Starting phenix.real_space_refine on Thu Sep 26 19:09:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uo5_26640/09_2024/7uo5_26640.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uo5_26640/09_2024/7uo5_26640.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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uo5_26640/09_2024/7uo5_26640.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uo5_26640/09_2024/7uo5_26640.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uo5_26640/09_2024/7uo5_26640.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uo5_26640/09_2024/7uo5_26640.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= 0.013 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: 7 Type Number sf(0) Gaussians Ca 7 9.91 5 P 372 5.49 5 S 2 5.16 5 C 4156 2.51 5 N 1688 2.21 5 O 2730 1.98 5 H 5024 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 13979 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 1898 Classifications: {'peptide': 112} Modifications used: {'COO': 1, 'NH1NOTPRO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 105} Chain: "B" Number of atoms: 12074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 12074 Classifications: {'RNA': 373} Modifications used: {'3*END': 1, '5*END': 1, 'rna2p_pur': 33, 'rna2p_pyr': 32, 'rna3p_pur': 185, 'rna3p_pyr': 123} Link IDs: {'rna2p': 64, 'rna3p': 308} Chain: "B" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Unusual residues: {' CA': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Residues with excluded nonbonded symmetry interactions: 47 residue: pdb=" P C B 20 " occ=0.00 ... (29 atoms not shown) pdb=" H6 C B 20 " occ=0.00 residue: pdb=" P C B 21 " occ=0.00 ... (29 atoms not shown) pdb=" H6 C B 21 " occ=0.00 residue: pdb=" P G B 22 " occ=0.00 ... (32 atoms not shown) pdb=" H22 G B 22 " occ=0.00 residue: pdb=" P C B 23 " occ=0.00 ... (29 atoms not shown) pdb=" H6 C B 23 " occ=0.00 residue: pdb=" P U B 24 " occ=0.00 ... (28 atoms not shown) pdb=" H6 U B 24 " occ=0.00 residue: pdb=" P U B 25 " occ=0.00 ... (28 atoms not shown) pdb=" H6 U B 25 " occ=0.00 residue: pdb=" P C B 26 " occ=0.00 ... (29 atoms not shown) pdb=" H6 C B 26 " occ=0.00 residue: pdb=" P G B 27 " occ=0.00 ... (32 atoms not shown) pdb=" H22 G B 27 " occ=0.00 residue: pdb=" P U B 28 " occ=0.00 ... (28 atoms not shown) pdb=" H6 U B 28 " occ=0.00 residue: pdb=" P C B 29 " occ=0.00 ... (29 atoms not shown) pdb=" H6 C B 29 " occ=0.00 residue: pdb=" P G B 30 " occ=0.00 ... (32 atoms not shown) pdb=" H22 G B 30 " occ=0.00 residue: pdb=" P U B 31 " occ=0.00 ... (28 atoms not shown) pdb=" H6 U B 31 " occ=0.00 ... (remaining 35 not shown) Time building chain proxies: 7.54, per 1000 atoms: 0.54 Number of scatterers: 13979 At special positions: 0 Unit cell: (89.7768, 120.107, 189.259, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 7 19.99 S 2 16.00 P 372 15.00 O 2730 8.00 N 1688 7.00 C 4156 6.00 H 5024 1.00 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: 3.29 Conformation dependent library (CDL) restraints added in 382.6 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: 5 helices and 1 sheets defined 45.5% alpha, 17.9% beta 96 base pairs and 146 stacking pairs defined. Time for finding SS restraints: 6.93 Creating SS restraints... Processing helix chain 'A' and resid 6 through 10 Processing helix chain 'A' and resid 13 through 23 removed outlier: 3.602A pdb=" N PHE A 17 " --> pdb=" O THR A 13 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL A 20 " --> pdb=" O GLN A 16 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLN A 23 " --> pdb=" O PHE A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 74 removed outlier: 3.934A pdb=" N ASN A 62 " --> pdb=" O ALA A 58 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N ILE A 64 " --> pdb=" O GLU A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 93 removed outlier: 4.302A pdb=" N ALA A 93 " --> pdb=" O LYS A 90 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 90 through 