Starting phenix.real_space_refine on Tue Mar 3 17:42:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6z1o_11031/03_2026/6z1o_11031.cif Found real_map, /net/cci-nas-00/data/ceres_data/6z1o_11031/03_2026/6z1o_11031.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/6z1o_11031/03_2026/6z1o_11031.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6z1o_11031/03_2026/6z1o_11031.map" model { file = "/net/cci-nas-00/data/ceres_data/6z1o_11031/03_2026/6z1o_11031.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6z1o_11031/03_2026/6z1o_11031.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= 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: 5 Type Number sf(0) Gaussians S 12 5.16 5 C 2436 2.51 5 N 714 2.21 5 O 810 1.98 5 H 3786 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-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7758 Number of models: 1 Model: "" Number of chains: 1 Chain: "D" Number of atoms: 1293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 1293 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 2, 'TRANS': 86} Chain breaks: 1 Restraints were copied for chains: E, F, C, B, A Time building chain proxies: 0.73, per 1000 atoms: 0.09 Number of scatterers: 7758 At special positions: 0 Unit cell: (83.2, 82.16, 46.8, 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 810 8.00 N 714 7.00 C 2436 6.00 H 3786 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 87 " distance=1.99 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 87 " distance=1.99 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 87 " distance=1.99 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 87 " distance=1.99 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 87 " distance=1.99 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 87 " distance=1.99 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: 0.71 Conformation dependent library (CDL) restraints added in 176.3 milliseconds 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 960 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 14 sheets defined 0.0% alpha, 43.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 14 Processing sheet with id=AA2, first strand: chain 'A' and resid 17 through 23 Processing sheet with id=AA3, first strand: chain 'A' and resid 25 through 26 Processing sheet with id=AA4, first strand: chain 'A' and resid 28 through 31 Processing sheet with id=AA5, first strand: chain 'A' and resid 34 through 37 Processing sheet with id=AA6, first strand: chain 'A' and resid 43 through 47 Processing sheet with id=AA7, first strand: chain 'A' and resid 60 through 62 Processing sheet with id=AA8, first strand: chain 'A' and resid 64 through 65 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 64 through 65 current: chain 'B' and resid 64 through 65 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 64 through 65 current: chain 'C' and resid 64 through 65 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 64 through 65 current: chain 'D' and resid 64 through 65 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 64 through 65 current: chain 'E' and resid 64 through 65 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 64 through 65 current: chain 'F' and resid 64 through 65 No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 72 through 75 Processing sheet with id=AB1, first strand: chain 'A' and resid 79 through 82 Processing sheet with id=AB2, first strand: chain 'A' and resid 85 through 86 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 85 through 86 current: chain 'B' and resid 85 through 86 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 85 through 86 current: chain 'C' and resid 85 through 86 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 85 through 86 current: chain 'D' and resid 85 through 86 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 85 through 86 current: chain 'E' and resid 85 through 86 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 85 through 86 current: chain 'F' and resid 85 through 86 No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 88 through 91 Processing sheet with id=AB4, first strand: chain 'A' and resid 95 through 97 Processing sheet with id=AB5, first strand: chain 'A' and resid 103 through 106 185 hydrogen bonds defined for protein. 555 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: 1.71 Time building geometry restraints manager: 0.