Starting phenix.real_space_refine on Tue Mar 3 10:49:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7m65_23689/03_2026/7m65_23689.cif Found real_map, /net/cci-nas-00/data/ceres_data/7m65_23689/03_2026/7m65_23689.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7m65_23689/03_2026/7m65_23689.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7m65_23689/03_2026/7m65_23689.map" model { file = "/net/cci-nas-00/data/ceres_data/7m65_23689/03_2026/7m65_23689.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7m65_23689/03_2026/7m65_23689.cif" } resolution = 4.1 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 ------------------------------------------------------------------------------- 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: 4 Type Number sf(0) Gaussians S 5 5.16 5 C 1235 2.51 5 N 370 2.21 5 O 415 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: 2025 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 237 Classifications: {'peptide': 32} Link IDs: {'TRANS': 31} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 167 Classifications: {'peptide': 23} Link IDs: {'TRANS': 22} Restraints were copied for chains: C, E, G, I, D, F, H, J Time building chain proxies: 0.44, per 1000 atoms: 0.22 Number of scatterers: 2025 At special positions: 0 Unit cell: (62.245, 68.575, 45.365, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 5 16.00 O 415 8.00 N 370 7.00 C 1235 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=5, symmetry=0 Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.16 Conformation dependent library (CDL) restraints added in 101.6 milliseconds 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 510 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 1 sheets defined 0.0% alpha, 5.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.03 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 7 through 10 removed outlier: 3.604A pdb=" N THR E 9 " --> pdb=" O ALA C 8 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR G 9 " --> pdb=" O ALA E 8 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N CYS A 7 " --> pdb=" O ALA G 8 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N GLN G 10 " --> pdb=" O CYS A 7 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N THR A 9 " --> pdb=" O GLN G 10 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR I 9 " --> pdb=" O ALA A 8 " (cutoff:3.500A) 6 hydrogen bonds defined for protein. 18 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: 0.16 Time building geometry restraints manager: 0.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 337 1.31 - 1.44: 613 1.44 - 1.56: 1090 1.56 - 1.68: 0 1.68 - 1.81: 5 Bond restraints: 2045 Sorted by residual: bond pdb=" CG ASN C 35 " pdb=" OD1 ASN C 35 " ideal model delta sigma weight residual 1.231 1.189 0.042 1.90e-02 2.77e+03 4.93e+00 bond pdb=" CG ASN E 35 " pdb=" OD1 ASN E 35 " ideal model delta sigma weight residual 1.231 1.189 0.042 1.90e-02 2.77e+03 4.78e+00 bond pdb=" CG ASN I 35 " pdb=" OD1 ASN I 35 " ideal model delta sigma weight residual 1.231 1.190 0.041 1.90e-02 2.77e+03 4.74e+00 bond pdb=" CG ASN G 35 " pdb=" OD1 ASN G 35 " ideal model delta sigma weight residual 1.231 1.190 0.041 1.90e-02 2.77e+03 4.59e+00 bond pdb=" CG ASN A 35 " pdb=" OD1 ASN A 35 " ideal model delta sigma weight residual 1.231 1.190 0.041 1.90e-02 2.77e+03 4.55e+00 ... (remaining 2040 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.33: 2598 2.33 - 4.67: 132 4.67 - 7.00: 30 7.00 - 9.33: 10 9.33 - 11.66: 5 Bond angle restraints: 2775 Sorted by residual: angle pdb=" N PHE F 15 " pdb=" CA PHE F 15 " pdb=" C PHE F 15 " ideal model delta sigma weight residual 112.41 119.39 -6.98 1.30e+00 5.92e-01 2.88e+01 angle pdb=" N PHE J 15 " pdb=" CA PHE J 15 " pdb=" C PHE J 15 " ideal model delta sigma weight residual 112.41 119.38 -6.97 1.30e+00 5.92e-01 2.87e+01 angle pdb=" N PHE B 15 " pdb=" CA PHE B 15 " pdb=" C PHE B 15 " ideal model delta sigma weight residual 112.41 119.37 -6.96 1.30e+00 5.92e-01 2.87e+01 angle pdb=" N PHE D 15 " pdb=" CA PHE D 15 " pdb=" C PHE D 15 " ideal model delta sigma weight residual 112.41 119.36 -6.95 1.30e+00 5.92e-01 2.86e+01 angle pdb=" N PHE H 15 " pdb=" CA PHE H 15 " pdb=" C PHE H 15 " ideal model delta sigma weight residual 112.41 119.34 -6.93 1.30e+00 5.92e-01 2.84e+01 ... (remaining 2770 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 8.26: 870 8.26 - 16.50: 195 16.50 - 24.75: 55 24.75 - 33.00: 35 33.00 - 41.24: 10 Dihedral angle restraints: 1165 sinusoidal: 385 harmonic: 780 Sorted by residual: dihedral pdb=" CA PHE H 15 " pdb=" C PHE H 15 " pdb=" N