Starting phenix.real_space_refine on Wed Sep 25 16:12:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uo0_26636/09_2024/7uo0_26636.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uo0_26636/09_2024/7uo0_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_26636/09_2024/7uo0_26636.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uo0_26636/09_2024/7uo0_26636.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uo0_26636/09_2024/7uo0_26636.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uo0_26636/09_2024/7uo0_26636.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 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. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 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 dihedrals: 1 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: 6.91, per 1000 atoms: 0.65 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.20 Conformation dependent library (CDL) restraints added in 174.7 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: 3.83 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: 3.19 Time building geometry restraints manager: 2.70 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: 0.00 - 15.47: 18310 15.47 - 30.94: 4 30.94 - 46.41: 0 46.41 - 61.88: 0 61.88 - 77.35: 5 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: 6290 35.89 - 71.77: 1215 71.77 - 107.66: 181 107.66 - 143.55: 28 143.55 - 179.43: 31 Dihedral angle restraints: 7745 sinusoidal: 7420 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 7742 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 3.120 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 3.040 nonbonded pdb=" O2' A B 248 " pdb=" O2' A C 74 " model vdw 2.186 3.040 nonbonded pdb=" O2' U B 366 " pdb=" O5' C B 367 " model vdw 2.207 3.040 ... (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 Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.91 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 26.100 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3191 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 : 29.933 179.431 7531 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 % Allowed : 7.14 % Favored : 90.82 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP A 108 HIS 0.004 0.002 HIS A 77 PHE 0.011 0.002 PHE A 72 ARG 0.005 0.000 ARG A 75 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 98 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 21 time to evaluate : 0.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.6386 (mmt) cc_final: 0.5867 (tpp) outliers start: 2 outliers final: 0 residues processed: 22 average time/residue: 0.2981 time to fit residues: 8.9813 Evaluate side-chains 11 residues out of total 98 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 11 time to evaluate : 0.381 ------------------------------------------------------------------------------- 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: 4.9990 chunk 23 optimal weight: 5.9990 chunk 14 optimal weight: 10.0000 chunk 28 optimal weight: 5.9990 chunk 22 optimal weight: 7.9990 chunk 43 optimal weight: 3.9990 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... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4484 moved from start: 1.0597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.065 11874 Z= 0.558 Angle : 1.590 12.386 18319 Z= 0.752 Chirality : 0.069 0.423 2412 Planarity : 0.013 0.209 619 Dihedral : 31.096 176.180 7286 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 30.77 Ramachandran Plot: Outliers : 0.91 % Allowed : 5.45 % Favored : 93.64 % Rotamer: Outliers : 8.16 % Allowed : 13.27 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.76), residues: 110 helix: -1.10 (0.73), residues: 40 sheet: -0.95 (0.99), residues: 29 loop : -1.49 (0.93), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.004 TRP A 108 HIS 0.032 0.010 HIS A 111 PHE 0.024 0.006 PHE A 21 ARG 0.014 0.002 ARG A 73 *********************** 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 27 residues out of total 98 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 19 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.6407 (OUTLIER) cc_final: 0.5828 (tpp) outliers start: 8 outliers final: 3 residues processed: 26 average time/residue: 0.3976 time to fit residues: 13.0610 Evaluate side-chains 15 residues out of total 98 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 11 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 107 LEU 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: 10.0000 chunk 50 optimal weight: 10.0000 chunk 55 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4585 moved from start: 1.2921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 11874 Z= 0.315 Angle : 1.065 9.295 18319 Z= 0.507 Chirality : 0.048 0.237 2412 Planarity : 0.008 0.110 619 Dihedral : 30.727 177.130 7286 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 17.