Starting phenix.real_space_refine on Tue Mar 3 11:51:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6j6j_0689/03_2026/6j6j_0689.cif Found real_map, /net/cci-nas-00/data/ceres_data/6j6j_0689/03_2026/6j6j_0689.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/6j6j_0689/03_2026/6j6j_0689.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6j6j_0689/03_2026/6j6j_0689.map" model { file = "/net/cci-nas-00/data/ceres_data/6j6j_0689/03_2026/6j6j_0689.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6j6j_0689/03_2026/6j6j_0689.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= 0.001 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 4 5.16 5 C 2264 2.51 5 N 628 2.21 5 O 728 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 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: 3624 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 887 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 117} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 887 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 117} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 887 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 117} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 887 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 117} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'BTN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'BTN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'BTN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'BTN': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Time building chain proxies: 0.91, per 1000 atoms: 0.25 Number of scatterers: 3624 At special positions: 0 Unit cell: (70.551, 60.021, 64.233, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 4 16.00 O 728 8.00 N 628 7.00 C 2264 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.28 Conformation dependent library (CDL) restraints added in 138.0 milliseconds 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 824 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 4 sheets defined 0.0% alpha, 47.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.10 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 21 removed outlier: 4.058A pdb=" N GLY A 41 " --> pdb=" O LEU A 56 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N VAL A 55 " --> pdb=" O ALA A 78 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ALA A 78 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N SER A 88 " --> pdb=" O TRP A 79 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 19 through 21 removed outlier: 4.058A pdb=" N GLY B 41 " --> pdb=" O LEU B 56 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N VAL B 55 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ALA B 78 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N SER B 88 " --> pdb=" O TRP B 79 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 19 through 21 removed outlier: 4.057A pdb=" N GLY C 41 " --> pdb=" O LEU C 56 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N VAL C 55 " --> pdb=" O ALA C 78 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ALA C 78 " --> pdb=" O VAL C 55 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N SER C 88 " --> pdb=" O TRP C 79 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 19 through 21 removed outlier: 4.059A pdb=" N GLY D 41 " --> pdb=" O LEU D 56 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N VAL D 55 " --> pdb=" O ALA D 78 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ALA D 78 " --> pdb=" O VAL D 55 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N SER D 88 " --> pdb=" O TRP D 79 " (cutoff:3.500A) 184 hydrogen bonds defined for protein. 