LEU H 16 " pdb=" CA LEU H 16 " ideal model delta harmonic sigma weight residual 180.00 152.44 27.56 0 5.00e+00 4.00e-02 3.04e+01 dihedral pdb=" CA PHE J 15 " pdb=" C PHE J 15 " pdb=" N LEU J 16 " pdb=" CA LEU J 16 " ideal model delta harmonic sigma weight residual 180.00 152.47 27.53 0 5.00e+00 4.00e-02 3.03e+01 dihedral pdb=" CA PHE D 15 " pdb=" C PHE D 15 " pdb=" N LEU D 16 " pdb=" CA LEU D 16 " ideal model delta harmonic sigma weight residual 180.00 152.49 27.51 0 5.00e+00 4.00e-02 3.03e+01 ... (remaining 1162 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.132: 312 0.132 - 0.264: 23 0.264 - 0.396: 0 0.396 - 0.528: 0 0.528 - 0.660: 5 Chirality restraints: 340 Sorted by residual: chirality pdb=" CB ILE B 26 " pdb=" CA ILE B 26 " pdb=" CG1 ILE B 26 " pdb=" CG2 ILE B 26 " both_signs ideal model delta sigma weight residual False 2.64 1.99 0.66 2.00e-01 2.50e+01 1.09e+01 chirality pdb=" CB ILE J 26 " pdb=" CA ILE J 26 " pdb=" CG1 ILE J 26 " pdb=" CG2 ILE J 26 " both_signs ideal model delta sigma weight residual False 2.64 1.99 0.66 2.00e-01 2.50e+01 1.09e+01 chirality pdb=" CB ILE F 26 " pdb=" CA ILE F 26 " pdb=" CG1 ILE F 26 " pdb=" CG2 ILE F 26 " both_signs ideal model delta sigma weight residual False 2.64 1.99 0.66 2.00e-01 2.50e+01 1.08e+01 ... (remaining 337 not shown) Planarity restraints: 360 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE E 15 " -0.015 2.00e-02 2.50e+03 1.24e-02 2.70e+00 pdb=" CG PHE E 15 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 PHE E 15 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE E 15 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE E 15 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE E 15 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE E 15 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE I 15 " -0.015 2.00e-02 2.50e+03 1.24e-02 2.69e+00 pdb=" CG PHE I 15 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 PHE I 15 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE I 15 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE I 15 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE I 15 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE I 15 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 15 " -0.015 2.00e-02 2.50e+03 1.24e-02 2.68e+00 pdb=" CG PHE A 15 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 PHE A 15 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE A 15 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE A 15 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE A 15 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A 15 " -0.003 2.00e-02 2.50e+03 ... (remaining 357 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 936 2.89 - 3.40: 2346 3.40 - 3.90: 3188 3.90 - 4.40: 3720 4.40 - 4.90: 6916 Nonbonded interactions: 17106 Sorted by model distance: nonbonded pdb=" O LEU J 16 " pdb=" CD2 LEU J 16 " model vdw 2.392 3.460 nonbonded pdb=" O LEU D 16 " pdb=" CD2 LEU D 16 " model vdw 2.392 3.460 nonbonded pdb=" O LEU B 16 " pdb=" CD2 LEU B 16 " model vdw 2.392 3.460 nonbonded pdb=" O LEU F 16 " pdb=" CD2 LEU F 16 " model vdw 2.392 3.460 nonbonded pdb=" O LEU H 16 " pdb=" CD2 LEU H 16 " model vdw 2.393 3.460 ... (remaining 17101 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 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.030 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 3.490 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:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 4.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 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 : 0.010 0.102 2050 Z= 0.636 Angle : 1.401 11.663 2775 Z= 0.744 Chirality : 0.102 0.660 340 Planarity : 0.004 0.012 360 Dihedral : 12.046 41.242 655 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 33.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.65 % Favored : 82.35 % Rotamer: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -6.09 (0.25), residues: 255 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.63 (0.19), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 11 TYR 0.008 0.002 TYR E 37 PHE 0.028 0.005 PHE E 15 HIS 0.006 0.004 HIS H 18 Details of bonding type rmsd covalent geometry : bond 0.00872 ( 2045) covalent geometry : angle 1.40085 ( 2775) hydrogen bonds : bond 0.27702 ( 6) hydrogen bonds : angle 12.33100 ( 18) Misc. bond : bond 0.10160 ( 5) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.079 Fit side-chains REVERT: C 15 PHE cc_start: 0.7309 (p90) cc_final: 0.5719 (t80) REVERT: C 28 SER cc_start: 0.8833 (t) cc_final: 0.8519 (p) REVERT: E 28 SER cc_start: 0.8925 (t) cc_final: 0.8482 (p) REVERT: G 28 SER cc_start: 0.9165 (t) cc_final: 0.8769 (p) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.0650 time to fit residues: 4.0492 Evaluate side-chains 34 residues out of total 235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 12 optimal weight: 8.9990 chunk 24 optimal weight: 10.0000 chunk 13 optimal weight: 20.0000 chunk 1 optimal weight: 7.9990 chunk 8 optimal weight: 8.9990 chunk 16 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 chunk 9 optimal weight: 6.9990 chunk 11 optimal weight: 10.0000 chunk 18 optimal weight: 7.9990 chunk 6 optimal weight: 0.7980 overall best weight: 5.