Starting phenix.real_space_refine on Sun Mar 10 15:29:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x34_32978/03_2024/7x34_32978.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x34_32978/03_2024/7x34_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_32978/03_2024/7x34_32978.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x34_32978/03_2024/7x34_32978.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x34_32978/03_2024/7x34_32978.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x34_32978/03_2024/7x34_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-dev-5265/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: 2.07, per 1000 atoms: 0.75 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: 1.63 Conformation dependent library (CDL) restraints added in 169.6 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: 1.32 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: 1.71 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: 1641 35.62 - 71.23: 237 71.23 - 106.85: 28 106.85 - 142.46: 0 142.46 - 178.08: 1 Dihedral angle restraints: 1907 sinusoidal: 1614 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 1904 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: 2.060 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: 9.400 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.740 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 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:2.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.790 ------------------------------------------------------------------------------- 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 : 24.837 178.075 1715 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 : 0.154 Fit side-chains REVERT: C 366 ASP cc_start: 0.9573 (m-30) cc_final: 0.9369 (m-30) REVERT: C 378 ASP cc_start: 0.8190 (m-30) cc_final: 0.7918 (m-30) outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.0877 time to fit residues: 2.1036 Evaluate side-chains 13 residues out of total 77 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.147 ------------------------------------------------------------------------------- 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: 10.0000 chunk 9 optimal weight: 10.0000 chunk 5 optimal weight: 6.9990 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: 8.7994 ------------------------------------------------------------------------------- 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: 0.7842 moved from start: 0.2462 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= 0.311 Angle : 0.820 9.924 4523 Z= 0.421 Chirality : 0.042 0.288 588 Planarity : 0.005 0.031 222 Dihedral : 25.972 160.346 1531 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 34.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 1.30 % Allowed : 19.48 % Favored : 79.22 % 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: -0.58 (0.82), residues: 98 helix: -0.06 (0.57), residues: 69 sheet: None (None), residues: 0 loop : -0.86 (1.31), residues: 29 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.011 0.004 PHE C 368 TYR 0.013 0.003 TYR C 367 ARG 0.002 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 17 residues out of total 77 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 16 time to evaluate : 0.156 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 16 average time/residue: 0.0792 time to fit residues: 1.8379 Evaluate side-chains 11 residues out of total 77 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 10 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 389 ASN 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: 9.9990 chunk 8 optimal weight: 5.9990 chunk 1 optimal weight: 7.9990 chunk 11 optimal weight: 20.0000 chunk 18 optimal weight: 10.0000 chunk 9 optimal weight: 4.9990 chunk 16 optimal weight: 20.0000 chunk 4 optimal weight: 5.9990 chunk 15 optimal weight: 10.0000 chunk 10 optimal weight: 10.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.3538 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= 0.262 Angle : 0.777 13.718 4523 Z= 0.397 Chirality : 0.040 0.304 588 Planarity : 0.005 0.020 222 Dihedral : 26.007 150.893 1531 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 32.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 1.30 % Allowed : 23.38 % 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: -0.43 (0.84), residues: 98 helix: 0.13 (0.60), residues: 69 sheet: None (None), residues: 0 loop : -1.07 (1.28), residues: 29 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.007 0.002 PHE C 432 TYR 0.007 0.003 TYR C 367 ARG 0.003 0.001 ARG C 356 *********************** 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 : 0.160 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 11 average time/residue: 0.0804 time to fit residues: 1.3620 Evaluate side-chains 10 residues out of total 77 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 9 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 389 ASN 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: 0.2980 chunk 15 optimal weight: 10.0000 chunk 12 optimal weight: 10.0000 chunk 9 optimal weight: 0.9990 chunk 16 optimal weight: 20.0000 chunk 4 optimal weight: 10.0000 chunk 6 optimal weight: 6.9990 chunk 3 optimal weight: 5.9990 chunk 10 optimal weight: 10.0000 overall best weight: 4.8590 ------------------------------------------------------------------------------- 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: 0.7797 moved from start: 0.3659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3009 Z= 0.202 Angle : 0.706 10.045 4523 Z= 0.366 Chirality : 0.038 0.277 588 Planarity : 0.004 0.018 222 Dihedral : 25.906 151.243 1531 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 28.