outliers start: 9 outliers final: 2 residues processed: 25 average time/residue: 0.2231 time to fit residues: 7.2753 Evaluate side-chains 19 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 16 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ARG Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 112 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 10 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 3 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 7 optimal weight: 0.4980 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 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.062145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.048650 restraints weight = 55889.143| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 1.20 r_work: 0.3425 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.4289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7440 Z= 0.215 Angle : 0.716 6.283 11400 Z= 0.359 Chirality : 0.037 0.255 1493 Planarity : 0.005 0.036 435 Dihedral : 27.018 174.330 4397 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 14.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.91 % Favored : 89.09 % Rotamer: Outliers : 6.12 % Allowed : 21.43 % Favored : 72.45 % 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: -3.18 (0.75), residues: 110 helix: -1.11 (0.78), residues: 46 sheet: -1.24 (1.17), residues: 14 loop : -3.41 (0.80), residues: 50 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 108 HIS 0.003 0.001 HIS A 43 PHE 0.007 0.002 PHE A 19 ARG 0.002 0.000 ARG A 113 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 20 time to evaluate : 0.302 Fit side-chains REVERT: A 10 ARG cc_start: 0.7443 (OUTLIER) cc_final: 0.7164 (mtt180) REVERT: A 31 GLN cc_start: 0.8214 (tp-100) cc_final: 0.7714 (tp-100) outliers start: 6 outliers final: 4 residues processed: 25 average time/residue: 0.2591 time to fit residues: 8.2612 Evaluate side-chains 24 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 19 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ARG Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 112 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 20 optimal weight: 4.9990 chunk 23 optimal weight: 9.9990 chunk 7 optimal weight: 0.0870 chunk 1 optimal weight: 0.9980 chunk 19 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 overall best weight: 2.2164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 111 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.060800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.047295 restraints weight = 56205.071| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 1.27 r_work: 0.3371 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.4823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 7440 Z= 0.339 Angle : 0.839 7.103 11400 Z= 0.417 Chirality : 0.043 0.263 1493 Planarity : 0.006 0.038 435 Dihedral : 27.238 173.099 4397 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 20.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.55 % Favored : 85.45 % Rotamer: Outliers : 5.10 % Allowed : 21.43 % Favored : 73.47 % 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: -3.45 (0.74), residues: 110 helix: -1.56 (0.74), residues: 46 sheet: -1.06 (1.14), residues: 14 loop : -3.42 (0.82), residues: 50 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP A 108 HIS 0.004 0.002 HIS A 43 PHE 0.009 0.002 PHE A 19 ARG 0.003 0.001 ARG A 10 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 19 time to evaluate : 0.313 Fit side-chains REVERT: A 10 ARG cc_start: 0.7412 (OUTLIER) cc_final: 0.7162 (mtt180) REVERT: A 31 GLN cc_start: 0.8261 (tp-100) cc_final: 0.7752 (tp-100) REVERT: A 108 TRP cc_start: 0.7714 (m-10) cc_final: 0.7219 (m-10) outliers start: 5 outliers final: 2 residues processed: 23 average time/residue: 0.2435 time to fit residues: 7.2922 Evaluate side-chains 22 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 19 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ARG Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 112 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 7 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 chunk 27 optimal weight: 6.9990 chunk 2 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.060449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.046969 restraints weight = 55564.518| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 1.30 r_work: 0.3366 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.5233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 7440 Z= 0.361 Angle : 0.877 7.409 11400 Z= 0.434 Chirality : 0.045 0.265 1493 Planarity : 0.006 0.039 435 Dihedral : 27.415 172.457 4397 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 20.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.64 % Favored : 86.36 % Rotamer: Outliers : 5.10 % Allowed : 23.47 % Favored : 71.43 % 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: -3.03 (0.76), residues: 110 helix: -1.17 (0.81), residues: 40 sheet: -1.25 (1.13), residues: 14 loop : -2.93 (0.82), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP A 108 HIS 0.004 0.002 HIS A 43 PHE 0.009 0.002 PHE A 84 ARG 0.003 0.001 ARG A 109 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 19 time to evaluate : 0.305 Fit side-chains REVERT: A 10 ARG cc_start: 0.7410 (OUTLIER) cc_final: 0.7141 (mtt180) REVERT: A 31 GLN cc_start: 0.8341 (tp-100) cc_final: 0.7897 (tp40) REVERT: A 108 TRP cc_start: 0.7821 (m-10) cc_final: 0.7311 (m-10) outliers start: 5 outliers final: 2 residues processed: 23 average time/residue: 0.2368 time to fit residues: 7.0986 Evaluate side-chains 21 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 18 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ARG Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 112 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 18 optimal weight: 3.9990 chunk 15 optimal weight: 6.9990 chunk 8 optimal weight: 0.8980 chunk 11 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.060156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.046651 restraints weight = 56091.402| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 1.40 r_work: 0.3357 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.5397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.075 7440 Z= 0.385 Angle : 0.904 7.858 11400 Z= 0.447 Chirality : 0.046 0.259 1493 Planarity : 0.007 0.038 435 Dihedral : 27.454 172.571 4397 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 21.