Starting phenix.real_space_refine on Fri Sep 27 14:42:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uo1_26637/09_2024/7uo1_26637.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uo1_26637/09_2024/7uo1_26637.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uo1_26637/09_2024/7uo1_26637.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uo1_26637/09_2024/7uo1_26637.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uo1_26637/09_2024/7uo1_26637.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uo1_26637/09_2024/7uo1_26637.cif" } resolution = 3.2 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 ------------------------------------------------------------------------------- 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= 1.000 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 10 9.91 5 P 454 5.49 5 S 2 5.16 5 C 4934 2.51 5 N 1993 2.21 5 O 3301 1.98 5 H 5894 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 16588 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 12071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 12071 Classifications: {'RNA': 373} Modifications used: {'3*END': 1, '5*END': 1, 'rna2p_pur': 25, 'rna2p_pyr': 26, 'rna3p_pur': 191, 'rna3p_pyr': 128} Link IDs: {'rna2p': 51, 'rna3p': 321} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 2622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 2622 Classifications: {'RNA': 82} Modifications used: {'3*END': 1, 'rna2p_pur': 3, 'rna2p_pyr': 6, 'rna3p_pur': 37, 'rna3p_pyr': 36} Link IDs: {'rna2p': 8, 'rna3p': 73} Chain: "A" Number of atoms: 1885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 1885 Classifications: {'peptide': 112} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 105} Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Unusual residues: {' CA': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Residues with excluded nonbonded symmetry interactions: 46 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 34 not shown) Time building chain proxies: 9.29, per 1000 atoms: 0.56 Number of scatterers: 16588 At special positions: 0 Unit cell: (99.6826, 116.048, 196.39, 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 10 19.99 S 2 16.00 P 454 15.00 O 3301 8.00 N 1993 7.00 C 4934 6.00 H 5894 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: 3.97 Conformation dependent library (CDL) restraints added in 592.9 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 45.5% alpha, 13.4% beta 109 base pairs and 164 stacking pairs defined. Time for finding SS restraints: 8.95 Creating SS restraints... Processing helix chain 'A' and resid 5 through 9 Processing helix chain 'A' and resid 12 through 21 removed outlier: 3.528A pdb=" N PHE A 16 " --> pdb=" O THR A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 74 Processing helix chain 'A' and resid 95 through 111 Processing sheet with id=AA1, first strand: chain 'A' and resid 24 through 27 45 hydrogen bonds defined for protein. 126 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 294 hydrogen bonds 544 hydrogen bond angles 0 basepair planarities 109 basepair parallelities 164 stacking parallelities Total time for adding SS restraints: 6.18 Time building geometry restraints manager: 4.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 5893 1.03 - 1.22: 78 1.22 - 1.42: 5415 1.42 - 1.61: 6364 1.61 - 1.81: 11 Bond restraints: 17761 Sorted by residual: bond pdb=" C1' C B 35 " pdb=" N1 C B 35 " ideal model delta sigma weight residual 1.470 1.493 -0.023 1.50e-02 4.44e+03 2.39e+00 bond pdb=" C1' C B 131 " pdb=" N1 C B 131 " ideal model delta sigma weight residual 1.470 1.491 -0.021 1.50e-02 4.44e+03 1.90e+00 bond pdb=" C1' C B 343 " pdb=" N1 C B 343 " ideal model delta sigma weight residual 1.470 1.489 -0.019 1.50e-02 4.44e+03 1.60e+00 bond pdb=" C1' A C 14 " pdb=" N9 A C 14 " ideal model delta sigma weight residual 1.465 1.484 -0.019 1.50e-02 4.44e+03 1.58e+00 bond pdb=" C3' G B 64 " pdb=" O3' G B 64 " ideal model delta sigma weight residual 1.417 1.435 -0.018 1.50e-02 4.44e+03 1.41e+00 ... (remaining 17756 not shown) Histogram of bond angle deviations from ideal: 0.00 - 17.92: 31738 17.92 - 35.84: 5 35.84 - 53.77: 0 53.77 - 71.69: 0 71.69 - 89.61: 42 Bond angle restraints: 