492 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: 0.39 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: 1.22 - 1.34: 1159 1.34 - 1.46: 1020 1.46 - 1.57: 1517 1.57 - 1.69: 4 1.69 - 1.81: 4 Bond restraints: 3704 Sorted by residual: bond pdb=" C3 BTN C5100 " pdb=" O3 BTN C5100 " ideal model delta sigma weight residual 1.220 1.405 -0.185 2.00e-02 2.50e+03 8.53e+01 bond pdb=" C3 BTN D5100 " pdb=" O3 BTN D5100 " ideal model delta sigma weight residual 1.220 1.404 -0.184 2.00e-02 2.50e+03 8.47e+01 bond pdb=" C3 BTN A5100 " pdb=" O3 BTN A5100 " ideal model delta sigma weight residual 1.220 1.403 -0.183 2.00e-02 2.50e+03 8.41e+01 bond pdb=" C3 BTN B5100 " pdb=" O3 BTN B5100 " ideal model delta sigma weight residual 1.220 1.403 -0.183 2.00e-02 2.50e+03 8.34e+01 bond pdb=" C2 BTN C5100 " pdb=" S1 BTN C5100 " ideal model delta sigma weight residual 1.824 1.663 0.161 2.00e-02 2.50e+03 6.44e+01 ... (remaining 3699 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 4656 1.68 - 3.37: 306 3.37 - 5.05: 71 5.05 - 6.73: 27 6.73 - 8.42: 8 Bond angle restraints: 5068 Sorted by residual: angle pdb=" C SER B 62 " pdb=" N ALA B 63 " pdb=" CA ALA B 63 " ideal model delta sigma weight residual 121.80 130.14 -8.34 2.44e+00 1.68e-01 1.17e+01 angle pdb=" C SER A 62 " pdb=" N ALA A 63 " pdb=" CA ALA A 63 " ideal model delta sigma weight residual 121.80 130.12 -8.32 2.44e+00 1.68e-01 1.16e+01 angle pdb=" C SER C 62 " pdb=" N ALA C 63 " pdb=" CA ALA C 63 " ideal model delta sigma weight residual 121.80 130.10 -8.30 2.44e+00 1.68e-01 1.16e+01 angle pdb=" C SER D 62 " pdb=" N ALA D 63 " pdb=" CA ALA D 63 " ideal model delta sigma weight residual 121.80 130.03 -8.23 2.44e+00 1.68e-01 1.14e+01 angle pdb=" C GLU A 51 " pdb=" N SER A 52 " pdb=" CA SER A 52 " ideal model delta sigma weight residual 121.54 127.63 -6.09 1.91e+00 2.74e-01 1.02e+01 ... (remaining 5063 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.87: 1724 13.87 - 27.74: 276 27.74 - 41.60: 52 41.60 - 55.47: 8 55.47 - 69.34: 4 Dihedral angle restraints: 2064 sinusoidal: 744 harmonic: 1320 Sorted by residual: dihedral pdb=" CA ALA C 63 " pdb=" C ALA C 63 " pdb=" N PRO C 64 " pdb=" CA PRO C 64 " ideal model delta harmonic sigma weight residual -180.00 -154.75 -25.25 0 5.00e+00 4.00e-02 2.55e+01 dihedral pdb=" CA ALA D 63 " pdb=" C ALA D 63 " pdb=" N PRO D 64 " pdb=" CA PRO D 64 " ideal model delta harmonic sigma weight residual -180.00 -154.81 -25.19 0 5.00e+00 4.00e-02 2.54e+01 dihedral pdb=" CA ALA A 63 " pdb=" C ALA A 63 " pdb=" N PRO A 64 " pdb=" CA PRO A 64 " ideal model delta harmonic sigma weight residual 180.00 -154.83 -25.17 0 5.00e+00 4.00e-02 2.53e+01 ... (remaining 2061 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 421 0.057 - 0.114: 99 0.114 - 0.172: 40 0.172 - 0.229: 4 0.229 - 0.286: 4 Chirality restraints: 568 Sorted by residual: chirality pdb=" C2 BTN C5100 " pdb=" C4 BTN C5100 " pdb=" C7 BTN C5100 " pdb=" S1 BTN C5100 " both_signs ideal model delta sigma weight residual False 3.08 2.80 0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" C2 BTN B5100 " pdb=" C4 BTN B5100 " pdb=" C7 BTN B5100 " pdb=" S1 BTN B5100 " both_signs ideal model delta sigma weight residual False 3.08 2.80 0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" C2 BTN D5100 " pdb=" C4 BTN D5100 " pdb=" C7 BTN D5100 " pdb=" S1 BTN D5100 " both_signs ideal model delta sigma weight residual False 3.08 2.80 0.28 2.00e-01 2.50e+01 1.98e+00 ... (remaining 565 not shown) Planarity restraints: 632 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C3 BTN B5100 " 0.002 2.00e-02 2.50e+03 3.58e-02 1.93e+01 pdb=" C4 BTN B5100 " -0.055 2.00e-02 2.50e+03 pdb=" C5 BTN B5100 " 0.046 2.00e-02 2.50e+03 pdb=" N1 BTN B5100 " -0.028 2.00e-02 2.50e+03 pdb=" N2 BTN B5100 " 0.041 2.00e-02 2.50e+03 pdb=" O3 BTN B5100 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C3 BTN A5100 " 0.002 2.00e-02 2.50e+03 3.56e-02 1.90e+01 pdb=" C4 BTN A5100 " -0.054 2.00e-02 2.50e+03 pdb=" C5 BTN A5100 " 0.046 2.00e-02 2.50e+03 pdb=" N1 BTN A5100 " -0.028 2.00e-02 2.50e+03 pdb=" N2 BTN A5100 " 0.041 2.00e-02 2.50e+03 pdb=" O3 BTN A5100 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C3 BTN D5100 " -0.002 2.00e-02 2.50e+03 3.55e-02 1.90e+01 pdb=" C4 BTN D5100 " 0.054 2.00e-02 2.50e+03 pdb=" C5 BTN D5100 " -0.046 2.00e-02 2.50e+03 pdb=" N1 BTN D5100 " 0.029 2.00e-02 2.50e+03 pdb=" N2 BTN D5100 " -0.041 2.00e-02 2.50e+03 pdb=" O3 BTN D5100 " 0.006 