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 21 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 = 0.3825 r_free = 0.3825 target = 0.087793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.080357 restraints weight = 8832.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.082126 restraints weight = 4659.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.083278 restraints weight = 2850.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.083968 restraints weight = 1937.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.084568 restraints weight = 1450.992| |-----------------------------------------------------------------------------| r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.3393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2050 Z= 0.159 Angle : 0.850 11.911 2775 Z= 0.402 Chirality : 0.046 0.138 340 Planarity : 0.003 0.016 360 Dihedral : 7.682 24.145 275 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 17.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.33 % Favored : 86.67 % Rotamer: Outliers : 0.00 % Allowed : 9.79 % Favored : 90.21 % 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: -5.76 (0.28), residues: 255 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.38 (0.21), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 11 TYR 0.005 0.001 TYR G 37 PHE 0.012 0.002 PHE J 23 HIS 0.005 0.002 HIS I 18 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 2045) covalent geometry : angle 0.84995 ( 2775) hydrogen bonds : bond 0.06248 ( 6) hydrogen bonds : angle 6.03463 ( 18) Misc. bond : bond 0.00007 ( 5) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.098 Fit side-chains REVERT: B 22 ASN cc_start: 0.8821 (p0) cc_final: 0.8614 (p0) REVERT: G 28 SER cc_start: 0.9157 (t) cc_final: 0.8743 (p) REVERT: J 22 ASN cc_start: 0.7689 (p0) cc_final: 0.7014 (t0) outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.0375 time to fit residues: 1.8927 Evaluate side-chains 28 residues out of total 235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 9 optimal weight: 20.0000 chunk 22 optimal weight: 6.9990 chunk 10 optimal weight: 20.0000 chunk 21 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 chunk 13 optimal weight: 40.0000 chunk 24 optimal weight: 10.0000 chunk 8 optimal weight: 9.9990 chunk 5 optimal weight: 10.0000 chunk 20 optimal weight: 5.9990 chunk 16 optimal weight: 30.0000 overall best weight: 8.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 ASN C 21 ASN C 35 ASN I 35 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.088083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.081093 restraints weight = 9856.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.082622 restraints weight = 5129.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.083621 restraints weight = 3133.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.084305 restraints weight = 2168.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.084606 restraints weight = 1624.099| |-----------------------------------------------------------------------------| r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.4141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 2050 Z= 0.183 Angle : 0.778 9.380 2775 Z= 0.391 Chirality : 0.045 0.145 340 Planarity : 0.003 0.029 360 Dihedral : 7.575 24.066 275 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 17.