Starting phenix.real_space_refine (version: dev) on Sun Feb 19 20:16:01 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uo0_26636/02_2023/7uo0_26636.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uo0_26636/02_2023/7uo0_26636.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uo0_26636/02_2023/7uo0_26636.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uo0_26636/02_2023/7uo0_26636.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uo0_26636/02_2023/7uo0_26636.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uo0_26636/02_2023/7uo0_26636.pdb" } resolution = 3.4 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= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "A PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.00s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 10697 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 922 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 6, 'TRANS': 105} Chain: "B" Number of atoms: 8024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 8024 Classifications: {'RNA': 373} Modifications used: {'5*END': 1, 'rna2p_pur': 27, 'rna2p_pyr': 26, 'rna3p_pur': 191, 'rna3p_pyr': 128} Link IDs: {'rna2p': 53, 'rna3p': 319} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 1744 Classifications: {'RNA': 82} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 8, 'rna3p_pur': 37, 'rna3p_pyr': 33} Link IDs: {'rna2p': 11, 'rna3p': 70} Chain: "B" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Unusual residues: {' CA': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Residues with excluded nonbonded symmetry interactions: 47 residue: pdb=" P C B 20 " occ=0.00 ... (18 atoms not shown) pdb=" C6 C B 20 " occ=0.00 residue: pdb=" P C B 21 " occ=0.00 ... (18 atoms not shown) pdb=" C6 C B 21 " occ=0.00 residue: pdb=" P G B 22 " occ=0.00 ... (21 atoms not shown) pdb=" C4 G B 22 " occ=0.00 residue: pdb=" P C B 23 " occ=0.00 ... (18 atoms not shown) pdb=" C6 C B 23 " occ=0.00 residue: pdb=" P U B 24 " occ=0.00 ... (18 atoms not shown) pdb=" C6 U B 24 " occ=0.00 residue: pdb=" P U B 25 " occ=0.00 ... (18 atoms not shown) pdb=" C6 U B 25 " occ=0.00 residue: pdb=" P C B 26 " occ=0.00 ... (18 atoms not shown) pdb=" C6 C B 26 " occ=0.00 residue: pdb=" P G B 27 " occ=0.00 ... (21 atoms not shown) pdb=" C4 G B 27 " occ=0.00 residue: pdb=" P U B 28 " occ=0.00 ... (18 atoms not shown) pdb=" C6 U B 28 " occ=0.00 residue: pdb=" P C B 29 " occ=0.00 ... (18 atoms not shown) pdb=" C6 C B 29 " occ=0.00 residue: pdb=" P G B 30 " occ=0.00 ... (21 atoms not shown) pdb=" C4 G B 30 " occ=0.00 residue: pdb=" P U B 31 " occ=0.00 ... (18 atoms not shown) pdb=" C6 U B 31 " occ=0.00 ... (remaining 35 not shown) Time building chain proxies: 6.56, per 1000 atoms: 0.61 Number of scatterers: 10697 At special positions: 0 Unit cell: (125.902, 115.322, 194.672, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 7 19.99 S 2 16.00 P 454 15.00 O 3303 8.00 N 1996 7.00 C 4935 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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: 5.01 Conformation dependent library (CDL) restraints added in 199.5 milliseconds 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 214 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 1 sheets defined 40.2% alpha, 11.6% beta 113 base pairs and 83 stacking pairs defined. Time for finding SS restraints: 3.63 Creating SS restraints... Processing helix chain 'A' and resid 6 through 10 Processing helix chain 'A' and resid 13 through 23 removed outlier: 3.778A pdb=" N PHE A 17 " --> pdb=" O THR A 13 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLN A 23 " --> pdb=" O PHE A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 75 Processing helix chain 'A' and resid 96 through 109 Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 28 removed outlier: 3.739A pdb=" N GLY A 36 " --> pdb=" O GLN A 25 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA A 27 " --> pdb=" O ILE A 34 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N GLY A 47 " --> pdb=" O VAL A 86 " (cutoff:3.500A) removed outlier: 8.903A pdb=" N ALA A 88 " --> pdb=" O GLY A 47 " (cutoff:3.500A) 34 hydrogen bonds defined for protein. 93 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 312 hydrogen bonds 598 hydrogen bond angles 0 basepair planarities 113 basepair parallelities 83 stacking parallelities Total time for adding SS restraints: 3.14 Time building geometry restraints manager: 5.