2.00e-02 2.50e+03 ... (remaining 629 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 1171 2.81 - 3.33: 2720 3.33 - 3.86: 6145 3.86 - 4.38: 6884 4.38 - 4.90: 12906 Nonbonded interactions: 29826 Sorted by model distance: nonbonded pdb=" OH TYR C 43 " pdb=" O3 BTN C5100 " model vdw 2.291 3.040 nonbonded pdb=" OH TYR D 43 " pdb=" O3 BTN D5100 " model vdw 2.291 3.040 nonbonded pdb=" OH TYR B 43 " pdb=" O3 BTN B5100 " model vdw 2.292 3.040 nonbonded pdb=" OH TYR A 43 " pdb=" O3 BTN A5100 " model vdw 2.292 3.040 nonbonded pdb=" ND2 ASN A 23 " pdb=" OG SER A 27 " model vdw 2.322 3.120 ... (remaining 29821 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.030 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.850 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 6.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6647 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 : 0.011 0.185 3704 Z= 0.524 Angle : 1.065 8.418 5068 Z= 0.564 Chirality : 0.061 0.286 568 Planarity : 0.005 0.036 632 Dihedral : 13.509 69.341 1240 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.11 % Favored : 88.89 % Rotamer: Outliers : 0.00 % Allowed : 19.77 % Favored : 80.23 % 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: -3.36 (0.33), residues: 468 helix: None (None), residues: 0 sheet: -1.47 (0.27), residues: 284 loop : -3.38 (0.35), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 84 TYR 0.016 0.002 TYR C 96 PHE 0.018 0.003 PHE A 29 TRP 0.013 0.002 TRP A 75 HIS 0.002 0.001 HIS B 87 Details of bonding type rmsd covalent geometry : bond 0.01066 ( 3704) covalent geometry : angle 1.06478 ( 5068) hydrogen bonds : bond 0.10890 ( 184) hydrogen bonds : angle 7.10031 ( 492) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.097 Fit side-chains REVERT: A 105 ASN cc_start: 0.8185 (m110) cc_final: 0.7865 (m110) REVERT: B 105 ASN cc_start: 0.7803 (m110) cc_final: 0.7563 (m-40) REVERT: D 83 TYR cc_start: 0.7863 (m-10) cc_final: 0.7403 (m-10) outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.0893 time to fit residues: 7.1907 Evaluate side-chains 54 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 2.9990 chunk 26 optimal weight: 8.9990 chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 9.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 9.9990 chunk 19 optimal weight: 4.9990 chunk 30 optimal weight: 0.4980 chunk 22 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 ASN B 81 ASN B 105 ASN B 107 GLN C 105 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.168480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.154345 restraints weight = 3845.254| |-----------------------------------------------------------------------------| r_work (start): 0.3785 rms_B_bonded: 1.63 r_work: 0.3724 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3606 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3704 Z= 0.159 Angle : 0.653 7.430 5068 Z= 0.352 Chirality : 0.045 0.145 568 Planarity : 0.004 0.038 632 Dihedral : 6.609 30.518 592 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 5.52 % Allowed : 15.99 % Favored : 78.49 % 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: -2.76 (0.36), residues: 468 helix: None (None), residues: 0 sheet: -0.93 (0.29), residues: 264 loop : -3.09 (0.40), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 84 TYR 0.014 0.002 TYR D 43 PHE 0.013 0.003 PHE C 29 TRP 0.012 0.001 TRP D 92 HIS 0.002 0.001 HIS D 87 Details of bonding type rmsd covalent geometry : bond 0.00367 ( 3704) covalent geometry : angle 0.65265 ( 5068) hydrogen bonds : bond 0.03356 ( 184) hydrogen bonds : angle 6.57486 ( 492) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 51 time to evaluate : 0.126 Fit side-chains REVERT: B 116 GLU cc_start: 0.7018 (pm20) cc_final: 0.6753 (mp0) REVERT: C 56 LEU cc_start: 0.7989 (OUTLIER) cc_final: 0.7769 (pp) outliers start: 19 outliers final: 7 residues processed: 68 average time/residue: 0.0703 time to fit residues: 5.9204 Evaluate side-chains 49 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 114 