Starting phenix.real_space_refine on Mon Sep 23 11:31:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a06_15051/09_2024/8a06_15051.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a06_15051/09_2024/8a06_15051.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a06_15051/09_2024/8a06_15051.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a06_15051/09_2024/8a06_15051.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a06_15051/09_2024/8a06_15051.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a06_15051/09_2024/8a06_15051.cif" } resolution = 4.0 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= 0.001 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 5 5.16 5 C 761 2.51 5 N 186 2.21 5 O 233 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 1185 Number of models: 1 Model: "" Number of chains: 1 Chain: "E" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1185 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 5, 'TRANS': 141} Time building chain proxies: 1.76, per 1000 atoms: 1.49 Number of scatterers: 1185 At special positions: 0 Unit cell: (55.35, 45.9, 81, 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) S 5 16.00 O 233 8.00 N 186 7.00 C 761 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.27 Conformation dependent library (CDL) restraints added in 141.5 milliseconds 290 Ramachandran restraints generated. 145 Oldfield, 0 Emsley, 145 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 286 Finding SS restraints... Secondary structure from input PDB file: 2 helices and 2 sheets defined 12.9% alpha, 39.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'E' and resid 14 through 26 removed outlier: 3.697A pdb=" N CYS E 18 " --> pdb=" O THR E 14 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 92 removed outlier: 3.795A pdb=" N ILE E 91 " --> pdb=" O SER E 87 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 34 through 42 removed outlier: 3.547A pdb=" N PHE E 39 " --> pdb=" O PHE E 137 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 95 through 102 removed outlier: 3.580A pdb=" N ARG E 101 " --> pdb=" O ILE E 78 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE E 78 " --> pdb=" O ARG E 101 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N VAL E 79 " --> pdb=" O SER E 125 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER E 125 " --> pdb=" O VAL E 79 " (cutoff:3.500A) 46 hydrogen bonds defined for protein. 132 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.29 Time building geometry restraints manager: 0.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 372 1.34 - 1.46: 236 1.46 - 1.57: 594 1.57 - 1.69: 0 1.69 - 1.81: 8 Bond restraints: 1210 Sorted by residual: bond pdb=" CG ARG E 93 " pdb=" CD ARG E 93 " ideal model delta sigma weight residual 1.520 1.545 -0.025 3.00e-02 1.11e+03 6.98e-01 bond pdb=" CB ASN E 110 " pdb=" CG ASN E 110 " ideal model delta sigma weight residual 1.516 1.536 -0.020 2.50e-02 1.60e+03 6.59e-01 bond pdb=" CA ASN E 110 " pdb=" C ASN E 110 " ideal model delta sigma weight residual 1.519 1.528 -0.008 1.14e-02 7.69e+03 5.51e-01 bond pdb=" CG GLU E 117 " pdb=" CD GLU E 117 " ideal model delta sigma weight residual 1.516 1.530 -0.014 2.50e-02 1.60e+03 3.32e-01 bond pdb=" CA ASN E 110 " pdb=" CB ASN E 110 " ideal model delta sigma weight residual 1.530 1.543 -0.013 2.22e-02 2.03e+03 3.30e-01 ... (remaining 1205 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.23: 1586 1.23 - 2.46: 40 2.46 - 3.69: 10 3.69 - 4.92: 3 4.92 - 6.15: 1 Bond angle restraints: 1640 Sorted by residual: angle pdb=" C ASN E 110 " pdb=" CA ASN E 110 " pdb=" CB ASN E 110 " ideal model delta sigma weight residual 110.34 114.00 -3.66 1.40e+00 5.10e-01 6.84e+00 angle pdb=" CA ASN E 110 " pdb=" CB ASN E 110 " pdb=" CG ASN E 110 " ideal model delta sigma weight residual 112.60 114.91 -2.31 1.00e+00 1.00e+00 5.34e+00 angle pdb=" CA GLU E 104 " pdb=" CB GLU E 104 " pdb=" CG GLU E 104 " ideal model delta sigma weight residual 114.10 117.71 -3.61 2.00e+00 2.50e-01 3.25e+00 angle pdb=" CG ARG E 93 " pdb=" CD ARG E 93 " pdb=" NE ARG E 93 " ideal model delta sigma weight residual 112.00 115.94 -3.94 2.20e+00 2.07e-01 3.21e+00 angle pdb=" CA LEU E 41 " pdb=" CB LEU E 41 " pdb=" CG LEU E 41 " ideal model delta sigma weight residual 116.30 122.45 -6.15 3.50e+00 8.16e-02 3.09e+00 ... (remaining 1635 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.63: 615 11.63 - 23.26: 69 23.26 - 34.89: 30 34.89 - 46.52: 9 46.52 - 58.15: 5 Dihedral angle restraints: 728 sinusoidal: 289 harmonic: 439 Sorted by residual: dihedral pdb=" CA PHE E 118 " pdb=" C