Starting phenix.real_space_refine on Fri Aug 22 12:38:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8az1_15729/08_2025/8az1_15729.cif Found real_map, /net/cci-nas-00/data/ceres_data/8az1_15729/08_2025/8az1_15729.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8az1_15729/08_2025/8az1_15729.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8az1_15729/08_2025/8az1_15729.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8az1_15729/08_2025/8az1_15729.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8az1_15729/08_2025/8az1_15729.map" } resolution = 3.1 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= 0.003 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 1130 2.51 5 N 330 2.21 5 O 370 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 1830 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 182 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B, C, D, E, F, G, H, I, J Time building chain proxies: 0.56, per 1000 atoms: 0.31 Number of scatterers: 1830 At special positions: 0 Unit cell: (38.64, 86.52, 38.64, 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 370 8.00 N 330 7.00 C 1130 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=10, symmetry=0 Number of additional bonds: simple=10, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.26 Conformation dependent library (CDL) restraints added in 81.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 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 10 sheets defined 0.0% alpha, 40.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 14 through 19 Processing sheet with id=AA2, first strand: chain 'A' and resid 22 through 23 removed outlier: 6.460A pdb=" N ASN A 22 " --> pdb=" O PHE C 23 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ASN C 22 " --> pdb=" O PHE E 23 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ASN E 22 " --> pdb=" O PHE G 23 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ASN G 22 " --> pdb=" O PHE I 23 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 26 through 27 Processing sheet with id=AA4, first strand: chain 'A' and resid 30 through 32 removed outlier: 8.551A pdb=" N THR A 30 " --> pdb=" O ASN C 31 " (cutoff:3.500A) removed outlier: 8.547A pdb=" N THR C 30 " --> pdb=" O ASN E 31 " (cutoff:3.500A) removed outlier: 8.532A pdb=" N THR E 30 " --> pdb=" O ASN G 31 " (cutoff:3.500A) removed outlier: 8.555A pdb=" N THR G 30 " --> pdb=" O ASN I 31 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 35 through 36 Processing sheet with id=AA6, first strand: chain 'B' and resid 14 through 19 Processing sheet with id=AA7, first strand: chain 'B' and resid 22 through 23 removed outlier: 6.442A pdb=" N ASN B 22 " --> pdb=" O PHE D 23 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ASN D 22 " --> pdb=" O PHE F 23 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ASN F 22 " --> pdb=" O PHE H 23 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ASN H 22 " --> pdb=" O PHE J 23 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 26 through 27 Processing sheet with id=AA9, first strand: chain 'B' and resid 30 through 32 removed outlier: 8.566A pdb=" N THR B 30 " --> pdb=" O ASN D 31 " (cutoff:3.500A) removed outlier: 8.533A pdb=" N THR D 30 " --> pdb=" O ASN F 31 " (cutoff:3.500A) removed outlier: 8.530A pdb=" N THR F 30 " --> pdb=" O ASN H 31 " (cutoff:3.500A) removed outlier: 8.551A pdb=" N THR H 30 " --> pdb=" O ASN J 31 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 35 through 36 56 hydrogen bonds defined for protein. 168 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: 0.36 Time building geometry restraints manager: 0.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.29: 300 1.29 - 1.35: 311 1.35 - 1.41: 228 1.41 - 1.48: 301 1.48 - 1.54: 710 Bond restraints: 1850 Sorted by residual: bond pdb=" C GLY H 33 " pdb=" O GLY H 33 " ideal model delta sigma weight residual 1.238 1.231 0.006 1.12e-02 7.97e+03 3.34e-01 bond pdb=" C GLY A 20 " pdb=" O GLY A 20 " ideal model delta sigma weight residual 1.238 1.232 0.006 1.13e-02 7.83e+03 3.07e-01 bond pdb=" C GLY E 20 " pdb=" O GLY E 20 " ideal model delta sigma weight residual 1.238 1.232 0.006 1.13e-02 7.83e+03 3.04e-01 bond pdb=" C GLY J 33 " pdb=" O GLY J 33 " ideal model delta sigma weight residual 1.238 1.231 0.006 1.12e-02 7.97e+03 2.93e-01 bond pdb=" C GLY I 20 " pdb=" O GLY I 20 " ideal model delta sigma weight residual 1.238 1.232 0.006 