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 31 optimal weight: 6.9990 chunk 18 optimal weight: 8.9990 chunk 9 optimal weight: 0.7980 chunk 33 optimal weight: 8.9990 chunk 40 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 43 optimal weight: 8.9990 chunk 7 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.173896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.158175 restraints weight = 3776.086| |-----------------------------------------------------------------------------| r_work (start): 0.3801 rms_B_bonded: 1.83 r_work: 0.3731 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3608 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.3165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3704 Z= 0.111 Angle : 0.600 7.229 5068 Z= 0.328 Chirality : 0.043 0.131 568 Planarity : 0.004 0.033 632 Dihedral : 5.999 28.325 592 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.04 % Favored : 89.96 % Rotamer: Outliers : 3.49 % Allowed : 20.06 % Favored : 76.45 % 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: -2.21 (0.37), residues: 468 helix: None (None), residues: 0 sheet: -0.27 (0.32), residues: 228 loop : -2.79 (0.38), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 84 TYR 0.008 0.001 TYR A 96 PHE 0.012 0.002 PHE C 29 TRP 0.011 0.001 TRP D 75 HIS 0.002 0.001 HIS D 87 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 3704) covalent geometry : angle 0.59976 ( 5068) hydrogen bonds : bond 0.03059 ( 184) hydrogen bonds : angle 6.23639 ( 492) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 50 time to evaluate : 0.130 Fit side-chains REVERT: A 131 THR cc_start: 0.9018 (m) cc_final: 0.8776 (m) REVERT: B 85 ASN cc_start: 0.7506 (t0) cc_final: 0.7305 (t0) outliers start: 12 outliers final: 9 residues processed: 57 average time/residue: 0.0772 time to fit residues: 5.3265 Evaluate side-chains 52 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 43 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 114 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 23 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 chunk 9 optimal weight: 5.9990 chunk 43 optimal weight: 8.9990 chunk 26 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 chunk 6 optimal weight: 6.9990 chunk 16 optimal weight: 7.9990 chunk 27 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.157602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.144674 restraints weight = 3994.087| |-----------------------------------------------------------------------------| r_work (start): 0.3708 rms_B_bonded: 1.51 r_work: 0.3639 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3525 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.3887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.064 3704 Z= 0.334 Angle : 0.829 7.675 5068 Z= 0.437 Chirality : 0.050 0.171 568 Planarity : 0.008 0.061 632 Dihedral : 7.476 32.251 592 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.97 % Favored : 91.03 % Rotamer: Outliers : 6.69 % Allowed : 18.02 % Favored : 75.29 % 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: -2.71 (0.38), residues: 468 helix: None (None), residues: 0 sheet: -1.28 (0.28), residues: 284 loop : -2.49 (0.49), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 84 TYR 0.017 0.003 TYR A 43 PHE 0.020 0.004 PHE B 29 TRP 0.012 0.002 TRP B 75 HIS 0.006 0.003 HIS C 127 Details of bonding type rmsd covalent geometry : bond 0.00792 ( 3704) covalent geometry : angle 0.82873 ( 5068) hydrogen bonds : bond 0.04458 ( 184) hydrogen bonds : angle 7.00363 ( 492) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 53 time to evaluate : 0.077 Fit side-chains REVERT: A 83 TYR cc_start: 0.7915 (m-10) cc_final: 0.7665 (m-10) REVERT: D 82 ASN cc_start: 0.8872 (m110) cc_final: 0.8631 (m110) REVERT: D 107 GLN cc_start: 0.8542 (OUTLIER) cc_final: 0.7951 (tp40) outliers start: 23 outliers final: 15 residues processed: 71 average time/residue: 0.0579 time to fit residues: 5.2382 Evaluate side-chains 67 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 51 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 