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.64 % Favored : 86.36 % Rotamer: Outliers : 4.08 % Allowed : 25.51 % Favored : 70.41 % 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: -3.64 (0.73), residues: 110 helix: -1.71 (0.74), residues: 46 sheet: -1.40 (1.09), residues: 14 loop : -3.45 (0.81), residues: 50 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP A 108 HIS 0.005 0.002 HIS A 43 PHE 0.012 0.003 PHE A 19 ARG 0.003 0.001 ARG A 56 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 20 time to evaluate : 0.312 Fit side-chains REVERT: A 10 ARG cc_start: 0.7361 (OUTLIER) cc_final: 0.7066 (mtt180) REVERT: A 31 GLN cc_start: 0.8228 (tp-100) cc_final: 0.7811 (tp-100) REVERT: A 108 TRP cc_start: 0.7826 (m-10) cc_final: 0.7237 (m-10) REVERT: A 109 ARG cc_start: 0.8514 (mtm110) cc_final: 0.7821 (mmp80) outliers start: 4 outliers final: 2 residues processed: 23 average time/residue: 0.2803 time to fit residues: 8.1281 Evaluate side-chains 22 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 19 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ARG Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 112 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 29 optimal weight: 10.0000 chunk 11 optimal weight: 6.9990 chunk 5 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.060549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.047118 restraints weight = 55440.362| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 1.23 r_work: 0.3372 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.5292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 7440 Z= 0.334 Angle : 0.846 6.956 11400 Z= 0.420 Chirality : 0.043 0.271 1493 Planarity : 0.006 0.038 435 Dihedral : 27.321 172.993 4397 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 20.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.82 % Favored : 88.18 % Rotamer: Outliers : 4.08 % Allowed : 24.49 % Favored : 71.43 % 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: -2.99 (0.78), residues: 110 helix: -1.10 (0.83), residues: 40 sheet: -1.17 (1.15), residues: 14 loop : -2.97 (0.83), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.003 TRP A 108 HIS 0.004 0.002 HIS A 43 PHE 0.011 0.002 PHE A 19 ARG 0.004 0.000 ARG A 10 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 21 time to evaluate : 0.297 Fit side-chains REVERT: A 10 ARG cc_start: 0.7529 (OUTLIER) cc_final: 0.7307 (mtt180) REVERT: A 31 GLN cc_start: 0.8355 (tp-100) cc_final: 0.7901 (tp-100) REVERT: A 108 TRP cc_start: 0.7792 (m-10) cc_final: 0.7219 (m-10) REVERT: A 109 ARG cc_start: 0.8399 (mtm110) cc_final: 0.7717 (mmp80) outliers start: 4 outliers final: 2 residues processed: 25 average time/residue: 0.2553 time to fit residues: 8.1311 Evaluate side-chains 23 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 20 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ARG Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 112 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 29 optimal weight: 9.9990 chunk 13 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 chunk 8 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 23 optimal weight: 10.0000 chunk 18 optimal weight: 3.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.061140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.047703 restraints weight = 56773.379| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 1.27 r_work: 0.3385 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.5142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 7440 Z= 0.277 Angle : 0.793 7.031 11400 Z= 0.396 Chirality : 0.041 0.269 1493 Planarity : 0.006 0.037 435 Dihedral : 27.229 173.869 4397 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 17.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.73 % Favored : 87.27 % Rotamer: Outliers : 3.06 % Allowed : 26.53 % Favored : 70.41 % 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: -3.27 (0.76), residues: 110 helix: -1.41 (0.77), residues: 46 sheet: -0.95 (1.20), residues: 14 loop : -3.32 (0.81), residues: 50 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP A 108 HIS 0.003 0.002 HIS A 43 PHE 0.011 0.002 PHE A 19 ARG 0.002 0.000 ARG A 10 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 21 time to evaluate : 0.327 Fit side-chains REVERT: A 10 ARG cc_start: 0.7260 (OUTLIER) cc_final: 0.7008 (mtt180) REVERT: A 31 GLN cc_start: 0.8251 (tp-100) cc_final: 0.7895 (tp-100) REVERT: A 108 TRP cc_start: 0.7716 (m-10) cc_final: 0.7138 (m-10) outliers start: 3 outliers final: 2 residues processed: 24 average time/residue: 0.2192 time to fit residues: 6.8627 Evaluate side-chains 22 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 19 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ARG Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 112 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 37 optimal weight: 5.9990 chunk 29 optimal weight: 10.0000 chunk 36 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 5 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 23 optimal weight: 8.9990 chunk 34 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- 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 = 0.3948 r_free = 0.3948 target = 0.060013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.046549 restraints weight = 56351.673| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 1.48 r_work: 0.3354 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.5599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 7440 Z= 0.407 Angle : 0.927 7.231 11400 Z= 0.457 Chirality : 0.047 0.277 1493 Planarity : 0.007 0.038 435 Dihedral : 27.466 172.478 4397 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 24.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.64 % Favored : 86.36 % Rotamer: Outliers : 4.08 % Allowed : 26.53 % Favored : 69.39 % 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: -2.96 (0.79), residues: 110 helix: -1.08 (0.85), residues: 40 sheet: -0.88 (1.16), residues: 14 loop : -3.03 (0.85), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP A 108 HIS 0.005 0.002 HIS A 111 PHE 0.011 0.003 PHE A 19 ARG 0.004 0.001 ARG A 10 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5294.87 seconds wall clock time: 90 minutes 53.18 seconds (5453.18 seconds total)