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.69 % Favored : 84.31 % Rotamer: Outliers : 0.00 % Allowed : 8.09 % Favored : 91.91 % 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: -5.74 (0.30), residues: 255 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.37 (0.23), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG I 11 TYR 0.005 0.001 TYR E 37 PHE 0.014 0.003 PHE J 15 HIS 0.006 0.003 HIS H 18 Details of bonding type rmsd covalent geometry : bond 0.00395 ( 2045) covalent geometry : angle 0.77846 ( 2775) hydrogen bonds : bond 0.07126 ( 6) hydrogen bonds : angle 5.73695 ( 18) Misc. bond : bond 0.00008 ( 5) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.149 Fit side-chains REVERT: E 32 VAL cc_start: 0.8328 (p) cc_final: 0.7887 (p) REVERT: J 22 ASN cc_start: 0.7869 (p0) cc_final: 0.6932 (t0) outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.0341 time to fit residues: 1.5049 Evaluate side-chains 22 residues out of total 235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 2 optimal weight: 10.0000 chunk 11 optimal weight: 7.9990 chunk 12 optimal weight: 20.0000 chunk 20 optimal weight: 40.0000 chunk 13 optimal weight: 30.0000 chunk 22 optimal weight: 7.9990 chunk 24 optimal weight: 30.0000 chunk 7 optimal weight: 20.0000 chunk 9 optimal weight: 20.0000 chunk 15 optimal weight: 30.0000 chunk 17 optimal weight: 20.0000 overall best weight: 13.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.082334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.075736 restraints weight = 9908.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.077176 restraints weight = 5098.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.078128 restraints weight = 3149.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.078693 restraints weight = 2184.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.079104 restraints weight = 1666.169| |-----------------------------------------------------------------------------| r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.4546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 2050 Z= 0.254 Angle : 0.871 10.295 2775 Z= 0.428 Chirality : 0.046 0.145 340 Planarity : 0.004 0.026 360 Dihedral : 8.265 23.697 275 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 18.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.86 % Favored : 83.14 % Rotamer: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -6.08 (0.27), residues: 255 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.63 (0.21), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG I 11 TYR 0.005 0.001 TYR E 37 PHE 0.016 0.004 PHE D 15 HIS 0.009 0.003 HIS B 18 Details of bonding type rmsd covalent geometry : bond 0.00545 ( 2045) covalent geometry : angle 0.87095 ( 2775) hydrogen bonds : bond 0.06041 ( 6) hydrogen bonds : angle 5.35322 ( 18) Misc. bond : bond 0.00008 ( 5) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.087 Fit side-chains REVERT: C 28 SER cc_start: 0.8652 (t) cc_final: 0.8434 (p) REVERT: E 10 GLN cc_start: 0.8114 (mp10) cc_final: 0.7619 (mp10) REVERT: J 27 LEU cc_start: 0.8138 (pt) cc_final: 0.7397 (tp) outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.0246 time to fit residues: 1.1258 Evaluate side-chains 23 residues out of total 235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 0 optimal weight: 40.0000 chunk 4 optimal weight: 20.0000 chunk 12 optimal weight: 30.0000 chunk 11 optimal weight: 30.0000 chunk 10 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 18 optimal weight: 0.7980 chunk 17 optimal weight: 9.9990 chunk 22 optimal weight: 30.0000 chunk 3 optimal weight: 10.0000 chunk 19 optimal weight: 6.9990 overall best weight: 7.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.084863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.077932 restraints weight = 9646.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.079518 restraints weight = 4947.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.080502 restraints weight = 3051.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.081141 restraints weight = 2081.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.081461 restraints weight = 1557.960| |-----------------------------------------------------------------------------| r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.4951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 2050 Z= 0.171 Angle : 0.794 10.603 2775 Z= 0.379 Chirality : 0.045 0.141 340 Planarity : 0.003 0.019 360 Dihedral : 7.522 21.614 275 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.94 % Favored : 87.06 % Rotamer: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -6.00 (0.27), residues: 255 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.57 (0.21), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG I 11 TYR 0.004 0.001 TYR E 37 PHE 0.012 0.003 PHE E 15 HIS 0.006 0.002 HIS H 18 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 2045) covalent geometry : angle 0.79413 ( 2775) hydrogen bonds : bond 0.05248 ( 6) hydrogen bonds : angle 4.87566 ( 18) Misc. bond : bond 0.00007 ( 5) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.081 Fit side-chains REVERT: C 28 SER