Starting phenix.real_space_refine (version: dev) on Wed Feb 22 03:52:53 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uo1_26637/02_2023/7uo1_26637.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uo1_26637/02_2023/7uo1_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_26637/02_2023/7uo1_26637.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uo1_26637/02_2023/7uo1_26637.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uo1_26637/02_2023/7uo1_26637.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uo1_26637/02_2023/7uo1_26637.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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 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: 8.80, per 1000 atoms: 0.53 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 - 3.50 Amino acid : False - 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: 13.55 Conformation dependent library (CDL) restraints added in 273.9 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: 6.74 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: 5.63 Time building geometry restraints manager: 13.90 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: 18.39 - 41.51: 42 41.51 - 64.62: 0 64.62 - 87.74: 0 87.74 - 110.86: 15953 110.86 - 133.97: 15790 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: 6459 36.00 - 72.00: 421 72.00 - 108.00: 64 108.00 - 143.99: 53 143.99 - 179.99: 52 Dihedral angle restraints: 7049 sinusoidal: 6676 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 7046 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 1.850 nonbonded pdb="HO2' C B 138 " pdb=" O5' A B 139 " model vdw 1.618 1.850 nonbonded pdb="HO2' G B 84 " pdb=" O5' C B 85 " model vdw 1.632 1.850 nonbonded pdb=" H62 A B 81 " pdb=" O2' G B 280 " model vdw 1.635 1.850 nonbonded pdb="HO2' C B 35 " pdb=" OP2 C B 36 " model vdw 1.638 1.850 ... (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 ========== 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 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. 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: 0.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.170 Extract box with map and model: 1.830 Check model and map are aligned: 0.240 Process input model: 54.170 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 0.140 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5377 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 : 27.215 179.992 5826 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 % 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 *********************** 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 : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 41 average time/residue: 0.5904 time to fit residues: 31.0614 Evaluate side-chains 33 residues out of total 98 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 0.537 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3772 ------------------------------------------------------------------------------- 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: 0.0370 chunk 42 optimal weight: 10.0000 chunk 23 optimal weight: 8.9990 chunk 14 optimal weight: 9.9990 chunk 28 optimal weight: 9.9990 chunk 22 optimal weight: 9.9990 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: 7.0066 ------------------------------------------------------------------------------- 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: 0.6486 moved from start: 0.5513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.037 11867 Z= 0.396 Angle : 2.015 34.390 18304 Z= 0.789 Chirality : 0.239 2.240 2410 Planarity : 0.007 0.078 619 Dihedral : 27.753 179.501 5581 Min Nonbonded Distance : 1.659 Molprobity Statistics. All-atom Clashscore : 34.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer Outliers : 5.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.82), residues: 110 helix: 0.54 (0.73), residues: 46 sheet: -1.58 (0.79), residues: 30 loop : -0.43 (1.36), residues: 34 *********************** 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: 5 poor density : 32 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 5 residues processed: 33 average time/residue: 0.6676 time to fit residues: 27.3785 Evaluate side-chains 34 residues out of total 98 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 29 time to evaluate : 0.560 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2207 time to fit residues: 2.1694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 28 optimal weight: 10.0000 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: 2.9990 chunk 55 optimal weight: 6.9990 chunk 45 optimal weight: 0.5980 chunk 17 optimal weight: 7.9990 chunk 40 optimal weight: 40.0000 chunk 38 optimal weight: 9.9990 overall best weight: 5.3188 ------------------------------------------------------------------------------- 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: 0.6587 moved from start: 0.6384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.036 11867 Z= 0.292 Angle : 1.912 31.011 18304 Z= 0.716 Chirality : 0.231 2.061 2410 Planarity : 0.006 0.047 619 Dihedral : 27.476 179.409 5581 Min Nonbonded Distance : 1.710 Molprobity Statistics. All-atom Clashscore : 25.