93' Processing helix chain 'A' and resid 96 through 109 removed outlier: 3.932A pdb=" N ALA A 103 " --> pdb=" O ALA A 99 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU A 105 " --> pdb=" O SER A 101 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LYS A 106 " --> pdb=" O GLU A 102 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 28 removed outlier: 6.511A pdb=" N ARG A 45 " --> pdb=" O PHE A 84 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N VAL A 86 " --> pdb=" O ARG A 45 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N GLY A 47 " --> pdb=" O VAL A 86 " (cutoff:3.500A) removed outlier: 8.698A pdb=" N ALA A 88 " --> pdb=" O GLY A 47 " (cutoff:3.500A) removed outlier: 8.415A pdb=" N THR A 49 " --> pdb=" O ALA A 88 " (cutoff:3.500A) 34 hydrogen bonds defined for protein. 93 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 253 hydrogen bonds 440 hydrogen bond angles 0 basepair planarities 96 basepair parallelities 146 stacking parallelities Total time for adding SS restraints: 5.17 Time building geometry restraints manager: 3.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.94 - 1.11: 5023 1.11 - 1.29: 488 1.29 - 1.46: 5570 1.46 - 1.64: 3868 1.64 - 1.81: 3 Bond restraints: 14952 Sorted by residual: bond pdb=" C5 C B 10 " pdb=" H5 C B 10 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.67e+01 bond pdb=" CD2 PHE A 84 " pdb=" HD2 PHE A 84 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.67e+01 bond pdb=" C5 C B 252 " pdb=" H5 C B 252 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.67e+01 bond pdb=" C2 A B 139 " pdb=" H2 A B 139 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.67e+01 bond pdb=" C6 C B 253 " pdb=" H6 C B 253 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.67e+01 ... (remaining 14947 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.22: 23959 3.22 - 6.44: 2518 6.44 - 9.66: 263 9.66 - 12.88: 23 12.88 - 16.10: 2 Bond angle restraints: 26765 Sorted by residual: angle pdb=" O3' G B 329 " pdb=" C3' G B 329 " pdb=" C2' G B 329 " ideal model delta sigma weight residual 109.50 125.60 -16.10 1.50e+00 4.44e-01 1.15e+02 angle pdb=" O3' G B 133 " pdb=" C3' G B 133 " pdb=" C2' G B 133 " ideal model delta sigma weight residual 109.50 123.51 -14.01 1.50e+00 4.44e-01 8.73e+01 angle pdb=" O4' G B 137 " pdb=" C1' G B 137 " pdb=" C2' G B 137 " ideal model delta sigma weight residual 107.60 98.64 8.96 1.00e+00 1.00e+00 8.03e+01 angle pdb=" C4' G B 175 " pdb=" O4' G B 175 " pdb=" C1' G B 175 " ideal model delta sigma weight residual 109.90 101.17 8.73 1.00e+00 1.00e+00 7.63e+01 angle pdb=" O3' A B 173 " pdb=" C3' A B 173 " pdb=" C2' A B 173 " ideal model delta sigma weight residual 109.50 121.88 -12.38 1.50e+00 4.44e-01 6.81e+01 ... (remaining 26760 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 6205 35.99 - 71.98: 1166 71.98 - 107.97: 169 107.97 - 143.96: 24 143.96 - 179.95: 42 Dihedral angle restraints: 7606 sinusoidal: 7232 harmonic: 374 Sorted by residual: dihedral pdb=" C5' A B 139 " pdb=" C4' A B 139 " pdb=" C3' A B 139 " pdb=" O3' A B 139 " ideal model delta sinusoidal sigma weight residual 147.00 61.67 85.33 1 8.00e+00 1.56e-02 1.38e+02 dihedral pdb=" C5' C B 122 " pdb=" C4' C B 122 " pdb=" C3' C B 122 " pdb=" O3' C B 122 " ideal model delta sinusoidal sigma weight residual 147.00 67.95 79.05 1 8.00e+00 1.56e-02 1.22e+02 dihedral pdb=" C5' A B 351 " pdb=" C4' A B 351 " pdb=" C3' A B 351 " pdb=" O3' A B 351 " ideal model delta sinusoidal sigma weight residual 147.00 68.43 78.57 1 8.00e+00 1.56e-02 1.20e+02 ... (remaining 7603 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.204: 1885 0.204 - 0.408: 90 0.408 - 0.611: 23 0.611 - 0.815: 4 0.815 - 1.019: 1 Chirality restraints: 2003 Sorted by residual: chirality pdb=" P C B 145 " pdb=" OP1 C B 145 " pdb=" OP2 C B 145 " pdb=" O5' C B 145 " both_signs ideal model delta sigma weight residual True 2.41 -1.39 1.02 2.00e-01 2.50e+01 2.59e+01 chirality pdb=" C3' G B 329 " pdb=" C4' G B 329 " pdb=" O3' G B 329 " pdb=" C2' G B 329 " both_signs ideal model delta sigma weight residual False -2.74 -1.94 -0.80 2.00e-01 2.50e+01 1.60e+01 chirality pdb=" C3' A B 192 " pdb=" C4' A B 192 " pdb=" O3' A B 192 " pdb=" C2' A B 192 " both_signs ideal model delta sigma weight residual False -2.74 -2.03 -0.72 2.00e-01 2.50e+01 1.29e+01 ... (remaining 2000 not shown) Planarity restraints: 960 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C B 145 " 0.971 2.00e-02 2.50e+03 3.80e-01 3.97e+03 pdb=" N1 C B 145 " -0.066 2.00e-02 2.50e+03 pdb=" C2 C B 145 " -0.167 2.00e-02 2.50e+03 pdb=" O2 C B 145 " -0.557 2.00e-02 2.50e+03 pdb=" N3 C B 145 " 0.079 2.00e-02 2.50e+03 pdb=" C4 C B 145 " 0.134 2.00e-02 2.50e+03 pdb=" N4 C B 145 " 0.343 2.00e-02 2.50e+03 pdb=" C5 C B 145 " -0.106 2.00e-02 2.50e+03 pdb=" C6 C B 145 " -0.216 2.00e-02 2.50e+03 pdb=" H5 C B 145 " -0.120 2.00e-02 2.50e+03 pdb=" H6 C B 145 " -0.295 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G B 336 " 0.672 2.00e-02 2.50e+03 2.38e-01 1.98e+03 pdb=" N9 G B 336 " -0.009 2.00e-02 2.50e+03 pdb=" C8 G B 336 " -0.141 2.00e-02 2.50e+03 pdb=" N7 G B 336 " -0.172 2.00e-02 2.50e+03 pdb=" C5 G B 336 " -0.097 2.00e-02 2.50e+03 pdb=" C6 G B 336 " 0.076 2.00e-02 2.50e+03 pdb=" O6 G B 336 " 0.282 2.00e-02 2.50e+03 pdb=" N1 G B 336 " 0.044 2.00e-02 2.50e+03 pdb=" C2 G B 336 " -0.167 2.00e-02 2.50e+03 pdb=" N2 G B 336 " -0.129 2.00e-02 2.50e+03 pdb=" N3 G B 336 " -0.246 2.00e-02 2.50e+03 pdb=" C4 G B 336 " -0.187 2.00e-02 2.50e+03 pdb=" H8 G B 336 " -0.121 2.00e-02 2.50e+03 pdb=" H1 G B 336 " 0.197 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G B 144 " 0.603 2.00e-02 2.50e+03 2.26e-01 1.78e+03 pdb=" N9 G B 144 " 0.017 2.00e-02 2.50e+03 pdb=" C8 G B 144 " -0.192 2.00e-02 2.50e+03 pdb=" N7 G B 144 " -0.149 2.00e-02 2.50e+03 pdb=" C5 G B 144 " -0.042 2.00e-02 2.50e+03 pdb=" C6 G B 144 " 0.119 2.00e-02 2.50e+03 pdb=" O6 G B 144 " 0.350 2.00e-02 2.50e+03 pdb=" N1 G B 144 " 0.061 2.00e-02 2.50e+03 pdb=" C2 G B 144 " -0.084 2.00e-02 2.50e+03 pdb=" N2 G B 144 " -0.250 2.00e-02 2.50e+03 pdb=" N3 G B 144 " -0.082 2.00e-02 2.50e+03 pdb=" C4 G B 144 " -0.078 2.00e-02 2.50e+03 pdb=" H8 G B 144 " -0.258 2.00e-02 2.50e+03 pdb=" H1 G B 144 " -0.013 2.00e-02 2.50e+03 ... (remaining 957 not shown) Histogram of nonbonded interaction distances: 1.45 - 2.08: 790 2.08 - 2.71: 14734 2.71 - 3.34: 35932 3.34 - 3.97: 54135 3.97 - 4.60: 74342 Nonbonded interactions: 179933 Sorted by model distance: nonbonded pdb="HO2' C B 343 " pdb=" H3' A B 344 " model vdw 1.453 2.270 nonbonded pdb="HO2' A B 181 " pdb=" OP2 A B 182 " model vdw 1.497 2.450 nonbonded pdb=" OP1 C B 145 " pdb="HO2' G B 147 " model vdw 1.562 2.450 nonbonded pdb="HO2' A B 193 " pdb=" OP1 G B 194 " model vdw 1.565 2.450 nonbonded pdb="HO2' G B 165 " pdb=" OP1 A B 166 " model vdw 1.566 2.450 ... (remaining 179928 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=0.00 max=1.00 mean=0.89 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.460 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.160 Extract box with map and model: 0.500 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 35.560 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5949 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 : 0.015 0.063 9928 Z= 0.873 Angle : 2.219 16.101 15291 Z= 1.426 Chirality : 0.120 1.019 2003 Planarity : 0.058 0.386 538 Dihedral : 31.483 179.953 6256 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 2.33 Ramachandran Plot: Outliers : 0.91 % Allowed : 6.36 % Favored : 92.73 % Rotamer: Outliers : 1.02 % Allowed : 10.20 % Favored : 88.78 % 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: -2.73 (0.76), residues: 110 helix: -3.09 (0.62), residues: 37 sheet: 1.09 (1.36), residues: 12 loop : -1.55 (0.83), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.021 TRP A 108 HIS 0.007 0.003 HIS A 59 PHE 0.043 0.012 PHE A 84 ARG 0.009 0.001 ARG A 75 *********************** 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 