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1461 1.33 - 1.45: 5697 1.45 - 1.57: 3806 1.57 - 1.69: 907 1.69 - 1.81: 3 Bond restraints: 11874 Sorted by residual: bond pdb=" C3' G C 19 " pdb=" O3' G C 19 " ideal model delta sigma weight residual 1.417 1.440 -0.023 1.50e-02 4.44e+03 2.27e+00 bond pdb=" C1' C B 35 " pdb=" N1 C B 35 " ideal model delta sigma weight residual 1.470 1.492 -0.022 1.50e-02 4.44e+03 2.14e+00 bond pdb=" C3' G B 137 " pdb=" O3' G B 137 " ideal model delta sigma weight residual 1.417 1.438 -0.021 1.50e-02 4.44e+03 2.04e+00 bond pdb=" C1' G B 190 " pdb=" N9 G B 190 " ideal model delta sigma weight residual 1.465 1.486 -0.021 1.50e-02 4.44e+03 2.03e+00 bond pdb=" C3' A B 352 " pdb=" O3' A B 352 " ideal model delta sigma weight residual 1.417 1.438 -0.021 1.50e-02 4.44e+03 1.96e+00 ... (remaining 11869 not shown) Histogram of bond angle deviations from ideal: 30.65 - 51.54: 5 51.54 - 72.43: 0 72.43 - 93.31: 0 93.31 - 114.20: 10229 114.20 - 135.09: 8085 Bond angle restraints: 18319 Sorted by residual: angle pdb=" O3' C B 14 " pdb=" P A B 15 " pdb=" OP1 A B 15 " ideal model delta sigma weight residual 108.00 30.65 77.35 3.00e+00 1.11e-01 6.65e+02 angle pdb=" O3' A B 15 " pdb=" P G B 16 " pdb=" OP1 G B 16 " ideal model delta sigma weight residual 108.00 34.51 73.49 3.00e+00 1.11e-01 6.00e+02 angle pdb=" O3' A B 130 " pdb=" P C B 131 " pdb=" OP1 C B 131 " ideal model delta sigma weight residual 108.00 34.71 73.29 3.00e+00 1.11e-01 5.97e+02 angle pdb=" O3' C B 70 " pdb=" P C B 71 " pdb=" OP1 C B 71 " ideal model delta sigma weight residual 108.00 35.06 72.94 3.00e+00 1.11e-01 5.91e+02 angle pdb=" O3' C B 252 " pdb=" P C B 253 " pdb=" OP1 C B 253 " ideal model delta sigma weight residual 108.00 36.18 71.82 3.00e+00 1.11e-01 5.73e+02 ... (remaining 18314 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.89: 5466 35.89 - 71.77: 452 71.77 - 107.66: 63 107.66 - 143.55: 28 143.55 - 179.43: 31 Dihedral angle restraints: 6040 sinusoidal: 5715 harmonic: 325 Sorted by residual: dihedral pdb=" C4' C C 63 " pdb=" C3' C C 63 " pdb=" C2' C C 63 " pdb=" C1' C C 63 " ideal model delta sinusoidal sigma weight residual -35.00 36.41 -71.41 1 8.00e+00 1.56e-02 1.02e+02 dihedral pdb=" C4' G B 190 " pdb=" C3' G B 190 " pdb=" C2' G B 190 " pdb=" C1' G B 190 " ideal model delta sinusoidal sigma weight residual -35.00 36.38 -71.38 1 8.00e+00 1.56e-02 1.02e+02 dihedral pdb=" C4' C C 49 " pdb=" C3' C C 49 " pdb=" C2' C C 49 " pdb=" C1' C C 49 " ideal model delta sinusoidal sigma weight residual -35.00 35.89 -70.89 1 8.00e+00 1.56e-02 1.01e+02 ... (remaining 6037 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.180: 2098 0.180 - 0.360: 286 0.360 - 0.540: 22 0.540 - 0.721: 2 0.721 - 0.901: 4 Chirality restraints: 2412 Sorted by residual: chirality pdb=" P C B 253 " pdb=" OP1 C B 253 " pdb=" OP2 C B 253 " pdb=" O5' C B 253 " both_signs ideal model delta sigma weight residual True 2.41 1.51 0.90 2.00e-01 2.50e+01 2.03e+01 chirality pdb=" P C B 71 " pdb=" OP1 C B 71 " pdb=" OP2 C B 71 " pdb=" O5' C B 71 " both_signs ideal model delta sigma weight residual True 2.41 1.52 0.89 2.00e-01 2.50e+01 1.98e+01 chirality pdb=" P C B 131 " pdb=" OP1 C B 131 " pdb=" OP2 C B 131 " pdb=" O5' C B 131 " both_signs ideal model delta sigma weight residual True 2.41 1.58 0.83 2.00e-01 2.50e+01 1.71e+01 ... (remaining 2409 not shown) Planarity restraints: 619 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C B 35 " -0.001 2.00e-02 2.50e+03 1.40e-02 4.43e+00 pdb=" N1 C B 35 " -0.003 2.00e-02 2.50e+03 pdb=" C2 C B 35 " 0.034 2.00e-02 2.50e+03 pdb=" O2 C B 35 " -0.022 2.00e-02 2.50e+03 pdb=" N3 C B 35 " 0.003 2.00e-02 2.50e+03 pdb=" C4 C B 35 " 0.004 2.00e-02 2.50e+03 pdb=" N4 C B 35 " -0.009 2.00e-02 2.50e+03 pdb=" C5 C B 35 " 0.000 2.00e-02 2.50e+03 pdb=" C6 C B 35 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G B 63 " -0.004 2.00e-02 2.50e+03 1.09e-02 3.54e+00 pdb=" N9 G B 63 " 0.002 2.00e-02 2.50e+03 pdb=" C8 G B 63 " 0.004 2.00e-02 2.50e+03 pdb=" N7 G B 63 " 0.005 2.00e-02 2.50e+03 pdb=" C5 G B 63 " 0.001 2.00e-02 2.50e+03 pdb=" C6 G B 63 " -0.001 2.00e-02 2.50e+03 pdb=" O6 G B 63 " -0.001 2.00e-02 2.50e+03 pdb=" N1 G B 63 " -0.003 2.00e-02 2.50e+03 pdb=" C2 G B 63 " -0.028 2.00e-02 2.50e+03 pdb=" N2 G B 63 " 0.024 2.00e-02 2.50e+03 pdb=" N3 G B 63 " -0.002 2.00e-02 2.50e+03 pdb=" C4 G B 63 