Starting phenix.real_space_refine on Sun Mar 10 14:16:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a06_15051/03_2024/8a06_15051.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a06_15051/03_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_15051/03_2024/8a06_15051.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a06_15051/03_2024/8a06_15051.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a06_15051/03_2024/8a06_15051.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a06_15051/03_2024/8a06_15051.pdb" } 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 Residue "E PHE -1": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 117": "OE1" <-> "OE2" 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: 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: 1.33, per 1000 atoms: 1.12 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 - 3.50 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: 0.34 Conformation dependent library (CDL) restraints added in 377.1 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: 0.14 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: 0.28 Time building geometry restraints manager: 0.40 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: 100.50 - 107.18: 32 107.18 - 113.85: 679 113.85 - 120.53: 439 120.53 - 127.21: 481 127.21 - 133.89: 9 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 2.520 nonbonded pdb=" OG1 THR E 53 " pdb=" OH TYR E 58 " model vdw 2.291 2.440 nonbonded pdb=" O THR E 27 " pdb=" OG1 THR E 28 " model vdw 2.333 2.440 nonbonded pdb=" N ASP E 44 " pdb=" OD1 ASP E 44 " model vdw 2.474 2.520 nonbonded pdb=" OE1 GLU E 83 " pdb=" OG SER E 94 " model vdw 2.481 2.440 ... (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: 0.000 Normalize map: mean=0, sd=1: 0.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 1.770 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 9.860 Find NCS groups from input model: 0.030 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.940 ------------------------------------------------------------------------------- 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 : 0.143 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: 0.0996 time to fit residues: 6.3772 Evaluate side-chains 51 residues out of total 137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 50 time to evaluate : 0.147 ------------------------------------------------------------------------------- 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: 9.9990 chunk 10 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 4 optimal weight: 9.9990 chunk 6 optimal weight: 7.9990 chunk 8 optimal weight: 5.9990 chunk 12 optimal weight: 8.9990 chunk 13 optimal weight: 7.9990 chunk 9 optimal weight: 3.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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: 0.7771 moved from start: 0.1468 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= 0.158 Angle : 0.570 6.164 1640 Z= 0.305 Chirality : 0.047 0.143 190 Planarity : 0.004 0.023 206 Dihedral : 4.294 14.180 160 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % 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: -0.77 (0.70), residues: 145 helix: 1.48 (1.87), residues: 11 sheet: 0.67 (0.67), residues: 58 loop : -1.88 (0.69), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP E 59 HIS 0.002 0.001 HIS E 26 PHE 0.020 0.002 PHE E 137 TYR 0.005 0.001 TYR E 21 ARG 0.003 0.000 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 : 0.156 Fit side-chains REVERT: E 18 CYS cc_start: 0.8106 (t) cc_final: 0.7852 (t) outliers start: 6 outliers final: 3 residues processed: 44 average time/residue: 0.0970 time to fit residues: 4.9747 Evaluate side-chains 36 residues out of total 137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 33 time to evaluate : 0.151 ------------------------------------------------------------------------------- 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: 5.9990 chunk 1 optimal weight: 0.2980 chunk 8 optimal weight: 9.9990 chunk 12 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 3 optimal weight: 6.9990 chunk 11 optimal weight: 8.9990 chunk 7 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 10 optimal weight: 8.9990 chunk 5 optimal weight: 20.0000 overall best weight: 3.4588 ------------------------------------------------------------------------------- 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: 0.7809 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 1210 Z= 0.191 Angle : 0.559 5.879 1640 Z= 0.299 Chirality : 0.047 0.135 190 Planarity : 0.004 0.023 206 Dihedral : 4.495 14.860 158 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 5.84 % Allowed : 16.79 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.73), residues: 145 helix: 1.84 (2.00), residues: 11 sheet: 0.80 (0.68), residues: 61 loop : -1.90 (0.73), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 59 HIS 0.002 0.001 HIS E 26 PHE 0.021 0.002 PHE E 137 TYR 0.008 0.001 TYR E 21 ARG 0.002 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 50 residues out of total 137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 42 time to evaluate : 0.150 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 46 average time/residue: 0.0984 time to fit residues: 5.2550 Evaluate side-chains 46 residues out of total 137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 40 time to evaluate : 0.149 ------------------------------------------------------------------------------- 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 43 SER 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: 6.9990 chunk 9 optimal weight: 40.0000 chunk 0 optimal weight: 20.0000 chunk 6 optimal weight: 6.9990 chunk 12 optimal weight: 8.9990 chunk 3 optimal weight: 7.9990 chunk 4 optimal weight: 10.0000 chunk 2 optimal weight: 4.9990 chunk 7 optimal weight: 9.9990 chunk 13 optimal weight: 7.9990 chunk 1 optimal weight: 7.9990 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: 0.7909 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 1210 Z= 0.341 Angle : 0.628 5.488 1640 Z= 0.337 Chirality : 0.049 0.139 190 Planarity : 0.004 0.024 206 Dihedral : 4.896 15.843 158 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 10.22 % Allowed : 16.06 % Favored : 73.72 % 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: -0.94 (0.73), residues: 145 helix: 2.14 (2.00), residues: 11 sheet: 0.34 (0.67), residues: 62 loop : -2.05 (0.74), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP E 59 HIS 0.003 0.001 HIS E 26 PHE 0.029 0.002 PHE E 137 TYR 0.012 0.002 TYR E 21 ARG 0.005 0.001 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 51 residues out of total 137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 37 time to evaluate : 0.146 Fit side-chains REVERT: E 95 GLU cc_start: 0.6230 (tt0) cc_final: 0.5933 (tt0) REVERT: E 108 PHE cc_start: 0.7678 (OUTLIER) cc_final: 0.6480 (t80) outliers start: 14 outliers final: 10 residues processed: 47 average time/residue: 0.1004 time to fit residues: 5.4300 Evaluate side-chains 47 residues out of total 137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 36 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 43 SER 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 4 optimal weight: 8.9990 chunk 7 optimal weight: 7.9990 chunk 13 optimal weight: 6.9990 chunk 1 optimal weight: 5.9990 chunk 9 optimal weight: 0.0170 chunk 11 optimal weight: 5.9990 chunk 8 optimal weight: 10.0000 chunk 6 optimal weight: 10.0000 chunk 5 optimal weight: 8.9990 chunk 2 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 overall best weight: 3.8026 ------------------------------------------------------------------------------- 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: 0.7875 moved from start: 0.2355 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= 0.204 Angle : 0.551 4.457 1640 Z= 0.303 Chirality : 0.046 0.137 190 Planarity : 0.004 0.025 206 Dihedral : 4.665 15.041 158 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 8.76 % Allowed : 21.90 % 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: -0.90 (0.73), residues: 145 helix: 2.08 (1.96), residues: 11 sheet: 0.51 (0.67), residues: 61 loop : -2.13 (0.74), 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 0.007 0.001 PHE E 118 TYR 0.007 0.001 TYR E 21 ARG 0.005 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 48 residues out of total 137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 36 time to evaluate : 0.150 Fit side-chains REVERT: E 95 GLU cc_start: 0.6203 (tt0) cc_final: 0.5900 (tt0) REVERT: E 108 PHE cc_start: 0.7541 (OUTLIER) cc_final: 0.6674 (t80) outliers start: 12 outliers final: 8 residues processed: 46 average time/residue: 0.0982 time to fit residues: 5.2535 Evaluate side-chains 45 residues out of total 137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 36 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 43 SER 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 12 optimal weight: 1.9990 chunk 11 optimal weight: 7.9990 chunk 7 optimal weight: 8.9990 chunk 5 optimal weight: 9.9990 chunk 9 optimal weight: 4.9990 chunk 3 optimal weight: 10.0000 chunk 8 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 6 optimal weight: 6.9990 chunk 1 optimal weight: 9.9990 chunk 10 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 1210 Z= 0.245 Angle : 0.572 4.504 1640 Z= 0.313 Chirality : 0.047 0.138 190 Planarity : 0.004 0.025 206 Dihedral : 4.759 15.571 158 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 9.49 % Allowed : 21.17 % 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: -1.09 (0.73), residues: 145 helix: 2.19 (1.98), residues: 11 sheet: 0.17 (0.66), residues: 64 loop : -2.15 (0.75), 