Starting phenix.real_space_refine on Wed Mar 5 14:16:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8a06_15051/03_2025/8a06_15051.cif Found real_map, /net/cci-nas-00/data/ceres_data/8a06_15051/03_2025/8a06_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/cci-nas-00/data/ceres_data/8a06_15051/03_2025/8a06_15051.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8a06_15051/03_2025/8a06_15051.map" model { file = "/net/cci-nas-00/data/ceres_data/8a06_15051/03_2025/8a06_15051.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8a06_15051/03_2025/8a06_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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 2.24, per 1000 atoms: 1.89 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: 0.20 Conformation dependent library (CDL) restraints added in 188.7 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: 0.10 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: 0.19 Time building geometry restraints manager: 0.27 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: 0.000 Normalize map: mean=0, sd=1: 0.330 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 8.420 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.200 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 1 poor density : 55 time to evaluate : 0.137 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: 0.1060 time to fit residues: 6.7832 Evaluate side-chains 51 residues out of total 137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 50 time to evaluate : 0.152 ------------------------------------------------------------------------------- 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: 5.9990 chunk 9 optimal weight: 0.9980 overall best weight: 1.6788 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.121578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.111841 restraints weight = 1935.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.114366 restraints weight = 993.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.116066 restraints weight = 606.391| |-----------------------------------------------------------------------------| r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.1507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 1210 Z= 0.146 Angle : 0.569 6.038 1640 Z= 0.305 Chirality : 0.047 0.140 190 Planarity : 0.004 0.023 206 Dihedral : 4.813 29.561 160 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.65 % Allowed : 14.60 % 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: -0.79 (0.70), residues: 145 helix: 1.40 (1.85), residues: 11 sheet: 0.65 (0.67), residues: 58 loop : -1.87 (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 0.018 0.002 PHE E 137 TYR 0.003 0.001 TYR E 21 ARG 0.002 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 46 residues out of total 137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 41 time to evaluate : 0.146 Fit side-chains REVERT: E 18 CYS cc_start: 0.8381 (t) cc_final: 0.8114 (t) REVERT: E 132 ASP cc_start: 0.7595 (OUTLIER) cc_final: 0.7389 (t0) outliers start: 5 outliers final: 2 residues processed: 42 average time/residue: 0.1321 time to fit residues: 6.3950 Evaluate side-chains 36 residues out of total 137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 33 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 41 LEU Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 132 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 12 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 3 optimal weight: 9.9990 chunk 9 optimal weight: 20.0000 chunk 1 optimal weight: 0.1980 chunk 4 optimal weight: 9.9990 chunk 13 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 overall best weight: 2.2388 ------------------------------------------------------------------------------- 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 = 0.3272 r_free = 0.3272 target = 0.119941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.110405 restraints weight = 1882.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.112776 restraints weight = 1002.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.114464 restraints weight = 626.972| |-----------------------------------------------------------------------------| r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 1210 Z= 0.150 Angle : 0.541 5.842 1640 Z= 0.289 Chirality : 0.046 0.133 190 Planarity : 0.004 0.022 206 Dihedral : 4.312 13.827 158 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 4.38 % Allowed : 16.79 % Favored : 78.83 % 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: -0.49 (0.72), residues: 145 helix: 1.96 (2.00), residues: 11 sheet: 0.87 (0.67), residues: 61 loop : -1.85 (0.72), residues: 73 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 0.020 0.002 PHE E 137 TYR 0.006 0.001 TYR E 102 ARG 0.004 0.001 ARG E 93 *********************** 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 48 residues out of total 137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.143 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 45 average time/residue: 0.0985 time to fit residues: 5.1286 Evaluate side-chains 45 residues out of total 137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 41 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 6 optimal weight: 9.9990 chunk 7 optimal weight: 0.7980 chunk 2 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 3 optimal weight: 7.9990 chunk 8 optimal weight: 9.9990 chunk 11 optimal weight: 0.0980 chunk 4 optimal weight: 8.9990 chunk 10 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- 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 = 0.3267 r_free = 0.3267 target = 0.119590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.109704 restraints weight = 1897.