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 3786 1.03 - 1.23: 133 1.23 - 1.42: 1637 1.42 - 1.61: 2250 1.61 - 1.81: 12 Bond restraints: 7818 Sorted by residual: bond pdb=" CA ALA D 94 " pdb=" CB ALA D 94 " ideal model delta sigma weight residual 1.530 1.472 0.058 1.24e-02 6.50e+03 2.15e+01 bond pdb=" CA ALA F 94 " pdb=" CB ALA F 94 " ideal model delta sigma weight residual 1.530 1.473 0.057 1.24e-02 6.50e+03 2.13e+01 bond pdb=" CA ALA E 94 " pdb=" CB ALA E 94 " ideal model delta sigma weight residual 1.530 1.473 0.057 1.24e-02 6.50e+03 2.11e+01 bond pdb=" CA ALA C 94 " pdb=" CB ALA C 94 " ideal model delta sigma weight residual 1.530 1.473 0.057 1.24e-02 6.50e+03 2.09e+01 bond pdb=" CA ALA B 94 " pdb=" CB ALA B 94 " ideal model delta sigma weight residual 1.530 1.474 0.056 1.24e-02 6.50e+03 2.06e+01 ... (remaining 7813 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 11065 1.89 - 3.79: 2260 3.79 - 5.68: 459 5.68 - 7.57: 124 7.57 - 9.47: 30 Bond angle restraints: 13938 Sorted by residual: angle pdb=" C PRO B 39 " pdb=" CA PRO B 39 " pdb=" CB PRO B 39 " ideal model delta sigma weight residual 111.11 103.02 8.09 1.17e+00 7.31e-01 4.78e+01 angle pdb=" C PRO F 39 " pdb=" CA PRO F 39 " pdb=" CB PRO F 39 " ideal model delta sigma weight residual 111.11 103.03 8.08 1.17e+00 7.31e-01 4.77e+01 angle pdb=" C PRO A 39 " pdb=" CA PRO A 39 " pdb=" CB PRO A 39 " ideal model delta sigma weight residual 111.11 103.05 8.06 1.17e+00 7.31e-01 4.74e+01 angle pdb=" C PRO C 39 " pdb=" CA PRO C 39 " pdb=" CB PRO C 39 " ideal model delta sigma weight residual 111.11 103.06 8.05 1.17e+00 7.31e-01 4.73e+01 angle pdb=" C PRO E 39 " pdb=" CA PRO E 39 " pdb=" CB PRO E 39 " ideal model delta sigma weight residual 111.11 103.08 8.03 1.17e+00 7.31e-01 4.71e+01 ... (remaining 13933 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.52: 3342 17.52 - 35.04: 300 35.04 - 52.56: 96 52.56 - 70.07: 6 70.07 - 87.59: 6 Dihedral angle restraints: 3750 sinusoidal: 2004 harmonic: 1746 Sorted by residual: dihedral pdb=" C CYS F 87 " pdb=" N CYS F 87 " pdb=" CA CYS F 87 " pdb=" CB CYS F 87 " ideal model delta harmonic sigma weight residual -122.60 -132.10 9.50 0 2.50e+00 1.60e-01 1.44e+01 dihedral pdb=" C CYS C 87 " pdb=" N CYS C 87 " pdb=" CA CYS C 87 " pdb=" CB CYS C 87 " ideal model delta harmonic sigma weight residual -122.60 -132.04 9.44 0 2.50e+00 1.60e-01 1.43e+01 dihedral pdb=" C CYS D 87 " pdb=" N CYS D 87 " pdb=" CA CYS D 87 " pdb=" CB CYS D 87 " ideal model delta harmonic sigma weight residual -122.60 -132.04 9.44 0 2.50e+00 1.60e-01 1.43e+01 ... (remaining 3747 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 222 0.072 - 0.144: 224 0.144 - 0.216: 122 0.216 - 0.289: 26 0.289 - 0.361: 18 Chirality restraints: 612 Sorted by residual: chirality pdb=" CA CYS F 87 " pdb=" N CYS F 87 " pdb=" C CYS F 87 " pdb=" CB CYS F 87 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.25e+00 chirality pdb=" CA CYS A 87 " pdb=" N CYS A 87 " pdb=" C CYS A 87 " pdb=" CB CYS A 87 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.23e+00 chirality pdb=" CA CYS B 87 " pdb=" N CYS B 87 " pdb=" C CYS B 87 " pdb=" CB CYS B 87 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.21e+00 ... (remaining 609 not shown) Planarity restraints: 1224 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 95 " 0.222 2.00e-02 2.50e+03 2.76e-01 1.14e+03 pdb=" CG ASN C 95 " -0.013 2.00e-02 2.50e+03 pdb=" OD1 ASN C 95 " -0.223 2.00e-02 2.50e+03 pdb=" ND2 ASN C 95 " 0.010 2.00e-02 2.50e+03 pdb="HD21 ASN C 95 " -0.421 2.00e-02 2.50e+03 pdb="HD22 ASN C 95 " 0.425 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 95 " 0.221 2.00e-02 2.50e+03 2.76e-01 1.14e+03 pdb=" CG ASN A 95 " -0.013 2.00e-02 2.50e+03 pdb=" OD1 ASN A 95 " -0.222 2.00e-02 2.50e+03 pdb=" ND2 ASN A 95 " 0.010 2.00e-02 2.50e+03 pdb="HD21 ASN A 95 " -0.421 2.00e-02 2.50e+03 pdb="HD22 ASN A 95 " 0.425 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 95 " 0.221 2.00e-02 2.50e+03 2.76e-01 1.14e+03 pdb=" CG ASN D 95 " -0.013 2.00e-02 2.50e+03 pdb=" OD1 ASN D 95 " -0.222 2.00e-02 2.50e+03 pdb=" ND2 ASN D 95 " 0.010 2.00e-02 2.50e+03 pdb="HD21 ASN D 95 " -0.421 2.00e-02 2.50e+03 pdb="HD22 ASN D 95 " 0.425 2.00e-02 2.50e+03 ... (remaining 1221 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.22: 675 2.22 - 2.82: 16052 2.82 - 3.41: 18599 3.41 - 4.01: 29086 4.01 - 4.60: 40908 Nonbonded interactions: 105320 Sorted by model distance: nonbonded pdb=" OD1 ASN B 68 " pdb=" HG SER B 71 " model vdw 1.628 2.450 nonbonded pdb=" OD1 ASN C 68 " pdb=" HG SER C 71 " model vdw 1.628 2.450 nonbonded pdb=" OD1 ASN D 68 " pdb=" HG SER D 71 " model vdw 1.628 2.450 nonbonded pdb=" OD1 ASN E 68 " pdb=" HG SER E 71 " model vdw 1.629 2.450 nonbonded pdb=" OD1 ASN F 68 " pdb=" HG SER F 71 " model vdw 1.629 2.450 ... (remaining 105315 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 'D' selection = chain 'E' selection = chain 'F' selection = chain 'C' selection = chain 'B' selection = chain 'A' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.920 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: 