cc_start: 0.8582 (t) cc_final: 0.8332 (p) REVERT: E 10 GLN cc_start: 0.8098 (mp10) cc_final: 0.7667 (mp10) REVERT: J 27 LEU cc_start: 0.8118 (pt) cc_final: 0.7389 (tp) outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.0224 time to fit residues: 1.1681 Evaluate side-chains 25 residues out of total 235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 22 optimal weight: 0.5980 chunk 9 optimal weight: 30.0000 chunk 1 optimal weight: 7.9990 chunk 6 optimal weight: 4.9990 chunk 16 optimal weight: 10.0000 chunk 8 optimal weight: 20.0000 chunk 7 optimal weight: 7.9990 chunk 2 optimal weight: 0.6980 chunk 14 optimal weight: 6.9990 chunk 3 optimal weight: 0.0970 chunk 17 optimal weight: 20.0000 overall best weight: 2.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 HIS E 21 ASN E 35 ASN G 18 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.092353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.083947 restraints weight = 8881.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.085744 restraints weight = 4822.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.086979 restraints weight = 3093.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.087811 restraints weight = 2143.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.088331 restraints weight = 1590.560| |-----------------------------------------------------------------------------| r_work (final): 0.3862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7141 moved from start: 0.5801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 2050 Z= 0.116 Angle : 0.723 11.190 2775 Z= 0.335 Chirality : 0.043 0.134 340 Planarity : 0.002 0.008 360 Dihedral : 6.238 20.968 275 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.20 % Favored : 89.80 % Rotamer: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % 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: -5.69 (0.28), residues: 255 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.33 (0.21), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 11 TYR 0.003 0.000 TYR E 37 PHE 0.011 0.002 PHE H 15 HIS 0.003 0.001 HIS B 18 Details of bonding type rmsd covalent geometry : bond 0.00233 ( 2045) covalent geometry : angle 0.72286 ( 2775) hydrogen bonds : bond 0.04030 ( 6) hydrogen bonds : angle 4.69551 ( 18) Misc. bond : bond 0.00005 ( 5) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.082 Fit side-chains REVERT: E 10 GLN cc_start: 0.7987 (mp10) cc_final: 0.7688 (mp10) REVERT: J 22 ASN cc_start: 0.7807 (p0) cc_final: 0.6234 (t0) REVERT: J 27 LEU cc_start: 0.7678 (pt) cc_final: 0.7315 (mt) outliers start: 0 outliers final: 0 residues processed: 44 average time/residue: 0.0255 time to fit residues: 1.5916 Evaluate side-chains 28 residues out of total 235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 22 optimal weight: 8.9990 chunk 6 optimal weight: 5.9990 chunk 15 optimal weight: 20.0000 chunk 21 optimal weight: 30.0000 chunk 23 optimal weight: 30.0000 chunk 24 optimal weight: 10.0000 chunk 10 optimal weight: 20.0000 chunk 16 optimal weight: 40.0000 chunk 7 optimal weight: 10.0000 chunk 17 optimal weight: 8.9990 chunk 3 optimal weight: 10.0000 overall best weight: 8.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 21 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.096318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.088874 restraints weight = 9994.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.090559 restraints weight = 4996.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.091685 restraints weight = 2958.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.092342 restraints weight = 1944.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.092883 restraints weight = 1435.198| |-----------------------------------------------------------------------------| r_work (final): 0.3830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.5698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 2050 Z= 0.185 Angle : 0.773 10.821 2775 Z= 0.380 Chirality : 0.045 0.156 340 Planarity : 0.003 0.017 360 Dihedral : 7.006 20.437 275 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 14.