Starting phenix.real_space_refine on Thu Dec 7 16:57:00 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x34_32978/12_2023/7x34_32978.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x34_32978/12_2023/7x34_32978.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x34_32978/12_2023/7x34_32978.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x34_32978/12_2023/7x34_32978.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x34_32978/12_2023/7x34_32978.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x34_32978/12_2023/7x34_32978.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 215 atoms to isotropic. 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: 4 Type Number sf(0) Gaussians P 94 5.49 5 C 1365 2.51 5 N 503 2.21 5 O 800 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C TYR 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.00s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 2762 Number of models: 1 Model: "" Number of chains: 2 Chain: "C" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 745 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 98} Chain: "3" Number of atoms: 2017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 2017 Classifications: {'RNA': 94} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 2, 'rna3p_pur': 54, 'rna3p_pyr': 36} Link IDs: {'rna2p': 3, 'rna3p': 90} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" P A 31756 " occ=0.55 ... (20 atoms not shown) pdb=" C4 A 31756 " occ=0.55 Time building chain proxies: 2.13, per 1000 atoms: 0.77 Number of scatterers: 2762 At special positions: 0 Unit cell: (141.024, 88.14, 172.212, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) P 94 15.00 O 800 8.00 N 503 7.00 C 1365 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: 1.69 Conformation dependent library (CDL) restraints added in 161.2 milliseconds 196 Ramachandran restraints generated. 98 Oldfield, 0 Emsley, 98 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 192 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 0 sheets defined 77.0% alpha, 0.0% beta 19 base pairs and 62 stacking pairs defined. Time for finding SS restraints: 1.21 Creating SS restraints... Processing helix chain 'C' and resid 334 through 365 removed outlier: 3.869A pdb=" N ALA C 338 " --> pdb=" O ALA C 334 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA C 350 " --> pdb=" O ALA C 346 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS C 351 " --> pdb=" O ALA C 347 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASN C 354 " --> pdb=" O ALA C 350 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LYS C 355 " --> pdb=" O LYS C 351 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ALA C 362 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N LYS C 363 " --> pdb=" O ARG C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 387 Processing helix chain 'C' and resid 389 through 403 Processing helix chain 'C' and resid 407 through 421 54 hydrogen bonds defined for protein. 162 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 48 hydrogen bonds 76 hydrogen bond angles 0 basepair planarities 19 basepair parallelities 62 stacking parallelities Total time for adding SS restraints: 0.83 Time building geometry restraints manager: 1.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.04 - 1.16: 1 1.16 - 1.27: 221 1.27 - 1.39: 849 1.39 - 1.50: 1042 1.50 - 1.62: 896 Bond restraints: 3009 Sorted by residual: bond pdb=" CG PRO C 425 " pdb=" CD PRO C 425 " ideal model delta sigma weight residual 1.503 1.043 0.460 3.40e-02 8.65e+02 1.83e+02 bond pdb=" N PRO C 425 " pdb=" CD PRO C 425 " ideal model delta sigma weight residual 1.473 1.540 -0.067 1.40e-02 5.10e+03 2.28e+01 bond pdb=" CA ASN C 403 " pdb=" C ASN C 403 " ideal model delta sigma weight residual 1.526 1.543 -0.017 1.08e-02 8.57e+03 2.52e+00 bond pdb=" N1 U 31708 " pdb=" C2 U 31708 " ideal model delta sigma weight residual 1.381 1.406 -0.025 2.00e-02 2.50e+03 1.62e+00 bond pdb=" CB ASN C 403 " pdb=" CG ASN C 403 " ideal model delta sigma weight residual 1.516 1.544 -0.028 2.50e-02 1.60e+03 1.24e+00 ... (remaining 3004 not shown) Histogram of bond angle deviations from ideal: 77.26 - 89.27: 2 89.27 - 101.28: 28 101.28 - 113.29: 2288 113.29 - 125.30: 1842 125.30 - 137.31: 363 Bond angle restraints: 4523 Sorted by residual: angle pdb=" N PRO C 425 " pdb=" CD PRO C 425 " pdb=" CG PRO C 425 " ideal model delta sigma weight residual 103.20 77.26 25.94 1.50e+00 4.44e-01 2.99e+02 angle pdb=" CA PRO C 425 " pdb=" CB PRO C 425 " pdb=" CG PRO C 425 " ideal model delta sigma weight residual 104.50 84.84 19.66 1.90e+00 2.77e-01 1.07e+02 angle pdb=" CA PRO C 425 " pdb=" N PRO C 425 " pdb=" CD PRO C 425 " ideal model delta sigma weight residual 112.00 100.92 11.08 1.40e+00 5.10e-01 6.27e+01 angle pdb=" CB PRO C 425 " pdb=" CG PRO C 425 " pdb=" CD PRO C 