Starting phenix.real_space_refine on Tue Mar 3 10:47:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8a06_15051/03_2026/8a06_15051.cif Found real_map, /net/cci-nas-00/data/ceres_data/8a06_15051/03_2026/8a06_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 { model { file = "/net/cci-nas-00/data/ceres_data/8a06_15051/03_2026/8a06_15051.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8a06_15051/03_2026/8a06_15051.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8a06_15051/03_2026/8a06_15051.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8a06_15051/03_2026/8a06_15051.map" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 5 5.16 5 C 761 2.51 5 N 186 2.21 5 O 233 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 0.26, per 1000 atoms: 0.22 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: 0.04 Conformation dependent library (CDL) restraints added in 25.7 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: 0.02 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: 0.07 Time building geometry restraints manager: 0.06 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: 0.240 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: 0.010 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 1.820 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:0.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 2.790 ------------------------------------------------------------------------------- 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= 0.121 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.009 0.001 ARG E 93 TYR 0.003 0.001 TYR E 102 PHE 0.010 0.001 PHE E 108 TRP 0.006 0.002 TRP E 59 HIS 0.002 0.001 HIS E 26 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 1210) covalent geometry : angle 0.55558 ( 1640) hydrogen bonds : bond 0.25470 ( 46) hydrogen bonds : angle 10.06785 ( 132) *********************** 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 : 0.024 Fit side-chains REVERT: E 18 CYS cc_start: 0.8242 (t) cc_final: 0.7953 (t) REVERT: E 43 SER cc_start: 0.9402 (p) cc_final: 0.9117 (p) REVERT: E 93 ARG cc_start: 0.7521 (mtp-110) cc_final: 0.7297 (mtp-110) outliers start: 1 outliers final: 1 residues processed: 56 average time/residue: 0.0205 time to fit residues: 1.3368 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 : 0.023 ------------------------------------------------------------------------------- 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 13 optimal weight: 6.9990 chunk 6 optimal weight: 10.0000 chunk 12 optimal weight: 0.8980 chunk 0 optimal weight: 20.0000 chunk 4 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 5 optimal weight: 20.0000 chunk 9 optimal weight: 10.0000 chunk 3 optimal weight: 5.9990 chunk 2 optimal weight: 6.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- 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 = 0.3249 r_free = 0.3249 target = 0.117964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.108363 restraints weight = 1926.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.110806 restraints weight = 997.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.112438 restraints weight = 615.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.113589 restraints weight = 422.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.114304 restraints weight = 310.144| |-----------------------------------------------------------------------------| r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.1620 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= 0.167 Angle : 0.604 6.160 1640 Z= 0.325 Chirality : 0.048 0.146 190 Planarity : 0.004 0.024 206 Dihedral : 4.998 27.041 160 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 4.38 % Allowed : 13.14 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.69), residues: 145 helix: 1.41 (1.83), residues: 11 sheet: 0.51 (0.66), residues: 58 loop : -1.96 (0.69), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG E 93 TYR 0.007 0.001 TYR E 21 PHE 0.021 0.002 PHE E 137 TRP 0.014 0.003 TRP E 59 HIS 0.002 0.001 HIS E 26 Details of bonding type rmsd covalent geometry : bond 0.00374 ( 1210) covalent geometry : angle 0.60400 ( 1640) hydrogen bonds : bond 0.04254 ( 46) hydrogen bonds : angle 7.10914 ( 132) *********************** 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 : 0.024 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 46 average time/residue: 0.0215 time to fit residues: 1.1556 Evaluate side-chains 39 residues out of total 137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 35 time to evaluate : 0.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 27 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 6 optimal weight: 10.0000 chunk 3 optimal weight: 7.9990 chunk 4 optimal weight: 10.0000 chunk 11 optimal weight: 7.9990 chunk 10 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 8 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 1 optimal weight: 8.9990 chunk 9 optimal weight: 5.9990 chunk 5 optimal weight: 20.0000 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 = 0.3202 r_free = 0.3202 target = 0.114441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.105555 restraints weight = 1987.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.107712 restraints weight = 1092.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.109230 restraints weight = 699.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.110239 restraints weight = 489.