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.51 % Favored : 85.49 % Rotamer: Outliers : 0.43 % Allowed : 1.28 % Favored : 98.30 % 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: -5.93 (0.27), residues: 255 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.52 (0.20), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG I 11 TYR 0.002 0.001 TYR E 37 PHE 0.014 0.003 PHE A 15 HIS 0.006 0.002 HIS B 18 Details of bonding type rmsd covalent geometry : bond 0.00404 ( 2045) covalent geometry : angle 0.77264 ( 2775) hydrogen bonds : bond 0.04605 ( 6) hydrogen bonds : angle 4.61020 ( 18) Misc. bond : bond 0.00006 ( 5) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 29 time to evaluate : 0.076 Fit side-chains REVERT: E 10 GLN cc_start: 0.8260 (mp10) cc_final: 0.7904 (mp10) REVERT: H 16 LEU cc_start: 0.6364 (mt) cc_final: 0.6130 (pp) outliers start: 1 outliers final: 0 residues processed: 29 average time/residue: 0.0238 time to fit residues: 1.0250 Evaluate side-chains 22 residues out of total 235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 3 optimal weight: 0.9990 chunk 1 optimal weight: 6.9990 chunk 6 optimal weight: 1.9990 chunk 5 optimal weight: 20.0000 chunk 14 optimal weight: 20.0000 chunk 0 optimal weight: 30.0000 chunk 15 optimal weight: 10.0000 chunk 13 optimal weight: 20.0000 chunk 17 optimal weight: 30.0000 chunk 4 optimal weight: 7.9990 chunk 19 optimal weight: 4.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.092982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.085649 restraints weight = 9247.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.087331 restraints weight = 4903.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.088435 restraints weight = 3033.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.089144 restraints weight = 2083.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.089543 restraints weight = 1552.196| |-----------------------------------------------------------------------------| r_work (final): 0.3879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 moved from start: 0.6072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2050 Z= 0.127 Angle : 0.708 9.310 2775 Z= 0.343 Chirality : 0.043 0.140 340 Planarity : 0.002 0.010 360 Dihedral : 6.543 21.638 275 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.98 % Favored : 89.02 % Rotamer: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % 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: -5.80 (0.27), residues: 255 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.41 (0.21), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 11 TYR 0.003 0.001 TYR E 37 PHE 0.013 0.002 PHE D 15 HIS 0.005 0.002 HIS B 18 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 2045) covalent geometry : angle 0.70774 ( 2775) hydrogen bonds : bond 0.03867 ( 6) hydrogen bonds : angle 4.53296 ( 18) Misc. bond : bond 0.00004 ( 5) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.084 Fit side-chains REVERT: E 10 GLN cc_start: 0.8123 (mp10) cc_final: 0.7840 (mp10) REVERT: J 27 LEU cc_start: 0.7680 (pt) cc_final: 0.7308 (mt) outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.0260 time to fit residues: 1.1445 Evaluate side-chains 25 residues out of total 235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 4 optimal weight: 20.0000 chunk 5 optimal weight: 40.0000 chunk 20 optimal weight: 5.9990 chunk 1 optimal weight: 4.9990 chunk 6 optimal weight: 20.0000 chunk 3 optimal weight: 0.9980 chunk 2 optimal weight: 20.0000 chunk 9 optimal weight: 20.0000 chunk 11 optimal weight: 7.9990 chunk 14 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 10 GLN ** 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 = 0.3915 r_free = 0.3915 target = 0.091866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.084150 restraints weight = 9366.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.085783 restraints weight = 5167.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.086849 restraints weight = 3280.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.087575 restraints weight = 2292.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.087951 restraints weight = 1725.700| |-----------------------------------------------------------------------------| r_work (final): 0.3824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 moved from start: 0.6178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2050 Z= 0.147 Angle : 0.736 10.729 2775 Z= 0.358 Chirality : 0.044 0.151 340 Planarity : 0.002 0.013 360 Dihedral : 6.678 20.307 275 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 15.