Starting phenix.real_space_refine on Mon Feb 10 19:26:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8a06_15051/02_2025/8a06_15051.cif Found real_map, /net/cci-nas-00/data/ceres_data/8a06_15051/02_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_15051/02_2025/8a06_15051.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8a06_15051/02_2025/8a06_15051.map" model { file = "/net/cci-nas-00/data/ceres_data/8a06_15051/02_2025/8a06_15051.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8a06_15051/02_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-5592/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: 1.50, per 1000 atoms: 1.27 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 482.6 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: 0.39 Time building geometry restraints manager: 0.26 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: 0.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.050 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 7.400 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.700 ------------------------------------------------------------------------------- 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 : 0.149 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: 0.1056 time to fit residues: 6.7333 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 : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 110 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 11 optimal weight: 8.9990 chunk 10 optimal weight: 7.9990 chunk 5 optimal weight: 20.0000 chunk 3 optimal weight: 0.0000 chunk 7 optimal weight: 0.3980 chunk 4 optimal weight: 9.9990 chunk 6 optimal weight: 10.0000 chunk 8 optimal weight: 7.9990 chunk 12 optimal weight: 0.9990 chunk 13 optimal weight: 7.9990 chunk 9 optimal weight: 0.8980 overall best weight: 2.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 110 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.121062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.111728 restraints weight = 1936.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.114072 restraints weight = 1011.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.115703 restraints weight = 627.026| |-----------------------------------------------------------------------------| r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 1210 Z= 0.157 Angle : 0.571 6.188 1640 Z= 0.307 Chirality : 0.047 0.142 190 Planarity : 0.004 0.023 206 Dihedral : 4.761 27.409 160 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 4.38 % Allowed : 13.87 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.70), residues: 145 helix: 1.39 (1.85), residues: 11 sheet: 0.65 (0.67), residues: 58 loop : -1.88 (0.69), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 59 HIS 0.001 0.000 HIS E 26 PHE 0.019 0.002 PHE E 137 TYR 0.004 0.001 TYR E 21 ARG 0.003 0.001 ARG E 93 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 290 Ramachandran restraints generated. 145 Oldfield, 0 Emsley, 145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 290 Ramachandran restraints generated. 145 Oldfield, 0 Emsley, 145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.194 Fit side-chains REVERT: E 18 CYS cc_start: 0.8351 (t) cc_final: 0.8074 (t) REVERT: E 132 ASP cc_start: 0.7614 (OUTLIER) cc_final: 0.7386 (t0) outliers start: 6 outliers final: 3 residues processed: 44 average time/residue: 0.1088 time to fit residues: 5.5643 Evaluate side-chains 40 residues out of total 137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 36 time to evaluate : 0.140 ------------------------------------------------------------------------------- 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 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: 20.0000 chunk 11 optimal weight: 20.0000 chunk 3 optimal weight: 6.9990 chunk 9 optimal weight: 0.3980 chunk 1 optimal weight: 0.5980 chunk 4 optimal weight: 10.0000 chunk 13 optimal weight: 7.9990 chunk 6 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 5 optimal weight: 8.9990 overall best weight: 3.1986 ------------------------------------------------------------------------------- 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 = 0.118545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.108658 restraints weight = 1894.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.111120 restraints weight = 998.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.112861 restraints weight = 618.980| |-----------------------------------------------------------------------------| r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.1874 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= 0.184 Angle : 0.562 5.948 1640 Z= 0.302 Chirality : 0.047 0.136 190 Planarity : 0.004 0.023 206 Dihedral : 4.454 14.618 158 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 4.38 % Allowed : 17.52 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.73), residues: 145 helix: 1.86 (2.00), residues: 11 sheet: 0.79 (0.67), residues: 61 loop : -1.86 (0.72), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 59 HIS 0.003 0.001 HIS E 26 PHE 0.021 0.002 PHE E 137 TYR 0.007 0.001 TYR E 102 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 to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.186 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 47 average time/residue: 0.0959 time to fit residues: 5.2090 Evaluate side-chains 47 residues out of total 137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 42 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 125 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 6 optimal weight: 10.0000 chunk 7 optimal weight: 0.0980 chunk 2 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 3 optimal weight: 5.9990 chunk 8 optimal weight: 20.0000 chunk 11 optimal weight: 6.9990 chunk 4 optimal weight: 6.9990 chunk 10 optimal weight: 8.9990 chunk 9 optimal weight: 7.9990 chunk 12 optimal weight: 10.0000 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 = 0.3226 r_free = 0.3226 target = 0.116386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.106334 restraints weight = 1936.