Starting phenix.real_space_refine on Sat Apr 4 20:06:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9m5l_63645/04_2026/9m5l_63645.cif Found real_map, /net/cci-nas-00/data/ceres_data/9m5l_63645/04_2026/9m5l_63645.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9m5l_63645/04_2026/9m5l_63645.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9m5l_63645/04_2026/9m5l_63645.map" model { file = "/net/cci-nas-00/data/ceres_data/9m5l_63645/04_2026/9m5l_63645.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9m5l_63645/04_2026/9m5l_63645.cif" } resolution = 3.27 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= 0.000 sd= 0.004 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: 3 Type Number sf(0) Gaussians C 1119 2.51 5 N 315 2.21 5 O 363 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 1797 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 599 Classifications: {'peptide': 87} Link IDs: {'TRANS': 86} Restraints were copied for chains: B, C Time building chain proxies: 0.25, per 1000 atoms: 0.14 Number of scatterers: 1797 At special positions: 0 Unit cell: (73.87, 77.19, 30.71, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 363 8.00 N 315 7.00 C 1119 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: 0.07 Conformation dependent library (CDL) restraints added in 44.9 milliseconds 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 444 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 6 sheets defined 0.0% alpha, 19.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 6.347A pdb=" N ALA A 29 " --> pdb=" O ALA C 30 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ALA C 29 " --> pdb=" O GLU B 28 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 46 through 51 removed outlier: 8.306A pdb=" N GLU A 46 " --> pdb=" O GLY C 47 " (cutoff:3.500A) removed outlier: 8.560A pdb=" N VAL C 49 " --> pdb=" O GLU A 46 " (cutoff:3.500A) removed outlier: 9.067A pdb=" N VAL A 48 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 9.019A pdb=" N GLY C 51 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N HIS A 50 " --> pdb=" O GLY C 51 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N VAL C 48 " --> pdb=" O GLY B 47 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N VAL B 49 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N HIS C 50 " --> pdb=" O VAL B 49 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 62 through 64 removed outlier: 6.607A pdb=" N VAL A 63 " --> pdb=" O THR C 64 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 69 through 71 removed outlier: 6.424A pdb=" N ALA B 69 " --> pdb=" O VAL C 70 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 76 through 78 removed outlier: 6.615A pdb=" N ALA A 76 " --> pdb=" O VAL C 77 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 88 through 92 removed outlier: 6.800A pdb=" N ALA C 91 " --> pdb=" O ALA A 90 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N THR A 92 " --> pdb=" O ALA C 91 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N ALA B 89 " --> pdb=" O ALA C 90 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N THR C 92 " --> pdb=" O ALA B 89 " (cutoff:3.500A) removed outlier: 9.063A pdb=" N ALA B 91 " --> pdb=" O THR C 92 " (cutoff:3.500A) 11 hydrogen bonds defined for protein. 33 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: 0.14 Time building geometry restraints manager: 0.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.28: 324 1.28 - 1.35: 289 1.35 - 1.41: 44 1.41 - 1.48: 345 1.48 - 1.54: 801 Bond restraints: 1803 Sorted by residual: bond pdb=" CB VAL C 49 " pdb=" CG2 VAL C 49 " ideal model delta sigma weight residual 1.521 1.457 0.064 3.30e-02 9.18e+02 3.73e+00 bond pdb=" CB VAL A 49 " pdb=" CG2 VAL A 49 " ideal model delta sigma weight residual 1.521 1.458 0.063 3.30e-02 9.18e+02 3.70e+00 bond pdb=" CB GLN B 79 " pdb=" CG GLN B 79 " ideal model delta sigma weight residual 1.520 1.463 0.057 3.00e-02 1.11e+03 3.66e+00 bond pdb=" CB GLN C 79 " pdb=" CG GLN C 79 " ideal model delta sigma weight residual 1.520 1.463 0.057 3.00e-02 1.11e+03 3.65e+00 bond pdb=" CB VAL B 49 " pdb=" CG2 VAL B 49 " ideal model delta sigma weight residual 1.521 1.458 0.063 3.30e-02 9.18e+02 3.65e+00 ... (remaining 1798 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 2161 1.61 - 3.22: 246 3.22 - 4.82: 14 4.82 - 6.43: 3 6.43 - 8.04: 6 Bond angle restraints: 2430 Sorted by residual: angle pdb=" CB LYS A 21 " pdb=" CG LYS A 21 " pdb=" CD LYS A 21 " ideal model delta sigma weight residual 111.30 118.08 -6.78 2.30e+00 1.89e-01 8.69e+00 angle pdb=" CB LYS C 21 " pdb=" CG LYS C 21 " pdb=" CD LYS C 21 " ideal model delta sigma weight residual 111.30 118.05 -6.75 2.30e+00 1.89e-01 8.62e+00 angle pdb=" CB LYS B 21 " pdb=" CG LYS B 21 " pdb=" CD LYS B 21 " ideal model delta sigma weight residual 111.30 118.05 -6.75 2.30e+00 1.89e-01 8.61e+00 angle pdb=" CG LYS B 21 " pdb=" CD LYS B 21 " pdb=" CE LYS B 21 " ideal model delta sigma weight residual 111.30 117.60 -6.30 2.30e+00 1.89e-01 7.50e+00 angle pdb=" CG LYS C 21 " pdb=" CD LYS C 21 " pdb=" CE LYS C 21 " ideal model delta sigma weight residual 111.30 117.55 -6.25 2.30e+00 1.89e-01 7.39e+00 ... (remaining 2425 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.72: 918 13.72 - 27.43: 105 27.43 - 41.14: 30 41.14 - 54.86: 9 54.86 - 68.57: 9 Dihedral angle restraints: 1071 sinusoidal: 366 harmonic: 705 Sorted by residual: dihedral pdb=" CA GLY B 36 " pdb=" C GLY B 36 " pdb=" N VAL B 37 " pdb=" CA VAL B 37 " ideal model delta harmonic sigma weight residual 180.00 -160.77 -19.23 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA GLY A 36 " pdb=" C GLY A 36 " pdb=" N VAL A 37 " pdb=" CA VAL A 37 " ideal model delta harmonic sigma weight residual -180.00 -160.79 -19.21 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA GLY C 36 " pdb=" C GLY C 36 " pdb=" N VAL C 37 " pdb=" CA VAL C 37 " ideal model delta harmonic sigma weight residual 180.00 -160.81 -19.19 0 5.00e+00 4.00e-02 1.47e+01 ... (remaining 1068 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 104 0.036 - 0.073: 90 0.073 - 0.109: 88 0.109 - 0.145: 24 0.145 - 0.182: 6 Chirality restraints: 312 Sorted by residual: chirality pdb=" CB THR C 22 " pdb=" CA THR C 22 " pdb=" OG1 THR C 22 " pdb=" CG2 THR C 22 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 8.25e-01 chirality pdb=" CB THR A 22 " pdb=" CA THR A 22 " pdb=" OG1 THR A 22 " pdb=" CG2 THR A 22 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 7.93e-01 chirality pdb=" CB THR B 22 " pdb=" CA THR B 22 " pdb=" OG1 THR B 22 " pdb=" CG2 THR B 22 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 7.91e-01 ... (remaining 309 not shown) Planarity restraints: 306 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR C 39 " -0.007 2.00e-02 2.50e+03 1.48e-02 2.19e+00 pdb=" C TYR C 39 " 0.026 2.00e-02 2.50e+03 pdb=" O TYR C 39 " -0.010 2.00e-02 2.50e+03 pdb=" N VAL C 40 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 39 " -0.007 2.00e-02 2.50e+03 1.48e-02 2.18e+00 pdb=" C TYR A 39 " 0.026 2.00e-02 2.50e+03 pdb=" O TYR A 39 " -0.010 2.00e-02 2.50e+03 pdb=" N VAL A 40 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR B 39 " -0.007 2.00e-02 2.50e+03 1.44e-02 2.07e+00 pdb=" C TYR B 39 " 0.025 2.00e-02 2.50e+03 pdb=" O TYR B 39 " -0.010 2.00e-02 2.50e+03 pdb=" N VAL B 40 " -0.008 2.00e-02 2.50e+03 ... (remaining 303 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 201 2.71 - 3.26: 1659 3.26 - 3.80: 2682 3.80 - 4.35: 3110 4.35 - 4.90: 6497 Nonbonded interactions: 14149 Sorted by model distance: nonbonded pdb=" NZ LYS A 80 " pdb=" OE1 GLU C 46 " model vdw 2.163 3.120 nonbonded pdb=" O GLY A 84 " pdb=" OG SER A 87 " model vdw 2.166 3.040 nonbonded pdb=" OE1 GLU B 46 " pdb=" NZ LYS C 80 " model vdw 2.166 3.120 nonbonded pdb=" O GLY C 84 " pdb=" OG SER C 87 " model vdw 2.167 3.040 nonbonded pdb=" O GLY B 84 " pdb=" OG SER B 87 " model vdw 2.167 3.040 ... (remaining 14144 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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 individual isotropic 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: 1.070 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: 0.010 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 2.220 Find NCS groups from input model: 0.000 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:0.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 4.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 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 : 0.016 0.064 1803 Z= 0.709 Angle : 1.094 8.038 2430 Z= 0.624 Chirality : 0.071 0.182 312 Planarity : 0.006 0.015 306 Dihedral : 15.129 68.572 627 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 21.18 % Favored : 78.82 % Rotamer: Outliers : 0.00 % Allowed : 13.56 % Favored : 86.44 % 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: -6.12 (0.31), residues: 255 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.66 (0.23), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.023 0.006 TYR C 39 PHE 0.008 0.004 PHE C 94 HIS 0.007 0.005 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.01564 ( 1803) covalent geometry : angle 1.09365 ( 2430) hydrogen bonds : bond 0.12773 ( 11) hydrogen bonds : angle 7.50279 ( 33) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.035 Fit side-chains REVERT: B 83 GLU cc_start: 0.7816 (tt0) cc_final: 0.7222 (tm-30) REVERT: C 83 GLU cc_start: 0.7595 (tt0) cc_final: 0.7308 (tm-30) outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.0737 time to fit residues: 1.6270 Evaluate side-chains 12 residues out of total 177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 12 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 1 optimal weight: 0.9980 chunk 8 optimal weight: 10.0000 chunk 16 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 9 optimal weight: 6.9990 chunk 11 optimal weight: 0.5980 chunk 18 optimal weight: 0.9980 chunk 6 optimal weight: 7.9990 chunk 4 optimal weight: 5.