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 0.006 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 51 residues out of total 137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 38 time to evaluate : 0.146 Fit side-chains REVERT: E 95 GLU cc_start: 0.6225 (tt0) cc_final: 0.5943 (tt0) REVERT: E 108 PHE cc_start: 0.7513 (OUTLIER) cc_final: 0.6825 (t80) REVERT: E 131 TYR cc_start: 0.7979 (m-80) cc_final: 0.7705 (m-80) outliers start: 13 outliers final: 9 residues processed: 47 average time/residue: 0.0975 time to fit residues: 5.2792 Evaluate side-chains 48 residues out of total 137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 38 time to evaluate : 0.147 ------------------------------------------------------------------------------- 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 27 THR Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 43 SER 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 1 optimal weight: 9.9990 chunk 3 optimal weight: 10.0000 chunk 11 optimal weight: 4.9990 chunk 4 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 chunk 9 optimal weight: 20.0000 chunk 0 optimal weight: 9.9990 chunk 8 optimal weight: 6.9990 chunk 12 optimal weight: 9.9990 chunk 7 optimal weight: 8.9990 chunk 5 optimal weight: 0.6980 overall best weight: 4.1388 ------------------------------------------------------------------------------- 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: 0.7880 moved from start: 0.2532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 1210 Z= 0.219 Angle : 0.560 4.515 1640 Z= 0.305 Chirality : 0.046 0.136 190 Planarity : 0.004 0.029 206 Dihedral : 4.680 15.635 158 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 9.49 % Allowed : 23.36 % Favored : 67.15 % 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: -1.18 (0.72), residues: 145 helix: 2.21 (1.98), residues: 11 sheet: 0.11 (0.65), residues: 64 loop : -2.23 (0.74), 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 0.009 0.001 TYR E 21 ARG 0.007 0.001 ARG E 93 *********************** 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 95 GLU cc_start: 0.5996 (tt0) cc_final: 0.5691 (tt0) REVERT: E 108 PHE cc_start: 0.7476 (OUTLIER) cc_final: 0.6897 (t80) REVERT: E 131 TYR cc_start: 0.7947 (m-80) cc_final: 0.7680 (m-80) outliers start: 13 outliers final: 9 residues processed: 47 average time/residue: 0.0962 time to fit residues: 5.2169 Evaluate side-chains 50 residues out of total 137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 40 time to evaluate : 0.144 ------------------------------------------------------------------------------- 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 27 THR Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 43 SER 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 5 optimal weight: 3.9990 chunk 13 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 2 optimal weight: 9.9990 chunk 1 optimal weight: 7.9990 chunk 11 optimal weight: 6.9990 chunk 3 optimal weight: 9.9990 chunk 9 optimal weight: 7.9990 chunk 4 optimal weight: 6.9990 chunk 7 optimal weight: 10.0000 chunk 10 optimal weight: 8.9990 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: 0.7921 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 1210 Z= 0.331 Angle : 0.625 4.956 1640 Z= 0.337 Chirality : 0.048 0.139 190 Planarity : 0.005 0.034 206 Dihedral : 4.952 16.598 158 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 8.76 % Allowed : 24.09 % Favored : 67.15 % 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: -1.46 (0.72), residues: 145 helix: 2.07 (1.96), residues: 11 sheet: -0.18 (0.64), residues: 64 loop : -2.31 (0.75), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP E 59 HIS 0.002 0.001 HIS E 26 PHE 0.008 0.002 PHE E 118 TYR 0.012 0.002 TYR E 21 ARG 0.007 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: 12 poor density : 39 time to evaluate : 0.143 Fit side-chains REVERT: E 86 LEU cc_start: 0.9153 (mm) cc_final: 0.8921 (mm) REVERT: E 95 GLU cc_start: 0.6408 (tt0) cc_final: 0.6105 (tt0) REVERT: E 108 PHE cc_start: 0.7494 (OUTLIER) cc_final: 0.6957 (t80) REVERT: E 131 TYR cc_start: 0.7980 (m-80) cc_final: 0.7695 (m-80) outliers start: 12 outliers final: 11 residues processed: 47 average time/residue: 0.0912 time to fit residues: 4.9833 Evaluate side-chains 51 residues out of total 137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 39 time to evaluate : 0.154 ------------------------------------------------------------------------------- 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 31 VAL Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 43 SER 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 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: 7.9990 chunk 13 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 4 optimal weight: 7.9990 chunk 3 