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.33 % Favored : 86.67 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.89 (0.27), residues: 255 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.48 (0.20), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG I 11 TYR 0.003 0.001 TYR E 37 PHE 0.015 0.002 PHE G 15 HIS 0.005 0.002 HIS B 18 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 2045) covalent geometry : angle 0.73649 ( 2775) hydrogen bonds : bond 0.05469 ( 6) hydrogen bonds : angle 4.81023 ( 18) Misc. bond : bond 0.00003 ( 5) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.067 Fit side-chains REVERT: E 10 GLN cc_start: 0.7992 (mp10) cc_final: 0.7708 (mp10) outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.0207 time to fit residues: 0.8721 Evaluate side-chains 26 residues out of total 235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 11 optimal weight: 20.0000 chunk 14 optimal weight: 7.9990 chunk 17 optimal weight: 40.0000 chunk 19 optimal weight: 10.0000 chunk 10 optimal weight: 7.9990 chunk 3 optimal weight: 5.9990 chunk 20 optimal weight: 0.5980 chunk 1 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 chunk 9 optimal weight: 30.0000 chunk 16 optimal weight: 0.3980 overall best weight: 4.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 18 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.093808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.086037 restraints weight = 9456.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.087713 restraints weight = 5160.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.088724 restraints weight = 3255.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.089505 restraints weight = 2303.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.089925 restraints weight = 1741.780| |-----------------------------------------------------------------------------| r_work (final): 0.3856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7169 moved from start: 0.6489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2050 Z= 0.125 Angle : 0.720 10.654 2775 Z= 0.341 Chirality : 0.043 0.134 340 Planarity : 0.002 0.009 360 Dihedral : 6.333 20.220 275 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.41 % Favored : 90.59 % Rotamer: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -5.78 (0.27), residues: 255 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.40 (0.20), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 11 TYR 0.002 0.000 TYR E 37 PHE 0.013 0.002 PHE D 15 HIS 0.005 0.002 HIS B 18 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 2045) covalent geometry : angle 0.72006 ( 2775) hydrogen bonds : bond 0.04277 ( 6) hydrogen bonds : angle 4.84520 ( 18) Misc. bond : bond 0.00003 ( 5) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.063 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 27 average time/residue: 0.0207 time to fit residues: 0.8298 Evaluate side-chains 21 residues out of total 235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 23 optimal weight: 6.9990 chunk 4 optimal weight: 30.0000 chunk 1 optimal weight: 6.9990 chunk 11 optimal weight: 20.0000 chunk 21 optimal weight: 2.9990 chunk 0 optimal weight: 40.0000 chunk 8 optimal weight: 5.9990 chunk 15 optimal weight: 9.9990 chunk 10 optimal weight: 6.9990 chunk 19 optimal weight: 8.9990 chunk 24 optimal weight: 20.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 10 GLN ** 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 = 0.3912 r_free = 0.3912 target = 0.090444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.082286 restraints weight = 9258.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.084026 restraints weight = 5118.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.085209 restraints weight = 3249.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.086000 restraints weight = 2261.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.086396 restraints weight = 1697.214| |-----------------------------------------------------------------------------| r_work (final): 0.3843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 moved from start: 0.6541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2050 Z= 0.142 Angle : 0.749 9.947 2775 Z= 0.361 Chirality : 0.043 0.138 340 Planarity : 0.002 0.013 360 Dihedral : 6.537 19.687 275 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.94 % Favored : 87.06 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -5.85 (0.25), residues: 255 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.45 (0.19), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 11 TYR 0.003 0.001 TYR E 37 PHE 0.016 0.002 PHE C 15 HIS 0.005 0.002 HIS B 18 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 2045) covalent geometry : angle 0.74878 ( 2775) hydrogen bonds : bond 0.05064 ( 6) hydrogen bonds : angle 5.01579 ( 18) Misc. bond : bond 0.00004 ( 5) =============================================================================== Job complete usr+sys time: 495.31 seconds wall clock time: 9 minutes 33.70 seconds (573.70 seconds total)