25 residues out of total 98 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 24 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 24 average time/residue: 0.8249 time to fit residues: 23.4405 Evaluate side-chains 17 residues out of total 98 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 17 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 40 optimal weight: 0.8980 chunk 36 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 22 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 43 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5847 moved from start: 0.3025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 9928 Z= 0.223 Angle : 1.025 9.777 15291 Z= 0.541 Chirality : 0.052 0.332 2003 Planarity : 0.006 0.037 538 Dihedral : 30.555 179.690 6011 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 17.42 Ramachandran Plot: Outliers : 0.91 % Allowed : 3.64 % Favored : 95.45 % Rotamer: Outliers : 1.02 % Allowed : 11.22 % 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: -2.84 (0.75), residues: 110 helix: -2.79 (0.52), residues: 54 sheet: 0.23 (1.07), residues: 19 loop : -1.20 (1.18), residues: 37 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 108 HIS 0.003 0.001 HIS A 111 PHE 0.015 0.002 PHE A 84 ARG 0.004 0.001 ARG A 109 *********************** 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 18 residues out of total 98 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 17 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 18 average time/residue: 0.8253 time to fit residues: 17.7918 Evaluate side-chains 14 residues out of total 98 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 13 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 7.9990 chunk 13 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 14 optimal weight: 10.0000 chunk 35 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6005 moved from start: 0.4105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 9928 Z= 0.424 Angle : 1.045 10.714 15291 Z= 0.534 Chirality : 0.055 0.363 2003 Planarity : 0.008 0.059 538 Dihedral : 30.739 178.994 6011 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 34.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.82 % Favored : 88.18 % Rotamer: Outliers : 3.06 % Allowed : 15.31 % 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: -3.74 (0.71), residues: 110 helix: -3.09 (0.52), residues: 54 sheet: -0.92 (1.00), residues: 19 loop : -1.95 (1.11), residues: 37 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.002 TRP A 108 HIS 0.012 0.004 HIS A 111 PHE 0.012 0.003 PHE A 84 ARG 0.011 0.001 ARG A 37 *********************** 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 18 residues out of total 98 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 15 time to evaluate : 0.447 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 18 average time/residue: 0.6426 time to fit residues: 14.2832 Evaluate side-chains 15 residues out of total 98 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 13 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 79 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 22 optimal weight: 6.9990 chunk 4 optimal weight: 0.4980 chunk 20 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 0 optimal weight: 0.8980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5927 moved from start: 0.4680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9928 Z= 0.230 Angle : 0.840 9.490 15291 Z= 0.437 Chirality : 0.044 0.299 2003 Planarity : 0.006 0.036 538 Dihedral : 30.419 179.806 6011 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 16.