425 " ideal model delta sigma weight residual 106.10 125.98 -19.88 3.20e+00 9.77e-02 3.86e+01 angle pdb=" CA ARG C 359 " pdb=" CB ARG C 359 " pdb=" CG ARG C 359 " ideal model delta sigma weight residual 114.10 122.09 -7.99 2.00e+00 2.50e-01 1.60e+01 ... (remaining 4518 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.62: 1598 35.62 - 71.23: 200 71.23 - 106.85: 28 106.85 - 142.46: 0 142.46 - 178.08: 1 Dihedral angle restraints: 1827 sinusoidal: 1534 harmonic: 293 Sorted by residual: dihedral pdb=" O4' U 31761 " pdb=" C1' U 31761 " pdb=" N1 U 31761 " pdb=" C2 U 31761 " ideal model delta sinusoidal sigma weight residual -128.00 50.08 -178.08 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' A 31707 " pdb=" C1' A 31707 " pdb=" N9 A 31707 " pdb=" C4 A 31707 " ideal model delta sinusoidal sigma weight residual 70.00 2.44 67.56 1 2.00e+01 2.50e-03 1.48e+01 dihedral pdb=" N PRO C 425 " pdb=" CG PRO C 425 " pdb=" CD PRO C 425 " pdb=" CB PRO C 425 " ideal model delta sinusoidal sigma weight residual 30.00 77.42 -47.42 1 1.50e+01 4.44e-03 1.38e+01 ... (remaining 1824 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 458 0.046 - 0.093: 89 0.093 - 0.139: 29 0.139 - 0.185: 8 0.185 - 0.231: 4 Chirality restraints: 588 Sorted by residual: chirality pdb=" CB ILE C 358 " pdb=" CA ILE C 358 " pdb=" CG1 ILE C 358 " pdb=" CG2 ILE C 358 " both_signs ideal model delta sigma weight residual False 2.64 2.88 -0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" C1' U 31752 " pdb=" O4' U 31752 " pdb=" C2' U 31752 " pdb=" N1 U 31752 " both_signs ideal model delta sigma weight residual False 2.47 2.26 0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" C1' G 31760 " pdb=" O4' G 31760 " pdb=" C2' G 31760 " pdb=" N9 G 31760 " both_signs ideal model delta sigma weight residual False 2.46 2.26 0.20 2.00e-01 2.50e+01 1.01e+00 ... (remaining 585 not shown) Planarity restraints: 222 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G 31747 " 0.036 2.00e-02 2.50e+03 1.52e-02 6.96e+00 pdb=" N9 G 31747 " -0.035 2.00e-02 2.50e+03 pdb=" C8 G 31747 " -0.003 2.00e-02 2.50e+03 pdb=" N7 G 31747 " 0.001 2.00e-02 2.50e+03 pdb=" C5 G 31747 " -0.004 2.00e-02 2.50e+03 pdb=" C6 G 31747 " 0.007 2.00e-02 2.50e+03 pdb=" O6 G 31747 " 0.009 2.00e-02 2.50e+03 pdb=" N1 G 31747 " 0.004 2.00e-02 2.50e+03 pdb=" C2 G 31747 " 0.000 2.00e-02 2.50e+03 pdb=" N2 G 31747 " -0.003 2.00e-02 2.50e+03 pdb=" N3 G 31747 " -0.006 2.00e-02 2.50e+03 pdb=" C4 G 31747 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U 31752 " 0.032 2.00e-02 2.50e+03 1.60e-02 5.75e+00 pdb=" N1 U 31752 " -0.031 2.00e-02 2.50e+03 pdb=" C2 U 31752 " -0.005 2.00e-02 2.50e+03 pdb=" O2 U 31752 " -0.006 2.00e-02 2.50e+03 pdb=" N3 U 31752 " 0.007 2.00e-02 2.50e+03 pdb=" C4 U 31752 " 0.002 2.00e-02 2.50e+03 pdb=" O4 U 31752 " 0.009 2.00e-02 2.50e+03 pdb=" C5 U 31752 " 0.002 2.00e-02 2.50e+03 pdb=" C6 U 31752 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G 31760 " 0.029 2.00e-02 2.50e+03 1.23e-02 4.57e+00 pdb=" N9 G 31760 " -0.028 2.00e-02 2.50e+03 pdb=" C8 G 31760 " -0.006 2.00e-02 2.50e+03 pdb=" N7 G 31760 " -0.000 2.00e-02 2.50e+03 pdb=" C5 G 31760 " 0.002 2.00e-02 2.50e+03 pdb=" C6 G 31760 " 0.004 2.00e-02 2.50e+03 pdb=" O6 G 31760 " 0.008 2.00e-02 2.50e+03 pdb=" N1 G 31760 " 0.003 2.00e-02 2.50e+03 pdb=" C2 G 31760 " -0.002 2.00e-02 2.50e+03 pdb=" N2 G 31760 " -0.003 2.00e-02 2.50e+03 pdb=" N3 G 31760 " -0.004 2.00e-02 2.50e+03 pdb=" C4 G 31760 " -0.003 2.00e-02 2.50e+03 ... (remaining 219 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 823 2.83 - 3.35: 2506 3.35 - 3.87: 6051 3.87 - 4.38: 6453 4.38 - 4.90: 8054 Nonbonded interactions: 23887 Sorted by model distance: nonbonded pdb=" N2 G 31697 " pdb=" O2 U 31704 " model vdw 2.316 2.496 nonbonded pdb=" O2 U 31684 " pdb=" N2 G 31717 " model vdw 2.356 2.496 nonbonded pdb=" O2' A 31755 " pdb=" O4' A 31756 " model vdw 2.383 2.440 nonbonded pdb=" O4 U 31684 " pdb=" O6 G 31717 " model vdw 2.411 2.432 nonbonded pdb=" O GLU C 392 " pdb=" OG1 THR C 396 " model vdw 2.422 2.440 ... (remaining 23882 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 Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.55 max=1.00 mean=1.00 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: 1.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 9.310 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.710 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.000 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 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 : 0.009 0.460 3009 Z= 0.669 Angle : 1.172 25.944 4523 Z= 0.608 Chirality : 0.047 0.231 588 Planarity : 0.007 0.070 222 Dihedral : 23.928 178.075 1635 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % 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: -2.86 (0.75), residues: 98 helix: -1.82 (0.46), residues: 79 sheet: None (None), residues: 0 loop : -1.15 (1.77), residues: 19 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.007 0.002 PHE C 368 TYR 0.014 0.002 TYR C 367 ARG 0.003 0.001 ARG C 356 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 196 Ramachandran restraints generated. 