Starting phenix.real_space_refine on Wed Aug 5 19:51:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k43_62042/08_2026/9k43_62042.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k43_62042/08_2026/9k43_62042.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9k43_62042/08_2026/9k43_62042.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k43_62042/08_2026/9k43_62042.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9k43_62042/08_2026/9k43_62042.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k43_62042/08_2026/9k43_62042.map" } resolution = 2.87 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= 0.002 sd= 0.052 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 289 5.49 5 S 10 5.16 5 C 6542 2.51 5 N 2197 2.21 5 O 2776 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11814 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 783 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "B" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 644 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "C" Number of atoms: 778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 778 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 3, 'TRANS': 99} Chain: "D" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 731 Classifications: {'peptide': 93} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 89} Chain: "E" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 783 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "F" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 644 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 778 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 3, 'TRANS': 99} Chain: "H" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 731 Classifications: {'peptide': 93} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 89} Chain: "I" Number of atoms: 2957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2957 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2985 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Time building chain proxies: 1.97, per 1000 atoms: 0.17 Number of scatterers: 11814 At special positions: 0 Unit cell: (118.992, 97.552, 114.704, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 10 16.00 P 289 15.00 O 2776 8.00 N 2197 7.00 C 6542 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: 0.65 Conformation dependent library (CDL) restraints added in 202.2 milliseconds 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1388 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 10 sheets defined 75.8% alpha, 2.7% beta 143 base pairs and 244 stacking pairs defined. Time for finding SS restraints: 1.67 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 removed outlier: 3.601A pdb=" N LYS A 56 " --> pdb=" O ARG A 52 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER A 57 " --> pdb=" O LYS A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.944A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.508A pdb=" N GLN B 27 " --> pdb=" O ASP B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 27 through 33 Processing helix chain 'C' and resid 37 through 49 Processing helix chain 'C' and resid 56 through 85 Processing helix chain 'C' and resid 91 through 102 removed outlier: 3.572A pdb=" N ASP C 102 " --> pdb=" O ALA C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 109 Processing helix chain 'C' and resid 123 through 127 removed outlier: 3.560A pdb=" N ILE C 127 " --> pdb=" O LYS C 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 60 through 72 Processing helix chain 'D' and resid 78 through 107 Processing helix chain 'D' and resid 113 through 125 Processing helix chain 'D' and resid 126 through 146 Processing helix chain 'E' and resid 44 through 57 removed outlier: 3.541A pdb=" N LYS E 56 " --> pdb=" O ARG E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 77 removed outlier: 3.927A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 24 through 29 removed outlier: 3.661A pdb=" N GLN F 27 " --> pdb=" O ASP F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.647A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 27 through 33 Processing helix chain 'G' and resid 37 through 49 Processing helix chain 'G' and resid 56 through 85 Processing helix chain 'G' and resid 91 through 102 removed outlier: 3.573A pdb=" N ASP G 102 " --> pdb=" O ALA G 98 " (cutoff:3.500A) Processing helix chain 'G' and resid 102 through 109 Processing helix chain 'G' and resid 123 through 127 removed outlier: 3.560A pdb=" N ILE G 127 " --> pdb=" O LYS G 124 " (cutoff:3.500A) Processing helix chain 'H' and resid 60 through 72 Processing helix chain 'H' and resid 78 through 107 Processing helix chain 'H' and resid 113 through 125 Processing helix chain 'H' and resid 126 through 147 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.092A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 54 through 55 removed outlier: 7.031A pdb=" N ARG C 54 " --> pdb=" O ILE D 112 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 89 through 90 Processing sheet with id=AA6, first strand: chain 'C' and resid 112 through 113 removed outlier: 6.451A pdb=" N THR C 112 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.269A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 54 through 55 removed outlier: 6.753A pdb=" N ARG G 54 " --> pdb=" O ILE H 112 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 89 through 90 417 hydrogen bonds defined for protein. 