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G C 53 " 0.022 2.00e-02 2.50e+03 1.04e-02 3.25e+00 pdb=" N9 G C 53 " -0.028 2.00e-02 2.50e+03 pdb=" C8 G C 53 " -0.001 2.00e-02 2.50e+03 pdb=" N7 G C 53 " 0.002 2.00e-02 2.50e+03 pdb=" C5 G C 53 " 0.001 2.00e-02 2.50e+03 pdb=" C6 G C 53 " 0.001 2.00e-02 2.50e+03 pdb=" O6 G C 53 " 0.005 2.00e-02 2.50e+03 pdb=" N1 G C 53 " 0.001 2.00e-02 2.50e+03 pdb=" C2 G C 53 " 0.001 2.00e-02 2.50e+03 pdb=" N2 G C 53 " -0.002 2.00e-02 2.50e+03 pdb=" N3 G C 53 " -0.002 2.00e-02 2.50e+03 pdb=" C4 G C 53 " 0.000 2.00e-02 2.50e+03 ... (remaining 616 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 640 2.67 - 3.23: 8176 3.23 - 3.79: 17008 3.79 - 4.34: 18215 4.34 - 4.90: 27169 Nonbonded interactions: 71208 Sorted by model distance: nonbonded pdb=" O4 U B 97 " pdb=" N6 A B 99 " model vdw 2.117 2.520 nonbonded pdb=" O4 U B 25 " pdb=" O6 G B 56 " model vdw 2.129 2.432 nonbonded pdb=" O2' G B 291 " pdb=" OP2 G B 293 " model vdw 2.139 2.440 nonbonded pdb=" O2' A B 248 " pdb=" O2' A C 74 " model vdw 2.186 2.440 nonbonded pdb=" O2' U B 366 " pdb=" O5' C B 367 " model vdw 2.207 2.440 ... (remaining 71203 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: 6 Type Number sf(0) Gaussians Ca 7 9.91 5 P 454 5.49 5 S 2 5.16 5 C 4935 2.51 5 N 1996 2.21 5 O 3303 1.98 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: 3.020 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: 0.000 Extract box with map and model: 10.930 Check model and map are aligned: 0.160 Process input model: 30.890 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 0.100 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3360 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 : 0.003 0.024 11874 Z= 0.176 Angle : 2.227 77.348 18319 Z= 0.847 Chirality : 0.111 0.901 2412 Planarity : 0.004 0.029 619 Dihedral : 24.661 179.431 5826 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % 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: -0.20 (0.84), residues: 110 helix: 1.29 (0.81), residues: 45 sheet: -0.19 (1.14), residues: 12 loop : -1.41 (0.95), residues: 53 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 98 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 21 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 22 average time/residue: 0.2925 time to fit residues: 8.7545 Evaluate side-chains 11 residues out of total 98 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 11 time to evaluate : 0.438 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2445 ------------------------------------------------------------------------------- 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: 4.9990 chunk 42 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 14 optimal weight: 9.9990 chunk 28 optimal weight: 5.9990 chunk 22 optimal weight: 6.9990 chunk 43 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 chunk 26 optimal weight: 9.9990 chunk 32 optimal weight: 4.9990 chunk 50 optimal weight: 8.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4607 moved from start: 1.0209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.069 11874 Z= 0.538 Angle : 1.501 13.351 18319 Z= 0.705 Chirality : 0.066 0.430 2412 Planarity : 0.011 0.165 619 Dihedral : 26.864 178.624 5581 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 34.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer Outliers : 6.12 % 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: -1.83 (0.77), residues: 110 helix: -0.89 (0.76), residues: 40 sheet: -0.91 (1.02), residues: 26 loop : -1.52 (0.93), residues: 44 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 98 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 17 time to evaluate : 0.411 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 23 average time/residue: 0.4536 time to fit residues: 12.9802 Evaluate side-chains 11 residues out of total 98 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 9 time to evaluate : 0.426 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0892 time to fit residues: 0.6190 ------------------------------------------------------------------------------- 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: 5.9990 chunk 15 optimal weight: 9.9990 chunk 42 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 14 optimal weight: 9.9990 chunk 50 optimal weight: 10.0000 chunk 55 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- 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: 0.4899 moved from start: 1.4247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.046 11874 Z= 0.386 Angle : 1.184 10.330 18319 Z= 0.568 Chirality : 0.053 0.269 2412 Planarity : 0.009 0.080 619 Dihedral : 27.193 177.688 5581 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 30.83 Ramachandran Plot: Outliers : 0.91 % Allowed : 10.91 % Favored : 88.18 % Rotamer Outliers : 6.