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.112174 restraints weight = 989.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.113904 restraints weight = 611.026| |-----------------------------------------------------------------------------| r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.1992 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= 0.165 Angle : 0.539 6.008 1640 Z= 0.289 Chirality : 0.046 0.134 190 Planarity : 0.004 0.022 206 Dihedral : 4.394 14.339 158 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 7.30 % Allowed : 17.52 % Favored : 75.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.72), residues: 145 helix: 2.18 (2.03), residues: 11 sheet: 0.92 (0.67), residues: 61 loop : -1.85 (0.71), 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 0.023 0.002 PHE E 137 TYR 0.007 0.001 TYR E 21 ARG 0.004 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 53 residues out of total 137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 43 time to evaluate : 0.142 Fit side-chains outliers start: 10 outliers final: 8 residues processed: 48 average time/residue: 0.0949 time to fit residues: 5.2698 Evaluate side-chains 47 residues out of total 137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 39 time to evaluate : 0.126 ------------------------------------------------------------------------------- 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 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 8 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 1 optimal weight: 5.9990 chunk 5 optimal weight: 6.9990 chunk 4 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 7 optimal weight: 9.9990 chunk 10 optimal weight: 0.4980 chunk 3 optimal weight: 0.0570 chunk 2 optimal weight: 5.9990 overall best weight: 3.5104 ------------------------------------------------------------------------------- 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 = 0.3252 r_free = 0.3252 target = 0.118320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.108002 restraints weight = 1922.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.110531 restraints weight = 1013.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.112321 restraints weight = 633.033| |-----------------------------------------------------------------------------| r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 1210 Z= 0.193 Angle : 0.554 5.407 1640 Z= 0.302 Chirality : 0.046 0.136 190 Planarity : 0.004 0.024 206 Dihedral : 4.471 14.511 158 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 7.30 % Allowed : 18.98 % 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: -0.55 (0.72), residues: 145 helix: 2.29 (2.02), residues: 11 sheet: 0.87 (0.67), residues: 61 loop : -2.02 (0.70), residues: 73 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 0.010 0.001 PHE E 108 TYR 0.009 0.001 TYR E 21 ARG 0.006 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 51 residues out of total 137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 41 time to evaluate : 0.146 Fit side-chains outliers start: 10 outliers final: 8 residues processed: 46 average time/residue: 0.0999 time to fit residues: 5.3220 Evaluate side-chains 48 residues out of total 137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 40 time to evaluate : 0.146 ------------------------------------------------------------------------------- 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 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 1 optimal weight: 9.9990 chunk 6 optimal weight: 7.9990 chunk 7 optimal weight: 6.9990 chunk 4 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 12 optimal weight: 6.9990 chunk 8 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 11 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.116069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.105735 restraints weight = 1914.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.108266 restraints weight = 1027.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.109734 restraints weight = 644.179| |-----------------------------------------------------------------------------| r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 1210 Z= 0.261 Angle : 0.584 4.822 1640 Z= 0.321 Chirality : 0.048 0.140 190 Planarity : 0.004 0.025 206 Dihedral : 4.674 14.941 158 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 10.22 % Allowed : 18.98 % Favored : 70.80 % 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: -0.87 (0.72), residues: 145 helix: 2.26 (2.01), residues: 11 sheet: 0.56 (0.67), residues: 60 loop : -2.12 (0.70), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 59 HIS 0.003 0.001 HIS E 26 PHE 0.013 0.001 PHE E 108 TYR 0.012 0.002 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 50 residues out of total 