Starting phenix.real_space_refine on Tue Feb 3 14:19:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9liy_63127/02_2026/9liy_63127.cif Found real_map, /net/cci-nas-00/data/ceres_data/9liy_63127/02_2026/9liy_63127.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9liy_63127/02_2026/9liy_63127.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9liy_63127/02_2026/9liy_63127.map" model { file = "/net/cci-nas-00/data/ceres_data/9liy_63127/02_2026/9liy_63127.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9liy_63127/02_2026/9liy_63127.cif" } resolution = 3.2 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= 0.002 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: 5 Type Number sf(0) Gaussians S 12 5.16 5 C 2196 2.51 5 N 588 2.21 5 O 744 1.98 5 H 48 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3588 Number of models: 1 Model: "" Number of chains: 1 Chain: "F" Number of atoms: 598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 598 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 3, 'TRANS': 76} Chain breaks: 1 Restraints were copied for chains: A, D, B, E, C Time building chain proxies: 0.61, per 1000 atoms: 0.17 Number of scatterers: 3588 At special positions: 0 Unit cell: (70.55, 185.09, 36.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 12 16.00 O 744 8.00 N 588 7.00 C 2196 6.00 H 48 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 89 " distance=2.03 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 89 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 89 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 89 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 89 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 89 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.29 Conformation dependent library (CDL) restraints added in 140.3 milliseconds 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 840 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 10 sheets defined 0.0% alpha, 20.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'F' and resid 19 through 23 removed outlier: 6.510A pdb=" N ILE F 20 " --> pdb=" O SER D 21 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N SER D 23 " --> pdb=" O ILE F 20 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N CYS F 22 " --> pdb=" O SER D 23 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ILE D 20 " --> pdb=" O SER E 21 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N SER E 23 " --> pdb=" O ILE D 20 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N CYS D 22 " --> pdb=" O SER E 23 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'F' and resid 27 through 28 removed outlier: 6.237A pdb=" N SER F 27 " --> pdb=" O ASN D 28 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N SER D 27 " --> pdb=" O ASN E 28 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'F' and resid 38 through 39 Processing sheet with id=AA4, first strand: chain 'F' and resid 46 through 51 removed outlier: 6.641A pdb=" N SER D 51 " --> pdb=" O TYR F 50 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N SER E 51 " --> pdb=" O TYR D 50 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 74 through 80 removed outlier: 6.943A pdb=" N ALA D 75 " --> pdb=" O LEU F 74 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ILE F 76 " --> pdb=" O ALA D 75 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N SER D 77 " --> pdb=" O ILE F 76 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N GLY F 78 " --> pdb=" O SER D 77 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ALA E 75 " --> pdb=" O LEU D 74 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ILE D 76 " --> pdb=" O ALA E 75 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N SER E 77 " --> pdb=" O ILE D 76 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N GLY D 78 " --> pdb=" O SER E 77 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 19 through 23 removed outlier: 6.543A pdb=" N ILE A 20 " --> pdb=" O SER B 21 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N SER B 23 " --> pdb=" O ILE A 20 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N CYS A 22 " --> pdb=" O SER B 23 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ILE B 20 " --> pdb=" O SER C 21 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N SER C 23 " --> pdb=" O ILE B 20 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N CYS B 22 " --> pdb=" O SER C 23 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 27 through 28 removed outlier: 6.228A pdb=" N SER A 27 " --> pdb=" O ASN B 28 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N