Starting phenix.real_space_refine on Thu Sep 10 21:11:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6j6j_0689/09_2026/6j6j_0689.cif Found real_map, /net/cci-nas-00/data/ceres_data/6j6j_0689/09_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_0689/09_2026/6j6j_0689.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6j6j_0689/09_2026/6j6j_0689.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6j6j_0689/09_2026/6j6j_0689.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6j6j_0689/09_2026/6j6j_0689.cif" model { file = "/net/cci-nas-00/data/ceres_data/6j6j_0689/09_2026/6j6j_0689.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6j6j_0689/09_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-2.2.1-6174/lib/python3.11/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: 0.84, per 1000 atoms: 0.23 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: 0.29 Conformation dependent library (CDL) restraints added in 92.0 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: 0.09 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: 0.47 Time building geometry restraints manager: 0.36 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: 1668 13.87 - 27.74: 272 27.74 - 41.60: 52 41.60 - 55.47: 8 55.47 - 69.34: 4 Dihedral angle restraints: 2004 sinusoidal: 684 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 2001 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: 0.110 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: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 4.120 Find NCS groups from input model: 0.020 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:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 5.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6853 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 : 13.735 69.341 1180 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/Z covalent geometry : bond 0.01066 / 0.52 ( 3704) covalent geometry : angle 1.06478 / 0.56 ( 5068) hydrogen bonds : bond 0.10890 / 6.10 ( 184) hydrogen bonds : angle 7.10031 / 4.70 ( 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 : 0.130 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: 0.0801 time to fit residues: 6.4821 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 : 0.092 ------------------------------------------------------------------------------- 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... 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 = 0.3941 r_free = 0.3941 target = 0.169933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.156624 restraints weight = 3820.219| |-----------------------------------------------------------------------------| r_work (start): 0.3796 rms_B_bonded: 1.52 r_work: 0.3734 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3622 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3704 Z= 0.156 Angle : 0.653 7.366 5068 Z= 0.353 Chirality : 0.044 0.136 568 Planarity : 0.004 0.039 632 Dihedral : 6.661 31.297 532 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer: Outliers : 5.52 % Allowed : 16.28 % Favored : 78.20 % 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: -2.43 (0.35), residues: 468 helix: None (None), residues: 0 sheet: -0.28 (0.32), residues: 220 loop : -3.02 (0.35), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 84 TYR 0.013 0.002 TYR D 43 PHE 0.013 0.003 PHE C 29 TRP 0.011 0.001 TRP C 75 HIS 0.002 0.001 HIS D 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 ( 3704) covalent geometry : angle 0.65340 / 0.35 ( 5068) hydrogen bonds : bond 0.03284 / 2.10 ( 184) hydrogen bonds : angle 6.57829 / 4.39 ( 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 : 0.101 Fit side-chains REVERT: B 116 GLU cc_start: 0.6969 (pm20) cc_final: 0.6754 (mp0) REVERT: C 56 LEU cc_start: 0.8006 (OUTLIER) cc_final: 0.7794 (pp) REVERT: D 83 TYR cc_start: 0.7987 (m-10) cc_final: 0.7656 (m-10) outliers start: 19 outliers final: 8 residues processed: 67 average time/residue: 0.0433 time to fit residues: 3.7639 Evaluate side-chains 49 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 40 time to evaluate : 0.112 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain D residue 131 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: 9.9990 chunk 9 optimal weight: 3.9990 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: 2.9990 chunk 32 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.163448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.147756 restraints weight = 3841.034| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 1.82 r_work: 0.3654 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3533 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.3386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3704 Z= 0.181 Angle : 0.689 7.570 5068 Z= 0.373 Chirality : 0.045 0.148 568 Planarity : 0.005 0.043 632 Dihedral : 6.698 31.440 532 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.04 % Favored : 89.96 % Rotamer: Outliers : 4.94 % Allowed : 17.73 % Favored : 77.33 % 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: -2.61 (0.37), residues: 468 helix: None (None), residues: 0 sheet: -1.15 (0.28), residues: 