1233 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 368 hydrogen bonds 736 hydrogen bond angles 0 basepair planarities 143 basepair parallelities 244 stacking parallelities Total time for adding SS restraints: 1.83 Time building geometry restraints manager: 0.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2090 1.33 - 1.45: 4235 1.45 - 1.57: 5699 1.57 - 1.69: 577 1.69 - 1.81: 18 Bond restraints: 12619 Sorted by residual: bond pdb=" C1' DC J -72 " pdb=" N1 DC J -72 " ideal model delta sigma weight residual 1.468 1.550 -0.082 1.40e-02 5.10e+03 3.43e+01 bond pdb=" C1' DC I 70 " pdb=" N1 DC I 70 " ideal model delta sigma weight residual 1.468 1.548 -0.080 1.40e-02 5.10e+03 3.23e+01 bond pdb=" C1' DC J 70 " pdb=" N1 DC J 70 " ideal model delta sigma weight residual 1.468 1.547 -0.079 1.40e-02 5.10e+03 3.15e+01 bond pdb=" O3' DG J 23 " pdb=" P DC J 24 " ideal model delta sigma weight residual 1.607 1.664 -0.057 1.20e-02 6.94e+03 2.27e+01 bond pdb=" O3' DT J 15 " pdb=" P DA J 16 " ideal model delta sigma weight residual 1.607 1.662 -0.055 1.20e-02 6.94e+03 2.14e+01 ... (remaining 12614 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.47: 17047 1.47 - 2.95: 1144 2.95 - 4.42: 82 4.42 - 5.89: 8 5.89 - 7.37: 4 Bond angle restraints: 18285 Sorted by residual: angle pdb=" N ASN F 25 " pdb=" CA ASN F 25 " pdb=" C ASN F 25 " ideal model delta sigma weight residual 113.15 107.42 5.73 1.19e+00 7.06e-01 2.32e+01 angle pdb=" N3 DT I 60 " pdb=" C4 DT I 60 " pdb=" O4 DT I 60 " ideal model delta sigma weight residual 119.90 122.58 -2.68 6.00e-01 2.78e+00 2.00e+01 angle pdb=" N3 DT J 9 " pdb=" C4 DT J 9 " pdb=" O4 DT J 9 " ideal model delta sigma weight residual 119.90 122.56 -2.66 6.00e-01 2.78e+00 1.97e+01 angle pdb=" N3 DT I -39 " pdb=" C4 DT I -39 " pdb=" O4 DT I -39 " ideal model delta sigma weight residual 119.90 122.52 -2.62 6.00e-01 2.78e+00 1.90e+01 angle pdb=" N3 DT I 43 " pdb=" C4 DT I 43 " pdb=" O4 DT I 43 " ideal model delta sigma weight residual 119.90 122.50 -2.60 6.00e-01 2.78e+00 1.88e+01 ... (remaining 18280 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.37: 4190 17.37 - 34.75: 1117 34.75 - 52.12: 1125 52.12 - 69.49: 375 69.49 - 86.87: 18 Dihedral angle restraints: 6825 sinusoidal: 4679 harmonic: 2146 Sorted by residual: dihedral pdb=" CA ASN F 64 " pdb=" CB ASN F 64 " pdb=" CG ASN F 64 " pdb=" OD1 ASN F 64 " ideal model delta sinusoidal sigma weight residual -90.00 -163.56 73.56 2 2.00e+01 2.50e-03 1.10e+01 dihedral pdb=" CG ARG F 39 " pdb=" CD ARG F 39 " pdb=" NE ARG F 39 " pdb=" CZ ARG F 39 " ideal model delta sinusoidal sigma weight residual 90.00 133.84 -43.84 2 1.50e+01 4.44e-03 1.02e+01 dihedral pdb=" CG ARG C 54 " pdb=" CD ARG C 54 " pdb=" NE ARG C 54 " pdb=" CZ ARG C 54 " ideal model delta sinusoidal sigma weight residual -180.00 -136.42 -43.58 2 1.50e+01 4.44e-03 1.01e+01 ... (remaining 6822 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1339 0.037 - 0.075: 531 0.075 - 0.112: 182 0.112 - 0.149: 38 0.149 - 0.186: 7 Chirality restraints: 2097 Sorted by residual: chirality pdb=" P DA J -71 " pdb=" OP1 DA J -71 " pdb=" OP2 DA J -71 " pdb=" O5' DA J -71 " both_signs ideal model delta sigma weight residual True 2.34 -2.52 -0.19 2.00e-01 2.50e+01 8.67e-01 chirality pdb=" C3' DG J 4 " pdb=" C4' DG J 4 " pdb=" O3' DG J 4 " pdb=" C2' DG J 4 " both_signs ideal model delta sigma weight residual False -2.73 -2.91 0.18 2.00e-01 2.50e+01 7.74e-01 chirality pdb=" C1' DC J 70 " pdb=" O4' DC J 70 " pdb=" C2' DC J 70 " pdb=" N1 DC J 70 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.38e-01 ... (remaining 2094 not shown) Planarity restraints: 1296 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU D 125 " -0.026 5.00e-02 4.00e+02 3.93e-02 2.48e+00 pdb=" N PRO D 126 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO D 126 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 126 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG E 42 " 0.025 5.00e-02 4.00e+02 3.78e-02 2.29e+00 pdb=" N PRO E 43 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO E 43 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO E 43 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 31 " 0.024 5.00e-02 4.00e+02 3.60e-02 2.08e+00 pdb=" N PRO B 32 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO B 32 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 32 " 0.020 5.00e-02 4.00e+02 ... (remaining 1293 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1806 2.77 - 3.30: 10340 3.30 - 3.83: 23767 3.83 - 4.37: 27537 4.37 - 4.90: 39377 Nonbonded interactions: 102827 Sorted by model distance: nonbonded pdb=" NZ LYS B 59 " pdb=" OE2 GLU B 63 " model vdw 2.234 3.120 nonbonded pdb=" NH2 ARG C 43 " pdb=" OE1 GLU D 58 " model vdw 2.298 3.120 nonbonded pdb=" NH2 ARG G 43 " pdb=" OE1 GLU H 58 " model vdw 2.322 3.120 nonbonded pdb=" OD2 ASP A 106 " pdb=" NH1 ARG A 131 " model vdw 2.325 3.120 nonbonded pdb=" OD2 ASP E 106 " pdb=" NH1 ARG E 131 " model vdw 2.328 3.120 ... (remaining 102822 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 10.290 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 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:7.