31785 Sorted by residual: angle pdb=" O3' U B 299 " pdb=" P G B 300 " pdb=" OP1 G B 300 " ideal model delta sigma weight residual 108.00 18.39 89.61 3.00e+00 1.11e-01 8.92e+02 angle pdb=" O3' C B 9 " pdb=" P C B 10 " pdb=" OP1 C B 10 " ideal model delta sigma weight residual 108.00 18.82 89.18 3.00e+00 1.11e-01 8.84e+02 angle pdb=" O3' A B 13 " pdb=" P C B 14 " pdb=" OP1 C B 14 " ideal model delta sigma weight residual 108.00 18.84 89.16 3.00e+00 1.11e-01 8.83e+02 angle pdb=" O3' C C 75 " pdb=" P C C 76 " pdb=" OP1 C C 76 " ideal model delta sigma weight residual 108.00 19.12 88.88 3.00e+00 1.11e-01 8.78e+02 angle pdb=" O3' G B 19 " pdb=" P C B 20 " pdb=" OP1 C B 20 " ideal model delta sigma weight residual 108.00 19.22 88.78 3.00e+00 1.11e-01 8.76e+02 ... (remaining 31780 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 36.00: 7509 36.00 - 72.00: 1257 72.00 - 108.00: 177 108.00 - 143.99: 53 143.99 - 179.99: 52 Dihedral angle restraints: 9048 sinusoidal: 8675 harmonic: 373 Sorted by residual: dihedral pdb=" C4' G B 101 " pdb=" C3' G B 101 " pdb=" C2' G B 101 " pdb=" C1' G B 101 " ideal model delta sinusoidal sigma weight residual -35.00 36.25 -71.25 1 8.00e+00 1.56e-02 1.02e+02 dihedral pdb=" C4' A B 351 " pdb=" C3' A B 351 " pdb=" C2' A B 351 " pdb=" C1' A B 351 " ideal model delta sinusoidal sigma weight residual -35.00 36.20 -71.20 1 8.00e+00 1.56e-02 1.02e+02 dihedral pdb=" C4' G B 332 " pdb=" C3' G B 332 " pdb=" C2' G B 332 " pdb=" C1' G B 332 " ideal model delta sinusoidal sigma weight residual -35.00 35.79 -70.79 1 8.00e+00 1.56e-02 1.01e+02 ... (remaining 9045 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.115: 2096 0.115 - 0.231: 83 0.231 - 0.346: 200 0.346 - 0.461: 23 0.461 - 0.577: 8 Chirality restraints: 2410 Sorted by residual: chirality pdb=" P A B 233 " pdb=" OP1 A B 233 " pdb=" OP2 A B 233 " pdb=" O5' A B 233 " both_signs ideal model delta sigma weight residual True 2.41 2.99 -0.58 2.00e-01 2.50e+01 8.31e+00 chirality pdb=" P C B 20 " pdb=" OP1 C B 20 " pdb=" OP2 C B 20 " pdb=" O5' C B 20 " both_signs ideal model delta sigma weight residual True 2.41 -2.95 -0.54 2.00e-01 2.50e+01 7.17e+00 chirality pdb=" P C B 14 " pdb=" OP1 C B 14 " pdb=" OP2 C B 14 " pdb=" O5' C B 14 " both_signs ideal model delta sigma weight residual True 2.41 -2.93 -0.52 2.00e-01 2.50e+01 6.88e+00 ... (remaining 2407 not shown) Planarity restraints: 1097 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C B 35 " -0.030 2.00e-02 2.50e+03 1.54e-02 6.50e+00 pdb=" N1 C B 35 " 0.031 2.00e-02 2.50e+03 pdb=" C2 C B 35 " -0.018 2.00e-02 2.50e+03 pdb=" O2 C B 35 " 0.019 2.00e-02 2.50e+03 pdb=" N3 C B 35 " -0.001 2.00e-02 2.50e+03 pdb=" C4 C B 35 " -0.004 2.00e-02 2.50e+03 pdb=" N4 C B 35 " -0.005 2.00e-02 2.50e+03 pdb=" C5 C B 35 " -0.000 2.00e-02 2.50e+03 pdb=" C6 C B 35 " 0.003 2.00e-02 2.50e+03 pdb=" H5 C B 35 " -0.000 2.00e-02 2.50e+03 pdb=" H6 C B 35 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G B 106 " -0.008 2.00e-02 2.50e+03 1.18e-02 4.87e+00 pdb=" N9 G B 106 " 0.004 2.00e-02 2.50e+03 pdb=" C8 G B 106 " 0.001 2.00e-02 2.50e+03 pdb=" N7 G B 106 " -0.001 2.00e-02 2.50e+03 pdb=" C5 G B 106 " 0.002 2.00e-02 2.50e+03 pdb=" C6 G B 106 " 0.009 2.00e-02 2.50e+03 pdb=" O6 G B 106 " -0.012 2.00e-02 2.50e+03 pdb=" N1 G B 106 " -0.006 2.00e-02 2.50e+03 pdb=" C2 G B 106 " 0.033 2.00e-02 2.50e+03 pdb=" N2 G B 106 " -0.022 2.00e-02 2.50e+03 pdb=" N3 G B 106 " 0.001 2.00e-02 2.50e+03 pdb=" C4 G B 106 " -0.002 2.00e-02 2.50e+03 pdb=" H8 G B 106 " -0.003 2.00e-02 2.50e+03 pdb=" H1 G B 106 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C C 76 " -0.018 2.00e-02 2.50e+03 1.26e-02 4.37e+00 pdb=" N1 C C 76 " 0.018 2.00e-02 2.50e+03 pdb=" C2 C C 76 " -0.025 2.00e-02 2.50e+03 pdb=" O2 C C 76 " 0.019 2.00e-02 2.50e+03 pdb=" N3 C C 76 " 0.004 2.00e-02 2.50e+03 pdb=" C4 C C 76 " -0.007 2.00e-02 2.50e+03 pdb=" N4 C C 76 " -0.002 2.00e-02 2.50e+03 pdb=" C5 C C 76 " -0.000 2.00e-02 2.50e+03 pdb=" C6 C C 76 " 0.003 2.00e-02 2.50e+03 pdb=" H5 C C 76 " 0.002 2.00e-02 2.50e+03 pdb=" H6 C C 76 " 0.005 2.00e-02 2.50e+03 ... (remaining 1094 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.21: 1249 2.21 - 2.81: 22703 2.81 - 3.41: 39051 3.41 - 4.00: 52292 4.00 - 4.60: 76175 Nonbonded interactions: 191470 Sorted by model distance: nonbonded pdb=" O6 G B 52 " pdb=" H ARG A 6 " model vdw 1.615 2.450 nonbonded pdb="HO2' C B 138 " pdb=" O5' A B 139 " model vdw 1.618 2.450 nonbonded pdb="HO2' G B 84 " pdb=" O5' C B 85 " model vdw 1.632 2.450 nonbonded pdb=" H62 A B 81 " pdb=" O2' G B 280 " model vdw 1.635 2.450 nonbonded pdb="HO2' C B 35 " pdb=" OP2 C B 36 " model vdw 1.638 2.450 ... (remaining 191465 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=0.91 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: 0.