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN A 50 HIS B 24 GLN B 50 HIS C 24 GLN C 50 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.115711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.097404 restraints weight = 2179.329| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 2.17 r_work: 0.3527 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3409 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 1803 Z= 0.100 Angle : 0.487 3.749 2430 Z= 0.281 Chirality : 0.054 0.143 312 Planarity : 0.002 0.006 306 Dihedral : 5.537 15.687 261 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.20 % Favored : 89.80 % Rotamer: Outliers : 0.00 % Allowed : 12.43 % Favored : 87.57 % 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: -5.29 (0.36), residues: 255 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.03 (0.27), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.002 TYR C 39 PHE 0.005 0.001 PHE C 94 HIS 0.001 0.000 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00205 ( 1803) covalent geometry : angle 0.48704 ( 2430) hydrogen bonds : bond 0.01282 ( 11) hydrogen bonds : angle 5.19929 ( 33) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 14 residues out of total 177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.035 Fit side-chains REVERT: B 23 LYS cc_start: 0.8242 (ttpt) cc_final: 0.7799 (tttt) outliers start: 0 outliers final: 0 residues processed: 14 average time/residue: 0.0620 time to fit residues: 1.0310 Evaluate side-chains 7 residues out of total 177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 7 time to evaluate : 0.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 17 optimal weight: 10.0000 chunk 23 optimal weight: 8.9990 chunk 22 optimal weight: 8.9990 chunk 15 optimal weight: 8.9990 chunk 2 optimal weight: 7.9990 chunk 1 optimal weight: 4.9990 chunk 12 optimal weight: 8.9990 chunk 8 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 20 optimal weight: 4.9990 chunk 16 optimal weight: 9.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- 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 = 0.3822 r_free = 0.3822 target = 0.114495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.094591 restraints weight = 2367.980| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 2.03 r_work: 0.3436 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3323 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.053 1803 Z= 0.515 Angle : 0.795 4.343 2430 Z= 0.465 Chirality : 0.063 0.141 312 Planarity : 0.005 0.013 306 Dihedral : 6.710 18.315 261 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 26.27 % Favored : 73.73 % Rotamer: Outliers : 1.13 % Allowed : 19.77 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -5.75 (0.34), residues: 255 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.37 (0.26), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.019 0.005 TYR C 39 PHE 0.012 0.004 PHE A 94 HIS 0.003 0.001 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.01165 ( 1803) covalent geometry : angle 0.79466 ( 2430) hydrogen bonds : bond 0.02097 ( 11) hydrogen bonds : angle 5.58075 ( 33) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 14 residues out of total 177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 12 time to evaluate : 0.053 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 13 average time/residue: 0.0684 time to fit residues: 1.0392 Evaluate side-chains 13 residues out of total 177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 11 time to evaluate : 0.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain C residue 79 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 2 optimal weight: 6.9990 chunk 19 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 4 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 9 optimal weight: 3.