SER B 27 " --> pdb=" O ASN C 28 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 38 through 39 Processing sheet with id=AA9, first strand: chain 'A' and resid 46 through 51 removed outlier: 6.630A pdb=" N SER B 51 " --> pdb=" O TYR A 50 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 74 through 80 removed outlier: 6.939A pdb=" N ALA B 75 " --> pdb=" O LEU A 74 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ILE A 76 " --> pdb=" O ALA B 75 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N SER B 77 " --> pdb=" O ILE A 76 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N GLY A 78 " --> pdb=" O SER B 77 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ALA C 75 " --> pdb=" O LEU B 74 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ILE B 76 " --> pdb=" O ALA C 75 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N SER C 77 " --> pdb=" O ILE B 76 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N GLY B 78 " --> pdb=" O SER C 77 " (cutoff:3.500A) 28 hydrogen bonds defined for protein. 84 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: 0.43 Time building geometry restraints manager: 0.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.85 - 1.04: 48 1.04 - 1.23: 210 1.23 - 1.42: 1344 1.42 - 1.61: 2040 1.61 - 1.80: 12 Bond restraints: 3654 Sorted by residual: bond pdb=" CA ILE D 76 " pdb=" CB ILE D 76 " ideal model delta sigma weight residual 1.540 1.529 0.011 1.36e-02 5.41e+03 6.99e-01 bond pdb=" CA ILE C 76 " pdb=" CB ILE C 76 " ideal model delta sigma weight residual 1.540 1.529 0.011 1.36e-02 5.41e+03 6.88e-01 bond pdb=" CA ILE A 76 " pdb=" CB ILE A 76 " ideal model delta sigma weight residual 1.540 1.529 0.011 1.36e-02 5.41e+03 6.81e-01 bond pdb=" CA ILE F 76 " pdb=" CB ILE F 76 " ideal model delta sigma weight residual 1.540 1.529 0.011 1.36e-02 5.41e+03 6.24e-01 bond pdb=" CA ILE B 76 " pdb=" CB ILE B 76 " ideal model delta sigma weight residual 1.540 1.529 0.011 1.36e-02 5.41e+03 6.15e-01 ... (remaining 3649 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.73: 4310 0.73 - 1.47: 533 1.47 - 2.20: 135 2.20 - 2.93: 32 2.93 - 3.67: 24 Bond angle restraints: 5034 Sorted by residual: angle pdb=" CA GLY E 31 " pdb=" C GLY E 31 " pdb=" N ASN E 32 " ideal model delta sigma weight residual 115.34 117.71 -2.37 8.40e-01 1.42e+00 7.98e+00 angle pdb=" CA GLY C 31 " pdb=" C GLY C 31 " pdb=" N ASN C 32 " ideal model delta sigma weight residual 115.34 117.70 -2.36 8.40e-01 1.42e+00 7.90e+00 angle pdb=" CA GLY B 31 " pdb=" C GLY B 31 " pdb=" N ASN B 32 " ideal model delta sigma weight residual 115.34 117.69 -2.35 8.40e-01 1.42e+00 7.83e+00 angle pdb=" CA GLY A 31 " pdb=" C GLY A 31 " pdb=" N ASN A 32 " ideal model delta sigma weight residual 115.34 117.68 -2.34 8.40e-01 1.42e+00 7.74e+00 angle pdb=" CA GLY D 31 " pdb=" C GLY D 31 " pdb=" N ASN D 32 " ideal model delta sigma weight residual 115.34 117.67 -2.33 8.40e-01 1.42e+00 7.69e+00 ... (remaining 5029 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 8.56: 1683 8.56 - 17.12: 243 17.12 - 25.69: 120 25.69 - 34.25: 30 34.25 - 42.81: 18 Dihedral angle restraints: 2094 sinusoidal: 762 harmonic: 1332 Sorted by residual: dihedral pdb=" CB CYS A 22 " pdb=" SG CYS A 22 " pdb=" SG CYS A 89 " pdb=" CB CYS A 89 " ideal model delta sinusoidal sigma weight residual 93.00 68.72 24.28 1 1.00e+01 1.00e-02 8.49e+00 dihedral pdb=" CB CYS D 22 " pdb=" SG CYS D 22 " pdb=" SG CYS D 89 " pdb=" CB CYS D 89 " ideal model delta sinusoidal sigma weight residual 93.00 68.73 24.27 1 1.00e+01 1.00e-02 8.48e+00 dihedral pdb=" CB CYS C 22 " pdb=" SG CYS C 22 " pdb=" SG CYS C 89 " pdb=" CB CYS C 89 " ideal model delta sinusoidal sigma weight residual 93.00 68.76 24.24 1 1.00e+01 1.00e-02 8.47e+00 ... (remaining 2091 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 348 0.026 - 0.052: 133 0.052 - 0.079: 48 0.079 - 0.105: 12 0.105 - 0.131: 23 Chirality restraints: 564 Sorted by residual: chirality pdb=" CA ILE D 76 " pdb=" N ILE D 76 " pdb=" C ILE D 76 " pdb=" CB ILE D 76 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.29e-01 chirality pdb=" CA ILE D 20 " pdb=" N ILE D 20 " pdb=" C ILE D 20 " pdb=" CB ILE D 20 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.28e-01 chirality pdb=" CA ILE E 76 " pdb=" N ILE E 76 " pdb=" C ILE E 76 " pdb=" CB ILE E 76 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.23e-01 ... (remaining 561 not shown) Planarity restraints: 642 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 40 " -0.011 5.00e-02 4.00e+02 1.72e-02 4.74e-01 pdb=" N PRO C 41 " 0.030 5.00e-02 4.00e+02 pdb=" CA PRO C 