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 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 : 0.006 0.082 12619 Z= 0.522 Angle : 0.744 7.369 18285 Z= 0.655 Chirality : 0.045 0.186 2097 Planarity : 0.004 0.039 1296 Dihedral : 28.505 86.868 5437 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 0.80 % Allowed : 24.60 % Favored : 74.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.81 (0.30), residues: 728 helix: 2.61 (0.22), residues: 544 sheet: None (None), residues: 0 loop : -0.51 (0.40), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 48 TYR 0.009 0.001 TYR B 51 PHE 0.007 0.001 PHE B 100 HIS 0.007 0.001 HIS C 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00591 / 0.52 (12619) covalent geometry : angle 0.74369 / 0.65 (18285) hydrogen bonds : bond 0.10775 / 6.98 ( 785) hydrogen bonds : angle 4.37290 / 3.16 ( 1969) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 177 time to evaluate : 0.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 88 TYR cc_start: 0.8627 (m-10) cc_final: 0.8137 (m-10) REVERT: D 106 TYR cc_start: 0.8802 (m-10) cc_final: 0.8577 (m-10) REVERT: H 85 MET cc_start: 0.8612 (mmm) cc_final: 0.8392 (tpp) outliers start: 5 outliers final: 2 residues processed: 181 average time/residue: 0.6048 time to fit residues: 116.8246 Evaluate side-chains 130 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 128 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain F residue 96 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 20.0000 chunk 53 optimal weight: 0.0030 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 0.0670 chunk 45 optimal weight: 0.9980 overall best weight: 0.6130 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 ASN B 75 HIS C 123 HIS E 39 HIS E 68 GLN F 64 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.054086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.039395 restraints weight = 56869.540| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 2.11 r_work: 0.2794 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 moved from start: 0.1219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 12619 Z= 0.150 Angle : 0.650 7.864 18285 Z= 0.390 Chirality : 0.045 0.246 2097 Planarity : 0.004 0.037 1296 Dihedral : 30.766 86.301 3979 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 3.22 % Allowed : 27.65 % Favored : 69.13 % 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: 2.96 (0.30), residues: 728 helix: 2.65 (0.21), residues: 556 sheet: None (None), residues: 0 loop : -0.45 (0.41), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 23 TYR 0.014 0.002 TYR B 51 PHE 0.020 0.001 PHE H 88 HIS 0.005 0.001 HIS D 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.15 (12619) covalent geometry : angle 0.65042 / 0.39 (18285) hydrogen bonds : bond 0.04801 / 3.20 ( 785) hydrogen bonds : angle 3.06373 / 2.29 ( 1969) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 141 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 88 TYR cc_start: 0.9238 (m-10) cc_final: 0.8482 (m-10) REVERT: C 102 ASP cc_start: 0.8763 (t0) cc_final: 0.8156 (t0) REVERT: D 106 TYR cc_start: 0.9005 (m-10) cc_final: 0.8482 (m-10) REVERT: D 136 GLU cc_start: 0.9274 (OUTLIER) cc_final: 0.9005 (tp30) REVERT: G 102 ASP cc_start: 0.8822 (t0) cc_final: 0.7928 (t0) REVERT: G 110 LYS cc_start: 0.9035 (mtmm) cc_final: 0.8661 (mmmm) REVERT: H 85 MET cc_start: 0.9502 (mmm) cc_final: 0.9175 (tpp) outliers start: 20 outliers final: 8 residues processed: 154 average time/residue: 0.5532 time to fit residues: 91.5460 Evaluate side-chains 137 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 128 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain D residue 136 GLU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 66 ILE Chi-restraints excluded: chain G residue 82 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 16 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 chunk 73 optimal weight: 30.0000 chunk 13 optimal weight: 0.9990 chunk 28 optimal weight: 0.0980 chunk 52 optimal weight: 4.9990 chunk 97 optimal weight: 20.0000 chunk 63 optimal weight: 5.9990 chunk 38 optimal weight: 6.9990 chunk 83 optimal weight: 20.0000 chunk 67 optimal weight: 6.9990 overall best weight: 3.