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.110883 restraints weight = 367.241| |-----------------------------------------------------------------------------| r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 1210 Z= 0.216 Angle : 0.630 5.345 1640 Z= 0.341 Chirality : 0.049 0.139 190 Planarity : 0.004 0.024 206 Dihedral : 4.859 15.595 158 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 6.57 % Allowed : 18.25 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.73), residues: 145 helix: 2.13 (2.00), residues: 11 sheet: 0.47 (0.67), residues: 62 loop : -1.98 (0.74), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG E 101 TYR 0.012 0.002 TYR E 21 PHE 0.023 0.002 PHE E 137 TRP 0.013 0.003 TRP E 59 HIS 0.003 0.001 HIS E 26 Details of bonding type rmsd covalent geometry : bond 0.00497 ( 1210) covalent geometry : angle 0.63035 ( 1640) hydrogen bonds : bond 0.03882 ( 46) hydrogen bonds : angle 6.81568 ( 132) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 290 Ramachandran restraints generated. 145 Oldfield, 0 Emsley, 145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 290 Ramachandran restraints generated. 145 Oldfield, 0 Emsley, 145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 36 time to evaluate : 0.025 Fit side-chains REVERT: E 108 PHE cc_start: 0.7653 (OUTLIER) cc_final: 0.7305 (t80) outliers start: 9 outliers final: 6 residues processed: 43 average time/residue: 0.0222 time to fit residues: 1.1349 Evaluate side-chains 41 residues out of total 137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 34 time to evaluate : 0.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 12 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 7 optimal weight: 5.9990 chunk 11 optimal weight: 7.9990 chunk 8 optimal weight: 5.9990 chunk 3 optimal weight: 4.9990 chunk 4 optimal weight: 9.9990 chunk 2 optimal weight: 3.9990 chunk 5 optimal weight: 8.9990 chunk 10 optimal weight: 8.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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 = 0.3207 r_free = 0.3207 target = 0.114986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.104790 restraints weight = 2033.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.107353 restraints weight = 1050.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.109077 restraints weight = 647.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.110289 restraints weight = 443.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.111150 restraints weight = 327.375| |-----------------------------------------------------------------------------| r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 1210 Z= 0.175 Angle : 0.579 5.011 1640 Z= 0.318 Chirality : 0.048 0.138 190 Planarity : 0.004 0.025 206 Dihedral : 4.783 15.219 158 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.74), residues: 145 helix: 2.27 (2.01), residues: 11 sheet: 0.16 (0.66), residues: 66 loop : -2.02 (0.75), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 93 TYR 0.009 0.001 TYR E 21 PHE 0.026 0.002 PHE E 137 TRP 0.011 0.002 TRP E 59 HIS 0.002 0.001 HIS E 26 Details of bonding type rmsd covalent geometry : bond 0.00396 ( 1210) covalent geometry : angle 0.57926 ( 1640) hydrogen bonds : bond 0.03407 ( 46) hydrogen bonds : angle 6.62586 ( 132) *********************** 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 50 residues out of total 137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 38 time to evaluate : 0.025 Fit side-chains REVERT: E 108 PHE cc_start: 0.7482 (OUTLIER) cc_final: 0.7129 (t80) outliers start: 12 outliers final: 8 residues processed: 47 average time/residue: 0.0217 time to fit residues: 1.1918 Evaluate side-chains 44 residues out of total 137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 35 time to evaluate : 0.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 66 ILE Chi-restraints excluded: chain E residue 108 PHE Chi-restraints excluded: chain E residue 125 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 9 optimal weight: 10.0000 chunk 4 optimal weight: 6.9990 chunk 13 optimal weight: 6.9990 chunk 10 optimal weight: 10.0000 chunk 6 optimal weight: 5.9990 chunk 5 optimal weight: 10.0000 chunk 11 optimal weight: 5.9990 chunk 1 optimal weight: 7.9990 chunk 7 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 chunk 2 optimal weight: 1.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- 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 = 0.3204 r_free = 0.3204 target = 0.114451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.104694 restraints weight = 1944.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.107094 restraints weight = 1018.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.108768 restraints weight = 632.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.109972 restraints weight = 435.