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.240 Extract box with map and model: 0.740 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 43.730 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.060 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:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5258 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 11867 Z= 0.144 Angle : 4.427 89.611 18304 Z= 1.518 Chirality : 0.099 0.577 2410 Planarity : 0.003 0.023 619 Dihedral : 31.568 179.992 7521 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 2.73 % Allowed : 4.55 % Favored : 92.73 % Rotamer: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.82), residues: 110 helix: 2.24 (0.74), residues: 46 sheet: -1.81 (0.82), residues: 30 loop : -1.24 (1.17), residues: 34 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP A 107 HIS 0.002 0.000 HIS A 58 PHE 0.003 0.000 PHE A 20 ARG 0.001 0.000 ARG A 56 *********************** 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 **************************** Residue LYS 1 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Evaluate side-chains 41 residues out of total 98 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.542 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 40 LEU cc_start: 0.7949 (mm) cc_final: 0.7599 (mm) REVERT: A 72 ARG cc_start: 0.6821 (tpt90) cc_final: 0.6203 (tpt90) outliers start: 0 outliers final: 0 residues processed: 41 average time/residue: 0.5787 time to fit residues: 30.3040 Evaluate side-chains 34 residues out of total 98 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 47 optimal weight: 0.0070 chunk 42 optimal weight: 10.0000 chunk 23 optimal weight: 8.9990 chunk 14 optimal weight: 10.0000 chunk 28 optimal weight: 9.9990 chunk 22 optimal weight: 10.0000 chunk 43 optimal weight: 10.0000 chunk 16 optimal weight: 20.0000 chunk 26 optimal weight: 20.0000 chunk 32 optimal weight: 8.9990 chunk 50 optimal weight: 6.9990 overall best weight: 7.0006 ------------------------------------------------------------------------------- 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: 0.6379 moved from start: 0.5140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 11867 Z= 0.410 Angle : 1.986 31.594 18304 Z= 0.780 Chirality : 0.246 2.247 2410 Planarity : 0.007 0.051 619 Dihedral : 31.555 179.930 7276 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 24.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 4.08 % Allowed : 13.27 % 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: -0.43 (0.81), residues: 110 helix: 0.94 (0.71), residues: 46 sheet: -1.15 (0.91), residues: 21 loop : -1.07 (1.13), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.004 TRP A 107 HIS 0.008 0.003 HIS A 42 PHE 0.016 0.004 PHE A 71 ARG 0.009 0.002 ARG A 6 *********************** 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 **************************** Residue LYS 1 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Evaluate side-chains 37 residues out of total 98 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 33 time to evaluate : 0.552 Fit side-chains revert: symmetry clash REVERT: A 28 THR cc_start: 0.7416 (p) cc_final: 0.7193 (p) REVERT: A 72 ARG cc_start: 0.6871 (tpt90) cc_final: 0.4638 (tpt90) REVERT: A 93 ASP cc_start: 0.8285 (p0) cc_final: 0.8069 (p0) outliers start: 4 outliers final: 4 residues processed: 34 average time/residue: 0.6873 time to fit residues: 29.0367 Evaluate side-chains 34 residues out of total 98 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 30 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 95 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 28 optimal weight: 9.9990 chunk 15 optimal weight: 30.0000 chunk 42 optimal weight: 9.9990 chunk 34 optimal weight: 7.9990 chunk 14 optimal weight: 9.9990 chunk 50 optimal weight: 0.7980 chunk 55 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 17 optimal weight: 7.9990 chunk 40 optimal weight: 40.0000 chunk 38 optimal weight: 9.9990 overall best weight: 5.