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer: Outliers : 2.04 % Allowed : 15.31 % Favored : 82.65 % 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: -3.04 (0.74), residues: 110 helix: -2.42 (0.60), residues: 54 sheet: -0.80 (1.06), residues: 19 loop : -1.66 (1.07), residues: 37 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 108 HIS 0.003 0.001 HIS A 111 PHE 0.017 0.002 PHE A 19 ARG 0.003 0.001 ARG A 37 *********************** 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 17 residues out of total 98 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 15 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.7961 (tp30) cc_final: 0.7041 (mm-30) REVERT: A 108 TRP cc_start: 0.7494 (OUTLIER) cc_final: 0.7264 (m-10) outliers start: 2 outliers final: 1 residues processed: 17 average time/residue: 0.7036 time to fit residues: 14.8803 Evaluate side-chains 17 residues out of total 98 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 15 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 108 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 34 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 39 optimal weight: 7.9990 chunk 32 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 15 optimal weight: 10.0000 chunk 9 optimal weight: 0.1980 chunk 27 optimal weight: 5.9990 overall best weight: 2.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6003 moved from start: 0.5134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 9928 Z= 0.336 Angle : 0.913 10.261 15291 Z= 0.468 Chirality : 0.048 0.336 2003 Planarity : 0.007 0.039 538 Dihedral : 30.585 179.229 6011 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 27.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.55 % Favored : 85.45 % Rotamer: Outliers : 3.06 % Allowed : 14.29 % Favored : 82.65 % 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: -3.39 (0.70), residues: 110 helix: -2.69 (0.54), residues: 54 sheet: -0.96 (1.01), residues: 19 loop : -1.85 (1.05), residues: 37 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 108 HIS 0.003 0.002 HIS A 111 PHE 0.009 0.002 PHE A 84 ARG 0.009 0.001 ARG A 37 *********************** 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 19 residues out of total 98 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 16 time to evaluate : 0.510 Fit side-chains revert: symmetry clash REVERT: A 82 MET cc_start: 0.8129 (mtp) cc_final: 0.7563 (mtp) REVERT: A 105 GLU cc_start: 0.7986 (tp30) cc_final: 0.7110 (mm-30) REVERT: A 108 TRP cc_start: 0.7566 (OUTLIER) cc_final: 0.7343 (m-10) outliers start: 3 outliers final: 2 residues processed: 19 average time/residue: 0.6287 time to fit residues: 15.0527 Evaluate side-chains 17 residues out of total 98 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 14 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 108 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 11 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 15 optimal weight: 10.0000 chunk 24 optimal weight: 7.9990 chunk 44 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 26 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5981 moved from start: 0.5645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 9928 Z= 0.292 Angle : 0.844 9.464 15291 Z= 0.435 Chirality : 0.045 0.313 2003 Planarity : 0.006 0.037 538 Dihedral : 30.447 179.588 6011 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 20.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.82 % Favored : 88.18 % Rotamer: Outliers : 4.08 % Allowed : 15.31 % Favored : 80.61 % 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: -3.36 (0.70), residues: 110 helix: -2.72 (0.56), residues: 52 sheet: -0.93 (1.01), residues: 19 loop : -1.85 (0.99), residues: 39 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 108 HIS 0.004 0.002 HIS A 111 PHE 0.022 0.003 PHE A 19 ARG 0.006 0.001 ARG A 37 *********************** 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 19 residues out of total 98 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 15 time to evaluate : 0.484 Fit side-chains revert: symmetry clash REVERT: A 105 GLU cc_start: 0.7947 (tp30) cc_final: 0.7127 (mm-30) outliers start: 4 outliers final: 3 residues processed: 19 average time/residue: 0.6292 time to fit residues: 14.8956 Evaluate side-chains 18 residues out of total 