PHE E 118 " pdb=" N PHE E 119 " pdb=" CA PHE E 119 " ideal model delta harmonic sigma weight residual -180.00 -164.13 -15.87 0 5.00e+00 4.00e-02 1.01e+01 dihedral pdb=" CA ASP E 16 " pdb=" CB ASP E 16 " pdb=" CG ASP E 16 " pdb=" OD1 ASP E 16 " ideal model delta sinusoidal sigma weight residual -30.00 -83.04 53.04 1 2.00e+01 2.50e-03 9.57e+00 dihedral pdb=" CA ASN E 110 " pdb=" CB ASN E 110 " pdb=" CG ASN E 110 " pdb=" OD1 ASN E 110 " ideal model delta sinusoidal sigma weight residual 120.00 178.15 -58.15 2 2.00e+01 2.50e-03 8.66e+00 ... (remaining 725 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 95 0.025 - 0.050: 48 0.050 - 0.075: 23 0.075 - 0.100: 12 0.100 - 0.125: 12 Chirality restraints: 190 Sorted by residual: chirality pdb=" CA ILE E 66 " pdb=" N ILE E 66 " pdb=" C ILE E 66 " pdb=" CB ILE E 66 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.88e-01 chirality pdb=" CA ILE E 82 " pdb=" N ILE E 82 " pdb=" C ILE E 82 " pdb=" CB ILE E 82 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.70e-01 chirality pdb=" CA ILE E 4 " pdb=" N ILE E 4 " pdb=" C ILE E 4 " pdb=" CB ILE E 4 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.11 2.00e-01 2.50e+01 3.21e-01 ... (remaining 187 not shown) Planarity restraints: 206 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN E 110 " 0.007 2.00e-02 2.50e+03 1.41e-02 1.98e+00 pdb=" C ASN E 110 " -0.024 2.00e-02 2.50e+03 pdb=" O ASN E 110 " 0.009 2.00e-02 2.50e+03 pdb=" N GLU E 111 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL E 74 " 0.005 2.00e-02 2.50e+03 1.08e-02 1.16e+00 pdb=" C VAL E 74 " -0.019 2.00e-02 2.50e+03 pdb=" O VAL E 74 " 0.007 2.00e-02 2.50e+03 pdb=" N ASN E 75 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 93 " -0.077 9.50e-02 1.11e+02 3.47e-02 9.92e-01 pdb=" NE ARG E 93 " 0.008 2.00e-02 2.50e+03 pdb=" CZ ARG E 93 " -0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG E 93 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG E 93 " 0.000 2.00e-02 2.50e+03 ... (remaining 203 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 80 2.74 - 3.28: 1111 3.28 - 3.82: 1731 3.82 - 4.36: 1919 4.36 - 4.90: 3475 Nonbonded interactions: 8316 Sorted by model distance: nonbonded pdb=" O ASN E 110 " pdb=" ND2 ASN E 110 " model vdw 2.201 3.120 nonbonded pdb=" OG1 THR E 53 " pdb=" OH TYR E 58 " model vdw 2.291 3.040 nonbonded pdb=" O THR E 27 " pdb=" OG1 THR E 28 " model vdw 2.333 3.040 nonbonded pdb=" N ASP E 44 " pdb=" OD1 ASP E 44 " model vdw 2.474 3.120 nonbonded pdb=" OE1 GLU E 83 " pdb=" OG SER E 94 " model vdw 2.481 3.040 ... (remaining 8311 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.010 Normalize map: mean=0, sd=1: 0.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.040 Check model and map are aligned: 0.000 Set scattering table: 0.030 Process input model: 9.780 Find NCS groups from input model: 0.020 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 1210 Z= 0.171 Angle : 0.556 6.151 1640 Z= 0.301 Chirality : 0.045 0.125 190 Planarity : 0.004 0.035 206 Dihedral : 13.754 58.146 442 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.73 % Allowed : 0.00 % Favored : 99.27 % 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: -0.86 (0.71), residues: 145 helix: 0.13 (1.83), residues: 11 sheet: 0.72 (0.69), residues: 59 loop : -1.85 (0.70), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP E 59 HIS 0.002 0.001 HIS E 26 PHE 0.010 0.001 PHE E 108 TYR 0.003 0.001 TYR E 102 ARG 0.009 0.001 ARG E 93 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 290 Ramachandran restraints generated. 145 Oldfield, 0 Emsley, 145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 290 Ramachandran restraints generated. 145 Oldfield, 0 Emsley, 145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 55 time to evaluate : 0.215 Fit side-chains REVERT: E 18 CYS cc_start: 0.8242 (t) cc_final: 0.7956 (t) REVERT: E 43 SER cc_start: 0.9402 (p) cc_final: 0.9117 (p) REVERT: E 93 ARG cc_start: 0.7520 (mtp-110) cc_final: 0.7296 (mtp-110) outliers start: 1 outliers final: 1 residues processed: 56 average time/residue: 0.1038 time to fit residues: 6.6358 Evaluate side-chains 51 residues out of total 137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 50 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 110 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 11 optimal weight: 8.9990 chunk 10 optimal weight: 7.9990 chunk 5 optimal weight: 20.0000 chunk 3 optimal weight: 0.0000 chunk 7 optimal weight: 0.3980 chunk 4 optimal weight: 9.9990 chunk 6 optimal weight: 10.0000 chunk 8 optimal weight: 7.9990 chunk 12 optimal weight: 0.9990 chunk 13 optimal weight: 7.9990 chunk 9 optimal weight: 0.8980 overall best weight: 2.