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 121 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.051677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.037024 restraints weight = 58159.775| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 2.11 r_work: 0.2712 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8844 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 12619 Z= 0.242 Angle : 0.699 10.375 18285 Z= 0.402 Chirality : 0.045 0.225 2097 Planarity : 0.004 0.034 1296 Dihedral : 31.198 88.060 3979 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 2.89 % Allowed : 27.65 % Favored : 69.45 % 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: 3.06 (0.31), residues: 728 helix: 2.73 (0.21), residues: 558 sheet: None (None), residues: 0 loop : -0.47 (0.43), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 40 TYR 0.023 0.002 TYR H 106 PHE 0.009 0.001 PHE D 88 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00479 / 0.24 (12619) covalent geometry : angle 0.69912 / 0.40 (18285) hydrogen bonds : bond 0.05546 / 3.72 ( 785) hydrogen bonds : angle 3.14155 / 2.37 ( 1969) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 134 time to evaluate : 0.187 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 68 GLU cc_start: 0.9074 (OUTLIER) cc_final: 0.8862 (tt0) REVERT: C 102 ASP cc_start: 0.8440 (t0) cc_final: 0.7921 (t0) REVERT: C 103 GLU cc_start: 0.8662 (tp30) cc_final: 0.8195 (tp30) REVERT: C 104 GLU cc_start: 0.8459 (mp0) cc_final: 0.8216 (mp0) REVERT: D 106 TYR cc_start: 0.9073 (m-10) cc_final: 0.8574 (m-10) REVERT: D 136 GLU cc_start: 0.9296 (OUTLIER) cc_final: 0.8991 (tp30) REVERT: E 120 MET cc_start: 0.8772 (mmm) cc_final: 0.8241 (mtm) REVERT: F 88 TYR cc_start: 0.9299 (m-10) cc_final: 0.8881 (m-10) REVERT: G 103 GLU cc_start: 0.8712 (tp30) cc_final: 0.8272 (tp30) REVERT: G 106 ASP cc_start: 0.9418 (t0) cc_final: 0.9168 (t0) REVERT: G 110 LYS cc_start: 0.9115 (mtmm) cc_final: 0.8719 (mmmm) REVERT: H 136 GLU cc_start: 0.9261 (OUTLIER) cc_final: 0.8995 (tp30) outliers start: 18 outliers final: 8 residues processed: 142 average time/residue: 0.5403 time to fit residues: 82.4971 Evaluate side-chains 132 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 121 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 68 GLU Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain D residue 136 GLU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 66 ILE Chi-restraints excluded: chain G residue 82 SER Chi-restraints excluded: chain H residue 136 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 77 optimal weight: 20.0000 chunk 57 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 chunk 89 optimal weight: 20.0000 chunk 29 optimal weight: 1.9990 chunk 73 optimal weight: 30.0000 chunk 36 optimal weight: 10.0000 chunk 72 optimal weight: 30.0000 chunk 8 optimal weight: 2.9990 chunk 87 optimal weight: 30.0000 overall best weight: 1.5788 ------------------------------------------------------------------------------- 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 = 0.3432 r_free = 0.3432 target = 0.051834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.037004 restraints weight = 57976.065| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 2.14 r_work: 0.2727 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8827 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12619 Z= 0.153 Angle : 0.627 7.463 18285 Z= 0.370 Chirality : 0.043 0.229 2097 Planarity : 0.004 0.034 1296 Dihedral : 31.206 89.142 3978 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 3.05 % Allowed : 28.94 % Favored : 68.01 % 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: 3.23 (0.31), residues: 728 helix: 2.88 (0.22), residues: 556 sheet: None (None), residues: 0 loop : -0.48 (0.42), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 40 TYR 0.015 0.002 TYR D 63 PHE 0.019 0.001 PHE H 88 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.15 (12619) covalent geometry : angle 0.62652 / 0.37 (18285) hydrogen bonds : bond 0.04257 / 2.84 ( 785) hydrogen bonds : angle 2.92165 / 2.20 ( 1969) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 133 time to evaluate : 0.211 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 44 LYS cc_start: 0.9233 (ttpt) cc_final: 0.8881 (ttmm) REVERT: C 68 GLU cc_start: 0.9051 (OUTLIER) cc_final: 0.8843 (tt0) REVERT: C 104 GLU cc_start: 0.8336 (mp0) cc_final: 0.7659 (mp0) REVERT: D 56 ASN cc_start: 0.9414 (m-40) cc_final: 0.9179 (m-40) REVERT: D 106 TYR cc_start: 0.8961 (m-10) cc_final: 0.8521 (m-10) REVERT: D 136 GLU cc_start: 0.9299 (OUTLIER) cc_final: 0.9008 (tp30) REVERT: E 56 LYS cc_start: 0.9319 (ttpp) cc_final: 0.9044 (tmmt) REVERT: F 85 ASP cc_start: 0.9097 (m-30) cc_final: 0.8897 (m-30) REVERT: G 30 SER cc_start: 0.9738 (OUTLIER) cc_final: 0.9478 (p) REVERT: G 102 ASP cc_start: 0.8714 (t0) cc_final: 0.7916 (t0) REVERT: G 110 LYS cc_start: 0.9138 (mtmm) cc_final: 0.8698 (mmmm) REVERT: H 136 GLU