118 ASN Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 42 THR Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 107 GLN Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 123 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 27 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 21 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- 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 = 0.3958 r_free = 0.3958 target = 0.169022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.153804 restraints weight = 4074.720| |-----------------------------------------------------------------------------| r_work (start): 0.3793 rms_B_bonded: 1.91 r_work: 0.3683 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3555 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.3973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 3704 Z= 0.266 Angle : 0.752 7.435 5068 Z= 0.400 Chirality : 0.048 0.151 568 Planarity : 0.006 0.046 632 Dihedral : 7.127 32.358 592 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.19 % Favored : 90.81 % Rotamer: Outliers : 8.72 % Allowed : 17.73 % Favored : 73.55 % 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: -2.72 (0.38), residues: 468 helix: None (None), residues: 0 sheet: -1.32 (0.27), residues: 284 loop : -2.43 (0.50), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 84 TYR 0.015 0.003 TYR A 43 PHE 0.017 0.003 PHE B 29 TRP 0.012 0.002 TRP A 75 HIS 0.005 0.003 HIS A 87 Details of bonding type rmsd covalent geometry : bond 0.00631 ( 3704) covalent geometry : angle 0.75183 ( 5068) hydrogen bonds : bond 0.03901 ( 184) hydrogen bonds : angle 6.86389 ( 492) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 53 time to evaluate : 0.102 Fit side-chains REVERT: B 49 ASN cc_start: 0.8115 (t0) cc_final: 0.7889 (t0) REVERT: D 82 ASN cc_start: 0.8869 (m110) cc_final: 0.8615 (m110) REVERT: D 107 GLN cc_start: 0.8548 (OUTLIER) cc_final: 0.8063 (tp40) outliers start: 30 outliers final: 23 residues processed: 77 average time/residue: 0.0632 time to fit residues: 6.0355 Evaluate side-chains 75 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 51 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 118 ASN Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 107 GLN Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 42 THR Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 69 SER Chi-restraints excluded: chain D residue 107 GLN Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 131 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 40 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 25 optimal weight: 7.9990 chunk 18 optimal weight: 7.9990 chunk 27 optimal weight: 0.7980 chunk 22 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 3 optimal weight: 8.9990 chunk 28 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN C 23 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.173777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.158271 restraints weight = 4095.003| |-----------------------------------------------------------------------------| r_work (start): 0.3824 rms_B_bonded: 1.96 r_work: 0.3714 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3583 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.4071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 3704 Z= 0.169 Angle : 0.659 7.434 5068 Z= 0.352 Chirality : 0.044 0.135 568 Planarity : 0.005 0.042 632 Dihedral : 6.482 29.401 592 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.97 % Favored : 91.03 % Rotamer: Outliers : 6.69 % Allowed : 20.64 % Favored : 72.67 % 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: -2.48 (0.38), residues: 468 helix: None (None), residues: 0 sheet: -0.87 (0.28), residues: 264 loop : -2.69 (0.46), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 84 TYR 0.012 0.002 TYR C 60 PHE 0.014 0.002 PHE A 29 TRP 0.011 0.001 TRP A 75 HIS 0.003 0.002 HIS B 87 Details of bonding type rmsd covalent geometry : bond 0.00401 ( 3704) covalent geometry : angle 0.65860 ( 5068) hydrogen bonds : bond 0.03305 ( 