1.13e-02 7.83e+03 2.85e-01 ... (remaining 1845 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.85: 2341 0.85 - 1.70: 124 1.70 - 2.55: 25 2.55 - 3.40: 0 3.40 - 4.25: 20 Bond angle restraints: 2510 Sorted by residual: angle pdb=" N GLY B 20 " pdb=" CA GLY B 20 " pdb=" C GLY B 20 " ideal model delta sigma weight residual 113.48 117.73 -4.25 1.46e+00 4.69e-01 8.49e+00 angle pdb=" N GLY I 20 " pdb=" CA GLY I 20 " pdb=" C GLY I 20 " ideal model delta sigma weight residual 113.48 117.71 -4.23 1.46e+00 4.69e-01 8.38e+00 angle pdb=" N GLY D 20 " pdb=" CA GLY D 20 " pdb=" C GLY D 20 " ideal model delta sigma weight residual 113.48 117.70 -4.22 1.46e+00 4.69e-01 8.35e+00 angle pdb=" N GLY C 20 " pdb=" CA GLY C 20 " pdb=" C GLY C 20 " ideal model delta sigma weight residual 113.48 117.67 -4.19 1.46e+00 4.69e-01 8.24e+00 angle pdb=" N GLY A 20 " pdb=" CA GLY A 20 " pdb=" C GLY A 20 " ideal model delta sigma weight residual 113.48 117.65 -4.17 1.46e+00 4.69e-01 8.17e+00 ... (remaining 2505 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 7.64: 820 7.64 - 15.28: 110 15.28 - 22.91: 40 22.91 - 30.55: 30 30.55 - 38.18: 10 Dihedral angle restraints: 1010 sinusoidal: 320 harmonic: 690 Sorted by residual: dihedral pdb=" N HIS A 18 " pdb=" CA HIS A 18 " pdb=" CB HIS A 18 " pdb=" CG HIS A 18 " ideal model delta sinusoidal sigma weight residual -180.00 -141.82 -38.18 3 1.50e+01 4.44e-03 6.71e+00 dihedral pdb=" N HIS G 18 " pdb=" CA HIS G 18 " pdb=" CB HIS G 18 " pdb=" CG HIS G 18 " ideal model delta sinusoidal sigma weight residual -180.00 -141.89 -38.11 3 1.50e+01 4.44e-03 6.69e+00 dihedral pdb=" N HIS C 18 " pdb=" CA HIS C 18 " pdb=" CB HIS C 18 " pdb=" CG HIS C 18 " ideal model delta sinusoidal sigma weight residual -180.00 -141.89 -38.11 3 1.50e+01 4.44e-03 6.69e+00 ... (remaining 1007 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 160 0.024 - 0.047: 74 0.047 - 0.071: 26 0.071 - 0.094: 15 0.094 - 0.118: 15 Chirality restraints: 290 Sorted by residual: chirality pdb=" CA ILE E 26 " pdb=" N ILE E 26 " pdb=" C ILE E 26 " pdb=" CB ILE E 26 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.46e-01 chirality pdb=" CA ILE F 26 " pdb=" N ILE F 26 " pdb=" C ILE F 26 " pdb=" CB ILE F 26 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.35e-01 chirality pdb=" CA ILE J 26 " pdb=" N ILE J 26 " pdb=" C ILE J 26 " pdb=" CB ILE J 26 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.31e-01 ... (remaining 287 not shown) Planarity restraints: 330 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER F 28 " -0.004 2.00e-02 2.50e+03 7.26e-03 5.27e-01 pdb=" C SER F 28 " 0.013 2.00e-02 2.50e+03 pdb=" O SER F 28 " -0.005 2.00e-02 2.50e+03 pdb=" N SER F 29 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER D 28 " -0.004 2.00e-02 2.50e+03 7.25e-03 5.26e-01 pdb=" C SER D 28 " 0.013 2.00e-02 2.50e+03 pdb=" O SER D 28 " -0.005 2.00e-02 2.50e+03 pdb=" N SER D 29 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER I 28 " 0.004 2.00e-02 2.50e+03 7.11e-03 5.06e-01 pdb=" C SER I 28 " -0.012 2.00e-02 2.50e+03 pdb=" O SER I 28 " 0.005 2.00e-02 2.50e+03 pdb=" N SER I 29 " 0.004 2.00e-02 2.50e+03 ... (remaining 327 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.88: 757 2.88 - 3.38: 1501 3.38 - 3.89: 3175 3.89 - 4.39: 3586 4.39 - 4.90: 7029 Nonbonded interactions: 16048 Sorted by model distance: nonbonded pdb=" O SER A 19 " pdb=" ND2 ASN A 21 " model vdw 2.374 3.120 nonbonded pdb=" O SER G 19 " pdb=" ND2 ASN G 21 " model vdw 2.374 3.120 nonbonded pdb=" O SER J 19 " pdb=" ND2 ASN J 21 " model vdw 2.375 3.120 nonbonded pdb=" O SER E 19 " pdb=" ND2 ASN E 21 " model vdw 2.375 3.120 nonbonded pdb=" O SER C 19 " pdb=" ND2 ASN C 21 " model vdw 2.375 3.120 ... (remaining 16043 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: 0.01 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: 1.710 Set stop_for_unknowns flag: 0.010 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: 0.040 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 5.380 Find NCS groups from input model: 0.020 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:1.