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 110 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 1210 Z= 0.157 Angle : 0.571 6.188 1640 Z= 0.307 Chirality : 0.047 0.142 190 Planarity : 0.004 0.023 206 Dihedral : 4.761 27.409 160 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 4.38 % Allowed : 13.87 % Favored : 81.75 % 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: -0.80 (0.70), residues: 145 helix: 1.39 (1.85), residues: 11 sheet: 0.65 (0.67), residues: 58 loop : -1.88 (0.69), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 59 HIS 0.001 0.000 HIS E 26 PHE 0.019 0.002 PHE E 137 TYR 0.004 0.001 TYR E 21 ARG 0.003 0.001 ARG E 93 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 290 Ramachandran restraints generated. 145 Oldfield, 0 Emsley, 145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 290 Ramachandran restraints generated. 145 Oldfield, 0 Emsley, 145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 43 time to evaluate : 0.139 Fit side-chains REVERT: E 18 CYS cc_start: 0.8100 (t) cc_final: 0.7840 (t) outliers start: 6 outliers final: 3 residues processed: 44 average time/residue: 0.0920 time to fit residues: 4.7116 Evaluate side-chains 39 residues out of total 137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 36 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 41 LEU Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 125 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 6 optimal weight: 10.0000 chunk 1 optimal weight: 5.9990 chunk 8 optimal weight: 20.0000 chunk 12 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 3 optimal weight: 9.9990 chunk 11 optimal weight: 5.9990 chunk 7 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 10 optimal weight: 8.9990 chunk 5 optimal weight: 6.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- 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: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 1210 Z= 0.222 Angle : 0.579 5.896 1640 Z= 0.312 Chirality : 0.047 0.137 190 Planarity : 0.004 0.023 206 Dihedral : 4.554 14.955 158 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 5.84 % Allowed : 16.06 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.72), residues: 145 helix: 1.79 (1.98), residues: 11 sheet: 0.66 (0.69), residues: 59 loop : -1.89 (0.71), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP E 59 HIS 0.003 0.001 HIS E 26 PHE 0.021 0.002 PHE E 137 TYR 0.010 0.001 TYR E 21 ARG 0.001 0.000 ARG E 101 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 290 Ramachandran restraints generated. 145 Oldfield, 0 Emsley, 145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 290 Ramachandran restraints generated. 145 Oldfield, 0 Emsley, 145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 37 time to evaluate : 0.137 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 42 average time/residue: 0.0996 time to fit residues: 4.8154 Evaluate side-chains 41 residues out of total 137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 36 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 125 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 11 optimal weight: 5.9990 chunk 9 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 6 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 4 optimal weight: 10.0000 chunk 2 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 13 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- 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: 0.7826 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 1210 Z= 0.184 Angle : 0.547 5.358 1640 Z= 0.294 Chirality : 0.047 0.137 190 Planarity : 0.004 0.023 206 Dihedral : 4.496 14.226 158 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 8.03 % Allowed : 17.52 % Favored : 74.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.73), residues: 145 helix: 2.21 (2.02), residues: 11 sheet: 0.76 (0.67), residues: 61 loop : -1.91 (0.73), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP E 59 HIS 0.002 0.001 HIS E 26 PHE 0.022 0.002 PHE E 137 TYR 0.008 0.001 TYR E 21 ARG 0.002 0.000 ARG E 93 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 290 Ramachandran restraints generated. 145 Oldfield, 0 Emsley, 145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 290 Ramachandran restraints generated. 