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 GLN C 79 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.125417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.105773 restraints weight = 2154.197| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 2.04 r_work: 0.3592 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3479 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 1803 Z= 0.100 Angle : 0.464 3.464 2430 Z= 0.268 Chirality : 0.054 0.128 312 Planarity : 0.001 0.007 306 Dihedral : 5.193 15.827 261 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.41 % Favored : 90.59 % Rotamer: Outliers : 3.39 % Allowed : 19.21 % Favored : 77.40 % 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: -5.16 (0.38), residues: 255 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.93 (0.29), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.002 TYR A 39 PHE 0.005 0.001 PHE C 94 HIS 0.001 0.001 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00221 ( 1803) covalent geometry : angle 0.46353 ( 2430) hydrogen bonds : bond 0.01044 ( 11) hydrogen bonds : angle 5.08157 ( 33) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 10 time to evaluate : 0.037 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 15 average time/residue: 0.0683 time to fit residues: 1.1937 Evaluate side-chains 11 residues out of total 177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 9 time to evaluate : 0.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain B residue 83 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 16 optimal weight: 20.0000 chunk 10 optimal weight: 0.0970 chunk 19 optimal weight: 5.9990 chunk 7 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 21 optimal weight: 10.0000 chunk 15 optimal weight: 7.9990 chunk 22 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 99 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.118232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.096894 restraints weight = 2062.779| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 2.24 r_work: 0.3548 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3424 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 1803 Z= 0.158 Angle : 0.476 2.890 2430 Z= 0.276 Chirality : 0.053 0.128 312 Planarity : 0.002 0.006 306 Dihedral : 5.134 16.001 261 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.29 % Favored : 84.71 % Rotamer: Outliers : 1.13 % Allowed : 23.16 % Favored : 75.71 % 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: -4.96 (0.40), residues: 255 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.77 (0.30), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.010 0.003 TYR C 39 PHE 0.007 0.002 PHE C 94 HIS 0.001 0.000 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 1803) covalent geometry : angle 0.47635 ( 2430) hydrogen bonds : bond 0.00874 ( 11) hydrogen bonds : angle 5.05959 ( 33) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 11 time to evaluate : 0.061 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 12 average time/residue: 0.0696 time to fit residues: 0.9997 Evaluate side-chains 13 residues out of total 177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 11 time to evaluate : 0.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain B residue 83 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 15 optimal weight: 10.0000 chunk 7 optimal weight: 1.9990 chunk 19 optimal weight: 8.9990 chunk 18 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 17 optimal weight: 7.9990 chunk 20 optimal weight: 6.9990 chunk 6 optimal weight: 4.9990 chunk 10 optimal weight: 0.0770 chunk 22 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 overall best weight: 1.9544 ------------------------------------------------------------------------------- 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 = 0.3962 r_free = 0.3962 target = 0.119486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.098265 restraints weight = 1978.183| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 2.20 r_work: 0.3553 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3428 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.2604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 1803 Z= 0.151 Angle : 0.458 2.487 2430 Z= 0.267 Chirality : 0.052 0.127 312 Planarity : 0.002 0.006 306 Dihedral : 5.009 15.360 261 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.33 % Favored : 86.67 % Rotamer: Outliers : 1.13 % Allowed : 24.86 % Favored : 74.01 % 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: -4.73 (0.41), residues: 255 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.60 (0.31), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.010 0.002 TYR C 39 PHE 0.007 0.002 PHE C 94 HIS 0.001 0.000 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 1803) covalent geometry : angle 0.45844 ( 2430) hydrogen bonds : bond 0.00857 ( 11) hydrogen bonds : angle 5.05590 ( 33) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 11 time to evaluate : 0.044 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 12 average time/residue: 0.0586 time to fit residues: 0.8533 Evaluate side-chains 11 residues out of total 177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 10 time to evaluate : 0.