284 loop : -2.55 (0.47), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 84 TYR 0.012 0.002 TYR C 43 PHE 0.015 0.003 PHE C 29 TRP 0.011 0.001 TRP B 75 HIS 0.003 0.002 HIS D 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.18 ( 3704) covalent geometry : angle 0.68934 / 0.37 ( 5068) hydrogen bonds : bond 0.03638 / 2.31 ( 184) hydrogen bonds : angle 6.57650 / 4.40 ( 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 68 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 51 time to evaluate : 0.081 Fit side-chains REVERT: A 131 THR cc_start: 0.9019 (m) cc_final: 0.8671 (p) REVERT: B 85 ASN cc_start: 0.7789 (t0) cc_final: 0.7568 (t0) REVERT: C 49 ASN cc_start: 0.8211 (t0) cc_final: 0.7958 (t0) REVERT: D 56 LEU cc_start: 0.7994 (OUTLIER) cc_final: 0.7651 (pp) outliers start: 17 outliers final: 12 residues processed: 64 average time/residue: 0.0582 time to fit residues: 4.7950 Evaluate side-chains 61 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 48 time to evaluate : 0.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 107 GLN Chi-restraints excluded: chain A residue 123 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 55 VAL Chi-restraints excluded: chain C residue 123 THR 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 Chi-restraints excluded: chain D residue 123 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 23 optimal weight: 0.8980 chunk 25 optimal weight: 0.1980 chunk 9 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 34 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 6 optimal weight: 6.9990 chunk 16 optimal weight: 0.0060 chunk 27 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 overall best weight: 0.8200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 85 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.174097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.158025 restraints weight = 3849.532| |-----------------------------------------------------------------------------| r_work (start): 0.3809 rms_B_bonded: 1.90 r_work: 0.3728 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3607 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.3600 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= 0.103 Angle : 0.578 7.010 5068 Z= 0.314 Chirality : 0.041 0.133 568 Planarity : 0.004 0.045 632 Dihedral : 5.859 27.525 532 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.83 % Favored : 90.17 % Rotamer: Outliers : 4.94 % Allowed : 19.19 % Favored : 75.87 % 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: -2.06 (0.37), residues: 468 helix: None (None), residues: 0 sheet: -0.22 (0.32), residues: 228 loop : -2.63 (0.39), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 84 TYR 0.009 0.001 TYR A 96 PHE 0.012 0.002 PHE A 29 TRP 0.010 0.001 TRP B 75 HIS 0.001 0.001 HIS A 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.10 ( 3704) covalent geometry : angle 0.57816 / 0.31 ( 5068) hydrogen bonds : bond 0.02917 / 1.89 ( 184) hydrogen bonds : angle 6.25923 / 4.19 ( 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 62 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 45 time to evaluate : 0.124 Fit side-chains revert: symmetry clash REVERT: A 83 TYR cc_start: 0.7961 (m-10) cc_final: 0.7726 (m-10) REVERT: A 131 THR cc_start: 0.8996 (m) cc_final: 0.8660 (p) REVERT: C 49 ASN cc_start: 0.8165 (t0) cc_final: 0.7928 (t0) REVERT: D 107 GLN cc_start: 0.8331 (OUTLIER) cc_final: 0.7935 (tp40) outliers start: 17 outliers final: 13 residues processed: 54 average time/residue: 0.0747 time to fit residues: 4.9131 Evaluate side-chains 56 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 42 time to evaluate : 0.129 ------------------------------------------------------------------------------- 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 118 ASN 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 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 107 GLN Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 131 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 27 optimal weight: 10.0000 chunk 38 optimal weight: 0.0020 chunk 0 optimal weight: 8.9990 chunk 22 optimal weight: 8.9990 chunk 11 optimal weight: 8.9990 chunk 37 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 chunk 21 optimal weight: 6.9990 chunk 17 optimal weight: 0.7980 chunk 13 optimal weight: 9.9990 chunk 33 optimal weight: 8.9990 overall best weight: 3.7594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.171786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.157238 restraints weight = 4093.356| |-----------------------------------------------------------------------------| r_work (start): 0.3818 rms_B_bonded: 1.85 r_work: 0.3706 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3580 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.3940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 3704 Z= 0.276 Angle : 0.744 7.297 5068 Z= 0.393 Chirality : 0.047 0.160 568 Planarity : 0.006 0.047 632 Dihedral : 6.895 31.150 532 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.55 % Favored : 91.45 % Rotamer: Outliers : 7.56 % Allowed : 18.60 % Favored : 73.84 % 