145 Oldfield, 0 Emsley, 145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 43 time to evaluate : 0.145 Fit side-chains REVERT: E 108 PHE cc_start: 0.7668 (OUTLIER) cc_final: 0.6428 (t80) outliers start: 11 outliers final: 8 residues processed: 49 average time/residue: 0.0949 time to fit residues: 5.3746 Evaluate side-chains 52 residues out of total 137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 43 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 108 PHE Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 132 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 4 optimal weight: 5.9990 chunk 7 optimal weight: 7.9990 chunk 13 optimal weight: 2.9990 chunk 1 optimal weight: 9.9990 chunk 9 optimal weight: 5.9990 chunk 11 optimal weight: 6.9990 chunk 8 optimal weight: 9.9990 chunk 6 optimal weight: 5.9990 chunk 5 optimal weight: 9.9990 chunk 2 optimal weight: 1.9990 chunk 10 optimal weight: 9.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 1210 Z= 0.235 Angle : 0.578 4.760 1640 Z= 0.315 Chirality : 0.048 0.140 190 Planarity : 0.004 0.023 206 Dihedral : 4.640 14.820 158 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 8.76 % Allowed : 19.71 % Favored : 71.53 % 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: -0.84 (0.73), residues: 145 helix: 2.19 (2.00), residues: 11 sheet: 0.59 (0.68), residues: 60 loop : -2.09 (0.71), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 59 HIS 0.002 0.001 HIS E 26 PHE 0.007 0.001 PHE E 118 TYR 0.010 0.001 TYR E 21 ARG 0.003 0.001 ARG E 93 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 290 Ramachandran restraints generated. 145 Oldfield, 0 Emsley, 145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 290 Ramachandran restraints generated. 145 Oldfield, 0 Emsley, 145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 38 time to evaluate : 0.138 Fit side-chains REVERT: E 108 PHE cc_start: 0.7532 (OUTLIER) cc_final: 0.6323 (t80) outliers start: 12 outliers final: 9 residues processed: 46 average time/residue: 0.0968 time to fit residues: 5.1460 Evaluate side-chains 46 residues out of total 137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 36 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 66 ILE Chi-restraints excluded: chain E residue 108 PHE Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 132 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 12 optimal weight: 3.9990 chunk 11 optimal weight: 6.9990 chunk 7 optimal weight: 10.0000 chunk 5 optimal weight: 10.0000 chunk 9 optimal weight: 7.9990 chunk 3 optimal weight: 7.9990 chunk 8 optimal weight: 0.5980 chunk 13 optimal weight: 6.9990 chunk 6 optimal weight: 5.9990 chunk 1 optimal weight: 7.9990 chunk 10 optimal weight: 7.9990 overall best weight: 4.9188 ------------------------------------------------------------------------------- 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: 0.7884 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 1210 Z= 0.250 Angle : 0.582 4.720 1640 Z= 0.317 Chirality : 0.048 0.142 190 Planarity : 0.004 0.023 206 Dihedral : 4.714 15.019 158 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 10.22 % Allowed : 20.44 % Favored : 69.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.72), residues: 145 helix: 2.19 (1.99), residues: 11 sheet: 0.16 (0.66), residues: 64 loop : -2.09 (0.73), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 59 HIS 0.002 0.001 HIS E 26 PHE 0.007 0.001 PHE E 118 TYR 0.010 0.001 TYR E 21 ARG 0.003 0.001 ARG E 93 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 290 Ramachandran restraints generated. 145 Oldfield, 0 Emsley, 145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 290 Ramachandran restraints generated. 145 Oldfield, 0 Emsley, 145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 38 time to evaluate : 0.134 Fit side-chains REVERT: E 108 PHE cc_start: 0.7491 (OUTLIER) cc_final: 0.6588 (t80) REVERT: E 131 TYR cc_start: 0.8086 (m-80) cc_final: 0.7763 (m-80) outliers start: 14 outliers final: 12 residues processed: 46 average time/residue: 0.1001 time to fit residues: 5.2908 Evaluate side-chains 51 residues out of total 137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 38 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue -1 PHE Chi-restraints excluded: chain E residue 18 CYS Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 66 ILE Chi-restraints excluded: chain E residue 108 PHE Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 132 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 1 optimal weight: 5.9990 chunk 3 optimal weight: 8.9990 chunk 11 optimal weight: 5.9990 chunk 4 optimal weight: 6.9990 chunk 2 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 8 optimal weight: 5.9990 chunk 12 optimal weight: 8.9990 chunk 7 optimal weight: 6.9990 chunk 5 optimal weight: 9.9990 overall best weight: 3.9786 ------------------------------------------------------------------------------- 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: 0.7871 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 1210 Z= 0.210 Angle : 0.560 4.507 1640 Z= 0.306 Chirality : 0.047 0.140 190 Planarity : 0.004 0.024 206 Dihedral : 4.629 14.888 158 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 9.49 % Allowed : 24.09 % Favored : 66.