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6485 moved from start: 0.6264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 11867 Z= 0.294 Angle : 1.917 31.436 18304 Z= 0.719 Chirality : 0.233 2.053 2410 Planarity : 0.006 0.046 619 Dihedral : 31.405 179.538 7276 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 15.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % 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: -0.14 (0.84), residues: 110 helix: 1.73 (0.72), residues: 46 sheet: -1.35 (0.90), residues: 21 loop : -1.43 (1.16), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP A 107 HIS 0.010 0.003 HIS A 58 PHE 0.012 0.002 PHE A 4 ARG 0.006 0.001 ARG A 97 *********************** 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 **************************** Residue LYS 1 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Evaluate side-chains 32 residues out of total 98 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 28 time to evaluate : 0.614 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 72 ARG cc_start: 0.6863 (tpt90) cc_final: 0.4592 (tpt90) REVERT: A 86 VAL cc_start: 0.6842 (OUTLIER) cc_final: 0.6593 (m) outliers start: 4 outliers final: 3 residues processed: 29 average time/residue: 0.6616 time to fit residues: 24.3011 Evaluate side-chains 31 residues out of total 98 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 27 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 110 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 26 optimal weight: 20.0000 chunk 5 optimal weight: 10.0000 chunk 24 optimal weight: 6.9990 chunk 34 optimal weight: 10.0000 chunk 51 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 48 optimal weight: 6.9990 chunk 14 optimal weight: 10.0000 chunk 45 optimal weight: 5.9990 chunk 30 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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: 0.6563 moved from start: 0.7268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 11867 Z= 0.296 Angle : 1.876 29.776 18304 Z= 0.709 Chirality : 0.240 2.112 2410 Planarity : 0.006 0.045 619 Dihedral : 31.418 179.941 7276 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 17.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 6.12 % Allowed : 14.29 % 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: -0.32 (0.83), residues: 110 helix: 1.63 (0.71), residues: 46 sheet: -1.44 (0.91), residues: 21 loop : -1.60 (1.13), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.003 TRP A 107 HIS 0.009 0.003 HIS A 58 PHE 0.007 0.002 PHE A 71 ARG 0.016 0.001 ARG A 97 *********************** 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 **************************** Residue LYS 1 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Evaluate side-chains 34 residues out of total 98 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 28 time to evaluate : 0.590 Fit side-chains REVERT: A 72 ARG cc_start: 0.6981 (tpt90) cc_final: 0.4667 (tpt90) outliers start: 6 outliers final: 4 residues processed: 30 average time/residue: 0.6559 time to fit residues: 24.6595 Evaluate side-chains 32 residues out of total 98 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 28 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 95 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 40 optimal weight: 40.0000 chunk 22 optimal weight: 9.9990 chunk 46 optimal weight: 3.9990 chunk 37 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 27 optimal weight: 10.0000 chunk 48 optimal weight: 3.9990 chunk 13 optimal weight: 10.0000 chunk 18 optimal weight: 10.0000 chunk 10 optimal weight: 7.9990 chunk 31 optimal weight: 7.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- 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: 0.6649 moved from start: 0.8084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 11867 Z= 0.363 Angle : 1.924 30.946 18304 Z= 0.730 Chirality : 0.236 2.086 2410 Planarity : 0.007 0.063 619 Dihedral : 31.523 179.328 7276 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 22.