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 7 optimal weight: 0.6980 chunk 15 optimal weight: 10.0000 chunk 12 optimal weight: 10.0000 chunk 5 optimal weight: 0.0670 chunk 3 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 14 optimal weight: 0.2980 chunk 22 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 10 optimal weight: 10.0000 chunk 1 optimal weight: 8.9990 overall best weight: 0.7720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.126099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.105585 restraints weight = 1965.175| |-----------------------------------------------------------------------------| r_work (start): 0.3768 rms_B_bonded: 2.12 r_work: 0.3659 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3537 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.3019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 1803 Z= 0.081 Angle : 0.417 4.342 2430 Z= 0.242 Chirality : 0.052 0.149 312 Planarity : 0.001 0.013 306 Dihedral : 4.435 14.413 261 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.98 % Favored : 89.02 % Rotamer: Outliers : 2.26 % Allowed : 23.16 % Favored : 74.58 % 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: -4.34 (0.43), residues: 255 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.30 (0.33), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.002 TYR B 39 PHE 0.005 0.001 PHE C 94 HIS 0.000 0.000 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00175 ( 1803) covalent geometry : angle 0.41723 ( 2430) hydrogen bonds : bond 0.00707 ( 11) hydrogen bonds : angle 4.89369 ( 33) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 11 residues out of total 177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 7 time to evaluate : 0.061 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 9 average time/residue: 0.0633 time to fit residues: 0.7329 Evaluate side-chains 9 residues out of total 177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 7 time to evaluate : 0.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain C residue 79 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 19 optimal weight: 7.9990 chunk 18 optimal weight: 5.9990 chunk 13 optimal weight: 8.9990 chunk 22 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 10 optimal weight: 0.6980 chunk 5 optimal weight: 0.0970 chunk 12 optimal weight: 6.9990 chunk 23 optimal weight: 9.9990 chunk 16 optimal weight: 10.0000 chunk 9 optimal weight: 7.9990 overall best weight: 4.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.114486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.092716 restraints weight = 2119.053| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 2.25 r_work: 0.3480 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3359 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.2532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.034 1803 Z= 0.319 Angle : 0.590 3.847 2430 Z= 0.346 Chirality : 0.055 0.133 312 Planarity : 0.003 0.009 306 Dihedral : 5.408 15.862 261 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.22 % Favored : 80.78 % Rotamer: Outliers : 1.13 % Allowed : 24.86 % Favored : 74.01 % 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: -4.73 (0.41), residues: 255 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.60 (0.31), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.016 0.004 TYR C 39 PHE 0.008 0.002 PHE C 94 HIS 0.001 0.001 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00722 ( 1803) covalent geometry : angle 0.58987 ( 2430) hydrogen bonds : bond 0.01293 ( 11) hydrogen bonds : angle 5.12487 ( 33) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 12 residues out of total 177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 10 time to evaluate : 0.101 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 11 average time/residue: 0.0569 time to fit residues: 0.7765 Evaluate side-chains 11 residues out of total 177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 10 time to evaluate : 0.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 83 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 9 optimal weight: 0.0980 chunk 21 optimal weight: 6.9990 chunk 3 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 1 optimal weight: 5.9990 chunk 10 optimal weight: 0.8980 chunk 8 optimal weight: 10.0000 chunk 4 optimal weight: 4.