137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 36 time to evaluate : 0.143 Fit side-chains REVERT: E 66 ILE cc_start: 0.8962 (OUTLIER) cc_final: 0.8719 (mp) outliers start: 14 outliers final: 11 residues processed: 44 average time/residue: 0.1059 time to fit residues: 5.3559 Evaluate side-chains 47 residues out of total 137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 35 time to evaluate : 0.149 ------------------------------------------------------------------------------- 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 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 11 optimal weight: 7.9990 chunk 6 optimal weight: 5.9990 chunk 1 optimal weight: 7.9990 chunk 10 optimal weight: 6.9990 chunk 3 optimal weight: 0.0770 chunk 13 optimal weight: 0.9990 chunk 9 optimal weight: 20.0000 chunk 5 optimal weight: 10.0000 chunk 7 optimal weight: 8.9990 chunk 4 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 overall best weight: 3.6146 ------------------------------------------------------------------------------- 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 = 0.3242 r_free = 0.3242 target = 0.117372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.107445 restraints weight = 1890.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.109815 restraints weight = 1039.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.111437 restraints weight = 662.220| |-----------------------------------------------------------------------------| r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 1210 Z= 0.201 Angle : 0.556 4.488 1640 Z= 0.305 Chirality : 0.047 0.138 190 Planarity : 0.004 0.026 206 Dihedral : 4.574 14.762 158 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 8.76 % Allowed : 22.63 % Favored : 68.61 % 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: -0.93 (0.72), residues: 145 helix: 2.22 (1.99), residues: 11 sheet: 0.53 (0.67), residues: 60 loop : -2.17 (0.69), residues: 74 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 0.010 0.001 PHE E 108 TYR 0.008 0.001 TYR E 21 ARG 0.005 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 49 residues out of total 137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 37 time to evaluate : 0.146 Fit side-chains outliers start: 12 outliers final: 10 residues processed: 46 average time/residue: 0.0943 time to fit residues: 5.0455 Evaluate side-chains 46 residues out of total 137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 36 time to evaluate : 0.143 ------------------------------------------------------------------------------- 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 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 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 4 optimal weight: 2.9990 chunk 9 optimal weight: 6.9990 chunk 12 optimal weight: 9.9990 chunk 8 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 11 optimal weight: 8.9990 chunk 3 optimal weight: 7.9990 chunk 6 optimal weight: 6.9990 chunk 1 optimal weight: 7.9990 chunk 5 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- 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 = 0.3206 r_free = 0.3206 target = 0.115145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.105557 restraints weight = 1949.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.107873 restraints weight = 1058.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.109477 restraints weight = 674.395| |-----------------------------------------------------------------------------| r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.2547 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= 0.270 Angle : 0.585 4.390 1640 Z= 0.321 Chirality : 0.048 0.141 190 Planarity : 0.004 0.027 206 Dihedral : 4.733 15.224 158 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 9.49 % Allowed : 24.82 % Favored : 65.69 % 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: -1.25 (0.71), residues: 145 helix: 2.14 (1.98), residues: 11 sheet: 0.04 (0.65), residues: 64 loop : -2.25 (0.71), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 59 HIS 0.003 0.001 HIS E 26 PHE 0.012 0.002 PHE E 108 TYR 0.011 0.001 TYR E 21 ARG 0.004 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 50 residues out of total 137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 37 time to evaluate : 0.149 Fit side-chains REVERT: E 66 ILE cc_start: 0.8978 (OUTLIER) cc_final: 0.8776 (mp) outliers start: 13 outliers final: 11 residues processed: 45 average time/residue: 0.1025 time to fit residues: 5.3248 Evaluate side-chains 49 residues out of total 137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 37 time to evaluate : 0.151 ------------------------------------------------------------------------------- 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 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 2 optimal weight: 10.0000 chunk 3 optimal weight: 9.9990 chunk 7 optimal weight: 7.9990 chunk 8 optimal weight: 7.9990 chunk 11 optimal weight: 9.9990 chunk 9 optimal weight: 8.9990 chunk 10 optimal weight: 10.0000 chunk 6 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 4 optimal weight: 8.9990 chunk 12 optimal weight: 0.