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 7.14 % Allowed : 15.31 % 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: -1.13 (0.79), residues: 110 helix: 0.86 (0.70), residues: 46 sheet: -1.57 (0.90), residues: 21 loop : -2.09 (1.05), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.004 TRP A 107 HIS 0.012 0.003 HIS A 58 PHE 0.009 0.003 PHE A 83 ARG 0.006 0.001 ARG A 97 *********************** 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 **************************** Residue LYS 1 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Evaluate side-chains 37 residues out of total 98 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 30 time to evaluate : 0.598 Fit side-chains revert: symmetry clash REVERT: A 72 ARG cc_start: 0.6992 (tpt90) cc_final: 0.4697 (tpt90) outliers start: 7 outliers final: 5 residues processed: 31 average time/residue: 0.6738 time to fit residues: 26.1878 Evaluate side-chains 34 residues out of total 98 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 29 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 73 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 13 optimal weight: 10.0000 chunk 54 optimal weight: 5.9990 chunk 44 optimal weight: 9.9990 chunk 25 optimal weight: 10.0000 chunk 4 optimal weight: 50.0000 chunk 17 optimal weight: 9.9990 chunk 28 optimal weight: 9.9990 chunk 52 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 chunk 30 optimal weight: 5.9990 chunk 39 optimal weight: 20.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- 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: 0.6662 moved from start: 0.8685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 11867 Z= 0.364 Angle : 1.901 30.109 18304 Z= 0.722 Chirality : 0.239 2.084 2410 Planarity : 0.007 0.045 619 Dihedral : 31.525 178.031 7276 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 22.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 4.08 % Allowed : 18.37 % 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: -1.47 (0.79), residues: 110 helix: 0.50 (0.69), residues: 46 sheet: -1.69 (0.91), residues: 21 loop : -2.20 (1.07), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.003 TRP A 107 HIS 0.009 0.003 HIS A 58 PHE 0.010 0.003 PHE A 71 ARG 0.009 0.001 ARG A 97 *********************** 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 **************************** Residue LYS 1 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Evaluate side-chains 36 residues out of total 98 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 32 time to evaluate : 0.661 Fit side-chains REVERT: A 9 ARG cc_start: 0.7452 (mtt180) cc_final: 0.7252 (mtt180) REVERT: A 72 ARG cc_start: 0.6963 (tpt90) cc_final: 0.4609 (tpt90) REVERT: A 109 ARG cc_start: 0.7093 (tpt90) cc_final: 0.6860 (tpt90) outliers start: 4 outliers final: 4 residues processed: 33 average time/residue: 0.6870 time to fit residues: 28.3574 Evaluate side-chains 36 residues out of total 98 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 32 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 63 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 30 optimal weight: 6.9990 chunk 45 optimal weight: 0.0980 chunk 53 optimal weight: 4.9990 chunk 33 optimal weight: 6.9990 chunk 32 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 21 optimal weight: 8.9990 chunk 16 optimal weight: 20.0000 chunk 10 optimal weight: 6.9990 chunk 34 optimal weight: 8.9990 chunk 36 optimal weight: 8.9990 overall best weight: 4.8188 ------------------------------------------------------------------------------- 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: 0.6632 moved from start: 0.8703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 11867 Z= 0.288 Angle : 1.869 29.894 18304 Z= 0.702 Chirality : 0.239 2.098 2410 Planarity : 0.006 0.043 619 Dihedral : 31.412 178.522 7276 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 18.