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.72), residues: 145 helix: 2.17 (1.98), residues: 11 sheet: 0.18 (0.66), residues: 64 loop : -2.12 (0.72), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP E 59 HIS 0.002 0.001 HIS E 26 PHE 0.006 0.001 PHE E 108 TYR 0.008 0.001 TYR E 21 ARG 0.002 0.000 ARG E 101 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 290 Ramachandran restraints generated. 145 Oldfield, 0 Emsley, 145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 290 Ramachandran restraints generated. 145 Oldfield, 0 Emsley, 145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 38 time to evaluate : 0.145 Fit side-chains REVERT: E 108 PHE cc_start: 0.7485 (OUTLIER) cc_final: 0.6805 (t80) outliers start: 13 outliers final: 12 residues processed: 47 average time/residue: 0.0868 time to fit residues: 4.7522 Evaluate side-chains 51 residues out of total 137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 38 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue -1 PHE Chi-restraints excluded: chain E residue 18 CYS Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 108 PHE Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 135 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 5 optimal weight: 0.9980 chunk 13 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 2 optimal weight: 10.0000 chunk 1 optimal weight: 3.9990 chunk 11 optimal weight: 6.9990 chunk 3 optimal weight: 5.9990 chunk 9 optimal weight: 9.9990 chunk 4 optimal weight: 6.9990 chunk 7 optimal weight: 8.9990 chunk 10 optimal weight: 10.0000 overall best weight: 4.9988 ------------------------------------------------------------------------------- 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: 0.7885 moved from start: 0.2652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 1210 Z= 0.256 Angle : 0.584 4.493 1640 Z= 0.318 Chirality : 0.047 0.142 190 Planarity : 0.004 0.025 206 Dihedral : 4.741 15.170 158 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 10.22 % Allowed : 24.82 % Favored : 64.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.71), residues: 145 helix: 2.19 (1.98), residues: 11 sheet: 0.08 (0.64), residues: 64 loop : -2.23 (0.72), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 59 HIS 0.002 0.001 HIS E 26 PHE 0.007 0.001 PHE E 118 TYR 0.010 0.002 TYR E 21 ARG 0.005 0.001 ARG E 93 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 290 Ramachandran restraints generated. 145 Oldfield, 0 Emsley, 145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 290 Ramachandran restraints generated. 145 Oldfield, 0 Emsley, 145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 37 time to evaluate : 0.144 Fit side-chains REVERT: E 108 PHE cc_start: 0.7515 (OUTLIER) cc_final: 0.6545 (t80) outliers start: 14 outliers final: 11 residues processed: 46 average time/residue: 0.0957 time to fit residues: 5.1023 Evaluate side-chains 50 residues out of total 137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 38 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue -1 PHE Chi-restraints excluded: chain E residue 18 CYS Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 108 PHE Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 135 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 11 optimal weight: 20.0000 chunk 12 optimal weight: 3.9990 chunk 2 optimal weight: 10.0000 chunk 9 optimal weight: 5.9990 chunk 13 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 4 optimal weight: 6.9990 chunk 3 optimal weight: 6.9990 chunk 8 optimal weight: 5.9990 chunk 6 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 1210 Z= 0.198 Angle : 0.557 4.508 1640 Z= 0.304 Chirality : 0.047 0.141 190 Planarity : 0.004 0.024 206 Dihedral : 4.668 15.031 158 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 8.76 % Allowed : 26.28 % Favored : 64.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.71), residues: 145 helix: 2.16 (1.97), residues: 11 sheet: 0.16 (0.64), residues: 64 loop : -2.20 (0.71), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP E 59 HIS 0.002 0.001 HIS E 26 PHE 0.007 0.001 PHE E 108 TYR 0.009 0.001 TYR E 131 ARG 0.004 0.001 ARG E 93 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 290 Ramachandran restraints generated. 