0.050 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.130 Find NCS groups from input model: 0.040 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 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 : 0.013 0.058 4038 Z= 0.959 Angle : 2.235 9.468 5466 Z= 1.581 Chirality : 0.128 0.361 612 Planarity : 0.013 0.047 714 Dihedral : 13.750 52.333 1404 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer: Outliers : 0.00 % Allowed : 11.27 % Favored : 88.73 % 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: -4.26 (0.25), residues: 510 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.24 (0.19), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG E 49 TYR 0.027 0.006 TYR A 86 PHE 0.018 0.005 PHE A 99 TRP 0.031 0.007 TRP E 34 HIS 0.008 0.005 HIS D 96 Details of bonding type rmsd covalent geometry : bond 0.01336 ( 4032) covalent geometry : angle 2.23067 ( 5454) SS BOND : bond 0.03904 ( 6) SS BOND : angle 3.70325 ( 12) hydrogen bonds : bond 0.11912 ( 185) hydrogen bonds : angle 7.23459 ( 555) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 0.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 80 GLU cc_start: 0.7716 (mt-10) cc_final: 0.7385 (mt-10) REVERT: E 48 PHE cc_start: 0.8219 (m-80) cc_final: 0.7779 (m-80) REVERT: E 104 LYS cc_start: 0.7713 (tttt) cc_final: 0.7414 (ttmt) REVERT: F 84 ASP cc_start: 0.8207 (t0) cc_final: 0.7766 (t0) REVERT: C 48 PHE cc_start: 0.8224 (m-80) cc_final: 0.7936 (m-80) REVERT: C 82 GLU cc_start: 0.8099 (mt-10) cc_final: 0.7602 (mt-10) REVERT: B 48 PHE cc_start: 0.8442 (m-80) cc_final: 0.8135 (m-80) REVERT: A 19 ARG cc_start: 0.7976 (ttt180) cc_final: 0.7148 (mmp-170) REVERT: A 34 TRP cc_start: 0.7391 (t-100) cc_final: 0.6958 (t60) REVERT: A 80 GLU cc_start: 0.6973 (mt-10) cc_final: 0.6766 (mt-10) REVERT: A 104 LYS cc_start: 0.7866 (tttt) cc_final: 0.7451 (tttt) outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 0.1845 time to fit residues: 34.7043 Evaluate side-chains 99 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.156 ------------------------------------------------------------------------------- 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: 0.9980 chunk 26 optimal weight: 0.5980 chunk 2 optimal weight: 0.7980 chunk 16 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 25 optimal weight: 0.5980 chunk 19 optimal weight: 0.3980 chunk 30 optimal weight: 0.6980 chunk 22 optimal weight: 0.5980 chunk 37 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 37 GLN D 68 ASN C 68 ASN A 36 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.129149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.121032 restraints weight = 20570.886| |-----------------------------------------------------------------------------| r_work (start): 0.3917 rms_B_bonded: 2.22 r_work: 0.3840 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3742 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.4049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 4038 Z= 0.158 Angle : 0.670 4.503 5466 Z= 0.375 Chirality : 0.047 0.133 612 Planarity : 0.005 0.044 714 Dihedral : 6.249 18.197 576 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 1.64 % Allowed : 17.14 % Favored : 81.22 % 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: -3.68 (0.27), residues: 510 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.79 (0.21), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 28 TYR 0.019 0.003 TYR E 86 PHE 0.009 0.001 PHE F 99 TRP 0.009 0.002 TRP C 34 HIS 0.002 0.001 HIS F 96 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 4032) covalent geometry : angle 0.66940 ( 5454) SS BOND : bond 0.00475 ( 6) SS BOND : angle 0.94968 ( 12) hydrogen bonds : bond 0.03165 ( 185) hydrogen bonds : angle 5.91624 ( 555) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 98 time to evaluate : 0.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 35 TYR cc_start: 0.8489 (m-10) cc_final: 0.8201 (m-10) REVERT: E 48 PHE cc_start: 0.8425 (m-80) cc_final: 0.8218 (t80) REVERT: E 104 LYS cc_start: 0.7813 (tttt) cc_final: 0.7179 (tmtt) REVERT: C 46 VAL cc_start: 0.9133 (m) cc_final: 0.8910 (t) REVERT: C 49 ARG cc_start: 0.6362 (tpt90) cc_final: 0.5835 (tpt90) REVERT: B 48 PHE cc_start: 0.8593 (m-80) cc_final: 0.8374 (m-80) REVERT: B 88 ASN cc_start: 0.8890 (m-40) cc_final: 0.8683 (m110) REVERT: B 97 GLN cc_start: 0.8975 (mp10) cc_final: 0.8597 (mt0) REVERT: A 19 ARG cc_start: 0.8438 (ttt180) cc_final: 0.7314 (mmp-170) REVERT: A 23 GLN cc_start: 0.8173 (tt0) cc_final: 0.7893 (tt0) REVERT: A 34 TRP cc_start: 0.8090 (t-100) cc_final: 0.7126 (t60) REVERT: A 104 LYS cc_start: 0.7728 (tttt) cc_final: 0.7227 (tttm) outliers start: 7 outliers final: 5 residues processed: 101 average time/residue: 0.1427 time