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer: Outliers : 4.08 % Allowed : 19.39 % 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: -1.04 (0.80), residues: 110 helix: 1.14 (0.72), residues: 46 sheet: -1.63 (0.93), residues: 21 loop : -2.24 (1.02), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.003 TRP A 107 HIS 0.009 0.002 HIS A 58 PHE 0.008 0.002 PHE A 18 ARG 0.006 0.001 ARG A 97 *********************** 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 **************************** Residue LYS 1 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Evaluate side-chains 33 residues out of total 98 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 29 time to evaluate : 0.636 Fit side-chains revert: symmetry clash REVERT: A 72 ARG cc_start: 0.6891 (tpt90) cc_final: 0.4649 (tpt90) outliers start: 4 outliers final: 4 residues processed: 30 average time/residue: 0.6389 time to fit residues: 24.2993 Evaluate side-chains 33 residues out of total 98 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 29 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 63 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 26 optimal weight: 20.0000 chunk 5 optimal weight: 9.9990 chunk 42 optimal weight: 9.9990 chunk 49 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 30 optimal weight: 6.9990 chunk 21 optimal weight: 8.9990 chunk 39 optimal weight: 20.0000 chunk 15 optimal weight: 20.0000 overall best weight: 2.5386 ------------------------------------------------------------------------------- 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: 0.6547 moved from start: 0.8517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 11867 Z= 0.181 Angle : 1.821 28.604 18304 Z= 0.675 Chirality : 0.240 2.155 2410 Planarity : 0.005 0.028 619 Dihedral : 31.209 179.386 7276 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 4.08 % Allowed : 19.39 % 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: -0.01 (0.85), residues: 110 helix: 2.38 (0.75), residues: 46 sheet: -1.39 (0.97), residues: 21 loop : -2.03 (1.06), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP A 107 HIS 0.006 0.002 HIS A 58 PHE 0.009 0.002 PHE A 18 ARG 0.004 0.001 ARG A 97 *********************** 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 **************************** Residue LYS 1 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Evaluate side-chains 35 residues out of total 98 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 31 time to evaluate : 0.570 Fit side-chains revert: symmetry clash REVERT: A 72 ARG cc_start: 0.6841 (tpt90) cc_final: 0.4568 (tpt90) REVERT: A 109 ARG cc_start: 0.7140 (tpt90) cc_final: 0.6896 (tpt90) outliers start: 4 outliers final: 4 residues processed: 31 average time/residue: 0.7014 time to fit residues: 27.1378 Evaluate side-chains 35 residues out of total 98 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 31 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 63 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 45 optimal weight: 0.2980 chunk 47 optimal weight: 6.9990 chunk 50 optimal weight: 5.9990 chunk 33 optimal weight: 7.9990 chunk 53 optimal weight: 2.9990 chunk 32 optimal weight: 8.9990 chunk 25 optimal weight: 9.9990 chunk 36 optimal weight: 9.9990 chunk 55 optimal weight: 4.9990 chunk 51 optimal weight: 0.5980 chunk 44 optimal weight: 10.0000 overall best weight: 2.9786 ------------------------------------------------------------------------------- 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: 0.6569 moved from start: 0.8559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 11867 Z= 0.204 Angle : 1.831 28.922 18304 Z= 0.679 Chirality : 0.239 2.131 2410 Planarity : 0.005 0.030 619 Dihedral : 31.202 179.119 7276 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 4.08 % Allowed : 20.41 % Favored : 75.