184) hydrogen bonds : angle 6.64886 ( 492) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 52 time to evaluate : 0.075 Fit side-chains REVERT: A 131 THR cc_start: 0.9023 (m) cc_final: 0.8661 (p) REVERT: D 82 ASN cc_start: 0.8914 (m110) cc_final: 0.8635 (m110) outliers start: 23 outliers final: 21 residues processed: 68 average time/residue: 0.0588 time to fit residues: 5.0412 Evaluate side-chains 72 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 51 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 107 GLN Chi-restraints excluded: chain B residue 118 ASN Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 107 GLN Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 69 SER Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 123 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 17 optimal weight: 0.2980 chunk 9 optimal weight: 2.9990 chunk 3 optimal weight: 0.4980 chunk 42 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 chunk 34 optimal weight: 6.9990 chunk 30 optimal weight: 8.9990 chunk 36 optimal weight: 0.7980 chunk 40 optimal weight: 0.5980 chunk 25 optimal weight: 6.9990 chunk 27 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 23 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.180213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.164436 restraints weight = 4028.704| |-----------------------------------------------------------------------------| r_work (start): 0.3916 rms_B_bonded: 1.93 r_work: 0.3793 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3662 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.4195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 3704 Z= 0.101 Angle : 0.572 6.809 5068 Z= 0.309 Chirality : 0.041 0.133 568 Planarity : 0.004 0.046 632 Dihedral : 5.486 23.307 592 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.83 % Favored : 90.17 % Rotamer: Outliers : 5.81 % Allowed : 22.67 % Favored : 71.51 % 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: -1.97 (0.38), residues: 468 helix: None (None), residues: 0 sheet: -0.37 (0.32), residues: 232 loop : -2.35 (0.40), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 84 TYR 0.016 0.001 TYR C 60 PHE 0.014 0.002 PHE A 29 TRP 0.009 0.001 TRP B 75 HIS 0.002 0.001 HIS B 87 Details of bonding type rmsd covalent geometry : bond 0.00220 ( 3704) covalent geometry : angle 0.57215 ( 5068) hydrogen bonds : bond 0.02777 ( 184) hydrogen bonds : angle 6.22601 ( 492) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 48 time to evaluate : 0.137 Fit side-chains REVERT: A 131 THR cc_start: 0.8999 (m) cc_final: 0.8672 (p) REVERT: D 62 SER cc_start: 0.7702 (m) cc_final: 0.7500 (p) REVERT: D 82 ASN cc_start: 0.8904 (m110) cc_final: 0.8633 (m110) REVERT: D 107 GLN cc_start: 0.8325 (OUTLIER) cc_final: 0.8064 (tp40) outliers start: 20 outliers final: 14 residues processed: 61 average time/residue: 0.0771 time to fit residues: 5.6783 Evaluate side-chains 60 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 45 time to evaluate : 0.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 118 ASN Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 107 GLN Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 123 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 39 optimal weight: 5.9990 chunk 22 optimal weight: 8.9990 chunk 1 optimal weight: 6.9990 chunk 21 optimal weight: 0.0570 chunk 28 optimal weight: 5.9990 chunk 14 optimal weight: 9.9990 chunk 31 optimal weight: 5.9990 chunk 15 optimal weight: 0.2980 chunk 41 optimal weight: 5.9990 chunk 32 optimal weight: 6.9990 chunk 10 optimal weight: 7.9990 overall best weight: 3.6704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 23 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.169687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.154674 restraints weight = 4191.629| |-----------------------------------------------------------------------------| r_work (start): 0.3798 rms_B_bonded: 1.91 r_work: 0.3685 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3557 