to fit residues: 17.8529 Evaluate side-chains 86 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 81 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 81 ASP Chi-restraints excluded: chain A residue 71 SER Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 93 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 13 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 96 HIS ** 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 = 0.3828 r_free = 0.3828 target = 0.115259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 20)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.108116 restraints weight = 20830.968| |-----------------------------------------------------------------------------| r_work (start): 0.3734 rms_B_bonded: 2.06 r_work: 0.3660 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3569 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.5636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 4038 Z= 0.203 Angle : 0.660 4.682 5466 Z= 0.366 Chirality : 0.045 0.126 612 Planarity : 0.005 0.037 714 Dihedral : 6.107 16.805 576 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 2.82 % Allowed : 16.90 % Favored : 80.28 % 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: -3.72 (0.27), residues: 510 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.83 (0.20), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 60 TYR 0.019 0.002 TYR F 85 PHE 0.011 0.001 PHE F 99 TRP 0.009 0.002 TRP E 34 HIS 0.002 0.001 HIS F 96 Details of bonding type rmsd covalent geometry : bond 0.00466 ( 4032) covalent geometry : angle 0.65692 ( 5454) SS BOND : bond 0.01065 ( 6) SS BOND : angle 1.47574 ( 12) hydrogen bonds : bond 0.03016 ( 185) hydrogen bonds : angle 5.04585 ( 555) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 0.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 48 PHE cc_start: 0.8315 (OUTLIER) cc_final: 0.8101 (t80) REVERT: C 48 PHE cc_start: 0.8275 (OUTLIER) cc_final: 0.7877 (t80) REVERT: B 48 PHE cc_start: 0.8652 (m-80) cc_final: 0.8439 (m-80) REVERT: B 88 ASN cc_start: 0.8927 (m-40) cc_final: 0.8696 (m110) REVERT: B 97 GLN cc_start: 0.9108 (mp10) cc_final: 0.8853 (mt0) REVERT: A 104 LYS cc_start: 0.7790 (tttt) cc_final: 0.7581 (tptt) outliers start: 12 outliers final: 7 residues processed: 83 average time/residue: 0.1379 time to fit residues: 14.3075 Evaluate side-chains 73 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 64 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 48 PHE Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain F residue 48 PHE Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain C residue 48 PHE Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain A residue 71 SER Chi-restraints excluded: chain A residue 93 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 44 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 36 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.114663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.107680 restraints weight = 21191.118| |-----------------------------------------------------------------------------| r_work (start): 0.3743 rms_B_bonded: 2.11 r_work: 0.3673 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3582 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.6192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 4038 Z= 0.165 Angle : 0.591 4.527 5466 Z= 0.326 Chirality : 0.044 0.133 612 Planarity : 0.004 0.035 714 Dihedral : 5.960 16.134 576 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 3.76 % Allowed : 16.90 % Favored : 79.34 % 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: -3.67 (0.27), residues: 510 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.79 (0.21), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 90 TYR 0.012 0.001 TYR F 85 PHE 0.004 0.001 PHE A 61 TRP 0.007 0.001 TRP B 34 HIS 0.002 0.001 HIS F 96 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 4032) covalent geometry : angle 0.59016 ( 5454) SS BOND : bond 0.00792 ( 6) SS BOND : angle 0.92612 ( 12) hydrogen bonds : bond 0.02659 ( 185) hydrogen bonds : angle 4.73878 ( 555) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 71 time to evaluate : 0.151 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 48 PHE cc_start: 0.8342 (OUTLIER) cc_final: 0.8081 (t80) REVERT: E 104 LYS cc_start: 0.7862 (tttt) cc_final: 0.7252 (tmtt) REVERT: C 48 PHE cc_start: 0.8232 (OUTLIER) cc_final: 0.7810 (t80) REVERT: B 84 ASP cc_start: 0.8520 (OUTLIER) cc_final: 0.8052 (t0) REVERT: B 97 GLN cc_start: 0.9118 (mp10) cc_final: 0.8877 (mt0) REVERT: A 90 ARG cc_start: 0.8414 (ttp80) cc_final: 0.6783 (tpm170) outliers start: 16 outliers final: 10 residues processed: 78 average time/residue: 0.1443 time to fit residues: 13.9199 Evaluate side-chains 