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.87), residues: 110 helix: 2.54 (0.77), residues: 46 sheet: -1.32 (0.97), residues: 21 loop : -1.78 (1.09), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP A 107 HIS 0.006 0.002 HIS A 58 PHE 0.010 0.002 PHE A 18 ARG 0.005 0.001 ARG A 97 *********************** 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 **************************** Residue LYS 1 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Evaluate side-chains 33 residues out of total 98 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 29 time to evaluate : 0.631 Fit side-chains revert: symmetry clash REVERT: A 72 ARG cc_start: 0.6870 (tpt90) cc_final: 0.4593 (tpt90) outliers start: 4 outliers final: 4 residues processed: 30 average time/residue: 0.6482 time to fit residues: 24.6857 Evaluate side-chains 33 residues out of total 98 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 29 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 63 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 4 optimal weight: 50.0000 chunk 34 optimal weight: 10.0000 chunk 27 optimal weight: 10.0000 chunk 35 optimal weight: 6.9990 chunk 47 optimal weight: 0.9980 chunk 13 optimal weight: 9.9990 chunk 40 optimal weight: 40.0000 chunk 6 optimal weight: 2.9990 chunk 12 optimal weight: 10.0000 chunk 44 optimal weight: 9.9990 chunk 18 optimal weight: 10.0000 overall best weight: 6.1988 ------------------------------------------------------------------------------- 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: 0.6676 moved from start: 0.9058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 11867 Z= 0.357 Angle : 1.902 30.145 18304 Z= 0.720 Chirality : 0.238 2.063 2410 Planarity : 0.007 0.057 619 Dihedral : 31.465 178.854 7276 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 21.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 4.08 % Allowed : 20.41 % Favored : 75.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.81), residues: 110 helix: 1.37 (0.74), residues: 46 sheet: -1.51 (0.95), residues: 21 loop : -2.09 (1.02), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.003 TRP A 107 HIS 0.009 0.003 HIS A 58 PHE 0.008 0.003 PHE A 18 ARG 0.006 0.001 ARG A 36 ********************** 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 **************************** Residue LYS 1 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Evaluate side-chains 35 residues out of total 98 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 31 time to evaluate : 0.610 Fit side-chains revert: symmetry clash REVERT: A 72 ARG cc_start: 0.6922 (tpt90) cc_final: 0.4662 (tpt90) REVERT: A 108 ARG cc_start: 0.6879 (ttt90) cc_final: 0.6616 (tpm170) outliers start: 4 outliers final: 4 residues processed: 32 average time/residue: 0.6066 time to fit residues: 24.7904 Evaluate side-chains 33 residues out of total 98 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 29 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 63 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 45 optimal weight: 0.5980 chunk 5 optimal weight: 9.9990 chunk 8 optimal weight: 9.9990 chunk 39 optimal weight: 20.0000 chunk 2 optimal weight: 4.9990 chunk 32 optimal weight: 7.9990 chunk 50 optimal weight: 0.8980 chunk 29 optimal weight: 10.0000 chunk 38 optimal weight: 9.9990 chunk 1 optimal weight: 7.9990 chunk 35 optimal weight: 3.9990 overall best weight: 3.6986 ------------------------------------------------------------------------------- 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 = 0.4680 r_free = 0.4680 target = 0.241168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.202147 restraints weight = 39551.815| |-----------------------------------------------------------------------------| r_work (start): 0.4253 rms_B_bonded: 0.89 r_work: 0.4093 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.4093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6446 moved from start: 0.8953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 11867 Z= 0.241 Angle : 1.845 29.169 18304 Z= 0.688 Chirality : 0.239 2.121 2410 Planarity : 0.006 0.033 619 Dihedral : 31.273 179.219 7276 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 15.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 4.08 % Allowed : 20.41 % Favored : 75.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.84), residues: 110 helix: 1.90 (0.74), residues: 46 sheet: -1.38 (0.98), residues: 21 loop : -1.80 (1.08), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 107 HIS 0.008 0.002 HIS A 58 PHE 0.008 0.002 PHE A 18 ARG 0.005 0.001 ARG A 97 =============================================================================== Job complete usr+sys time: 5287.19 seconds wall clock time: 92 minutes 11.94 seconds (5531.94 seconds total)