Starting phenix.real_space_refine on Tue Mar 3 10:47:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vw2_21410/03_2026/6vw2_21410.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vw2_21410/03_2026/6vw2_21410.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6vw2_21410/03_2026/6vw2_21410.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vw2_21410/03_2026/6vw2_21410.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6vw2_21410/03_2026/6vw2_21410.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vw2_21410/03_2026/6vw2_21410.map" } resolution = 3.4 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 ------------------------------------------------------------------------------- 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= 1.000 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 1110 2.51 5 N 310 2.21 5 O 380 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 1800 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 180 Classifications: {'peptide': 24} Modifications used: {'COO': 1} Link IDs: {'TRANS': 23} Restraints were copied for chains: B, C, D, E, F, G, H, I, J Time building chain proxies: 0.17, per 1000 atoms: 0.09 Number of scatterers: 1800 At special positions: 0 Unit cell: (50.008, 75.544, 39.368, 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 380 8.00 N 310 7.00 C 1110 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: 0.08 Conformation dependent library (CDL) restraints added in 49.9 milliseconds 440 Ramachandran restraints generated. 220 Oldfield, 0 Emsley, 220 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 440 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 6 sheets defined 0.0% alpha, 33.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.04 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'H' and resid 15 through 16 removed outlier: 5.819A pdb=" N PHE A 15 " --> pdb=" O LEU E 16 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N PHE E 15 " --> pdb=" O LEU I 16 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 22 through 23 removed outlier: 7.473A pdb=" N ASN D 22 " --> pdb=" O PHE H 23 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N ASN A 22 " --> pdb=" O PHE D 23 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 26 through 32 removed outlier: 6.927A pdb=" N SER D 29 " --> pdb=" O SER H 28 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N THR H 30 " --> pdb=" O SER D 29 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N SER A 29 " --> pdb=" O SER D 28 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N THR D 30 " --> pdb=" O SER A 29 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ILE A 26 " --> pdb=" O LEU E 27 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N SER E 29 " --> pdb=" O ILE A 26 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N SER A 28 " --> pdb=" O SER E 29 " (cutoff:3.500A) removed outlier: 10.094A pdb=" N ASN E 31 " --> pdb=" O SER A 28 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N THR A 30 " --> pdb=" O ASN E 31 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ILE E 26 " --> pdb=" O LEU I 27 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N SER I 29 " --> pdb=" O ILE E 26 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N SER E 28 " --> pdb=" O SER I 29 " (cutoff:3.500A) removed outlier: 10.093A pdb=" N ASN I 31 " --> pdb=" O SER E 28 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N THR E 30 " --> pdb=" O ASN I 31 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 15 through 16 removed outlier: 5.808A pdb=" N PHE C 15 " --> pdb=" O LEU G 16 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N PHE B 15 " --> pdb=" O LEU C 16 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 22 through 23 removed outlier: 7.460A pdb=" N ASN B 22 " --> pdb=" O PHE F 23 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N ASN F 22 " --> pdb=" O PHE J 23 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 26 through 32 removed outlier: 6.870A pdb=" N ILE C 26 " --> pdb=" O LEU G 27 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N SER G 29 " --> pdb=" O ILE C 26 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N SER C 28 " --> pdb=" O SER G 29 " (cutoff:3.500A) removed outlier: 10.094A pdb=" N ASN G 31 " --> pdb=" O SER C 28 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N THR C 30 " --> pdb=" O ASN G 31 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ILE B 26 " --> pdb=" O LEU C 27 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N SER C 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N SER B 28 " --> pdb=" O SER C 29 " (cutoff:3.500A) removed outlier: 10.093A pdb=" N ASN C 31 " --> pdb=" O SER B 28 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N THR B 30 " --> pdb=" O ASN C 31 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N SER B 29 " --> pdb=" O SER F 28 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N THR F 30 " --> pdb=" O SER B 29 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N SER F 29 " --> pdb=" O SER J 28 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N THR J 30 " --> pdb=" O SER F 29 " (cutoff:3.500A) 24 hydrogen bonds defined for protein. 