98 Oldfield, 0 Emsley, 98 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 196 Ramachandran restraints generated. 98 Oldfield, 0 Emsley, 98 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 77 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 17 time to evaluate : 0.156 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.0870 time to fit residues: 2.0778 Evaluate side-chains 11 residues out of total 77 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 11 time to evaluate : 0.155 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 16 optimal weight: 20.0000 chunk 14 optimal weight: 20.0000 chunk 7 optimal weight: 6.9990 chunk 4 optimal weight: 8.9990 chunk 9 optimal weight: 0.0050 chunk 5 optimal weight: 7.9990 chunk 11 optimal weight: 9.9990 chunk 17 optimal weight: 20.0000 chunk 18 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 chunk 13 optimal weight: 20.0000 overall best weight: 6.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 360 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3009 Z= 0.266 Angle : 0.764 9.057 4523 Z= 0.389 Chirality : 0.038 0.279 588 Planarity : 0.005 0.025 222 Dihedral : 25.034 160.819 1451 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 31.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 1.30 % Allowed : 20.78 % Favored : 77.92 % 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: -0.37 (0.85), residues: 98 helix: 0.14 (0.58), residues: 69 sheet: None (None), residues: 0 loop : -0.93 (1.36), residues: 29 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.008 0.003 PHE C 368 TYR 0.009 0.002 TYR C 367 ARG 0.003 0.001 ARG C 359 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 196 Ramachandran restraints generated. 98 Oldfield, 0 Emsley, 98 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 196 Ramachandran restraints generated. 98 Oldfield, 0 Emsley, 98 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 77 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 17 time to evaluate : 0.150 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 17 average time/residue: 0.0798 time to fit residues: 1.9492 Evaluate side-chains 10 residues out of total 77 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 9 time to evaluate : 0.144 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0380 time to fit residues: 0.1983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 17 optimal weight: 20.0000 chunk 12 optimal weight: 10.0000 chunk 8 optimal weight: 10.0000 chunk 1 optimal weight: 9.9990 chunk 11 optimal weight: 20.0000 chunk 18 optimal weight: 10.0000 chunk 9 optimal weight: 10.0000 chunk 16 optimal weight: 20.0000 chunk 4 optimal weight: 4.9990 chunk 15 optimal weight: 10.0000 chunk 10 optimal weight: 10.0000 overall best weight: 8.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.3907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 3009 Z= 0.329 Angle : 0.863 13.308 4523 Z= 0.441 Chirality : 0.045 0.321 588 Planarity : 0.005 0.020 222 Dihedral : 25.327 147.602 1451 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 40.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.30 % Allowed : 28.57 % Favored : 70.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.83), residues: 98 helix: -0.03 (0.59), residues: 69 sheet: None (None), residues: 0 loop : -1.08 (1.28), residues: 29 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.012 0.004 PHE C 432 TYR 0.019 0.005 TYR C 367 ARG 0.003 0.001 ARG C 359 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 196 Ramachandran restraints generated. 98 Oldfield, 0 Emsley, 98 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 196 Ramachandran restraints generated. 98 Oldfield, 0 Emsley, 98 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 12 residues out of total 77 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 11 time to evaluate : 0.146 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 11 average time/residue: 0.0750 time to fit residues: 1.2748 Evaluate side-chains 9 residues out of total 77 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 9 time to evaluate : 0.147 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 0 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 7 optimal weight: 2.9990 chunk 15 optimal weight: 10.0000 chunk 12 optimal weight: 10.0000 chunk 9 optimal weight: 6.9990 chunk 16 optimal weight: 20.0000 chunk 4 optimal weight: 10.0000 chunk 6 optimal weight: 5.9990 chunk 3 optimal weight: 0.0470 chunk 10 optimal weight: 10.0000 overall best weight: 5.2088 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.3899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3009 Z= 0.209 Angle : 0.724 13.380 4523 Z= 0.372 Chirality : 0.038 0.273 588 Planarity : 0.004 0.018 222 Dihedral : 25.088 148.941 1451 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 27.