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % 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: -0.22 (0.82), residues: 98 helix: 0.35 (0.59), residues: 69 sheet: None (None), residues: 0 loop : -1.16 (1.21), residues: 29 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.012 0.004 PHE C 432 TYR 0.019 0.004 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 14 residues out of total 77 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 12 time to evaluate : 0.164 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 12 average time/residue: 0.0800 time to fit residues: 1.4694 Evaluate side-chains 11 residues out of total 77 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 10 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 389 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 4 optimal weight: 9.9990 chunk 18 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 chunk 8 optimal weight: 8.9990 chunk 1 optimal weight: 6.9990 chunk 6 optimal weight: 5.9990 chunk 9 optimal weight: 9.9990 chunk 17 optimal weight: 10.0000 chunk 2 optimal weight: 6.9990 chunk 10 optimal weight: 10.0000 chunk 13 optimal weight: 20.0000 overall best weight: 7.7990 ------------------------------------------------------------------------------- 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: 0.7824 moved from start: 0.3878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 3009 Z= 0.279 Angle : 0.778 14.866 4523 Z= 0.396 Chirality : 0.041 0.282 588 Planarity : 0.004 0.019 222 Dihedral : 25.945 147.003 1531 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 34.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % 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: -0.09 (0.82), residues: 98 helix: 0.44 (0.60), residues: 69 sheet: None (None), residues: 0 loop : -1.08 (1.17), residues: 29 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.008 0.003 PHE C 432 TYR 0.024 0.004 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 11 residues out of total 77 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 10 time to evaluate : 0.159 Fit side-chains REVERT: C 367 TYR cc_start: 0.6324 (m-80) cc_final: 0.5902 (m-80) outliers start: 1 outliers final: 1 residues processed: 10 average time/residue: 0.0796 time to fit residues: 1.2591 Evaluate side-chains 11 residues out of total 77 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 10 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 389 ASN 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: 0.0010 chunk 3 optimal weight: 2.9990 chunk 12 optimal weight: 10.0000 chunk 9 optimal weight: 8.9990 chunk 1 optimal weight: 5.9990 overall best weight: 4.9994 ------------------------------------------------------------------------------- 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: 0.7795 moved from start: 0.3932 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= 0.205 Angle : 0.717 13.962 4523 Z= 0.368 Chirality : 0.038 0.256 588 Planarity : 0.004 0.018 222 Dihedral : 25.932 149.161 1531 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 28.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 1.30 % Allowed : 23.38 % 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: -0.07 (0.83), residues: 98 helix: 0.51 (0.61), residues: 70 sheet: None (None), residues: 0 loop : -1.29 (1.16), residues: 28 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.008 0.002 PHE C 432 TYR 0.016 0.003 TYR C 367 ARG 0.003 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 12 residues out of total 77 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 11 time to evaluate : 0.139 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 11 average time/residue: 0.0747 time to fit residues: 1.2877 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 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 389 ASN 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: 20.0000 chunk 5 optimal weight: 0.2980 chunk 15 optimal weight: 10.0000 chunk 11 optimal weight: 10.0000 chunk 18 optimal weight: 10.0000 chunk 8 optimal weight: 6.9990 overall best weight: 7.2592 ------------------------------------------------------------------------------- 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: 0.7823 moved from start: 0.4185 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= 0.276 Angle : 0.775 13.912 4523 Z= 0.397 Chirality : 0.040 0.275 588 Planarity : 0.004 0.019 222 Dihedral : 25.952 143.758 1531 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 34.91 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: -0.15 (0.84), residues: 98 helix: 0.12 (0.60), residues: 75 sheet: None (None), residues: 0 loop : -0.35 (1.34), residues: 23 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.006 0.002 PHE C 368 TYR 0.025 0.006 TYR C 367 ARG 0.003 0.001 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 11 residues out of total 77 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 10 time to evaluate : 0.155 Fit side-chains REVERT: C 367 TYR cc_start: 0.6527 (m-80) cc_final: 0.6157 (m-80) outliers start: 1 outliers final: 1 residues processed: 10 average time/residue: 0.0769 time to fit residues: 1.2180 Evaluate side-chains 11 residues out of total 77 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 10 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 389 ASN 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: 6.9990 chunk 11 optimal weight: 20.0000 chunk 9 optimal weight: 6.9990 chunk 16 optimal weight: 20.0000 chunk 4 optimal weight: 6.9990 chunk 13 optimal weight: 10.0000 chunk 2 optimal weight: 10.0000 overall best weight: 8.1992 ------------------------------------------------------------------------------- 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: 0.7857 moved from start: 0.4573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 3009 Z= 0.310 Angle : 0.833 14.112 4523 Z= 0.428 Chirality : 0.043 0.298 588 Planarity : 0.005 0.021 222 Dihedral : 26.084 136.881 1531 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 38.