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer Outliers : 0.00 % 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 (0.82), residues: 110 helix: 1.46 (0.73), residues: 46 sheet: -1.31 (0.85), residues: 30 loop : -0.90 (1.26), residues: 34 *********************** 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 30 residues out of total 98 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 30 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.6685 time to fit residues: 25.3105 Evaluate side-chains 29 residues out of total 98 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.540 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 9.9990 chunk 24 optimal weight: 6.9990 chunk 34 optimal weight: 9.9990 chunk 51 optimal weight: 4.9990 chunk 54 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 14 optimal weight: 10.0000 chunk 45 optimal weight: 0.9990 chunk 30 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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: 0.6644 moved from start: 0.7204 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= 0.275 Angle : 1.857 29.565 18304 Z= 0.696 Chirality : 0.238 2.118 2410 Planarity : 0.006 0.048 619 Dihedral : 27.550 179.487 5581 Min Nonbonded Distance : 1.736 Molprobity Statistics. All-atom Clashscore : 25.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer Outliers : 5.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.82), residues: 110 helix: 1.52 (0.73), residues: 46 sheet: -1.29 (0.88), residues: 30 loop : -1.09 (1.22), residues: 34 *********************** 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 32 residues out of total 98 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 27 time to evaluate : 0.564 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 29 average time/residue: 0.6399 time to fit residues: 23.6711 Evaluate side-chains 30 residues out of total 98 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 27 time to evaluate : 0.621 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1811 time to fit residues: 1.4008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 37 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 27 optimal weight: 10.0000 chunk 48 optimal weight: 2.9990 chunk 13 optimal weight: 9.9990 chunk 18 optimal weight: 10.0000 chunk 10 optimal weight: 7.9990 chunk 31 optimal weight: 6.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- 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: 0.6732 moved from start: 0.8186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.048 11867 Z= 0.360 Angle : 1.920 30.156 18304 Z= 0.726 Chirality : 0.234 2.077 2410 Planarity : 0.007 0.069 619 Dihedral : 27.923 179.340 5581 Min Nonbonded Distance : 1.694 Molprobity Statistics. All-atom Clashscore : 33.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer Outliers : 1.02 % 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: -1.00 (0.82), residues: 110 helix: 0.61 (0.72), residues: 46 sheet: -1.40 (0.84), residues: 30 loop : -1.52 (1.31), residues: 34 *********************** 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 33 residues out of total 98 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 32 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 32 average time/residue: 0.6813 time to fit residues: 27.1313 Evaluate side-chains 32 residues out of total 98 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 0.605 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 44 optimal weight: 8.9990 chunk 25 optimal weight: 9.9990 chunk 4 optimal weight: 50.0000 chunk 17 optimal weight: 10.0000 chunk 28 optimal weight: 9.9990 chunk 52 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 30 optimal weight: 6.9990 chunk 39 optimal weight: 20.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6724 moved from start: 0.8520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.056 11867 Z= 0.334 Angle : 1.878 28.899 18304 Z= 0.706 Chirality : 0.237 2.080 2410 Planarity : 0.006 0.051 619 Dihedral : 27.863 179.859 5581 Min Nonbonded Distance : 1.702 Molprobity Statistics. All-atom Clashscore : 30.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer Outliers : 4.08 % 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: -1.03 (0.83), residues: 110 helix: 0.71 (0.76), residues: 46 sheet: -1.36 (0.86), residues: 30 loop : -1.80 (1.27), residues: 34 *********************** 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 34 residues out of total 98 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 30 time to evaluate : 0.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 4 residues processed: 30 average time/residue: 0.5543 time to fit residues: 21.7992 Evaluate side-chains 33 residues out of total 98 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 29 time to evaluate : 0.573 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1722 time to fit residues: 1.6450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 53 optimal weight: 4.9990 chunk 33 optimal weight: 6.9990 chunk 32 optimal weight: 6.9990 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: 5.9990 ------------------------------------------------------------------------------- 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: 0.6746 moved from start: 0.8888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.039 11867 Z= 0.342 Angle : 1.892 30.003 18304 Z= 0.711 Chirality : 0.236 2.061 2410 Planarity : 0.007 0.061 619 Dihedral : 27.890 179.863 5581 Min Nonbonded Distance : 1.694 Molprobity Statistics. All-atom Clashscore : 32.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer Outliers : 2.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.79), residues: 110 helix: 0.48 (0.75), residues: 46 sheet: -1.48 (0.86), residues: 30 loop : -1.98 (1.14), residues: 34 *********************** 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 30 residues out of total 98 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 28 time to evaluate : 0.