41 " -0.009 5.00e-02 4.00e+02 pdb=" CD PRO C 41 " -0.010 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 40 " -0.011 5.00e-02 4.00e+02 1.70e-02 4.65e-01 pdb=" N PRO A 41 " 0.029 5.00e-02 4.00e+02 pdb=" CA PRO A 41 " -0.009 5.00e-02 4.00e+02 pdb=" CD PRO A 41 " -0.009 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 40 " -0.011 5.00e-02 4.00e+02 1.70e-02 4.62e-01 pdb=" N PRO B 41 " 0.029 5.00e-02 4.00e+02 pdb=" CA PRO B 41 " -0.009 5.00e-02 4.00e+02 pdb=" CD PRO B 41 " -0.009 5.00e-02 4.00e+02 ... (remaining 639 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.61: 155 2.61 - 3.11: 2918 3.11 - 3.60: 4033 3.60 - 4.10: 6025 4.10 - 4.60: 8357 Nonbonded interactions: 21488 Sorted by model distance: nonbonded pdb=" H CYS E 22 " pdb=" HA CYS E 22 " model vdw 2.111 1.816 nonbonded pdb=" H CYS C 22 " pdb=" HA CYS C 22 " model vdw 2.111 1.816 nonbonded pdb=" H CYS A 22 " pdb=" HA CYS A 22 " model vdw 2.113 1.816 nonbonded pdb=" H CYS F 22 " pdb=" HA CYS F 22 " model vdw 2.114 1.816 nonbonded pdb=" H CYS D 22 " pdb=" HA CYS D 22 " model vdw 2.115 1.816 ... (remaining 21483 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 'F' selection = chain 'A' selection = chain 'D' selection = chain 'B' selection = chain 'E' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.360 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: 0.020 Extract box with map and model: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.940 Find NCS groups from input model: 0.030 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:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 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 : 0.004 0.020 3612 Z= 0.201 Angle : 0.580 3.668 4926 Z= 0.334 Chirality : 0.040 0.131 564 Planarity : 0.002 0.017 630 Dihedral : 11.549 42.808 1224 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 33.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.21 % Favored : 90.79 % Rotamer: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % 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: -5.99 (0.25), residues: 456 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.56 (0.19), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 17 TYR 0.007 0.002 TYR E 88 PHE 0.003 0.001 PHE B 101 TRP 0.006 0.001 TRP A 92 HIS 0.001 0.000 HIS A 39 Details of bonding type rmsd covalent geometry : bond 0.00450 ( 3606) covalent geometry : angle 0.57907 ( 4914) SS BOND : bond 0.00432 ( 6) SS BOND : angle 0.76832 ( 12) hydrogen bonds : bond 0.09201 ( 28) hydrogen bonds : angle 7.49910 ( 84) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.137 Fit side-chains REVERT: A 16 GLN cc_start: 0.6825 (mt0) cc_final: 0.6561 (mt0) REVERT: A 83 ASP cc_start: 0.8364 (t0) cc_final: 0.8092 (t0) REVERT: B 16 GLN cc_start: 0.6909 (mt0) cc_final: 0.6579 (mt0) REVERT: B 83 ASP cc_start: 0.8066 (t0) cc_final: 0.7827 (t0) outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.0591 time to fit residues: 4.7009 Evaluate side-chains 60 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 0.1980 chunk 26 optimal weight: 0.3980 chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 7.9990 chunk 32 optimal weight: 0.8980 chunk 31 optimal weight: 10.0000 chunk 25 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 chunk 30 optimal weight: 8.9990 chunk 22 optimal weight: 9.9990 chunk 37 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 28 ASN A 16 GLN A 28 ASN D 28 ASN B 16 GLN B 28 ASN E 16 GLN E 28 ASN C 28 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.133866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.113802 restraints weight = 5867.562| |-----------------------------------------------------------------------------| r_work (start): 0.3786 rms_B_bonded: 2.43 r_work: 0.3689 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3593 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.1109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3612 Z= 0.076 Angle : 0.394 3.474 4926 Z= 0.198 Chirality : 0.037 0.127 564 Planarity : 0.002 0.020 630 Dihedral : 3.080 7.895 498 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 29.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 2.27 % Allowed : 9.09 % Favored : 88.