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 1.30 % Allowed : 22.08 % Favored : 76.62 % 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: -0.11 (0.84), residues: 98 helix: 0.37 (0.59), residues: 69 sheet: None (None), residues: 0 loop : -0.94 (1.30), residues: 29 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.008 0.003 PHE C 432 TYR 0.013 0.003 TYR C 367 ARG 0.002 0.001 ARG C 356 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 196 Ramachandran restraints generated. 98 Oldfield, 0 Emsley, 98 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 196 Ramachandran restraints generated. 98 Oldfield, 0 Emsley, 98 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 77 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 12 time to evaluate : 0.164 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 12 average time/residue: 0.0780 time to fit residues: 1.4415 Evaluate side-chains 11 residues out of total 77 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 10 time to evaluate : 0.160 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0308 time to fit residues: 0.2250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 4 optimal weight: 7.9990 chunk 18 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 chunk 8 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 6 optimal weight: 6.9990 chunk 9 optimal weight: 0.0270 chunk 17 optimal weight: 20.0000 chunk 2 optimal weight: 10.0000 chunk 10 optimal weight: 10.0000 chunk 13 optimal weight: 20.0000 overall best weight: 5.4046 ------------------------------------------------------------------------------- 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: 0.7805 moved from start: 0.3992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3009 Z= 0.222 Angle : 0.725 12.198 4523 Z= 0.374 Chirality : 0.039 0.269 588 Planarity : 0.004 0.018 222 Dihedral : 25.102 147.803 1451 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 30.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.00 % Allowed : 22.08 % Favored : 77.92 % 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: 0.15 (0.84), residues: 98 helix: 0.56 (0.61), residues: 69 sheet: None (None), residues: 0 loop : -0.81 (1.23), residues: 29 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.021 0.005 PHE C 432 TYR 0.029 0.006 TYR C 367 ARG 0.002 0.001 ARG C 356 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 196 Ramachandran restraints generated. 98 Oldfield, 0 Emsley, 98 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 196 Ramachandran restraints generated. 98 Oldfield, 0 Emsley, 98 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 10 residues out of total 77 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 10 time to evaluate : 0.150 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.0810 time to fit residues: 1.2524 Evaluate side-chains 10 residues out of total 77 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 10 time to evaluate : 0.152 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 10 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 chunk 18 optimal weight: 10.0000 chunk 11 optimal weight: 20.0000 chunk 8 optimal weight: 8.9990 chunk 7 optimal weight: 6.9990 chunk 5 optimal weight: 7.9990 chunk 3 optimal weight: 10.0000 chunk 12 optimal weight: 10.0000 chunk 9 optimal weight: 7.9990 chunk 1 optimal weight: 8.9990 overall best weight: 8.1990 ------------------------------------------------------------------------------- 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: 0.7835 moved from start: 0.4186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 3009 Z= 0.297 Angle : 0.778 11.489 4523 Z= 0.401 Chirality : 0.041 0.271 588 Planarity : 0.004 0.019 222 Dihedral : 25.148 143.219 1451 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 37.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.60 % Allowed : 20.78 % Favored : 76.62 % 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: 0.24 (0.83), residues: 98 helix: 0.55 (0.59), residues: 69 sheet: None (None), residues: 0 loop : -0.56 (1.28), residues: 29 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.017 0.004 PHE C 432 TYR 0.034 0.007 TYR C 367 ARG 0.001 0.001 ARG C 356 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 196 Ramachandran restraints generated. 98 Oldfield, 0 Emsley, 98 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 196 Ramachandran restraints generated. 