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: -2.50 (0.38), residues: 468 helix: None (None), residues: 0 sheet: -1.16 (0.27), residues: 284 loop : -2.31 (0.51), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 84 TYR 0.014 0.002 TYR B 43 PHE 0.017 0.003 PHE B 29 TRP 0.010 0.002 TRP B 75 HIS 0.006 0.003 HIS C 127 Details of bonding type rmsd/Z covalent geometry : bond 0.00655 / 0.28 ( 3704) covalent geometry : angle 0.74426 / 0.39 ( 5068) hydrogen bonds : bond 0.04045 / 2.60 ( 184) hydrogen bonds : angle 6.79521 / 4.57 ( 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 82 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 56 time to evaluate : 0.132 Fit side-chains REVERT: A 83 TYR cc_start: 0.7957 (m-10) cc_final: 0.7628 (m-10) REVERT: D 107 GLN cc_start: 0.8596 (OUTLIER) cc_final: 0.7950 (tp40) outliers start: 26 outliers final: 18 residues processed: 73 average time/residue: 0.0522 time to fit residues: 4.8551 Evaluate side-chains 72 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 53 time to evaluate : 0.094 ------------------------------------------------------------------------------- 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 69 SER Chi-restraints excluded: chain A residue 107 GLN 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 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 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 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: 5.9990 chunk 14 optimal weight: 0.6980 chunk 25 optimal weight: 5.9990 chunk 18 optimal weight: 7.9990 chunk 27 optimal weight: 4.9990 chunk 22 optimal weight: 6.9990 chunk 38 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 3 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.173755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.158288 restraints weight = 4093.819| |-----------------------------------------------------------------------------| r_work (start): 0.3817 rms_B_bonded: 1.95 r_work: 0.3706 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3578 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.4020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 3704 Z= 0.198 Angle : 0.665 7.388 5068 Z= 0.355 Chirality : 0.044 0.139 568 Planarity : 0.005 0.045 632 Dihedral : 6.519 30.956 532 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.83 % Favored : 90.17 % Rotamer: Outliers : 7.85 % Allowed : 18.90 % Favored : 73.26 % 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: -2.43 (0.38), residues: 468 helix: None (None), residues: 0 sheet: -1.13 (0.27), residues: 284 loop : -2.25 (0.51), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 84 TYR 0.012 0.002 TYR B 43 PHE 0.015 0.003 PHE B 29 TRP 0.010 0.001 TRP A 75 HIS 0.004 0.002 HIS A 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.20 ( 3704) covalent geometry : angle 0.66549 / 0.36 ( 5068) hydrogen bonds : bond 0.03505 / 2.26 ( 184) hydrogen bonds : angle 6.68008 / 4.50 ( 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 81 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 54 time to evaluate : 0.130 Fit side-chains REVERT: A 49 ASN cc_start: 0.7539 (t0) cc_final: 0.7332 (t0) REVERT: D 62 SER cc_start: 0.7930 (m) cc_final: 0.7509 (p) REVERT: D 107 GLN cc_start: 0.8526 (OUTLIER) cc_final: 0.8000 (tp40) outliers start: 27 outliers final: 24 residues processed: 71 average time/residue: 0.0507 time to fit residues: 4.5835 Evaluate side-chains 78 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 53 time to evaluate : 0.123 ------------------------------------------------------------------------------- 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 107 GLN Chi-restraints excluded: chain A residue 118 ASN 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 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 118 ASN 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 17 optimal weight: 7.9990 chunk 9 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 42 optimal weight: 4.9990 chunk 39 optimal weight: 10.0000 chunk 34 optimal weight: 5.9990 chunk 30 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 40 optimal weight: 0.9990 chunk 25 optimal weight: 9.9990 chunk 27 optimal weight: 0.4980 overall best weight: 2.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 23 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.172104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.156749 restraints weight = 4207.403| |-----------------------------------------------------------------------------| r_work (start): 0.3809 rms_B_bonded: 1.96 r_work: 0.3689 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3560 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.4140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 3704 Z= 0.223 Angle : 0.686 7.154 5068 Z= 0.365 Chirality : 0.045 0.149 568 Planarity : 0.005 0.044 632 Dihedral : 6.672 30.800 532 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.62 % Favored : 90.38 % Rotamer: Outliers : 7.85 % Allowed : 19.77 % Favored : 72.38 % 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: -2.50 (0.38), residues: 468 helix: None (None), residues: 0 sheet: -1.18 (0.27), residues: 284 loop : -2.27 (0.52), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 84 TYR 0.013 0.002 TYR B 43 PHE 0.016 0.003 PHE B 29 TRP 0.011 0.001 TRP D 75 HIS 0.004 0.002 HIS A 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00532 / 0.22 ( 3704) covalent geometry : angle 0.68602 / 0.37 ( 5068) hydrogen bonds : bond 0.03677 / 2.37 ( 184) hydrogen bonds : angle 6.76125 / 4.55 ( 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 78 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 51 time to evaluate : 0.081 Fit side-chains REVERT: D 107 GLN cc_start: 0.8548 (OUTLIER) cc_final: 0.8012 (tp40) outliers start: 27 outliers final: 24 residues processed: 68 average time/residue: 0.0455 time to fit residues: 4.0088 Evaluate side-chains 75 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 50 time to evaluate : 0.085 ------------------------------------------------------------------------------- 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 107 GLN 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 39 optimal weight: 3.9990 chunk 22 optimal weight: 7.9990 chunk 1 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 14 optimal weight: 8.9990 chunk 31 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 81 ASN B 23 ASN D 23 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.170728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.155390 restraints weight = 4160.348| |-----------------------------------------------------------------------------| r_work (start): 0.3812 rms_B_bonded: 1.96 r_work: 0.3692 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3561 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.4233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 3704 Z= 0.241 Angle : 0.692 6.720 5068 Z= 0.369 Chirality : 0.046 0.147 568 Planarity : 0.006 0.046 632 Dihedral : 6.686 30.475 532 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.55 % Favored : 91.45 % Rotamer: Outliers : 7.85 % Allowed : 20.93 % 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: -2.57 (0.38), residues: 468 helix: None (None), residues: 0 sheet: -1.22 (0.27), residues: 284 loop : -2.33 (0.52), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 84 TYR 0.013 0.002 TYR B 43 PHE 0.016 0.003 PHE B 29 TRP 0.010 0.001 TRP A 75 HIS 0.005 0.002 HIS A 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00577 / 0.24 ( 3704) covalent geometry : angle 0.69223 / 0.37 ( 5068) hydrogen bonds : bond 0.03763 / 2.42 ( 184) hydrogen bonds : angle 6.82527 / 4.59 ( 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 76 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 49 time to evaluate : 0.124 Fit side-chains REVERT: D 53 ARG cc_start: 0.8674 (ttm170) cc_final: 0.8397 (ttp-170) REVERT: D 107 GLN cc_start: 0.8566 (OUTLIER) cc_final: 0.8015 (tp40) outliers start: 27 outliers final: 25 residues processed: 66 average time/residue: 0.0501 time to fit residues: 4.2230 Evaluate side-chains 75 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 49 time to evaluate : 0.101 ------------------------------------------------------------------------------- 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 107 GLN 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 118 ASN 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 43 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 28 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 35 optimal weight: 6.9990 chunk 31 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.178889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.163307 restraints weight = 4057.821| |-----------------------------------------------------------------------------| r_work (start): 0.3871 rms_B_bonded: 1.98 r_work: 0.3753 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3621 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 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 : 0.002 0.037 3704 Z= 0.106 Angle : 0.551 6.354 5068 Z= 0.301 Chirality : 0.041 0.131 568 Planarity : 0.004 0.041 632 Dihedral : 5.733 27.355 532 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.97 % Favored : 91.03 % Rotamer: Outliers : 5.23 % Allowed : 22.97 % 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: -1.94 (0.38), residues: 468 helix: None (None), residues: 0 sheet: -0.26 (0.32), residues: 224 loop : -2.38 (0.41), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 103 TYR 0.011 0.001 TYR A 96 PHE 0.015 0.002 PHE A 29 TRP 0.010 0.001 TRP B 75 HIS 0.002 0.001 HIS A 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 ( 3704) covalent geometry : angle 0.55087 / 0.30 ( 5068) hydrogen bonds : bond 0.02858 / 1.85 ( 184) hydrogen bonds : angle 6.36810 / 4.29 ( 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 70 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 52 time to evaluate : 0.123 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 SER cc_start: 0.7633 (m) cc_final: 0.7285 (p) REVERT: A 131 THR cc_start: 0.9060 (m) cc_final: 0.8762 (p) REVERT: B 62 SER cc_start: 0.7520 (m) cc_final: 0.7273 (p) REVERT: C 107 GLN cc_start: 0.8341 (OUTLIER) cc_final: 0.8064 (mt0) REVERT: D 53 