72 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: 0.13 Time building geometry restraints manager: 0.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.28: 300 1.28 - 1.35: 300 1.35 - 1.41: 240 1.41 - 1.47: 290 1.47 - 1.54: 700 Bond restraints: 1830 Sorted by residual: bond pdb=" CA SER G 20 " pdb=" C SER G 20 " ideal model delta sigma weight residual 1.528 1.514 0.014 1.32e-02 5.74e+03 1.08e+00 bond pdb=" CA SER E 20 " pdb=" C SER E 20 " ideal model delta sigma weight residual 1.528 1.514 0.014 1.32e-02 5.74e+03 1.06e+00 bond pdb=" CA SER J 20 " pdb=" C SER J 20 " ideal model delta sigma weight residual 1.528 1.514 0.013 1.32e-02 5.74e+03 1.05e+00 bond pdb=" CA SER H 20 " pdb=" C SER H 20 " ideal model delta sigma weight residual 1.528 1.515 0.013 1.32e-02 5.74e+03 1.00e+00 bond pdb=" CA SER C 20 " pdb=" C SER C 20 " ideal model delta sigma weight residual 1.528 1.515 0.013 1.32e-02 5.74e+03 9.91e-01 ... (remaining 1825 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.28: 2050 1.28 - 2.56: 320 2.56 - 3.84: 90 3.84 - 5.13: 20 5.13 - 6.41: 10 Bond angle restraints: 2490 Sorted by residual: angle pdb=" C SER B 19 " pdb=" N SER B 20 " pdb=" CA SER B 20 " ideal model delta sigma weight residual 122.35 127.41 -5.06 1.46e+00 4.69e-01 1.20e+01 angle pdb=" C SER J 19 " pdb=" N SER J 20 " pdb=" CA SER J 20 " ideal model delta sigma weight residual 122.35 127.41 -5.06 1.46e+00 4.69e-01 1.20e+01 angle pdb=" C SER I 19 " pdb=" N SER I 20 " pdb=" CA SER I 20 " ideal model delta sigma weight residual 122.35 127.40 -5.05 1.46e+00 4.69e-01 1.20e+01 angle pdb=" C SER D 19 " pdb=" N SER D 20 " pdb=" CA SER D 20 " ideal model delta sigma weight residual 122.35 127.40 -5.05 1.46e+00 4.69e-01 1.19e+01 angle pdb=" C SER G 19 " pdb=" N SER G 20 " pdb=" CA SER G 20 " ideal model delta sigma weight residual 122.35 127.39 -5.04 1.46e+00 4.69e-01 1.19e+01 ... (remaining 2485 not shown) Histogram of dihedral angle deviations from ideal: 0.08 - 7.54: 700 7.54 - 14.99: 140 14.99 - 22.45: 100 22.45 - 29.90: 60 29.90 - 37.36: 20 Dihedral angle restraints: 1020 sinusoidal: 340 harmonic: 680 Sorted by residual: dihedral pdb=" CA ALA G 25 " pdb=" C ALA G 25 " pdb=" N ILE G 26 " pdb=" CA ILE G 26 " ideal model delta harmonic sigma weight residual 180.00 154.48 25.52 0 5.00e+00 4.00e-02 2.61e+01 dihedral pdb=" CA ALA I 25 " pdb=" C ALA I 25 " pdb=" N ILE I 26 " pdb=" CA ILE I 26 " ideal model delta harmonic sigma weight residual 180.00 154.51 25.49 0 5.00e+00 4.00e-02 2.60e+01 dihedral pdb=" CA ALA D 25 " pdb=" C ALA D 25 " pdb=" N ILE D 26 " pdb=" CA ILE D 26 " ideal model delta harmonic sigma weight residual 180.00 154.51 25.49 0 5.00e+00 4.00e-02 2.60e+01 ... (remaining 1017 not shown) Histogram of chiral volume deviations from ideal: 0.002 - 0.030: 132 0.030 - 0.059: 58 0.059 - 0.087: 60 0.087 - 0.116: 10 0.116 - 0.144: 30 Chirality restraints: 290 Sorted by residual: chirality pdb=" CG LEU C 27 " pdb=" CB LEU C 27 " pdb=" CD1 LEU C 27 " pdb=" CD2 LEU C 27 " both_signs ideal model delta sigma weight residual False -2.59 -2.73 0.14 2.00e-01 2.50e+01 5.21e-01 chirality pdb=" CG LEU G 27 " pdb=" CB LEU G 27 " pdb=" CD1 LEU G 27 " pdb=" CD2 LEU G 27 " both_signs ideal model delta sigma weight residual False -2.59 -2.73 0.14 2.00e-01 2.50e+01 5.19e-01 chirality pdb=" CA SER J 20 " pdb=" N SER J 20 " pdb=" C SER J 20 " pdb=" CB SER J 20 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.16e-01 ... (remaining 287 not shown) Planarity restraints: 330 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR G 36 " 0.017 2.00e-02 2.50e+03 3.47e-02 1.20e+01 pdb=" C THR G 36 " -0.060 2.00e-02 2.50e+03 pdb=" O THR G 36 " 0.023 2.00e-02 2.50e+03 pdb=" N TYR G 37 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR E 36 " -0.017 2.00e-02 2.50e+03 3.46e-02 1.20e+01 pdb=" C THR E 36 " 0.060 2.00e-02 2.50e+03 pdb=" O THR E 36 " -0.023 2.00e-02 2.50e+03 pdb=" N TYR E 37 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR D 36 " -0.017 2.00e-02 2.50e+03 3.46e-02 1.20e+01 pdb=" C THR D 36 " 0.060 2.00e-02 