cc_start: 0.9263 (OUTLIER) cc_final: 0.8966 (tp30) outliers start: 19 outliers final: 9 residues processed: 146 average time/residue: 0.5044 time to fit residues: 79.0920 Evaluate side-chains 139 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 126 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain C residue 68 GLU Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain D residue 136 GLU Chi-restraints excluded: chain E residue 53 LYS Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 66 ILE Chi-restraints excluded: chain G residue 82 SER Chi-restraints excluded: chain H residue 101 SER Chi-restraints excluded: chain H residue 136 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 79 optimal weight: 20.0000 chunk 88 optimal weight: 20.0000 chunk 11 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 85 optimal weight: 30.0000 chunk 46 optimal weight: 1.9990 chunk 14 optimal weight: 6.9990 chunk 56 optimal weight: 4.9990 chunk 95 optimal weight: 20.0000 chunk 50 optimal weight: 2.9990 chunk 26 optimal weight: 9.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 27 GLN E 68 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.050081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.035108 restraints weight = 57864.879| |-----------------------------------------------------------------------------| r_work (start): 0.2830 rms_B_bonded: 2.22 r_work: 0.2663 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8906 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 12619 Z= 0.261 Angle : 0.723 8.055 18285 Z= 0.405 Chirality : 0.046 0.225 2097 Planarity : 0.004 0.032 1296 Dihedral : 31.480 89.391 3978 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 4.02 % Allowed : 27.97 % Favored : 68.01 % 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: 3.11 (0.31), residues: 728 helix: 2.80 (0.22), residues: 556 sheet: None (None), residues: 0 loop : -0.55 (0.44), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 40 TYR 0.030 0.002 TYR H 106 PHE 0.021 0.002 PHE D 88 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00523 / 0.26 (12619) covalent geometry : angle 0.72327 / 0.40 (18285) hydrogen bonds : bond 0.06153 / 4.14 ( 785) hydrogen bonds : angle 3.21288 / 2.43 ( 1969) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 122 time to evaluate : 0.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 68 GLU cc_start: 0.9096 (OUTLIER) cc_final: 0.8879 (tt0) REVERT: D 136 GLU cc_start: 0.9357 (OUTLIER) cc_final: 0.9026 (tp30) REVERT: E 56 LYS cc_start: 0.9337 (ttpp) cc_final: 0.9071 (tmmt) REVERT: E 120 MET cc_start: 0.8892 (mmm) cc_final: 0.8424 (mtm) REVERT: G 30 SER cc_start: 0.9737 (OUTLIER) cc_final: 0.9442 (p) REVERT: G 102 ASP cc_start: 0.8522 (t0) cc_final: 0.7936 (t0) REVERT: G 106 ASP cc_start: 0.9408 (t0) cc_final: 0.9165 (t0) REVERT: G 110 LYS cc_start: 0.9232 (mtmm) cc_final: 0.8841 (mmmm) REVERT: H 136 GLU cc_start: 0.9324 (OUTLIER) cc_final: 0.9056 (tp30) outliers start: 25 outliers final: 12 residues processed: 138 average time/residue: 0.5095 time to fit residues: 75.4571 Evaluate side-chains 134 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 118 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 68 GLU Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain D residue 136 GLU Chi-restraints excluded: chain E residue 53 LYS Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 66 ILE Chi-restraints excluded: chain G residue 82 SER Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 136 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 33 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 chunk 41 optimal weight: 0.7980 chunk 86 optimal weight: 30.0000 chunk 56 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 50 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 27 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.050747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.036191 restraints weight = 58099.881| |-----------------------------------------------------------------------------| r_work (start): 0.2867 rms_B_bonded: 2.15 r_work: 0.2704 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8858 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 12619 Z= 0.136 Angle : 0.639 8.618 18285 Z= 0.372 Chirality : 0.043 0.235 2097 Planarity : 0.004 0.036 1296 Dihedral : 31.308 88.406 3978 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.22 % Allowed : 29.58 % Favored : 67.20 % 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: 3.24 (0.31), residues: 728 helix: 2.89 (0.22), residues: 556 sheet: None (None), residues: 0 loop : -0.48 (0.43), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 95 TYR 0.019 0.002 TYR H 106 PHE 0.007 0.001 PHE B 61 HIS 0.002 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.14 (12619) covalent geometry : angle 0.63852 / 0.37 (18285) hydrogen bonds : bond 0.04130 / 2.77 ( 785) hydrogen bonds : angle 2.86586 / 2.16 ( 1969) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 137 time to evaluate : 0.