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 6 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 1210 Z= 0.267 Angle : 0.593 5.004 1640 Z= 0.321 Chirality : 0.047 0.140 190 Planarity : 0.005 0.037 206 Dihedral : 4.884 16.061 158 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % 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: -1.58 (0.71), residues: 145 helix: 2.13 (1.96), residues: 11 sheet: -0.29 (0.63), residues: 64 loop : -2.39 (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 0.030 0.002 PHE E 137 TYR 0.010 0.002 TYR E 131 ARG 0.008 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 53 residues out of total 137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 40 time to evaluate : 0.151 Fit side-chains REVERT: E 86 LEU cc_start: 0.9060 (mm) cc_final: 0.8845 (mm) REVERT: E 95 GLU cc_start: 0.6382 (tt0) cc_final: 0.6072 (tt0) REVERT: E 108 PHE cc_start: 0.7534 (OUTLIER) cc_final: 0.7158 (t80) REVERT: E 131 TYR cc_start: 0.7930 (m-80) cc_final: 0.7713 (m-80) outliers start: 13 outliers final: 11 residues processed: 49 average time/residue: 0.1021 time to fit residues: 5.7537 Evaluate side-chains 51 residues out of total 137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 39 time to evaluate : 0.121 ------------------------------------------------------------------------------- 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 31 VAL Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 43 SER 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: 5.9990 chunk 4 optimal weight: 6.9990 chunk 5 optimal weight: 6.9990 chunk 11 optimal weight: 10.0000 chunk 3 optimal weight: 20.0000 chunk 0 optimal weight: 9.9990 chunk 10 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 8 optimal weight: 7.9990 chunk 9 optimal weight: 10.0000 chunk 2 optimal weight: 5.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 1210 Z= 0.309 Angle : 0.623 4.856 1640 Z= 0.338 Chirality : 0.048 0.139 190 Planarity : 0.005 0.039 206 Dihedral : 4.988 16.362 158 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 8.76 % Allowed : 27.01 % 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: -1.69 (0.70), residues: 145 helix: 1.76 (1.94), residues: 11 sheet: -0.41 (0.63), residues: 64 loop : -2.35 (0.74), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP E 59 HIS 0.002 0.001 HIS E 26 PHE 0.029 0.002 PHE E 137 TYR 0.021 0.002 TYR E 131 ARG 0.009 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 50 residues out of total 137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 38 time to evaluate : 0.149 Fit side-chains REVERT: E 86 LEU cc_start: 0.9079 (mm) cc_final: 0.8855 (mm) REVERT: E 95 GLU cc_start: 0.6398 (tt0) cc_final: 0.6113 (tt0) REVERT: E 108 PHE cc_start: 0.7623 (OUTLIER) cc_final: 0.7191 (t80) REVERT: E 131 TYR cc_start: 0.7884 (m-80) cc_final: 0.7666 (m-80) outliers start: 12 outliers final: 11 residues processed: 47 average time/residue: 0.0953 time to fit residues: 5.1676 Evaluate side-chains 50 residues out of total 137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 38 time to evaluate : 0.154 ------------------------------------------------------------------------------- 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 31 VAL Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 43 SER 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: 5.9990 chunk 3 optimal weight: 0.9980 chunk 8 optimal weight: 6.9990 chunk 5 optimal weight: 1.9990 chunk 12 optimal weight: 7.9990 chunk 7 optimal weight: 10.0000 chunk 9 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 6 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 10 optimal weight: 7.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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 = 0.3249 r_free = 0.3249 target = 0.117422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.107605 restraints weight = 1991.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.110053 restraints weight = 1039.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.111729 restraints weight = 645.848| |-----------------------------------------------------------------------------| r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 1210 Z= 0.190 Angle : 0.567 4.878 1640 Z= 0.306 Chirality : 0.046 0.139 190 Planarity : 0.005 0.039 206 Dihedral : 4.662 15.181 158 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 8.76 % Allowed : 27.01 % 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: -1.52 (0.71), residues: 145 helix: 1.70 (1.96), residues: 11 sheet: -0.21 (0.64), residues: 64 loop : -2.30 (0.72), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP E 59 HIS 0.001 0.000 HIS E 26 PHE 0.026 0.002 PHE E 137 TYR 0.015 0.001 TYR E 131 ARG 0.009 0.001 ARG E 93 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 687.27 seconds wall clock time: 14 minutes 0.03 seconds (840.03 seconds total)