2.50e+03 pdb=" O THR D 36 " -0.023 2.00e-02 2.50e+03 pdb=" N TYR D 37 " -0.020 2.00e-02 2.50e+03 ... (remaining 327 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 618 2.81 - 3.34: 1772 3.34 - 3.86: 3038 3.86 - 4.38: 3852 4.38 - 4.90: 6750 Nonbonded interactions: 16030 Sorted by model distance: nonbonded pdb=" O SER D 20 " pdb=" OG SER D 20 " model vdw 2.292 3.040 nonbonded pdb=" O SER F 20 " pdb=" OG SER F 20 " model vdw 2.292 3.040 nonbonded pdb=" O SER H 20 " pdb=" OG SER H 20 " model vdw 2.292 3.040 nonbonded pdb=" O SER E 20 " pdb=" OG SER E 20 " model vdw 2.292 3.040 nonbonded pdb=" O SER A 20 " pdb=" OG SER A 20 " model vdw 2.293 3.040 ... (remaining 16025 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' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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: 0.110 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: 0.030 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 2.280 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:0.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 3.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6966 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 : 0.006 0.024 1830 Z= 0.332 Angle : 1.134 6.407 2490 Z= 0.640 Chirality : 0.062 0.144 290 Planarity : 0.012 0.035 330 Dihedral : 14.199 37.360 580 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 24.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 27.27 % Favored : 72.73 % Rotamer: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % 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: -4.46 (0.43), residues: 220 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.40 (0.32), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.002 TYR G 37 PHE 0.016 0.004 PHE D 23 HIS 0.015 0.010 HIS D 18 Details of bonding type rmsd covalent geometry : bond 0.00641 ( 1830) covalent geometry : angle 1.13394 ( 2490) hydrogen bonds : bond 0.21521 ( 24) hydrogen bonds : angle 13.48610 ( 72) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 440 Ramachandran restraints generated. 220 Oldfield, 0 Emsley, 220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 440 Ramachandran restraints generated. 220 Oldfield, 0 Emsley, 220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.035 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.0126 time to fit residues: 0.4404 Evaluate side-chains 23 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 12 optimal weight: 20.0000 chunk 13 optimal weight: 3.9990 chunk 1 optimal weight: 6.9990 chunk 8 optimal weight: 20.0000 chunk 16 optimal weight: 2.9990 chunk 15 optimal weight: 9.9990 chunk 9 optimal weight: 1.9990 chunk 11 optimal weight: 7.9990 chunk 18 optimal weight: 5.9990 chunk 6 optimal weight: 20.0000 chunk 4 optimal weight: 2.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4563 r_free = 0.4563 target = 0.145544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.125004 restraints weight = 2668.147| |-----------------------------------------------------------------------------| r_work (start): 0.4328 rms_B_bonded: 3.70 r_work: 0.4182 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.4182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6736 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.014 1830 Z= 0.159 Angle : 0.695 5.336 2490 Z= 0.389 Chirality : 0.049 0.145 290 Planarity : 0.003 0.009 330 Dihedral : 9.775 37.326 250 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.45 % Favored : 79.55 % Rotamer: Outliers : 2.38 % Allowed : 13.81 % Favored : 83.81 % 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: -4.58 (0.39), residues: 220 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.48 (0.30), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.002 TYR H 37 PHE 0.009 0.002 PHE B 23 HIS 0.009 0.004 HIS D 18 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 1830) covalent geometry : angle 0.69473 ( 2490) hydrogen bonds : bond 0.04161 ( 24) hydrogen bonds : angle 8.28137 ( 72) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 440 Ramachandran restraints generated. 220 Oldfield, 0 Emsley, 220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 440 Ramachandran restraints generated. 220 Oldfield, 0 Emsley, 220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 29 time to evaluate : 0.035 Fit side-chains outliers start: 5 outliers final: 5 residues processed: 33 average time/residue: 0.0149 time to fit residues: 0.6906 Evaluate side-chains 34 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 29 time to evaluate : 0.