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 84 MET cc_start: 0.9139 (mmm) cc_final: 0.8730 (mmm) REVERT: C 68 GLU cc_start: 0.9038 (OUTLIER) cc_final: 0.8836 (tt0) REVERT: D 56 ASN cc_start: 0.9459 (m-40) cc_final: 0.9206 (m-40) REVERT: D 91 ASP cc_start: 0.9265 (t0) cc_final: 0.8905 (t0) REVERT: D 128 GLU cc_start: 0.8529 (pm20) cc_final: 0.8304 (pm20) REVERT: D 136 GLU cc_start: 0.9285 (OUTLIER) cc_final: 0.8936 (tp30) REVERT: E 40 ARG cc_start: 0.8543 (OUTLIER) cc_final: 0.8145 (tpt90) REVERT: E 56 LYS cc_start: 0.9306 (ttpp) cc_final: 0.9021 (tmmt) REVERT: G 30 SER cc_start: 0.9725 (OUTLIER) cc_final: 0.9472 (p) REVERT: G 102 ASP cc_start: 0.8301 (t0) cc_final: 0.7789 (t0) REVERT: G 106 ASP cc_start: 0.9374 (t0) cc_final: 0.9130 (t0) REVERT: G 110 LYS cc_start: 0.9158 (mtmm) cc_final: 0.8776 (mmmm) REVERT: H 136 GLU cc_start: 0.9300 (OUTLIER) cc_final: 0.8970 (tp30) outliers start: 20 outliers final: 8 residues processed: 148 average time/residue: 0.5505 time to fit residues: 87.3208 Evaluate side-chains 143 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 130 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 68 GLU Chi-restraints excluded: chain D residue 136 GLU Chi-restraints excluded: chain E residue 40 ARG Chi-restraints excluded: chain E residue 53 LYS Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 66 ILE Chi-restraints excluded: chain H residue 136 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 20.0000 chunk 40 optimal weight: 2.9990 chunk 88 optimal weight: 20.0000 chunk 70 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 73 optimal weight: 30.0000 chunk 12 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 81 optimal weight: 20.0000 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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 = 0.3380 r_free = 0.3380 target = 0.049743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.035410 restraints weight = 58629.303| |-----------------------------------------------------------------------------| r_work (start): 0.2841 rms_B_bonded: 2.14 r_work: 0.2678 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8883 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 12619 Z= 0.197 Angle : 0.678 7.496 18285 Z= 0.385 Chirality : 0.043 0.226 2097 Planarity : 0.004 0.032 1296 Dihedral : 31.329 89.763 3977 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 4.02 % Allowed : 28.94 % Favored : 67.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.28 (0.31), residues: 728 helix: 2.95 (0.22), residues: 552 sheet: None (None), residues: 0 loop : -0.52 (0.43), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 100 TYR 0.036 0.002 TYR D 106 PHE 0.020 0.001 PHE H 88 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.20 (12619) covalent geometry : angle 0.67822 / 0.39 (18285) hydrogen bonds : bond 0.04830 / 3.24 ( 785) hydrogen bonds : angle 3.04823 / 2.30 ( 1969) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 121 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 68 GLU cc_start: 0.9058 (OUTLIER) cc_final: 0.8855 (tt0) REVERT: C 102 ASP cc_start: 0.8973 (t0) cc_final: 0.8603 (t0) REVERT: D 91 ASP cc_start: 0.9308 (t0) cc_final: 0.8944 (t0) REVERT: D 136 GLU cc_start: 0.9320 (OUTLIER) cc_final: 0.8983 (tp30) REVERT: E 56 LYS cc_start: 0.9315 (ttpp) cc_final: 0.9028 (tmmt) REVERT: E 120 MET cc_start: 0.8840 (mmm) cc_final: 0.8285 (mtm) REVERT: G 30 SER cc_start: 0.9735 (OUTLIER) cc_final: 0.9475 (p) REVERT: G 102 ASP cc_start: 0.8379 (t0) cc_final: 0.7856 (t0) REVERT: G 106 ASP cc_start: 0.9363 (t0) cc_final: 0.9139 (t0) REVERT: G 110 LYS cc_start: 0.9198 (mtmm) cc_final: 0.8796 (mmmm) REVERT: H 136 GLU cc_start: 0.9335 (OUTLIER) cc_final: 0.9002 (tp30) outliers start: 25 outliers final: 13 residues processed: 138 average time/residue: 0.5828 time to fit residues: 86.2871 Evaluate side-chains 139 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 122 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 68 GLU Chi-restraints excluded: chain D residue 136 GLU Chi-restraints excluded: chain E residue 53 LYS Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 66 ILE Chi-restraints excluded: chain G residue 82 SER Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 101 SER Chi-restraints excluded: chain H residue 136 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 4.9990 chunk 90 optimal weight: 20.0000 chunk 96 optimal weight: 20.0000 chunk 33 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 77 optimal weight: 20.0000 chunk 21 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 82 optimal weight: 20.0000 chunk 56 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.050309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.035757 restraints weight = 58299.470| |-----------------------------------------------------------------------------| r_work (start): 0.2861 rms_B_bonded: 