145 Oldfield, 0 Emsley, 145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 290 Ramachandran restraints generated. 145 Oldfield, 0 Emsley, 145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 38 time to evaluate : 0.117 Fit side-chains REVERT: E 108 PHE cc_start: 0.7484 (OUTLIER) cc_final: 0.6842 (t80) outliers start: 12 outliers final: 11 residues processed: 46 average time/residue: 0.0917 time to fit residues: 4.8582 Evaluate side-chains 50 residues out of total 137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 38 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue -1 PHE Chi-restraints excluded: chain E residue 18 CYS Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 108 PHE Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 135 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 7 optimal weight: 10.0000 chunk 4 optimal weight: 5.9990 chunk 5 optimal weight: 20.0000 chunk 11 optimal weight: 0.8980 chunk 3 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 10 optimal weight: 8.9990 chunk 13 optimal weight: 1.9990 chunk 8 optimal weight: 6.9990 chunk 9 optimal weight: 7.9990 chunk 2 optimal weight: 0.8980 overall best weight: 3.1586 ------------------------------------------------------------------------------- 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: 0.7854 moved from start: 0.2682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 1210 Z= 0.192 Angle : 0.557 5.033 1640 Z= 0.302 Chirality : 0.046 0.141 190 Planarity : 0.004 0.024 206 Dihedral : 4.656 15.192 158 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 9.49 % Allowed : 25.55 % Favored : 64.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.70), residues: 145 helix: 2.20 (1.98), residues: 11 sheet: 0.19 (0.64), residues: 64 loop : -2.24 (0.69), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP E 59 HIS 0.002 0.001 HIS E 26 PHE 0.006 0.001 PHE E 108 TYR 0.018 0.001 TYR E 131 ARG 0.003 0.001 ARG E 93 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 290 Ramachandran restraints generated. 145 Oldfield, 0 Emsley, 145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 290 Ramachandran restraints generated. 145 Oldfield, 0 Emsley, 145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 41 time to evaluate : 0.139 Fit side-chains REVERT: E 39 PHE cc_start: 0.9124 (p90) cc_final: 0.8893 (p90) REVERT: E 108 PHE cc_start: 0.7539 (OUTLIER) cc_final: 0.6927 (t80) outliers start: 13 outliers final: 11 residues processed: 50 average time/residue: 0.0926 time to fit residues: 5.3948 Evaluate side-chains 51 residues out of total 137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 39 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue -1 PHE Chi-restraints excluded: chain E residue 18 CYS Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 108 PHE Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 135 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 4 optimal weight: 7.9990 chunk 3 optimal weight: 9.9990 chunk 8 optimal weight: 8.9990 chunk 5 optimal weight: 20.0000 chunk 12 optimal weight: 0.9990 chunk 7 optimal weight: 7.9990 chunk 9 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 6 optimal weight: 10.0000 chunk 2 optimal weight: 0.9990 chunk 10 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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 = 0.3254 r_free = 0.3254 target = 0.118208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.108141 restraints weight = 1953.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.110581 restraints weight = 1016.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.112284 restraints weight = 632.120| |-----------------------------------------------------------------------------| r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 1210 Z= 0.237 Angle : 0.575 5.965 1640 Z= 0.310 Chirality : 0.047 0.142 190 Planarity : 0.004 0.025 206 Dihedral : 4.808 15.628 158 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 9.49 % Allowed : 26.28 % Favored : 64.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.70), residues: 145 helix: 2.17 (1.98), residues: 11 sheet: 0.23 (0.65), residues: 64 loop : -2.30 (0.69), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP E 59 HIS 0.002 0.001 HIS E 26 PHE 0.006 0.001 PHE E 118 TYR 0.026 0.002 TYR E 131 ARG 0.003 0.001 ARG E 101 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 690.20 seconds wall clock time: 13 minutes 0.76 seconds (780.76 seconds total)