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.35 (0.79), residues: 110 helix: -1.65 (0.74), residues: 40 sheet: -1.61 (0.89), residues: 31 loop : -1.01 (1.10), residues: 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 98 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 18 time to evaluate : 0.412 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 22 average time/residue: 0.2946 time to fit residues: 8.9056 Evaluate side-chains 18 residues out of total 98 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 15 time to evaluate : 0.591 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1063 time to fit residues: 0.9513 ------------------------------------------------------------------------------- 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: 10.0000 chunk 5 optimal weight: 0.8980 chunk 24 optimal weight: 6.9990 chunk 34 optimal weight: 5.9990 chunk 51 optimal weight: 20.0000 chunk 54 optimal weight: 10.0000 chunk 48 optimal weight: 4.9990 chunk 14 optimal weight: 9.9990 chunk 45 optimal weight: 3.9990 chunk 30 optimal weight: 6.9990 chunk 0 optimal weight: 1.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- 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: 0.5172 moved from start: 1.8031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.069 11874 Z= 0.460 Angle : 1.299 13.413 18319 Z= 0.623 Chirality : 0.057 0.252 2412 Planarity : 0.008 0.074 619 Dihedral : 27.842 176.595 5581 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 40.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.64 % Favored : 86.36 % Rotamer Outliers : 3.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.48 (0.71), residues: 110 helix: -2.07 (0.72), residues: 41 sheet: -1.69 (0.90), residues: 31 loop : -2.84 (0.83), residues: 38 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 98 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 15 time to evaluate : 0.414 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 17 average time/residue: 0.3581 time to fit residues: 8.0754 Evaluate side-chains 15 residues out of total 98 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 13 time to evaluate : 0.386 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1048 time to fit residues: 0.6862 ------------------------------------------------------------------------------- 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: 3.9990 chunk 22 optimal weight: 8.9990 chunk 46 optimal weight: 2.9990 chunk 37 optimal weight: 9.9990 chunk 0 optimal weight: 1.9990 chunk 27 optimal weight: 8.9990 chunk 48 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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: 0.5217 moved from start: 1.9230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.066 11874 Z= 0.389 Angle : 1.074 10.466 18319 Z= 0.519 Chirality : 0.051 0.363 2412 Planarity : 0.007 0.069 619 Dihedral : 27.651 177.769 5581 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 32.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.73 % Favored : 87.27 % 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: -2.96 (0.81), residues: 110 helix: -1.97 (0.75), residues: 41 sheet: -2.15 (0.84), residues: 31 loop : -1.34 (1.20), residues: 38 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 98 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 16 time to evaluate : 0.377 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 18 average time/residue: 0.2840 time to fit residues: 7.2167 Evaluate side-chains 15 residues out of total 98 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 14 time to evaluate : 0.431 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1410 time to fit residues: 0.5029 ------------------------------------------------------------------------------- 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: 3.9990 chunk 54 optimal weight: 10.0000 chunk 44 optimal weight: 2.9990 chunk 25 optimal weight: 8.9990 chunk 4 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 28 optimal weight: 6.9990 chunk 52 optimal weight: 30.0000 chunk 6 optimal weight: 0.8980 chunk 30 optimal weight: 4.9990 chunk 39 optimal weight: 8.