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 22 ASN Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain E residue 22 ASN Chi-restraints excluded: chain G residue 22 ASN Chi-restraints excluded: chain I residue 22 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 15 optimal weight: 9.9990 chunk 2 optimal weight: 20.0000 chunk 1 optimal weight: 9.9990 chunk 17 optimal weight: 9.9990 chunk 12 optimal weight: 20.0000 chunk 8 optimal weight: 40.0000 chunk 0 optimal weight: 5.9990 chunk 16 optimal weight: 6.9990 chunk 3 optimal weight: 9.9990 chunk 10 optimal weight: 10.0000 chunk 11 optimal weight: 0.0570 overall best weight: 6.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.136103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.115118 restraints weight = 2734.939| |-----------------------------------------------------------------------------| r_work (start): 0.4174 rms_B_bonded: 3.48 r_work: 0.4042 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.4042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6918 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.025 1830 Z= 0.256 Angle : 0.841 5.672 2490 Z= 0.473 Chirality : 0.054 0.163 290 Planarity : 0.003 0.010 330 Dihedral : 11.153 44.294 250 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 18.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.91 % Favored : 79.09 % Rotamer: Outliers : 2.86 % Allowed : 25.71 % Favored : 71.43 % 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: -4.61 (0.40), residues: 220 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.51 (0.30), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.011 0.002 TYR E 37 PHE 0.007 0.002 PHE H 15 HIS 0.010 0.005 HIS E 18 Details of bonding type rmsd covalent geometry : bond 0.00525 ( 1830) covalent geometry : angle 0.84077 ( 2490) hydrogen bonds : bond 0.04703 ( 24) hydrogen bonds : angle 8.11137 ( 72) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 440 Ramachandran restraints generated. 220 Oldfield, 0 Emsley, 220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 440 Ramachandran restraints generated. 220 Oldfield, 0 Emsley, 220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 32 time to evaluate : 0.037 Fit side-chains REVERT: A 35 ASN cc_start: 0.7767 (p0) cc_final: 0.7506 (p0) REVERT: F 35 ASN cc_start: 0.7832 (p0) cc_final: 0.7550 (p0) REVERT: I 35 ASN cc_start: 0.8248 (p0) cc_final: 0.8029 (p0) outliers start: 6 outliers final: 6 residues processed: 36 average time/residue: 0.0148 time to fit residues: 0.7572 Evaluate side-chains 38 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 32 time to evaluate : 0.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 22 ASN Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain E residue 22 ASN Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain G residue 22 ASN Chi-restraints excluded: chain I residue 22 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 2 optimal weight: 20.0000 chunk 7 optimal weight: 5.9990 chunk 4 optimal weight: 20.0000 chunk 13 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 15 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 16 optimal weight: 10.0000 chunk 11 optimal weight: 5.9990 chunk 3 optimal weight: 4.9990 chunk 10 optimal weight: 9.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4517 r_free = 0.4517 target = 0.141162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.121253 restraints weight = 2715.301| |-----------------------------------------------------------------------------| r_work (start): 0.4260 rms_B_bonded: 3.45 r_work: 0.4131 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.4131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6829 moved from start: 0.3020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.014 1830 Z= 0.173 Angle : 0.714 5.061 2490 Z= 0.400 Chirality : 0.048 0.152 290 Planarity : 0.002 0.008 330 Dihedral : 9.919 41.150 250 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.45 % Favored : 89.55 % Rotamer: Outliers : 3.81 % Allowed : 26.19 % Favored : 70.00 % 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: -4.69 (0.39), residues: 220 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.57 (0.30), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.001 TYR E 37 PHE 0.005 0.001 PHE C 23 HIS 0.008 0.004 HIS B 18 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 1830) covalent geometry : angle 0.71398 ( 2490) hydrogen bonds : bond 0.03951 ( 24) hydrogen bonds : angle 7.17207 ( 72) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 440 Ramachandran restraints generated. 220 Oldfield, 0 Emsley, 220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 440 Ramachandran restraints generated. 