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.22 (0.28), residues: 456 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.97 (0.21), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG A 17 TYR 0.004 0.001 TYR A 37 PHE 0.003 0.001 PHE D 101 TRP 0.005 0.001 TRP F 92 HIS 0.001 0.000 HIS E 39 Details of bonding type rmsd covalent geometry : bond 0.00210 ( 3606) covalent geometry : angle 0.39381 ( 4914) SS BOND : bond 0.00216 ( 6) SS BOND : angle 0.38004 ( 12) hydrogen bonds : bond 0.00803 ( 28) hydrogen bonds : angle 4.77356 ( 84) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 62 time to evaluate : 0.135 Fit side-chains REVERT: B 82 ASP cc_start: 0.8661 (m-30) cc_final: 0.8383 (m-30) outliers start: 9 outliers final: 6 residues processed: 62 average time/residue: 0.0555 time to fit residues: 4.4809 Evaluate side-chains 64 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain C residue 106 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 13 optimal weight: 7.9990 chunk 33 optimal weight: 10.0000 chunk 43 optimal weight: 0.3980 chunk 0 optimal weight: 8.9990 chunk 9 optimal weight: 4.9990 chunk 15 optimal weight: 8.9990 chunk 29 optimal weight: 2.9990 chunk 30 optimal weight: 9.9990 chunk 5 optimal weight: 6.9990 chunk 38 optimal weight: 0.0870 chunk 17 optimal weight: 4.9990 overall best weight: 2.6964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 28 ASN A 28 ASN D 28 ASN B 16 GLN B 28 ASN E 16 GLN E 28 ASN C 16 GLN C 28 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.127900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.108245 restraints weight = 5925.535| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 2.41 r_work: 0.3606 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3512 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8828 moved from start: 0.1218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.020 3612 Z= 0.194 Angle : 0.497 3.519 4926 Z= 0.255 Chirality : 0.040 0.134 564 Planarity : 0.003 0.016 630 Dihedral : 3.788 10.709 498 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 28.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.62 % Favored : 88.38 % Rotamer: Outliers : 4.29 % Allowed : 11.11 % Favored : 84.60 % 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: -5.03 (0.29), residues: 456 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.83 (0.22), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 17 TYR 0.014 0.002 TYR B 37 PHE 0.002 0.000 PHE B 101 TRP 0.005 0.001 TRP B 92 HIS 0.001 0.000 HIS E 39 Details of bonding type rmsd covalent geometry : bond 0.00460 ( 3606) covalent geometry : angle 0.49630 ( 4914) SS BOND : bond 0.00453 ( 6) SS BOND : angle 0.77760 ( 12) hydrogen bonds : bond 0.01101 ( 28) hydrogen bonds : angle 4.76587 ( 84) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 61 time to evaluate : 0.150 Fit side-chains REVERT: A 83 ASP cc_start: 0.8587 (t0) cc_final: 0.8360 (t0) REVERT: B 82 ASP cc_start: 0.8675 (m-30) cc_final: 0.8424 (m-30) outliers start: 17 outliers final: 11 residues processed: 68 average time/residue: 0.0545 time to fit residues: 4.8765 Evaluate side-chains 71 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 60 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 106 LYS Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 70 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 8.9990 chunk 0 optimal weight: 8.9990 chunk 34 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 36 optimal weight: 8.9990 chunk 13 optimal weight: 1.9990 chunk 10 optimal weight: 7.9990 chunk 38 optimal weight: 0.7980 chunk 11 optimal weight: 4.9990 chunk 29 optimal weight: 0.8980 chunk 28 optimal weight: 10.0000 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 16 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.130231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.110628 restraints weight = 5810.697| |-----------------------------------------------------------------------------| r_work (start): 0.3734 rms_B_bonded: 2.38 r_work: 0.3633 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3541 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.1323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 3612 Z= 0.129 Angle : 0.434 3.504 4926 Z= 0.220 Chirality : 0.038 0.130 564 Planarity : 0.002 0.015 630 Dihedral : 3.500 11.012 498 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 28.