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 28 average time/residue: 0.5792 time to fit residues: 21.1768 Evaluate side-chains 28 residues out of total 98 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 27 time to evaluate : 0.588 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1825 time to fit residues: 0.7401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 10.0000 chunk 49 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 50 optimal weight: 0.5980 chunk 30 optimal weight: 6.9990 chunk 21 optimal weight: 8.9990 chunk 39 optimal weight: 20.0000 chunk 15 optimal weight: 30.0000 overall best weight: 3.3186 ------------------------------------------------------------------------------- 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: 0.6674 moved from start: 0.8739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 11867 Z= 0.212 Angle : 1.828 27.991 18304 Z= 0.677 Chirality : 0.237 2.079 2410 Planarity : 0.005 0.040 619 Dihedral : 27.600 179.980 5581 Min Nonbonded Distance : 1.781 Molprobity Statistics. All-atom Clashscore : 24.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer Outliers : 2.04 % 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: -0.62 (0.83), residues: 110 helix: 1.25 (0.79), residues: 46 sheet: -1.27 (0.86), residues: 30 loop : -1.80 (1.18), residues: 34 *********************** 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 30 residues out of total 98 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 28 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 29 average time/residue: 0.5601 time to fit residues: 21.2493 Evaluate side-chains 30 residues out of total 98 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 28 time to evaluate : 0.558 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1728 time to fit residues: 0.9933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 45 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 50 optimal weight: 4.9990 chunk 33 optimal weight: 7.9990 chunk 53 optimal weight: 0.8980 chunk 32 optimal weight: 7.9990 chunk 25 optimal weight: 9.9990 chunk 36 optimal weight: 9.9990 chunk 55 optimal weight: 6.9990 chunk 51 optimal weight: 0.8980 chunk 44 optimal weight: 10.0000 overall best weight: 1.7382 ------------------------------------------------------------------------------- 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: 0.6568 moved from start: 0.8422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 11867 Z= 0.147 Angle : 1.801 27.969 18304 Z= 0.659 Chirality : 0.237 2.079 2410 Planarity : 0.005 0.053 619 Dihedral : 27.187 179.578 5581 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 18.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer Outliers : 0.00 % 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 (0.85), residues: 110 helix: 2.24 (0.76), residues: 46 sheet: -1.16 (0.88), residues: 30 loop : -1.26 (1.24), residues: 34 *********************** 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 28 residues out of total 98 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.582 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.5726 time to fit residues: 20.7642 Evaluate side-chains 28 residues out of total 98 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.616 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 9.9990 chunk 35 optimal weight: 6.9990 chunk 47 optimal weight: 0.0970 chunk 13 optimal weight: 9.9990 chunk 40 optimal weight: 40.0000 chunk 6 optimal weight: 3.9990 chunk 12 optimal weight: 10.0000 chunk 44 optimal weight: 10.0000 chunk 18 optimal weight: 9.9990 overall best weight: 6.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6737 moved from start: 0.9017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.047 11867 Z= 0.346 Angle : 1.888 29.603 18304 Z= 0.709 Chirality : 0.236 2.062 2410 Planarity : 0.007 0.056 619 Dihedral : 27.709 179.714 5581 Min Nonbonded Distance : 1.707 Molprobity Statistics. All-atom Clashscore : 30.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer Outliers : 4.08 % 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: -0.91 (0.81), residues: 110 helix: 0.87 (0.76), residues: 46 sheet: -1.29 (0.87), residues: 30 loop : -1.85 (1.14), residues: 34 ********************** 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 30 residues out of total 98 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 26 time to evaluate : 0.540 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 4 residues processed: 26 average time/residue: 0.5919 time to fit residues: 19.9887 Evaluate side-chains 30 residues out of total 98 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 26 time to evaluate : 0.529 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.3187 time to fit residues: 2.2516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 45 optimal weight: 0.8980 chunk 5 optimal weight: 9.9990 chunk 8 optimal weight: 10.0000 chunk 39 optimal weight: 20.0000 chunk 2 optimal weight: 4.9990 chunk 32 optimal weight: 7.9990 chunk 50 optimal weight: 4.9990 chunk 29 optimal weight: 10.0000 chunk 38 optimal weight: 9.9990 chunk 1 optimal weight: 6.9990 chunk 35 optimal weight: 4.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4658 r_free = 0.4658 target = 0.238436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.196398 restraints weight = 39262.502| |-----------------------------------------------------------------------------| r_work (start): 0.4197 rms_B_bonded: 0.92 r_work: 0.4078 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.4078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6566 moved from start: 0.9029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.041 11867 Z= 0.275 Angle : 1.852 28.703 18304 Z= 0.688 Chirality : 0.236 2.063 2410 Planarity : 0.006 0.047 619 Dihedral : 27.623 179.919 5581 Min Nonbonded Distance : 1.728 Molprobity Statistics. All-atom Clashscore : 26.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer Outliers : 0.00 % 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: -0.76 (0.82), residues: 110 helix: 1.13 (0.78), residues: 46 sheet: -1.44 (0.86), residues: 30 loop : -1.75 (1.15), residues: 34 =============================================================================== Job complete usr+sys time: 5056.79 seconds wall clock time: 89 minutes 56.70 seconds (5396.70 seconds total)