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer: Outliers : 4.08 % Allowed : 20.41 % Favored : 75.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.68 (0.74), residues: 110 helix: -1.59 (0.72), residues: 39 sheet: -1.67 (0.92), residues: 30 loop : -1.76 (0.94), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 108 HIS 0.007 0.003 HIS A 59 PHE 0.047 0.008 PHE A 19 ARG 0.015 0.001 ARG A 98 *********************** 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 22 residues out of total 98 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 18 time to evaluate : 0.403 Fit side-chains REVERT: A 82 MET cc_start: 0.6378 (mmt) cc_final: 0.5875 (tpp) REVERT: A 96 ASP cc_start: 0.8626 (t0) cc_final: 0.8412 (t0) REVERT: A 102 GLU cc_start: 0.8494 (pp20) cc_final: 0.7718 (tm-30) REVERT: A 105 GLU cc_start: 0.7996 (tp30) cc_final: 0.7688 (tp30) REVERT: A 106 LYS cc_start: 0.9160 (mtmm) cc_final: 0.8559 (mtmm) outliers start: 4 outliers final: 2 residues processed: 21 average time/residue: 0.3007 time to fit residues: 8.5550 Evaluate side-chains 19 residues out of total 98 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 17 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain A residue 107 LEU 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: 1.9990 chunk 24 optimal weight: 7.9990 chunk 34 optimal weight: 5.9990 chunk 51 optimal weight: 20.0000 chunk 54 optimal weight: 9.9990 chunk 48 optimal weight: 4.9990 chunk 14 optimal weight: 10.0000 chunk 45 optimal weight: 3.9990 chunk 30 optimal weight: 6.9990 chunk 0 optimal weight: 3.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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: 0.5027 moved from start: 1.7666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.086 11874 Z= 0.526 Angle : 1.412 12.871 18319 Z= 0.683 Chirality : 0.062 0.298 2412 Planarity : 0.009 0.063 619 Dihedral : 31.487 179.000 7286 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 34.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.73 % Favored : 87.27 % Rotamer: Outliers : 5.10 % Allowed : 22.45 % Favored : 72.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.24 (0.71), residues: 110 helix: -1.53 (0.70), residues: 39 sheet: -2.16 (0.93), residues: 31 loop : -2.52 (0.86), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.002 TRP A 108 HIS 0.004 0.002 HIS A 77 PHE 0.047 0.006 PHE A 19 ARG 0.006 0.001 ARG A 37 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 98 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 18 time to evaluate : 0.415 Fit side-chains REVERT: A 102 GLU cc_start: 0.8845 (pp20) cc_final: 0.8226 (tm-30) REVERT: A 106 LYS cc_start: 0.9180 (mtmm) cc_final: 0.8579 (mtmm) outliers start: 5 outliers final: 4 residues processed: 21 average time/residue: 0.2533 time to fit residues: 7.5993 Evaluate side-chains 17 residues out of total 98 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 13 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain A residue 107 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 40 optimal weight: 2.9990 chunk 22 optimal weight: 7.9990 chunk 46 optimal weight: 1.9990 chunk 37 optimal weight: 8.9990 chunk 0 optimal weight: 0.9980 chunk 27 optimal weight: 9.9990 chunk 48 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 31 optimal weight: 4.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- 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: 0.4911 moved from start: 1.7676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 11874 Z= 0.273 Angle : 0.924 11.308 18319 Z= 0.445 Chirality : 0.043 0.285 2412 Planarity : 0.006 0.052 619 Dihedral : 30.877 176.809 7286 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 15.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 4.08 % Allowed : 24.49 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.35 (0.71), residues: 110 helix: -0.47 (0.70), residues: 40 sheet: -2.03 (0.84), residues: 31 loop : -2.08 (0.92), residues: 39 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP A 108 HIS 0.005 0.002 HIS A 59 PHE 0.018 0.004 PHE A 19 ARG 0.004 0.001 ARG A 37 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 98 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 17 time to evaluate : 0.436 Fit side-chains REVERT: A 102 GLU cc_start: 0.8869 (pp20) cc_final: 0.8117 (tm-30) REVERT: A 106 LYS cc_start: 0.9185 (mtmm) cc_final: 0.8536 (mtmm) outliers start: 4 outliers final: 2 residues processed: 20 average time/residue: 0.2683 time to fit residues: 7.6925 Evaluate side-chains 17 residues out of total 98 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 15 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain A residue 107 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 13 optimal weight: 4.9990 chunk 54 optimal weight: 10.0000 chunk 44 optimal weight: 3.9990 chunk 25 optimal weight: 10.0000 chunk 4 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 52 optimal weight: 30.0000 chunk 6 optimal weight: 0.7980 chunk 30 optimal weight: 4.9990 chunk 39 optimal weight: 8.