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.30 % Allowed : 25.97 % 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: -0.33 (0.83), residues: 98 helix: -0.01 (0.60), residues: 75 sheet: None (None), residues: 0 loop : -0.45 (1.26), residues: 23 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.009 0.003 PHE C 432 TYR 0.025 0.005 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 11 residues out of total 77 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 10 time to evaluate : 0.151 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 10 average time/residue: 0.0769 time to fit residues: 1.2212 Evaluate side-chains 12 residues out of total 77 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 11 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 389 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 4 optimal weight: 8.9990 chunk 15 optimal weight: 10.0000 chunk 6 optimal weight: 6.9990 chunk 1 optimal weight: 5.9990 chunk 2 optimal weight: 8.9990 chunk 13 optimal weight: 10.0000 chunk 0 optimal weight: 2.9990 chunk 10 optimal weight: 10.0000 chunk 17 optimal weight: 20.0000 chunk 12 optimal weight: 10.0000 chunk 11 optimal weight: 20.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- 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: 0.7827 moved from start: 0.4712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 3009 Z= 0.256 Angle : 0.771 12.625 4523 Z= 0.399 Chirality : 0.040 0.309 588 Planarity : 0.005 0.021 222 Dihedral : 26.052 134.203 1531 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 32.93 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: -0.44 (0.82), residues: 98 helix: 0.03 (0.59), residues: 76 sheet: None (None), residues: 0 loop : -0.99 (1.18), residues: 22 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.016 0.003 PHE C 432 TYR 0.019 0.004 TYR C 367 ARG 0.004 0.002 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 11 residues out of total 77 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 10 time to evaluate : 0.149 Fit side-chains REVERT: C 367 TYR cc_start: 0.6056 (m-80) cc_final: 0.5730 (m-80) outliers start: 1 outliers final: 1 residues processed: 10 average time/residue: 0.0746 time to fit residues: 1.1791 Evaluate side-chains 11 residues out of total 77 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 10 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 389 ASN 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: 9.9990 chunk 18 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 3 optimal weight: 7.9990 chunk 2 optimal weight: 3.9990 chunk 4 optimal weight: 5.9990 chunk 15 optimal weight: 10.0000 chunk 17 optimal weight: 10.0000 chunk 8 optimal weight: 7.9990 chunk 1 optimal weight: 8.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.4764 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= 0.264 Angle : 0.782 13.163 4523 Z= 0.404 Chirality : 0.041 0.312 588 Planarity : 0.004 0.018 222 Dihedral : 26.064 133.065 1531 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 32.49 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: -0.15 (0.83), residues: 98 helix: 0.10 (0.59), residues: 75 sheet: None (None), residues: 0 loop : -0.31 (1.29), residues: 23 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.006 0.002 PHE C 432 TYR 0.030 0.006 TYR C 367 ARG 0.003 0.001 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 11 residues out of total 77 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 10 time to evaluate : 0.148 Fit side-chains REVERT: C 367 TYR cc_start: 0.6230 (m-80) cc_final: 0.5858 (m-80) outliers start: 1 outliers final: 1 residues processed: 10 average time/residue: 0.0719 time to fit residues: 1.1310 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 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 389 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 4 optimal weight: 8.9990 chunk 12 optimal weight: 9.9990 chunk 6 optimal weight: 6.9990 chunk 3 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 1 optimal weight: 8.9990 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: 7.1990 ------------------------------------------------------------------------------- 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 = 0.4045 r_free = 0.4045 target = 0.055209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.047668 restraints weight = 32492.941| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 3.31 r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3496 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3496 r_free = 0.3496 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 = 0.3494 r_free = 0.3494 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3494 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.4777 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= 0.269 Angle : 0.781 12.987 4523 Z= 0.404 Chirality : 0.041 0.312 588 Planarity : 0.004 0.018 222 Dihedral : 26.065 132.822 1531 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 32.71 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: -0.13 (0.83), residues: 98 helix: 0.13 (0.60), residues: 75 sheet: None (None), residues: 0 loop : -0.34 (1.28), residues: 23 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.005 0.002 PHE C 368 TYR 0.024 0.004 TYR C 367 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: 839.39 seconds wall clock time: 15 minutes 58.32 seconds (958.32 seconds total)