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.65 % Favored : 90.35 % Rotamer: Outliers : 5.05 % Allowed : 10.10 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.84 (0.32), residues: 456 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.68 (0.24), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 17 TYR 0.009 0.001 TYR B 37 PHE 0.002 0.000 PHE D 101 TRP 0.005 0.001 TRP B 92 HIS 0.000 0.000 HIS F 39 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 3606) covalent geometry : angle 0.43387 ( 4914) SS BOND : bond 0.00362 ( 6) SS BOND : angle 0.53961 ( 12) hydrogen bonds : bond 0.00817 ( 28) hydrogen bonds : angle 4.51487 ( 84) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 63 time to evaluate : 0.086 Fit side-chains REVERT: A 83 ASP cc_start: 0.8608 (t0) cc_final: 0.8383 (t0) REVERT: B 82 ASP cc_start: 0.8652 (m-30) cc_final: 0.8362 (m-30) outliers start: 20 outliers final: 18 residues processed: 70 average time/residue: 0.0527 time to fit residues: 4.8174 Evaluate side-chains 80 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 62 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 26 ASN Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 26 ASN Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 26 ASN Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 26 ASN Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 26 ASN Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 105 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 36 optimal weight: 10.0000 chunk 15 optimal weight: 9.9990 chunk 4 optimal weight: 8.9990 chunk 17 optimal weight: 6.9990 chunk 46 optimal weight: 8.9990 chunk 24 optimal weight: 9.9990 chunk 30 optimal weight: 10.0000 chunk 25 optimal weight: 7.9990 chunk 42 optimal weight: 6.9990 chunk 11 optimal weight: 6.9990 chunk 18 optimal weight: 5.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.123472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.104188 restraints weight = 5993.498| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 2.40 r_work: 0.3541 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3444 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8884 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.049 3612 Z= 0.474 Angle : 0.737 5.312 4926 Z= 0.387 Chirality : 0.047 0.145 564 Planarity : 0.005 0.032 630 Dihedral : 4.791 15.139 498 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 27.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.20 % Favored : 81.80 % Rotamer: Outliers : 5.56 % Allowed : 12.63 % Favored : 81.82 % 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: -5.04 (0.30), residues: 456 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.84 (0.23), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 17 TYR 0.028 0.004 TYR A 37 PHE 0.002 0.000 PHE A 101 TRP 0.008 0.003 TRP A 92 HIS 0.002 0.001 HIS E 39 Details of bonding type rmsd covalent geometry : bond 0.01111 ( 3606) covalent geometry : angle 0.73499 ( 4914) SS BOND : bond 0.01259 ( 6) SS BOND : angle 1.33845 ( 12) hydrogen bonds : bond 0.01127 ( 28) hydrogen bonds : angle 5.12429 ( 84) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 62 time to evaluate : 0.170 Fit side-chains REVERT: A 83 ASP cc_start: 0.8667 (t0) cc_final: 0.8411 (t0) REVERT: B 82 ASP cc_start: 0.8722 (m-30) cc_final: 0.8460 (m-30) outliers start: 22 outliers final: 22 residues processed: 75 average time/residue: 0.0542 time to fit residues: 5.2996 Evaluate side-chains 83 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 61 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 26 ASN Chi-restraints excluded: chain F residue 105 THR Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 26 ASN Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 26 ASN Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 26 ASN Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 106 LYS Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 26 ASN Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 26 ASN Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 105 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 46 optimal weight: 10.0000 chunk 38 optimal weight: 9.9990 chunk 33 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 3 optimal weight: 0.0040 overall best weight: 0.7192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN B 28 ASN C 28 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.131434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.111658 restraints weight = 5834.306| |-----------------------------------------------------------------------------| r_work (start): 0.3768 rms_B_bonded: 2.40 r_work: 0.3672 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3577 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 3612 Z= 0.078 Angle : 0.409 3.458 4926 Z= 0.209 Chirality : 0.037 0.128 564 Planarity : 0.002 0.015 630 Dihedral : 3.306 10.962 498 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 30.