2.15 r_work: 0.2699 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8865 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12619 Z= 0.149 Angle : 0.656 9.117 18285 Z= 0.378 Chirality : 0.042 0.230 2097 Planarity : 0.004 0.034 1296 Dihedral : 31.286 89.439 3977 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.70 % Allowed : 30.55 % Favored : 65.76 % 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: 3.20 (0.31), residues: 728 helix: 2.89 (0.22), residues: 552 sheet: None (None), residues: 0 loop : -0.54 (0.43), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 95 TYR 0.054 0.003 TYR D 106 PHE 0.007 0.001 PHE B 61 HIS 0.003 0.001 HIS D 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.15 (12619) covalent geometry : angle 0.65643 / 0.38 (18285) hydrogen bonds : bond 0.04049 / 2.71 ( 785) hydrogen bonds : angle 2.93920 / 2.20 ( 1969) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 135 time to evaluate : 0.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 68 GLU cc_start: 0.9061 (OUTLIER) cc_final: 0.8860 (tt0) REVERT: D 56 ASN cc_start: 0.9464 (m-40) cc_final: 0.9167 (m-40) REVERT: D 58 GLU cc_start: 0.8758 (mm-30) cc_final: 0.8313 (tp30) REVERT: D 91 ASP cc_start: 0.9296 (t0) cc_final: 0.8957 (t0) REVERT: D 136 GLU cc_start: 0.9315 (OUTLIER) cc_final: 0.8986 (tp30) REVERT: E 56 LYS cc_start: 0.9303 (ttpp) cc_final: 0.9008 (tmmt) REVERT: G 30 SER cc_start: 0.9738 (OUTLIER) cc_final: 0.9486 (p) REVERT: G 102 ASP cc_start: 0.8250 (t0) cc_final: 0.7744 (t0) REVERT: G 106 ASP cc_start: 0.9345 (t0) cc_final: 0.9091 (t0) REVERT: G 110 LYS cc_start: 0.9194 (mtmm) cc_final: 0.8775 (mmmm) REVERT: H 136 GLU cc_start: 0.9320 (OUTLIER) cc_final: 0.8966 (tp30) outliers start: 23 outliers final: 10 residues processed: 148 average time/residue: 0.5250 time to fit residues: 83.7461 Evaluate side-chains 139 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 125 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 68 GLU Chi-restraints excluded: chain C residue 113 ILE Chi-restraints excluded: chain D residue 136 GLU Chi-restraints excluded: chain E residue 53 LYS Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 66 ILE Chi-restraints excluded: chain G residue 82 SER Chi-restraints excluded: chain H residue 101 SER Chi-restraints excluded: chain H residue 136 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 71 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 93 optimal weight: 20.0000 chunk 72 optimal weight: 30.0000 chunk 47 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 59 optimal weight: 0.5980 chunk 78 optimal weight: 9.9990 chunk 57 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 94 optimal weight: 10.0000 overall best weight: 1.3188 ------------------------------------------------------------------------------- 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 = 0.3409 r_free = 0.3409 target = 0.050516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.035817 restraints weight = 57148.932| |-----------------------------------------------------------------------------| r_work (start): 0.2872 rms_B_bonded: 2.24 r_work: 0.2708 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8856 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12619 Z= 0.149 Angle : 0.664 10.544 18285 Z= 0.380 Chirality : 0.042 0.225 2097 Planarity : 0.004 0.037 1296 Dihedral : 31.238 89.803 3977 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.73 % Allowed : 32.32 % Favored : 64.95 % 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: 3.21 (0.31), residues: 728 helix: 2.93 (0.22), residues: 546 sheet: None (None), residues: 0 loop : -0.54 (0.42), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 105 TYR 0.059 0.003 TYR B 88 PHE 0.023 0.001 PHE H 88 HIS 0.004 0.001 HIS D 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.15 (12619) covalent geometry : angle 0.66415 / 0.38 (18285) hydrogen bonds : bond 0.04129 / 2.77 ( 785) hydrogen bonds : angle 2.95007 / 2.21 ( 1969) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 128 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 68 GLU cc_start: 0.9058 (OUTLIER) cc_final: 0.8854 (tt0) REVERT: D 58 GLU cc_start: 0.8749 (mm-30) cc_final: 0.8299 (tp30) REVERT: D 91 ASP cc_start: 0.9303 (t0) cc_final: 0.8968 (t0) REVERT: D 136 GLU cc_start: 0.9352 (OUTLIER) cc_final: 0.9035 (tp30) REVERT: E 56 LYS cc_start: 0.9296 (ttpp) cc_final: 0.8996 (tmmt) REVERT: G 30 SER cc_start: 0.9748 (OUTLIER) cc_final: 0.9491 (p) REVERT: G 102 ASP cc_start: 0.8123 (t0) cc_final: 0.7671 (t0) REVERT: G 106 ASP cc_start: 0.9327 (t0) cc_final: 0.9085 (t0) REVERT: G 110 LYS cc_start: 0.9194 (mtmm) cc_final: 0.8770 (mmmm) REVERT: H 136 GLU cc_start: 0.9380 (OUTLIER) cc_final: 0.9056 (tp30) outliers start: 17 outliers final: 9 residues processed: 138 average time/residue: 0.6050 time to fit residues: 89.6403 Evaluate side-chains 139 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 126 