220 Oldfield, 0 Emsley, 220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 33 time to evaluate : 0.042 Fit side-chains outliers start: 8 outliers final: 7 residues processed: 39 average time/residue: 0.0183 time to fit residues: 1.0002 Evaluate side-chains 39 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 32 time to evaluate : 0.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 22 ASN Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain E residue 22 ASN Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain H residue 27 LEU Chi-restraints excluded: chain I residue 22 ASN Chi-restraints excluded: chain J residue 27 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 19 optimal weight: 4.9990 chunk 15 optimal weight: 9.9990 chunk 9 optimal weight: 9.9990 chunk 10 optimal weight: 20.0000 chunk 2 optimal weight: 3.9990 chunk 6 optimal weight: 30.0000 chunk 1 optimal weight: 3.9990 chunk 12 optimal weight: 20.0000 chunk 8 optimal weight: 30.0000 chunk 16 optimal weight: 10.0000 chunk 7 optimal weight: 2.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4465 r_free = 0.4465 target = 0.137011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.117361 restraints weight = 2745.083| |-----------------------------------------------------------------------------| r_work (start): 0.4216 rms_B_bonded: 3.42 r_work: 0.4085 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.4085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6908 moved from start: 0.3151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 1830 Z= 0.210 Angle : 0.756 5.339 2490 Z= 0.424 Chirality : 0.050 0.161 290 Planarity : 0.002 0.009 330 Dihedral : 10.214 42.044 250 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.45 % Favored : 84.55 % Rotamer: Outliers : 5.24 % Allowed : 28.57 % Favored : 66.19 % 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: -4.86 (0.38), residues: 220 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.69 (0.29), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.001 TYR E 37 PHE 0.005 0.002 PHE E 23 HIS 0.009 0.005 HIS B 18 Details of bonding type rmsd covalent geometry : bond 0.00425 ( 1830) covalent geometry : angle 0.75647 ( 2490) hydrogen bonds : bond 0.04088 ( 24) hydrogen bonds : angle 7.24684 ( 72) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 440 Ramachandran restraints generated. 220 Oldfield, 0 Emsley, 220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 440 Ramachandran restraints generated. 220 Oldfield, 0 Emsley, 220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 36 time to evaluate : 0.067 Fit side-chains REVERT: A 15 PHE cc_start: 0.7441 (OUTLIER) cc_final: 0.7060 (m-80) outliers start: 11 outliers final: 8 residues processed: 44 average time/residue: 0.0283 time to fit residues: 1.6930 Evaluate side-chains 42 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 33 time to evaluate : 0.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 PHE Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain E residue 22 ASN Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain G residue 22 ASN Chi-restraints excluded: chain H residue 27 LEU Chi-restraints excluded: chain I residue 18 HIS Chi-restraints excluded: chain I residue 22 ASN Chi-restraints excluded: chain J residue 27 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 17 optimal weight: 6.9990 chunk 5 optimal weight: 7.9990 chunk 13 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 8 optimal weight: 20.0000 chunk 12 optimal weight: 2.9990 chunk 6 optimal weight: 30.0000 chunk 2 optimal weight: 20.0000 chunk 11 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.137598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.118309 restraints weight = 2728.791| |-----------------------------------------------------------------------------| r_work (start): 0.4241 rms_B_bonded: 3.46 r_work: 0.4107 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.4107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6874 moved from start: 0.3341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.018 1830 Z= 0.189 Angle : 0.727 6.206 2490 Z= 0.405 Chirality : 0.048 0.159 290 Planarity : 0.002 0.008 330 Dihedral : 9.913 41.214 250 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.36 % Favored : 88.64 % Rotamer: Outliers : 4.76 % Allowed : 30.48 % Favored : 64.76 % 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: -4.95 (0.38), residues: 220 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.77 (0.29), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.001 TYR E 37 PHE 0.008 0.001 PHE A 15 HIS 0.008 0.004 HIS B 18 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 1830) covalent geometry : angle 0.72732 ( 2490) hydrogen bonds : bond 0.03813 ( 24) hydrogen bonds : angle 7.00533 ( 72) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 440 Ramachandran restraints generated. 