76 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 63 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 48 PHE Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain D residue 84 ASP Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain F residue 48 PHE Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain C residue 48 PHE Chi-restraints excluded: chain C residue 84 ASP Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain A residue 71 SER Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 93 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 9 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 11 optimal weight: 0.0970 chunk 5 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 95 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.113803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.106869 restraints weight = 21061.417| |-----------------------------------------------------------------------------| r_work (start): 0.3735 rms_B_bonded: 2.12 r_work: 0.3669 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3579 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.6477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 4038 Z= 0.160 Angle : 0.583 4.569 5466 Z= 0.320 Chirality : 0.043 0.129 612 Planarity : 0.004 0.033 714 Dihedral : 5.857 18.393 576 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 4.23 % Allowed : 15.73 % Favored : 80.05 % 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: -3.65 (0.27), residues: 510 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.77 (0.21), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 49 TYR 0.011 0.001 TYR E 85 PHE 0.005 0.001 PHE F 99 TRP 0.006 0.001 TRP E 34 HIS 0.003 0.001 HIS F 96 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 4032) covalent geometry : angle 0.58157 ( 5454) SS BOND : bond 0.00781 ( 6) SS BOND : angle 0.92875 ( 12) hydrogen bonds : bond 0.02526 ( 185) hydrogen bonds : angle 4.54598 ( 555) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 67 time to evaluate : 0.228 Fit side-chains REVERT: D 48 PHE cc_start: 0.8306 (OUTLIER) cc_final: 0.8068 (t80) REVERT: E 80 GLU cc_start: 0.8531 (mm-30) cc_final: 0.8276 (mm-30) REVERT: E 104 LYS cc_start: 0.7872 (tttt) cc_final: 0.7245 (tmtt) REVERT: C 48 PHE cc_start: 0.8227 (OUTLIER) cc_final: 0.7786 (t80) REVERT: B 84 ASP cc_start: 0.8325 (OUTLIER) cc_final: 0.7936 (t0) REVERT: B 97 GLN cc_start: 0.9105 (mp10) cc_final: 0.8894 (mt0) REVERT: A 90 ARG cc_start: 0.8454 (ttp80) cc_final: 0.6875 (tpm170) outliers start: 18 outliers final: 12 residues processed: 73 average time/residue: 0.1508 time to fit residues: 13.6265 Evaluate side-chains 79 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 64 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 48 PHE Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain D residue 84 ASP Chi-restraints excluded: chain E residue 48 PHE Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain F residue 48 PHE Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 81 ASP Chi-restraints excluded: chain C residue 48 PHE Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain A residue 34 TRP Chi-restraints excluded: chain A residue 71 SER Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 93 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 11 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 44 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 27 optimal weight: 0.1980 chunk 4 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 96 HIS ** 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 = 0.3805 r_free = 0.3805 target = 0.112761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.106047 restraints weight = 21415.192| |-----------------------------------------------------------------------------| r_work (start): 0.3724 rms_B_bonded: 2.10 r_work: 0.3664 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3574 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.6701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 4038 Z= 0.166 Angle : 0.580 4.568 5466 Z= 0.319 Chirality : 0.044 0.129 612 Planarity : 0.004 0.033 714 Dihedral : 5.859 17.497 576 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 4.46 % Allowed : 15.73 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.60 (0.27), residues: 510 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.74 (0.21), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 49 TYR 0.012 0.001 TYR F 85 PHE 0.004 0.001 PHE F 99 TRP 0.006 0.001 TRP E 34 HIS 0.003 0.001 HIS F 96 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 4032) covalent geometry : angle 0.57881 ( 5454) SS BOND : bond 0.00811 ( 6) SS BOND : angle 0.95584 ( 12) hydrogen bonds : bond 0.02510 ( 185) hydrogen bonds : angle 