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- 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: 0.5112 moved from start: 1.9851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.099 11874 Z= 0.400 Angle : 1.123 12.115 18319 Z= 0.537 Chirality : 0.051 0.341 2412 Planarity : 0.007 0.059 619 Dihedral : 31.315 178.948 7286 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 24.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer: Outliers : 4.08 % Allowed : 26.53 % Favored : 69.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.52 (0.73), residues: 110 helix: -0.73 (0.71), residues: 39 sheet: -1.96 (0.86), residues: 31 loop : -2.17 (0.97), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.004 TRP A 108 HIS 0.011 0.003 HIS A 59 PHE 0.016 0.004 PHE A 19 ARG 0.011 0.002 ARG A 61 *********************** 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 20 residues out of total 98 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 16 time to evaluate : 0.389 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 19 average time/residue: 0.2008 time to fit residues: 5.8891 Evaluate side-chains 18 residues out of total 98 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 16 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain A residue 107 LEU 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: 10.0000 chunk 33 optimal weight: 6.9990 chunk 32 optimal weight: 4.9990 chunk 24 optimal weight: 6.9990 chunk 21 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 34 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5257 moved from start: 2.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.084 11874 Z= 0.490 Angle : 1.250 12.970 18319 Z= 0.593 Chirality : 0.057 0.351 2412 Planarity : 0.007 0.041 619 Dihedral : 31.647 179.931 7286 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 33.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer: Outliers : 6.12 % Allowed : 26.53 % Favored : 67.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.99 (0.76), residues: 110 helix: -1.36 (0.78), residues: 40 sheet: -2.20 (0.81), residues: 31 loop : -2.16 (1.01), residues: 39 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP A 108 HIS 0.007 0.003 HIS A 59 PHE 0.019 0.005 PHE A 19 ARG 0.011 0.001 ARG A 57 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 98 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 18 time to evaluate : 0.405 Fit side-chains revert: symmetry clash REVERT: A 89 LYS cc_start: 0.8497 (mmmt) cc_final: 0.8232 (mmmt) REVERT: A 110 ARG cc_start: 0.8660 (ptt90) cc_final: 0.8175 (mmm160) outliers start: 6 outliers final: 3 residues processed: 21 average time/residue: 0.2816 time to fit residues: 8.1704 Evaluate side-chains 18 residues out of total 98 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 15 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 107 LEU 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: 0.8980 chunk 42 optimal weight: 2.9990 chunk 49 optimal weight: 9.9990 chunk 51 optimal weight: 20.0000 chunk 47 optimal weight: 4.9990 chunk 50 optimal weight: 9.9990 chunk 30 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 chunk 39 optimal weight: 8.9990 chunk 15 optimal weight: 10.0000 overall best weight: 3.7788 ------------------------------------------------------------------------------- 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: 0.5295 moved from start: 2.3294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 11874 Z= 0.440 Angle : 1.151 11.785 18319 Z= 0.546 Chirality : 0.053 0.355 2412 Planarity : 0.007 0.050 619 Dihedral : 31.493 179.528 7286 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 29.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.91 % Favored : 89.09 % Rotamer: Outliers : 3.06 % Allowed : 30.61 % Favored : 66.33 % 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: -3.01 (0.78), residues: 110 helix: -1.41 (0.77), residues: 41 sheet: -2.27 (0.80), residues: 31 loop : -2.09 (1.12), residues: 38 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP A 108 HIS 0.010 0.003 HIS A 59 PHE 0.031 0.004 PHE A 19 ARG 0.009 0.001 ARG A 37 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 98 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 17 time to evaluate : 0.395 Fit side-chains revert: symmetry clash REVERT: A 110 ARG cc_start: 0.8549 (ptt90) cc_final: 0.8145 (mmm160) outliers start: 3 outliers final: 2 residues processed: 18 average time/residue: 0.3447 time to fit residues: 8.2477 Evaluate side-chains 19 residues out of total 98 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 17 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 107 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 45 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 50 optimal weight: 9.9990 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: 5.9990 chunk 51 optimal weight: 20.0000 chunk 44 optimal weight: 1.