98 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 15 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 79 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 26 optimal weight: 5.9990 chunk 39 optimal weight: 7.9990 chunk 25 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 chunk 8 optimal weight: 0.7980 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5984 moved from start: 0.6061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 9928 Z= 0.271 Angle : 0.820 9.251 15291 Z= 0.423 Chirality : 0.044 0.301 2003 Planarity : 0.006 0.036 538 Dihedral : 30.393 179.046 6011 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 21.60 Ramachandran Plot: Outliers : 0.91 % Allowed : 8.18 % Favored : 90.91 % Rotamer: Outliers : 3.06 % Allowed : 17.35 % Favored : 79.59 % 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: -3.59 (0.69), residues: 110 helix: -2.56 (0.57), residues: 48 sheet: -1.28 (1.06), residues: 21 loop : -2.50 (0.93), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 108 HIS 0.005 0.002 HIS A 77 PHE 0.039 0.003 PHE A 19 ARG 0.008 0.001 ARG A 37 *********************** 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 18 residues out of total 98 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 15 time to evaluate : 0.480 Fit side-chains REVERT: A 82 MET cc_start: 0.8103 (mtp) cc_final: 0.7608 (mtp) REVERT: A 105 GLU cc_start: 0.7902 (tp30) cc_final: 0.7097 (mm-30) outliers start: 3 outliers final: 3 residues processed: 18 average time/residue: 0.6422 time to fit residues: 14.3909 Evaluate side-chains 17 residues out of total 98 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 14 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 79 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 29 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 22 optimal weight: 7.9990 chunk 4 optimal weight: 0.5980 chunk 36 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6011 moved from start: 0.6326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 9928 Z= 0.317 Angle : 0.859 9.019 15291 Z= 0.440 Chirality : 0.045 0.320 2003 Planarity : 0.006 0.036 538 Dihedral : 30.415 178.390 6011 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 24.08 Ramachandran Plot: Outliers : 0.91 % Allowed : 10.91 % Favored : 88.18 % Rotamer: Outliers : 3.06 % Allowed : 17.35 % Favored : 79.59 % 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: -3.55 (0.72), residues: 110 helix: -2.49 (0.62), residues: 46 sheet: -1.27 (1.07), residues: 21 loop : -2.56 (0.94), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 108 HIS 0.006 0.002 HIS A 77 PHE 0.008 0.002 PHE A 84 ARG 0.009 0.001 ARG A 37 *********************** 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 19 residues out of total 98 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 16 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.7993 (mtp) cc_final: 0.7471 (mtp) REVERT: A 105 GLU cc_start: 0.7947 (tp30) cc_final: 0.7131 (mm-30) REVERT: A 110 ARG cc_start: 0.7315 (ttm170) cc_final: 0.7000 (ttp80) outliers start: 3 outliers final: 3 residues processed: 19 average time/residue: 0.6147 time to fit residues: 14.5760 Evaluate side-chains 18 residues out of total 98 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 15 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 79 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 33 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6048 moved from start: 0.6582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 9928 Z= 0.397 Angle : 0.943 9.165 15291 Z= 0.477 Chirality : 0.049 0.341 2003 Planarity : 0.007 0.038 538 Dihedral : 30.618 179.900 6011 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 31.71 Ramachandran Plot: Outliers : 0.91 % Allowed : 14.55 % Favored : 84.55 % Rotamer: Outliers : 3.06 % Allowed : 17.35 % Favored : 79.59 % 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: -4.10 (0.68), residues: 110 helix: -2.96 (0.54), residues: 48 