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 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 : 0.008 0.103 1860 Z= 0.771 Angle : 0.577 4.255 2510 Z= 0.355 Chirality : 0.041 0.118 290 Planarity : 0.002 0.007 330 Dihedral : 10.899 38.181 570 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % 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 aren not related in a simple way. whole: -1.57 (0.45), residues: 230 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.19 (0.34), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.001 0.001 TYR H 37 PHE 0.002 0.001 PHE F 23 HIS 0.002 0.001 HIS B 18 Details of bonding type rmsd covalent geometry : bond 0.00379 ( 1850) covalent geometry : angle 0.57704 ( 2510) hydrogen bonds : bond 0.08598 ( 56) hydrogen bonds : angle 7.59905 ( 168) Misc. bond : bond 0.10204 ( 10) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 11 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.085 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 11 average time/residue: 0.0357 time to fit residues: 0.5933 Evaluate side-chains 10 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.074 ------------------------------------------------------------------------------- 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: 10.0000 chunk 13 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 9 optimal weight: 0.6980 chunk 11 optimal weight: 0.7980 chunk 18 optimal weight: 4.9990 chunk 6 optimal weight: 10.0000 chunk 4 optimal weight: 7.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN A 35 ASN B 14 ASN B 35 ASN C 14 ASN ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 14 ASN ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 14 ASN ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 14 ASN ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 14 ASN ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 14 ASN ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 14 ASN I 21 ASN ** I 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 14 ASN J 21 ASN ** J 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.090102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.073397 restraints weight = 2208.026| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 2.58 r_work: 0.3195 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.024 1860 Z= 0.234 Angle : 0.539 3.078 2510 Z= 0.318 Chirality : 0.046 0.125 290 Planarity : 0.002 0.006 330 Dihedral : 4.926 14.800 250 Min Nonbonded Distance : 2.670 Molprobity Statistics. All-atom Clashscore : 2.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % 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 aren not related in a simple way. whole: -1.76 (0.42), residues: 230 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.33 (0.32), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.002 TYR B 37 PHE 0.010 0.002 PHE C 23 HIS 0.005 0.003 HIS F 18 Details of bonding type rmsd covalent geometry : bond 0.00546 ( 1850) covalent geometry : angle 0.53898 ( 2510) hydrogen bonds : bond 0.02466 ( 56) hydrogen bonds : angle 5.28425 ( 168) Misc. bond : bond 0.00029 ( 10) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 10 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.073 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.0340 time to fit residues: 0.5158 Evaluate side-chains 10 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 5 optimal weight: 6.9990 chunk 7 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 10 optimal weight: 10.0000 chunk 0 optimal weight: 8.9990 chunk 15 optimal weight: 0.8980 chunk 12 optimal weight: 9.9990 chunk 1 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 13 optimal weight: 5.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 35 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 = 0.3522 r_free = 0.3522 target = 0.095189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.077788 restraints weight = 2168.795| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 2.65 r_work: 0.3276 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.012 1860 Z= 0.109 Angle : 0.444 2.706 2510 Z= 0.260 Chirality : 0.044 0.124 290 Planarity : 0.001 0.004 330 Dihedral : 4.158 13.109 250 Min Nonbonded Distance : 2.665 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Rotamer: Outliers : 0.00 % Allowed : 8.50 % Favored : 91.