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.110764 restraints weight = 318.621| |-----------------------------------------------------------------------------| r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 1210 Z= 0.193 Angle : 0.592 4.773 1640 Z= 0.325 Chirality : 0.048 0.139 190 Planarity : 0.004 0.025 206 Dihedral : 4.912 15.641 158 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 10.22 % Allowed : 23.36 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.73), residues: 145 helix: 2.29 (2.00), residues: 11 sheet: 0.03 (0.66), residues: 66 loop : -2.08 (0.76), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 93 TYR 0.011 0.001 TYR E 21 PHE 0.023 0.002 PHE E 137 TRP 0.012 0.002 TRP E 59 HIS 0.002 0.001 HIS E 26 Details of bonding type rmsd covalent geometry : bond 0.00445 ( 1210) covalent geometry : angle 0.59240 ( 1640) hydrogen bonds : bond 0.03474 ( 46) hydrogen bonds : angle 6.48202 ( 132) *********************** 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: 14 poor density : 37 time to evaluate : 0.025 Fit side-chains REVERT: E 86 LEU cc_start: 0.9001 (mm) cc_final: 0.8792 (mm) REVERT: E 108 PHE cc_start: 0.7785 (OUTLIER) cc_final: 0.7457 (t80) outliers start: 14 outliers final: 12 residues processed: 47 average time/residue: 0.0214 time to fit residues: 1.1846 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 : 0.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue -1 PHE Chi-restraints excluded: chain E residue 18 CYS Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 66 ILE Chi-restraints excluded: chain E residue 108 PHE Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 135 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 0 optimal weight: 20.0000 chunk 6 optimal weight: 9.9990 chunk 2 optimal weight: 7.9990 chunk 12 optimal weight: 8.9990 chunk 3 optimal weight: 6.9990 chunk 1 optimal weight: 6.9990 chunk 9 optimal weight: 0.4980 chunk 10 optimal weight: 6.9990 chunk 5 optimal weight: 9.9990 chunk 4 optimal weight: 5.9990 chunk 7 optimal weight: 9.9990 overall best weight: 5.4988 ------------------------------------------------------------------------------- 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 = 0.3207 r_free = 0.3207 target = 0.114376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.104608 restraints weight = 1961.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.107028 restraints weight = 1016.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.108687 restraints weight = 627.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.109895 restraints weight = 430.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.110680 restraints weight = 315.846| |-----------------------------------------------------------------------------| r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 1210 Z= 0.191 Angle : 0.589 4.669 1640 Z= 0.323 Chirality : 0.048 0.139 190 Planarity : 0.005 0.026 206 Dihedral : 4.935 15.368 158 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 5.52 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.72), residues: 145 helix: 2.32 (1.97), residues: 11 sheet: -0.10 (0.64), residues: 66 loop : -2.10 (0.76), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 93 TYR 0.010 0.002 TYR E 21 PHE 0.029 0.002 PHE E 137 TRP 0.011 0.002 TRP E 59 HIS 0.002 0.001 HIS E 26 Details of bonding type rmsd covalent geometry : bond 0.00441 ( 1210) covalent geometry : angle 0.58935 ( 1640) hydrogen bonds : bond 0.03351 ( 46) hydrogen bonds : angle 6.47679 ( 132) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 290 Ramachandran restraints generated. 145 Oldfield, 0 Emsley, 145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 290 Ramachandran restraints generated. 145 Oldfield, 0 Emsley, 145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 38 time to evaluate : 0.045 Fit side-chains REVERT: E 108 PHE cc_start: 0.7503 (OUTLIER) cc_final: 0.7186 (t80) outliers start: 14 outliers final: 12 residues processed: 47 average time/residue: 0.0314 time to fit residues: 1.7286 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 : 0.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue -1 PHE Chi-restraints excluded: chain E residue 18 CYS Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 66 ILE Chi-restraints excluded: chain E residue 108 PHE Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 135 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 13 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 chunk 7 optimal weight: 7.9990 chunk 9 optimal weight: 7.9990 chunk 11 optimal weight: 6.9990 chunk 12 optimal weight: 3.9990 chunk 2 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 6 optimal weight: 2.9990 chunk 5 optimal weight: 8.9990 chunk 4 optimal weight: 8.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 = 0.3221 r_free = 0.3221 target = 0.115355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.105839 restraints weight = 1941.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.108232 restraints weight = 995.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.109915 restraints weight = 609.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.111064 restraints weight = 413.