220 Oldfield, 0 Emsley, 220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 440 Ramachandran restraints generated. 220 Oldfield, 0 Emsley, 220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 34 time to evaluate : 0.071 Fit side-chains REVERT: A 15 PHE cc_start: 0.7391 (OUTLIER) cc_final: 0.7028 (m-80) outliers start: 10 outliers final: 7 residues processed: 42 average time/residue: 0.0280 time to fit residues: 1.6097 Evaluate side-chains 39 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 31 time to evaluate : 0.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 PHE Chi-restraints excluded: chain C residue 22 ASN Chi-restraints excluded: chain E residue 22 ASN Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain G residue 22 ASN Chi-restraints excluded: chain H residue 27 LEU Chi-restraints excluded: chain I residue 22 ASN Chi-restraints excluded: chain J residue 27 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 6 optimal weight: 30.0000 chunk 12 optimal weight: 30.0000 chunk 15 optimal weight: 9.9990 chunk 17 optimal weight: 9.9990 chunk 0 optimal weight: 7.9990 chunk 8 optimal weight: 30.0000 chunk 18 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 chunk 9 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 2 optimal weight: 20.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.133058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.113618 restraints weight = 2765.455| |-----------------------------------------------------------------------------| r_work (start): 0.4164 rms_B_bonded: 3.45 r_work: 0.4023 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.4023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6941 moved from start: 0.3377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.025 1830 Z= 0.261 Angle : 0.831 6.342 2490 Z= 0.463 Chirality : 0.053 0.172 290 Planarity : 0.003 0.011 330 Dihedral : 10.648 42.493 250 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 15.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.91 % Favored : 84.09 % Rotamer: Outliers : 6.67 % Allowed : 30.00 % Favored : 63.33 % 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: -5.02 (0.37), residues: 220 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.82 (0.28), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.002 TYR E 37 PHE 0.007 0.002 PHE A 15 HIS 0.011 0.005 HIS A 18 Details of bonding type rmsd covalent geometry : bond 0.00530 ( 1830) covalent geometry : angle 0.83144 ( 2490) hydrogen bonds : bond 0.04365 ( 24) hydrogen bonds : angle 7.40499 ( 72) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 440 Ramachandran restraints generated. 220 Oldfield, 0 Emsley, 220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 440 Ramachandran restraints generated. 220 Oldfield, 0 Emsley, 220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 35 time to evaluate : 0.070 Fit side-chains REVERT: A 15 PHE cc_start: 0.7441 (OUTLIER) cc_final: 0.7108 (m-10) REVERT: B 18 HIS cc_start: 0.6011 (OUTLIER) cc_final: 0.5524 (p-80) REVERT: F 35 ASN cc_start: 0.7801 (p0) cc_final: 0.7534 (p0) outliers start: 14 outliers final: 10 residues processed: 47 average time/residue: 0.0258 time to fit residues: 1.6816 Evaluate side-chains 45 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 33 time to evaluate : 0.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 PHE Chi-restraints excluded: chain B residue 18 HIS Chi-restraints excluded: chain C residue 22 ASN Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain E residue 22 ASN Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain G residue 18 HIS Chi-restraints excluded: chain G residue 22 ASN Chi-restraints excluded: chain H residue 27 LEU Chi-restraints excluded: chain I residue 18 HIS Chi-restraints excluded: chain I residue 22 ASN Chi-restraints excluded: chain J residue 27 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 18 optimal weight: 9.9990 chunk 5 optimal weight: 8.9990 chunk 11 optimal weight: 9.9990 chunk 17 optimal weight: 1.9990 chunk 8 optimal weight: 30.0000 chunk 13 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 15 optimal weight: 9.9990 chunk 4 optimal weight: 20.0000 chunk 19 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.138623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.119232 