4.48837 ( 555) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 68 time to evaluate : 0.183 Fit side-chains revert: symmetry clash REVERT: D 48 PHE cc_start: 0.8285 (OUTLIER) cc_final: 0.8073 (t80) REVERT: E 80 GLU cc_start: 0.8505 (mt-10) cc_final: 0.8240 (mm-30) REVERT: E 104 LYS cc_start: 0.7932 (tttt) cc_final: 0.7376 (tmtt) REVERT: C 48 PHE cc_start: 0.8237 (OUTLIER) cc_final: 0.7854 (t80) REVERT: B 84 ASP cc_start: 0.8513 (OUTLIER) cc_final: 0.8076 (t0) REVERT: B 97 GLN cc_start: 0.9157 (mp10) cc_final: 0.8908 (mt0) REVERT: A 80 GLU cc_start: 0.8581 (mt-10) cc_final: 0.8245 (mt-10) REVERT: A 90 ARG cc_start: 0.8531 (ttp80) cc_final: 0.6974 (tpm170) outliers start: 19 outliers final: 14 residues processed: 74 average time/residue: 0.1502 time to fit residues: 13.5136 Evaluate side-chains 81 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 64 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 34 TRP Chi-restraints excluded: chain D residue 48 PHE Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain D residue 84 ASP Chi-restraints excluded: chain E residue 48 PHE Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain F residue 48 PHE Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 81 ASP Chi-restraints excluded: chain C residue 48 PHE Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain A residue 34 TRP Chi-restraints excluded: chain A residue 48 PHE Chi-restraints excluded: chain A residue 71 SER Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 93 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 17 optimal weight: 0.6980 chunk 28 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 43 optimal weight: 0.4980 chunk 46 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 30 optimal weight: 0.5980 chunk 18 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 11 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: ** E 96 HIS ** 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 = 0.3827 r_free = 0.3827 target = 0.114305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.107652 restraints weight = 21337.046| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 2.10 r_work: 0.3666 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3574 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.6823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 4038 Z= 0.158 Angle : 0.573 4.534 5466 Z= 0.314 Chirality : 0.043 0.126 612 Planarity : 0.004 0.032 714 Dihedral : 5.790 17.656 576 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 4.23 % Allowed : 16.20 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.54 (0.28), residues: 510 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.69 (0.21), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 49 TYR 0.011 0.001 TYR F 85 PHE 0.004 0.001 PHE F 99 TRP 0.006 0.001 TRP E 34 HIS 0.003 0.001 HIS F 96 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 4032) covalent geometry : angle 0.57170 ( 5454) SS BOND : bond 0.00709 ( 6) SS BOND : angle 0.86360 ( 12) hydrogen bonds : bond 0.02463 ( 185) hydrogen bonds : angle 4.41052 ( 555) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 66 time to evaluate : 0.143 Fit side-chains REVERT: D 48 PHE cc_start: 0.8315 (OUTLIER) cc_final: 0.8085 (t80) REVERT: D 80 GLU cc_start: 0.8251 (mt-10) cc_final: 0.7878 (mt-10) REVERT: E 80 GLU cc_start: 0.8590 (mt-10) cc_final: 0.8261 (mm-30) REVERT: E 104 LYS cc_start: 0.7953 (tttt) cc_final: 0.7302 (tmtt) REVERT: C 48 PHE cc_start: 0.8239 (OUTLIER) cc_final: 0.7855 (t80) REVERT: A 90 ARG cc_start: 0.8458 (ttp80) cc_final: 0.6812 (tpm170) outliers start: 18 outliers final: 15 residues processed: 72 average time/residue: 0.1409 time to fit residues: 12.6292 Evaluate side-chains 83 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 66 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 48 PHE Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain D residue 84 ASP Chi-restraints excluded: chain E residue 48 PHE Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain F residue 48 PHE Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 81 ASP Chi-restraints excluded: chain F residue 84 ASP Chi-restraints excluded: chain C residue 48 PHE Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain A residue 34 TRP Chi-restraints excluded: chain A residue 48 PHE Chi-restraints excluded: chain A residue 71 SER Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 93 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 38 optimal weight: 1.9990 chunk 17 optimal weight: 0.0980 chunk 34 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 96 HIS ** 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 = 0.3786 r_free = 0.3786 target = 0.111592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 