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.111836 restraints weight = 300.851| |-----------------------------------------------------------------------------| r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 1210 Z= 0.152 Angle : 0.566 4.558 1640 Z= 0.309 Chirality : 0.046 0.139 190 Planarity : 0.005 0.030 206 Dihedral : 4.817 15.944 158 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 11.68 % Allowed : 24.09 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.72), residues: 145 helix: 2.34 (1.99), residues: 11 sheet: 0.07 (0.65), residues: 64 loop : -2.21 (0.73), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 93 TYR 0.008 0.001 TYR E 21 PHE 0.025 0.002 PHE E 137 TRP 0.009 0.002 TRP E 59 HIS 0.002 0.001 HIS E 26 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 1210) covalent geometry : angle 0.56592 ( 1640) hydrogen bonds : bond 0.03067 ( 46) hydrogen bonds : angle 6.43301 ( 132) *********************** 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 56 residues out of total 137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 40 time to evaluate : 0.045 Fit side-chains REVERT: E 108 PHE cc_start: 0.7475 (OUTLIER) cc_final: 0.7152 (t80) REVERT: E 132 ASP cc_start: 0.7897 (OUTLIER) cc_final: 0.7654 (t0) outliers start: 16 outliers final: 9 residues processed: 50 average time/residue: 0.0350 time to fit residues: 2.0559 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 : 0.049 ------------------------------------------------------------------------------- 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 108 PHE Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 132 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 0 optimal weight: 20.0000 chunk 8 optimal weight: 6.9990 chunk 12 optimal weight: 0.9990 chunk 7 optimal weight: 6.9990 chunk 6 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 9 optimal weight: 6.9990 chunk 1 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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 = 0.115440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.106054 restraints weight = 1923.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.108325 restraints weight = 1013.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.109890 restraints weight = 638.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.111014 restraints weight = 445.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.111761 restraints weight = 332.635| |-----------------------------------------------------------------------------| r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 1210 Z= 0.184 Angle : 0.606 4.577 1640 Z= 0.330 Chirality : 0.048 0.140 190 Planarity : 0.005 0.034 206 Dihedral : 5.010 17.804 158 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 10.95 % Allowed : 25.55 % Favored : 63.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.36 (0.71), residues: 145 helix: 2.26 (1.98), residues: 11 sheet: -0.04 (0.64), residues: 64 loop : -2.36 (0.72), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 93 TYR 0.012 0.002 TYR E 131 PHE 0.024 0.002 PHE E 137 TRP 0.011 0.002 TRP E 59 HIS 0.002 0.001 HIS E 26 Details of bonding type rmsd covalent geometry : bond 0.00438 ( 1210) covalent geometry : angle 0.60577 ( 1640) hydrogen bonds : bond 0.03230 ( 46) hydrogen bonds : angle 6.49123 ( 132) *********************** 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 53 residues out of total 137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 38 time to evaluate : 0.048 Fit side-chains REVERT: E 39 PHE cc_start: 0.9102 (p90) cc_final: 0.8836 (p90) REVERT: E 108 PHE cc_start: 0.7554 (OUTLIER) cc_final: 0.6995 (t80) REVERT: E 132 ASP cc_start: 0.7930 (OUTLIER) cc_final: 0.7672 (t0) outliers start: 15 outliers final: 12 residues processed: 49 average time/residue: 0.0369 time to fit residues: 2.1035 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 : 0.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue -1 PHE Chi-restraints excluded: chain E residue 7 VAL Chi-restraints excluded: chain E residue 18 CYS Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 108 PHE Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 132 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 1 optimal weight: 6.9990 chunk 10 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 2 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 5 optimal weight: 0.0020 chunk 12 optimal weight: 10.0000 chunk 3 optimal weight: 0.1980 chunk 4 optimal weight: 6.9990 chunk 6 optimal weight: 5.9990 overall best weight: 3.6394 ------------------------------------------------------------------------------- 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 = 0.3245 r_free = 0.3245 target = 0.116808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.107375 restraints weight = 1892.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.109764 restraints weight = 979.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.111326 restraints weight = 605.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.112413 restraints weight = 419.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.113233 restraints weight = 312.162| |-----------------------------------------------------------------------------| r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 1210 Z= 0.148 Angle : 0.585 4.709 1640 Z= 0.317 Chirality : 0.046 0.139 190 Planarity : 0.004 0.036 206 Dihedral : 4.936 18.160 158 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 10.22 % Allowed : 26.28 % Favored : 63.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.70), residues: 145 helix: 2.22 (1.99), residues: 11 sheet: 0.08 (0.64), residues: 64 loop : -2.33 (0.70), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 93 TYR 0.009 0.001 TYR E 131 PHE 0.007 0.001 PHE E 39 TRP 0.009 0.002 TRP E 59 HIS 0.001 0.001 HIS E 26 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 1210) covalent geometry : angle 0.58499 ( 1640) hydrogen bonds : bond 0.02954 ( 46) hydrogen bonds : angle 6.43451 ( 132) *********************** 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 52 residues out of total 137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 38 time to evaluate : 0.054 Fit side-chains REVERT: E 39 PHE cc_start: 0.9098 (p90) cc_final: 0.8859 (p90) REVERT: E 108 PHE cc_start: 0.7527 (OUTLIER) cc_final: 0.7005 (t80) REVERT: E 132 ASP cc_start: 0.7928 (OUTLIER) cc_final: 0.7686 (t0) outliers start: 14 outliers final: 11 residues processed: 48 average time/residue: 0.0362 time to fit residues: 2.0249 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 : 0.