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 3.28 % Allowed : 14.90 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.74 (0.31), residues: 456 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.61 (0.24), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 17 TYR 0.005 0.001 TYR A 50 PHE 0.002 0.000 PHE E 101 TRP 0.007 0.001 TRP B 92 HIS 0.001 0.001 HIS F 39 Details of bonding type rmsd covalent geometry : bond 0.00216 ( 3606) covalent geometry : angle 0.40934 ( 4914) SS BOND : bond 0.00176 ( 6) SS BOND : angle 0.25946 ( 12) hydrogen bonds : bond 0.00658 ( 28) hydrogen bonds : angle 4.26500 ( 84) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 63 time to evaluate : 0.144 Fit side-chains REVERT: A 83 ASP cc_start: 0.8651 (t0) cc_final: 0.8388 (t0) REVERT: B 82 ASP cc_start: 0.8625 (m-30) cc_final: 0.8334 (m-30) outliers start: 13 outliers final: 12 residues processed: 70 average time/residue: 0.0519 time to fit residues: 4.8026 Evaluate side-chains 73 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 61 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 26 ASN Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain D residue 26 ASN Chi-restraints excluded: chain B residue 26 ASN Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 106 LYS Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 26 ASN Chi-restraints excluded: chain C residue 105 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 1 optimal weight: 5.9990 chunk 44 optimal weight: 9.9990 chunk 0 optimal weight: 7.9990 chunk 24 optimal weight: 8.9990 chunk 34 optimal weight: 3.9990 chunk 27 optimal weight: 8.9990 chunk 15 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 33 optimal weight: 6.9990 chunk 5 optimal weight: 1.9990 chunk 26 optimal weight: 7.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN B 28 ASN C 28 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.126004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.106208 restraints weight = 5948.847| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 2.43 r_work: 0.3594 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3499 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8846 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.025 3612 Z= 0.235 Angle : 0.528 3.964 4926 Z= 0.272 Chirality : 0.040 0.135 564 Planarity : 0.003 0.021 630 Dihedral : 3.976 13.653 498 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 28.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.11 % Favored : 82.89 % Rotamer: Outliers : 6.06 % Allowed : 14.14 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.74 (0.31), residues: 456 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.61 (0.24), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG F 17 TYR 0.016 0.002 TYR B 37 PHE 0.001 0.000 PHE B 101 TRP 0.006 0.001 TRP D 92 HIS 0.001 0.000 HIS B 39 Details of bonding type rmsd covalent geometry : bond 0.00554 ( 3606) covalent geometry : angle 0.52726 ( 4914) SS BOND : bond 0.00633 ( 6) SS BOND : angle 0.87187 ( 12) hydrogen bonds : bond 0.00899 ( 28) hydrogen bonds : angle 4.62899 ( 84) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 63 time to evaluate : 0.085 Fit side-chains REVERT: A 83 ASP cc_start: 0.8627 (t0) cc_final: 0.8397 (t0) REVERT: D 84 GLU cc_start: 0.8437 (tp30) cc_final: 0.8150 (tp30) outliers start: 24 outliers final: 23 residues processed: 76 average time/residue: 0.0320 time to fit residues: 3.2448 Evaluate side-chains 86 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 63 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 26 ASN Chi-restraints excluded: chain F residue 105 THR Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 26 ASN Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 26 ASN Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 106 LYS Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 26 ASN Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 26 ASN Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 105 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 25 optimal weight: 8.9990 chunk 28 optimal weight: 7.9990 chunk 45 optimal weight: 0.2980 chunk 37 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 14 optimal weight: 10.0000 chunk 8 optimal weight: 7.9990 chunk 38 optimal weight: 10.0000 chunk 18 optimal weight: 6.9990 chunk 43 optimal weight: 6.9990 chunk 20 optimal weight: 9.9990 overall best weight: 3.3986 ------------------------------------------------------------------------------- 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 = 0.3966 r_free = 0.3966 target = 0.127018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.107528 restraints weight = 5949.183| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 2.43 r_work: 0.3593 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3497 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8849 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.024 3612 Z= 0.235 Angle : 0.535 3.904 4926 Z= 0.276 Chirality : 0.041 0.137 564 Planarity : 0.003 0.021 630 Dihedral : 4.073 14.238 498 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 27.