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.58 (0.43), residues: 230 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.19 (0.33), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.001 TYR E 37 PHE 0.004 0.001 PHE I 15 HIS 0.003 0.001 HIS A 18 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 1850) covalent geometry : angle 0.44436 ( 2510) hydrogen bonds : bond 0.01710 ( 56) hydrogen bonds : angle 4.81151 ( 168) Misc. bond : bond 0.00036 ( 10) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 10 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.070 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.0325 time to fit residues: 0.5036 Evaluate side-chains 10 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 3 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 chunk 16 optimal weight: 7.9990 chunk 1 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 18 optimal weight: 7.9990 chunk 2 optimal weight: 7.9990 chunk 14 optimal weight: 6.9990 chunk 8 optimal weight: 9.9990 chunk 17 optimal weight: 1.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 35 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.092147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.074291 restraints weight = 2140.292| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 2.63 r_work: 0.3315 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.027 1860 Z= 0.281 Angle : 0.538 3.114 2510 Z= 0.323 Chirality : 0.047 0.125 290 Planarity : 0.002 0.007 330 Dihedral : 5.426 16.772 250 Min Nonbonded Distance : 2.659 Molprobity Statistics. All-atom Clashscore : 2.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.67 (0.42), residues: 230 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.26 (0.32), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.011 0.002 TYR C 37 PHE 0.009 0.002 PHE H 23 HIS 0.006 0.003 HIS A 18 Details of bonding type rmsd covalent geometry : bond 0.00644 ( 1850) covalent geometry : angle 0.53845 ( 2510) hydrogen bonds : bond 0.02511 ( 56) hydrogen bonds : angle 4.94315 ( 168) Misc. bond : bond 0.00064 ( 10) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 10 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.080 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.0392 time to fit residues: 0.5912 Evaluate side-chains 10 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 2 optimal weight: 7.9990 chunk 11 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 7 optimal weight: 0.0870 chunk 15 optimal weight: 0.8980 chunk 8 optimal weight: 9.9990 chunk 9 optimal weight: 1.9990 chunk 18 optimal weight: 7.9990 chunk 17 optimal weight: 0.8980 chunk 10 optimal weight: 10.0000 chunk 19 optimal weight: 2.9990 overall best weight: 1.1762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 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 = 0.3530 r_free = 0.3530 target = 0.096401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.078904 restraints weight = 2086.498| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 2.57 r_work: 0.3304 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.012 1860 Z= 0.113 Angle : 0.448 2.807 2510 Z= 0.264 Chirality : 0.044 0.125 290 Planarity : 0.001 0.004 330 Dihedral : 4.369 14.244 250 Min Nonbonded Distance : 2.666 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % 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 aren not related in a simple way. whole: -1.76 (0.42), residues: 230 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.33 (0.32), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.001 TYR C 37 PHE 0.003 0.001 PHE H 23 HIS 0.003 0.002 HIS G 18 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 1850) covalent geometry : angle 0.44790 ( 2510) hydrogen bonds : bond 0.01780 ( 56) hydrogen bonds : angle 4.61647 ( 168) Misc. bond : bond 0.00030 ( 10) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 10 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.071 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.0337 time to fit residues: 0.5157 Evaluate side-chains 10 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 10 optimal weight: 10.0000 chunk 14 optimal weight: 0.9990 chunk 3 optimal weight: 5.9990 chunk 11 optimal weight: 6.9990 chunk 13 optimal weight: 1.9990 chunk 17 optimal weight: 0.0870 chunk 1 optimal weight: 2.9990 chunk 12 optimal weight: 9.9990 chunk 0 optimal weight: 7.9990 chunk 18 optimal weight: 0.0980 chunk 15 optimal weight: 2.9990 overall best weight: 1.2364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 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 = 0.3550 r_free = 0.3550 target = 0.097397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.079553 restraints weight = 2135.716| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 2.63 r_work: 0.3345 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.013 1860 