19)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.105099 restraints weight = 21940.275| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 2.09 r_work: 0.3645 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3556 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.6968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 4038 Z= 0.202 Angle : 0.605 4.691 5466 Z= 0.333 Chirality : 0.044 0.126 612 Planarity : 0.004 0.032 714 Dihedral : 5.922 17.690 576 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 4.46 % Allowed : 15.96 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.54 (0.27), residues: 510 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.69 (0.21), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 49 TYR 0.014 0.002 TYR F 85 PHE 0.004 0.001 PHE F 99 TRP 0.006 0.001 TRP F 34 HIS 0.002 0.001 HIS F 96 Details of bonding type rmsd covalent geometry : bond 0.00460 ( 4032) covalent geometry : angle 0.60380 ( 5454) SS BOND : bond 0.00920 ( 6) SS BOND : angle 1.13904 ( 12) hydrogen bonds : bond 0.02629 ( 185) hydrogen bonds : angle 4.44547 ( 555) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 67 time to evaluate : 0.175 Fit side-chains REVERT: D 48 PHE cc_start: 0.8330 (OUTLIER) cc_final: 0.8090 (t80) REVERT: E 104 LYS cc_start: 0.7958 (tttt) cc_final: 0.7235 (tmtt) REVERT: C 48 PHE cc_start: 0.8273 (OUTLIER) cc_final: 0.7883 (t80) REVERT: B 84 ASP cc_start: 0.8638 (OUTLIER) cc_final: 0.8174 (t0) REVERT: A 90 ARG cc_start: 0.8440 (ttp80) cc_final: 0.6910 (tpm170) outliers start: 19 outliers final: 14 residues processed: 75 average time/residue: 0.1611 time to fit residues: 14.5148 Evaluate side-chains 78 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 61 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 48 PHE Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain D residue 84 ASP Chi-restraints excluded: chain E residue 48 PHE Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain F residue 48 PHE Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 81 ASP Chi-restraints excluded: chain C residue 48 PHE Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain A residue 34 TRP Chi-restraints excluded: chain A residue 48 PHE Chi-restraints excluded: chain A residue 71 SER Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 93 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 4 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 chunk 41 optimal weight: 0.5980 chunk 11 optimal weight: 0.5980 chunk 6 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 43 optimal weight: 0.2980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 96 HIS ** 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 = 0.3832 r_free = 0.3832 target = 0.114178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.107717 restraints weight = 21437.655| |-----------------------------------------------------------------------------| r_work (start): 0.3747 rms_B_bonded: 2.11 r_work: 0.3678 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3586 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.7041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4038 Z= 0.134 Angle : 0.570 5.767 5466 Z= 0.310 Chirality : 0.043 0.125 612 Planarity : 0.003 0.032 714 Dihedral : 5.743 17.614 576 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 4.23 % Allowed : 15.96 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.51 (0.28), residues: 510 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.67 (0.21), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 49 TYR 0.010 0.001 TYR F 85 PHE 0.003 0.001 PHE A 99 TRP 0.004 0.001 TRP B 34 HIS 0.003 0.001 HIS A 96 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 4032) covalent geometry : angle 0.56998 ( 5454) SS BOND : bond 0.00589 ( 6) SS BOND : angle 0.73867 ( 12) hydrogen bonds : bond 0.02372 ( 185) hydrogen bonds : angle 4.37886 ( 555) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 69 time to evaluate : 0.207 Fit side-chains revert: symmetry clash REVERT: D 48 PHE cc_start: 0.8301 (OUTLIER) cc_final: 0.8076 (t80) REVERT: E 80 GLU cc_start: 0.8638 (mm-30) cc_final: 0.8130 (mm-30) REVERT: E 104 LYS cc_start: 0.7953 (tttt) cc_final: 0.7235 (tmtt) REVERT: C 48 PHE cc_start: 0.8242 (OUTLIER) cc_final: 0.7827 (t80) REVERT: B 84 ASP cc_start: 0.8342 (OUTLIER) cc_final: 0.7909 (t0) REVERT: A 80 GLU cc_start: 0.8497 (mt-10) cc_final: 0.8142 (mt-10) REVERT: A 90 ARG cc_start: 0.8397 (ttp80) cc_final: 0.6921 (tpm170) outliers start: 18 outliers final: 13 residues processed: 75 average time/residue: 0.1419 time to fit residues: 13.2299 Evaluate side-chains 81 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 65 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 48 