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.50 % Favored : 87.50 % Rotamer: Outliers : 6.31 % Allowed : 14.65 % Favored : 79.04 % 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: -4.85 (0.30), residues: 456 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.69 (0.23), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG F 17 TYR 0.015 0.002 TYR B 37 PHE 0.002 0.000 PHE D 101 TRP 0.006 0.001 TRP A 92 HIS 0.001 0.000 HIS F 39 Details of bonding type rmsd covalent geometry : bond 0.00556 ( 3606) covalent geometry : angle 0.53409 ( 4914) SS BOND : bond 0.00628 ( 6) SS BOND : angle 0.83803 ( 12) hydrogen bonds : bond 0.00857 ( 28) hydrogen bonds : angle 4.64596 ( 84) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 60 time to evaluate : 0.086 Fit side-chains REVERT: A 83 ASP cc_start: 0.8660 (t0) cc_final: 0.8428 (t0) REVERT: B 82 ASP cc_start: 0.8673 (m-30) cc_final: 0.8386 (m-30) outliers start: 25 outliers final: 25 residues processed: 74 average time/residue: 0.0337 time to fit residues: 3.3258 Evaluate side-chains 85 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 60 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 26 ASN Chi-restraints excluded: chain F residue 105 THR Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 26 ASN Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 26 ASN Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 26 ASN Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 106 LYS Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 26 ASN Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 26 ASN Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 105 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 23 optimal weight: 10.0000 chunk 8 optimal weight: 7.9990 chunk 40 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 46 optimal weight: 10.0000 chunk 32 optimal weight: 4.9990 chunk 20 optimal weight: 10.0000 chunk 30 optimal weight: 0.9980 chunk 26 optimal weight: 5.9990 chunk 19 optimal weight: 6.9990 chunk 11 optimal weight: 0.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- 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 = 0.3957 r_free = 0.3957 target = 0.126568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.107105 restraints weight = 5919.268| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 2.41 r_work: 0.3587 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3490 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8852 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.026 3612 Z= 0.250 Angle : 0.548 3.976 4926 Z= 0.283 Chirality : 0.041 0.138 564 Planarity : 0.003 0.023 630 Dihedral : 4.123 14.213 498 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 28.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.01 % Favored : 83.99 % Rotamer: Outliers : 6.31 % Allowed : 15.66 % Favored : 78.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.87 (0.30), residues: 456 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.70 (0.23), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG F 17 TYR 0.016 0.002 TYR B 37 PHE 0.002 0.000 PHE D 101 TRP 0.007 0.001 TRP C 92 HIS 0.001 0.000 HIS F 39 Details of bonding type rmsd covalent geometry : bond 0.00589 ( 3606) covalent geometry : angle 0.54695 ( 4914) SS BOND : bond 0.00664 ( 6) SS BOND : angle 0.90125 ( 12) hydrogen bonds : bond 0.00863 ( 28) hydrogen bonds : angle 4.67610 ( 84) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 61 time to evaluate : 0.083 Fit side-chains REVERT: A 83 ASP cc_start: 0.8626 (t0) cc_final: 0.8426 (t0) REVERT: B 82 ASP cc_start: 0.8668 (m-30) cc_final: 0.8385 (m-30) outliers start: 25 outliers final: 25 residues processed: 75 average time/residue: 0.0328 time to fit residues: 3.2477 Evaluate side-chains 86 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 61 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 26 ASN Chi-restraints excluded: chain F residue 105 THR Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 26 ASN Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 26 ASN Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 26 ASN Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 106 LYS Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 26 ASN Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 26 ASN Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 105 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 22 optimal weight: 9.9990 chunk 6 optimal weight: 9.9990 chunk 21 optimal weight: 4.9990 chunk 31 optimal weight: 9.9990 chunk 8 optimal weight: 6.9990 chunk 12 optimal weight: 5.9990 chunk 30 optimal weight: 9.9990 chunk 25 optimal weight: 6.9990 chunk 24 optimal weight: 0.9980 chunk 36 optimal weight: 6.9990 chunk 14 optimal weight: 1.