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.108860 restraints weight = 1016.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.110573 restraints weight = 632.988| |-----------------------------------------------------------------------------| r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 1210 Z= 0.263 Angle : 0.594 5.484 1640 Z= 0.321 Chirality : 0.048 0.140 190 Planarity : 0.004 0.024 206 Dihedral : 4.771 14.941 158 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 8.03 % Allowed : 18.25 % 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: -0.88 (0.72), residues: 145 helix: 2.19 (2.01), residues: 11 sheet: 0.50 (0.68), residues: 60 loop : -2.07 (0.71), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP E 59 HIS 0.003 0.001 HIS E 26 PHE 0.025 0.002 PHE E 137 TYR 0.011 0.002 TYR E 21 ARG 0.002 0.001 ARG E 101 *********************** 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 48 residues out of total 137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 37 time to evaluate : 0.154 Fit side-chains REVERT: E 95 GLU cc_start: 0.6468 (tt0) cc_final: 0.6214 (tt0) REVERT: E 108 PHE cc_start: 0.7525 (OUTLIER) cc_final: 0.6065 (t80) outliers start: 11 outliers final: 7 residues processed: 45 average time/residue: 0.0983 time to fit residues: 5.1188 Evaluate side-chains 42 residues out of total 137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 34 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 108 PHE Chi-restraints excluded: chain E residue 125 SER 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: 0.9980 chunk 5 optimal weight: 0.0570 chunk 4 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 12 optimal weight: 9.9990 chunk 7 optimal weight: 10.0000 chunk 10 optimal weight: 7.9990 chunk 3 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 overall best weight: 2.8104 ------------------------------------------------------------------------------- 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 = 0.3250 r_free = 0.3250 target = 0.117986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.107874 restraints weight = 1923.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.110416 restraints weight = 999.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.112149 restraints weight = 619.689| |-----------------------------------------------------------------------------| r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.2402 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= 0.171 Angle : 0.548 4.829 1640 Z= 0.299 Chirality : 0.046 0.135 190 Planarity : 0.004 0.024 206 Dihedral : 4.530 14.992 158 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 9.49 % Allowed : 19.71 % 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: -0.74 (0.72), residues: 145 helix: 2.37 (2.02), residues: 11 sheet: 0.64 (0.67), residues: 61 loop : -2.08 (0.71), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP E 59 HIS 0.002 0.001 HIS E 26 PHE 0.005 0.001 PHE E 39 TYR 0.007 0.001 TYR E 21 ARG 0.003 0.000 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 49 residues out of total 137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 36 time to evaluate : 0.142 Fit side-chains REVERT: E 66 ILE cc_start: 0.8992 (OUTLIER) cc_final: 0.8760 (mp) REVERT: E 108 PHE cc_start: 0.7462 (OUTLIER) cc_final: 0.6264 (t80) outliers start: 13 outliers final: 8 residues processed: 45 average time/residue: 0.1025 time to fit residues: 5.3128 Evaluate side-chains 45 residues out of total 137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 35 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue -1 PHE Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 66 ILE Chi-restraints excluded: chain E residue 108 PHE Chi-restraints excluded: chain E residue 125 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 1 optimal weight: 5.9990 chunk 6 optimal weight: 7.9990 chunk 7 optimal weight: 6.9990 chunk 4 optimal weight: 3.9990 chunk 5 optimal weight: 20.0000 chunk 12 optimal weight: 8.9990 chunk 8 optimal weight: 5.9990 chunk 2 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 11 optimal weight: 6.9990 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.116570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.106428 restraints weight = 1905.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.108860 restraints weight = 1018.