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue -1 PHE Chi-restraints excluded: chain E residue 7 VAL Chi-restraints excluded: chain E residue 18 CYS Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 108 PHE Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 132 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 13 optimal weight: 5.9990 chunk 8 optimal weight: 0.6980 chunk 11 optimal weight: 5.9990 chunk 5 optimal weight: 10.0000 chunk 9 optimal weight: 5.9990 chunk 3 optimal weight: 0.2980 chunk 4 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 2 optimal weight: 0.9980 chunk 12 optimal weight: 6.9990 chunk 6 optimal weight: 3.9990 overall best weight: 2.3984 ------------------------------------------------------------------------------- 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 = 0.3274 r_free = 0.3274 target = 0.118977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.109472 restraints weight = 1907.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.111863 restraints weight = 992.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.113527 restraints weight = 604.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.114662 restraints weight = 411.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.115477 restraints weight = 301.562| |-----------------------------------------------------------------------------| r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 1210 Z= 0.122 Angle : 0.577 5.709 1640 Z= 0.309 Chirality : 0.046 0.134 190 Planarity : 0.004 0.037 206 Dihedral : 4.733 15.942 158 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 8.76 % Allowed : 27.74 % Favored : 63.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.69), residues: 145 helix: 2.33 (2.02), residues: 11 sheet: 0.16 (0.62), residues: 65 loop : -2.34 (0.68), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 93 TYR 0.007 0.001 TYR E 131 PHE 0.006 0.001 PHE E 39 TRP 0.008 0.002 TRP E 59 HIS 0.001 0.000 HIS E 26 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 1210) covalent geometry : angle 0.57735 ( 1640) hydrogen bonds : bond 0.02738 ( 46) hydrogen bonds : angle 6.35803 ( 132) ********************** 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 51 residues out of total 137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 39 time to evaluate : 0.053 Fit side-chains REVERT: E 93 ARG cc_start: 0.8057 (mtp-110) cc_final: 0.7638 (mtp-110) REVERT: E 108 PHE cc_start: 0.7530 (OUTLIER) cc_final: 0.6992 (t80) outliers start: 12 outliers final: 9 residues processed: 48 average time/residue: 0.0360 time to fit residues: 2.0291 Evaluate side-chains 48 residues out of total 137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 38 time to evaluate : 0.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue -1 PHE Chi-restraints excluded: chain E residue 7 VAL Chi-restraints excluded: chain E residue 18 CYS Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 35 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 5 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 7 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 11 optimal weight: 7.9990 chunk 10 optimal weight: 8.9990 chunk 4 optimal weight: 4.9990 chunk 9 optimal weight: 0.6980 chunk 3 optimal weight: 7.9990 chunk 2 optimal weight: 2.9990 chunk 13 optimal weight: 8.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- 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 = 0.3286 r_free = 0.3286 target = 0.119995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.110513 restraints weight = 1933.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.112874 restraints weight = 1004.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.114474 restraints weight = 628.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.115530 restraints weight = 435.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.116365 restraints weight = 327.491| |-----------------------------------------------------------------------------| r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.2878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 1210 Z= 0.126 Angle : 0.588 6.305 1640 Z= 0.312 Chirality : 0.046 0.136 190 Planarity : 0.004 0.036 206 Dihedral : 4.684 14.363 158 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 9.49 % Allowed : 27.01 % Favored : 63.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.70), residues: 145 helix: 2.37 (2.02), residues: 11 sheet: 0.33 (0.65), residues: 64 loop : -2.41 (0.66), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 93 TYR 0.007 0.001 TYR E 131 PHE 0.009 0.001 PHE E 39 TRP 0.009 0.002 TRP E 59 HIS 0.001 0.000 HIS E 26 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 1210) covalent geometry : angle 0.58754 ( 1640) hydrogen bonds : bond 0.02742 ( 46) hydrogen bonds : angle 6.27873 ( 132) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 369.58 seconds wall clock time: 7 minutes 20.33 seconds (440.33 seconds total)