restraints weight = 2792.540| |-----------------------------------------------------------------------------| r_work (start): 0.4234 rms_B_bonded: 3.47 r_work: 0.4092 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.4092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6929 moved from start: 0.3543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.017 1830 Z= 0.178 Angle : 0.725 6.505 2490 Z= 0.403 Chirality : 0.048 0.161 290 Planarity : 0.002 0.008 330 Dihedral : 9.820 40.576 250 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.18 % Favored : 86.82 % Rotamer: Outliers : 4.76 % Allowed : 32.38 % Favored : 62.86 % 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: -5.07 (0.38), residues: 220 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.85 (0.29), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.001 TYR G 37 PHE 0.006 0.001 PHE J 15 HIS 0.009 0.004 HIS A 18 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 1830) covalent geometry : angle 0.72482 ( 2490) hydrogen bonds : bond 0.03797 ( 24) hydrogen bonds : angle 6.93453 ( 72) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 440 Ramachandran restraints generated. 220 Oldfield, 0 Emsley, 220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 440 Ramachandran restraints generated. 220 Oldfield, 0 Emsley, 220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 34 time to evaluate : 0.070 Fit side-chains outliers start: 10 outliers final: 8 residues processed: 43 average time/residue: 0.0264 time to fit residues: 1.5634 Evaluate side-chains 41 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 33 time to evaluate : 0.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 22 ASN Chi-restraints excluded: chain E residue 22 ASN Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain G residue 22 ASN Chi-restraints excluded: chain H residue 27 LEU Chi-restraints excluded: chain I residue 18 HIS Chi-restraints excluded: chain I residue 22 ASN Chi-restraints excluded: chain J residue 27 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 0 optimal weight: 20.0000 chunk 3 optimal weight: 10.0000 chunk 16 optimal weight: 20.0000 chunk 12 optimal weight: 20.0000 chunk 18 optimal weight: 20.0000 chunk 6 optimal weight: 20.0000 chunk 10 optimal weight: 9.9990 chunk 13 optimal weight: 6.9990 chunk 14 optimal weight: 4.9990 chunk 8 optimal weight: 6.9990 chunk 15 optimal weight: 9.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.132412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.113369 restraints weight = 2820.372| |-----------------------------------------------------------------------------| r_work (start): 0.4127 rms_B_bonded: 3.24 r_work: 0.3991 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7041 moved from start: 0.3587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.029 1830 Z= 0.302 Angle : 0.903 6.727 2490 Z= 0.501 Chirality : 0.056 0.171 290 Planarity : 0.003 0.011 330 Dihedral : 10.901 42.491 250 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 17.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.27 % Favored : 82.73 % Rotamer: Outliers : 6.19 % Allowed : 33.33 % Favored : 60.48 % 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: -5.19 (0.37), residues: 220 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.95 (0.28), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.011 0.002 TYR E 37 PHE 0.008 0.002 PHE A 15 HIS 0.011 0.005 HIS A 18 Details of bonding type rmsd covalent geometry : bond 0.00618 ( 1830) covalent geometry : angle 0.90346 ( 2490) hydrogen bonds : bond 0.04604 ( 24) hydrogen bonds : angle 7.53003 ( 72) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 440 Ramachandran restraints generated. 220 Oldfield, 0 Emsley, 220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 440 Ramachandran restraints generated. 220 Oldfield, 0 Emsley, 220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 38 time to evaluate : 0.064 Fit side-chains REVERT: A 15 PHE cc_start: 0.7565 (OUTLIER) cc_final: 0.7219 (m-80) REVERT: F 35 ASN cc_start: 0.7907 (p0) cc_final: 0.7580 (p0) REVERT: G 14 ASN cc_start: 0.6287 (t0) cc_final: 0.5833 (t0) outliers start: 13 outliers final: 11 residues processed: 48 average time/residue: 0.0239 time to fit residues: 1.5886 Evaluate side-chains 48 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 36 time to evaluate : 0.