PHE Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain D residue 84 ASP Chi-restraints excluded: chain E residue 48 PHE Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain F residue 48 PHE Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 81 ASP Chi-restraints excluded: chain C residue 48 PHE Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain A residue 34 TRP Chi-restraints excluded: chain A residue 48 PHE Chi-restraints excluded: chain A residue 71 SER Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 93 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 4 optimal weight: 2.9990 chunk 18 optimal weight: 0.4980 chunk 3 optimal weight: 0.5980 chunk 40 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 43 optimal weight: 0.3980 chunk 29 optimal weight: 1.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 96 HIS ** 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 = 0.3816 r_free = 0.3816 target = 0.112875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.106360 restraints weight = 21660.299| |-----------------------------------------------------------------------------| r_work (start): 0.3728 rms_B_bonded: 2.13 r_work: 0.3660 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3571 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.7102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4038 Z= 0.149 Angle : 0.594 5.500 5466 Z= 0.319 Chirality : 0.044 0.123 612 Planarity : 0.003 0.031 714 Dihedral : 5.737 17.322 576 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 3.99 % Allowed : 17.14 % Favored : 78.87 % 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: -3.48 (0.28), residues: 510 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.64 (0.21), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 90 TYR 0.011 0.001 TYR F 85 PHE 0.004 0.001 PHE D 48 TRP 0.004 0.001 TRP B 34 HIS 0.002 0.001 HIS A 96 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 4032) covalent geometry : angle 0.59256 ( 5454) SS BOND : bond 0.00686 ( 6) SS BOND : angle 0.93390 ( 12) hydrogen bonds : bond 0.02363 ( 185) hydrogen bonds : angle 4.34440 ( 555) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 62 time to evaluate : 0.231 Fit side-chains revert: symmetry clash REVERT: E 80 GLU cc_start: 0.8623 (mm-30) cc_final: 0.8107 (mm-30) REVERT: E 104 LYS cc_start: 0.7953 (tttt) cc_final: 0.7294 (tmtt) REVERT: C 48 PHE cc_start: 0.8249 (OUTLIER) cc_final: 0.7815 (t80) REVERT: B 84 ASP cc_start: 0.8516 (OUTLIER) cc_final: 0.8055 (t0) REVERT: A 90 ARG cc_start: 0.8399 (ttp80) cc_final: 0.6946 (tpm170) outliers start: 17 outliers final: 13 residues processed: 68 average time/residue: 0.1513 time to fit residues: 12.8143 Evaluate side-chains 78 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 63 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain D residue 84 ASP Chi-restraints excluded: chain E residue 48 PHE Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain F residue 48 PHE Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 81 ASP Chi-restraints excluded: chain C residue 48 PHE Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain A residue 34 TRP Chi-restraints excluded: chain A residue 48 PHE Chi-restraints excluded: chain A residue 71 SER Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 93 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 13 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 96 HIS ** 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 = 0.3786 r_free = 0.3786 target = 0.111384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.104910 restraints weight = 21882.743| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 2.11 r_work: 0.3641 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3551 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.7152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 4038 Z= 0.198 Angle : 0.626 6.207 5466 Z= 0.338 Chirality : 0.044 0.124 612 Planarity : 0.003 0.030 714 Dihedral : 5.880 17.804 576 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 3.99 % Allowed : 17.37 % Favored : 78.64 % 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: -3.44 (0.28), residues: 510 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.61 (0.21), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 28 TYR 0.014 0.002 TYR F 85 PHE 0.003 0.001 PHE F 99 TRP 0.005 0.001 TRP E 34 HIS 0.002 0.001 HIS F 96 Details of bonding type rmsd covalent geometry : bond 0.00453 ( 4032) covalent geometry : angle 0.62492 ( 5454) SS BOND : bond 0.00903 ( 6) SS BOND : angle 1.12682 ( 12) hydrogen bonds : bond 0.02589 ( 185) hydrogen bonds : angle 4.40757 ( 555) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2184.79 seconds wall clock time: 37 minutes 43.40 seconds (2263.40 seconds total)