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- 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 = 0.3951 r_free = 0.3951 target = 0.126196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.106574 restraints weight = 5982.899| |-----------------------------------------------------------------------------| r_work (start): 0.3678 rms_B_bonded: 2.42 r_work: 0.3582 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3488 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8851 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.031 3612 Z= 0.288 Angle : 0.581 4.184 4926 Z= 0.302 Chirality : 0.042 0.139 564 Planarity : 0.004 0.027 630 Dihedral : 4.278 14.904 498 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 27.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.47 % Favored : 85.53 % Rotamer: Outliers : 6.31 % Allowed : 15.66 % Favored : 78.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.99 (0.28), residues: 456 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.80 (0.22), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 17 TYR 0.017 0.003 TYR B 37 PHE 0.002 0.000 PHE D 101 TRP 0.006 0.002 TRP D 92 HIS 0.001 0.000 HIS E 39 Details of bonding type rmsd covalent geometry : bond 0.00679 ( 3606) covalent geometry : angle 0.58016 ( 4914) SS BOND : bond 0.00759 ( 6) SS BOND : angle 0.96672 ( 12) hydrogen bonds : bond 0.00906 ( 28) hydrogen bonds : angle 4.72881 ( 84) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 60 time to evaluate : 0.150 Fit side-chains REVERT: B 82 ASP cc_start: 0.8674 (m-30) cc_final: 0.8397 (m-30) outliers start: 25 outliers final: 25 residues processed: 74 average time/residue: 0.0526 time to fit residues: 5.0997 Evaluate side-chains 85 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 60 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 26 ASN Chi-restraints excluded: chain F residue 105 THR Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 26 ASN Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 26 ASN Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 26 ASN Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 106 LYS Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 26 ASN Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 26 ASN Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 105 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 0 optimal weight: 6.9990 chunk 46 optimal weight: 9.9990 chunk 17 optimal weight: 5.9990 chunk 4 optimal weight: 4.9990 chunk 2 optimal weight: 0.0980 chunk 39 optimal weight: 8.9990 chunk 11 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 25 optimal weight: 5.9990 chunk 23 optimal weight: 0.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- 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 = 0.4019 r_free = 0.4019 target = 0.132261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.112888 restraints weight = 5816.266| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 2.31 r_work: 0.3651 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3559 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8813 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3612 Z= 0.100 Angle : 0.427 3.444 4926 Z= 0.218 Chirality : 0.038 0.130 564 Planarity : 0.002 0.018 630 Dihedral : 3.434 12.109 498 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 30.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.55 % Favored : 91.45 % Rotamer: Outliers : 4.29 % Allowed : 17.93 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.77 (0.30), residues: 456 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.63 (0.23), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 17 TYR 0.007 0.001 TYR A 37 PHE 0.002 0.001 PHE C 101 TRP 0.007 0.001 TRP C 92 HIS 0.001 0.001 HIS D 39 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 3606) covalent geometry : angle 0.42683 ( 4914) SS BOND : bond 0.00375 ( 6) SS BOND : angle 0.48625 ( 12) hydrogen bonds : bond 0.00749 ( 28) hydrogen bonds : angle 4.26240 ( 84) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1204.42 seconds wall clock time: 21 minutes 23.67 seconds (1283.67 seconds total)