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.110599 restraints weight = 642.626| |-----------------------------------------------------------------------------| r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 1210 Z= 0.245 Angle : 0.579 4.904 1640 Z= 0.315 Chirality : 0.047 0.140 190 Planarity : 0.004 0.023 206 Dihedral : 4.721 14.826 158 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % 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: -0.92 (0.72), residues: 145 helix: 2.24 (2.00), residues: 11 sheet: 0.52 (0.67), residues: 60 loop : -2.15 (0.71), residues: 74 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 0.007 0.001 PHE E 118 TYR 0.011 0.001 TYR E 21 ARG 0.004 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 49 residues out of total 137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 36 time to evaluate : 0.124 Fit side-chains REVERT: E 108 PHE cc_start: 0.7469 (OUTLIER) cc_final: 0.6571 (t80) outliers start: 13 outliers final: 11 residues processed: 45 average time/residue: 0.0988 time to fit residues: 5.1175 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 : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue -1 PHE Chi-restraints excluded: chain E residue 18 CYS Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 66 ILE Chi-restraints excluded: chain E residue 108 PHE Chi-restraints excluded: chain E residue 125 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 11 optimal weight: 5.9990 chunk 6 optimal weight: 8.9990 chunk 1 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 chunk 3 optimal weight: 1.9990 chunk 13 optimal weight: 6.9990 chunk 9 optimal weight: 20.0000 chunk 5 optimal weight: 6.9990 chunk 7 optimal weight: 7.9990 chunk 4 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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 = 0.3224 r_free = 0.3224 target = 0.116139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.106164 restraints weight = 1897.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.108597 restraints weight = 1010.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.110204 restraints weight = 638.922| |-----------------------------------------------------------------------------| r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.2545 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= 0.222 Angle : 0.568 4.850 1640 Z= 0.309 Chirality : 0.047 0.139 190 Planarity : 0.004 0.024 206 Dihedral : 4.661 14.792 158 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 8.76 % Allowed : 24.82 % 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: -1.00 (0.72), residues: 145 helix: 2.18 (1.98), residues: 11 sheet: 0.44 (0.67), residues: 60 loop : -2.18 (0.70), 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 0.006 0.001 PHE E 108 TYR 0.009 0.001 TYR E 21 ARG 0.003 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 : 0.141 Fit side-chains REVERT: E 108 PHE cc_start: 0.7455 (OUTLIER) cc_final: 0.6626 (t80) outliers start: 12 outliers final: 11 residues processed: 44 average time/residue: 0.0987 time to fit residues: 5.0216 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 : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue -1 PHE Chi-restraints excluded: chain E residue 18 CYS Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 66 ILE Chi-restraints excluded: chain E residue 108 PHE Chi-restraints excluded: chain E residue 125 SER 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: 9.9990 chunk 12 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 11 optimal weight: 20.0000 chunk 3 optimal weight: 20.0000 chunk 6 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 chunk 5 optimal weight: 5.9990 chunk 2 optimal weight: 0.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 = 0.3236 r_free = 0.3236 target = 0.116909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.106835 restraints weight = 1937.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.109290 restraints weight = 1022.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.111001 restraints weight = 639.193| |-----------------------------------------------------------------------------| r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 1210 Z= 0.199 Angle : 0.556 5.063 1640 Z= 0.302 Chirality : 0.046 0.139 190 Planarity : 0.004 0.024 206 Dihedral : 4.580 14.677 158 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % 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: -1.15 (0.71), residues: 145 helix: 2.16 (1.98), residues: 11 sheet: 0.12 (0.65), residues: 64 loop : -2.19 (0.70), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP E 59 HIS 0.002 0.001 HIS E 26 PHE 0.006 0.001 PHE E 108 TYR 0.008 0.001 TYR E 21 ARG 0.002 0.000 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 to be fit. rotamer outliers: 13 poor density : 38 time to evaluate : 0.145 Fit side-chains REVERT: E 39 PHE cc_start: 0.9099 (p90) cc_final: 0.8865 (p90) REVERT: E 66 ILE cc_start: 0.8952 (OUTLIER) cc_final: 0.8705 (mp) REVERT: E 108 PHE cc_start: 0.7458 (OUTLIER) cc_final: 0.6725 (t80) outliers start: 13 outliers final: 9 residues processed: 45 average time/residue: 0.1128 time to fit residues: 5.8727 Evaluate side-chains 49 residues out of total 137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 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 28 THR Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 66 ILE Chi-restraints excluded: chain E residue 108 PHE Chi-restraints excluded: chain E residue 125 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 2 optimal weight: 7.9990 chunk 3 optimal weight: 9.9990 chunk 7 optimal weight: 10.0000 chunk 8 optimal weight: 6.9990 chunk 11 optimal weight: 7.9990 chunk 9 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 6 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 4 optimal weight: 8.9990 chunk 12 optimal weight: 2.9990 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 = 0.3211 r_free = 0.3211 target = 0.115525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.105436 restraints weight = 1921.