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 PHE Chi-restraints excluded: chain B residue 15 PHE Chi-restraints excluded: chain C residue 22 ASN Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain E residue 22 ASN Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain G residue 18 HIS Chi-restraints excluded: chain G residue 22 ASN Chi-restraints excluded: chain H residue 27 LEU Chi-restraints excluded: chain I residue 18 HIS Chi-restraints excluded: chain I residue 22 ASN Chi-restraints excluded: chain J residue 27 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 9 optimal weight: 8.9990 chunk 14 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 2 optimal weight: 20.0000 chunk 15 optimal weight: 7.9990 chunk 8 optimal weight: 10.0000 chunk 18 optimal weight: 20.0000 chunk 13 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.137051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.117857 restraints weight = 2792.892| |-----------------------------------------------------------------------------| r_work (start): 0.4210 rms_B_bonded: 3.42 r_work: 0.4069 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.4069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6992 moved from start: 0.3681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.019 1830 Z= 0.193 Angle : 0.770 6.742 2490 Z= 0.425 Chirality : 0.050 0.161 290 Planarity : 0.002 0.008 330 Dihedral : 10.004 40.202 250 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.09 % Favored : 85.91 % Rotamer: Outliers : 4.29 % Allowed : 36.19 % Favored : 59.52 % 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: 220 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.93 (0.29), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.001 TYR E 37 PHE 0.005 0.001 PHE A 15 HIS 0.009 0.004 HIS A 18 Details of bonding type rmsd covalent geometry : bond 0.00395 ( 1830) covalent geometry : angle 0.76956 ( 2490) hydrogen bonds : bond 0.03920 ( 24) hydrogen bonds : angle 7.09463 ( 72) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 440 Ramachandran restraints generated. 220 Oldfield, 0 Emsley, 220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 440 Ramachandran restraints generated. 220 Oldfield, 0 Emsley, 220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 32 time to evaluate : 0.066 Fit side-chains REVERT: B 18 HIS cc_start: 0.6303 (OUTLIER) cc_final: 0.5827 (p-80) outliers start: 9 outliers final: 8 residues processed: 40 average time/residue: 0.0255 time to fit residues: 1.4109 Evaluate side-chains 40 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 31 time to evaluate : 0.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 HIS Chi-restraints excluded: chain C residue 22 ASN Chi-restraints excluded: chain E residue 22 ASN Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain G residue 22 ASN Chi-restraints excluded: chain H residue 27 LEU Chi-restraints excluded: chain I residue 18 HIS Chi-restraints excluded: chain I residue 22 ASN Chi-restraints excluded: chain J residue 27 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 1 optimal weight: 7.9990 chunk 6 optimal weight: 10.0000 chunk 14 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 2 optimal weight: 20.0000 chunk 4 optimal weight: 10.0000 chunk 16 optimal weight: 20.0000 chunk 11 optimal weight: 9.9990 chunk 18 optimal weight: 9.9990 chunk 13 optimal weight: 7.9990 chunk 8 optimal weight: 20.0000 overall best weight: 8.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.127990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.109122 restraints weight = 2805.361| |-----------------------------------------------------------------------------| r_work (start): 0.4092 rms_B_bonded: 3.38 r_work: 0.3957 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7042 moved from start: 0.3724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.031 1830 Z= 0.324 Angle : 0.948 6.891 2490 Z= 0.525 Chirality : 0.058 0.172 290 Planarity : 0.003 0.011 330 Dihedral : 11.150 42.389 250 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 17.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.73 % Favored : 82.27 % Rotamer: Outliers : 5.71 % Allowed : 34.76 % Favored : 59.52 % 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: -5.22 (0.37), residues: 220 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.97 (0.29), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.011 0.002 TYR E 37 PHE 0.009 0.002 PHE A 15 HIS 0.012 0.005 HIS A 18 Details of bonding type rmsd covalent geometry : bond 0.00664 ( 1830) covalent geometry : angle 0.94842 ( 2490) hydrogen bonds : bond 0.04805 ( 24) hydrogen bonds : angle 7.74236 ( 72) =============================================================================== Job complete usr+sys time: 506.52 seconds wall clock time: 9 minutes 34.39 seconds (574.39 seconds total)