Z= 0.118 Angle : 0.433 2.718 2510 Z= 0.255 Chirality : 0.044 0.124 290 Planarity : 0.001 0.003 330 Dihedral : 4.199 13.640 250 Min Nonbonded Distance : 2.669 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % 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 aren not related in a simple way. whole: -1.81 (0.43), residues: 230 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.37 (0.33), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.001 TYR C 37 PHE 0.003 0.001 PHE J 15 HIS 0.003 0.002 HIS A 18 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 1850) covalent geometry : angle 0.43284 ( 2510) hydrogen bonds : bond 0.01753 ( 56) hydrogen bonds : angle 4.58049 ( 168) Misc. bond : bond 0.00019 ( 10) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 10 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.066 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.0305 time to fit residues: 0.4667 Evaluate side-chains 10 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 16 optimal weight: 0.4980 chunk 1 optimal weight: 2.9990 chunk 10 optimal weight: 10.0000 chunk 15 optimal weight: 5.9990 chunk 18 optimal weight: 0.7980 chunk 9 optimal weight: 6.9990 chunk 2 optimal weight: 8.9990 chunk 5 optimal weight: 0.7980 chunk 8 optimal weight: 10.0000 chunk 7 optimal weight: 0.0570 chunk 3 optimal weight: 1.9990 overall best weight: 0.8300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 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 = 0.3587 r_free = 0.3587 target = 0.099714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.081583 restraints weight = 2178.585| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 2.67 r_work: 0.3332 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3207 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.010 1860 Z= 0.088 Angle : 0.421 2.972 2510 Z= 0.246 Chirality : 0.044 0.125 290 Planarity : 0.001 0.004 330 Dihedral : 3.907 12.708 250 Min Nonbonded Distance : 2.666 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Rotamer: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % 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 aren not related in a simple way. whole: -1.82 (0.43), residues: 230 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.37 (0.33), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.010 0.001 TYR B 37 PHE 0.002 0.000 PHE I 15 HIS 0.002 0.001 HIS A 18 Details of bonding type rmsd covalent geometry : bond 0.00197 ( 1850) covalent geometry : angle 0.42118 ( 2510) hydrogen bonds : bond 0.01649 ( 56) hydrogen bonds : angle 4.50032 ( 168) Misc. bond : bond 0.00020 ( 10) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 10 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.068 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.0358 time to fit residues: 0.5435 Evaluate side-chains 10 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 6 optimal weight: 9.9990 chunk 17 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 15 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 14 optimal weight: 9.9990 chunk 0 optimal weight: 8.9990 chunk 12 optimal weight: 10.0000 chunk 3 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 35 ASN ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.095203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.076684 restraints weight = 2239.551| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 2.69 r_work: 0.3285 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.019 1860 Z= 0.176 Angle : 0.461 2.938 2510 Z= 0.275 Chirality : 0.045 0.124 290 Planarity : 0.002 0.005 330 Dihedral : 4.591 14.816 250 Min Nonbonded Distance : 2.670 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.84 (0.43), residues: 230 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.39 (0.33), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.011 0.002 TYR B 37 PHE 0.005 0.001 PHE C 23 HIS 0.004 0.002 HIS A 18 Details of bonding type rmsd covalent geometry : bond 0.00405 ( 1850) covalent geometry : angle 0.46128 ( 2510) hydrogen bonds : bond 0.01980 ( 56) hydrogen bonds : angle 4.70672 ( 168) Misc. bond : bond 0.00050 ( 10) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 10 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.073 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.0344 time to fit residues: 0.5393 Evaluate side-chains 10 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 13 optimal weight: 5.9990 