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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: 0.5359 moved from start: 2.4376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.088 11874 Z= 0.492 Angle : 1.218 12.852 18319 Z= 0.579 Chirality : 0.056 0.346 2412 Planarity : 0.007 0.048 619 Dihedral : 31.668 179.818 7286 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 33.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 5.10 % Allowed : 28.57 % Favored : 66.33 % 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: -3.11 (0.77), residues: 110 helix: -1.65 (0.74), residues: 40 sheet: -2.37 (0.78), residues: 31 loop : -1.89 (1.14), residues: 39 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.004 TRP A 108 HIS 0.009 0.003 HIS A 59 PHE 0.021 0.004 PHE A 19 ARG 0.008 0.001 ARG A 57 *********************** 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 22 residues out of total 98 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 17 time to evaluate : 0.367 Fit side-chains revert: symmetry clash REVERT: A 89 LYS cc_start: 0.8720 (mmmt) cc_final: 0.8490 (mmmt) REVERT: A 106 LYS cc_start: 0.9376 (mtmm) cc_final: 0.9077 (mtmm) outliers start: 5 outliers final: 3 residues processed: 19 average time/residue: 0.3388 time to fit residues: 8.6242 Evaluate side-chains 20 residues out of total 98 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 17 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 107 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 4 optimal weight: 0.9990 chunk 34 optimal weight: 4.9990 chunk 27 optimal weight: 9.9990 chunk 35 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 6 optimal weight: 0.6980 chunk 12 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5243 moved from start: 2.4148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 11874 Z= 0.283 Angle : 0.917 10.358 18319 Z= 0.437 Chirality : 0.043 0.314 2412 Planarity : 0.006 0.037 619 Dihedral : 31.086 179.650 7286 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 17.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 2.04 % Allowed : 30.61 % Favored : 67.35 % 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: -2.74 (0.75), residues: 110 helix: -1.43 (0.70), residues: 41 sheet: -2.20 (0.77), residues: 31 loop : -1.53 (1.12), residues: 38 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP A 108 HIS 0.004 0.002 HIS A 59 PHE 0.011 0.002 PHE A 19 ARG 0.008 0.001 ARG A 73 ********************** 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 20 residues out of total 98 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 18 time to evaluate : 0.429 Fit side-chains REVERT: A 82 MET cc_start: 0.5678 (mtt) cc_final: 0.5361 (mtm) REVERT: A 89 LYS cc_start: 0.8734 (mmmt) cc_final: 0.8501 (mmmt) REVERT: A 106 LYS cc_start: 0.9403 (mtmm) cc_final: 0.9003 (ptpp) REVERT: A 110 ARG cc_start: 0.8433 (ptt90) cc_final: 0.8089 (mmm160) outliers start: 2 outliers final: 1 residues processed: 19 average time/residue: 0.2981 time to fit residues: 7.8361 Evaluate side-chains 17 residues out of total 98 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 16 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 45 optimal weight: 4.9990 chunk 5 optimal weight: 0.0000 chunk 8 optimal weight: 0.8980 chunk 39 optimal weight: 9.9990 chunk 2 optimal weight: 0.8980 chunk 32 optimal weight: 4.9990 chunk 50 optimal weight: 10.0000 chunk 29 optimal weight: 7.9990 chunk 38 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- 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 = 0.4417 r_free = 0.4417 target = 0.115722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.103648 restraints weight = 91348.342| |-----------------------------------------------------------------------------| r_work (start): 0.4112 rms_B_bonded: 1.35 r_work (final): 0.4112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5996 moved from start: 2.4025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 11874 Z= 0.212 Angle : 0.802 9.833 18319 Z= 0.384 Chirality : 0.038 0.321 2412 Planarity : 0.005 0.029 619 Dihedral : 30.683 178.941 7286 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 1.02 % Allowed : 30.61 % Favored : 68.37 % 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: -2.30 (0.76), residues: 110 helix: -0.93 (0.77), residues: 40 sheet: -2.25 (0.77), residues: 30 loop : -1.22 (1.04), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP A 108 HIS 0.004 0.002 HIS A 111 PHE 0.014 0.002 PHE A 19 ARG 0.009 0.001 ARG A 26 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1790.98 seconds wall clock time: 32 minutes 54.80 seconds (1974.80 seconds total)