ARG cc_start: 0.8652 (ttm170) cc_final: 0.8388 (ttp-170) REVERT: D 107 GLN cc_start: 0.8388 (OUTLIER) cc_final: 0.8012 (tp40) outliers start: 18 outliers final: 16 residues processed: 62 average time/residue: 0.0721 time to fit residues: 5.4437 Evaluate side-chains 67 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 49 time to evaluate : 0.130 ------------------------------------------------------------------------------- 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 107 GLN 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 118 ASN Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 107 GLN Chi-restraints excluded: chain C residue 118 ASN Chi-restraints excluded: chain D residue 18 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 131 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 39 optimal weight: 8.9990 chunk 31 optimal weight: 5.9990 chunk 6 optimal weight: 6.9990 chunk 33 optimal weight: 8.9990 chunk 16 optimal weight: 0.0030 chunk 0 optimal weight: 8.9990 chunk 30 optimal weight: 0.0970 chunk 41 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 13 optimal weight: 8.9990 chunk 40 optimal weight: 5.9990 overall best weight: 1.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.174891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.159915 restraints weight = 4136.833| |-----------------------------------------------------------------------------| r_work (start): 0.3855 rms_B_bonded: 1.95 r_work: 0.3727 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3594 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.4332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3704 Z= 0.144 Angle : 0.578 5.583 5068 Z= 0.315 Chirality : 0.042 0.129 568 Planarity : 0.004 0.036 632 Dihedral : 5.862 30.431 532 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.55 % Favored : 91.45 % Rotamer: Outliers : 6.10 % Allowed : 22.97 % Favored : 70.93 % 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: -2.26 (0.38), residues: 468 helix: None (None), residues: 0 sheet: -0.76 (0.28), residues: 268 loop : -2.52 (0.48), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 84 TYR 0.009 0.002 TYR A 96 PHE 0.013 0.002 PHE A 29 TRP 0.011 0.001 TRP C 75 HIS 0.003 0.001 HIS A 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.14 ( 3704) covalent geometry : angle 0.57821 / 0.31 ( 5068) hydrogen bonds : bond 0.03156 / 2.04 ( 184) hydrogen bonds : angle 6.45563 / 4.35 ( 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 72 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 51 time to evaluate : 0.131 Fit side-chains revert: symmetry clash REVERT: A 131 THR cc_start: 0.9122 (m) cc_final: 0.8810 (p) REVERT: C 62 SER cc_start: 0.7907 (m) cc_final: 0.7444 (p) REVERT: D 53 ARG cc_start: 0.8594 (ttm170) cc_final: 0.8340 (ttp-170) REVERT: D 107 GLN cc_start: 0.8466 (OUTLIER) cc_final: 0.7896 (tp40) outliers start: 21 outliers final: 20 residues processed: 62 average time/residue: 0.0695 time to fit residues: 5.2656 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 : 0.129 ------------------------------------------------------------------------------- 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 107 GLN 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 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 118 ASN 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 Chi-restraints excluded: chain D residue 131 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 2 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 chunk 14 optimal weight: 6.9990 chunk 29 optimal weight: 9.9990 chunk 34 optimal weight: 6.9990 chunk 4 optimal weight: 5.9990 chunk 7 optimal weight: 10.0000 chunk 37 optimal weight: 0.9990 chunk 39 optimal weight: 8.9990 chunk 24 optimal weight: 6.9990 chunk 17 optimal weight: 0.7980 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.169346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.154612 restraints weight = 4169.168| |-----------------------------------------------------------------------------| r_work (start): 0.3809 rms_B_bonded: 1.89 r_work: 0.3689 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3558 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.4375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 3704 Z= 0.264 Angle : 0.697 6.742 5068 Z= 0.372 Chirality : 0.046 0.146 568 Planarity : 0.006 0.046 632 Dihedral : 6.519 30.429 532 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.55 % Favored : 91.45 % 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: -2.51 (0.38), residues: 468 helix: None (None), residues: 0 sheet: -1.14 (0.27), residues: 284 loop : -2.36 (0.51), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 84 TYR 0.014 0.002 TYR B 43 PHE 0.016 0.003 PHE B 29 TRP 0.010 0.002 TRP D 75 HIS 0.005 0.003 HIS A 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00630 / 0.26 ( 3704) covalent geometry : angle 0.69695 / 0.37 ( 5068) hydrogen bonds : bond 0.03848 / 2.48 ( 184) hydrogen bonds : angle 6.81864 / 4.59 ( 492) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 878.58 seconds wall clock time: 15 minutes 46.96 seconds (946.96 seconds total)