chunk 10 optimal weight: 10.0000 chunk 16 optimal weight: 0.5980 chunk 4 optimal weight: 8.9990 chunk 15 optimal weight: 2.9990 chunk 2 optimal weight: 8.9990 chunk 18 optimal weight: 0.3980 chunk 8 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 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 = 0.3582 r_free = 0.3582 target = 0.099327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.080914 restraints weight = 2230.785| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 2.71 r_work: 0.3328 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.011 1860 Z= 0.086 Angle : 0.423 3.149 2510 Z= 0.248 Chirality : 0.044 0.126 290 Planarity : 0.001 0.004 330 Dihedral : 3.973 12.982 250 Min Nonbonded Distance : 2.670 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Rotamer: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.90 (0.43), residues: 230 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.44 (0.33), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.001 TYR B 37 PHE 0.003 0.000 PHE J 15 HIS 0.003 0.001 HIS B 18 Details of bonding type rmsd covalent geometry : bond 0.00192 ( 1850) covalent geometry : angle 0.42334 ( 2510) hydrogen bonds : bond 0.01644 ( 56) hydrogen bonds : angle 4.45382 ( 168) Misc. bond : bond 0.00021 ( 10) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 10 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.073 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.0344 time to fit residues: 0.5148 Evaluate side-chains 10 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 14 optimal weight: 9.9990 chunk 16 optimal weight: 0.5980 chunk 1 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 2 optimal weight: 8.9990 chunk 17 optimal weight: 0.9980 chunk 7 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 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 = 0.3546 r_free = 0.3546 target = 0.097101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.078040 restraints weight = 2317.003| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.79 r_work: 0.3297 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.014 1860 Z= 0.122 Angle : 0.434 3.161 2510 Z= 0.256 Chirality : 0.044 0.124 290 Planarity : 0.001 0.004 330 Dihedral : 4.179 13.595 250 Min Nonbonded Distance : 2.669 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.90 (0.43), residues: 230 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.44 (0.33), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.010 0.001 TYR B 37 PHE 0.003 0.001 PHE I 15 HIS 0.003 0.002 HIS A 18 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 1850) covalent geometry : angle 0.43363 ( 2510) hydrogen bonds : bond 0.01745 ( 56) hydrogen bonds : angle 4.54892 ( 168) Misc. bond : bond 0.00036 ( 10) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 10 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.070 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.0352 time to fit residues: 0.5339 Evaluate side-chains 10 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 3 optimal weight: 5.9990 chunk 6 optimal weight: 10.0000 chunk 11 optimal weight: 6.9990 chunk 8 optimal weight: 9.9990 chunk 18 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 1 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 35 ASN ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 35 ASN ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 35 ASN ** I 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.094740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.075102 restraints weight = 2336.184| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 2.86 r_work: 0.3337 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.026 1860 Z= 0.263 Angle : 0.510 3.352 2510 Z= 0.308 Chirality : 0.046 0.120 290 Planarity : 0.002 0.006 330 Dihedral : 5.083 16.156 250 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.01 (0.43), residues: 230 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.53 (0.33), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.014 0.002 TYR B 37 PHE 0.009 0.002 PHE C 23 HIS 0.005 0.003 HIS F 18 Details of bonding type rmsd covalent geometry : bond 0.00602 ( 1850) covalent geometry : angle 0.51027 ( 2510) hydrogen bonds : bond 0.02390 ( 56) hydrogen bonds : angle 4.74556 ( 168) Misc. bond : bond 0.00087 ( 10) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 825.76 seconds wall clock time: 15 minutes 8.61 seconds (908.61 seconds total)