sheet: -1.26 (1.07), residues: 21 loop : -2.97 (0.92), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 108 HIS 0.006 0.002 HIS A 77 PHE 0.009 0.002 PHE A 84 ARG 0.008 0.001 ARG A 37 *********************** 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 19 residues out of total 98 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 16 time to evaluate : 0.472 Fit side-chains revert: symmetry clash REVERT: A 82 MET cc_start: 0.8043 (mtp) cc_final: 0.7540 (mtp) REVERT: A 105 GLU cc_start: 0.7980 (tp30) cc_final: 0.7178 (mm-30) outliers start: 3 outliers final: 3 residues processed: 19 average time/residue: 0.7653 time to fit residues: 17.6189 Evaluate side-chains 19 residues out of total 98 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 16 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 79 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 44 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 29 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6008 moved from start: 0.6687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 9928 Z= 0.283 Angle : 0.833 9.028 15291 Z= 0.428 Chirality : 0.044 0.311 2003 Planarity : 0.006 0.039 538 Dihedral : 30.436 179.427 6011 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 22.24 Ramachandran Plot: Outliers : 0.91 % Allowed : 11.82 % Favored : 87.27 % Rotamer: Outliers : 2.04 % Allowed : 20.41 % Favored : 77.55 % 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: -3.59 (0.71), residues: 110 helix: -2.57 (0.59), residues: 46 sheet: -0.96 (1.15), residues: 21 loop : -2.73 (0.92), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 108 HIS 0.004 0.001 HIS A 77 PHE 0.008 0.002 PHE A 84 ARG 0.005 0.001 ARG A 37 ********************** 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 18 residues out of total 98 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 16 time to evaluate : 0.465 Fit side-chains revert: symmetry clash REVERT: A 82 MET cc_start: 0.7974 (mtp) cc_final: 0.7448 (mtp) REVERT: A 105 GLU cc_start: 0.7933 (tp30) cc_final: 0.7121 (mm-30) REVERT: A 109 ARG cc_start: 0.8532 (tpp80) cc_final: 0.8280 (tmm160) outliers start: 2 outliers final: 2 residues processed: 18 average time/residue: 0.7109 time to fit residues: 15.7104 Evaluate side-chains 18 residues out of total 98 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 16 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 79 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 38 optimal weight: 3.9990 chunk 15 optimal weight: 9.9990 chunk 39 optimal weight: 6.9990 chunk 4 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 33 optimal weight: 5.9990 chunk 2 optimal weight: 0.9980 chunk 27 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- 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 = 0.4492 r_free = 0.4492 target = 0.118743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.104520 restraints weight = 115364.922| |-----------------------------------------------------------------------------| r_work (start): 0.4037 rms_B_bonded: 1.63 r_work: 0.3873 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6558 moved from start: 0.7083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 9928 Z= 0.275 Angle : 0.796 8.659 15291 Z= 0.410 Chirality : 0.042 0.306 2003 Planarity : 0.006 0.041 538 Dihedral : 30.318 178.867 6011 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 20.47 Ramachandran Plot: Outliers : 0.91 % Allowed : 9.09 % Favored : 90.00 % Rotamer: Outliers : 2.04 % Allowed : 20.41 % Favored : 77.55 % 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: -3.47 (0.72), residues: 110 helix: -2.43 (0.59), residues: 46 sheet: -0.80 (1.22), residues: 21 loop : -2.77 (0.91), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 108 HIS 0.003 0.001 HIS A 77 PHE 0.011 0.002 PHE A 19 ARG 0.004 0.001 ARG A 109 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5081.38 seconds wall clock time: 91 minutes 42.94 seconds (5502.94 seconds total)