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.107826 restraints weight = 1026.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.109507 restraints weight = 646.949| |-----------------------------------------------------------------------------| r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.2710 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= 0.269 Angle : 0.594 5.495 1640 Z= 0.321 Chirality : 0.048 0.141 190 Planarity : 0.004 0.024 206 Dihedral : 4.746 15.037 158 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 10.22 % Allowed : 24.82 % Favored : 64.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.71), residues: 145 helix: 2.07 (1.97), residues: 11 sheet: 0.05 (0.65), residues: 64 loop : -2.28 (0.71), residues: 70 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 0.007 0.001 PHE E 108 TYR 0.011 0.001 TYR E 21 ARG 0.002 0.001 ARG E 101 *********************** 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 54 residues out of total 137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 40 time to evaluate : 0.147 Fit side-chains REVERT: E 39 PHE cc_start: 0.9069 (p90) cc_final: 0.8843 (p90) REVERT: E 108 PHE cc_start: 0.7481 (OUTLIER) cc_final: 0.6853 (t80) REVERT: E 131 TYR cc_start: 0.8139 (m-80) cc_final: 0.7888 (m-80) outliers start: 14 outliers final: 13 residues processed: 47 average time/residue: 0.0948 time to fit residues: 5.1634 Evaluate side-chains 54 residues out of total 137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 40 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 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 108 PHE Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 132 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 4 optimal weight: 6.9990 chunk 3 optimal weight: 6.9990 chunk 5 optimal weight: 6.9990 chunk 1 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 chunk 11 optimal weight: 9.9990 chunk 12 optimal weight: 6.9990 chunk 8 optimal weight: 8.9990 chunk 10 optimal weight: 5.9990 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 = 0.3217 r_free = 0.3217 target = 0.115936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.106296 restraints weight = 1908.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.108653 restraints weight = 1009.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.110305 restraints weight = 630.245| |-----------------------------------------------------------------------------| r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 1210 Z= 0.271 Angle : 0.605 5.707 1640 Z= 0.328 Chirality : 0.048 0.141 190 Planarity : 0.004 0.024 206 Dihedral : 4.809 15.238 158 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 10.22 % Allowed : 25.55 % 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: -1.32 (0.71), residues: 145 helix: 1.78 (1.94), residues: 11 sheet: 0.06 (0.65), residues: 64 loop : -2.31 (0.71), 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 108 TYR 0.009 0.001 TYR E 21 ARG 0.002 0.000 ARG E 101 ********************** 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 52 residues out of total 137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 38 time to evaluate : 0.151 Fit side-chains REVERT: E 108 PHE cc_start: 0.7483 (OUTLIER) cc_final: 0.6951 (t80) REVERT: E 131 TYR cc_start: 0.8151 (m-80) cc_final: 0.7925 (m-80) outliers start: 14 outliers final: 13 residues processed: 46 average time/residue: 0.0970 time to fit residues: 5.1865 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 : 0.145 ------------------------------------------------------------------------------- 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 108 PHE Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 132 ASP 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 8 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 chunk 2 optimal weight: 8.9990 chunk 3 optimal weight: 9.9990 chunk 5 optimal weight: 10.0000 chunk 6 optimal weight: 5.9990 chunk 9 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 10 optimal weight: 9.9990 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 = 0.3217 r_free = 0.3217 target = 0.115933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.105887 restraints weight = 1946.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.108331 restraints weight = 1030.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.110049 restraints weight = 643.145| |-----------------------------------------------------------------------------| r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.2727 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= 0.269 Angle : 0.603 4.884 1640 Z= 0.328 Chirality : 0.048 0.143 190 Planarity : 0.004 0.024 206 Dihedral : 4.831 15.171 158 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 10.22 % Allowed : 25.55 % 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: -1.29 (0.71), residues: 145 helix: 1.64 (1.94), residues: 11 sheet: 0.18 (0.66), residues: 64 loop : -2.38 (0.69), 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 0.008 0.002 PHE E 108 TYR 0.009 0.001 TYR E 21 ARG 0.002 0.000 ARG E 101 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 804.80 seconds wall clock time: 15 minutes 47.51 seconds (947.51 seconds total)