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 GLN A 111 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5234 moved from start: 2.0240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.050 11874 Z= 0.305 Angle : 0.950 10.721 18319 Z= 0.459 Chirality : 0.045 0.270 2412 Planarity : 0.006 0.054 619 Dihedral : 27.212 177.239 5581 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 26.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer Outliers : 3.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.23 (0.76), residues: 110 helix: -2.00 (0.74), residues: 42 sheet: -2.21 (0.80), residues: 31 loop : -1.81 (1.09), residues: 37 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 98 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 20 time to evaluate : 0.378 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 22 average time/residue: 0.3840 time to fit residues: 10.7917 Evaluate side-chains 17 residues out of total 98 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 15 time to evaluate : 0.429 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1059 time to fit residues: 0.6896 ------------------------------------------------------------------------------- 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: 8.9990 chunk 33 optimal weight: 8.9990 chunk 32 optimal weight: 4.9990 chunk 24 optimal weight: 7.9990 chunk 21 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 10 optimal weight: 0.2980 chunk 34 optimal weight: 5.9990 chunk 36 optimal weight: 4.9990 overall best weight: 3.8588 ------------------------------------------------------------------------------- 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: 0.5423 moved from start: 2.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.060 11874 Z= 0.457 Angle : 1.269 12.388 18319 Z= 0.600 Chirality : 0.058 0.356 2412 Planarity : 0.008 0.056 619 Dihedral : 28.357 179.933 5581 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 45.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % 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: -3.59 (0.75), residues: 110 helix: -2.41 (0.71), residues: 41 sheet: -2.16 (0.83), residues: 31 loop : -2.12 (1.06), residues: 38 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 98 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 16 time to evaluate : 0.400 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 19 average time/residue: 0.2724 time to fit residues: 7.3657 Evaluate side-chains 16 residues out of total 98 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 15 time to evaluate : 0.407 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1044 time to fit residues: 0.5194 ------------------------------------------------------------------------------- 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: 9.9990 chunk 5 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 chunk 49 optimal weight: 10.0000 chunk 51 optimal weight: 20.0000 chunk 47 optimal weight: 3.9990 chunk 50 optimal weight: 9.9990 chunk 30 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 39 optimal weight: 8.9990 chunk 15 optimal weight: 10.0000 overall best weight: 3.5588 ------------------------------------------------------------------------------- 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: 0.5422 moved from start: 2.3162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.091 11874 Z= 0.397 Angle : 1.085 10.508 18319 Z= 0.516 Chirality : 0.050 0.271 2412 Planarity : 0.007 0.053 619 Dihedral : 27.833 179.889 5581 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 34.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.91 % Favored : 89.09 % 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: -3.63 (0.74), residues: 110 helix: -2.76 (0.64), residues: 42 sheet: -2.30 (0.78), residues: 31 loop : -1.56 (1.16), residues: 37 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 98 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 17 time to evaluate : 0.390 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 19 average time/residue: 0.3741 time to fit residues: 9.2828 Evaluate side-chains 18 residues out of total 98 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 15 time to evaluate : 0.413 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0965 time to fit residues: 0.8408 ------------------------------------------------------------------------------- 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: 4.9990 chunk 47 optimal weight: 4.9990 chunk 50 optimal weight: 10.0000 chunk 33 optimal weight: 7.9990 chunk 53 optimal weight: 7.9990 chunk 32 optimal weight: 4.9990 chunk 25 optimal weight: 8.9990 chunk 36 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 chunk 51 optimal weight: 20.0000 chunk 44 optimal weight: 3.9990 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: 0.5528 moved from start: 2.4665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.081 11874 Z= 0.548 Angle : 1.347 14.317 18319 Z= 0.630 Chirality : 0.060 0.393 2412 Planarity : 0.010 0.145 619 Dihedral : 28.549 179.632 5581 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 52.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.73 % Favored : 87.27 % 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: -4.38 (0.66), residues: 110 helix: -3.01 (0.61), residues: 42 sheet: -2.71 (0.74), residues: 31 loop : -2.49 (0.95), residues: 37 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 98 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 15 time to evaluate : 0.409 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 16 average time/residue: 0.3676 time to fit residues: 7.8647 Evaluate side-chains 16 residues out of total 98 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 15 time to evaluate : 0.393 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1063 time to fit residues: 0.5141 ------------------------------------------------------------------------------- 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: 0.4980 chunk 34 optimal weight: 4.9990 chunk 27 optimal weight: 9.9990 chunk 35 optimal weight: 0.8980 chunk 47 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 6 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- 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: 0.5385 moved from start: 2.4125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 11874 Z= 0.241 Angle : 0.908 10.407 18319 Z= 0.432 Chirality : 0.042 0.283 2412 Planarity : 0.006 0.072 619 Dihedral : 27.372 179.971 5581 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 24.47 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: -3.09 (0.79), residues: 110 helix: -2.17 (0.68), residues: 42 sheet: -2.61 (0.71), residues: 31 loop : -0.84 (1.32), residues: 37 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 98 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 16 time to evaluate : 0.407 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 17 average time/residue: 0.3887 time to fit residues: 8.7023 Evaluate side-chains 13 residues out of total 98 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.440 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3082 ------------------------------------------------------------------------------- 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: 5.9990 chunk 5 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 39 optimal weight: 9.9990 chunk 2 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 50 optimal weight: 10.0000 chunk 29 optimal weight: 7.9990 chunk 38 optimal weight: 4.9990 chunk 1 optimal weight: 0.7980 chunk 35 optimal weight: 4.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- 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 = 0.4369 r_free = 0.4369 target = 0.113619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.101768 restraints weight = 92606.024| |-----------------------------------------------------------------------------| r_work (start): 0.4063 rms_B_bonded: 1.43 r_work (final): 0.4063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6247 moved from start: 2.4323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 11874 Z= 0.257 Angle : 0.876 10.942 18319 Z= 0.418 Chirality : 0.040 0.236 2412 Planarity : 0.006 0.044 619 Dihedral : 26.946 179.788 5581 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 25.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % 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: -3.19 (0.77), residues: 110 helix: -2.16 (0.64), residues: 42 sheet: -2.71 (0.70), residues: 31 loop : -0.97 (1.28), residues: 37 =============================================================================== Job complete usr+sys time: 1735.02 seconds wall clock time: 32 minutes 57.65 seconds (1977.65 seconds total)