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 68 GLU Chi-restraints excluded: chain C residue 113 ILE Chi-restraints excluded: chain D residue 136 GLU Chi-restraints excluded: chain E residue 53 LYS Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 66 ILE Chi-restraints excluded: chain G residue 82 SER Chi-restraints excluded: chain H residue 101 SER Chi-restraints excluded: chain H residue 136 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 87 optimal weight: 30.0000 chunk 95 optimal weight: 20.0000 chunk 49 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 72 optimal weight: 30.0000 chunk 97 optimal weight: 20.0000 chunk 91 optimal weight: 20.0000 chunk 11 optimal weight: 2.9990 chunk 89 optimal weight: 20.0000 chunk 41 optimal weight: 0.9980 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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 = 0.3388 r_free = 0.3388 target = 0.049572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.034781 restraints weight = 58065.075| |-----------------------------------------------------------------------------| r_work (start): 0.2843 rms_B_bonded: 2.26 r_work: 0.2679 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8885 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 12619 Z= 0.202 Angle : 0.707 11.051 18285 Z= 0.397 Chirality : 0.043 0.225 2097 Planarity : 0.004 0.035 1296 Dihedral : 31.379 88.968 3977 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.41 % Allowed : 32.48 % Favored : 65.11 % 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: 3.01 (0.31), residues: 728 helix: 2.78 (0.22), residues: 546 sheet: None (None), residues: 0 loop : -0.56 (0.42), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 105 TYR 0.073 0.003 TYR D 106 PHE 0.006 0.001 PHE H 65 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.20 (12619) covalent geometry : angle 0.70684 / 0.40 (18285) hydrogen bonds : bond 0.04759 / 3.20 ( 785) hydrogen bonds : angle 3.14406 / 2.35 ( 1969) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 119 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 68 GLU cc_start: 0.9084 (OUTLIER) cc_final: 0.8878 (tt0) REVERT: C 102 ASP cc_start: 0.8807 (t0) cc_final: 0.8564 (t0) REVERT: D 91 ASP cc_start: 0.9332 (t0) cc_final: 0.9003 (t0) REVERT: D 136 GLU cc_start: 0.9363 (OUTLIER) cc_final: 0.9051 (tp30) REVERT: E 56 LYS cc_start: 0.9318 (ttpp) cc_final: 0.9024 (tmmt) REVERT: G 30 SER cc_start: 0.9753 (OUTLIER) cc_final: 0.9484 (p) REVERT: G 102 ASP cc_start: 0.8126 (t0) cc_final: 0.7696 (t0) REVERT: G 106 ASP cc_start: 0.9356 (t0) cc_final: 0.9137 (t0) REVERT: G 110 LYS cc_start: 0.9218 (mtmm) cc_final: 0.8788 (mmmm) outliers start: 15 outliers final: 8 residues processed: 130 average time/residue: 0.5779 time to fit residues: 80.4712 Evaluate side-chains 131 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 120 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 68 GLU Chi-restraints excluded: chain D residue 136 GLU Chi-restraints excluded: chain E residue 53 LYS Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 66 ILE Chi-restraints excluded: chain G residue 82 SER Chi-restraints excluded: chain H residue 101 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 94 optimal weight: 10.0000 chunk 19 optimal weight: 0.4980 chunk 50 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 96 optimal weight: 20.0000 chunk 63 optimal weight: 5.9990 chunk 92 optimal weight: 10.0000 chunk 14 optimal weight: 0.8980 chunk 97 optimal weight: 20.0000 chunk 60 optimal weight: 0.9980 chunk 43 optimal weight: 5.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- 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 = 0.3397 r_free = 0.3397 target = 0.049879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.035154 restraints weight = 57757.980| |-----------------------------------------------------------------------------| r_work (start): 0.2857 rms_B_bonded: 2.27 r_work: 0.2692 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8874 moved from start: 0.3042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12619 Z= 0.159 Angle : 0.681 11.423 18285 Z= 0.385 Chirality : 0.043 0.228 2097 Planarity : 0.004 0.037 1296 Dihedral : 31.339 89.521 3977 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.25 % Allowed : 33.28 % Favored : 64.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.03 (0.31), residues: 728 helix: 2.79 (0.22), residues: 546 sheet: None (None), residues: 0 loop : -0.55 (0.42), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 40 TYR 0.067 0.003 TYR B 88 PHE 0.028 0.001 PHE H 88 HIS 0.004 0.001 HIS D 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.16 (12619) covalent geometry : angle 0.68066 / 0.39 (18285) hydrogen bonds : bond 0.04203 / 2.82 ( 785) hydrogen bonds : angle 3.04525 / 2.27 ( 1969) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3006.21 seconds wall clock time: 51 minutes 51.62 seconds (3111.62 seconds total)