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- 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 = 0.3205 r_free = 0.3205 target = 0.115151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.105151 restraints weight = 1940.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.107459 restraints weight = 1063.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.109071 restraints weight = 684.249| |-----------------------------------------------------------------------------| r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 1210 Z= 0.314 Angle : 0.605 4.605 1640 Z= 0.333 Chirality : 0.049 0.142 190 Planarity : 0.005 0.036 206 Dihedral : 4.897 15.419 158 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 10.22 % Allowed : 24.09 % Favored : 65.69 % 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: -1.36 (0.71), residues: 145 helix: 2.08 (1.96), residues: 11 sheet: -0.04 (0.64), residues: 64 loop : -2.31 (0.71), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP E 59 HIS 0.003 0.001 HIS E 26 PHE 0.014 0.002 PHE E 108 TYR 0.011 0.002 TYR E 21 ARG 0.009 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 51 residues out of total 137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 37 time to evaluate : 0.146 Fit side-chains REVERT: E 66 ILE cc_start: 0.8971 (OUTLIER) cc_final: 0.8758 (mp) outliers start: 14 outliers final: 12 residues processed: 47 average time/residue: 0.1001 time to fit residues: 5.4519 Evaluate side-chains 49 residues out of total 137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 36 time to evaluate : 0.151 ------------------------------------------------------------------------------- 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 78 ILE 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: 5.9990 chunk 5 optimal weight: 7.9990 chunk 1 optimal weight: 0.0980 chunk 9 optimal weight: 8.9990 chunk 13 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 11 optimal weight: 20.0000 chunk 12 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 10 optimal weight: 9.9990 overall best weight: 5.2188 ------------------------------------------------------------------------------- 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 = 0.3222 r_free = 0.3222 target = 0.115849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.106015 restraints weight = 1937.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.108335 restraints weight = 1052.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.109976 restraints weight = 671.132| |-----------------------------------------------------------------------------| r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 1210 Z= 0.275 Angle : 0.603 4.333 1640 Z= 0.331 Chirality : 0.048 0.142 190 Planarity : 0.005 0.031 206 Dihedral : 4.876 15.957 158 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 5.94 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: -1.46 (0.70), residues: 145 helix: 1.74 (1.93), residues: 11 sheet: -0.10 (0.63), residues: 64 loop : -2.34 (0.70), 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 0.026 0.002 PHE E 137 TYR 0.020 0.002 TYR E 131 ARG 0.007 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 48 residues out of total 137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 35 time to evaluate : 0.153 Fit side-chains outliers start: 13 outliers final: 11 residues processed: 44 average time/residue: 0.0988 time to fit residues: 5.0381 Evaluate side-chains 48 residues out of total 137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 37 time to evaluate : 0.156 ------------------------------------------------------------------------------- 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 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: 7.9990 chunk 8 optimal weight: 7.9990 chunk 13 optimal weight: 6.9990 chunk 12 optimal weight: 5.9990 chunk 2 optimal weight: 0.9990 chunk 3 optimal weight: 7.9990 chunk 5 optimal weight: 8.9990 chunk 6 optimal weight: 6.9990 chunk 9 optimal weight: 9.9990 chunk 1 optimal weight: 5.9990 chunk 10 optimal weight: 6.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- 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 = 0.3216 r_free = 0.3216 target = 0.115519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.105191 restraints weight = 1972.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.107718 restraints weight = 1046.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.109419 restraints weight = 655.424| |-----------------------------------------------------------------------------| r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.2663 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= 0.282 Angle : 0.603 4.318 1640 Z= 0.331 Chirality : 0.048 0.143 190 Planarity : 0.005 0.027 206 Dihedral : 4.923 16.644 158 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 8.03 % Allowed : 27.74 % 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: -1.54 (0.69), residues: 145 helix: 1.65 (1.93), residues: 11 sheet: -0.11 (0.63), residues: 64 loop : -2.43 (0.69), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 59 HIS 0.003 0.001 HIS E 26 PHE 0.028 0.002 PHE E 137 TYR 0.020 0.002 TYR E 131 ARG 0.006 0.001 ARG E 93 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 829.40 seconds wall clock time: 15 minutes 31.75 seconds (931.75 seconds total)