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.4282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 3704 Z= 0.275 Angle : 0.753 7.206 5068 Z= 0.401 Chirality : 0.047 0.144 568 Planarity : 0.007 0.062 632 Dihedral : 6.916 33.198 592 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer: Outliers : 6.69 % Allowed : 22.09 % Favored : 71.22 % 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: -2.47 (0.38), residues: 468 helix: None (None), residues: 0 sheet: -1.15 (0.27), residues: 284 loop : -2.27 (0.52), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 84 TYR 0.013 0.002 TYR A 43 PHE 0.017 0.003 PHE C 29 TRP 0.010 0.002 TRP B 75 HIS 0.006 0.003 HIS A 87 Details of bonding type rmsd covalent geometry : bond 0.00656 ( 3704) covalent geometry : angle 0.75268 ( 5068) hydrogen bonds : bond 0.03957 ( 184) hydrogen bonds : angle 6.87857 ( 492) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 49 time to evaluate : 0.123 Fit side-chains REVERT: A 53 ARG cc_start: 0.8660 (ttm170) cc_final: 0.8440 (ttp-170) REVERT: A 131 THR cc_start: 0.9057 (m) cc_final: 0.8713 (p) REVERT: D 62 SER cc_start: 0.8010 (m) cc_final: 0.7715 (p) REVERT: D 82 ASN cc_start: 0.8948 (m110) cc_final: 0.8685 (m110) REVERT: D 107 GLN cc_start: 0.8600 (OUTLIER) cc_final: 0.7965 (tp40) outliers start: 23 outliers final: 21 residues processed: 67 average time/residue: 0.0663 time to fit residues: 5.5427 Evaluate side-chains 71 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 49 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 107 GLN Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 42 THR Chi-restraints excluded: chain D residue 69 SER Chi-restraints excluded: chain D residue 107 GLN Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 123 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 43 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 17 optimal weight: 8.9990 chunk 35 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.4038 r_free = 0.4038 target = 0.178695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.163408 restraints weight = 4081.060| |-----------------------------------------------------------------------------| r_work (start): 0.3883 rms_B_bonded: 1.95 r_work: 0.3761 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3637 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.4341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3704 Z= 0.117 Angle : 0.595 6.895 5068 Z= 0.325 Chirality : 0.041 0.130 568 Planarity : 0.004 0.040 632 Dihedral : 5.703 27.435 592 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.62 % Favored : 90.38 % Rotamer: Outliers : 3.78 % Allowed : 24.13 % Favored : 72.09 % 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: -2.35 (0.38), residues: 468 helix: None (None), residues: 0 sheet: -0.90 (0.28), residues: 276 loop : -2.47 (0.48), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 84 TYR 0.017 0.001 TYR C 60 PHE 0.013 0.002 PHE A 29 TRP 0.010 0.001 TRP B 75 HIS 0.003 0.001 HIS B 87 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 3704) covalent geometry : angle 0.59539 ( 5068) hydrogen bonds : bond 0.02905 ( 184) hydrogen bonds : angle 6.41354 ( 492) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 49 time to evaluate : 0.131 Fit side-chains REVERT: A 131 THR cc_start: 0.9020 (m) cc_final: 0.8661 (p) REVERT: B 62 SER cc_start: 0.7484 (m) cc_final: 0.6970 (p) REVERT: C 53 ARG cc_start: 0.8607 (ttm170) cc_final: 0.8373 (ttp-170) REVERT: D 82 ASN cc_start: 0.8960 (m110) cc_final: 0.8700 (m110) REVERT: D 107 GLN cc_start: 0.8405 (OUTLIER) cc_final: 0.7918 (tp40) outliers start: 13 outliers final: 11 residues processed: 56 average time/residue: 0.0882 time to fit residues: 5.9756 Evaluate side-chains 61 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 49 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 107 GLN Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 107 GLN Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 123 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 39 optimal weight: 6.9990 chunk 31 optimal weight: 5.9990 chunk 6 optimal weight: 9.9990 chunk 33 optimal weight: 8.9990 chunk 16 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 30 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 13 optimal weight: 8.9990 chunk 40 optimal weight: 5.