98 Oldfield, 0 Emsley, 98 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 77 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 11 time to evaluate : 0.142 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 12 average time/residue: 0.0740 time to fit residues: 1.3791 Evaluate side-chains 12 residues out of total 77 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 11 time to evaluate : 0.143 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0330 time to fit residues: 0.2028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 14 optimal weight: 20.0000 chunk 16 optimal weight: 20.0000 chunk 17 optimal weight: 10.0000 chunk 10 optimal weight: 10.0000 chunk 7 optimal weight: 8.9990 chunk 13 optimal weight: 10.0000 chunk 5 optimal weight: 6.9990 chunk 15 optimal weight: 10.0000 chunk 11 optimal weight: 10.0000 chunk 18 optimal weight: 10.0000 chunk 8 optimal weight: 10.0000 overall best weight: 9.1996 ------------------------------------------------------------------------------- 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: 0.7890 moved from start: 0.5178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 3009 Z= 0.343 Angle : 0.919 18.215 4523 Z= 0.468 Chirality : 0.047 0.330 588 Planarity : 0.005 0.019 222 Dihedral : 25.490 136.381 1451 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 43.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.30 % Allowed : 24.68 % Favored : 74.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.82), residues: 98 helix: 0.19 (0.59), residues: 69 sheet: None (None), residues: 0 loop : -0.47 (1.23), residues: 29 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.005 0.002 PHE C 432 TYR 0.037 0.007 TYR C 367 ARG 0.005 0.002 ARG C 356 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 196 Ramachandran restraints generated. 98 Oldfield, 0 Emsley, 98 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 196 Ramachandran restraints generated. 98 Oldfield, 0 Emsley, 98 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 12 residues out of total 77 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 11 time to evaluate : 0.159 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 12 average time/residue: 0.0777 time to fit residues: 1.4262 Evaluate side-chains 12 residues out of total 77 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 11 time to evaluate : 0.161 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0333 time to fit residues: 0.2131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 12 optimal weight: 9.9990 chunk 18 optimal weight: 10.0000 chunk 17 optimal weight: 20.0000 chunk 15 optimal weight: 10.0000 chunk 1 optimal weight: 9.9990 chunk 11 optimal weight: 20.0000 chunk 9 optimal weight: 0.1980 chunk 16 optimal weight: 20.0000 chunk 4 optimal weight: 0.4980 chunk 13 optimal weight: 10.0000 chunk 2 optimal weight: 7.9990 overall best weight: 5.7386 ------------------------------------------------------------------------------- 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: 0.7817 moved from start: 0.5119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3009 Z= 0.233 Angle : 0.771 14.442 4523 Z= 0.397 Chirality : 0.041 0.317 588 Planarity : 0.004 0.018 222 Dihedral : 25.310 129.602 1451 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 31.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 0.00 % Allowed : 24.68 % Favored : 75.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.82), residues: 98 helix: 0.48 (0.60), residues: 70 sheet: None (None), residues: 0 loop : -0.64 (1.14), residues: 28 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.005 0.002 PHE C 368 TYR 0.015 0.004 TYR C 367 ARG 0.004 0.001 ARG C 356 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 196 Ramachandran restraints generated. 98 Oldfield, 0 Emsley, 98 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 196 Ramachandran restraints generated. 98 Oldfield, 0 Emsley, 98 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 10 residues out of total 77 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 10 time to evaluate : 0.139 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.0717 time to fit residues: 1.1530 Evaluate side-chains 9 residues out of total 77 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 9 time to evaluate : 0.142 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 4 optimal weight: 0.9990 chunk 15 optimal weight: 10.0000 chunk 6 optimal weight: 6.9990 chunk 1 optimal weight: 6.9990 chunk 2 optimal weight: 9.9990 chunk 13 optimal weight: 20.0000 chunk 0 optimal weight: 3.9990 chunk 10 optimal weight: 10.0000 chunk 17 optimal weight: 20.0000 chunk 12 optimal weight: 9.9990 chunk 11 optimal weight: 20.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- 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: 0.7814 moved from start: 0.5178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3009 Z= 0.236 Angle : 0.784 16.056 4523 Z= 0.401 Chirality : 0.040 0.326 588 Planarity : 0.004 0.018 222 Dihedral : 25.329 131.652 1451 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 30.