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- 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 = 0.3960 r_free = 0.3960 target = 0.120061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.099428 restraints weight = 2063.619| |-----------------------------------------------------------------------------| r_work (start): 0.3678 rms_B_bonded: 2.12 r_work: 0.3566 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3443 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 1803 Z= 0.145 Angle : 0.481 3.989 2430 Z= 0.276 Chirality : 0.052 0.127 312 Planarity : 0.002 0.013 306 Dihedral : 4.948 15.331 261 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.33 % Favored : 86.67 % Rotamer: Outliers : 1.13 % Allowed : 24.86 % Favored : 74.01 % 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: -4.60 (0.41), residues: 255 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.50 (0.32), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.010 0.002 TYR B 39 PHE 0.006 0.002 PHE C 94 HIS 0.001 0.000 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 1803) covalent geometry : angle 0.48076 ( 2430) hydrogen bonds : bond 0.00776 ( 11) hydrogen bonds : angle 4.87230 ( 33) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 11 time to evaluate : 0.050 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 12 average time/residue: 0.0750 time to fit residues: 1.0403 Evaluate side-chains 11 residues out of total 177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 10 time to evaluate : 0.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 3 optimal weight: 3.9990 chunk 17 optimal weight: 10.0000 chunk 20 optimal weight: 9.9990 chunk 21 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 5 optimal weight: 0.4980 chunk 16 optimal weight: 9.9990 chunk 12 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 13 optimal weight: 7.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- 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 = 0.3965 r_free = 0.3965 target = 0.120605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.099775 restraints weight = 2067.630| |-----------------------------------------------------------------------------| r_work (start): 0.3676 rms_B_bonded: 2.13 r_work: 0.3571 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3449 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.2859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 1803 Z= 0.148 Angle : 0.473 4.007 2430 Z= 0.271 Chirality : 0.052 0.127 312 Planarity : 0.002 0.013 306 Dihedral : 4.843 15.159 261 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.51 % Favored : 85.49 % Rotamer: Outliers : 0.56 % Allowed : 25.42 % Favored : 74.01 % 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: -4.50 (0.42), residues: 255 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.42 (0.32), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.010 0.002 TYR B 39 PHE 0.007 0.002 PHE C 94 HIS 0.001 0.000 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 1803) covalent geometry : angle 0.47279 ( 2430) hydrogen bonds : bond 0.00700 ( 11) hydrogen bonds : angle 4.91176 ( 33) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 10 residues out of total 177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 9 time to evaluate : 0.042 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 10 average time/residue: 0.0772 time to fit residues: 0.9042 Evaluate side-chains 10 residues out of total 177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 9 time to evaluate : 0.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 3 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 chunk 18 optimal weight: 5.9990 chunk 13 optimal weight: 0.0980 chunk 11 optimal weight: 0.0770 chunk 14 optimal weight: 1.9990 chunk 17 optimal weight: 7.9990 chunk 19 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 20 optimal weight: 10.0000 chunk 1 optimal weight: 2.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- 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 = 0.4077 r_free = 0.4077 target = 0.127849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.107230 restraints weight = 2015.753| |-----------------------------------------------------------------------------| r_work (start): 0.3807 rms_B_bonded: 2.16 r_work: 0.3705 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3580 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.3293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 1803 Z= 0.072 Angle : 0.412 4.190 2430 Z= 0.235 Chirality : 0.051 0.127 312 Planarity : 0.001 0.013 306 Dihedral : 4.278 13.816 261 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 1.13 % Allowed : 25.42 % Favored : 73.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -4.10 (0.45), residues: 255 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.11 (0.34), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.002 TYR B 39 PHE 0.004 0.001 PHE C 94 HIS 0.001 0.000 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00157 ( 1803) covalent geometry : angle 0.41195 ( 2430) hydrogen bonds : bond 0.00690 ( 11) hydrogen bonds : angle 4.56934 ( 33) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 647.85 seconds wall clock time: 12 minutes 57.09 seconds (777.09 seconds total)