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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 = 0.3978 r_free = 0.3978 target = 0.171417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.156475 restraints weight = 4186.413| |-----------------------------------------------------------------------------| r_work (start): 0.3817 rms_B_bonded: 1.93 r_work: 0.3703 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3577 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.4377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 3704 Z= 0.218 Angle : 0.690 7.007 5068 Z= 0.372 Chirality : 0.045 0.139 568 Planarity : 0.006 0.071 632 Dihedral : 6.493 32.009 592 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer: Outliers : 4.65 % Allowed : 23.55 % Favored : 71.80 % 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: -2.40 (0.38), residues: 468 helix: None (None), residues: 0 sheet: -1.09 (0.27), residues: 288 loop : -2.27 (0.52), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 84 TYR 0.015 0.002 TYR C 60 PHE 0.015 0.003 PHE B 29 TRP 0.011 0.001 TRP A 75 HIS 0.005 0.002 HIS B 87 Details of bonding type rmsd covalent geometry : bond 0.00518 ( 3704) covalent geometry : angle 0.68980 ( 5068) hydrogen bonds : bond 0.03587 ( 184) hydrogen bonds : angle 6.72844 ( 492) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 48 time to evaluate : 0.151 Fit side-chains REVERT: A 131 THR cc_start: 0.9065 (m) cc_final: 0.8736 (p) REVERT: B 62 SER cc_start: 0.7708 (m) cc_final: 0.7264 (t) REVERT: C 53 ARG cc_start: 0.8572 (ttm170) cc_final: 0.8334 (ttp-170) REVERT: D 82 ASN cc_start: 0.8953 (m110) cc_final: 0.8694 (m110) REVERT: D 107 GLN cc_start: 0.8547 (OUTLIER) cc_final: 0.7972 (tp40) outliers start: 16 outliers final: 14 residues processed: 60 average time/residue: 0.0565 time to fit residues: 4.3209 Evaluate side-chains 62 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 47 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 107 GLN Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 107 GLN Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 123 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 2 optimal weight: 4.9990 chunk 41 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 29 optimal weight: 8.9990 chunk 34 optimal weight: 6.9990 chunk 4 optimal weight: 0.9980 chunk 7 optimal weight: 7.9990 chunk 37 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 24 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 = 0.4026 r_free = 0.4026 target = 0.176578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.161672 restraints weight = 4011.323| |-----------------------------------------------------------------------------| r_work (start): 0.3876 rms_B_bonded: 1.90 r_work: 0.3765 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3639 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.4453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3704 Z= 0.123 Angle : 0.588 6.290 5068 Z= 0.322 Chirality : 0.041 0.130 568 Planarity : 0.005 0.051 632 Dihedral : 5.630 28.259 592 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.62 % Favored : 90.38 % Rotamer: Outliers : 4.07 % Allowed : 24.42 % Favored : 71.51 % 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: -1.84 (0.39), residues: 468 helix: None (None), residues: 0 sheet: -0.38 (0.32), residues: 232 loop : -2.14 (0.43), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 84 TYR 0.017 0.002 TYR C 60 PHE 0.013 0.002 PHE A 29 TRP 0.011 0.001 TRP B 75 HIS 0.003 0.001 HIS B 87 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 3704) covalent geometry : angle 0.58841 ( 5068) hydrogen bonds : bond 0.02931 ( 184) hydrogen bonds : angle 6.40260 ( 492) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 945.86 seconds wall clock time: 16 minutes 52.19 seconds (1012.19 seconds total)