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 1.30 % Allowed : 24.68 % Favored : 74.03 % 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: 0.28 (0.82), residues: 98 helix: 0.61 (0.62), residues: 69 sheet: None (None), residues: 0 loop : -0.63 (1.07), residues: 29 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.004 0.002 PHE C 432 TYR 0.011 0.003 TYR C 431 ARG 0.005 0.001 ARG C 356 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 196 Ramachandran restraints generated. 98 Oldfield, 0 Emsley, 98 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 196 Ramachandran restraints generated. 98 Oldfield, 0 Emsley, 98 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 10 residues out of total 77 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 9 time to evaluate : 0.171 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 9 average time/residue: 0.0685 time to fit residues: 1.0353 Evaluate side-chains 9 residues out of total 77 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 8 time to evaluate : 0.136 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0296 time to fit residues: 0.1866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 10 optimal weight: 10.0000 chunk 7 optimal weight: 2.9990 chunk 18 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 3 optimal weight: 8.9990 chunk 2 optimal weight: 6.9990 chunk 4 optimal weight: 7.9990 chunk 15 optimal weight: 10.0000 chunk 17 optimal weight: 10.0000 chunk 8 optimal weight: 4.9990 chunk 1 optimal weight: 9.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 389 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.5470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3009 Z= 0.251 Angle : 0.775 9.876 4523 Z= 0.404 Chirality : 0.043 0.342 588 Planarity : 0.005 0.030 222 Dihedral : 25.357 133.903 1451 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 33.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 0.00 % Allowed : 25.97 % Favored : 74.03 % 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: -0.18 (0.81), residues: 98 helix: 0.31 (0.60), residues: 70 sheet: None (None), residues: 0 loop : -0.97 (1.10), residues: 28 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.006 0.002 PHE C 432 TYR 0.010 0.003 TYR C 431 ARG 0.004 0.002 ARG C 356 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 196 Ramachandran restraints generated. 98 Oldfield, 0 Emsley, 98 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 196 Ramachandran restraints generated. 98 Oldfield, 0 Emsley, 98 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 9 residues out of total 77 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 9 time to evaluate : 0.128 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 9 average time/residue: 0.0619 time to fit residues: 0.9226 Evaluate side-chains 8 residues out of total 77 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 8 time to evaluate : 0.127 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 4 optimal weight: 10.0000 chunk 12 optimal weight: 9.9990 chunk 6 optimal weight: 10.0000 chunk 3 optimal weight: 9.9990 chunk 9 optimal weight: 0.7980 chunk 0 optimal weight: 20.0000 chunk 1 optimal weight: 7.9990 chunk 18 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 chunk 17 optimal weight: 10.0000 overall best weight: 7.7590 ------------------------------------------------------------------------------- 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 = 0.3681 r_free = 0.3681 target = 0.046730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.039665 restraints weight = 39376.398| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 3.99 r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3525 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3525 r_free = 0.3525 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3523 r_free = 0.3523 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3523 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.5932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 3009 Z= 0.292 Angle : 0.850 18.304 4523 Z= 0.432 Chirality : 0.044 0.368 588 Planarity : 0.005 0.024 222 Dihedral : 25.540 136.178 1451 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 38.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 0.00 % Allowed : 27.27 % Favored : 72.73 % 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: 0.11 (0.83), residues: 98 helix: 0.48 (0.61), residues: 70 sheet: None (None), residues: 0 loop : -0.73 (1.16), residues: 28 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.007 0.002 PHE C 432 TYR 0.009 0.002 TYR C 431 ARG 0.005 0.002 ARG C 356 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 827.72 seconds wall clock time: 16 minutes 7.95 seconds (967.95 seconds total)